record_id,title,abstract,keywords,authors,year,date,doi,label_included
1,15th International Conference on Human Retroviruses: HTLV and Related Viruses,The proceedings contain 253 papers. The topics discussed include: altered CD4+/CD8+ T-cell ratio in splenocytes of human T-cell leukemia virus type I tax transgenic mice with inflammatory arthropathy; viral expression directs the fate of B cells in BLV-infected sheep; tet-inducible lymphoma in a new tax transgenic mouse model; bovine immunodeficiency virus as a potentiating cofactor for the experimental bovine leukemia virus infection in sheep; bovine MHC class II DR molecule plays a key role in bovine leukemia virus (BLV)-induced lymphoma; comparative proteomic analysis of cancer stem cells in a tax-transgenic (Tax-Tg) mouse model of adult T-cell leukemia/lymphoma; a life-attenuated BLV deletant as a candidate vaccine to inhibit viral transmission in bovine herds; and high-throughput sequencing reveals novel microRNAs in the bovine leukemia virus (blv)-induced ovine model of leukemia.,microRNA;CD8 antigen;CD4 antigen;vaccine;human;Retroviridae;virus;human T cell leukemia virus;tax;mouse;Bovine leukemia virus;sheep;mouse model;lymphoma;T lymphocyte;transgenic mouse;B lymphocyte;virus transmission;virus expression;adult;cancer stem cell;virus infection;arthropathy;immune deficiency;leukemia;herd;high throughput sequencing;ovine model;virus typing,,2011,,,0
2,"102nd Annual Meeting of the American Association of Immunologist, IMMUNOLOGY 2015","The proceedings contain 1758 papers. The topics discussed include: de novo detection and HLA-association of public t cell responses to cytomegalovirus using high-throughput immune repertoire sequencing; abrogation of CD59 function restores activities of neutralizing and non-neutralizing antibodies in triggering antibody-dependent complement-mediated lysis of HIV-1 virions and provirus-activated latently infected cells; evaluation of bone marrow in cowpox virus infection in cynomolgus macaques; glycosylphosphatidylinositol deficiency attenuates the production of infectious HIV-1 and renders the virions sensitive to complement attack; and immune restoration, activation and viral reservoirs in gut-associated lymphoid tissue in SIV-infected long-term non-progressing chinese rhesus macaques on antiretroviral therapy.",neutralizing antibody;glycosylphosphatidylinositol;antibody;immunologist;American;human;virion;Cytomegalovirus;T lymphocyte;virus infection;bone marrow;Cowpox virus;lysis;Macaca fascicularis;rhesus monkey;intestine lymphatic tissue;therapy;provirus;Human immunodeficiency virus;Simian immunodeficiency virus,,2015,,,0
3,"Recommendations for a Standardized Avian Coronavirus (AvCoV) Nomenclature: Outcome from Discussions Within the Framework of the European Union COST Action FA1207: ""Towards Control of Avian Coronaviruses: Strategies for Vaccination, Diagnosis and Surveillance""","Viruses within the Coronaviridae family show variations within their genome sequences, especially within the major structural protein, the Spike (S) glycoprotein gene. Therefore, many different antigenic forms, serotypes, or variant strains of avian coronaviruses (AvCoV) exist worldwide. Only a few of them, the so called protectotypes, cross protect against different serotypes. New serotypes arise by recombination or spontaneous mutations. From time to time, antigenic virus variants appear which differ significantly from known serotypes. The result of this variability is an inconsistent nomenclature and classification of virus strains. Furthermore, there are currently no standard classification methods defined. Within the framework of the COST Action FA1207 ""Towards control of avian coronaviruses: strategies for diagnosis, surveillance, and vaccination"" (working groups ""Molecular virology"" and ""Epidemiology""), we aimed at defining and developing a unified and internationally standardized nomenclature and classification of AvCoVs. We recommend the use of ""CoV Genus/AvCov/host/country/specimen id/year"" to refer to AvCoV strains.",animal;bird disease;classification;Coronaviridae;Coronaviridae infection;nomenclature;veterinary medicine;virology,,2016,,10.1637/0005-2086-60.2.411,0
4,First genome sequence of Newcastle disease virus of Genotype VIII from Jordan,Newcastle disease virus (NDV) was detected by reverse transcriptase PCR (RT-PCR) from total RNA isolated from a chicken spleen of a backyard flock in Jordan. The complete coding genome sequence of NDV/chicken/Jordan/J11-spleen/ 2018 was obtained with MiSeq (Illumina) sequencing. Phylogenetic analysis of the concatenated coding sequences classified the virus as class II subgenotype VIIi.,RNA;article;gene sequence;genetic code;genotype;Jordan;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;RNA extraction;RNA isolation;spleen;virus genome,"Ababneh, M.;Ferreira, H. L.;Khalifeh, M.;Suarez, D. L.;Afonso, C. L.",2018,,10.1128/mra.01136-18,0
5,"Genotyping the isolates of bovine leukemia virus, circulating in the stavropol territory","The bovine leukemia virus (BLV) circulating on the territory of the Stavropol Territory of Russia is characterized according to the modern classification of subspecies membership. Proviral deoxyribonucleic acid (DNA) of BLV has been separated out of the peripheral blood of animals that had been naturally infected with this virus. Subsequent amplification, sequencing and phylogenetic analysis of a fragment of the env-gene with the length of 444 pairs of nucleotides (p.n.) made it possible to classify the studied isolates as genotypes 4 and 6. Besides, we have separated out the BLV isolate located apart from clusters of isolates of all eight known genotypes, which made it possible to classify it as atypical. In course of sequencing a section of the env gene of BLV provirus isolates separatedin this area, the presence of 31 point mutation in the studied locus has been detected, with 11 of them being significant: 2 transversions and 9 transitions.",virus DNA;virus envelope protein;article;Bovine leukemia virus;Bovine leukemia virus genotype 4;Bovine leukemia virus genotype 6;controlled study;envelope gene;gene amplification;gene locus;gene sequence;genotype;mutational analysis;nonhuman;phylogenetic tree;point mutation;Russian Federation;sequence analysis;virus gene;virus isolation,"Abakin, S. S.;Krasovskaya, T. L.;Surgikova, E. S.;Gendzhieva, O. B.",2016,,,0
6,"Identification and phylogentic analysis of sheep pox during an outbreak of sheep in Sharkia governorate, Egypt","Sheeppox virus (SPPV) is one of the listed and notifiable disease affect sheep production with major effect on the trade of new breed of sheep. This study was conducted to identify sheep pox by using cell culture, electron microscope (EM) and open reading frame (ORF) 103 gene during an outbreak of local breed of sheep occurred in Sharkia Governorate, Egypt in April 2017. Affected adult sheep showed typical skin pox lesion on face, the inner side of lips, inner aspect of the thigh and under the tail. The incidence rate of infection was 23.5% and the mortality rate in young lambs aged 3 to 6 months old was 8.2%. Forty-three scabs and tissue samples from clinically diseased adult sheep and dead lambs were collected and subjected to culture on Vero cell. The cytopathic effect (CPE) was observed within 3 to 7 days in 40 samples. A typical Poxvirus was a brick-like shape with round ends by negative staining of EM and ovoid like structure with dumb-bell shaped DNA core with concave bodies sides by positive staining of EM. By conventional PCR utilizing ORF103 gene and obtained bands of about 570 bp referred to SPPV. The sequence amplicon was analyzed by NCBI-BLAST and register in GeneBank under accession N. MG873537 and phylogentic tree was designed which revealed that the isolated strain of SPPV was resembled with other strains of SPPV isolated in Egypt, India, China, and USA. Finally, both EM and PCR are considered as sensitives, rapids, and powerful methods to identify SPPV from tissue and scab’s samples without the need of further culture in addition to the useful and easily use of ORF103 gene to differentiate SPPV from other Capripoxvirus.",adult;amplicon;animal tissue;article;Capripoxvirus;cell culture;controlled study;cytopathogenic effect;Egypt;electron microscopy;epidemic;incidence;infection rate;mortality rate;nonhuman;nucleotide sequence;ORF103 gene;phylogeny;polymerase chain reaction;sequence analysis;sheeppox;virus gene;virus morphology,"Abd-Elfatah, E. B.;El-Mekkawi, M. F.;Bastawecy, I. M.;Fawzi, E. M.",2018,,10.4238/gmr16039901,0
7,Isolation and Molecular Characterization of Novel Infectious Bronchitis Virus Variants from Vaccinated Broiler Flocks in Egypt,"The present study aimed to determine the molecular characteristics of circulating infectious bronchitis virus (IBV) strains in vaccinated broiler flocks in the Giza and Fayoum governorates. Thirty-four isolates were collected, and egg propagation revealed their ability to induce typical IBV lesions after three to five successive passages. Three selected isolates were identified as IBV using a real-time reverse transcriptase-PCR assay targeted the nucleocapsid (N) gene and further characterized by partial spike (S) gene sequence analysis. Phylogenetic analysis revealed their clustering into two variant groups. Group I consisted of one variant (VSVRI_F3), which had 99.1% nucleotide sequence identity to the Q1 reference strain. Group II consisted of variants VSVRI_G4 and VSVRI_G9, which showed 92.8%-94.3% nucleotide identity with the Egyptian variants Eg/12120S/2012, Eg/12197B/2012, and Eg/1265B/2012. Regarding the deduced amino acid sequence, the three variants had 77.1%-85.2% similarity with the vaccine strains currently used in Egypt. These findings highlight the importance of monitoring the prevalence of IBV variants in vaccinated broiler flocks as well as adopting an appropriate vaccination strategy.","coronavirus spike glycoprotein;nucleocapsid protein;nucleocapsid protein, Coronavirus;amino acid sequence;animal;Avian infectious bronchitis virus;bird disease;chemistry;chicken;Coronavirus infection;Egypt;genetic variation;genetics;isolation and purification;metabolism;phylogeny;real time polymerase chain reaction;veterinary medicine;virology","Abdel-Sabour, M. A.;Al-Ebshahy, E. M.;Khaliel, S. A.;Abdel-Wanis, N. A.;Yanai, T.",2017,,10.1637/11566-121516-RegR,0
8,"Retrotransposable elements on the W chromosome of the silkworm, Bombyx mori","The sex chromosomes of the silkworm, Bombyxmori, are designated ZW(XY) for females and ZZ(XX) for males. The W chromosome of B. mori does not recombine with the Z chromosome and autosomes and no genes for morphological characters have been mapped to the W chromosome as yet. Furthermore, femaleness is determined by the presence of a single W chromosome, regardless of the number of autosomes or Z chromosomes. To understand these interesting features of the W chromosome, it is necessary to analyze the W chromosome at the molecular biology level. Initially to isolate DNA sequences specific for the W chromosome as randomly amplified polymorphic DNA (RAPD) markers, we compared the genomic DNAs between males and females by PCR with arbitrary 10-mer primers. To the present, we have identified 12 W-specific RAPD markers, and with the exception of one RAPD marker, all of the deduced amino acid sequences of these W-specific RAPD markers show similarity to previously reported amino acid sequences of retrotransposable elements from various organisms. After constructing a genomic DNA lambda phage library of B. mori we obtained two lambda phage clones, one containing the W-Kabuki RAPD sequence and one containing the W-Samurai RAPD sequence and found that these DNA sequences comprised nested structures of many retrotransposable elements. To further analyze the W chromosome, we obtained 14 W-specific bacterial artificial chromosome (BAC) clones from three BAC libraries and subjected these clones to shotgun sequencing. The resulting assembly of sequences did not produce a single contiguous sequence due to the presence of many retrotransposable elements. Therefore, we coupled PCR with shotgun sequencing. Through these analyses, we found that many long terminal repeat (LTR) and non-LTR retrotransposons, retroposons, DNA transposons and their derivatives, have accumulated on the W chromosome as strata. These results strongly indicate that retrotransposable elements are the main structural component of the W chromosome.","Animals;Bacteriophage lambda/ge [Genetics];Bacteriophage lambda/ip [Isolation & Purification];*Bombyx/ge [Genetics];Bombyx/vi [Virology];*Chromosome Mapping;Female;Insect Proteins/ge [Genetics];Male;Models, Genetic;Random Amplified Polymorphic DNA Technique;*Retroelements;*Sex Chromosomes;0 (Insect Proteins);0 (Retroelements)","Abe, H.;Mita, K.;Yasukochi, Y.;Oshiki, T.;Shimada, T.",2005,,,0
9,A novel sapelovirus-like virus isolation from wild boar,"A novel sapelovirus-like virus was isolated from a wild boar (Sus scrofa). In this study, partial viral genomic nucleotide sequences were determined using the rapid determination system of viral nucleic acid sequences (RDV) ver. 3.1, which we recently developed for discovering novel viruses. Phylogenetic analysis of VP1 and 3A proteins and their encoding nucleotide sequences of enteroviruses and sapeloviruses indicated that the isolated virus was closely related to porcine sapelovirus. RT-PCR detected viral sequences in six of 48 wild boar fecal samples. © 2011 Springer Science+Business Media, LLC.",complementary DNA;protein VP1;protein VP3A;unclassified drug;virus DNA;viral protein;animal cell;article;controlled study;cytopathogenic effect;embryo;Enterovirus;feces culture;kidney cell;molecular phylogeny;nonhuman;nucleotide sequence;Picornaviridae;Porcine sapelovirus like virus;priority journal;protein analysis;reverse transcription polymerase chain reaction;RNA sequence;RNA virus;sequence homology;virus detection;virus identification;virus isolation;European wild boar;wild boar sapelovirus 1,"Abe, M.;Ito, N.;Sakai, K.;Kaku, Y.;Oba, M.;Nishimura, M.;Kurane, I.;Saijo, M.;Morikawa, S.;Sugiyama, M.;Mizutani, T.",2011,,10.1007/s11262-011-0628-2,0
10,Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus,"Infectious bronchitis virus (IBV) is a Gammacoronavirus that causes a highly contagious respiratory disease in chickens. A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. Thirteen open reading frames (ORFs) in the order 5'-UTR-1a-1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3'UTR were predicted. The relative frequencies of missense: silent SNPs were calculated to obtain a comparative measure of variability in specific genes. The most variable ORFs in descending order were E, 3b, 5'UTR, N, 1a, S, 1ab, M, 4c, 5a, 6b. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5'UTR did not alter the predicted secondary structure. The frequency of SNPs in the Spike (S) protein ORF of 0.67% was below the genomic average of 0.76%. Only three SNPS were identified in the S1 subunit, none of which were located in hypervariable region (HVR) 1 or HVR2. The S2 subunit was considerably more variable containing 87% of the polymorphisms detected across the entire S protein. The S2 subunit also contained a previously unreported multi-A insertion site and a stretch of four consecutive mutated amino acids, which mapped to the stalk region of the spike protein. Template-based protein structure modelling produced the first theoretical model of the IBV spike monomer. Given the lack of diversity observed at the sub-consensus level, the tenet that the HVRs in the S1 subunit are very tolerant of amino acid changes produced by genetic drift is questioned.",amino acid;virus spike protein;3' untranslated region;5' untranslated region;amino acid substitution;animal tissue;article;Avian infectious bronchitis virus;chicken;controlled study;Coronavirinae;gene insertion;genetic drift;genetic variability;genomics;high throughput screening;missense mutation;nonhuman;nucleotide sequence;open reading frame;priority journal;protein secondary structure;protein structure;protein subunit;respiratory tract disease;RNA folding;single nucleotide polymorphism;theoretical model;virus genome;virus strain;virus virulence,"Abolnik, C.",2015,,10.1016/j.meegid.2015.03.033,0
11,Evolution of H5 highly pathogenic avian influenza: sequence data indicate stepwise changes in the cleavage site,"The genetic composition of an H5 subtype hemagglutinin gene quasispecies, obtained from ostrich tissues that had been infected with H5 subtype influenza virus was analysed using a next generation sequencing approach. The first evidence for the reiterative copying of a poly (U) stretch in the connecting peptide region in the haemagglutinin cleavage site (HACS) by the viral RNA-dependent RNA polymerase (RdRp) is provided. Multiple non-consensus species of RNA were detected in the infected host, corresponding to likely intermediate sequences between the putative low pathogenic precursor nucleotide sequence of the H5 influenza strain and the highly pathogenic avian influenza virus gene sequence. In silico analysis of the identified RNA sequences predicted that the intermediary H5 sequence PQREKRGLF plays an important role in subsequent mutational events that relocate the HACS coding region from stable base-paired RNA regions to a single-stranded bulge, thereby priming the connecting peptide coding region for RdRp slippage.","hemagglutinin, avian influenza A virus;Influenza virus hemagglutinin;RNA directed RNA polymerase;virus RNA;animal;avian influenza;genetics;high throughput sequencing;human;influenza;Influenza A virus (H5N1);isolation and purification;poultry;virology","Abolnik, C.",2017,,10.1007/s00705-017-3337-x,0
12,Outbreaks of avian influenza H6N2 viruses in chickens arose by a reassortment of H6N8 and H9N2 ostrich viruses,"The first recorded outbreak of avian influenza (AI) in South African chickens (low pathogenicity H6N2) occurred at Camperdown, KwaZulu/Natal Province (KZN) in June 2002. To determine the source of the outbreak, we defined the phylogenetic relationships between various H6N2 isolates, and the previously unpublished gene sequences of an H6N8 virus isolated in 1998 from ostriches in the Leeu Gamka region (A/Ostrich/South Africa/KK98/98). We demonstrated that two distinct genetic H6N2 lineages (sub-lineages I and II) circulated in the Camperdown area, which later spread to other regions. Sub-lineages I and II shared a recent common H6N2 ancestor, which arose from a reassortment event between two South African ostrich isolates A/Ostrich/South Africa/9508103/95 and (H9N2) A/Ostrich/South Africa/KK98/98 (H6N8). Furthermore, the H6N2 sub-lineage I viruses had several molecular genetic markers including a 22-amino acid stalk deletion in the neuraminidase (NA) protein gene, a predicted increased N-glycosylation, and a D144 mutation of the HA protein gene, all of which are associated with the adaptation of AI viruses to chickens. The H6N2 NS1 and PB1 genes shared recent common ancestors with those of contemporary Asian HPAI H5N1 viruses. Our results suggest that ostriches are potential mixing vessels for avian influenza viruses (AIV) outbreak strains and support other reports that H6 viruses are capable of forming stable lineages in chickens. © 2006 Springer Science+Business Media, LLC.",amino acid;gene product;sialidase;article;avian influenza;chicken;controlled study;evolutionary adaptation;gene deletion;gene sequence;genetic line;genetic marker;genetic reassortment;glycosylation;H6N2 virus;Influenza virus;molecular genetics;mutation;nonhuman;ostrich;phylogeny;priority journal;South Africa;virus isolation;virus strain,"Abolnik, C.;Bisschop, S.;Gerdes, T.;Olivier, A.;Horner, R.",2007,,10.1007/s11262-006-0007-6,0
13,Phylogenetic analysis of low-pathogenicity avian influenza H6N2 viruses from chicken outbreaks (2001-2005) suggest that they are reassortants of historic ostrich low-pathogenicity avian influenza H9N2 and H6N8 viruses,"Low-pathogenicity (LPAI) and high-pathogenicity (HPAI) avian influenza viruses are periodically isolated from South African ostriches, but during 2002 the first recorded outbreak of LPAI (H6N2) in South African chickens occurred on commercial farms in the Camperdown area of KwaZulu/Natal (KZN) Province. Sequence analysis of all eight genes were performed and phylogenetic analysis was done based on the hemagglutinin and neuraminidasc sequences. Results from phylogenetic analyses indicated that the H6N2 chicken viruses most likely arose from a reassortment between two South African LPAI ostrich isolates: an H9N2 virus isolated in 1995 and an H6N8 virus isolated in 1998. Two cocirculating sublineages of H6N2 viruses were detected, both sharing a recent common ancestor. One of these sublineages was restricted to the KZN province. The neuraminidase gene contained a 22-amino acid deletion in the NA-stalk region, which is associated with adaptation to growth in chickens, whereas the other group, although lacking the NA-stalk deletion, spread to commercial farms in other provinces. The persistence of particular H6N2 types in some regions for at least 2 yr supports reports from Asia and southern California suggesting that H6N2 viruses can form stable lineages in chickens. It is probable that the ostrich H6N8 and H9N2 progenitors of the chicken H6N2 viruses were introduced to ostriches by wild birds. Ostriches, in which AI infections are often subclinical, may serve as mixing vessels for LPAI strains that occasionally spill over into other poultry.",hemagglutinin;animal;animal disease;avian influenza;chicken;conference paper;epidemic;genetic reassortment;genetics;Influenza A virus;nucleotide sequence;ostrich;pathogenicity;phylogeny;South Africa;virology,"Abolnik, C.;Bisschop, S. P. R.;Gerdes, G. H.;Olivier, A. J.;Horner, R. F.",2007,,,0
14,Full genomic sequence of an African avian paramyxovirus type 4 strain isolated from a wild duck,"A random amplification/deep sequencing approach was applied to determine the complete genomic sequence of an Avian Paramyxovirus Type 4 (APMV-4) strain isolated from a wild duck in South Africa in 2010. This sequence represents the fourth full genome of APMV-4 in public sequence databases and the first for the African continent. A total of 87,402,081 Illumina paired-end reads were obtained of which 47,338,867 (54.16 %) mapped to the reference genome EU877976. The entire genomic sequence of 15,054 nt, including the intact termini, was recovered at a high redundancy (coverage per base: average = 198,861.06, minimum = 52 and maximum = 1,790,889). Pairwise comparison of full genomic nucleotide sequences indicated that APMV-4/Egyptian goose/South Africa/N1468/10 shared 97.3 % sequence identity with APMV-4/KR/YJ/06, 96.4 % sequence identity with APMV-4/mallard/Belgium/15129/07 and 90.8 % nucleotide sequence identity with APMV-4/duck/HK/D3/75. Genomic features were consistent with previously sequenced viruses including predicted open reading frames for the NP, P, F and L genes, but variations in coding regions for the M and HN genes were identified. The sequencing approach adopted in this study could successfully indicate quasispecies in the viral stock.","Alleles;Animals;Avulavirus/ge [Genetics];*Avulavirus/ip [Isolation & Purification];Avulavirus/py [Pathogenicity];*Avulavirus Infections/ve [Veterinary];Avulavirus Infections/vi [Virology];Base Sequence;Chromosome Mapping;Databases, Genetic;*Ducks/vi [Virology];Gene Frequency;Gene Library;*Genome, Viral;High-Throughput Nucleotide Sequencing;Open Reading Frames;Phosphoproteins/ge [Genetics];Sequence Homology, Nucleic Acid;South Africa;Viral Proteins/ge [Genetics];0 (L protein, paramyxoviridae);0 (P protein, Sendai virus);0 (Phosphoproteins);0 (Viral Proteins)","Abolnik, C.;de Castro, M.;Rees, J.",2012,Dec,,0
15,Characterization of pigeon paramyxoviruses (Newcastle disease virus) isolated in South Africa from 2001 to 2006,"Pigeon paramyxovirus type 1 (PPMV-1), a variant of Newcastle disease virus that primarily affects doves and pigeons has been isolated in South Africa since the mid-1980s. Phylogenetic evidence indicates that pigeon paramyxovirus type 1 viruses were introduced into South Africa on multiple occasions, based on the presence of two separate lineages, 4bi and 4bii, that have been circulating in Europe and the Far East since the early 1990s. During 2006, a PPMV-1 virus was isolated from an African ground hornbill (Bucorvus leadbeateri) which became acutely infected with PPMV-1 and died, probably after scavenging off infected dove carcasses in the region, since a closely-related PPMV-1 strain was also isolated from doves collected nearby. The hornbill isolate had ICPI and MDT values characteristic of PPMV-1 strains. The threat of PPMV-1 to poultry production and biodiversity in southern Africa highlights the importance of monitoring the spread of this strain.",virus RNA;amino acid sequence;animal;animal disease;article;bird disease;classification;disease transmission;food chain;isolation and purification;molecular genetics;Newcastle disease virus;pathogenicity;phylogeny;Columbidae;reverse transcription polymerase chain reaction;sequence alignment;South Africa;species difference;virology,"Abolnik, C.;Gerdes, G. H.;Kitching, J.;Swanepoel, S.;Romito, M.;Bisschop, S. P. R.",2008,,,0
16,Characterisation of a highly pathogenic influenza A virus of subtype H5N2 isolated from ostriches in South Africa in 2004,"Objectives: The HPAI H5N2 strain that caused an outbreak in ostriches of the Eastern Cape Province, South Africa in 2004 was characterized. Design: Haemagglutination inhibition (HI) and agar gel immunodiffusion (AGID) were performed on sera from ostrich farms in the outbreak region, and intravenous pathogenicity (IVPI) tests, reverse-transcriptase-polymerase-chain reaction (RT-PCR), nucleic acid sequencing and phylogenetic comparisons were performed on the HPAI H5N2 virus isolated during the outbreak. Results: The deduced amino acid sequence at the HA0 cleavage site determined by RT-PCR and nucleotide sequencing was PQREKRRKKRGLF and thus the virus fell within the definition of a highly pathogenic virus, but in an IVPI test in chickens on the virus isolated from the index case and a value of 0.63 was recorded, which is below the criterion for highly pathogenic viruses in this in vivo test. After a further passage in embryonated eggs a second IVPI was carried out and an elevated value of 1.19 was obtained. Cloacal swabs were taken from the initial IVPI birds, inoculated into embryonated chickens eggs and a third IVPI was then performed on the resulting haemagglutinating, infective allantoic fluid. An index of 2.73 was recorded. Conclusions: HI tests appeared to be the more sensitive test compared to AGID when testing for antibodies to avian influenza in sera. An ostrich-derived virus with a virulent HA0 cleavage site was not initially virulent in chickens but after passage in the latter the virulence increased. Phylogenetic analyses demonstrated the link between AI viruses carried by wild ducks and those infecting ostriches. © 2009 Blackwell Publishing Ltd.",hemagglutination inhibiting antibody;Africa;amino acid sequence;animal experiment;article;controlled study;immunodiffusion;Influenza A virus (H5N2);intermethod comparison;nonhuman;nucleotide sequence;ostrich;pathogenicity;phylogeny;priority journal;reverse transcription polymerase chain reaction;sensitivity and specificity;species comparison;virus classification;virus isolation;virus strain;virus virulence,"Abolnik, C.;Londt, B. Z.;Manvell, R. J.;Shell, W.;Banks, J.;Gerdes, G. H.;Akol, G.;Brown, I. H.",2009,,10.1111/j.1750-2659.2009.00074.x,0
17,Complete genome sequence of a velogenic newcastle disease virus isolated in Mexico,"In Mexico, the number of cases of the highly virulent Newcastle disease virus is increasing. In 2005, an outbreak of Newcastle disease occurred on an egg laying hen farm in the state of Puebla despite vaccination with the LaSota strain. Farmers experienced a major drop in egg production as a consequence of a field challenge virus. In this study, we characterize the virus, APMV1/chicken/ Mexico/P05/2005, responsible for the outbreak. The virus is categorized as a velogenic virus with an intracranial pathogenicity index of 1.99 and a chicken embryo mean death time of 36 h. The complete genome length of the virus was sequenced as consisting of 15,192 bp. In addition, phylogenetic analysis classified the virus as a member of the class II, genotype V. The highly pathogenic nature of the virus has been linked to the amino acid sequence at the fusion protein cleavage site, which contains multiple basic amino acids (RRQKR;F). © Springer Science+Business Media, LLC 2012.",amino acid;fusion protein;agricultural worker;amino acid sequence;animal cell;animal tissue;article;controlled study;egg production;embryo;gene sequence;genotype;Mexico;Newcastle disease;Newcastle disease virus;nonhuman;nucleotide sequence;pathotype;phylogeny;priority journal;protein cleavage;vaccination;velogenic virus;virus;virus genome;virus isolation;virus strain;virus virulence,"Absalón, A. E.;Mariano-Matías, A.;Vásquez-Márquez, A.;Morales-Garzón, A.;Cortés-Espinosa, D. V.;Ortega-García, R.;Lucio-Decanini, E.",2012,,10.1007/s11262-012-0782-1,0
18,Avian infuenza: Global assessment of potential pandemic of the twenty first century,"The emergence of highly pathogenic avian influenza (HPAI) of Asian lineage and the subsequent spillover to other part of the globe and on going spread of Eurasian-Africa H5N1 epidemic into domestic, wild birds and human have generated unprecedented attention in recent times and threat of potential pandemic via the avian-human link. Historically, from 1878 through 1955, fowl plaque was described as a high mortality disease of poultry in many countries throughout Europe, Asia, North and South America and Africa and the etiology was proved to be a filterable virus. In the 1930s through the 1950s, fowl plaque disappeared as an endemic disease in most part of the world. In 1949, the first report of a low virulent disease in chickens caused by LPAI virus was reported. In 1955, the etiological of fowl plaque was determined to be influenza A virus, which subsequently was identified as the H7 subtype. In 1959, a ""fowl plaque-like"" outbreak was described in chickens, which was the first report of fowl plaque caused by a non-H7 AI virus, i.e. first fowl plaque outbreak from H5 subtype of AI virus. In 1961 the first wild birds infection and deaths were reported in common terns of South Africa. In 1966 and 1971, the first H5 and H7 LPAI viruses, respectively were identified; prior to this period, only HPAI viruses had H5 and H7 subtypes. In 1970, the AGID serological test was introduced, which allowed easy and rapid identification of AI virus-infected poultry flocks. In 1972, there was the first isolation of LPAI viruses in asymptomatic wild birds: ducks in the United State and shorebirds in Australia. In 1981, the term ""highly pathogenic avian influenza"" was accepted as standard nomenclature for fowl plaque and related synonyms. In 1983, LPAI virus was observed mutating to HPAI virus during LPAI field outbreak, and specific genomic changes were identified in the proteolytic cleavage site of the hemagglutinin responsible for the virulence change. In the late 1980s and early 1990s, molecular criteria were added to the definition for classifying an AI virus as HPAI. In 2002, there were the first reported infections and deaths in a wide variety of wild bird species from AI virus H5N1 HPAI virus. The primary goal of this review is to highlight the global situation of HPAI and provide baseline information to show the potential pandemic nature of the virus, so that control and prevention strategies can be improved.",hemagglutinin;Africa;Asia;Australia;avian influenza;death;duckling;endemic disease;Europe;fowl;genomics;human;infection control;infection prevention;Influenza A virus;Influenza A virus (H7N7);mortality;nomenclature;nonhuman;North America;note;pandemic;protein degradation;shorebird;South America;virus identification;virus mutation;virus virulence,"Abubakar, M. B.;Aini, I.;Omar, A. R.;Hair Bejo, M.",2009,,,0
19,Phylogenetic and molecular characterization of coronavirus affecting species of bovine and birds in cuba,"Avian infectious bronchitis virus (IBV) and bovine coronavirus (BCoV) are pathogens of veterinary importance that affect birds and bovine in Cuba; however, molecular characteristics and genetic diversity of these viruses are unknown. This study was aimed at determining the molecular characteristics and genetic diversity of both agents, based in the spike S gene. A molecular analysis was carried out from fi eld strains of BCoV collected between 2009 and 2011 and phylogenetic studies were conducted using partial or complete S gene sequences as phylogenetic markers. Besides, studies of phylogenetic inference were carried out in S1 region of recent isolates of IBV. All Cuban bovine coronavirus sequences were located in a single cluster supported by 100 % bootstrap and 1.00 posterior probability values. The Cuban BCoV sequences were also clustered with the USA BCoV strains corresponding to the GenBank accession numbers EF424621 and EF424623, suggesting a common origin for these viruses. This phylogenetic cluster was also the only group of sequences in which no recombination events were detected. Of the 45 amino acid changes found in the Cuban strains, four were unique. On the other hand, two putative genotypes genetically different to the Massachusetts genotype H120 strain used in the Cuban vaccination program were found in the fl ocks assessed. In addition, a potential nephropathogenic IBV isolate was found by fi rst time in Cuba. This research won the 2012 Award of the Cuban National Academy of Sciences. © Biotecnología Aplicada 2013.",article;bird;Coronavirinae;cow;Cuba;gene sequence;genetic variability;genotype;nonhuman;nucleotide sequence;phylogeny;virus characterization,"Acevedo, A. M.;Martínez, N.;Brandão, P.;Perera, C. L.;Frías, M. T.;Barrera, M.;Pérez, L. J.",2013,,,0
20,Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses,"Detection of viruses in the environment is heavily dependent on PCR-based approaches that require reference sequences for primer design. While this strategy can accurately detect known viruses, it will not find novel genotypes or emerging and invasive viral species. In this study, we investigated the use of viromics, i.e., high-throughput sequencing of the biosphere's viral fraction, to detect human-/animal-pathogenic RNA viruses in the Conwy river catchment area in Wales, United Kingdom. Using a combination of filtering and nuclease treatment, we extracted the viral fraction from wastewater and estuarine river water and sediment, followed by high-throughput RNA sequencing (RNA-Seq) analysis on the Illumina HiSeq platform, for the discovery of RNA virus genomes. We found a higher richness of RNA viruses in wastewater samples than in river water and sediment, and we assembled a complete norovirus genotype GI.2 genome from wastewater effluent, which was not contemporaneously detected by conventional reverse transcription-quantitative PCR (qRT-PCR). The simultaneous presence of diverse rotavirus signatures in wastewater indicated the potential for zoonotic infections in the area and suggested runoff from pig farms as a possible origin of these viruses. Our results show that viromics can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided appropriate and rigorous controls are included. <b>IMPORTANCE</b> Enteric viruses cause gastrointestinal illness and are commonly transmitted through the fecal-oral route. When wastewater is released into river systems, these viruses can contaminate the environment. Our results show that we can use viromics to find the range of potentially pathogenic viruses that are present in the environment and identify prevalent genotypes. The ultimate goal is to trace the fate of these pathogenic viruses from origin to the point where they are a threat to human health, informing reference-based detection methods and water quality management.",,"Adriaenssens, E. M.;Farkas, K.;Harrison, C.;Jones, D. L.;Allison, H. E.;McCarthy, A. J.",2018,May-Jun,,0
21,Prevalence of porcine parvoviruses in some South African swine herds with background of porcine circovirus type 2 infection,"The classical porcine parvovirus is an important pathogen of reproductive disorders in pigs with a confirmed history of global distribution. The detection of many novel porcine parvoviruses has however been on the increase for the past few years, but there is a dearth of information on the occurrence and prevalence of these viruses in South Africa. Molecular detection of some known parvoviruses, namely porcine parvoviruses (PPVs) - 1, 2, 3 and 4, porcine bocavirus-like virus (PBo-likeV) and porcine bocaviruses (PBoV1/2), was carried out from 110 randomly selected archived swine samples collected in the year 2015 and 2016. Samples were drawn from previously screened and confirmed porcine circovirus type 2 (PCV2) infected farms, with farm-level occurrence ranged from 5.6 to 60%. The findings showed that all the screened parvoviruses were present as follows: PPV1 (29.1%), PPV2 (21.8%), PPV3 (5.5%), PPV4 (43.6%), PBo-likeV (21.8%) and PBoV1/2 (44.6%). The frequency of double infections of the viruses was as high as 18.2% of PPV2/PPV4 and PPV4/PBoVs; while 17.3% and 7.3% of the screened samples showed multiple infections of the three and four viruses respectively. Further phylogenetic analyses of partial PPV1, 2 and PBoV1/2 sequences showed two major clades for each of the viruses. This study reports the first epidemiological survey and molecular characterisation of the classical and emerging porcine parvoviruses in South African swine herds. It also gives insights into the diversity and distribution of these viral pathogens within the herds of the study area and confirms their co-infection potentials with PCV2.",article;Bocaparvovirus;Circoviridae infection;gene sequence;herd;mixed infection;nonhuman;parvovirus infection;phylogeny;pig;Porcine bocavirus 1;Porcine bocavirus 2;Porcine bocavirus like virus;Porcine circovirus 2;Porcine parvovirus;Porcine parvovirus 1;Porcine parvovirus 2;Porcine parvovirus 3;Porcine parvovirus 4;prevalence;South Africa,"Afolabi, K. O.;Iweriebor, B. C.;Obi, L. C.;Okoh, A. I.",2019,,10.1016/j.actatropica.2018.10.010,0
22,Biological characterization and next-generation genome sequencing of the unclassified cotia virus SPAn232 (Poxviridae),"Cotia virus (COTV) SPAn232 was isolated in 1961 from sentinel mice at Cotia field station, São Paulo, Brazil. Attempts to classify COTV within a recognized genus of the Poxviridae have generated contradictory findings. Studies by different researchers suggested some similarity to myxoma virus and swinepox virus, whereas another investigation characterized COTV SPAn232 as a vaccinia virus strain. Because of the lack of consensus, we have conducted an independent biological and molecular characterization of COTV. Virus growth curves reached maximum yields at approximately 24 to 48 h and were accompanied by virus DNA replication and a characteristic early/late pattern of viral protein synthesis. Interestingly, COTV did not induce detectable cytopathic effects in BSC-40 cells until 4 days postinfection and generated viral plaques only after 8 days. We determined the complete genomic sequence of COTV by using a combination of the next-generation DNA sequencing technologies 454 and Illumina. A unique contiguous sequence of 185,139 bp containing 185 genes, including the 90 genes conserved in all chordopoxviruses, was obtained. COTV has an interesting panel of open reading frames (ORFs) related to the evasion of host defense, including two novel genes encoding C-C chemokine-like proteins, each present in duplicate copies. Phylogenetic analysis revealed the highest amino acid identity scores with Cervidpoxvirus, Capripoxvirus, Suipoxvirus, Leporipoxvirus, and Yatapoxvirus. However, COTV grouped as an independent branch within this clade, which clearly excluded its classification as an Orthopoxvirus. Therefore, our data suggest that COTV could represent a new poxvirus genus. © 2012, American Society for Microbiology.",animal cell;article;Capripoxvirus;Cervidpoxvirus;Chordopoxvirinae;Cotia virus;cytopathogenic effect;DNA replication;DNA sequence;host range;human;human cell;immune evasion;Leporipoxvirus;molecular phylogeny;nonhuman;nucleotide sequence;open reading frame;Orthopovirus;Poxviridae;priority journal;protein synthesis;Suipoxvirus;virogenesis;virus classification;virus gene;virus genome;virus morphology;virus plaque;virus replication,"Afonso, P. P.;Silva, P. M.;Schnellrath, L. C.;Jesus, D. M.;Hu, J.;Yang, Y.;Renne, R.;Attias, M.;Condit, R. C.;Moussatché, N.;Damaso, C. R.",2012,,10.1128/jvi.07162-11,0
23,"Lumpy skin disease outbreaks in Greece during 2015–16, implementation of emergency immunization and genetic differentiation between field isolates and vaccine virus strains","The objective of this study is to present epizootiological data from the lumpy skin disease (LSD) outbreaks in Greece during 2015–16, following the implementation of emergency vaccination and total stamping-out, along with laboratory data regarding the genetic differentiation between field isolates and live attenuated vaccine virus strains. Descriptive geographical chronology analysis was conducted to present the progressive shift of the outbreaks westwards, and at the same time, the absence of further outbreaks in previously affected regional units where high vaccination coverage was achieved. Isolation and molecular characterization of LSDV from the first recorded case in Greece (Evros/GR/15 isolate) was performed. The two live attenuated LSD vaccine viruses, currently used for emergency immunization in Greece, were sequenced and compared to the Evros/GR/15 isolate, in 3 genomic regions (GPCR gene, RPO30 gene, and partial LSDV126/LSDV127 genes). Sequence comparisons revealed prominent differences between the Evros/GR/15 isolate and the vaccine strains. Phylogenetic analysis resulted in the classification of the Evros/GR/15 isolate in the same clade with all field LSDV isolates, whereas vaccine strains were grouped in a distinct cluster within the LSDV clade. Additional samples from animals presenting skin nodules (N = 13) were characterized by sequencing in the 3 aforementioned genomic regions. Among them, in 5 animals that were vaccinated, the attenuated vaccine virus was identified. A PCR-RFLP method targeting the LSDV127 gene was developed and proved to be able to discriminate between the characterized field and vaccine strains. The findings of the present study substantiate the importance of timely and intensive vaccinations for the control of LSDV epizootic and the genetic differences between the Evros/GR/15 isolate and the vaccine strains. This provides the basis for the development of PCR-based DIVA assays, which would be of major importance for effective disease surveillance and stamping-out during LSD vaccination campaigns.",live vaccine;lumpy skin disease virus vaccine;restriction endonuclease;unclassified drug;virus vaccine;analysis;animal tissue;article;bovine;cladistics;controlled study;emergency care;epidemic;gene cluster;gene sequence;genetic difference;GPCR gene;Greece;LSDV126 gene;LSDV127 gene;lumpy skin disease;Lumpy skin disease virus;nonhuman;phylogeny;polymerase chain reaction;restriction fragment length polymorphism;restriction site;RPO30 gene;sequence analysis;skin nodule;strain difference;vaccination;virus gene;virus isolation;virus strain;lumpyvax,"Agianniotaki, E. I.;Tasioudi, K. E.;Chaintoutis, S. C.;Iliadou, P.;Mangana-Vougiouka, O.;Kirtzalidou, A.;Alexandropoulos, T.;Sachpatzidis, A.;Plevraki, E.;Dovas, C. I.;Chondrokouki, E.",2017,,10.1016/j.vetmic.2016.12.037,0
24,Spread of the newly emerging infectious laryngotracheitis viruses in Australia,"Infectious laryngotracheitis (ILT) is a significant viral disease of chickens in many countries around the globe. In this report the status of ILT in Australia has been used as a model to evaluate the evolution of the ILT viruses (ILTVs). Due to its geographical isolation, Australia harbored a distinct lineage of ILT viruses (ILTV) up to 2007. However examination of the ILT viruses (ILTV) involved in outbreaks between 2007 and 2009 has revealed that many of the outbreaks were caused by two new viral genotypes, class 8 and class 9. These two recombinant viruses were found to emerge as a result of recombination between previously existing live vaccine strains (SA2 and A20), and another live vaccine strain (Serva) introduced into the country in 2007. The new recombinant ILTVs were also shown to possess significantly higher virulence and replication capacity compared with a previously predominant ILTV, class 2. In the current study, examination of a large number of ILTVs isolated from outbreaks between 2009 and 2015 revealed the emergence of yet another recombinant virus (class 10) that appears to have become a predominant genotype in New South Wales. In Victoria however, the recombinant class 9 gradually became the predominant virus, replacing class 2. Therefore, there was an unusual pattern in geographical spread of the newly emerged viruses in different states of the country. These results suggest that ILTV is fast evolving towards a greater transmissibility and therefore greater capacity to spread into ILTV-free areas.","Animals;Australia/ep [Epidemiology];*Chickens/vi [Virology];Gene Transfer, Horizontal;*Herpesviridae Infections/ep [Epidemiology];*Herpesviridae Infections/ve [Veterinary];Herpesviridae Infections/vi [Virology];*Herpesvirus 1, Gallid/cl [Classification];Herpesvirus 1, Gallid/ge [Genetics];Herpesvirus 1, Gallid/ip [Isolation & Purification];High-Throughput Nucleotide Sequencing/ve [Veterinary];Phylogeny;Poultry Diseases/ep [Epidemiology];*Poultry Diseases/vi [Virology];Sequence Analysis, DNA/ve [Veterinary];Virulence;Virus Replication","Agnew-Crumpton, R.;Vaz, P. K.;Devlin, J. M.;O'Rourke, D.;Blacker-Smith, H. P.;Konsak-Ilievski, B.;Hartley, C. A.;Noormohammadi, A. H.",2016,09,,0
25,Detection and phylogenetic analysis of Orf virus in Kashmir Himalayas,"Orf virus (ORFV) is a zoonotic pathogen that primarily infects sheep and goats, and is responsible for significant economic losses. ORFV is endemic in all the major sheep and goat rearing areas of the world including Indian subcontinent. However, the nature of ORFV circulating among sheep and goat in Kashmir Himalayas has not yet been characterized. In the present study, we describe natural outbreaks of ORFV in sheep and goats of Kashmir Himalayas. We detected the presence of ORFV in the scab lesion by PCR amplification of the major envelope protein (B2L) gene. We sequenced the virus interferon resistance (VIR) gene and determined their phylogenetic relationship with that of the published reference sequences. Phylogenetic analysis based on VIR gene revealed that the ORFV isolates from Kashmir Himalayas separated into main two clusters. The sheep isolates showed genetic homology with the sheep strains reported from Greece and Italy, whereas the goat-specific strain show homology with the goat strains reported from China. This study demonstrates the presence of ORFV infection in sheep and goats, and report first phylogenetic analysis of the ORFV strains prevalent in the Kashmir Himalayas.",antiviral activity;article;bluetongue;Capripoxvirus;contagious ecthyma;DNA base composition;endemic disease;foot and mouth disease;gene sequence;genetic variation;Greece;Italy;lamb;molecular epidemiology;morbidity;nonhuman;Orf virus;phylogenetic tree;phylogeny;prevalence;pyoderma gangrenosum;sequence alignment;virus replication;virus virulence,"Ahanger, S. A.;Parveen, R.;Nazki, S.;Dar, Z.;Dar, T.;Dar, K. H.;Dar, A.;Rai, N.;Dar, P.",2018,,10.1007/s13337-018-0473-1,0
26,"Host-parasite relations of bacteria and phages can be unveiled by Oligostickiness, a measure of relaxed sequence similarity","Motivation: The recent metagenome analysis has been producing a large number of host-unassigned viruses. Although assigning viruses to their hosts is basically important not only for virology but also for prevention of epidemic, it has been a laborious and difficult task to date. The only effective method for this purpose has been to find them in a same microscopic view. Now, we tried a computational approach based on genome sequences of bacteria and phages, introducing a physicochemical parameter, SOSS (set of oligostickiness similarity score) derived from oligostickiness, a measure of binding affinity of oligonucleotides to template DNA. Results: We could confirm host-parasite relationships of bacteria and their phages by SOSS analysis: all phages tested (25 species) had a remarkably higher SOSS value with its host than with unrelated bacteria. Interestingly, according to SOSS values, lysogenic phages such as lambda phage (host: Escherichia coli) or SPP1 (host: Bacillus subtilis) have distinctively higher similarity with its host than its non-lysogenic (excretive or virulent) ones such as fd and T4 (host: E. coli) or phages gamma and PZA (host: B.subtilis). This finding is very promising for assigning host-unknown viruses to its host. We also investigated the relationship in codon usage frequency or G + C content of genomes to interpret the phenomenon revealed by SOSS analysis, obtaining evidences which support the hypothesis that higher SOSS values resulted from the cohabitation in the same environment which may cause the common biased mutation. Thus, lysogenic phages which stay inside longer resemble the host. © The Author 2009. Published by Oxford University Press. All rights reserved.",cytosine;guanine;oligonucleotide;verotoxin 1;verotoxin 2;article;Bacillus subtilis;bacteriophage;bacteriophage gamma;Enterobacteria phage lambda;bacteriophage PZA;Enterobacteria phage T4;Enterobacteria phage T7;bacterium;binding affinity;Clostridium botulinum;Peptoclostridium difficile;codon usage;controlled study;DNA template;Escherichia coli;gene mutation;gene sequence;genetic code;genetic similarity;genetic variability;host parasite interaction;Mycobacterium;nonhuman;nucleotide sequence;oligostickiness;priority journal;set of oligostickiness similarity score;species comparison;Streptococcus pyogenes;Streptococcus thermophilus;Vibrio cholerae,"Ahmed, S.;Saito, A.;Suzuki, M.;Nemoto, N.;Nishigaki, K.",2009,,10.1093/bioinformatics/btp003,0
27,Genetic diversity and comparison of diagnostic tests for characterization of foot-and-mouth disease virus strains from Pakistan 2008–2012,"We report the laboratory analysis of 125 clinical samples from suspected cases of foot-and-mouth disease (FMD) in cattle and Asian buffalo collected in Pakistan between 2008 and 2012. Of these samples, 89 were found to contain viral RNA by rRT-PCR, of which 88 were also found to contain infectious FMD virus (FMDV) by virus isolation (VI), with strong correlation between these tests (κ = 0.96). Samples that were VI-positive were serotyped by antigen detection ELISA (Ag-ELISA) and VP1 sequence acquisition and analysis. Sequence data identified FMDV serotypes A (n = 13), O (n = 36) and Asia-1 (n = 41), including three samples from which both serotypes Asia-1 and O were detected. Serotype A viruses were classified within three different Iran-05 sublineages: HER-10, FAR-11 and ESF-10. All serotype Asia-1 were within Group VII (Sindh-08 lineage), in a genetic clade that differs from viruses isolated prior to 2010. All serotypes O were classified as PanAsia-2 within two different sublineages: ANT-10 and BAL-09. Using VP1 sequencing as the gold standard for serotype determination, the overall sensitivity of Ag-ELISA to correctly determine serotype was 74%, and serotype-specific sensitivity was 8% for serotype A, 88% for Asia-1 and 89% for O. Serotype-specific specificity was 100% for serotype A, 93% for Asia-1 and 94% for O. Interestingly, 12 of 13 serotype A viruses were not detected by Ag-ELISA. This study confirms earlier accounts of regional genetic diversity of FMDV in Pakistan and highlights the importance of continued validation of diagnostic tests for rapidly evolving pathogens such as FMDV.",article;diagnostic test;enzyme linked immunosorbent assay;foot and mouth disease;genetic variability;human;Pakistan;reverse transcription polymerase chain reaction;screening test;virus detection;virus isolation,"Ahmed, Z.;Pauszek, S. J.;Ludi, A.;LaRocco, M.;Khan, E. U. H.;Afzal, M.;Arshed, M. J.;Farooq, U.;Arzt, J.;Bertram, M.;Brito, B.;Naeem, K.;Abubakar, M.;Rodriguez, L. L.",2018,,10.1111/tbed.12737,0
28,"Human endophthalmitis caused by pseudorabies virus infection, China, 2017",We report human endophthalmitis caused by pseudorabies virus infection after exposure to sewage on a hog farm in China. High-throughput sequencing and real-time PCR of vitreous humor showed pseudorabies virus sequences. This case showed that pseudorabies virus might infect humans after direct contact with contaminants.,aciclovir;meropenem;vancomycin;adult;article;case report;cerebrospinal fluid;China;clinical article;Cytomegalovirus;endophthalmitis;Epstein Barr virus;female;fever;follow up;headache;human;immunoprecipitation;latex agglutination test;middle aged;next generation sequencing;nucleotide sequence;ophthalmoscopy;Pseudorabies virus;Pseudorabies virus infection;real time polymerase chain reaction;retina degeneration;slit lamp microscopy;virus infection;visual acuity;visual impairment;vitrectomy;vitreous opacity,"Ai, J. W.;Weng, S. S.;Cheng, Q.;Cui, P.;Li, Y. J.;Wu, H. L.;Zhu, Y. M.;Xu, B.;Zhang, W. H.",2018,,10.3201/eid2406.171612,0
29,Complete genome analysis of porcine kobuviruses from the feces of pigs in Japan,"Porcine kobuviruses (PoKoVs) are ubiquitously distributed in pig populations worldwide and are thought to be enteric viruses in swine. Although PoKoVs have been detected in pigs in Japan, no complete genome data for Japanese PoKoVs are available. In the present study, 24 nearly complete or complete sequences of the PoKoV genome obtained from 10 diarrheic feces and 14 non-diarrheic feces of Japanese pigs were analyzed using a metagenomics approach. Japanese PoKoVs shared 85.2–100% identity with the complete coding nucleotide (nt) sequences and the closest relationship of 85.1–98.3% with PoKoVs from other countries. Twenty of 24 Japanese PoKoVs carried a deletion of 90 nt in the 2B coding region. Phylogenetic tree analyses revealed that PoKoVs were not grouped according to their geographical region of origin and the phylogenetic trees of the L, P1, P2, and P3 genetic regions showed topologies different from each other. Similarity plot analysis using strains from a single farm revealed partially different similarity patterns among strains from identical farm origins, suggesting that recombination events had occurred. These results indicate that various PoKoV strains are prevalent and not restricted geographically on pig farms worldwide and the coexistence of multiple strains leads to recombination events of PoKoVs and contributes to the genetic diversity and evolution of PoKoVs.",article;controlled study;feces;gene deletion;gene sequence;genetic variability;genome analysis;Japan;Kobuvirus;metagenomics;nonhuman;nucleotide sequence;phylogenetic tree;pig;porcine kobuvirus;priority journal;virus genome;virus recombination;virus strain,"Akagami, M.;Ito, M.;Niira, K.;Kuroda, M.;Masuda, T.;Haga, K.;Tsuchiaka, S.;Naoi, Y.;Kishimoto, M.;Sano, K.;Omatsu, T.;Aoki, H.;Katayama, Y.;Oba, M.;Oka, T.;Ichimaru, T.;Yamasato, H.;Ouchi, Y.;Shirai, J.;Katayama, K.;Mizutani, T.;Nagai, M.",2017,,10.1007/s11262-017-1464-9,1
30,Two new 'legumoviruses' (genus Begomovirus) naturally infecting soybean in Nigeria,"Two new 'legumoviruses' (genus Begomovirus; family Geminiviridae) naturally infecting soybean (Glycine max L. Merr.) in Nigeria were molecularly characterized. Based on characteristic symptoms in soybean, the two viruses are provisionally designated as Soybean mild mottle virus (SbMMV) and Soybean chlorotic blotch virus (SbCBV). SbCBV has a bipartite genome, whereas SbMMV has only a DNA A component. The DNA A component of SbMMV is 2,768 nucleotides (nt) long and the DNA A and DNA B components of SbCBV are 2,708 and 2,647 nt long, respectively. In pairwise comparisons, the DNA A component of SbMMV and SbCBV showed 62% nt sequence identity, indicating that these two viruses are distinct. Whereas the DNA A of SbMMV contains two virion- and four complementary-sense open reading frames, that of SbCBV lacks the virus-sense AV2, a signature gene present in 'Old World' begomoviruses. A pairwise comparison with the corresponding nucleotide sequence of other begomoviruses in the databases indicated that SbCBV had a maximum of 74% identity with cowpea golden mosaic virus and SbMMV had a maximum of 65% identity with mungbean yellow mosaic India virus and kudzu mosaic virus. Phylogenetic analysis of the DNA A component of SbCBV and SbMMV together with those of other begomoviruses available in the databases showed clustering of the two viruses within the 'legumovirus' clade of the begomovirus phylogenetic tree. In addition, the DNA A and B components of SbCBV from Centrosema pubescens Benth were found to be identical to those from soybean, indicating that leguminous wild species are a potential alternative host for the virus. Since soybean is an introduced crop, the identification of two distinct begomoviruses naturally infecting soybean in Nigeria suggests the occurrence of 'legumoviruses' in plant species indigenous to Africa and underscores their potential threat to sustainable cultivation of soybean on the African continent. © Springer-Verlag 2010.",virus DNA;amino acid sequence;article;Begomovirus;classification;genetic recombination;genetics;isolation and purification;molecular genetics;Nigeria;nomenclature;phylogeny;soybean;virology,"Alabi, O. J.;Kumar, P. L.;Mgbechi-Ezeri, J. U.;Naidu, R. A.",2010,,10.1007/s00705-010-0630-3,0
31,Serologic and Antigenic Properties of Malaysian Orf Virus Isolates - an in-Vitro Comparative-Study,"Three Malaysian orf virus isolates from goats (GV1, GV2 and GV3) were compared to three orf viruses from sheep (LBV Malaysian isolate, ORFII and NZ2 reference strains) in their serologic properties and protein profiles. Serologic tests such as cross agar gel precipitation test (AGPT), serum neutralization test (SNT), ELISA, indirect immunofluorescent test (IIF) and indirect immunoperoxidase test (IIP) revealed that the viruses were greatly related to each other. However,serotyping of these isolates by the use of homologous and heterologous titration of their hyperimmune sera (HIS) in SNT and ELISA showed opposite results and did not allow for the classification of these viruses as the goat and sheep origin. Protein analysis of these isolates was carried out by the use of SDS-Poly acrylamide gel electrophoresis (SDS-PAGE), Western blotting and physical staining and immunodetection of blotted protein profiles. The results revealed that these isolates were different mainly in the polypeptides bands of 41.5, 39.5 and 37.5 kD. These analytical techniques allowed the classification of these isolates into four groups, GV1 and GV2 in the first, GV3 in the second, LBV and ORFII in the third, and NZ2 in the fourth.",SULFATE-POLYACRYLAMIDE GELS;CONTAGIOUS ECTHYMA;ELECTROPHORETIC;TRANSFER;PROTEINS;VIRION;SHEEP;DIFFERENTIATION;PARAPOXVIRUSES;NITROCELLULOSE;HETEROGENEITY,"Alajeeli, K. S. A.;Iskander, F.;Ibrahim, A. L.;Zamrisaad, M.",1995,Dec,,0
32,Insights into Reston virus spillovers and adaption from virus whole genome sequences,"Reston virus (family Filoviridae) is unique among the viruses of the Ebolavirus genus in that it is considered non-pathogenic in humans, in contrast to the other members which are highly virulent. The virus has however, been associated with several outbreaks of highly lethal hemorrhagic fever in non-human primates (NHPs), specifically cynomolgus monkeys (Macaca fascicularis) originating in the Philippines. In addition, Reston virus has been isolated from domestic pigs in the Philippines. To better understand virus spillover events and potential adaption to new hosts, the whole genome sequences of representative Reston virus isolates were obtained using a next generation sequencing (NGS) approach and comparative genomic analysis and virus fitness analyses were performed. Nine virus genome sequences were completed for novel and previously described isolates obtained from a variety of hosts including a human case, non-human primates and pigs.","Animals;Disease Outbreaks/ve [Veterinary];Ebolavirus/ge [Genetics];Ebolavirus/py [Pathogenicity];*Filoviridae/ge [Genetics];Filoviridae/py [Pathogenicity];Filoviridae Infections/ve [Veterinary];Filoviridae Infections/vi [Virology];Genetic Markers/ge [Genetics];*Genome, Viral/ge [Genetics];Hemorrhagic Fever, Ebola/ve [Veterinary];Hemorrhagic Fever, Ebola/vi [Virology];High-Throughput Nucleotide Sequencing;Humans;Macaca fascicularis/vi [Virology];Swine/vi [Virology];0 (Genetic Markers)","Albarino, C. G.;Wiggleton Guerrero, L.;Jenks, H. M.;Chakrabarti, A. K.;Ksiazek, T. G.;Rollin, P. E.;Nichol, S. T.",2017,,,0
33,A molecular epidemiological study of avian paramyxovirus type 1 (Newcastle disease virus) isolates by phylogenetic analysis of a partial nucleotide sequence of the fusion protein gene,"A sequence 375 nucleotides in length, which included the region encoding the cleavage activation site and signal peptide of the fusion protein gene, was determined for 174 isolates of Newcastle disease virus (avian paramyxovirus type 1). These were compared with the sequences of 164 isolates published on GenBank, and the resulting alignment was analysed phylogenetically using maximum likelihood. The results are presented as unrooted phylogenetic trees. Briefly, the isolates divided into six broadly distinct groups (lineages 1 to 6). Lineages 3 and 4 were further subdivided into four sublineages (a to d) and lineage 5 into five lineages (a to e). Considerable genetic heterogeneity was detected within avian paramyxoviruses type 1, which appears to be influenced by host, time and geographical origin. It is concluded that by using this dataset it will be possible to type future virus isolates rapidly on the basis of their nucleotide sequence and make inferences about their origins.","Animals;Evolution, Molecular;Geography;*Newcastle Disease/ep [Epidemiology];Newcastle Disease/vi [Virology];Newcastle disease virus/cl [Classification];*Newcastle disease virus/ge [Genetics];*Phylogeny;Poultry/vi [Virology];*Viral Fusion Proteins/ge [Genetics];0 (Viral Fusion Proteins)","Aldous, E. W.;Mynn, J. K.;Banks, J.;Alexander, D. J.",2003,Jun,,0
34,"Genome characterization of a pathogenic porcine rotavirus B strain identified in Buryat republic, Russia in 2015","An outbreak of enteric disease of unknown etiology with 60% morbidity and 8% mortality in weaning piglets occurred in November 2015 on a farm in Buryat Republic, Russia. Metagenomic sequencing revealed the presence of rotavirus B in feces from diseased piglets while no other pathogens were identified. Clinical disease was reproduced in experimentally infected piglets, yielding the 11 RVB gene segments for strain Buryat15, with an RVB genotype constellation of G12-P[4]-I13-R4-C4-M4-A8-N10-T4-E4-H7. This genotype constellation has also been identified in the United States. While the Buryat15 VP7 protein lacked unique amino acid differences in the predicted neutralizing epitopes compared to the previously published swine RVB G12 strains, this report of RVB in Russian swine increases our epidemiological knowledge on the global prevalence and genetic diversity of RVB.",epitope;protein VP7;animal cell;animal experiment;animal model;article;diarrhea;enzyme linked immunosorbent assay;genetic variability;genotype;metagenomics;mortality rate;newborn;next generation sequencing;nonhuman;pathogenesis;phylogeny;piglet;polymerase chain reaction;porcine rotavirus;prevalence;RNA extraction;Rotavirus B;virus detection;virus virulence,"Alekseev, K. P.;Penin, A. A.;Mukhin, A. N.;Khametova, K. M.;Grebennikova, T. V.;Yuzhakov, A. G.;Moskvina, A. S.;Musienko, M. I.;Raev, S. A.;Mishin, A. M.;Kotelnikov, A. P.;Verkhovsky, O. A.;Aliper, T. I.;Nepoklonov, E. A.;Herrera-Ibata, D. M.;Shepherd, F. K.;Marthaler, D. G.",2018,,10.3390/pathogens7020046,1
35,The long view: a selective review of 40 years of Newcastle disease research,"This review is written for the series celebrating the 40th year since the first issue of Avian Pathology. The aim of the authors was to cover the developments in Newcastle disease (ND) research over the last 40 years that they considered significant. During those 40 years there have been several panzootics of this serious disease in poultry and for the last 30 years there has been a continuing panzootic in domestic pigeons, which has spread to wild birds and poultry. The 40-year period began with worldwide outbreaks of severe ND, which served as an important impetus for ND research work. Although early work was concerned with controlling the disease, specifically by improving and developing new vaccines and vaccine regimens, even prior to the 1970s ND virus was seen as a useful laboratory virus for replication and virulence studies. This review covers the historical developments in the following areas: understanding the molecular basis of virulence; epidemiology and relatedness of different ND strains, both antigenically and genetically; the emergence of virulent strains and their relationship with viruses of low virulence; sequencing and understanding the viral genome and genes; the development of rapid molecular-based diagnostic tests; and the phylogeny and molecular taxonomy of ND virus. The authors suggest areas in which future research could or should be undertaken. © 2012 Copyright Crown Copyright.",animal;animal disease;bird;bird disease;classification;genetics;human;Newcastle disease;Newcastle disease virus;pandemic;pathogenicity;phylogeny;poultry;review;virology;virulence;virus genome,"Alexander, D. J.;Aldous, E. W.;Fuller, C. M.",2012,,10.1080/03079457.2012.697991,0
36,Development of methodology based on commercialized SERS-active substrates for rapid discrimination of Poxviridae virions,"Surface-enhanced Raman spectroscopy (SERS) can be made an attractive approach for identification of Raman-active compounds and biological materials (i.e., toxins, viruses, or intact bacterial cells/spores) through development of reproducible, spatially uniform SERS-active substrates. Recently, reproducible (from substrate-to-substrate), spatially homogeneous (over large areas) SERS-active substrates have been commercialized and are now available in the marketplace. We have utilized these patterned surfaces to acquire SERS spectral signatures of intact bovine papular stomatitis, pseudocowpox, and Yaba monkey tumor viruses. Salient spectral signature features make it possible to discriminate among these genetically distinct Poxviridae-Chordopoxvirinae virions. In addition, partial least-squares, a multivariate calibration method, has been used to develop personal computer-borne algorimms useful for classification of unknown Parapoxvirus (e.g., bovine papular stomatitis virus and pseudocowpox virus) samples based solely on SERS spectral signatures. To our knowledge, this is the first report detailing application of these commercial-off-the-shelf (COTS) SERS-active substrates to identification of intact poxviruses.",article;Chordopoxvirinae;controlled study;microcomputer;nonhuman;Poxviridae;Raman spectrometry;sensitivity analysis;validation study;virion;virus classification,"Alexander, T. A.",2008,,10.1021/ac702464w,0
37,Etiology and pathology of epidemic outbreaks of avian influenza H5N1 infection in Egyptian chicken farms,"Epidemic outbreaks of avian influenza (AI) virus H5N1 have been frequently reported in Egypt during the last nine years. Here we investigate the involvement of AI H5N1 in outbreaks of acute respiratory disease that occurred in several commercial chicken farms in Egypt in 2011, and we describe to the pathology caused by the virus in the course of the outbreak. Twenty-one chicken farms with history of acute respiratory symptoms and high mortalities were screened for AI H5N1. Virus identification was based on hemagglutination inhibition test, and PCR detection and sequencing of the hemagglutinin and neuraminidase genes. Virus distribution was determined by immunohistochemical staining of AI antigens in organs of infected birds. Standard H&E staining was performed for histological examination of affected organs. Eighty-one % of the examined birds, representing 100% of the screened farms, were positive for AI H5N1 virus. Phylogenetic analysis of the hemagglutinin and neuraminidase genes of the isolated virus reveals its affiliation to clade 2.2.1. Viral antigens were localized in the endothelial cells of the heart, liver, lungs and skin, where pathological lesions including congestion, hemorrhages, multifocal inflammation and necrosis were concurrently observed. According to the pattern of the viral antigen and lesion distribution in the visceral organs, we suggest cardiovascular and circulatory failures as the probable cause of death during these outbreaks. In conclusion, the present study further confirms the epidemic status of AI H5N1 virus in Egypt and reveals the highly pathogenic nature of the local isolates.",animal;chicken;Egypt;epidemic;genetics;Influenza A virus (H5N1);avian influenza;isolation and purification;pathology;phylogeny;veterinary medicine;virology,"Ali, A.;Elmowalid, G.;Abdel-Glil, M.;Sharafeldin, T.;Abdallah, F.;Mansour, S.;Nagy, A.;Ahmed, B.;Abdelmoneim, M.",2015,,10.1515/pjvs-2015-0101,0
38,"Molecular characterization of the complete genomes of two new field isolates of Cowpea chlorotic mottle virus, and their phylogenetic analysis","Cowpea chlorotic mottle virus (CCMV, family Bromoviridae) is found worldwide and has been used as a model virus for a long time, but no data is available about the genetic diversity of field isolates. Recently, two new field isolates (Car1 and Car2) of CCMV obtained from cowpea showed distinct phenotypic symptoms when inoculated to cowpea. CCMV-Car1 induced severe mosaic and interveinal chlorosis, while CCMV-Car2 produced mild mottling and leaf rolling. Both isolates produced asymptomatic infection in Nicotiana benthamiana. The complete genome of both isolates was amplified by reverse transcription-polymerase chain reaction using specific primers against the CCMV sequences available in the GenBank database, cloned and sequenced. Both nucleotide and amino acid sequences were compared between the newly sequenced CCMV isolates and the three previously characterized CCMV strains (T, M1, and R). Phylogenetic analysis of the RNA 1 sequence showed that CCMV-Car1 was in a separate branch from the rest of the CCMV isolates while CCMV-Car2 grouped together with CCMV-R. On the basis of RNA 2 and RNA 3 sequences, two major groupings were obtained. One group included CCMV-Car1 and CCMV-Car2 isolates while the other contained CCMV-T, CCMV-M1, and CCMV-R strains. Recombination programs detected a potential recombination event in the RNA 1 sequence of CCMV-Car2 isolate but not in RNA 2 and RNA 3 sequences. The results showed that both mutations and recombination have played an important role in the genetic diversity of these two new isolates of CCMV. © 2011 Springer Science+Business Media, LLC.",virus RNA;5' untranslated region;article;Bromovirus;controlled study;cowpea chlorotic mottle virus;gene sequence;genetic database;genetic variability;molecular dynamics;nonhuman;nucleotide sequence;open reading frame;phenotype;phylogeny;priority journal;reverse transcription polymerase chain reaction;RNA recombination;sequence alignment;stop codon;virus genome;virus isolation,"Ali, A.;Shafiekhani, M.;Olsen, J.",2011,,10.1007/s11262-011-0613-9,0
39,Hendra and Nipah infection: Emerging paramyxoviruses,"Since their first emergence in mid 1990s henipaviruses continued to re emerge in Australia and South East Asia almost every year. In total there has been more than 12 Nipah and 48 Hendra virus outbreaks reported in South East Asia and Australia, respectively. These outbreaks are associated with significant economic and health damages that most high risks countries (particularly in South East Asia) cannot bear the burden of such economical threats. Up until recently, there were no actual therapeutics available to treat or prevent these lethal infections. However, an international collaborative research has resulted in the identification of a potential equine Hendra vaccine capable of providing antibody protection against Hendra virus infections. Consequently, with the current findings and after nearly 2 decades since their first detection, are we there yet? This review recaps the chronicle of the henipavirus emergence and briefly evaluates potential anti-henipavirus vaccines and antivirals. © 2013 Elsevier B.V.",adenovirus vaccine;antivirus agent;brilliant green;chloroquine;crystal violet;equivac hev;gliotoxin;human monoclonal antibody;human monoclonal antibody m102.4;lj 001;measles vaccine;mibefradil;peptide;praziquantel;quinoline derived antiinfective agent;recombinant protein;ribavirin;thrombospondin;unclassified drug;verapamil;virus vaccine;antiviral therapy;cell line;chemical structure;clinical feature;hemolytic anemia;Hendra virus;Hendra virus infection;Henipavirus;Henipavirus infection;human;infection prevention;infection sensitivity;molecular dynamics;Nipah virus;Nipah virus infection;nonhuman;Paramyxoviridae;priority journal;review;viral tropism;virus classification;virus encephalitis;virus virulence,"Aljofan, M.",2013,,10.1016/j.virusres.2013.08.002,0
40,"[Genetic characterization of the Wad Medani virus (WMV) (Reoviridae, Orbivirus), isolated from the ticks Hyalomma asiaticum Schulze et Schlottke, 1930 (Ixodidae: Hyalomminae) in Turkmenistan, Kazakhstan, and Armenia and from the ticks H. anatolicum Koch, 1844 in Tajikistan]",,animal;Armenia;genetics;high throughput sequencing;Ixodidae;Kazakhstan;molecular genetics;pathogenicity;phylogeny;Reoviridae;reovirus infection;sheep;Tajikistan;Turkmenistan;virology;virus genome,"Al'khovskiĭ, S. V.;L'Vov D, K.;Shchelkanov, M. Iu;Shchetinin, A. M.;Deriabin, P. G.;Gitel'man, A. K.;Aristova, V. A.;Botikov, A. G.",2014,,,0
41,A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species,"Identification of previously unrecognized viral agents in serum or plasma samples is of great medical interest but remains a major challenge, primarily because of abundant host DNA. The current methods, library screening or representational difference analysis (RDA), are very laborious and require selected sample sets. We have developed a simple and reproducible method for discovering viruses in single serum samples that is based on DNase treatment of the serum followed by restriction enzyme digestion and sequence-independent single primer amplification (SISPA) of the fragments, and have evaluated its performance on known viruses. Both DNA viruses and RNA viruses at a concentration of ≈106 genome equivalents per mi were reproducibly identified in 50 μl of serum. While evaluating the method, two previously unknown parvoviruses were discovered in the bovine sera used as diluent. The near complete genome sequence of each virus was determined; their classification as two species (provisionally named bovine parvoviruses 2 and 3) was confirmed by phylogenetic analysis. Both viruses were found to be frequent contaminants of commercial bovine serum. DNase treatment of serum samples may prove to be a very useful tool for virus discovery. The DNase-SISPA method is suitable for screening of a large number of samples and also enables rapid sequence determination of high-titer viruses.",complementary DNA;DNA;nucleic acid;RNA;article;bovine;DNA virus;nonhuman;nucleotide sequence;Parvoviridae;polymerase chain reaction;priority journal;RNA virus;virus genome,"Allander, T.;Emerson, S. U.;Engle, R. E.;Purcell, R. H.;Bukh, J.",2001,,10.1073/pnas.211424698,0
42,Cloning of a human parvovirus by molecular screening of respiratory tract samples,"The identification of new virus species is a key issue for the study of infectious disease but is technically very difficult. We developed a system for large-scale molecular virus screening of clinical samples based on host DNA depletion, random PCR amplification, large-scale sequencing, and bioinformatics. The technology was applied to pooled human respiratory tract samples. The first experiments detected seven human virus species without the use of any specific reagent. Among the detected viruses were one coronavirus and one parvovirus, both of which were at that time uncharacterized. The parvovirus, provisionally named human bocavirus, was in a retrospective clinical study detected in 17 additional patients and associated with lower respiratory tract infections in children. The molecular virus screening procedure provides a general culture-independent solution to the problem of detecting unknown virus species in single or pooled samples. We suggest that a systematic exploration of the viruses that infect humans, ""the human virome,"" can be initiated.",bioinformatics;nucleotide sequencing;respiratory tract infection;virus;MINUTE VIRUS;BOVINE PARVOVIRUS;SYNCYTIAL VIRUS;CANINES MVC;SEQUENCE;IDENTIFICATION;CHILDREN;CORONAVIRUS;HOSPITALIZATIONS;PATHOGENICITY,"Allander, T.;Tammi, M. T.;Eriksson, M.;Bjerkner, A.;Tiveljung-Lindell, A.;Andersson, B.",2005,Sep,,0
43,Estimation of viral richness from shotgun metagenomes using a frequency count approach,"BACKGROUND: Viruses are important drivers of ecosystem functions, yet little is known about the vast majority of viruses. Viral shotgun metagenomics enables the investigation of broad ecological questions in phage communities. One ecological characteristic is species richness, which is the number of different species in a community. Viruses do not have a phylogenetic marker analogous to the bacterial 16S rRNA gene with which to estimate richness, and so contig spectra are employed to measure the number of virus taxa in a given community. A contig spectrum is generated from a viral shotgun metagenome by assembling the random sequence reads into groups of sequences that overlap (contigs) and counting the number of sequences that group within each contig. Current tools available to analyze contig spectra to estimate phage richness are limited by relying on rank-abundance data. RESULTS: We present statistical estimates of virus richness from contig spectra. The program CatchAll (http://www.northeastern.edu/catchall/) was used to analyze contig spectra in terms of frequency count data rather than rank-abundance, thus enabling formal statistical analyses. Also, the influence of potentially spurious low-frequency counts on richness estimates was minimized by two methods, empirical and statistical. The results show greater estimates of viral richness than previous calculations in nearly all environments analyzed, including swine feces and reclaimed fresh water. CONCLUSIONS: CatchAll yielded consistent estimates of richness across viral metagenomes from the same or similar environments. Additionally, analysis of pooled viral metagenomes from different environments via mixed contig spectra resulted in greater richness estimates than those of the component metagenomes. Using CatchAll to analyze contig spectra will improve estimations of richness from viral shotgun metagenomes, particularly from large datasets, by providing statistical measures of richness.",,"Allen, H. K.;Bunge, J.;Foster, J. A.;Bayles, D. O.;Stanton, T. B.",2013,Feb 04,,0
44,Antibiotics in feed induce prophages in swine fecal microbiomes,"Antibiotics are a cost-effective tool for improving feed efficiency and preventing disease in agricultural animals, but the full scope of their collateral effects is not understood. Antibiotics have been shown to mediate gene transfer by inducing prophages in certain bacterial strains; therefore, one collateral effect could be prophage induction in the gut microbiome at large. Here we used metagenomics to evaluate the effect of two antibiotics in feed (carbadox and ASP250 [chlortetracycline, sul-famethazine, and penicillin]) on swine intestinal phage metagenomes (viromes). We also monitored the bacterial communities using 16S rRNA gene sequencing. ASP250, but not carbadox, caused significant population shifts in both the phage and bacterial communities. Antibiotic resistance genes, such as multidrug resistance efflux pumps, were identified in the viromes, but in-feed antibiotics caused no significant changes in their abundance. The abundance of phage integrase-encoding genes was significantly increased in the viromes of medicated swine over that in the viromes of nonmedicated swine, demonstrating the induction of prophages with antibiotic treatment. Phage-bacterium population dynamics were also examined. We observed a decrease in the relative abundance of Streptococcus bacteria (prey) when Streptococcus phages (predators) were abundant, supporting the ""kill-the-winner"" ecological model of population dynamics in the swine fecal microbiome. The data show that gut ecosystem dynamics are influenced by phages and that prophage induction is a collateral effect of in-feed antibiotics. © 2011 Allen et al.",antibiotic agent;carbadox;chlortetracycline;penicillin G;RNA 16S;sulfadimidine;animal experiment;antibiotic resistance gene;article;bacterial gene;controlled study;drug effect;feces microflora;female;gene sequence;gene transfer;integrase gene;intestine flora;metagenome;metagenomics;microbial diversity;microbial population dynamics;microbiome;multidrug resistance;nonhuman;population abundance;priority journal;prophage;Streptococcus;pig,"Allen, H. K.;Looft, T.;Bayles, D. O.;Humphrey, S.;Levine, U. Y.;Alt, D.;Stanton, T. B.",2011,,10.1128/mBio.00260-11,1
45,The Baltic Sea virome: diversity and transcriptional activity of DNA and RNA viruses,,,"Allen, L. Z.;McCrow, J. P.;Ininbergs, K.;Dupont, C. L.",2017,,,0
46,ICTV virus taxonomy profile: Asfarviridae,"The family Asfarviridae includes the single species African swine fever virus, isolates of which have linear dsDNA genomes of 170-194 kbp. Virions have an internal core, an internal lipid membrane, an icosahedral capsid and an outer lipid envelope. Infection of domestic pigs and wild boar results in an acute haemorrhagic fever with transmission by contact or ingestion, or by ticks of the genus Ornithodoros. Indigenous pigs act as reservoirs in Africa, where infection is endemic, and from where introductions occur periodically to Europe. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Asfarviridae, which is available at www.ictv.global/report/asfarviridae.",African swine fever virus;article;Asfarviridae;DNA virus infection;domestic pig;electron microscopy;Europe;European wild boar;genus;hemorrhagic fever;host range;lipid membrane;nonhuman;Ornithodoros;priority journal;RNA translation;taxonomy;tick borne disease;virion;virus genome;virus replication;virus transmission;virus virulence,"Alonso, C.;Borca, M.;Dixon, L.;Revilla, Y.;Rodriguez, F.;Escribano, J. M.;Lefkowitz, E. J.;Davison, A. J.;Siddell, S. G.;Simmonds, P.;Sabanadzovic, S.;Smith, D. B.;Orton, R. J.;Harrach, B.",2018,,10.1099/jgv.0.001049,0
47,Epidemiological study of air filtration systems for preventing PRRSV infection in large sow herds,"Porcine reproductive and respiratory syndrome virus (PRRSV) is the most economically significant pathogen in the US swine industry. Aerosol transmission among herds is a major concern in pig dense regions and filtration of incoming air, in combination with standard biosecurity procedures, has been demonstrated to prevent transmission of PRRSV into susceptible herds. To quantify the impact of air filtration on reducing risk of PRRSV outbreaks, we compared the incidence rate of new PRRSV introductions in 20 filtered and 17 non-filtered control sow herds in a swine dense region of North America during a 7. year study period. Events of novel virus introduction were ascertained by phylogenetic analysis of PRRSV ORF5 gene sequences. Putative new viruses were defined as exogenous (introduced) based on ORF5 nucleotide sequence differences compared to previous farm isolates. The influence of sequence difference cut-off values ranging from 2 to 10% on case definition and relative risk were evaluated. Non-filtered farms incurred about 0.5 outbreaks per year, with a seasonal increase in risk in cooler periods. Baseline risk, prior to filtration, in treatment farms was approximately 0.75 per year, approximately 50% higher than in control farms. Air filtration significantly reduced risk of PRRSV introduction events to 0.06-0.22 outbreaks per year, depending on the cut-off values used to classify a virus isolate as new to the herd. Overall, air filtration led to an approximately 80% reduction in risk of introduction of novel PRRSV, indicating that on large sow farms with good biosecurity in swine-dense regions, approximately four-fifths of PRRSV outbreaks may be attributable to aerosol transmission. © 2013 Elsevier B.V.",virus RNA;aerosol;air;air filtration;animal;animal disease;animal husbandry;Arterivirus;article;biosecurity;epidemic;epidemiology;evaluation study;female;filtration;genetics;incidence;isolation and purification;methodology;phylogeny;polymerase chain reaction;porcine reproductive and respiratory syndrome;prospective study;PRRS;retrospective study;season;sequence analysis;pig;United States;virology,"Alonso, C.;Murtaugh, M. P.;Dee, S. A.;Davies, P. R.",2013,,10.1016/j.prevetmed.2013.06.001,0
48,Characterization of H5N1 influenza a virus that caused the first highly pathogenic avian influenza outbreak in Saudi Arabia,"Introduction: Saudi Arabia (SA) experienced a highly pathogenic avian influenza (HPAI) H5N1 outbreak in domesticated birds in 2007. Methodology: Forty-three hemagglutinin (HA) and 41 neuraminidase (NA) genes of HPAI H5N1 viruses were sequenced and phylogenetic analyses of completely sequenced genes were performed to compare with other viral HA and NA gene sequences available in the public databases. Results: Molecular characterization of the H5N1 viruses revealed two genetically distinct clades, 2.2.2 and 2.3.1, of H5N1 viruses circulating in the area. Amino acid sequence analysis of the HA gene indicated that the virus from 2.2.2 contained the sequence SPQGERRRK-R/G at the cleavage site, while the virus from 2.3.1 contained the sequence SPQRERRRK-R/G. Additionally, a few mutations with amino acid substitutions such as M226I at N-link glycosylation site were identified in two of these isolates. Amino acid sequence of the NA gene showed a 20-amino-acid deletion in the NA stalk region, required for enhanced virulence of influenza viruses and its adaptation from wild birds to domestic chickens. As close contact between humans and birds is unavoidable, there is a need for a thorough understanding of the virus epidemiology, factors affecting the spread of the virus, and molecular characterization such as phylogeny and substitution rates of H5N1 viruses circulating in the region. Conclusion: Two genetically distinct clades were found to be circulating in the country, which could likely result in recombination and emergence of more virulent viral strains. These findings could be helpful for the authorities devising control measures against these viruses.",complementary DNA;Influenza virus hemagglutinin;virus RNA;virus sialidase;amino acid sequence;article;avian influenza;cladistics;codon;DNA cleavage;DNA sequence;gene mutation;genetic similarity;genetic variability;glycosylation;human;Influenza A virus (H5N1);Influenza virus hemagglutinin gene;neighbor joining method;nonhuman;nucleic acid base substitution;phylogeny;polymerase chain reaction;Saudi Arabia;virus gene;virus sialidase gene;virus virulence,"Al-Qahtani, A. A.;Mubin, M.;Almajhdi, F. N.;Alarifi, S.;Cruz, D. M. D.;ul Rehman, M. S. N.;Ismail, M. M.;Ahmed, N.;Al-Blowi, M. H.;Khalak, H.;Al-Ahdal, M. N.",2015,,10.3855/jidc.6546,0
49,"DISTRIBUTION OF CHICKEN ANAEMIA VIRUS IN TISSUES, FAECES AND ENVIRONMENTAL SAMPLES UP TO DAY 56 FOLLOWING ARTIFICIAL …",,,"Alsharari, M.;Islam, Afmf;Renz, K. G.;Burgess, S. K.",,,,0
50,Molecular characterization of the first bovine herpesvirus 4 (BoHV-4) strains isolated from in vitro bovine embryos production in Argentina,"Bovine herpesvirus 4 (BoHV-4) is increasingly considered as responsible for various problems of the reproductive tract. The virus infects mainly blood mononuclear cells and displays specific tropism for vascular endothelia, reproductive and fetal tissues. Epidemiological studies suggest its impact on reproductive performance, and its presence in various sites in the reproductive tract highlights its potential transmission in transfer-stage embryos. This work describes the biological and genetic characterization of BoHV-4 strains isolated from an in vitro bovine embryo production system. BoHV-4 strains were isolated in 2011 and 2013 from granulosa cells and bovine oocytes from ovary batches collected at a local abattoir, used as ""starting material"" for in vitro production of bovine embryos. Compatible BoHV-4-CPE was observed in the co-culture of granulosa cells and oocytes with MDBK cells. The identity of the isolates was confirmed by PCR assays targeting three ORFs of the viral genome. The phylogenetic analyses of the strains suggest that they were evolutionary unlinked. Therefore it is possible that BoHV-4 ovary infections occurred regularly along the evolution of the virus, at least in Argentina, which can have implications in the systems of in vitro embryo production. Thus, although BoHV-4 does not appear to be a frequent risk factor for in vitro embryo production data are still limited. This study reveals the potential of BoHV-4 transmission via embryo transfer. Moreover, the high variability among the BoHV-4 strains isolated from aborted cows in Argentina highlights the importance of further research on the role of this virus as an agent with the potential to cause reproductive disease in cattle. The genetic characterization of the isolated strains provides data to better understand the pathogenesis of BoHV-4 infections. Furthermore, it will lead to fundamental insights into the molecular aspects of the virus and the means by which these strains circulate in the herds.",animal cell;animal tissue;Argentina;article;bovine;Bovine herpesvirus 4;embryo;embryo transfer;gene sequence;genetic analysis;granulosa cell;in vitro study;molecular evolution;nonhuman;nucleotide sequence;oocyte;open reading frame;phylogeny;polymerase chain reaction;viral genetics;virus detection;virus isolation;virus strain;virus transmission,"Altamiranda, E. G.;Manrique, J. M.;Pérez, S. E.;Ríos, G. L.;Odeón, A. C.;Leunda, M. R.;Jones, L. R.;Verna, A.",2015,,10.1371/journal.pone.0132212,0
51,Enteric virome of Ethiopian children participating in a clean water intervention trial,,,"Altan, E.;Aiemjoy, K.;Phan, T. G.;Deng, X.;Aragie, S.",2018,,,0
52,Small circular rep-encoding single-stranded DNA genomes in Peruvian diarrhea virome,,,"Altan, E.;Mendoza, J. D. V.;Deng, X.;Phan, T. G.",2017,,,0
53,0440 The development of a cecum-cannulated gnotobiotic piglet model to study the human gut microbiota,,,"Aluthge, N. D.;Tom, W.;Burkey, T. E.",2016,,,0
54,"A broad spectrum, one-step reverse-transcription PCR amplification of the neuraminidase gene from multiple subtypes of influenza A virus","BACKGROUND: The emergence of high pathogenicity strains of Influenza A virus in a variety of human and animal hosts, with wide geographic distribution, has highlighted the importance of rapid identification and subtyping of the virus for outbreak management and treatment. Type A virus can be classified into subtypes according to the viral envelope glycoproteins, hemagglutinin and neuraminidase. Here we review the existing specificity and amplification of published primers to subtype neuraminidase genes and describe a new broad spectrum primer pair that can detect all 9 neuraminidase subtypes. RESULTS: Bioinformatic analysis of 3,337 full-length influenza A neuraminidase segments in the NCBI database revealed semi-conserved regions not previously targeted by primers. Two degenerate primers with M13 tags, NA8F-M13 and NA10R-M13 were designed from these regions and used to generate a 253 bp cDNA product. One-step RT-PCR testing was successful in 31/32 (97%) cases using a touchdown protocol with RNA from over 32 different cultured influenza A virus strains representing the 9 neuraminidase subtypes. Frozen blinded clinical nasopharyngeal aspirates were also assayed and were mostly of subtype N2. The region amplified was direct sequenced and then used in database searches to confirm the identity of the template RNA. The RT-PCR fragment generated includes one of the mutation sites related to oseltamivir resistance, H274Y. CONCLUSION: Our one-step RT-PCR assay followed by sequencing is a rapid, accurate, and specific method for detection and subtyping of different neuraminidase subtypes from a range of host species and from different geographical locations.","Adolescent;Adult;Aged;Aged, 80 and over;Animals;Charadriiformes/vi [Virology];Chickens/vi [Virology];Child;Child, Preschool;DNA Primers;Ducks/vi [Virology];Female;Horses/vi [Virology];Humans;Infant;Influenza A Virus, H9N2 Subtype;*Influenza A virus/cl [Classification];*Influenza A virus/ge [Genetics];Influenza A virus/ip [Isolation & Purification];Influenza in Birds/vi [Virology];Influenza, Human/vi [Virology];Male;Middle Aged;Nasopharynx/vi [Virology];*Neuraminidase/ge [Genetics];Orthomyxoviridae Infections/ve [Veterinary];Orthomyxoviridae Infections/vi [Virology];RNA, Viral/an [Analysis];RNA, Viral/ge [Genetics];*Reverse Transcriptase Polymerase Chain Reaction/mt [Methods];Sensitivity and Specificity;Sequence Analysis, DNA;0 (DNA Primers);0 (RNA, Viral)","Alvarez, A. C.;Brunck, M. E.;Boyd, V.;Lai, R.;Virtue, E.;Chen, W.;Bletchly, C.;Heine, H. G.;Barnard, R.",2008,Jul 09,,0
55,Double-stranded RNA high-throughput sequencing reveals a new cytorhabdovirus in a bean golden mosaic virus-resistant common bean transgenic line,"Using double-strand RNA (dsRNA) high-throughput sequencing, we identified five RNA viruses in a bean golden mosaic virus (BGMV)-resistant common bean transgenic line with symptoms of viral infection. Four of the identified viruses had already been described as infecting common bean (cowpea mild mottle virus, bean rugose mosaic virus, Phaseolus vulgaris alphaendornavirus 1, and Phaseolus vulgaris alphaendornavirus 2) and one is a putative new plant rhabdovirus (genus Cytorhabdovirus), tentatively named bean-associated cytorhabdovirus (BaCV). The BaCV genome presented all five open reading frames (ORFs) found in most rhabdoviruses: nucleoprotein (N) (ORF1) (451 amino acids, aa), phosphoprotein (P) (ORF2) (445 aa), matrix (M) (ORF4) (287 aa), glycoprotein (G) (ORF5) (520 aa), and an RNA-dependent RNA polymerase (L) (ORF6) (114 aa), as well as a putative movement protein (P3) (ORF3) (189 aa) and the hypothetical small protein P4. The predicted BaCV proteins were compared to homologous proteins from the closest cytorhabdoviruses, and a low level of sequence identity (15–39%) was observed. The phylogenetic analysis shows that BaCV clustered with yerba mate chlorosis-associated virus (YmCaV) and rice stripe mosaic virus (RSMV). Overall, our results provide strong evidence that BaCV is indeed a new virus species in the genus Cytorhabdovirus (family Rhabdoviridae), the first rhabdovirus to be identified infecting common bean.",Nextera;pCR 2 TOPO vector;PCR assay kit;SuperScript;double stranded RNA;matrix protein;plant virus movement protein;RNA directed RNA polymerase;viral protein;virus glycoprotein;virus nucleoprotein;Alphaendornavirus;article;bean;Carlavirus;Comovirus;Cytorhabdovirus;high throughput sequencing;metagenomics;molecular diagnosis;open reading frame;phylogenetic tree;phylogeny;plant virus;real time polymerase chain reaction;reverse transcription polymerase chain reaction;Rhabdoviridae;RNA extraction;Sanger sequencing;sequence analysis;transgenic plant;viral plant disease;virus genome;virus infection;virus isolation,"Alves-Freitas, D. M. T.;Pinheiro-Lima, B.;Faria, J. C.;Lacorte, C.;Ribeiro, S. G.;Melo, F. L.",2019,,10.3390/v11010090,0
56,"Serpins, viruses, and the virome: new directions in therapy",,,"Ambadapadi, S.;Chen, H.;Zheng, D.;Liu, L.;Dai, E.",2015,,,0
57,Bovine-like coronaviruses in domestic and wild ruminants,"Coronaviruses (CoVs) produce a wide spectrum of disease syndromes in different mammalian and avian host species. These viruses are well-recognized for their ability to change tissue tropism, to hurdle the interspecies barriers and to adapt ecological variations. It is predicted that the inherent genetic diversity of CoVs caused by accumulation of point mutations and high frequency of homologous recombination is the principal determinant of these competences. Several CoVs (e.g. Severe acute respiratory syndrome-CoV, Middle East respiratory syndrome-CoV) have been recorded to cross the interspecies barrier, inducing different disease conditions in variable animal hosts. Bovine CoV (BCoV) is a primary cause of gastroenteritis and respiratory disease in cattle calves, winter dysentery in lactating cows and shipping fever pneumonia in feedlot cattle. Although it has long been known as a restrictive cattle pathogen, CoVs that are closely related to BCoV have been recognized in dogs, humans and in other ruminant species. Biologic, antigenic and genetic analyses of the so-called 'bovine-like CoVs' proposed classification of these viruses as host-range variants rather than distinct virus species. In this review, the different bovine-like CoVs that have been identified in domesticated ruminants (water buffalo, sheep, goat, dromedary camel, llama and alpaca) and wild ruminants (deer, wild cattle, antelopes, giraffes and wild goats) are discussed in terms of epidemiology, transmission and virus characteristics. The presented data denote the importance of these viruses in the persistence of BCoV in nature, spread to new geographical zones, and continuous emergence of disease epidemics in cattle farms.",agricultural land;alpaca;animal experiment;animal model;antelope;article;bird;calf (mammal);cow;dog;dromedary;dysentery;epidemic;female;gastroenteritis;genetic analysis;genetic variability;giraffe;goat;homologous recombination;host range;llama;Middle East respiratory syndrome;nonhuman;pneumonic pasteurellosis;point mutation;severe acute respiratory syndrome;sheep;tropism;virus transmission;water buffalo;wildlife;winter;biological product,"Amer, H. M.",2019,,10.1017/s1466252318000117,0
58,Metagenomic analysis demonstrates the diversity of the fecal virome in asymptomatic pigs in East Africa,"Pigs harbor a variety of viruses that are closely related to human viruses and are suspected to have zoonotic potential. Little is known about the presence of viruses in smallholder farms where pigs are in close contact with humans and wildlife. This study provides insight into viral communities and the prevalence and characteristics of enteric viral co-infections in smallholder pigs in East Africa. Sequence-independent amplification and high-throughput sequencing were applied to the metagenomics analysis of viruses in feces collected from asymptomatic pigs. A total of 47,213 de novo-assembled contigs were constructed and compared with sequences from the GenBank database. Blastx search results revealed that 1039 contigs (>200 nt) were related to viral sequences in the GenBank database. Of the 1039 contigs, 612 were not assigned to any viral taxa because they had little similarity to known viral genomic or protein sequences, while 427 contigs had a high level of sequence similarity to known viruses and were assigned to viral taxa. The most frequent contigs related to mammalian viruses resembling members of the viral genera Astrovirus, Rotavirus, Bocavirus, Circovirus, and Kobuvirus. Other less abundant contigs were related to members of the genera Sapelovirus, Pasivirus, Posavirus, Teschovirus and Picobirnavirus. This is the first report on the diversity of the fecal virome of pig populations in East Africa. The findings of the present study help to elucidate the etiology of diarrheal diseases in pigs and identify potential zoonotic and emerging viruses in the region. Further investigations are required to compare the incidence of these viruses in healthy and diseased pigs in order to better elucidate their pathogenic role.",Africa;animal;classification;feces;genetics;isolation and purification;phylogeny;pig;swine disease;veterinary medicine;virology;virus;virus infection;zoonosis,"Amimo, J. O.;El Zowalaty, M. E.;Githae, D.;Wamalwa, M.;Djikeng, A.;Nasrallah, G. K.",2016,,10.1007/s00705-016-2819-6,1
59,Association of increased rate of condemnation of broiler carcasses due to hepatic abnormalities with immunosuppressive diseases in the broiler chicken industry in Saskatchewan,"The objective of this study was to identify the causative agents of hepatitis observed in broiler chickens at processing. Livers of chickens from 16 broiler farms in Saskatchewan with gross lesions of hepatitis were collected at processing. In addition to routine bacterial isolation and histopathological examination, serologic studies for infectious bursal disease virus (IBDV) and Chicken anaemia virus (CAV), calculation of the ratio of the weight of the bursa of Fabricius (BF) to body weight (BBW), and histopathological examination of the BF were done. Of the 264 livers with gross lesions, 83% had multifocal to coalescing necrotizing hepatitis, 16% had perihepatitis, and 1% had hemorrhages. No definitive causative microorganisms were isolated from the hepatic lesions; however, no significant bacterial isolations were made. Bursal atrophy, low BBW ratio, and high titer of antibody against IBDV each correlated with the rate of total condemnations (P = 0.0188, P = 0.0001, and P = 0.0073, respectively). Nucleotide sequencing of IBDV isolated from the BF identified the variant strains Delaware-E and 586. Condemnation because of hepatic lesions was correlated with titer of antibody against IBDV and BBW (P = 0.016 and P = 0.027). The results of this study demonstrate that hepatic lesions in Saskatchewan chickens are not currently caused by a primary bacterial pathogen but are associated with indicators of immunosuppression that is likely due to variant IBDV.",animal experiment;animal model;animal tissue;article;biochemical analysis;body weight;broiler;Canada;controlled study;enzyme linked immunosorbent assay;high throughput sequencing;histopathology;immunosuppressive treatment;liver disease;liver injury;nonhuman;perihepatitis;polymerase chain reaction,"Amini, K.;Zachar, T.;Popowich, S.;Knezacek, T.;Goodhope, B.;Willson, P.;Gomis, S.",2015,,,0
60,"Kiyoshi Tajima1 and Rustam Aminov2* National Agriculture and Food Research Organization, National Institute of Livestock",,,"Aminov, R.",,,,0
61,Pet rodents and fatal lymphocytic choriomeningitis in transplant patients,"In April 2005, 4 transplant recipients became ill after receiving organs infected with lymphocytic choriomeningitis virus (LCMV); 3 subsequently died. All organs came from a donor who had been exposed to a hamster infected with LCMV. The hamster was traced back through a Rhode Island pet store to a distribution center in Ohio, and more LCMV-infected hamsters were discovered in both. Rodents from the Ohio facility and its parent facility in Arkansas were tested for the same LCMV strain as the 1 involved in the transplant-associated deaths. Phylogenetic analysis of virus sequences linked the rodents from the Ohio facility to the Rhode Island pet store, the index hamster, and the transplant recipients. This report details the animal traceback and the supporting laboratory investigations.","Animals;*Animals, Domestic/vi [Virology];*Contact Tracing;Guinea Pigs;Humans;*Immunocompromised Host;*Lymphocytic Choriomeningitis/tm [Transmission];Lymphocytic choriomeningitis virus/cl [Classification];Lymphocytic choriomeningitis virus/ge [Genetics];*Lymphocytic choriomeningitis virus;Mice;Phylogeny;Rats;*Rodentia/vi [Virology];Transplants/ae [Adverse Effects];United States/ep [Epidemiology];Zoonoses/tm [Transmission];Zoonoses/vi [Virology]","Amman, B. R.;Pavlin, B. I.;Albarino, C. G.;Comer, J. A.;Erickson, B. R.;Oliver, J. B.;Sealy, T. K.;Vincent, M. J.;Nichol, S. T.;Paddock, C. D.;Tumpey, A. J.;Wagoner, K. D.;Glauer, R. D.;Smith, K. A.;Winpisinger, K. A.;Parsely, M. S.;Wyrick, P.;Hannafin, C. H.;Bandy, U.;Zaki, S.;Rollin, P. E.;Ksiazek, T. G.",2007,May,,0
62,"Genetic characterization of 2008 reassortant influenza A virus (H5N1), Thailand","In January and November 2008, outbreaks of avian influenza have been reported in 4 provinces of Thailand. Eight Influenza A H5N1 viruses were recovered from these 2008 AI outbreaks and comprehensively characterized and analyzed for nucleotide identity, genetic relatedness, virulence determinants, and possible sites of reassortment. The results show that the 2008 H5N1 viruses displayed genetic drift characteristics (less than 3% genetic differences), as commonly found in influenza A viruses. Based on phylogenetic analysis, clade 1 viruses in Thailand were divided into 3 distinct branches (subclades 1, 1.1 and 1.2). Six out of 8 H5N1 isolates have been identified as reassorted H5N1 viruses, while other isolates belong to an original H5N1 clade. These viruses have undergone inter-lineage reassortment between subclades 1.1 and 1.2 and thus represent new reassorted 2008 H5N1 viruses. The reassorted viruses have acquired gene segments from H5N1, subclade 1.1 (PA, HA, NP and M) and subclade 1.2 (PB2, PB1, NA and NS) in Thailand. Bootscan analysis of concatenated whole genome sequences of the 2008 H5N1 viruses supported the reassortment sites between subclade 1.1 and 1.2 viruses. Based on estimating of the time of the most recent common ancestors of the 2008 H5N1 viruses, the potential point of genetic reassortment of the viruses could be traced back to 2006. Genetic analysis of the 2008 H5N1 viruses has shown that most virulence determinants in all 8 genes of the viruses have remained unchanged. In summary, two predominant H5N1 lineages were circulating in 2008. The original CUK2-like lineage mainly circulated in central Thailand and the reassorted lineage (subclades 1.1 and 1.2) predominantly circulated in lower-north Thailand. To prevent new reassortment, emphasis should be put on prevention of H5N1 viruses circulating in high risk areas. In addition, surveillance and whole genome sequencing of H5N1 viruses should be routinely performed for monitoring the genetic drift of the virus and new reassorted strains, especially in light of potential reassortment between avian and mammalian H5N1 viruses.","Animals;Birds;Cluster Analysis;*Disease Outbreaks;Genotype;*Influenza A Virus, H5N1 Subtype/ge [Genetics];Influenza A Virus, H5N1 Subtype/ip [Isolation & Purification];*Influenza in Birds/ep [Epidemiology];*Influenza in Birds/vi [Virology];Molecular Sequence Data;Phylogeny;Poultry;RNA, Viral/ge [Genetics];*Reassortant Viruses/ge [Genetics];Reassortant Viruses/ip [Isolation & Purification];Sequence Analysis, DNA;Sequence Homology;Thailand/ep [Epidemiology];0 (RNA, Viral)","Amonsin, A.;Lapkuntod, J.;Suwannakarn, K.;Kitikoon, P.;Suradhat, S.;Tantilertcharoen, R.;Boonyapisitsopa, S.;Bunpapong, N.;Wongphatcharachai, M.;Wisedchanwet, T.;Theamboonlers, A.;Poovorawan, Y.;Sasipreeyajan, J.;Thanawongnuwech, R.",2010,Sep 16,,0
63,"Multi-year evolutionary dynamics of West Nile virus in suburban Chicago, USA, 2005-2007","West Nile virus has evolved in concert with its expansion across North America, but little is known about the evolutionary dynamics of the virus on local scales. We analysed viral nucleotide sequences from mosquitoes collected in 2005, 2006, and 2007 from a known transmission 'hot spot' in suburban Chicago, USA. Within this approximately 11 × 14 km area, the viral envelope gene has increased approximately 0.1% yr-1 in nucleotide-level genetic diversity. In each year, viral diversity was higher in 'residential' sites characterized by dense housing than in more open 'urban green space' sites such as cemeteries and parks. Phylodynamic analyses showed an increase in incidence around 2005, consistent with a higher-than-average peak in mosquito and human infection rates that year. Analyses of times to most recent common ancestor suggest that WNV in 2005 and 2006 may have arisen predominantly from viruses present during 2004 and 2005, respectively, but that WNV in 2007 had an older common ancestor, perhaps indicating a predominantly mixed or exogenous origin. These results show that the population of WNV in suburban Chicago is an admixture of viruses that are both locally derived and introduced from elsewhere, containing evolutionary information aggregated across a breadth of spatial and temporal scales. © 2010 The Royal Society.",virus envelope protein;virus RNA;animal;article;chemistry;Culex;DNA sequence;genetic variability;genetics;human;molecular evolution;molecular genetics;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;sequence alignment;United States;virology;West Nile fever;West Nile virus,"Amore, G.;Bertolotti, L.;Hamer, G. L.;Kitron, U. D.;Walker, E. D.;Ruiz, M. O.;Brawn, J. D.;Goldberg, T. L.",2010,,10.1098/rstb.2010.0054,0
64,Genetic analysis of Akabane virus isolates from cattle in Korea,"Bayesian Inference (BI) and Neighbor Joining (NJ) analyses of the phylogenetic relationships between the nucleotide sequences of the N gene of Akabane virus revealed an unclear topology among genogroups I-III, which was probably caused by genetic reassortment or recombination between these genogroups. In contrast, nucleotide and amino acid phylogenetic tree analyses of the M RNA segment agreed with the topologies obtained by using the BI and NJ methods. Therefore, distinct genogrouping of Akabane virus isolates should be performed using the M RNA segment. Four Korea isolates were classified into genogroup II together with Akabane virus strains isolated from all areas of Japan, including Okinawa Island. However, more nationwide isolates and more clinical data from Korean cattle farms will be required in the future to confirm the precise relationships between genotypes and pathogenicity. © 2009 Elsevier B.V. All rights reserved.",Akabane virus;amino acid sequence;article;Bunyaviridae;bovine;controlled study;genetic analysis;genotype;Korea;molecular phylogeny;nonhuman;nucleotide sequence;phylogenetic tree;sequence alignment;viral genetics;virus isolation;virus virulence,"An, D. J.;Yoon, S. H.;Jeong, W.;Kim, H. J.;Park, B. K.",2010,,10.1016/j.vetmic.2009.07.018,0
65,The UL31 to UL35 gene sequences of duck enteritis virus correspond to their homologs in herpes simplex virus,"Five ORFs in the genome of Duck enteritis virus (DEV) corresponding to UL31, UL32, UL33, UL34, and UL35 genes of Herpes simplex virus 1 (HSV-1) were amplified by a modified ""targeted gene walking"" PCR, cloned, and sequenced. UL33, UL34, and UL35 genes were oriented from the left to the right of genome, while UL31 and UL32 had an opposite orientation. A comparison of deduced amino acid sequences of the DEV ORFs with their alphaherpesvirus homologs showed well-conserved regions except for the UL34 and UL35 genes. Phylogenetic analysis revealed that DEV was closer to the genus Mardivirus than to any other genus of the subfamily Alphaherpesvirinae. Based on this evidence, we proposed to assign DEV to the subfamily Alphaherpesvirinae.",amino acid sequence;article;controlled study;Coronavirinae;enteritis;gene amplification;gene sequence;gene targeting;genetic transcription;Human alphaherpesvirus 1;Herpesviridae;Mardivirus;molecular cloning;nonhuman;nucleotide sequence;open reading frame;phylogeny;polymerase chain reaction,"An, R.;Li, H.;Han, Z.;Shao, Y.;Liu, S.;Kong, X.",2008,,,0
66,Whole genome analysis of epizootic hemorrhagic disease virus identified limited genome constellations and preferential reassortment,"Epizootic hemorrhagic disease virus (EHDV) is a Culicoides transmitted orbivirus that causes haemorrhagic disease in wild and domestic ruminants. A collection of 44 EHDV isolated from 2008 to 2012 was fully sequenced and analysed phylogenetically. Serotype 2 viruses were the dominant serotype all years except 2012 when serotype 6 viruses represented 63% of the isolates. High genetic similarity (>94% identity) between serotype 1 and 2 virus VP1, VP3, VP4, VP6, NS1, NS2 and NS3 segments prevented identification of reassortment events for these segments. Additionally, there was little genetic diversity (>96% identity) within serotypes for VP2, VP5 and VP7. Preferential reassortment within the homologous serotype was observed for VP2, VP5 and VP7 segments for type 1 and type 2 viruses. In contrast, type 6 viruses were all reassortants containing VP2 and VP5 derived from an exotic type 6 with the remaining segments most similar to type 2 viruses. These results suggest that reassortment between type 1 and type 2 viruses requires conservation of the VP2, VP5 and VP7 segment constellation while type 6 viruses only require VP2 and VP5 and are restricted to type 2-lineage VP7. As type 6 VP2 and VP5 segments were exclusively identified in viruses with type 2-derived VP7, these results suggest functional complementation between type 2 and type 6 VP7 proteins. © 2014 SGM.",nonstructural protein 1;nonstructural protein 2;nonstructural protein 3;protein VP1;protein VP2;protein VP3;protein VP4;protein VP5;protein VP6;protein VP7;unclassified drug;viral protein;animal tissue;article;controlled study;epizootic hemorrhagic disease virus;gene sequence;genetic complementation;genetic reassortment;genetic similarity;genetic variability;microbial population dynamics;molecular phylogeny;nonhuman;nucleotide sequence;Orbivirus;priority journal;serotype;virus genome;virus isolation;virus strain,"Anbalagan, S.;Cooper, E.;Klumper, P.;Simonson, R. R.;Hause, B. M.",2014,,10.1099/vir.0.059659-0,0
67,Dietary energy drives the dynamic response of bovine rumen viral communities,"BACKGROUND: Rumen microbes play a greater role in host energy acquisition than that of gut-associated microbes in monogastric animals. Although genome-enabled advancements are providing access to the vast diversity of uncultivated microbes, our understanding of variables shaping rumen microbial communities is in its infancy. Viruses have been shown to impact microbial populations through a myriad of processes, including cell lysis and reprogramming of host metabolism. However, little is known about the processes shaping the distribution of rumen viruses or how viruses may modulate microbial-driven processes in the rumen. To this end, we investigated how rumen bacterial and viral community structure and function responded in five steers fed four randomized dietary treatments in a crossover design. RESULTS: Total digestible nutrients (TDN), a measure of dietary energy, best explained the variation in bacterial and viral communities. Additional ecological drivers of viral communities included dietary zinc content and microbial functional diversity. Using partial least squares regression, we demonstrate significant associations between the abundances of 267 viral populations and variables driving the variation in rumen viral communities. While rumen viruses were dynamic, 14 near ubiquitous viral populations were identified, suggesting the presence of a core rumen virome largely comprised of novel viruses. Moreover, analysis of virally encoded auxiliary metabolic genes (AMGs) indicates rumen viruses have glycosidic hydrolases to potentially augment the breakdown of complex carbohydrates to increase energy production. Other AMGs identified have a role in redirecting carbon to the pentose phosphate pathway and one carbon pools by folate to boost viral replication. CONCLUSIONS: We demonstrate that rumen bacteria and viruses have differing responses and ecological drivers to dietary perturbation. Our results show that rumen viruses have implications for understanding the structuring of the previously identified core rumen microbiota and impacting microbial metabolism through a vast array of AMGs. AMGs in the rumen appear to have consequences for microbial metabolism that are largely in congruence with the current paradigm established in marine systems. This study provides a foundation for future hypotheses regarding the dynamics of viral-mediated processes in the rumen.",virus DNA;zinc;animal;bacteriophage;bovine;classification;crossover procedure;diet;DNA sequence;drug effect;food;genetics;isolation and purification;metagenome;metagenomics;microbiology;microflora;procedures;rumen;virology;virus,"Anderson, C. L.;Sullivan, M. B.;Fernando, S. C.",2017,,10.1186/s40168-017-0374-3,0
68,Characterization of co-circulating swine influenza A viruses in North America and the identification of a novel H1 genetic clade with antigenic significance,"Multiple genetically and antigenically distinct hemagglutinin genes of the H1 and H3 influenza A virus (IAV) subtypes co-circulate in North American swine. This diversity has evolved by repeated transmission of IAVs from humans to swine and subsequent antigenic drift in swine. To understand the evolutionary dynamics of these diverse HA lineages in North American swine, we undertook a phylogenetic analysis of 1576 H1 and 607 H3 HA gene segments, as well as 834 N1 and 1293 N2 NA gene segments, and 2126 M gene segments. These data revealed yearly co-circulation of H1N1, H1N2, and H3N2 viruses, with three HA clades representing the majority of the HA sequences: of the H1 viruses, 42% were classified as H1δ1 and 40.6% were classified as H1γ and of the H3 viruses 53% were classified as cluster IV-A H3N2. We detected a genetically distinct minor clade consisting of 37 H1 viruses isolated between 2003 and 2013, which we classified as H1γ-2. We estimated that this clade circulated in swine since approximately 1995, but it was not detected in swine until 2003. Though this clade only represents 1.07% of swine H1 sequences reported over the past 10 years, hemagglutination inhibition (HI) assays demonstrated that representatives of this clade of viruses are antigenically distinct, and, when measured using antigenic cartography, were as many as 7 antigenic units from other H1γ viruses. Therefore vaccines against the contemporary H1γ viruses are not likely to cross-protect against γ-2 viruses. The long-term circulation of these γ-2 viruses suggests that minor populations of viruses may be underreported in the national dataset given the long branch lengths and gaps in detections. The identification of these γ-2 viruses demonstrates the need for robust surveillance to capture the full diversity IAVs in swine in the USA and the importance of antigenic drift in the diversification and emergence of new antigenic variants in swine, which complicates vaccine design.",antigenicity;article;bacteriophage;cladistics;gene identification;gene sequence;hemagglutination inhibition;Influenza A virus (H1N1);Influenza A virus (H1N2);Influenza A virus (H3N2);nonhuman;North America;phylogeny;priority journal;swine influenza A virus;swine influenza virus;virus characterization;virus gene,"Anderson, T. K.;Campbell, B. A.;Nelson, M. I.;Lewis, N. S.;Janas-Martindale, A.;Killian, M. L.;Vincent, A. L.",2015,,10.1016/j.virusres.2015.02.009,0
69,A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses,"The H1 subtype of influenza A viruses (IAVs) has been circulating in swine since the 1918 human influenza pandemic. Over time, and aided by further introductions from nonswine hosts, swine H1 viruses have diversified into three genetic lineages. Due to limited global data, these H1 lineages were named based on colloquial context, leading to a proliferation of inconsistent regional naming conventions. In this study, we propose rigorous phylogenetic criteria to establish a globally consistent nomenclature of swine H1 virus hemagglutinin (HA) evolution. These criteria applied to a data set of 7,070 H1 HA sequences led to 28 distinct clades as the basis for the nomenclature. We developed and implemented a web-accessible annotation tool that can assign these biologically informative categories to new sequence data. The annotation tool assigned the combined data set of 7,070 H1 sequences to the correct clade more than 99% of the time. Our analyses indicated that 87% of the swine H1 viruses from 2010 to the present had HAs that belonged to 7 contemporary cocirculating clades. Our nomenclature and web-accessible classification tool provide an accurate method for researchers, diagnosticians, and health officials to assign clade designations to HA sequences. The tool can be updated readily to track evolving nomenclature as new clades emerge, ensuring continued relevance. A common global nomenclature facilitates comparisons of IAVs infecting humans and pigs, within and between regions, and can provide insight into the diversity of swine H1 influenza virus and its impact on vaccine strain selection, diagnostic reagents, and test performance, thereby simplifying communication of such data. <b>IMPORTANCE</b> A fundamental goal in the biological sciences is the definition of groups of organisms based on evolutionary history and the naming of those groups. For influenza A viruses (IAVs) in swine, understanding the hemagglutinin (HA) genetic lineage of a circulating strain aids in vaccine antigen selection and allows for inferences about vaccine efficacy. Previous reporting of H1 virus HA in swine relied on colloquial names, frequently with incriminating and stigmatizing geographic toponyms, making comparisons between studies challenging. To overcome this, we developed an adaptable nomenclature using measurable criteria for historical and contemporary evolutionary patterns of H1 global swine IAVs. We also developed a web-accessible tool that classifies viruses according to this nomenclature. This classification system will aid agricultural production and pandemic preparedness through the identification of important changes in swine IAVs and provides terminology enabling discussion of swine IAVs in a common context among animal and human health initiatives.",,"Anderson, T. K.;Macken, C. A.;Lewis, N. S.;Scheuermann, R. H.;Van Reeth, K.;Brown, I. H.;Swenson, S. L.;Simon, G.;Saito, T.;Berhane, Y.;Ciacci-Zanella, J.;Pereda, A.;Davis, C. T.;Donis, R. O.;Webby, R. J.;Vincent, A. L.",2016,Nov-Dec,,0
70,Genetic classification of 'Norwalk-like viruses',"Reverse transcription-polymerase chain reaction has been used worldwide for the diagnosis of Norwalk-like virus (NLV) infection, yet a commonly accepted genetic classification scheme has not been established. Amino acid sequences from four regions of open-reading frame 2 (ORF2) were used to analyze 101 NLV strains, including 2 bovine strains. On the basis of this analysis, a genetic classification scheme is proposed that differentiates 99 human strains into 2 major genetic groups consisting of 5 and 10 genetic clusters, respectively. The 2 bovine strains constitute a newly defined third major genetic group composed of 2 putative clusters represented by each strain. This classification scheme is well supported by the analysis of the entire ORF2 sequences from 38 strains selected to represent the genetic diversity of the human strains used above. This scheme should provide a firm scientific basis for the unified classification of NLV strains detected around the world.",amino acid sequence;conference paper;nonhuman;Norwalk virus;nucleotide sequence;open reading frame;priority journal;sequence analysis;strain difference;viral genetics;virus classification,"Ando, T.;Noel, J. S.;Fankhauser, R. L.",2000,,10.1086/315589,0
71,Nipah virus infection,"Nipah virus, a paramyxovirus related to Hendra virus, first emerged in Malaysia in 1998. Clinical presentation ranges from asymptomatic infection to fatal encephalitis. Malaysia has had no more cases since 1999, but outbreaks continue to occur in Bangladesh and India. In the Malaysia-Singapore outbreak, transmission occurred primarily through contact with pigs, whereas in Bangladesh and India, it is associated with ingestion of contaminated date palm sap and human-to-human transmission. Bats are the main reservoir for this virus, which can cause disease in humans and animals. There are currently no effective therapeutics, and supportive care and prevention are the mainstays of management.",article;biosafety;clinical feature;disease association;disease transmission;epidemic;genetic variability;genome size;human;incubation time;infection prevention;infection risk;neuroradiology;Nipah virus infection;nonhuman;outcome assessment;pathology;priority journal;respiratory tract disease;risk factor;virus classification;virus morphology,"Ang, B. S. P.;Lim, T. C. C.;Wang, L.",2018,,10.1128/jcm.01875-17,0
72,Molecular epidemiology and phylogeny of Nipah virus infection: A mini review,"Nipah virus (NiV) is a member of the genus Henipavirus of the family Paramyxoviridae, characterized by high pathogenicity and endemic in South Asia. It is classified as a Biosafety Level-4 (BSL-4) agent. The case-fatality varies from 40% to 70% depending on the severity of the disease and on the availability of adequate healthcare facilities. At present no antiviral drugs are available for NiV disease and the treatment is just supportive. Phylogenetic and evolutionary analyses can be used to help in understanding the epidemiology and the temporal origin of this virus. This review provides an overview of evolutionary studies performed on Nipah viruses circulating in different countries. Thirty phylogenetic studies have been published from 2000 to 2015 years, searching on pub-med using the key words ‘Nipah virus AND phylogeny’ and twenty-eight molecular epidemiological studies from 2006 to 2015 have been performed, typing the key words ‘Nipah virus AND molecular epidemiology’. Overall data from the published study demonstrated as phylogenetic and evolutionary analysis represent promising tools to evidence NiV epidemics, to study their origin and evolution and finally to act with effective preventive measure.",biosafety;case fatality rate;controlled study;disease severity;endemic disease;health care facility;Henipavirus;molecular epidemiology;Nipah virus;Nipah virus infection;nonhuman;Paramyxoviridae;pathogenicity;phylogeny;priority journal;review;South Asia,"Angeletti, S.;Lo Presti, A.;Cella, E.;Ciccozzi, M.",2016,,10.1016/j.apjtm.2016.05.012,0
73,"Emerging Coxsackievirus A6 Causing Hand, Foot and Mouth Disease, Vietnam","Hand, foot and mouth disease (HFMD) is a major public health issue in Asia and has global pandemic potential. Coxsackievirus A6 (CV-A6) was detected in 514/2,230 (23%) of HFMD patients admitted to 3 major hospitals in southern Vietnam during 2011-2015. Of these patients, 93 (18%) had severe HFMD. Phylogenetic analysis of 98 genome sequences revealed they belonged to cluster A and had been circulating in Vietnam for 2 years before emergence. CV-A6 movement among localities within Vietnam occurred frequently, whereas viral movement across international borders appeared rare. Skyline plots identified fluctuations in the relative genetic diversity of CV-A6 corresponding to large CV-A6-associated HFMD outbreaks worldwide. These data show that CV-A6 is an emerging pathogen and emphasize the necessity of active surveillance and understanding the mechanisms that shape the pathogen evolution and emergence, which is essential for development and implementation of intervention strategies.","Adolescent;Adult;Child;*Communicable Diseases, Emerging/ep [Epidemiology];*Communicable Diseases, Emerging/vi [Virology];*Coxsackievirus Infections/ep [Epidemiology];*Coxsackievirus Infections/vi [Virology];Enterovirus A, Human/cl [Classification];Enterovirus A, Human/ge [Genetics];Enterovirus A, Human/ip [Isolation & Purification];*Enterovirus A, Human;Female;Genome, Viral;Genomics/mt [Methods];*Hand, Foot and Mouth Disease/ep [Epidemiology];*Hand, Foot and Mouth Disease/vi [Virology];Humans;Male;Phylogeny;Phylogeography;Vietnam/ep [Epidemiology];Whole Genome Sequencing;Young Adult","Anh, N. T.;Nhu, L. N. T.;Van, H. M. T.;Hong, N. T. T.;Thanh, T. T.;Hang, V. T. T.;Ny, N. T. H.;Nguyet, L. A.;Phuong, T. T. L.;Nhan, L. N. T.;Hung, N. T.;Khanh, T. H.;Tuan, H. M.;Viet, H. L.;Nam, N. T.;Viet, D. C.;Qui, P. T.;Wills, B.;Sabanathan, S.;Chau, N. V. V.;Thwaites, L.;Rogier van Doorn, H.;Thwaites, G.;Rabaa, M. A.;Van Tan, L.",2018,04,,0
74,Origin of the 1918 pandemic H1N1 influenza A virus as studied by codon usage patterns and phylogenetic analysis,"The pandemic of 1918 was caused by an H1N1 influenza A virus, which is a negative strand RNA virus; however, little is known about the nature of its direct ancestral strains. Here we applied a broad genetic and phylogenetic analysis of a wide range of influenza virus genes, in particular the PB1 gene, to gain information about the phylogenetic relatedness of the 1918 H1N1 virus. We compared the RNA genome of the 1918 strain to many other influenza strains of different origin by several means, including relative synonymous codon usage (RSCU), effective number of codons (ENC), and phylogenetic relationship. We found that the PB1 gene of the 1918 pandemic virus had ENC values similar to the H1N1 classical swine and human viruses, but different ENC values from avian as well as H2N2 and H3N2 human viruses. Also, according to the RSCU of the PB1 gene, the 1918 virus grouped with all human isolates and ""classical'' swine H1N1 viruses. The phylogenetic studies of all eight RNA gene segments of influenza A viruses may indicate that the 1918 pandemic strain originated from a H1N1 swine virus, which itself might be derived from a H1N1 avian precursor, which was separated from the bulk of other avian viruses in toto a long time ago. The high stability of the RSCU pattern of the PB1 gene indicated that the integrity of RNA structure is more important for influenza virus evolution than previously thought. Copyright © 2011 RNA Society.",codon usage;fowl;genetic analysis;genome;human;Influenza A virus;Influenza A virus (H1N1);Influenza A virus (H2N2);Influenza A virus (H3N2);nonhuman;nucleotide sequence;pandemic influenza;phylogeny;priority journal;review;virus gene;virus strain,"Anhlan, D.;Grundmann, N.;Makalowski, W. H.;Ludwig, S.;Scholtissek, C.",2011,,10.1261/rna.2395211,0
75,Characterization of highly pathogenic avian influenza H5N8 virus from Egyptian domestic waterfowl in 2017,"In 2016, the highly pathogenic avian influenza (HPAI) H5N8 virus was detected in wild birds for the first time in Egypt. In the present study, we identified the HPAI virus H5N8 of clade 2.3.4.4 from domestic waterfowl in Egypt, suggesting its transmission to the domestic poultry from the migratory birds. Based on partial haemagglutinin gene sequence, this virus has a close genetic relationship with subtype H5N8 viruses circulating in Asia and Europe. Pathologically, H5N8 virus in hybrid duck induced nervous signs accompanied by encephalomalacia, haemorrhages, nonsuppurative encephalitis and nonsuppurative vasculitis. The granular layer of cerebellum showed multifocal areas of hydropic degeneration and the Purkinje cell neurons were necrotized or lost. Additionally, the lung, kidney and spleen were congested, and necrotizing pancreatitis was also observed. The co-circulation of both HPAI H5N1 and H5N8 subtypes with the low pathogenic avian influenza H9N2 subtype complicate the control of avian influenza in Egypt with the possibility of emergence of new reassortant viruses. Therefore, continuous monitoring with implementation of strict control measures is required. Research highlights: HPAI H5N8 virus clade 2.3.4.4 was detected in domestic ducks and geese in Egypt in 2017. Phylogenetically, the virus was closely related to HPAI H5N8 viruses identified in Asia and Europe Nonsuppurative encephalitis was widely observed in HPAI H5N8 virus-infected ducks. Degeneration of the cerebellar granular layer was found in most of the brain tissues examined.",acute hemorrhagic pancreatitis;animal experiment;animal tissue;article;avian influenza;avian influenza (H5N1);cladistics;domestic animal;Egyptian;encephalitis;encephalomalacia;gene sequence;highly pathogenic avian influenza;Influenza A virus (H5N8);Influenza A virus (H9N2);molecular phylogeny;nonhuman;phylogenetic tree;Purkinje cell;vasculitis;virus characterization;virus identification;waterfowl,"Anis, A.;AboElkhair, M.;Ibrahim, M.",2018,,10.1080/03079457.2018.1470606,0
76,Two novel bocaparvovirus species identified in wild Himalayan marmots,"Bocaparvovirus (BOV) is a genetically diverse group of DNA viruses and a possible cause of respiratory, enteric, and neurological diseases in humans and animals. Here, two highly divergent BOVs (tentatively named as Himalayan marmot BOV, HMBOV1 and HMBOV2) were identified in the livers and feces of wild Himalayan marmots in China, by viral metagenomic analysis. Five of 300 liver samples from Himalayan marmots were positive for HMBOV1 and five of 99 fecal samples from these animals for HMBOV2. Their nearly complete genome sequences are 4,672 and 4,887 nucleotides long, respectively, with a standard genomic organization and containing protein-coding motifs typical for BOVs. Based on their NS1, NP1, and VP1, HMBOV1 and HMBOV2 are most closely related to porcine BOV SX/1-2 (approximately 77.0%/50.0%, 50.0%/53.0%, and 79.0%/54.0% amino acid identity, respectively). Phylogenetic analysis of these three proteins showed that HMBOV1 and HMBOV2 formed two distinctly independent branches in BOVs. According to these results, HMBOV1 and HMBOV2 are two different novel species in the Bocaparvovirus genus. Their identification expands our knowledge of the genetic diversity and evolution of BOVs. Further studies are needed to investigate their potential pathogenicity and their impact on Himalayan marmots and humans.",animal;Bocaparvovirus;China;classification;DNA sequence;feces;genetics;geography;liver;Marmota;metagenomics;nucleotide sequence;open reading frame;parvovirus infection;phylogeny;physiology;rodent disease;sequence homology;virology;virus genome,"Ao, Y.;Li, X.;Li, L.;Xie, X.;Jin, D.;Yu, J.;Lu, S.;Duan, Z.",2017,,10.1007/s11427-017-9231-4,0
77,Diverse novel astroviruses identified in wild Himalayan marmots,"With advances in viral surveillance and next-generation sequencing, highly diverse novel astroviruses (AstVs) and different animal hosts had been discovered in recent years. However, the existence of AstVs in marmots had yet to be shown. Here, we identified two highly divergent strains of AstVs (tentatively named Qinghai Himalayanmarmot AstVs, HHMAstV1 and HHMAstV2), by viral metagenomic analysis in liver tissues isolated from wild Marmota himalayana in China. Overall, 12 of 99 (12.1 %) M. himalayana faecal samples were positive for the presence of genetically diverse AstVs, while only HHMAstV1 and HHMAstV2 were identified in 300 liver samples. The complete genomic sequences of HHMAstV1 and HHMAstV2 were 6681 and 6610 nt in length, respectively, with the typical genomic organization of AstVs. Analysis of the complete ORF 2 sequence showed that these novel AstVs are most closely related to the rabbit AstV, mamastrovirus 23 (with 31.0 and 48.0% shared amino acid identity, respectively). Phylogenetic analysis of the amino acid sequences of ORF1a, ORF1b and ORF2 indicated that HHMAstV1 and HHMAstV2 form two distinct clusters among the mamastroviruses, and may share a common ancestor with the rabbit-specific mamastrovirus 23. These results suggest that HHMAstV1 and HHMAstV2 are two novel species of the genus Mamastrovirus in the Astroviridae. The remarkable diversity of these novel AstVs will contribute to a greater understanding of the evolution and ecology of AstVs, although additional studies will be needed to understand the clinical significance of these novel AstVs in marmots, as well as in humans.",novel astroviruses;species;Himalayan marmots;complete genome;phylogenetic analysis;COMPLETE GENOME SEQUENCE;MOLECULAR CHARACTERIZATION;RESPIRATORY;SYNDROME;MIDDLE-EAST;ENCEPHALITIS;VIRUS;CORONAVIRUS;HEPATITIS;CATTLE;WOODCHUCK,"Ao, Y. Y.;Yu, J. M.;Li, L. L.;Cao, J. Y.;Deng, H. Y.;Xin, Y. Y.;Liu, M. M.;Lin, L.;Lu, S.;Xu, J. G.;Duan, Z. J.",2017,Apr,,0
78,Wild-type gross leukemia virus: classification of soluble antigens (GSA),,,"Aoki, T.;Herberman, R. B.;Johnson, P. A.;Liu, M.",1972,,,0
79,Airborne infection by enteric bacteria among poultry,,,"Applegate, T.",2017,,,0
80,Phylodynamics of avian influenza clade 2.2.1 H5N1 viruses in Egypt,"Background: Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are widely distributed within poultry populations in Egypt and have caused multiple human infections. Linking the epidemiological and sequence data is important to understand the transmission, persistence and evolution of the virus. This work describes the phylogenetic dynamics of H5N1 based on molecular characterization of the hemagglutinin (HA) gene of isolates collected from February 2006 to May 2014. Methods: Full-length HA sequences of 368 H5N1 viruses were generated and were genetically analysed to study their genetic evolution. They were collected from different poultry species, production sectors, and geographic locations in Egypt. The Bayesian Markov Chain Monte Carlo (BMCMC) method was applied to estimate the evolutionary rates among different virus clusters; additionally, an analysis of selection pressures in the HA gene was performed using the Single Likelihood Ancestor Counting (SLAC) method. Results: The phylogenetic analysis of the H5 gene from 2006-14 indicated the presence of one virus introduction of the classic clade (2.2.1) from which two main subgroups were originated, the variant subgroup which was further subdivided into 2 sub-divisions (2.2.1.1 and 2.2.1.1a) and the endemic subgroup (2.2.1.2). The clade 2.2.1.2 showed a high evolution rate over a period of 6 years (6.9 × 10-3 sub/site/year) in comparison to the 2.2.1.1a variant cluster (7.2 × 10-3 over a period of 4 years). Those two clusters are under positive selection as they possess 5 distinct positively selected sites in the HA gene. The mutations at 120, 154, and 162 HA antigenic sites and the other two mutations (129Δ, I151T) that occurred from 2009-14 were found to be stable in the 2.2.1.2 clade. Additionally, 13 groups of H5N1 HPAI viruses were identified based on their amino acid sequences at the cleavage site and ""EKRRKKR"" became the dominant pattern beginning in 2013. Conclusions: Continuous evolution of H5N1 HPAI viruses in Egypt has been observed in all poultry farming and production systems in almost all regions of the country. The wide circulation of the 2.2.1.2 clade carrying triple mutations (120, 129Δ, I151T) associated with increased binding affinity to human receptors is an alarming finding of public health importance.",avian influenza vaccine;virus antigen;amino acid sequence;article;avian influenza (H5N1);cladistics;controlled study;Egypt;endemic disease;gene cluster;gene isolation;gene mutation;gene sequence;geography;hemagglutinin gene;Influenza A virus (H5N1);molecular dynamics;molecular evolution;nonhuman;nucleotide sequence;phylogeny;poultry;protein cleavage;virus gene;virus identification,"Arafa, A.;El-Masry, I.;Kholosy, S.;Hassan, M. K.;Dauphin, G.;Lubroth, J.;Makonnen, Y. J.",2016,,10.1186/s12985-016-0477-7,0
81,Complete genome characterization of avian influenza virus subtype H9N2 from a commercial quail flock in Egypt,"The suspected presence of avian influenza virus subtype H9N2 in poultry in Egypt is a major concern since this subtype is widely distributed in different countries in the Middle East, here we describe the full genetic characterization of an avian influenza A virus (Qa/Egypt/11; H9N2) of subtype H9N2 that was previously isolated from a clinically normal quail flock in Giza, Egypt in May 2011. The nucleotide sequence analysis of the hemagglutinin gene of the isolated Egyptian virus showed the highest similarity with one group of recent Israeli strains (97 %) circulating from 2006-2010. Sequence homology and phylogenetic analysis indicated that the Qa/Egypt/11 isolate belonged to the A/quail/Hong Kong/G1/1997-like lineage with new mutations identified in all viral proteins. The phylogenetic analysis for the eight genes indicated placement of the Egyptian virus within the same lineage of H9N2 viruses that circulated in the region from 2006, especially with one group of recent Israeli strains. However, phylogenetic analysis of the internal genes like PB2, NP, and PA genes identified possible reassortment events for these genes with singular Israeli strains. This study indicates progressive evolution of this subtype in the Middle East region and possible mechanism of virus adaptation in land-based poultry like in quails. © Springer Science+Business Media, LLC 2012.",hemagglutinin;viral protein;adaptation;animal cell;article;avian influenza virus;avian influenza virus H9N2;controlled study;Egypt;gene mutation;genetic reassortment;molecular evolution;nonhuman;nucleotide sequence;phylogeny;poultry;priority journal;quail;sequence analysis;sequence homology;virus genome;virus isolation;virus strain,"Arafa, A. S.;Hagag, N.;Erfan, A.;Mady, W.;El-Husseiny, M.;Adel, A.;Nasef, S.",2012,,10.1007/s11262-012-0775-0,0
82,Characterization of Sri Lanka rabies virus isolates using nucleotide sequence analysis of nucleoprotein gene,"Thirty-four suspected rabid brain samples from 2 humans, 24 dogs, 4 cats, 2 mongooses, 1 jackal and 1 water buffalo were collected in 1995-1996 in Sri Lanka. Total RNA was extracted directly from brain suspensions and examined using a one-step reverse transcription-polymerase chain reaction (RT-PCR) for the rabies virus nucleoprotein (N) gene. Twenty-eight samples were found positive for the virus N gene by RT-PCR and also for the virus antigens by fluorescent antibody (FA) test. Rabies virus isolates obtained from different animal species in different regions of Sri Lanka were genetically homogenous. Sequences of 203 nucleotides (nt)-long RT-PCR products obtained from 16 of 27 samples were found identical. Sequences of 1350 nt of N genes of 14 RT-PCR products were determined. The Sri Lanka isolates under study formed a specific cluster that included also an earlier isolate from India but did not include the known isolates from China, Thailand, Malaysia, Israel, Iran, Oman, Saudi Arabia, Russia, Nepal, Philippines, Japan and from several other countries. These results suggest that one type of rabies virus is circulating among human, dog, cat, mongoose, jackal and water buffalo living near Colombo City and in other five remote regions in Sri Lanka.",virus antigen;virus nucleoprotein;virus RNA;agar gel electrophoresis;amino acid sequence;animal tissue;article;brain;buffalo;Carnivora;cat;controlled study;dog;fluorescent antibody technique;human;human tissue;nonhuman;nucleotide sequence;phylogeny;Rabies virus;reverse transcription polymerase chain reaction;Sri Lanka;virus characterization;virus isolation,"Arai, Y. T.;Takahashi, H.;Kameoka, Y.;Shiino, T.;Wimalaratne, O.;Lodmell, D. L.",2001,,,0
83,Phylogenetic analysis of classical swine fever virus isolates from Peru,"Classical swine fever (CSF) is considered to be endemic in Peru with outbreaks reported to the World Organization for Animal Health as recently as 2008 and 2009. Nevertheless, little is known regarding the genetic subgroup(s) of CSF virus that are circulating in Peru or their relationship to recent CSF viruses that have been isolated from neighbouring South American countries or other parts of the world. In this study, we molecularly characterize CSF viruses that were isolated from domestic pigs from different regions of Peru from the middle of 2007 to early 2008. All virus isolates were found to belong to genetic subgroup 1.1, consistent with the subgroup of viruses that have been identified from other South American countries. Although the Peruvian isolates are most closely related to viruses from Colombia and Brazil, they form a monophyletic clade, which suggests they have a distinct evolutionary history. ©2010 Canadian Food Inspection Agency.",animal;article;classical swine fever;classification;genetics;Peru;Pestivirus;phylogeny;reverse transcription polymerase chain reaction;pig;virology,"Araínga, M.;Hisanaga, T.;Hills, K.;Handel, K.;Rivera, H.;Pasick, J.",2010,,10.1111/j.1865-1682.2010.01144.x,0
84,Migratory birds in southern Brazil are a source of multiple avian influenza virus subtypes,"BACKGROUND: There is insufficient knowledge about the relation of avian influenza virus (AIV) to migratory birds in South America. Accordingly, we studied samples obtained over a 4-year period (2009-2012) from wild birds at a major wintering site in southern Brazil. METHODS: We obtained 1212 oropharyngeal/cloacal samples from wild birds at Lagoa do Peixe National Park and screened them for influenza A virus by RT-PCR amplification of the matrix gene. Virus isolates were subjected to genomic sequencing and antigenic characterization. RESULTS: Forty-eight samples of 1212 (3.96%) contained detectable influenza virus RNA. Partial viral sequences were obtained from 12 of these samples, showing the presence of H2N2 (1), H6Nx (1), H6N1 (8), H9N2 (1), and H12N5 (1) viruses. As H6 viruses predominated, we generated complete genomes from all 9 H6 viruses. Phylogenetic analyses showed that they were most similar to viruses of South American lineage. The H6N1 viruses caused no disease signs in infected ferrets and, despite genetic differences, were antigenically similar to North American isolates. CONCLUSIONS: Lagoa do Peixe National Park is a source of multiple AIV subtypes, with the levels of influenza virus in birds being highest at the end of their wintering period in this region. H6N1 viruses were the predominant subtype identified. These viruses were more similar to viruses of South American lineage than to those of North American lineage.","Animals;Antigens, Viral/an [Analysis];*Birds/vi [Virology];Brazil;Cloaca/vi [Virology];*Genetic Variation;*Influenza A virus/cl [Classification];Influenza A virus/ge [Genetics];*Influenza A virus/ip [Isolation & Purification];*Influenza in Birds/vi [Virology];Oropharynx/vi [Virology];Reverse Transcriptase Polymerase Chain Reaction;Sequence Analysis, DNA;Viral Matrix Proteins/ge [Genetics];0 (Antigens, Viral);0 (M1 protein, Influenza A virus);0 (Viral Matrix Proteins)","Araujo, J.;Petry, M. V.;Fabrizio, T.;Walker, D.;Ometto, T.;Thomazelli, L. M.;Scherer, A. L.;Serafini, P. P.;Neto, I. S.;Krauss, S.;Webster, R. G.;Webby, R. J.;Durigon, E. L.",2018,03,,0
85,Isolation and rapid identification of a Kerala isolate of duck enteritis virus using polymerase chain reaction,"Duck enteritis virus (DEV) is a herpes virus that cause an acute, contagious, and fatal disease. In this present article, we introduce a polymerase chain reaction (PCR) assay for DEV DNA. The method employed primer sets targeting the viral DNA polymerase gene (UL30), type I membrane protein that binds to heparin sulphate (glycoprotein C) and glycoprotein E of DEV and was able to amplify DNA fragments of the expected size from infected samples. The method will provide a valuable tool for a rapid laboratory diagnosis of DEV infection. By virtue of its high throughput format, the method may be useful for large epidemiological surveys and clarification of pathogenesis, such as latency of the virus.",DNA fragment;DNA polymerase;envelope protein;glycoprotein E;protein C;virus DNA;animal cell;animal tissue;article;controlled study;duck;duck enteritis virus;envelope gene;gene amplification;Herpesviridae;high throughput sequencing;molecular size;nonhuman;polymerase chain reaction;virus envelope;virus gene;virus identification;virus isolation;virus latency,"Aravind, S.;Kamble, N. M.;Gaikad, S. S.;Shukla, S. K.;Khulpae, S. A.;Dey, S.;Mohan, C. M.",2014,,,0
86,Molecular features of influenza A (H1N1) pdm09 prevalent in Mexico during winter seasons 2012-2014,"Since the emergence of the pandemic H1N1pdm09 virus in Mexico and California, biannual increases in the number of cases have been detected in Mexico. As observed in previous seasons, pandemic A/H1N1 09 virus was detected in severe cases during the 2011-2012 winter season and finally, during the 2013-2014 winter season it became the most prevalent influenza virus. Molecular and phylogenetic analyses of the whole viral genome are necessary to determine the antigenic and pathogenic characteristics of influenza viruses that cause severe outcomes of the disease. In this paper, we analyzed the evolution, antigenic and genetic drift of Mexican isolates from 2009, at the beginning of the pandemic, to 2014. We found a clear variation of the virus in Mexico from the 2011-2014 season due to different markers and in accordance with previous reports. In this study, we identified 13 novel substitutions with important biological effects, including virulence, T cell epitope presented by MHC and host specificity shift and some others substitutions might have more than one biological function. The systematic monitoring of mutations on whole genome of influenza A pH1N1 (2009) virus circulating at INER in Mexico City might provide valuable information to predict the emergence of new pathogenic influenza virus",VIRUS RNA-POLYMERASE;INCREASED VIRULENCE;STRUCTURAL BASIS;BINDING-SITE;SWINE;IDENTIFICATION;MUTATIONS;PROTEIN;NS1;HEMAGGLUTININ,"Arellano-Llamas, R.;Alfaro-Ruiz, L.;Canon, C. A.;Rosshandler, II;Cruz-Lagunas, A.;Zuniga, J.;Vega, R. R.;Wong, C. W.;Maurer-Stroh, S.;Cordoba, S. R.;Liu, E. T.;Hidalgo-Miranda, A.;Vazquez-Perez, J. A.",2017,Jul,,0
87,Eradication strategies of infectious diseases: African swine fever and porcine reproductive and respiratory syndrome (PRRS),"This publication gives a brief overview of two economically important diseases that affect the porcine species, Although they are caused by taxonomically distant viruses which produce different symptomatology and disease, successful strategies were used for their control and eradication. African swine fever (ASE) is included in the list A of OIE, and its importance in Europe comes out from the increase of outbreaks in the sub-Saharan countries of Africa in the last years, and porcine reproductive and respiratory syndrome (PRRS), a disease currently not included in the OIE list but nowadays perhaps one of the biggest problem in the international animal health. The authors review in this paper both diseases and the current strategies used for eradication of ASFV and for the removal of PRRS virus from endemic herds.",LINKED-IMMUNOSORBENT-ASSAY;IMMUNOPEROXIDASE MONOLAYER ASSAY;POLYMERASE-CHAIN-REACTION;SYNDROME VIRUS;LELYSTAD VIRUS;ANTIBODIES;ELISA;INFERTILITY;SURVIVAL;PROTEIN,"Arias, M.;Romero, L.;Aguero, M.;Canals, A.;Zamora, M. J.;Sanchez-Vizcaino, J. M.",2001,Jan,,0
88,"Co-circulation dynamics and persistence of newly introduced clades of 2012 outbreak associated West Nile Virus in Texas, 2012–2015","The second largest outbreak of West Nile encephalitis and West Nile fever ever recorded occurred in the United States (U.S) in the summer of 2012. The outbreak was related to the widespread circulation of closely related clades, or groups, of West Nile virus (WNV) into multiple states where they were not previously found. Whether the invading 2012 strains were able to circulate and overwinter in states with their own endemic population of WNV is unknown and the effect of viral genetics on adaptation and persistence in a new ecological niche is unclear. In this study, we sequenced 70 mosquito isolates from multiple counties throughout Texas in 2012–2015. We identified isolates representative of previously described 2012 WNV groups (Groups 8–10) and discovered a novel group which we called Group 11. Although we identified isolates representative of WNV endemic (2/70) to Texas, most isolates (68/70) were related to the invading 2012 strains, and of these Group 10 (45/68) was predominant. We also observed differences among the 2012 WNV groups correlating to their genotype. Group 10 WNV in Texas, which carry two putative positively selected variants, had limited introductions into Texas, wide circulation, and strong evidence of continued persistence perhaps indicative of overwintering. In contrast, Groups 8 and 11, without positively selected variants, had multiple introductions into Texas, limited circulation, and limited persistence. Lastly, we identified a potential transmission source in New York for incoming Group 8 WNV into Texas. Altogether our study suggests that mutations in the WNV genome may influence the range and dynamics of WNV circulation, and the ability of different strains to persist in new ecological niches.",animal experiment;article;cladistics;epidemic;genotype;mosquito;nonhuman;nucleotide sequence;overwintering;phylogeny;population genetics;priority journal;Texas;viral genetics;virus encephalitis;virus genome;virus identification;virus isolation;virus morphology;virus mutation;virus strain;virus survival;virus transmission;West Nile fever;West Nile virus,"Aroh, C.;Liang, C.;Raj, P.;Wakeland, B.;Yan, N.;Wakeland, E.",2018,,10.1016/j.meegid.2018.08.025,0
89,Letter to the editor: Drift in the nucleoprotein gene of swine influenza virus (H1N1) causing respiratory disease in pigs,"The nucleoprotein (NP) gene of swine influenza H1N1 variant, A/Sw/Quebec/5393/91 (SwQc91) was sequenced. When compared with other H1N1 strains, 12 amino acid (aa) replacements were observed in the 101-484 aa region of the NP protein including two aas, 345 and 430, representing the unique lineage of swine viruses. Phylogenetic analysis showed a drift in the NP gene.",virus nucleoprotein;amino acid sequence;amino acid substitution;article;gene sequence;genetic drift;nonhuman;phylogeny;priority journal;swine influenza virus;virus gene;virus strain,"Arora, D. J. S.",2002,,10.1023/a:1020134511510,0
90,Porcine Astrovirus Type 3 in Central Nervous System of Swine with Polioencephalomyelitis,"Using next-generation sequencing, we identified and genetically characterized a porcine astrovirus type 3 strain found in tissues from the central nervous system of 1 piglet and 3 sows with neurologic signs and nonsuppurative polioencephalomyelitis. Further studies are needed to understand the potential for cross-species transmission and clinical impact.","Animals;Astroviridae Infections/ep [Epidemiology];Astroviridae Infections/pa [Pathology];*Astroviridae Infections/ve [Veterinary];Astroviridae Infections/vi [Virology];Capsid Proteins/ge [Genetics];Capsid Proteins/me [Metabolism];Central Nervous System/pa [Pathology];Central Nervous System/vi [Virology];Encephalitis, Viral/ep [Epidemiology];Encephalitis, Viral/pa [Pathology];*Encephalitis, Viral/ve [Veterinary];Encephalitis, Viral/vi [Virology];*Encephalomyelitis, Enzootic Porcine/ep [Epidemiology];Encephalomyelitis, Enzootic Porcine/pa [Pathology];Encephalomyelitis, Enzootic Porcine/vi [Virology];Farms;Gene Expression;*Genome, Viral;Iowa/ep [Epidemiology];Mamastrovirus/cl [Classification];*Mamastrovirus/ge [Genetics];Mamastrovirus/ip [Isolation & Purification];Mamastrovirus/py [Pathogenicity];*Phylogeny;RNA Replicase/ge [Genetics];RNA Replicase/me [Metabolism];Swine;*Swine Diseases/ep [Epidemiology];Swine Diseases/pa [Pathology];Swine Diseases/vi [Virology];Whole Genome Sequencing;0 (Capsid Proteins)","Arruda, B.;Arruda, P.;Hensch, M.;Chen, Q.;Zheng, Y.;Yang, C.;Gatto, I. R. H.;Ferreyra, F. M.;Gauger, P.;Schwartz, K.;Bradner, L.;Harmon, K.;Hause, B.;Li, G.",2017,12,,1
91,Identification of a Divergent Lineage Porcine Pestivirus in Nursing Piglets with Congenital Tremors and Reproduction of Disease following Experimental Inoculation,"Congenital tremors is a sporadic disease of neonatal pigs characterized by action-related repetitive myoclonus. A majority of outbreaks of congenital tremors have been attributed to an unidentified virus. The objectives of this project were to 1) detect potential pathogen(s) in samples from piglets with congenital tremors and 2) develop an infection model to reproduce disease. Using next-generation sequencing, a divergent lineage pestivirus was detected in piglets with congenital tremors. The virus was originally most closely related to a bat pestivirus but is now more closely related to a recently published novel porcine pestivirus provisionally named atypical porcine pestivirus. A quantitative real-time PCR detected the virus in samples from neonatal piglets with congenital tremors from two separate farms, but not in samples from unaffected piglets from the same farm. To fulfill the second objective, pregnant sows were inoculated with either serum containing the pestivirus or PBS (control) by intravenous and intranasal routes simultaneously with direct inoculation of fetal amniotic vesicles by ultrasound-guided surgical technique. Inoculations were performed at either 45 or 62 days of gestation. All sows inoculated with the novel pestivirus farrowed piglets affected with congenital tremors while PBS-inoculated control piglets were unaffected. Tremor severity for each piglet was scored from videos taken 0, 1 and 2 days post-farrowing. Tremor severity remained relatively constant from 0 to 2 days post-farrowing for a majority of piglets. The prevalence of congenital tremors in pestivirus-inoculated litters ranged from 57% (4 out of 7 affected piglets) to 100% (10 out of 10 affected piglets). The virus was consistently detected by PCR in tissues from piglets with congenital tremors but was not detected in control piglets. Samples positive by PCR in greater than 90% of piglets sampled included brainstem (37 out of 41), mesenteric lymph node (37 out of 41), tracheobronchial lymph node (37 out of 41), and whole blood (19 out of 20). Although the first description of congenital tremors was in 1922, this is the first reported reproduction of congenital tremors following experimental inoculation with a divergent lineage porcine pestivirus. Studies investigating disease mechanism, epidemiology, and diagnostic assay development are needed to better understand the pathophysiology of congenital tremors due to this pestivirus.","Animals;Female;High-Throughput Nucleotide Sequencing;Pestivirus/ge [Genetics];*Pestivirus/ip [Isolation & Purification];*Pestivirus/ph [Physiology];Pregnancy;RNA, Viral/ge [Genetics];*Swine/vi [Virology];*Swine Diseases/cn [Congenital];*Swine Diseases/vi [Virology];*Tremor/cn [Congenital];*Tremor/vi [Virology];0 (RNA, Viral)","Arruda, B. L.;Arruda, P. H.;Magstadt, D. R.;Schwartz, K. J.;Dohlman, T.;Schleining, J. A.;Patterson, A. R.;Visek, C. A.;Victoria, J. G.",2016,,,1
92,Genetic ancestor of external antigens of pandemic influenza A/H1N1 virus,"The aim of the present investigation was to discover the genetic relationships of 2009 pandemic novel influenza A/H1N1 virus (NIV) external antigens Hemagglutinin (HA) and Neuraminidase (NA) with other influenza viruses by performing phylogenetic, comparative and statistical analyses. Phylogenetic trees of these two antigens show that the sequences of the NIV viruses are relatively homogeneous and these were derived from several viruses circulating in swine. The phylogenetic tree of HA shows that NIV had the closest relationship with North-American pig lineages whereas NA had with European pig lineages. In both segments, NIVs had the closest genetic relationship with swine influenza virus lineages. It strongly suggests that pigs are the most possible animal reservoir. Comparative analysis shows that among clade A, NIVs had very low genetic divergence as well as high similarity and also suffered strong purifying selection whereas neighbor clade B shows moderate values when compared to those of clades C-F. It indicates that classical swine influenza viruses present in clade B might be an ancestor of NIVs external antigens. The process of re-assortment occurred in classical swine influenza viruses. The mutation sites exclusively fixed in the NIV of swine and human along with vaccine strain provide an important suggestion for disease diagnosis and vaccine research.",Influenza virus hemagglutinin;sialidase;virus antigen;animal;article;genetics;human;influenza;Influenza A virus (H1N1);molecular evolution;mutation;nucleotide sequence;orthomyxovirus infection;phylogeny;pig;swine disease;virology,"Arunachalam, R.;Paulkumar, K.;Annadurai, G.",2012,,10.1007/s12539-012-0136-7,0
93,Phylogenetic analysis of pandemic influenza A/H1N1 virus,"The principle of the present study was to determine the evolution of pandemic novel influenza A/H1N1 2009 virus (NIV) by phylogenetic, comparative and statistical analyses. The phylogenetic trees of eight genomic segments illustrate that, so far, the sequences of the NIVs (outbreak group A) are relatively homogeneous and derived by the event of multiple genetic reassortment of Eurasian and North American swine, avian and human viruses (group B). It implies that some of the influenza viruses in group B had higher potential to evolve and getting the ability to transmit from human-to-human after animal-to-human cross-species transmission. The second analysis shows that NIV had attempted a little evolutionary change among humans and before introduction into human it had long evolutionary history. Statistical analysis shows that viruses from both outbreak and nearest group have homologous genes in their genomes which might be reflecting the phylogenetic relationship of strains, and also the presence of unique mutations between groups A-B may associate with increased virulence of NIVs. Both phylogenetic and cluster analyses confirm that the gene exchange takes place between viruses originated from different species and it could be generated NIV with unpredictable pandemic potential. Hence, we conclude that an extensive study should be made to recognize, which reassortment groups are closely related to NIVs, and to determine the sites in the genes of NIV under greatest or least selection pressure, which will ultimately be important in the effective design of vaccine and drugs for 'swine flu'.",pandemic 2009 NIV;genomic sequence;phylogeny;reassortment;evolution.;EVOLUTIONARY GENOMICS;NATURAL-SELECTION;A VIRUSES;ORIGIN;HUMANS;EMERGENCE;GENES,"Arunachalam, R.;Paulkumar, K.;Annadurai, G.",2012,Feb,,0
94,Subgroup determination of group a rotaviruses recovered from piglets in Nigeria,"Subgroup analysis using subgroup-specific monoclonal ELISA revealed a preponderance of subgroup 2-specific antigens of group A porcine rotaviruses over subgroup 1. Of 113 polyacrylamide gel electrophoresis-positive test samples, obtained from 4 States of Nigeria, 31 (27.4%) and 45 (39.8%) were determined to have subgroup 1 and 2 specificities, respectively. However, 37 (32.7%) test samples could not be classified into any of the known group A rotavirus subgroups. These 'unclassifiable' samples probably had neither subgroup 1 nor 2 specificities in ELISA or could belong to a third subgroup unknown or not investigated in this study. In all age groups investigated, subgroup 1 and 2 specific antigens were prevalent. This was also observed after yearly analysis of subgroup specificity; however, a higher prevalence of subgroup 2 specificity was observed in 1990 and 1991. Subgroup 1 rotaviruses were found in all the 4 States sampled (Plateau, Benue, Oyo, and Cross River), whereas subgroup 2 rotaviruses were detected only in Plateau State. All rotaviruses recovered in this study had long genome electrophoretic migration patterns, irrespective of subgroup. Thus genomic diversity of group A rotaviruses does not necessarily reflect antigenic diversity, as there is no mandatory correlation between genome electropherotype pattern and subgroup specificity.",virus antigen;antigenic variation;article;electrophoretic mobility;enzyme linked immunosorbent assay;geographic distribution;Nigeria;nonhuman;polyacrylamide gel electrophoresis;Rotavirus;pig;virus classification;virus genome,"Atii, D. J. I.;Ojeh, C. K.",1995,,,0
95,Metagenomic virome analysis of Culex mosquitoes from Kenya and China,,,"Atoni, E.;Wang, Y.;Karungu, S.;Waruhiu, C.;Zohaib, A.",2018,,,0
96,Integrated use of three machine learning techniques for influenza virus classification,,,"Attaluri, P. K.;Chen, Z.;Lu, G.",,,,0
97,Effects of orally administered Bdellovibrio bacteriovorus on the well-being and Salmonella colonization of young chicks,"Bdellovibrio bacteriovorus is a bacterium which preys upon and kills Gram-negative bacteria, including the zoonotic pathogens Escherichia coli and Salmonella. Bdellovibrio has potential as a biocontrol agent, but no reports of it being tested in living animals have been published, and no data on whether Bdellovibrio might spread between animals are available. In this study, we tried to fill this knowledge gap, using B. bacteriovorus HD100 doses in poultry with a normal gut microbiota or predosed with a colonizing Salmonella strain. In both cases, Bdellovibrio was dosed orally along with antacids. After dosing non-Salmonella-infected birds with Bdellovibrio, we measured the health and well-being of the birds and any changes in their gut pathology and culturable microbiota, finding that although a Bdellovibrio dose at 2 days of age altered the overall diversity of the natural gut microbiota in 28-day-old birds, there were no adverse effects on their growth and well-being. Drinking water and fecal matter from the pens in which the birds were housed as groups showed no contamination by Bdellovibrio after dosing. Predatory Bdellovibrio orally administered to birds that had been predosed with a gut-colonizing Salmonella enterica serovar Enteritidis phage type 4 strain (an important zoonotic pathogen) significantly reduced Salmonella numbers in bird gut cecal contents and reduced abnormal cecal morphology, indicating reduced cecal inflammation, compared to the ceca of the untreated controls or a nonpredatory ΔpilA strain, suggesting that these effects were due to predatory action. This work is a first step to applying Bdellovibrio therapeutically for other animal, and possibly human, infections. © 2011, American Society for Microbiology.","animal;animal salmonellosis;article;bacterial count;bacterial gene;bacteriophage;Bdellovibrio;biological control agent;cecum;chicken;clinical trial;controlled clinical trial;controlled study;cell culture technique;Escherichia coli;feces;genetics;growth, development and aging;male;metagenome;microbiology;oral drug administration;pathogenicity;pathology;physiology;randomized controlled trial;Salmonella enterica serovar Enteritidis;body weight gain","Atterbury, R. J.;Hobley, L.;Till, R.;Lambert, C.;Capeness, M. J.;Lerner, T. R.;Fenton, A. K.;Barrow, P.;Sockett, R. E.",2011,,10.1128/aem.00426-11,0
98,"Genetic characterization of foot-and-mouth disease viruses, Ethiopia, 1981-2007","Foot-and-mouth disease (FMD) is endemic to sub-Saharan Africa. To further understand its complex epidemiology, which involves multiple virus serotypes and host species, we characterized the viruses recovered from FMD outbreaks in Ethiopia during 1981-2007. We detected 5 of the 7 FMDV serotypes (O, A, C, Southern African Territories [SAT] 1, and SAT 2). Serotype O predominated, followed by serotype A; type C was not recognized after 1983. Phylogenetic analysis of virus protein 1 sequences indicated emergence of a new topotype within serotype O, East Africa 4. In 2007, serotype SAT 1 was detected in Ethiopia and formed a new distinct topotype (IX), and serotype SAT 2 reappeared after an apparent gap of 16 years. The diversity of viruses highlights the role of this region as a reservoir for FMD virus, and their continuing emergence in Ethiopia will greatly affect spread and consequent control strategy of the disease on this continent.",viral protein;amino acid sequence;article;controlled study;Ethiopia;Foot and mouth disease virus;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;serotype;unindexed sequence,"Ayelet, G.;Mahapatra, M.;Gelaye, E.;Egziabher, B. G.;Rufeal, T.;Sahle, M.;Ferris, N. P.;Wadsworth, J.;Hutchings, G. H.;Knowles, N. J.",2009,,10.3201/eid1509.090091,0
99,Differentiation of Proteins and Viruses Using Pyrolysis Gas Chromatography Differential Mobility Spectrometry (PY/GC/DMS) and Pattern Recognition,"It is extremely important to develop novel analytical sensors for pathogen detection. Applications of such sensors range from ensuring environmental monitoring, to providing human health diagnostic measures, and to early warning systems for bioterrorism. Certain viruses and bacteria pathogens are of special concern for their ability to spread rapidly in human populations during a pandemic, and emerging variants of these pathogens are challenging to detect. This paper provides a reliable detection strategy to classify viruses from innocuous proteins. Our novel instrumentation is based on pyrolysis gas chromatography differential mobility spectrometry (PY/GC/DMS), and couples a genetic algorithm based machine learning method for pattern recognition with a microfabricated solid state biosensor. Together, this hardware and software combination allowed for an extremely high classification accuracy (94%) between the T4 bacteriophage from bovine serum albumin (BSA), an unrelated protein. This study suggests that this portable sensor can be used along with the sophisticated data mining method as a fast, reliable, and accurate tool for the recognition of viruses.",Biosensor;differential mobility spectrometer (DMS);genetic algorithm;microelectronics;neural networks;pyrolysis;TRANSFORM-INFRARED-SPECTROSCOPY;HEPATITIS-A VIRUS;MASS-SPECTROMETRY;GENETIC ALGORITHM;PCR;TECHNOLOGY;ROTAVIRUS;COMPLEXES;SPECIMENS;BACTERIA,"Ayer, S.;Zhao, W. X.;Davis, C. E.",2008,Sep-Oct,,0
100,"Evaluation of oxidative stress via total antioxidant status, sialic acid, malondialdehyde and RT-PCR findings in sheep affected with bluetongue","INTRODUCTION: Bluetongue (BT) is a non-contagious infectious disease of ruminants. The disease agent bluetongue virus (BTV) is classified in the Reoviridae family Orbivirus. AIMS AND OBJECTIVES: The aim of this study was to determine serum malondialdehyde (MDA), total antioxidative stres (TAS), total sialic acid (TSA), ceruloplasmin, triglyceride, alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma-glutamyltransferase (GGT), cholesterol, creatinine, albumin, and total protein levels in sheep with and without bluetongue (BT). MATERIALS AND METHODS: The study included 13 Sakiz crossbreed sheep, aged 1-4 years and usually in the last stage of pregnancy, as the BT group and a control group consisting of 10 healthy sheep. All sheep were clinically examined before collecting blood samples. Serum ALT, AST, cholesterol, triglyceride, albumin, GGT, total protein, creatinine and TAS levels were measured using commercially available kits as per manufacturer's recommendations using a Biochemistry Auto Analyzer (Sinnowa D280, China). Serum lipid peroxidation was estimated through a previously described method in which MDA reacts with thiobarbituric acid (TBA) to form a coloured complex at a maximum absorbance of 535 nm. The TSA value was measured at 549 nm using the method described by Warren (1959): sialic acid was oxidised to formyl-pyruvic acid, which reacts with TBA to form a pink product. The ceruloplasmin concentration was measured according to Sunderman and Nomoto (1970): ceruloplasmin and p-phenylenediamine formed a coloured oxidation product that was proportional to the concentration of serum ceruloplasmin. Real time RT-PCR and conventional RT-PCR were performed as described by Shaw and others (2007). RESULTS: Biochemistry analysis of serum showed that in the BT group, TSA, MDA, triglyceride and ALT and AST were higher and that ceruloplasmin and TAS were lower than in the control group. Serum albumin, cholesterol, creatinine, total protein and GGT did not differ significantly between the two groups. CONCLUSIONS: Serum triglyceride, ceruloplasmin, TSA, MDA and TAS concentrations may prove beneficial to the diagnosis, prognosis and biochemical analysis of BT.",,"Aytekin, I.;Aksit, H.;Sait, A.;Kaya, F.;Aksit, D.;Gokmen, M.;Baca, A. U.",2015,,,0
101,"Shift of Enterovirus species among children in Cameroon--identification of a new enterovirus, EV-A119","BACKGROUND: Infections caused by human enteroviruses (EVs) are often asymptomatic or mild, although they may cause more severe illnesses as meningitis and acute flaccid paralysis. EVs have globally posed a threat to children, and outbreaks of aseptic meningitis and hand, foot and mouth disease are frequently reported. OBJECTIVE: To identify EV strains circulating among healthy children in a small community in Limbe, Cameroon two years apart. STUDY DESIGN: Species and EV types were obtained by partial 5'UTR-VP4 and VP1 sequencing of RNA from stool samples collected in October 2009 and September 2011 from 150 children in Cameroon. RESULTS: In all, 74 children (49%) were infected with 28 different types of EV. There were 29 (54%) infected children in 2009, and 45 (47%) in 2011. There was a significant difference between detected species of EV, with 15 (47%) children infected with EV-A in 2009, and 22 (71%) with EV-B in 2011 (p=0.0001). In 2009, one child was infected by a divergent EV, which was most similar to EV-A90. Based on the complete VP1 sequence, it was shown to be a new EV designated EV-A119. CONCLUSION: The current study shows a high heterogeneity of circulating EV types among children in Limbe, Cameroon, and a previously not described shift in predominating EV species.","5' Untranslated Regions;Adolescent;Cameroon/ep [Epidemiology];Child;Child, Preschool;Cluster Analysis;*Enterovirus/cl [Classification];Enterovirus/ge [Genetics];*Enterovirus/ip [Isolation & Purification];*Enterovirus Infections/ep [Epidemiology];*Enterovirus Infections/vi [Virology];Feces/vi [Virology];Female;*Genetic Variation;Humans;Male;Molecular Sequence Data;Phylogeny;RNA, Viral/ge [Genetics];Sequence Analysis, DNA;Viral Proteins/ge [Genetics];0 (5' Untranslated Regions);0 (RNA, Viral);0 (Viral Proteins)","Ayukekbong, J.;Kabayiza, J. C.;Lindh, M.;Nkuo-Akenji, T.;Tah, F.;Bergstrom, T.;Norder, H.",2013,Sep,,0
102,Phylogenic analysis of serotype Asia1 foot-and-mouth disease virus from Sulaimani/Iraq using VP1 protein: Heterogeneity with vaccine strain As1/Shamir/89,"Foot-and-mouth disease virus (FMDV) serotypes O, A and Asia1 are responsible for a significant number of disease outbreaks in Iraq. The current study can be considered as the first molecular characterization of serotype Asia1 in Iraq. The present investigation reports the detection of serotype FMDV Asia1 from local farms in Sulaimani districts in 2012 and 2014 outbreaks. Phylogenetic analysis of the complete VP1 gene has shown that FMDV Asia1 field isolates were under genetic novel variant Sindh-08 (group VII) including PAK/iso/11 and TUR/13 strains. The VP1 protein sequence of circulatory FMDV Asia1 genotype showed heterogeneity of nine amino acid substitutions within the G-H loop with the vaccine strain As1/Shamir/89 (JF739177) that is currently used in vaccination program in Iraq. Our result indicated that differences in VP1 protein at G-H loop of the locally circulated FMDV serotype Asia1 strain may be a reason for current vaccination failure.",protein VP1;article;cell heterogeneity;epidemic;epithelium;Foot and mouth disease virus;gene;genotype;Iraq;neighbor joining method;nonhuman;phylogenetic tree;phylogeny;reverse transcription polymerase chain reaction;RNA extraction;sampling;sequence analysis;serotype;vaccine failure;VP1 gene,"Baba Sheikh, M. O.;Rashid, P. M. A.;Marouf, A. S.;Raheem, Z. H.;Janga, S. C.",2017,,10.22099/ijvr.2017.4226,0
103,Origin of the 2009 Mexico influenza virus: a comparative phylogenetic analysis of the principal external antigens and matrix protein,"Triple-reassortant swine influenza A (H1) viruses, containing genes from avian, human, and swine influenza viruses, emerged and became an outbreak among humans worldwide. Over a 1,000 cases were identified within the first month, chiefly in Mexico and the United States. Here, the phylogenetic analysis of haemagglutin (HA), neuraminidase (NA), and matrix protein (MP) was carried out. The analysis showed that the H1 of this reassortant originated from American pigs, while NA and MP were more likely from European pigs. All of the 2009 isolates appear homogeneous and cluster together, although they are distinct from classical human A (H1N1) viruses.","hemagglutinin, human influenza A virus;HN protein;Influenza virus hemagglutinin;M1 protein, Influenza A virus;matrix protein;virus antigen;animal;article;classification;epidemic;Europe;genetic reassortment;genetics;human;influenza;Influenza A virus (H1N1);Mexico;phylogeny;pig;United States;virology","Babakir-Mina, M.;Dimonte, S.;Perno, C. F.;Ciotti, M.",2009,,10.1007/s00705-009-0438-1,0
104,Analysis of the genome of leporid herpesvirus 4,"The genome of a herpesvirus highly pathogenic to rabbits, leporid herpesvirus 4 (LHV-4), was analyzed using high-throughput DNA sequencing technology and primer walking. The assembled DNA sequences were further verified by restriction endonuclease digestion and Southern blot analyses. The total length of the LHV-4 genome was determined to be about 124. kb. Genes encoded in the LHV-4 genome are most closely related to herpesvirus of the Simplexvirus genus, including human herpesviruses (HHV-1 and HHV-2), monkey herpesviruses including cercopithicine (CeHV-2 and CeHV-16), macacine (McHV-1), bovine herpesvirus 2 (BHV-2), and a lineage of wallaby (macropodid) herpesviruses (MaHV-1 and -2). Similar to other simplexvirus genomes, LHV-4 has a high overall G+C content of 65-70% in the unique regions and 75-77% in the inverted repeat regions. Orthologs of ICP34.5 and US5 were not identified in the LHV-4 genome. This study shows that LHV-4 has the smallest simplexvirus genome characterized to date. © 2012 Elsevier Inc.",virus DNA;animal cell;article;Bovine herpes virus 2;Cercopithicine herpes virus 16;Cercopithicine herpes virus 2;controlled study;DNA base composition;DNA sequence;gene;genetic code;genetic identification;genome analysis;Human alphaherpesvirus 1;Herpes simplex virus 2;Herpesviridae;high throughput sequencing;Leporid herpes virus 4;Macacine herpesvirus 1;Macropodid herpes virus 1;Macropodid herpes virus 2;nonhuman;nucleotide sequence;priority journal;Leporidae;restriction mapping;Southern blotting;UL27 gene;virus genome,"Babra, B.;Watson, G.;Xu, W.;Jeffrey, B. M.;Xu, J. R.;Rockey, D. D.;Rohrmann, G. F.;Jin, L.",2012,,10.1016/j.virol.2012.08.002,0
105,Genome Sequence of Foot-and-Mouth Disease Virus Serotype O Isolated from Morocco in 2015,"The genome of a virus isolated from an outbreak of foot-and-mouth disease (FMD) in Morocco in 2015 is described here. This virus is classified as lineage Ind-2001d within serotype O, topotype ME-SA (Middle East-South Asia). This lineage is endemic on the Indian subcontinent but has caused outbreaks in the Middle East and North Africa since 2013.",,"Bachanek-Bankowska, K.;Wadsworth, J.;Gray, A.;Abouchoaib, N.;King, D. P.;Knowles, N. J.",2016,Apr 21,,0
106,Identification of a novel hepacivirus in domestic cattle from Germany,"Hepatitis C virus (HCV) continues to represent one of the most significant threats to human health. In recent years, HCV-related sequences have been found in bats, rodents, horses, and dogs, indicating a widespread distribution of hepaciviruses among animals. By applying unbiased high-throughput sequencing, a novel virus of the genus Hepacivirus was discovered in a bovine serum sample. De novo assembly yielded a nearly full-length genome coding for a polyprotein of 2,779 amino acids. Phylogenetic analysis confirmed that the virus represents a novel species within the genus Hepacivirus. Viral RNA screening determined that 1.6% (n = 5) of 320 individual animals and 3.2% (n = 5) of 158 investigated cattle herds in Germany were positive for bovine hepacivirus. Repeated reverse transcription-PCR (RT-PCR) analyses of animals from one dairy herd proved that a substantial percentage of cows were infected, with some of them being viremic for over 6 months. Clinical and postmortem examination revealed no signs of disease, including liver damage. Interestingly, quantitative RT-PCR from different organs and tissues, together with the presence of an miR-122 binding site in the viral genome, strongly suggests a liver tropism for bovine hepacivirus, making this novel virus a promising animal model for HCV infections in humans.",complementary DNA;microRNA 122;virus RNA;animal tissue;article;autopsy;binding site;clinical examination;cow;dairy cattle;domestic cattle;Flaviviridae infection;genetic code;genetic variability;genome analysis;Germany;Hepacivirus;Hepacivirus infection;Hepatitis C virus;high throughput screening;nonhuman;nucleotide sequence;phylogeny;priority journal;quantitative analysis;reverse transcription polymerase chain reaction;RNA analysis;RNA binding;viral tropism;virus genome;virus identification,"Baechlein, C.;Fischer, N.;Grundhoff, A.;Alawi, M.;Indenbirken, D.;Postel, A.;Baron, A. L.;Offinger, J.;Becker, K.;Beineke, A.;Rehage, J.;Becher, P.",2015,,10.1128/jvi.00534-15,1
107,"Pegivirus infection in domestic pigs, Germany",,domestic pig;Flaviviridae;gene sequence;Germany;high throughput sequencing;letter;nonhuman;nucleotide sequence;open reading frame;Pegivirus;Pegivirus infection;phylogeny;reverse transcription polymerase chain reaction;virus infection,"Baechlein, C.;Grundhoff, A.;Fischer, N.;Alawi, M.;Hoeltig, D.;Waldmann, K. H.;Becher, P.",2016,,10.3201/eid2207.160024,1
108,Surveillance and characterization of low pathogenic H5 avian influenza viruses isolated from wild migratory birds in Korea,"Migratory waterfowls are the natural reservoir of influenza A viruses. However, interspecies transmission had occasionally caused outbreaks in various hosts including humans. To characterize the genetic origins of H5 avian influenza viruses isolated from migratory birds in South Korea, phylogenetic analysis were conducted. A total of 53 H5 viruses were isolated between October 2005 and November 2008. Full genetic characterization indicated that most of these viruses belong to the Eurasian-like avian lineage. However, some segments of the AB/Korea/W235/07 and the AB/Korea/W236/07 isolates were clustered with North American lineage viruses rather than those of the Eurasian lineage, suggesting the occurrence of reassortment between these two avian virus lineages. Phylogenetic analysis further demonstrated that the H5N2 and H5N3 virus isolates were of the low pathogenicity H5 phenotype. The H5 viruses appear to be antigenically similar to each other, but could be distinguished from a recent HPAI H5N1 (EM/Korea/W149/06) virus by hemagglutinin inhibition (HI) assays. Experimental inoculation of representative viruses indicated that certain isolates, particularly AB/Korea/W163/07 (H5N2), could be detected in trachea and lungs of chickens but none could be transmitted by direct contact. Furthermore, all of the viruses could be detected in mice lung without prior adaptation which is indicative of their pathogenic potential in a mammalian host. Overall, our results emphasize the important role that migratory birds play in the perpetuation, transport, and reassortment of avian influenza viruses stressing the need for continued surveillance of influenza virus activity in these avian populations. © 2010 Elsevier B.V.",animal experiment;animal model;animal tissue;article;avian influenza;bird;controlled study;female;genetic similarity;hemagglutination inhibition test;Influenza A virus;Influenza A virus (H5N2);Influenza A virus (H5N3);lung;migratory species;molecular phylogeny;mouse;nonhuman;phenotype;priority journal;South Korea;trachea;viral genetics;virus characterization;virus detection;virus isolation;virus replication;virus transmission;virus virulence,"Baek, Y. H.;Pascua, P. N. Q.;Song, M. S.;Park, K. J.;Kwon, H. I.;Lee, J. H.;Kim, S. Y.;Moon, H. J.;Kim, C. J.;Choi, Y. K.",2010,,10.1016/j.virusres.2010.03.002,0
109,Novel Rath peptide for intracellular delivery of protein and nucleic acids,"In the present study, a novel cell penetrating peptide (CPP) named as Rath, has been identified from the avian infectious bursal disease virus. It has the potential to penetrate and translocate cargo molecules into cells independent of temperature. Additionally, it can deliver oligonucleotide in 30 min and antibodies within an hour intracellular to chicken embryonic fibroblast primary cells. As an ideal delivery vehicle, it has the ability to protect the cargo molecules in the presence of serum, nucleases and has minimal or no cytotoxicity at even higher peptide concentrations studied. The biophysical characterizations showed that Rath has a dominant β structure with a small α helix and has remarkable binding ability with protein and DNA. Thus, the characterization of unique Rath peptide to deliver protein or nucleic acid into the cells with non-covalent interaction could be used as an effective delivery method for various cell based assays. © 2008 Elsevier Inc. All rights reserved.",cell penetrating peptide;oligonucleotide;Rath peptide;unclassified drug;viral protein;alpha helix;animal cell;animal tissue;article;avian infectious bursal disease virus;binding affinity;chick embryo;controlled study;covalent bond;cytotoxicity;intracellular transport;molecular interaction;nonhuman;nucleic acid analysis;nucleic acid transport;peptide analysis;priority journal;protein DNA binding;protein structure;protein transport;temperature dependence;virus classification,"Bais, M. V.;Kumar, S.;Tiwari, A. K.;Kataria, R. S.;Nagaleekar, V. K.;Shrivastava, S.;Chindera, K.",2008,,10.1016/j.bbrc.2008.03.023,0
110,Poxviruses in bats ... so what?,"Poxviruses are important pathogens of man and numerous domestic and wild animal species. Cross species (including zoonotic) poxvirus infections can have drastic consequences for the recipient host. Bats are a diverse order of mammals known to carry lethal viral zoonoses such as Rabies, Hendra, Nipah, and SARS. Consequent targeted research is revealing bats to be infected with a rich diversity of novel viruses. Poxviruses were recently identified in bats and the settings in which they were found were dramatically different. Here, we review the natural history of poxviruses in bats and highlight the relationship of the viruses to each other and their context in the Poxviridae family. In addition to considering the zoonotic potential of these viruses, we reflect on the broader implications of these findings. Specifically, the potential to explore and exploit this newfound relationship to study coevolution and cross species transmission together with fundamental aspects of poxvirus host tropism as well as bat virology and immunology. © 2014 by the authors; licensee MDPI, Basel, Switzerland.",bat;coevolution;gene sequence;host;human;immunology;metagenomics;nonhuman;phylogeny;Poxviridae;poxvirus infection;review;tropism;virus detection;virus isolation;zoonosis,"Baker, K. S.;Murcia, P. R.",2014,,10.3390/v6041564,0
111,"Novel, potentially zoonotic paramyxoviruses from the African straw-colored fruit bat Eidolon helvum","Bats carry a variety of paramyxoviruses that impact human and domestic animal health when spillover occurs. Recent studies have shown a great diversity of paramyxoviruses in an urban-roosting population of straw-colored fruit bats in Ghana. Here, we investigate this further through virus isolation and describe two novel rubulaviruses: Achimota virus 1 (AchPV1) and Achimota virus 2 (AchPV2). The viruses form a phylogenetic cluster with each other and other bat-derived rubulaviruses, such as Tuhoko viruses, Menangle virus, and Tioman virus. We developed AchPV1- and AchPV2-specific serological assays and found evidence of infection with both viruses in Eidolon helvum across sub-Saharan Africa and on islands in the Gulf of Guinea. Longitudinal sampling of E. helvum indicates virus persistence within fruit bat populations and suggests spread of AchPVs via horizontal transmission. We also detected possible serological evidence of human infection with AchPV2 in Ghana and Tanzania. It is likely that clinically significant zoonotic spillover of chiropteran paramyxoviruses could be missed throughout much of Africa where health surveillance and diagnostics are poor and comorbidities, such as infection with HIV or Plasmodium sp., are common. © 2013, American Society for Microbiology.",Achimota virus 1;Achimota virus 2;adolescent;article;bat;child;cross reaction;Eidolon helvum;female;Ghana;Guinea;human;human cell;infant;major clinical study;male;Menangle virus;nonhuman;nucleotide sequence;Paramyxoviridae;persistent virus infection;phylogenetic tree;preschool child;priority journal;school child;strain difference;strain identification;Tanzania;taxonomic rank;Tioman virus;Tuhoko virus;virus isolation;virus strain;virus transmission;zoonosis,"Baker, K. S.;Todd, S.;Marsh, G. A.;Crameri, G.;Barr, J.;Kamins, A. O.;Peel, A. J.;Yu, M.;Hayman, D. T. S.;Nadjm, B.;Mtove, G.;Amos, B.;Reyburn, H.;Nyarko, E.;Suu-Ire, R.;Murcia, P. R.;Cunningham, A. A.;Wood, J. L. N.;Wang, L. F.",2013,,10.1128/jvi.01202-12,0
112,Peste des petits ruminants virus detected in tissues from an Asiatic lion (Panthera leo persico) belongs to Asian lineage IV,"In this study, peste des petits ruminants virus (PPRV) was detected in frozen pooled tissue samples from a dead Asiatic lion (Panthera leo persica). The samples were negative for canine distemper virus and positive for PPRV nucleic acids when tested with one-step RT-PCR using the appropriate virus-specific primers. Subsequent amplification, cloning, and sequencing of the partial nucleocapsid, matrix, and fusion genes confirmed the presence of PPRV nucleic acid. Comparative sequence and phylogenetic analyses of the structural genes of the isolated virus confirmed that the virus belonged to Asian lineage IV and was closely related to PPRV circulating in India. © 2012 The Korean Society of Veterinary Science.",animal;animal disease;article;genetics;isolation and purification;lion;Measles virus;molecular cloning;phylogeny;reverse transcription polymerase chain reaction,"Balamurugan, V.;Sen, A.;Venkatesan, G.;Bhanot, V.;Yadav, V.;Bhanuprakash, V.;Singh, R. K.",2012,,10.4142/jvs.2012.13.2.203,0
113,Sequence and phylogenetic analyses of the structural genes of virulent isolates and vaccine strains of peste des petits ruminants virus from India,"Peste des petits ruminants (PPR) is an acute, highly contagious, notifiable and economically important transboundary viral disease of sheep and goats. In this study, sequence and phylogenetic analyses of structural protein genes, namely the nucleocapsid (N), the matrix (M), the fusion (F) and the haemagglutinin (H) coding sequences of virulent and vaccine strains of PPR virus (PPRV), were undertaken to determine the genetic variations between field isolates and vaccine strains. The open reading frame (ORF) of these genes of the isolates/strains was amplified by RT-PCR, cloned and sequenced. The ORF of N, M, F and H genes was 1578, 1008, 1641 and 1830 nucleotides (nt) in length and encodes polypeptides of 525, 335, 546 and 609 amino acids (aa), respectively, as reported earlier. Comparative sequence analyses of these four genes of isolates/strains were carried out with published sequences. It revealed an identity of 97.7-100% and 97.7-99.8% among the Asian lineage IV and 89.6-98.7% and 89.8-98.9% with other lineages of PPRV at nt and aa levels, respectively. The phylogenetic analyses of these isolates based on the aa sequences showed that all the viruses belonged to lineage IV along with other Asian isolates. This is in agreement with earlier observations that only PPRV lineage IV is in circulation in India since the disease was first reported. Further, sequence analysis of the thermostable/thermo-adapted vaccine strains showed no significant changes in the functional or structural surface protein-coding gene sequences. It is important to monitor the circulation of the PPRV in susceptible animals by H gene-based sequence comparisons in addition to the F gene- and N gene-based approaches to identify the distribution and spread of virus in the regular outbreaks that occur in endemic countries like India. ©2010 Blackwell Verlag GmbH.",animal;article;genetics;India;Measles virus;peste des petits ruminants;virology,"Balamurugan, V.;Sen, A.;Venkatesan, G.;Yadav, V.;Bhanot, V.;Riyesh, T.;Bhanuprakash, V.;Singh, R. K.",2010,,10.1111/j.1865-1682.2010.01156.x,0
114,Infectious bronchitis virus in different avian physiological systems - A field study in Brazilian poultry flocks,"Avian infectious bronchitis is a highly contagious viral disease with economic effects on poultry agribusiness. The disease presents multi-systemic clinical signs (respiratory, renal, enteric, and reproductive) and is caused by one coronavirus (infectious bronchitis virus, IBV). Infectious bronchitis virus is classified into different serotypes and genotypes (vaccine strains and field variants). This study aimed to evaluate the occurrence of IBV in commercial poultry flocks from 3 important producing regions in Brazil and to determine the tropism of the main circulating genotypes to 3 different avian physiological systems (respiratory, digestive, urinary/reproductive). Clinical samples with suggestive signs of IBV infection were collected from 432 different poultry commercial flocks (198 from broilers and 234 from breeders). The total number of biological samples consisted of organ pools from the 3 above physiological systems obtained of farms from 3 important producing regions: midwest, northeast, and south. Infectious bronchitis virus was detected by reverse-transcription, real-time PCR of the 5′ untranslated region. The results showed 179 IBV-positive flocks (41.4% of the flocks), with 107 (24.8%) from broilers and 72 (16.8%) from breeders. There were similar frequencies of IBV-positive flocks in farms from different regions of the country, most often in broilers (average 54%) compared with breeders (average 30.8%). reverse-transcription was more frequently detected in the digestive system of breeders (40%), and in the digestive (43.5%) and respiratory (37.7%) systems of broilers. Infectious bronchitis virus genotyping was performed by a reverse-transcription nested PCR and sequencing of the S1 gene from a selection of 79 IBV-positive flocks (45 from broilers and 34 from breeders). The majority of the flocks were infected with Brazilian variant genotype than with Massachusetts vaccine genotype. These results demonstrate the predominance of the Brazilian variant (mainly in the enteric tract) in commercial poultry flocks from 3 important producing regions in Brazil. © 2014 Poultry Science Association Inc.",viral protein;animal;animal disease;article;Avian infectious bronchitis virus;bird;bird disease;Brazil;chicken;classification;Coronavirus infection;genetics;genotype;isolation and purification;metabolism;physiology;poultry;real time polymerase chain reaction;reverse transcription polymerase chain reaction;viral tropism;virology,"Balestrin, E.;Fraga, A. P.;Ikuta, N.;Canal, C. W.;Fonseca, A. S. K.;Lunge, V. R.",2014,,10.3382/ps.2014-03875,0
115,Full-length genome sequence analysis of a Hungarian porcine reproductive and respiratory syndrome virus isolated from a pig with severe respiratory disease,"Here, we report the isolation of a type 1 porcine reproductive and respiratory syndrome virus (PRRSV) strain from a clinical outbreak of severe respiratory problems and high fever. Next-generation sequencing was used to determine the complete genome sequence of the isolate (9625/2012). The virus belongs to a new branch within subtype 1, clade D, and shows the highest similarity to PRRSV Olot/1991 and to the Amervac vaccine strain. Mutation analysis of 9625/2012 revealed no evidence of recombination but did show a high proportion of amino acid substitutions in the putative neutralizing epitopes, suggesting an important role of selective immune pressure in the evolution of PRRSV 9625/2012.",virus RNA;amino acid sequence;amino acid substitution;animal;classification;epidemic;genetics;high throughput sequencing;Hungary;isolation and purification;mixed infection;molecular genetics;mutation;Mycoplasma hyopneumoniae;mycoplasmal pneumonia of swine;nucleotide sequence;pathology;pig;porcine reproductive and respiratory syndrome;Porcine reproductive and respiratory syndrome virus;sequence alignment;sequence analysis;veterinary medicine;virology;virus genome,"Bálint, Á;Balka, G.;Horváth, P.;Kecskeméti, S.;Dán, Á;Farsang, A.;Szeredi, L.;Bányai, K.;Bartha, D.;Olasz, F.;Belák, S.;Zádori, Z.",2015,,10.1007/s00705-014-2265-2,0
116,"Full genome sequence analysis of a wild, non-MLV-related type 2 Hungarian PRRSV variant isolated in Europe","Porcine reproductive and respiratory syndrome virus (PRRSV) is a widespread pathogen of pigs causing significant economic losses to the swine industry. The expanding diversity of PRRSV strains makes the diagnosis, control and eradication of the disease more and more difficult. In the present study, the authors report the full genome sequencing of a type 2 PRRSV strain isolated from piglet carcasses in Hungary. Next generation sequencing was used to determine the complete genome sequence of the isolate (PRRSV-2/Hungary/102/2012). Recombination analysis performed with the available full-length genome sequences showed no evidence of such event with other known PRRSV. Unique deletions and an insertion were found in the nsp2 region of PRRSV-2/Hungary/102/2012 when it was compared to the highly virulent VR2332 and JXA-1 prototype strains. The majority of amino acid alterations in GP4 and GP5 of the virus were in the known antigenic regions suggesting an important role for immunological pressure in PRRSV-2/Hungary/102/2012 evolution. Phylogenetic analysis revealed that it belongs to lineage 1 or 2 of type 2 PRRSV. Considering the lack of related PRRSV in Europe, except for a partial sequence from Slovakia, the ancestor of PRRSV-2/Hungary/102/2012 was most probably transported from North-America. It is the first documented type 2 PRRSV isolated in Europe that is not related to the Ingelvac MLV.","Amino Acid Sequence;Animals;Base Sequence;Europe;*Genome, Viral;Genotype;High-Throughput Nucleotide Sequencing;Hungary;Molecular Sequence Data;Phylogeny;*Porcine Reproductive and Respiratory Syndrome/vi [Virology];Porcine respiratory and reproductive syndrome virus/ch [Chemistry];Porcine respiratory and reproductive syndrome virus/cl [Classification];Porcine respiratory and reproductive syndrome virus/ge [Genetics];*Porcine respiratory and reproductive syndrome virus/ip [Isolation & Purification];Swine;Viral Proteins/ch [Chemistry];Viral Proteins/ge [Genetics];0 (Viral Proteins)","Balka, G.;Wang, X.;Olasz, F.;Balint, A.;Kiss, I.;Banyai, K.;Rusvai, M.;Stadejek, T.;Marthaler, D.;Murtaugh, M. P.;Zadori, Z.",2015,Mar 16,,0
117,Two amino acid changes at the N-terminus of transmissible gastroenteritis coronavirus spike protein result in the loss of enteric tropism,"To study the molecular basis of TGEV tropism, a collection of recombinants between the PUR46-MAD strain of transmissible gastroenteritis coronavirus (TGEV) infecting the enteric and respiratory tracts and the PTV strain, which only infects the respiratory tract, was generated. The recombinant isolation frequency was about 10-9 recombinants per nucleotide and was 3.7-fold higher at the 5'-end of the S gene than in other areas of the genome. Thirty recombinants were plaque purified and characterized phenotypically and genetically. All recombinant viruses had a single crossover and had inherited the 5'- and 3'-halves of their genome from the enteric and respiratory parents, respectively. Recombinant viruses were classified into three groups, named 1 to 3, according to the location of the crossover. Group 1 recombinants had the crossover in the S gene, while in Groups 2 and 3 the crossovers were located in ORF1b and ORF1a, respectively. The tropism of the recombinants was studied. Recombinants of Group 1 had enteric and respiratory tropism, while Group 2 recombinants infected the respiratory, but not the enteric, tract. Viruses of both groups differed by two nucleotide changes at positions 214 and 655. Both changes may be in principle responsible for the loss of enteric tropism but only the change in nucleotide 655 was specifically found in the respiratory isolates and most likely this single nucleotide change, which leads to a substitution in amino acid 219 of the S protein, was responsible for the loss of enteric tropism in the closely related PUR46 isolates. The available data indicate that in order to infect enteric tract cells with TGEV, two different domains of the S protein, mapping between amino acids 522 and 744 and around amino acid 219, respectively, are involved. The first domain binds to porcine aminopeptidase N, the cellular receptor for TGEV. In the other domain maps a second factor of undefined nature but which may be the binding site for a coreceptor essential for the enteric tropism of TGEV.",viral protein;animal cell;article;cell invasion;controlled study;Coronavirinae;gastroenteritis;gene mutation;nonhuman;priority journal;protein domain;radioimmunoassay;spike;virus cell interaction;virus recombinant,"Ballesteros, M. L.;Sánchez, C. M.;Enjuanes, L.",1997,,10.1006/viro.1996.8344,0
118,Investigation of foot-and-mouth disease outbreaks in the Mbala and Kazungula districts of Zambia,"Foot-and-mouth disease (FMD) is an acute, highly contagious viral infection of domestic and wild cloven-hoofed animals. It is known to be endemic in Zambia, with periodic outbreaks occurring in different geographical areas of the country. This study was conducted to investigate the presence of FMD virus (FMDV) in reported FMD-suspected cases in cattle from the Kazungula and Mbala districts of Zambia. Sixty epithelial tissues or oesophageal-pharyngeal (OP) scrapings (probang samples) were collected from Mbala (n = 51) and Kazungula (n = 9) and examined for FMDV. The FMDV viral RNA and serotypes were examined by realtime reverse transcription polymerase chain reaction (qRT-PCR) and antigen Enzyme- linked immunosorbent assay (ELISA), respectively. Twenty-two samples (36.7%) were positive for the FMDV genome by qRT-PCR with Cycle threshold (Ct) values ranging from 13 to 31. The FMDV-positive samples from epithelial tissues showed relatively higher Ct values compared to those obtained from OP scrapings, irrespective of geographical location. Forty percent (40%; n = 4) of epithelial tissues from Mbala were serotyped into SAT 2 serotype by antigen ELISA. Kazungula samples were serotyped into SAT 1. These findings indicated that Mbala and Kazungula districts had FMD outbreaks in 2012 that were ascribed to at least FMDV serotype SAT 2 and SAT 1 field strains. Furthermore, regular interaction between buffalos from the Mosi-o Tunya Park and domestic animals from surrounding areas could contribute to the occurrence of regular FMD outbreaks in Kazungula, whilst the uncontrolled animal movements across borders between Mbala and Nsumbawanga could be responsible for disease outbreaks in Mbala. In-depth molecular biological studies, including sequencing and phylogeny of the viruses, should be conducted to elucidate the complex epidemiology of FMD in Zambia, thereby providing valuable information needed for the rational control strategy of FMD in Zambia and neighbouring countries.",animal;bovine;cattle disease;classification;epidemic;Foot and mouth disease virus;foot and mouth disease;isolation and purification;pathology;veterinary medicine;virology;Zambia,"Banda, F.;Kasanga, C. J.;Sallu, R.;Sinkala, Y.;Sinkombe, T. W.;Mulumba, M.;Rweyemamu, M. M.;Wambura, P. N.",2014,,,0
119,Isolation and Metagenomic Identification of Avian Leukosis Virus Associated with Mortality in Broiler Chicken,"Avian leukosis virus (ALV) belongs to the family Retroviridae and causes considerable economic losses to the poultry industry. Following an outbreak associated with high mortality in a broiler flock in northern part of Malaysia, kidney tissues from affected chickens were submitted for virus isolation and identification in chicken embryonated egg and MDCK cells. Evidence of virus growth was indicated by haemorrhage and embryo mortality in egg culture. While viral growth in cell culture was evidenced by the development of cytopathic effects. The isolated virus was purified by sucrose gradient and identified using negative staining transmission electron microscopy. Further confirmation was achieved through next-generation sequencing and nucleotide sequence homology search. Analysis of the viral sequences using the NCBI BLAST tool revealed 99-100% sequence homology with exogenous ALV viral envelope protein. Phylogenetic analysis based on partial envelope sequences showed the Malaysian isolate clustered with Taiwanese and Japanese ALV strains, which were closer to ALV subgroup J, ALV subgroup E, and recombinant A/E isolates. Based on these findings, ALV was concluded to be associated with the present outbreak. It was recommended that further studies should be conducted on the molecular epidemiology and pathogenicity of the identified virus isolate.",,"Bande, F.;Arshad, S. S.;Omar, A. R.",2016,,,0
120,Unique genomic organization of a novel Avipoxvirus detected in turkey (Meleagris gallopavo),"Avipoxviruses are emerging pathogens affecting over 200 bird species worldwide. Genetic characterization of avipoxviruses is performed by analysis of genomic regions encoding the 4b and DNA polymerase. Whole genome sequence data are limited to a few avipoxvirus isolates. Based on phylogenetic analysis three major genetic clades are distinguished. In this study we report a novel avipoxvirus strain causing skin lesions in domestic turkey. The virus was identified in Hungary during 2011 in a flock of turkey vaccinated against avipoxvirus infection. The genome of the isolated strain, TKPV-HU1124/2011, was uniquely short (~188.5. kbp) and was predicted to encode reduced number of proteins. Phylogenetic analysis of the genes encoding the 4b and DNA polymerase separated TKPV-HU1124/2011 from other turkey origin avipoxviruses and classified it into a new genetic clade. This study permits new insight into the genetic and genomic heterogeneity of avipoxviruses and pinpoints the importance of strain diversity in vaccine efficacy.",DNA polymerase;article;Avipoxvirus;cladistics;gene structure;genetic heterogeneity;genetic variability;Meleagris gallopavo;nonhuman;phylogeny;poxvirus infection;priority journal;skin defect;strain difference;vaccination;virus classification;virus detection;virus genome;virus identification;virus isolation;virus strain,"Bányai, K.;Palya, V.;Dénes, B.;Glávits, R.;Ivanics, É;Horváth, B.;Farkas, S. L.;Marton, S.;Bálint, Á;Gyuranecz, M.;Erdélyi, K.;Dán, Á",2015,,10.1016/j.meegid.2015.08.001,0
121,Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013–2014,"Peste des petits ruminants virus (PPRV) causes a highly contagious disease, peste des petits ruminants (PPR), in sheep and goats which has been considered as a serious threat to the local economy in Africa and Asia. However, the in-depth evolutionary dynamics of PPRV during an epidemic is not well understood. We conducted phylogenetic analysis on genomic sequences of 25 PPRV strains from China 2013–2014 outbreaks. All these strains clustered into a novel clade in lineage 4. An evolutionary rate of 2.61 × 10−6 nucleotide substitutions per site per day was estimated, dating the most recent common ancestor of PPRV China 2013–2014 strains to early August 2013. Transmission network analysis revealed that all the virus sequences could be grouped into five clusters of infection, suggesting long-distance animal transmission play an important role in the spread of PPRV in China. These results expanded our knowledge for PPRV evolution to achieve effective control measures.",nucleotide;animal tissue;article;China;evolutionary rate;female;gene cluster;gene sequence;genetic variability;goat;male;nonhuman;nucleotide sequence;Peste-des-petits-ruminants virus;phylogeny;population dynamics;priority journal;sequence analysis;sheep;virus strain;virus transmission,"Bao, J.;Wang, Q.;Li, L.;Liu, C.;Zhang, Z.;Li, J.;Wang, S.;Wu, X.;Wang, Z.",2017,,10.1016/j.virol.2017.07.018,0
122,"Detection and genetic characterization of peste des petits ruminants virus in free-living bharals (Pseudois nayaur) in Tibet, China","Peste des petits ruminants (PPR) is an important viral disease of sheep and goats. The wildlife hosts of PPR, which may play an important role in the epidemiology of this disease, are not well characterized. The research was undertaken to study the infection of PPR virus (PPRV) in free-living bharals (Pseudois nayaur) in Tibet, China. In 2007, PPRV infection was confirmed in two bharals in Rutog County of Tibet based on clinical signs and detection of PPRV RNA in tissue samples. In 2008, PPRV infection was found in one bharal in Ge'gyai County of Tibet by competitive ELISA, reverse transcription-polymerase chain reaction, and sequence analysis of PPRV fusion protein (F) and nucleoprotein (N) gene segments. The PPRV variant identified in infected bharal was closely related to other circulating PPRV variants recently identified in sheep and goats from Tibet. This is the first report of PPRV infection in free-living bharals. © 2010.",fusion protein;nucleoprotein;article;chemical reaction;China;controlled study;gene amplification;gene sequence;genetic analysis;genetic variability;goat;nonhuman;nucleotide sequence;peste des petits ruminants;phylogenetic tree;phylogeny;protein purification;reverse transcription polymerase chain reaction;sequence analysis;sheep;wildlife,"Bao, J.;Wang, Z.;Li, L.;Wu, X.;Sang, P.;Wu, G.;Ding, G.;Suo, L.;Liu, C.;Wang, J.;Zhao, W.;Li, J.;Qi, L.",2011,,10.1016/j.rvsc.2010.05.031,0
123,Isolation and full-genome sequence of two reticuloendotheliosis virus strains from mixed infections with Marek’s disease virus in China,"Reticuloendotheliosis virus (REV), classified as a gammaretrovirus, has a variety of hosts, including chickens, ducks, geese, turkeys, and wild birds. REV causes a series of pathological syndromes, especially the immunosuppression of the host, which may lead to an increased susceptibility to other pathogens, thus greatly damaging the poultry industry. Mixed infections of REV and Marek’s disease virus (MDV) have been reported in many countries, including China. Previous reports revealed that MDV vaccines were not efficacious, and even less-virulent MDV strains would cause some losses due to mixed infections with REV. Additionally, contaminants in the MDV vaccine might be the main source of REV. In this study, two clinical samples were collected from two flocks of chickens that were diagnosed with MDV. Subsequently, two REV isolates were obtained from the clinical samples. The isolates, named CY1111 and SY1209, were further confirmed through an indirect immunofluorescence assay and electron microscopy. Complete genome sequences of the two REV strains were determined to test the relationship between them and other REV strains. Phylogenetic trees showed that the two REV strains were closely related to most REV strains that were isolated from a variety of hosts. Therefore, REVs might spread freely among these hosts under natural conditions. Additionally, most REV strains in China were in the same clade. The present work offers some information regarding REV in China.",animal cell;animal tissue;article;chicken;China;controlled study;electron microscopy;embryo;fibroblast;gene sequence;immunofluorescence;Marek disease;Gallid alphaherpesvirus 2;mixed infection;molecular cloning;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;priority journal;Reticuloendotheliosis virus;strain difference;strain identification;tissue homogenate;virus identification;virus isolation;virus strain,"Bao, K. Y.;Zhang, Y. P.;Zheng, H. W.;Lv, H. C.;Gao, Y. L.;Wang, J. F.;Gao, H. L.;Qi, X. L.;Cui, H. Y.;Wang, Y. Q.;Ren, X. G.;Wang, X. M.;Liu, C. J.",2015,,10.1007/s11262-015-1191-z,0
124,"Blood-feeding, susceptibility to infection with Schmallenberg virus and phylogenetics of Culicoides (Diptera: Ceratopogonidae) from the United Kingdom","Background: Culicoides biting midges (Diptera: Ceratopogonidae) are responsible for the biological transmission of internationally important arboviruses of livestock. In 2011, a novel Orthobunyavirus was discovered in northern Europe causing congenital malformations and abortions in ruminants. From field studies, Culicoides were implicated in the transmission of this virus which was subsequently named Schmallenberg virus (SBV), but to date no assessment of susceptibility to infection of field populations under standardised laboratory conditions has been carried out. We assessed the influence of membrane type (chick skin, collagen, Parafilm M®) when offered in conjunction with an artificial blood-feeding system (Hemotek, UK) on field-collected Culicoides blood-feeding rates. Susceptibility to infection with SBV following blood-feeding on an SBV-blood suspension provided via either (i) the Hemotek system or via (ii) a saturated cotton wool pledglet was then compared. Schmallenberg virus susceptibility was defined by RT-qPCR of RNA extractions of head homogenates and related to Culicoides species and haplotype identifications based on the DNA barcode region of the mitochondrial cytochrome c oxidase 1 (cox1) gene. Results: Culicoides blood-feeding rates were low across all membrane types tested (7.5% chick skin, 0.0% for collagen, 4.4% Parafilm M®, with 6029 female Culicoides being offered a blood meal in total). Susceptibility to infection with SBV through membrane blood-feeding (8 of 109 individuals tested) and pledglet blood-feeding (1 of 94 individuals tested) was demonstrated for the Obsoletus complex, with both C. obsoletus (Meigen) and C. scoticus Downes & Kettle susceptible to infection with SBV through oral feeding. Potential evidence of cryptic species within UK populations was found for the Obsoletus complex in phylogenetic analyses of cox1 DNA barcodes of 74 individuals assessed from a single field-site. Conclusions: Methods described in this study provide the means to blood-feed Palaearctic Culicoides for vector competence studies and colonisation attempts. Susceptibility to SBV infection was 7.3% for membrane-fed members of the subgenus Avaritia and 1.1% for pledglet-fed. Both C. obsoletus and C. scoticus were confirmed as being susceptible to infection with SBV, with potential evidence of cryptic species within UK Obsoletus complex specimens, however the implications of cryptic diversity in the Obsoletus complex on arbovirus transmission remains unknown.",collagen;RNA;article;controlled study;cox1 gene;Culicoides;DNA barcoding;female;gene;gene sequence;homogenate;infection sensitivity;nonhuman;phylogeny;reverse transcription polymerase chain reaction;Schmallenberg virus;skin;United Kingdom;virus detection,"Barber, J.;Harrup, L. E.;Silk, R.;Veronesi, E.;Gubbins, S.;Bachanek-Bankowska, K.;Carpenter, S.",2018,,10.1186/s13071-018-2650-x,0
125,Persistence mechanisms in tick-borne diseases,"The use of new, highly sensitive diagnostic methods has revealed persistent infections to be a common feature of different tick-borne diseases, such as babesiosis, anaplasmosis and heartwater. Antigenic variation can contribute to disease persistence through the continual elaboration of new surface structures, and we know in several instances how this is achieved. Known or suspected mechanisms of persistence in babesial parasites include cytoadhesion and rapid variation of the adhesive ligand in Babesia bovis and genetic diversity in several merozoite stage proteins of different Babesia spp. In Anaplasma, extensive variation in the pfam01617 gene family accompanies cycling of organism levels in chronic infection. One result from the pioneering research at Onderstepoort is the definition of a related polymorphic gene family that is likely involved in immunity against heartwater disease. We are beginning to understand the sizes of the antigenic repertoires and full definition is close, with the possibility of applying simultaneous high-throughput sequencing to the order of 1000 small genomes. We also, for the first time, can consider modifying these genomes and looking at effects on persistence and virulence. However, important biological questions remain unanswered; for example, why we are seeing a new emerging Anaplasma infection of humans and is infection of endothelial cells by Anaplasma significant to persistence in vivo.",*Anaplasma/ge [Genetics];Anaplasma/im [Immunology];Animals;Antigenic Variation/ge [Genetics];*Babesia bovis/ge [Genetics];Babesia bovis/im [Immunology];Cattle;*Ehrlichia ruminantium/ge [Genetics];Ehrlichia ruminantium/im [Immunology];Genetic Variation/ge [Genetics];*Genetic Variation;Humans;Tick-Borne Diseases/mi [Microbiology];Tick-Borne Diseases/ps [Parasitology];*Tick-Borne Diseases/ve [Veterinary],"Barbet, A. F.",2009,Mar,,0
126,DNA sequencing and phylogenetic analysis of the protease gene of ovine adenovirus 3 suggest that adenoviruses of sheep belong to two different genera,"Until now, the only published ovine adenovirus DNA sequence was the complete genome of ovine adenovirus isolate 287 (OAV287) which, compared to other mammalian adenoviruses, possesses strikingly unique genomic organisation and should properly be classified into a new adenovirus genus. The protease gene sequence of ovine adenovirus type 3 (OAdV-3) was determined and analysed. The results of phylogenetic analysis of the 205 residue long protein demonstrated that OAdV-3 belongs to the genus Mastadenovirus, and is surprisingly closely related to bovine adenovirus type 2. In spite of the common host origin, the evolutionary distance between OAdV-3 and OAV287 proved to be great suggesting that sheep, similarly to cattle and fowl, might be infected by distantly related adenoviruses belonging to different genera. (C) 2000 Elsevier Science B.V.",Adenoviridae;article;DNA binding;DNA sequence;genetic analysis;Mastadenovirus;nonhuman;nucleotide sequence;phylogeny;priority journal;sheep;virus classification,"Barbezange, C.;Benkö, M.;Dán, A.;Harrach, B.",2000,,10.1016/s0168-1702(99)00123-9,0
127,Search antigenic proteins of porcine circovirus type 2 by the technique of immunohistochemistry,"Porcine circovirus type 2 (PCV2) is a virus classified in the family Circoviridae and is associated with post-weaning multisystemic wasting syndrome (PMWS). The diagnosis should be on three main points: The presence of compatible clinical signs, histopathological lesions and demonstration of the nucleic acid and / or viral antigen inside lesions. Immunohistochemistry (IHC) method allows the demonstration of viral antigens by using specific antibodies and probes. In this study, two groups of samples were analyzed by IHC. Group I consists of 32 necropsied pigs with clinical signs indicative of the PMWS from commercial farms in Minas Gerais State. Group II consists of 109 tissues received by histopathology laboratory, with lesions suggestive of PMWS. The first and second sampling revealed, respectively, 7,60% and 60,55% positivity for the presence of antigen PCV2. In both groups, the viral antigens were demonstrated more frequent in lymph nodes and lungs evidenced by the intense immunoreactivity of histiocytes. The application of IHC allowed the comparison of between histopathological changes and the distribution of viral antigen in tissue.",diagnosis;disease;swine;virus,"Barbosa, C. N.;Freitas, T. R. P.",2011,Apr-Jun,,0
128,Research of antigen and antibodies against Porcine Circovirus Type-2 in pigs with and without postweaning multsystemic wasting syndrome from commercial farms of Minas Gerais State,"Porcine Circovirus Type 2 (PCV-2) is a non-enveloped circular single stranded DNA virus classified in the Circoviridae family related to post weaning multi systemic wasting syndrome (PMWS) in piglets. Immune-Histochemical (IHC) techniques are applied to detected PCV-2 antigen in the animal tissue injuries. Although, asymptomatic or sub clinic PCV-2 infected pigs could disseminate the virus in the flock. Serologic survey on apparently health pigs could suggest the virus ingression risk. In this work, antigens and antibodies against PCVS-2 in swine from commercial farms of seven and eight mesorregions of Minas Gerais State (MG) were investigated. 32 pigs with ages from five to eleven weeks which presented SMDS clinical signs were submitted to necropsy. PCV-2 antigens were investigated either from sacrificed pigs (Group I) and diagnosis demand samples (Group II) by IHC. 7,60% and more than 60% of the first and second groups, respectively, were positive for viral antigen. In both of them, intense marking of macrophages and histiocytes, especially in the lymph nodes and lung, evidenced antigens to CVS-2. In parallel, Immunoperoxidase Monolayer Assay (IPMA) was applied to antibody against PCV-2 screened in 955 pigs from 35 complete cycle commercial farms from same mesorregions. All pig flocks (100%) presented positive animals (confidence level 90% to 100%) and the frequency of reacting pigs varied 96.6% (confidence level 94,7% to 98,6%). PCV-2 antibody titers ranged 1: 320 (medium) to 1: 10.240 (high). The results suggest that 2.66% and 9% of pigs from Triangulo Mineiro and Zona da Mata regions respectively, would be able to develop clinical SMDS and that percentage reach 3.35% in the total serum.",Porcine circovirus type 2;viral Antigen (IHC);antibody (IPMA);IN-SITU HYBRIDIZATION;SYNDROME PMWS;INFECTION;BRAZIL;HERDS;SPAIN,"Barbosa, C. N.;Martins, N. R.;Esteves, E. G.;Freitas, T. R. P.",2011,,,0
129,Cloning and sequence analysis of the matrix (M) protein gene of rinderpest virus and evidence for another bovine morbillivirus,"We have cloned and sequenced the entire M gene of the vaccine strain of rinderpest virus and that of the virulent Kabete 'O' strain from which it was derived. The sequences of these two genes are essentially identical (99% at the nucleotide level), but were very different from a previously published Kabete O M gene sequence (M. Limo and T. Yilma, 1990, Virology 175, 323- 327). Inspection of the nucleotide and deduced amino acid sequences of known morbillivirus M genes showed that the earlier sequence was clearly from a morbillivirus, but neither from rinderpest virus nor from peste des petits ruminants virus.",matrix protein;article;Rinderpest virus;controlled study;gene sequence;Measles virus;molecular cloning;nonhuman;priority journal;virus classification,"Baron, M. D.;Goatley, L.;Barrett, T.",1994,,10.1006/viro.1994.1170,0
130,Isolation of multiple novel paramyxoviruses from pteropid bat urine,"Bats have been found to harbour a number of new emerging viruses with zoonotic potential, and there has been a great deal of interest in identifying novel bat pathogens to determine the risk to human and animal health. Many groups have identified novel viruses in bats by detection of viral nucleic acid; however, virus isolation is still a challenge, and there are few reports of viral isolates from bats. In recent years, our group has developed optimized procedures for virus isolation from bat urine, including the use of primary bat cells. In previous reports, we have described the isolation of Hendra virus, Menangle virus and Cedar virus in Queensland, Australia. Here, we report the isolation of four additional novel bat paramyxoviruses from urine collected from beneath pteropid tat (flying fox) colonies in Queensland and New South Wales during 2009-2011.",EMERGING VIRUSES;FRUIT BATS;METAGENOMIC ANALYSIS;TIOMAN-VIRUS;RESERVOIR;VIROME;HUMANS;ORIGIN;CHINA;PIGS,"Barr, J.;Smith, C.;Smith, I.;de Jong, C.;Todd, S.;Melville, D.;Broos, A.;Crameri, S.;Haining, J.;Marsh, G.;Crameri, G.;Field, H.;Wang, L. F.",2015,Jan,,0
131,Current perspectives on the phylogeny of Filoviridae,"Sporadic fatal outbreaks of disease in humans and non-human primates caused by Ebola or Marburg viruses have driven research into the characterization of these viruses with the hopes of identifying host tropisms and potential reservoirs. Such an understanding of the relatedness of newly discovered filoviruses may help to predict risk factors for outbreaks of hemorrhagic disease in humans and/or non-human primates. Recent discoveries such as three distinct genotypes of Reston ebolavirus, unexpectedly discovered in domestic swine in the Philippines; as well as a new species, Bundibugyo ebolavirus; the recent discovery of Lloviu virus as a potential new genus, Cuevavirus, within Filoviridae; and germline integrations of filovirus-like sequences in some animal species bring new insights into the relatedness of filoviruses, their prevalence and potential for transmission to humans. These new findings reveal that filoviruses are more diverse and may have had a greater influence on the evolution of animals than previously thought. Herein we review these findings with regard to the implications for understanding the host range, prevalence and transmission of Filoviridae. © 2011.",virus RNA;Bundibugyo Ebola virus;Cueva virus;disease surveillance;domestic pig;Ebola hemorrhagic fever;Ebolavirus;epidemic;Filoviridae;genetic variability;genotype;germ line;host pathogen interaction;host susceptibility;human;infection risk;infection sensitivity;mixed infection;molecular evolution;molecular phylogeny;new species;nonhuman;nucleotide sequence;Philippines;prediction;priority journal;Reston Ebola virus;review;risk assessment;RNA virus;viral tropism;virus carrier;virus genome;virus identification;virus transmission;virus virulence,"Barrette, R. W.;Xu, L.;Rowland, J. M.;McIntosh, M. T.",2011,,10.1016/j.meegid.2011.06.017,0
132,"Up-date of the new 2nd generation vaccines against rotavirus authorized in Spain: Perspectives, challenges and opportunities","A general review and update are done on the importance of the rotavirus and its implication as a source of gastroenteritis in the child. Comments are made on the structure of the virus, classification, pathogeny, symptoms and treatment. The immunological response of the host on protection of wild virus disease is reviewed, indicating how, after the first infection, reinfection is increasingly less severe as serious diarrheic disease is prevented. Briefly, the epidemiology and disease load are explained, indicating how the rotavirus is the cause of more than 600,000 deaths yearly in underdeveloped countries, elevated number of hospitalizations, outpatient visits and nosocomial infections and, consequently, the elevated morbidity and mortality that it represents for public health. It stands out that the only possible intervention is the preventive one, since the improvement achieved with health care hygienic conditions, water potability, access to oral rehydration, etc. have not led to a significant decrease in the disease incidence in both industrialized countries and developing ones. The most prevalent rotavirus serotypes and genotypes known in the world and in our country are described. Emphasis is placed on the current emergent serotypes. An extensive review is made of the principal studies that have recently appeared in the scientific literature on the new 2nd generation vaccines against the rotavirus authorized by the European Drug Agency (EMEA) and also in the United States. Although the two vaccines authorized in Spain come from different active ingredients, they have a common objective, the prevention of serious diarrhea due to rotavirus in the child. Wide designs of safety studies including more than 70,000 children have been necessary given the events that have occurred with Rotashield® (first human-bovine reassortant rotavirus vaccine used in the United States and currently withdrawn from the market) and its association with bowel intussusception. It has been sufficiently proven that there is no increased risk of bowel invagination associated with the vaccination with both vaccines, Rotarix® and RotaTeq™. Trials on efficacy, immunogenicity, adverse events, etc. have also been reviewed. They have been statistically significant and sufficiently tested within the permissible ranges in relationship with the placebos. A list is given of the recently appeared ACID (Advisory Committee Immunization Practices) recommendations for the RotaTeq™. Brief comments are made on several of the pharmacoeconomic studies found in the literature, some of them being cost-effective, although more advanced ones will be necessary once the vaccines are functioning and the immunization prices established for the public health system. Finally, the opportunities, challenges and perspectives of the current 2nd generation vaccines are discussed. In some of the future ones, the difficulties that they will have to face are indicated. The conclusion is reached on the importance of convincing the pediatricians on the use of these new vaccines, making the parents aware of it, providing both the regulatory authorities and them with health care education in order to include it within the common routine practice of immunizations. This requires pharmacoeconomic studies, with up-dated and real costs of the disease.",Rotavirus vaccine;child health care;cost benefit analysis;diarrhea;drug efficacy;drug safety;gastroenteritis;genotype;health education;hospital infection;hospitalization;human;immune response;immunization;morbidity;mortality;pediatrician;prevalence;public health;review;Rotavirus;serotype;virus infection;rotarix;rotashield;rotateq,"Barrio Corrales, F.;Cuenca Burgos, M. J.;García Fernández, M. A.;Trillo Belizón, C.",2006,,,0
133,Molecular epidemiology of bluetongue virus in Portugal during 2004-2006 outbreak,"After 44 years of epidemiological silence, bluetongue virus (BTV) was reintroduced in Portugal in the autumn of 2004. The first clinical cases of bluetongue disease (BT) were notified in sheep farms located in the South of Portugal, close to the Spanish border. A total of six BTV, five of serotype 4 and one of serotype 2 were isolated from sheep and cattle during the 2004-2006 epizootics. The nucleotide sequence of gene segments L2, S7 and S10 of BTV-4 prototype strain (BTV4/22045/PT04) obtained from the initial outbreak and of BTV-2 (BTV2/26629/PT05) was fully determined and compared with those from other parts of the world. The phylogenetic analysis revealed that BTV4/22045/PT04 is related to other BTV-4 strains that circulate in the Mediterranean basin since 1998, showing the highest identity (99%) with BTV-4 isolates of 2003 from Sardinia and Corsica, whereas BTV2/26629/PT05 is almost indistinguishable from the Onderstepoort BTV-2 live-attenuated vaccine strain and its related field strain isolated in Italy. Since live-attenuated BTV-2 vaccine was never used in Portugal, the isolation of this strain may represent a natural circulation of the vaccine virus used in other countries in Mediterranean Europe. © 2007 Elsevier B.V. All rights reserved.",animal cell;article;Bluetongue orbivirus;chick embryo;embryo;epidemic;molecular epidemiology;nonhuman;nucleotide sequence;phylogeny;Portugal;sheep disease;Southern Europe;unindexed sequence;viral genetics;virus isolation;virus strain;virus typing,"Barros, S. C.;Ramos, F.;Luís, T. M.;Vaz, A.;Duarte, M.;Henriques, M.;Cruz, B.;Fevereiro, M.",2007,,10.1016/j.vetmic.2007.04.014,0
134,Infection of macrophages by a lymphotropic herpesvirus: A new tropism for Marek's disease virus,"Marek's disease virus (MDV) is classified as an oncogenic lymphotropic herpesvirus of chickens. MDV productively and cytolytically infects B, αβT and γδT lymphocytes and latently infects T-helper lymphocytes. The aims of this study were to identify whether MDV infects macrophages in vivo and, if so, whether quantitative differences in macrophage infection are associated with MDV strain virulence. Chickens were infected with either virulent MDV (HPRS-16) or 'hypervirulent' MDV (C12/130). Flow cytometry with monoclonal antibodies recognizing MDV pp38 antigen and leukocyte antigens was used to identify MDV lytically infected cells. Macrophages from HPRS-16- and C12/130-infected chickens were pp38+. It is demonstrated that macrophages are pp38+ because they are infected and not because they have phagocytosed MDV antigens, as assessed by confocal microscopy using antibodies recognizing MDV antigens of the three herpesvirus kinetic classes: infected cell protein 4 (ICP4, immediate early), pp38 (early) and glycoprotein B (gB, late). Spleen macrophages from MDV-infected chickens were ICP4+, pp38+ and gB+, and ICP4 had nuclear localization denoting infection. Finally, MDV pp38+ macrophages had high inherent death rates, confirming cytolytic MDV infection, although production of virus particles has not been detected yet. These results have two fundamental implications for understanding MDV pathogenesis: (i) MDV evolved to perturb innate, in addition to acquired, immunity and (ii) macrophages are excellent candidates for transporting MDV to primary lymphoid organs during the earliest stages of pathogenesis.",cell protein;glycoprotein B;leukocyte antigen;monoclonal antibody;virus antigen;animal cell;animal experiment;animal model;antigen detection;antigen recognition;article;Gallid alphaherpesvirus 2;chicken;confocal microscopy;controlled study;cytolysis;flow cytometry;immunity;in vivo study;lymphoid organ;macrophage;mortality;nonhuman;nuclear localization signal;pathogenesis;phagocytosis;priority journal;spleen cell;virogenesis;virus infection;virus particle;virus strain;virus virulence,"Barrow, A. D.;Burgess, S. C.;Baigent, S. J.;Howes, K.;Nair, V. K.",2003,,10.1099/vir.0.19206-0,0
135,Tick-borne viruses,"Tick-borne viruses (TBVs) belong to the largest biological group known as arboviruses with unique mode of transmission by blood-feeding arthropods (ticks, mosquitoes, sand flies, biting midges, etc.) to a susceptible vertebrate host. Taxonomically, it is a heterogenous group of vertebrate viruses found in several viral families. With only one exception, African swine fever virus, all TBVs have a RNA genome. To date, at least 160 tick-borne viruses are known, some of them pose a significant threat to human and animal health worldwide. Recently, a number of established TBVs has re-emerged and spread to new geographic locations due to the influence of anthropogenic activities and few available vaccines. Moreover, new emerging tick-borne diseases are constantly being reported. Major advances in molecular biotechnologies have led to discoveries of new TBVs and further genetic characterization of unclassified viruses resulting in changes in TBVs classification created by the International Committee for the Taxonomy of Viruses. Although TBVs spend over 95% of their life cycle within tick vectors and the role of ticks as vectors has been known for over 100 years, our knowledge about TBVs and molecular processes involved in the virus-tick interactions is scarce.",virus vector;African swine fever virus;Arbovirus;Bunyavirales;DNA virus;Flaviviridae;life cycle;Lumpy skin disease virus;Mononegavirales;Murid herpesvirus 4;nonhuman;Nyamiviridae;Orthomyxoviridae;Reoviridae;review;Rhabdoviridae;RNA virus;taxonomy;tick;tick borne disease;Tick borne flavivirus;Tick borne virus;tick vector;virus classification;virus forms;virus transmission,"Bartíková, P.;Holíková, V.;Kazimírová, M.;Štibrániová, I.",2017,,10.4149/av_2017_403,0
136,Comparative characteristics of the biological properties of small ruminant lentiviruses,"The infections caused by small ruminant lentiviruses include diseases, such as Maedi-Visna (MV) and caprine arthritis- encephalitis (CAE). According to phylogenetic findings and their common origination, small ruminant lentiviruses were divided into Groups A, B, C, D, and E. Cultivation of the lentiviruses displayed the cytopathic effect of the CAE virus strain 75 G-63 in the primary culture of goatling synovial membrane cells, which was shown by monolayer destruction and polynuclear cell formation; this was uncharacteristic for M-88, K-796, and Tverskoy strains. A high homology was found for the Tverskoy strain with Group B small ruminant lentiviruses and the M- 88 and K-796 strains with their Group A.",virus DNA;viral protein;animal;article;Caprine arthritis encephalitis virus;cell culture;classification;comparative study;cytology;genetics;goat;isolation and purification;ovine progressive pneumonia;phylogeny;prenatal development;sensitivity and specificity;synovium;virology;virus replication;Visna virus,"Baryshnikova, E. I.;Malogolovkin, A. S.;Kolbasova, O. L.;Tsybanov, S. Zh",2011,,,0
137,"Novel West Nile virus lineage 1a full genome sequences from human cases of infection in north-eastern Italy, 2011","During 2008-2009, several human cases of WNV disease caused by an endemic lineage 1a strain were reported in areas surrounding the Po river in north-eastern Italy. Since 2010, cases have been recorded in nearby northern areas, where, in 2011, both lineage 1a and 2 were detected. We describe here two new WNV complete genome sequences from human cases of WNV infection occurring in 2011 in the Veneto Region. Phylogenetic analysis showed that both genome sequences belonged to lineage 1a and were related to WNV strains of the Western Mediterranean subtype. The novel WNV genomes had high nucleotide and amino acid sequence divergence from each other and from the WNV strain circulating in Italy in 2008-2009. The presence of different WNV strains in a relatively small geographical area is a novel finding with unpredictable impact on human disease that requires further investigation. © 2012 The Authors. Clinical Microbiology and Infection © 2012 European Society of Clinical Microbiology and Infectious Diseases.",amino acid sequence;article;cell lineage;gene sequence;human;Italy;nonhuman;nucleotide sequence;phylogeny;priority journal;virus gene;virus strain;West Nile fever;West Nile virus,"Barzon, L.;Pacenti, M.;Franchin, E.;Squarzon, L.;Lavezzo, E.;Toppo, S.;Martello, T.;Cattai, M.;Cusinato, R.;Palù, G.",2012,,10.1111/1469-0691.12001,0
138,Swine influenza viruses in Northern Vietnam in 2013-2014 article,"Swine are an important intermediate host for emergence of pandemic influenza. Vietnam is the largest swine producer in South East Asia. Systematic virological and serological surveillance of swine influenza viruses was carried out in Northern Vietnam from May 2013 to June 2014 with monthly sampling of pigs in local and large collective slaughterhouses and in a live pig market. Influenza A seroprevalence in the local slaughterhouses and in the large collective slaughterhouse was 48.7% and 29.1%, respectively. Seventy-seven influenza A viruses were isolated, all from the large collective slaughterhouse. Genetic analysis revealed six virus genotypes including H1N1 2009 pandemic (H1N1pdm09) viruses, H1N2 with H1 of human origin, H3N2 and H1N1pdm09 reassortants, and triple-reassortant H3N2 viruses. Phylogenetic analysis of swine and human H1N1pdm09 viruses showed evidence of repeated spill-over from humans to swine rather than the establishment of H1N1pdm09 as long-term distinct lineage in swine. Surveillance at the large collective slaughterhouse proved to be the most efficient, cost-effective, and sustainable method of surveillance for swine influenza viruses in Vietnam.",virus RNA;article;controlled study;genetic analysis;genetic reassortment;genotype;Influenza A virus (H1N1);Influenza A virus (H1N2);Influenza A virus (H3N2);nonhuman;nose smear;phylogenetic tree;pig;priority journal;seroprevalence;slaughterhouse;swine influenza virus;Viet Nam;virus genome;virus identification;virus isolation;virus strain,"Baudon, E.;Chu, D. K. W.;Tung, D. D.;Thi Nga, P.;Vu Mai Phuong, H.;Le Khanh Hang, N.;Thanh, L. T.;Thuy, N. T.;Khanh, N. C.;Mai, L. Q.;Khong, N. V.;Cowling, B. J.;Peyre, M.;Peiris, M.",2018,,10.1038/s41426-018-0109-y,0
139,A novel bovine papillomavirus type in the genus Dyokappapapillomavirus,"Papillomaviruses are a diverse group of viruses that are known to infect a wide range of animal species. Bovine papillomaviruses (BPVs) are divided into at least 21 genotypes (BPV1 to BPV21),  with most BPV isolates/strains described to date belonging to one of four genera, including Deltapapillomavirus, Xipapillomavirus, Epsilonpapillomavirus and Dyoxipapillomavirus. Here, we describe the identification and genetic characterization of a new BPV type in the genus Dyokappapapillomavirus. A farm in the state of New York, USA, reported chronic cases of vulvovaginitis in Holstein cows in 2016. Biopsies and/or swab samples collected from the vaginal mucosa were subjected to diagnostic investigation. Conventional diagnostic assays yielded negative results, and vaginal swab samples were subjected to viral metagenomic sequencing. Notably, BLAST searches revealed a papillomavirus genome with 7480 bp in length (67% nt sequence identity to BPV16). Additionally, phylogenetic analysis of the L1 gene of the papillomavirus identified here (tentatively named BPV22) revealed that it clusters with members of the genus Dyokappapapillomavirus. Interestingly, the recently identified BPV16, which was detected in fibropapilloma lesions in cattle also clusters within the Dyokappapapillomavirus group. Each virus, however, forms a separate branch in the phylogenetic tree. These results indicate that the putative BPV22 represents the second BPV within the genus Dyokappapapillomavirus.",animal;bovine;cattle disease;female;genetics;isolation and purification;Papillomaviridae;papillomavirus infection;phylogeny;veterinary medicine;virology;vulvovaginitis,"Bauermann, F. V.;Joshi, L. R.;Mohr, K. A.;Kutish, G. F.;Meier, P.;Chase, C.;Christopher-Hennings, J.;Diel, D. G.",2017,,10.1007/s00705-017-3443-9,1
140,Analysis of porcine circovirus type 1 detected in Rotarix vaccine,"A metagenomic analysis of live human vaccines has recently demonstrated the presence of porcine circovirus type 1 (PCV1) DNA in the paediatric vaccine Rotarix used in the prevention of acute gastroenteritis. Using real-time PCR for PCV1, titres of PCV1 DNA in several batches of Rotarix were found to be in the order of 6-7log10 copies per dose. Pre-treatment of the reconstituted vaccine with the nuclease Benzonase, followed by extraction of nucleic acid and quantification of PCV1 DNA by real-time PCR, revealed that there was no loss of PCV1 DNA titre compared to untreated controls, suggesting that the porcine viral DNA was present in the vaccine in an encapsidated form. PCV1 permissive PS cells, human HEK293 and Vero cells, used for vaccine production, were infected with Rotarix or PCV1, respectively, and subjected to immune fluorescence and RT-PCR. Viral genomes were present in Rotarix-incubated as well as PCV1-infected cells, while viral transcription was seen only in PCV1-infected cells. Similarly, PCV1-specific protein expression was observed in PCV1-infected cells, but not in cells treated with Rotarix. Passaging of the supernatant indicated productive infection in PCV1-infected PS cells, but not in HEK293 and Vero cells or in any cell line incubated with Rotarix. PCV1 DNA present in Rotarix was protected from Benzonase digestion; however, PCV1 was not recognized in immune electron microscopy and unable to infect PS, HEK293 or Vero cells, suggesting that the high amount of PCV1 DNA present in Rotarix does not reflect a corresponding proportion of biologically active virus particles. © 2010 Elsevier Ltd.",nucleic acid;Rotavirus vaccine;virus DNA;animal cell;article;Circovirus;controlled study;extraction;human;human cell;immunofluorescence;incubation time;nonhuman;nucleotide sequence;priority journal;protein expression;real time polymerase chain reaction;virus detection;virus transcription,"Baylis, S. A.;Finsterbusch, T.;Bannert, N.;Blümel, J.;Mankertz, A.",2011,,10.1016/j.vaccine.2010.11.028,0
141,Complete genome sequences of a cytophatic/noncytophatic pair of bovine viral diarrhea virus subtype 1a viruses,The complete genome sequences of both biotypes of a pair of bovine viral diarrhea viruses isolated from a bovid affected by mucosal disease were determined by next generation sequencing. The cytopathic virus possessed a 423-base insertion derived from bovine poly ubiquitin in the NS2/3 coding region and one nucleotide change. Both biotypes showed an additional glycosylation site in their N-terminus.,virus RNA;animal;bovine;bovine viral diarrhea;Bovine viral diarrhea virus 1;classification;cytopathogenic effect;genetics;high throughput sequencing;isolation and purification;nucleotide sequence;phylogeny;physiology;virology;virus genome,"Bazzucchi, M.;Bertolotti, L.;Giammarioli, M.;De Mia, G. M.",2018,,10.1007/s00705-018-3959-7,0
142,Identification and genetic characterization of bovine enterovirus by combination of two next generation sequencing platforms,"Prompt and accurate diagnosis is warranted for infectious diseases of domestic animals which may have a significant impact on animal production or clinical practice. In this study, the identification and genetic characterization of a bovine enterovirus (BEV) strain isolated from a calf with diarrhea, are described. Two different next generation sequencing platforms were employed. Shotgun metagenomic accomplished by MinION sequencing (Oxford Nanopore Technologies) allowed the identification of BEV RNA from a cell-culture isolate. BEV was then confirmed by a specific real time RT-PCR assay. To achieve the whole genome of this isolate, sequence reads obtained by MinION were coupled with those originating from NextSeq500 (Illumina). Genomic relatedness and phylogeny with extant BEV strains is also reported. Overall, this manuscript highlights the use of the portable MinION sequence technology as a tool for support diagnostics in veterinary practice.",complementary DNA;virus RNA;article;Bovine enterovirus;calf (bovine);cell culture;diarrhea;gene sequence;genetic identification;metagenomics;molecular phylogeny;next generation sequencing;nonhuman;priority journal;real time polymerase chain reaction;RNA analysis;virus genome;virus isolation;virus strain,"Beato, M. S.;Marcacci, M.;Schiavon, E.;Bertocchi, L.;Di Domenico, M.;Peserico, A.;Mion, M.;Zaccaria, G.;Cavicchio, L.;Mangone, I.;Soranzo, E.;Patavino, C.;Cammà, C.;Lorusso, A.",2018,,10.1016/j.jviromet.2018.07.002,0
143,Genetic and antigenic characterization of novel pestivirus genotypes: Implications for classification,"Currently, the genus Pestivirus comprises the four approved species Bovine viral diarrhea virus 1 (BVDV-1), BVDV-2, Classical swine fever virus (CSFV), and Border disease virus (BDV) and one tentative fifth species represented by a single strain (H138) isolated from a giraffe in Kenya more than 30 years ago. To further address the issue of heterogeneity of pestiviruses we have determined the entire Npro and E2 coding sequences for several new pestivirus isolates. Interestingly, phylogenetic analysis revealed that one pestivirus isolated in the 1990s in Africa is closely related to strain H138. Moreover, several novel pestiviruses isolated from sheep group together with the previously described strain V60 (Reindeer-1) isolated from a reindeer, whereas one ovine pestivirus strain (Gifhorn) significantly differs from all previously described pestiviruses, including BDV. We propose to term these mainly sheep-derived pestiviruses BDV-2 (V60-like isolates) and BDV-3 (Gifhorn); consequently, the ""classical"" BDV isolates should be termed BDV-1. As an additional criterion for segregation of pestiviruses, the antigenic relatedness of pestivirus isolates covering all observed major genotypes was studied by cross-neutralization assays. Analysis of the antigenic similarities indicated the presence of seven major antigenic groups corresponding to BVDV-1, BVDV-2, CSFV, BDV-1, BDV-2, BDV-3, and ""giraffe"". Taking into account the host origin, the lack of differences concerning the course of disease, and the results of our genetic and antigenic analyses, we suggest that BDV-1, BDV-2, and BDV-3 should be considered as major genotypes within the species BDV. © 2003 Elsevier Science (USA). All rights reserved.",Africa;animal cell;antigenicity;article;Bovine viral diarrhea virus 1;controlled study;genetic analysis;genotype;nonhuman;nucleotide sequence;Pestivirus;phylogeny;priority journal;reindeer;sheep;viral genetics;virus classification;virus isolation;virus strain,"Becher, P.;Ramirez, R. A.;Orlich, M.;Rosales, S. C.;König, M.;Schweizer, M.;Stalder, H.;Schirrmeier, H.;Thiel, H. J.",2003,,10.1016/s0042-6822(03)00192-2,0
144,Genetic typing of Croatian bovine viral diarrhea virus isolates,"Between 2007 and 2011, a total of 1937 sera samples and five spleen samples from nine Croatian dairy herds were tested for the bovine viral diarrhea virus (BVDV) using virus isolation and the immunoperoxidase test. BVDV was detected in 13 persistently infected (PI) cattle with a non-cytopathogenic biotype, while in five animals with fatal mucosal disease, isolates from spleen samples were of the cytopathogenic biotype. To reveal the genetic typing of Croatian BVDV isolates, viral RNA was extracted from infected cell cultures and amplified by RT-PCR, with primers targeting the 5'-UTR and the Npro gene, followed by direct sequencing of purified PCR products. Sequence and phylogenetic analysis of the 5'-UTR genome region determined that all Croatian isolates belonged to BVDV genotype 1; 11 isolates were grouped with BVDV-lb and 7 with BVDV-If viruses. The phylogenetic tree inferred by the Bayesian approach, using combined 5'-UTR/Npro, supported clustering of Croatian isolates in two subgroups. The deduced aminoacid sequence of the Npro region revealed 5 sites unique for four domestic BVDV-If isolates.",BVDV;immunoperoxidase test;Npro;phylogenetic analysis;PHYLOGENETIC ANALYSIS;POINT MUTATIONS;STRAIN OREGON;IDENTIFICATION;PESTIVIRUSES;DIVERSITY;GENOTYPE-1;BVDV;PREVALENCE;SEQUENCE,"Bedekovic, T.;Lojkic, I.;Lemo, N.;Cac, Z.;Cvetnic, Z.;Lojkic, M.;Madic, J.",2012,Sep-Oct,,0
145,"""Schmallenberg virus"" - A novel orthobunyavirus emerging in Europe","SUMMARY In 2011, a novel orthobunyavirus of the Simbu serogroup, the Schmallenberg virus (SBV), was discovered using a metagenomic approach. SBV caused a large epidemic in Europe in ruminants. As with related viruses such as Akabane virus, it appears to be transmitted by biting midges. Transplacental infection often results in the birth of malformed calves, lambs and goat kids. In more than 5000 farms in Germany, The Netherlands, Belgium, France, UK, Italy, Spain, Luxembourg, Denmark and Switzerland acute infections of adult ruminants or malformed SBV-positive offspring were detected, and high seroprevalences were seen in adult ruminants in the core regions in The Netherlands, Germany and Belgium. The discovery of SBV, the spread of the epidemic, the role of vectors, the impact on livestock, public health issues, SBV diagnosis and measures taken are described in this review. Lessons to be learned from the Schmallenberg virus epidemic and the consequences for future outbreaks are discussed. Copyright © Cambridge University Press 2012.",bovid;Ceratopogonidae;congenital malformation;Culicoides;disease carrier;epidemic;Europe;infection control;livestock;mandatory reporting;nonhuman;Orthobunyavirus;Orthobunyavirus infection;reverse transcription polymerase chain reaction;review;Schmallenberg virus;Schmallenberg virus infection;seroprevalence;vertical transmission;viremia;virus detection;virus transmission;zoonosis,"Beer, M.;Conraths, F. J.;Van Der Poel, W. H. M.",2013,,10.1017/s0950268812002245,0
146,"Multiple reassorted viruses as cause of highly pathogenic avian influenza A(H5N8) virus epidemic, the Netherlands, 2016","In 2016, an epidemic of highly pathogenic avian influenza A virus subtype H5N8 in the Netherlands caused mass deaths among wild birds, and several commercial poultry farms and captive bird holdings were affected. We performed complete genome sequencing to study the relationship between the wild bird and poultry viruses. Phylogenetic analysis showed that the viruses are related to H5 clade 2.3.4.4 viruses detected in Russia in May 2016 but contained novel polymerase basic 2 and nucleoprotein gene segments and 2 different variants of the polymerase acidic segment. Molecular dating suggests that the reassortment events most likely occurred in wild birds in Russia or Mongolia. Furthermore, 2 genetically distinct H5N5 reassortant viruses were detected in wild birds in the Netherlands. Our study provides evidence for fast and continuing reassortment of H5 clade 2.3.4.4 viruses, which might lead to rapid changes in virus characteristics, such as pathogenicity, infectivity, transmission, and zoonotic potential.",matrix protein;virus hemagglutinin;virus nucleoprotein;virus sialidase;article;avian influenza (H5N8);avian influenza;avian influenza virus;gene cluster;genetic analysis;genetic difference;genetic reassortment;geographic distribution;Netherlands;nonhuman;phylogeny;poultry;Sanger sequencing;virus detection;whole genome sequencing,"Beerens, N.;Heutink, R.;Bergervoet, S. A.;Harders, F.;Bossers, A.;Koch, G.",2017,,10.3201/eid2312.171062,0
147,Molecular analysis of swine hepatitis E virus from north India,"Background & objectives: Hepatitis E is the main cause of enterically transmitted non-A, non-B hepatitis in developing countries. In the developed countries such as the USA, Japan and Taiwan, the viruses infecting humans and swine share the same genotype with a high sequence similarity. Genotype 1 circulates in humans whereas genotype 4 in pigs in India. The present study was designed to investigate the presence of anti-HEV antibodies and HEV-RNA in swine population from north India, to investigate the genotype prevalent in it, and to compare it with other swine and human HEV strains from India.Methods: A total of 67 serum samples were collected from pigs of age period (1-6 months) from Indian Veterinary Research Institute (IVRI), Izatnagar, Bareily and subjected to anti-HEV IgG and HEV RNA detection. A phylogenetic tree was constructed using the neighbor-joining method and evaluated using the interior branch test method with MEGA 4 software.Results: Anti-HEV IgG and HEV RNA was found in 38.8 and 4.5 per cent of swine samples studied respectively. The above samples were observed to be of genotype 4e. The three new sequences had nucleotide similarity with other swine sequences in genotype 4 ranging from 80-98 per cent.Interpretation & conclusions: The three sequences observed in the present study showed nucleotide similarity with other swine sequences from southern and western India. The present study suggests that genotype 4 'e' is prevalent in the north India.",immunoglobulin G antibody;virus RNA;antibody detection;article;developing country;enzyme linked immunosorbent assay;genotype;hepatitis E;Hepatitis E virus;India;neighbor joining method;nonhuman;nucleotide sequence;open reading frame;phylogenetic tree;polymerase chain reaction;sequence homology;strain difference;pig;virus genome;virus transmission,"Begum, N.;Polipalli, S. K.;Husain, S. A.;Kar, P.",2010,,,0
148,Relationships and history of live Newcastle disease vaccine strains,"Formerly, NDV (Newcastle disease virus) strains were classified solely on the basis of virulence, but recently grouping based on genetic relationships of strains are the method of choice. Live vaccine strains belong to mild (lentogenic) or moderately virulent (mesogenic) categories, as opposed to the highly pathogenic epidemic viruses of the velogenic group. Using their genetic properties and lineage, the placement of vaccine strains in 'the NDV world' can be viewed as described below (Figure 1). 1. Lentogenic vaccine strains are found in two of the dozen or so genotypes of NDV resident in chickens. One of them is the American group 11 (comprising vaccine strains B-1, LaSota and F), the other is genotype I (with strains Ulster 2C, V4/Queensland and NDV-6/10) also residing in wild water-birds. 2. Mesogenic strains too, are present in only two genotypes: group 11 (strains Roakin and Komarov) and the Asian genogroup III (strains H and Mukteswar). 3. While vaccine strains of groups I and 11 aro of natural origin, strains H, Mukteswar and Komarov were artificially attenuated as claimed by reports in the 1940s. However, discrepancies were discerned between the actual genetic identity and the postulated origin of mesogenic vaccine strains (Figure 2). a) Since the mesogenic strain H is unrelated to the virulent Herts'33, its ostensible parent, the reduced virulence of H can not be attributed to the egg passage procedures performed in England and even the presence of this strain there is a riddle. b) Strains H and Mukteswar with less than 0.3% nucleotide distance between them must have been derived from the same isolate therefore can not be the result of independent developments in England and India. c) The reduced virulence (mesogenic) of strain H/Mukteswar can not be associated with attenuation either; most likely it is a naturally occurring Indian field isolate. d) The mesogenic strain Komarov, which is said to be attenuated through the intracerebral passage in ducklings of a local velogenic virus in Palestine, is identical with the American (genotype 11) vaccine strain Roakin, for which no scientific explanation can be given.",VIRUS;ORIGIN,"Bela, L.",2008,Jun,,0
149,"New viruses in veterinary medicine, detected by metagenomic approaches","In our world, which is faced today with exceptional environmental changes and dramatically intensifying globalisation, we are encountering challenges due to many new factors, including the emergence or re-emergence of novel, so far "" unknown"" infectious diseases. Although a broad arsenal of diagnostic methods is at our disposal, the majority of the conventional diagnostic tests is highly virus-specific or is targeted entirely towards a limited group of infectious agents. This specificity complicates or even hinders the detection of new or unexpected pathogens, such as new, emerging or re-emerging viruses or novel viral variants. The recently developed approaches of viral metagenomics provide an effective novel way to screen samples and detect viruses without previous knowledge of the infectious agent, thereby enabling a better diagnosis and disease control, in line with the "" One World, One Health"" principles (www.oneworldonehealth.org). Using metagenomic approaches, we have recently identified a broad variety of new viruses, such as novel bocaviruses, Torque Teno viruses, astroviruses, rotaviruses and kobuviruses in porcine disease syndromes, new virus variants in honeybee populations, as well as a range of other infectious agents in further host species. These findings indicate that the metagenomic detection of viral pathogens is becoming now a powerful, cultivation-independent, and useful novel diagnostic tool in veterinary diagnostic virology. © 2013 Elsevier B.V.",Astroviridae;bioinformatics;Bocaparvovirus;diagnostic test;diarrhea;disease control;honeybee;interstitial nephritis;Kobuvirus;metagenomics;nonhuman;nucleic acid amplification;review;Rotavirus;swine disease;Torque teno virus 1;veterinary medicine;virus detection;virus gene,"Belák, S.;Karlsson, O. E.;Blomström, A. L.;Berg, M.;Granberg, F.",2013,,10.1016/j.vetmic.2013.01.022,0
150,Advances in viral disease diagnostic and molecular epidemiological technologies,"The early and rapid detection and characterization of specific nucleic acids of medico-veterinary pathogens have proven invaluable for diagnostic purposes. The integration of amplification and signal detection systems, including online real-time devices, have increased speed and sensitivity and greatly facilitated the quantification of target nucleic acids. They have also allowed for sequence characterization using melting or hybridization curves. The newer-generation molecular diagnostic technologies offer, hitherto, unparalleled detection and discrimination methodologies, which are vital for the positive detection and identification of pathogenic agents, as well as the effects of the pathogens on the production of antibodies. The development phase of the novel technologies entails a thorough understanding of accurate diagnosis and discrimination of present and emerging diseases. The development of novel technologies can only be successful if they are transferred and used in the field with a sustainable quality-assured application to allow for the optimal detection and effective control of diseases. The aim of these new tools is to detect the presence of a pathogen agent before the onset of disease. This manuscript focuses mainly on the experiences of two World Organisation for Animal Health collaborating centers in context to molecular diagnosis and molecular epidemiology of transboundary and endemic animal diseases of viral origin, food safety and zoonoses. © 2009 Expert Reviews Ltd.",animal health;antibody production;diagnostic accuracy;diagnostic procedure;early diagnosis;endemic disease;enzyme linked immunosorbent assay;food contamination;food safety;foot and mouth disease;Foot and mouth disease virus;gene amplification;hepatitis E;Hepatitis E virus;human;microfluidics;molecular cloning;molecular epidemiology;nonhuman;Pestivirus;real time polymerase chain reaction;review;robotics;swine disease;veterinary medicine;viral contamination;virus detection;virus diagnosis;virus genome;virus infection;World Health Organization;zoonosis,"Belák, S.;Thorén, P.;LeBlanc, N.;Viljoen, G.",2009,,10.1586/erm.09.19,0
151,African swine fever virus and AIDS,,acquired immune deficiency syndrome;African swine fever virus;blood and hemopoietic system;classification;etiology;nonhuman;priority journal;virology;virus classification,"Beldekas, J.;Teas, J.;Hebert, J. R.",1986,,,0
152,Propidium monoazide (PMA) and ethidium bromide monoazide (EMA) improve DNA array and high-throughput sequencing of porcine reproductive and respiratory syndrome virus identification,"Pan-viral DNA array (PVDA) and high-throughput sequencing (HTS) are useful tools to identify novel viruses of emerging diseases. However, both techniques have difficulties to identify viruses in clinical samples because of the host genomic nucleic acid content (hg/cont). Both propidium monoazide (PMA) and ethidium bromide monoazide (EMA) have the capacity to bind free DNA/RNA, but are cell membrane-impermeable. Thus, both are unable to bind protected nucleic acid such as viral genomes within intact virions. However, EMA/PMA modified genetic material cannot be amplified by enzymes. In order to assess the potential of EMA/PMA to lower the presence of amplifiable hg/cont in samples and improve virus detection, serum and lung tissue homogenates were spiked with porcine reproductive and respiratory virus (PRRSV) and were processed with EMA/PMA. In addition, PRRSV RT-qPCR positive clinical samples were also tested. EMA/PMA treatments significantly decreased amplifiable hg/cont and significantly increased the number of PVDA positive probes and their signal intensity compared to untreated spiked lung samples. EMA/PMA treatments also increased the sensitivity of HTS by increasing the number of specific PRRSV reads and the PRRSV percentage of coverage. Interestingly, EMA/PMA treatments significantly increased the sensitivity of PVDA and HTS in two out of three clinical tissue samples. Thus, EMA/PMA treatments offer a new approach to lower the amplifiable hg/cont in clinical samples and increase the success of PVDA and HTS to identify viruses.",azide;ethidium bromide monoazide;propidium monoazide;unclassified drug;animal tissue;article;blood analysis;controlled study;DNA binding;DNA microarray;DNA sequence;gene amplification;high throughput sequencing;lung homogenate;molecular dynamics;nonhuman;Porcine reproductive and respiratory syndrome virus;priority journal;reverse transcription polymerase chain reaction;sensitivity and specificity;ultracentrifugation;virion;virus genome;virus identification,"Bellehumeur, C.;Boyle, B.;Charette, S. J.;Harel, J.;L'Homme, Y.;Masson, L.;Gagnon, C. A.",2015,,10.1016/j.jviromet.2015.06.014,0
153,High-throughput sequencing revealed the presence of an unforeseen parvovirus species in Canadian swine: The porcine partetravirus,,animal;animal disease;article;Canada;classification;genetics;Parvoviridae;parvovirus infection;phylogeny;pig;swine disease;virology,"Bellehumeur, C.;Boyle, B.;Mandeville, I.;Gagnon, C. A.",2013,,,1
154,Atypical rotavirus in chickens in Argentina,"In Argentina the presence of rotavirus was investigated in a chicken flock experiencing periodic episodes of diarrhoea during the winter of 1986. All the samples analysed were negative by the enzyme-linked immunosorbent assay (ELISA). However, when samples were observed by electron microscopy, particles which were indistinguishable from standard rotaviruses were detected in some samples. Ten of the 36 samples were positive after polyacrylamide gel electrophoresis (PAGE) analysis, all of them showing the same electropherotype. Based on these results these viruses were classified as rotavirus-like or atypical rotaviruses.",animal;animal disease;Argentina;article;bird disease;chicken;isolation and purification;microbiology;Rotavirus;virus infection,"Bellinzoni, R.;Mattion, N.;Vallejos, L.;La Torre, J. L.;Scodeller, E. A.",1987,,,0
155,Serological characterization of bovine rotaviruses isolated from dairy and beef herds in Argentina,"Bovine rotaviruses isolated from beef and dairy herds in Argentina were serotyped by the immunoperoxidase focus reduction assay as previously described (G. Gerna, M. Battaglia, G. Milenesi, N. Passarani, E. Percivalle, and E. Cattaneo, Infect. Immun. 43:722-729, 1984). Three strains from beef herds were related to the UK and NCDV bovine rotavirus strains defined as serotype 6 (Y. Hoshino, T.G. Wyatt, H.B. Greenberg, J. Flores, and A.Z. Kapikian, J. Infect. Dis. 149:694-702, 1984). Two other strains from dairy herds were classified as bovine viruses related to the bovine B223 strain reported by Woode and co-workers (G.N. Woode, N.E. Kelso, T.F. Simpson, S.K. Gaul, L.E. Evans, and L. Babiuk, J. Clin. Microbiol. 18:258-264, 1983) in the United States. A serotyping antibody-capture enzyme-linked immunoassay to detect serotype 6 rotavirus using a serotype 6-specific monoclonal antibody was developed and evaluated for strain characterization. Characterization of 72 group A rotavirus-positive fecal samples from beef herds and 43 fecal samples from dairy herds showed a predominance of serotype 6 rotavirus in beef herds but both serotype 6 and non-serotype 6 rotaviruses in dairy herds. Analysis of genomic double-stranded RNA by polyacrylamide gel electrophoresis showed that when outbreaks were caused by one serotype only a single electropherotype was present in all samples.",animal cell;Argentina;bovine;nonhuman;polyacrylamide gel electrophoresis;priority journal;Rotavirus;serotype;virus infection;virus strain,"Bellinzoni, R. C.;Blackhall, J. O.;Mattion, N. M.;Estes, M. K.;Snodgrass, D. R.;LaTorre, J. L.;Scodeller, E. A.",1989,,,0
156,Genotype Diversity of Newcastle Disease Virus in Nigeria: Disease Control Challenges and Future Outlook,"Newcastle disease (ND) is one of the most important avian diseases with considerable threat to the productivity of poultry all over the world. The disease is associated with severe respiratory, gastrointestinal, and neurological lesions in chicken leading to high mortality and several other production related losses. The aetiology of the disease is an avian paramyxovirus type-1 or Newcastle disease virus (NDV), whose isolates are serologically grouped into a single serotype but genetically classified into a total of 19 genotypes, owing to the continuous emergence and evolution of the virus. In Nigeria, molecular characterization of NDV is generally very scanty and majorly focuses on the amplification of the partial F gene for genotype assignment. However, with the introduction of the most objective NDV genotyping criteria which utilize complete fusion protein coding sequences in phylogenetic taxonomy, the enormous genetic diversity of the virus in Nigeria became very conspicuous. In this review, we examine the current ecological distribution of various NDV genotypes in Nigeria based on the available complete fusion protein nucleotide sequences (1662 bp) in the NCBI database. We then discuss the challenges of ND control as a result of the wide genetic distance between the currently circulating NDV isolates and the commonest vaccines used to combat the disease in the country. Finally, we suggest future directions in the war against the economically devastating ND in Nigeria.",b1 vaccine;fusion protein;i2 vaccine;komarov vaccine;lasota vaccine;Newcastle disease vaccine;unclassified drug;v4 vaccine;vgga vaccine;disease control;ecology;evolution;genetic distance;genetic variability;genotype;molecular phylogeny;Newcastle disease;Newcastle disease virus;Nigeria;nonhuman;nucleotide sequence;review;taxonomy;vaccination;virus classification;virus isolation,"Bello, M. B.;Yusoff, K. M.;Ideris, A.;Hair-Bejo, M.;Peeters, B. P. H.;Jibril, A. H.;Tambuwal, F. M.;Omar, A. R.",2018,,10.1155/2018/6097291,0
157,"Novel polyphenol oxidase mined from a metagenome expression library of bovine rumen: Biochemical properties, structural analysis, and phylogenetic relationships","RL5, a gene coding for a novel polyphenol oxidase, was identified through activity screening of a metagenome expression library from bovine rumen microflora. Characterization of the recombinant protein produced in Escherichia coli revealed a multipotent capacity to oxidize a wide range of substrates (syringaldazine > 2,6-dimethoxyphenol > veratryl alcohol > guaiacol > tetramethylbenzidine > 4-methoxybenzyl alcohol > 2,2′-azino- bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) ≫ henol red) over an unusually broad range of pH from 3.5 to 9.0. Apparent Km and k cat values for ABTS, syringaldazine, and 2,6-dimetoxyphenol obtained from steady-state kinetic measurements performed at 40°C, pH 4.5, yielded values of 26, 0.43, and 0.45 μM and 18, 660, and 1175 s-1, respectively. The Km values for syringaldazine and 2,6-dimetoxyphenol are up to 5 times lower, and the kcat values up to 40 times higher, than values previously reported for this class of enzyme. RL5 is a 4-copper oxidase with oxidation potential values of 745, 400, and 500 mV versus normal hydrogen electrode for the T1, T2, and T3 copper sites. A three-dimensional model of RL5 and site-directed mutants were generated to identify the copper ligands. Bioinformatic analysis of the gene sequence and the sequences and contexts of neighboring genes suggested a tentative phylogenetic assignment to the genus Bacteroides. Kinetic, electrochemical, and EPR analyses provide unequivocal evidence that the hypothetical proteins from Bacteroides thetaiotaomicron and from E. coli, which are closely related to the deduced protein encoded by the RL5 gene, are also multicopper proteins with polyphenol oxidase activity. The present study shows that these three newly characterized enzymes form a new family of functional multicopper oxidases with laccase activity related to conserved hypothetical proteins harboring the domain of unknown function DUF152 and suggests that some other of these proteins may also be laccases. © 2006 by The American Society for Biochemistry and Molecular Biology, Inc.","2,2' azino bis(3 ethylbenzthiazoline 6 sulfonic acid);4 methoxybenzyl alcohol;alcohol derivative;bacterial protein;catechol oxidase;guaiacol;laccase;phenol derivative;phenolsulfonphthalein;protein bt4389;protein duf152;protein rl5;protein yifh;sulfonic acid derivative;syringaldazine;syringol;tetramethylbenzidine;unclassified drug;veratryl alcohol;article;bacteriophage;catalysis;cow;electrochemistry;electron spin resonance;enzyme activity;enzyme structure;Escherichia coli;gene expression;gene identification;gene library;gene sequence;genetic code;microflora;nonhuman;nucleotide sequence;oxidation;oxidation reduction reaction;pH electrode;phylogeny;priority journal;protein analysis;protein function;protein structure;ruminant stomach;site directed mutagenesis;steady state","Beloqui, A.;Pita, M.;Polaina, J.;Martínez-Arias, A.;Golyshina, O. V.;Zumárraga, M.;Yakimov, M. M.;García-Arellano, H.;Alcalde, M.;Fernández, V. M.;Elborough, K.;Andreu, J. M.;Ballesteros, A.;Plou, F. J.;Timmis, K. N.;Ferrer, M.;Golyshin, P. N.",2006,,10.1074/jbc.M600577200,0
158,Molecular characterisation of epizootic haemorrhagic disease virus associated with a Tunisian outbreak among cattle in 2006,"In 2006, epizootic haemorrhagic disease (EHD) outbreaks were recorded in the Maghreb (Tunisia, Morocco and Algeria) among cattle, resulting in severe repercussions on herds (oedema of the head, necrotic lesions of the oral mucosa, hyperthermia of the teats, accompanied by anorexia and respiratory distress) and economic losses. The present study gives new information on the molecular characterisation of the EHD virus (EHDV) that had circulated in Tunisia. Genome segments 2, 3, 6, 7 and 10 of EHDV, corresponding to the VP2, VP3, VP5, VP7 and NS3/NS3A proteins, respectively, were amplified from the blood of one animal by RT-PCR and sequenced. Nucleotide sequence comparisons of these five segments with sequences available in the GenBank demonstrated that an EHDV serotype 6 (EHDV-6) had been present in Tunisia in 2006. The possible origin of this strain is discussed.",animal;bovine;cattle disease;epidemic;genetics;isolation and purification;Orbivirus;phylogeny;reovirus infection;Tunisia;veterinary medicine;virology,"Ben Dhaou, S.;Sailleau, C.;Babay, B.;Viarouge, C.;Sghaier, S.;Zientara, S.;Hammami, S.;Bréard, E.",2016,,10.1556/004.2016.025,0
159,"Prioritization of zoonotic viral diseases in feral pigs, domestic pigs and humans interface","INTRODUCTION: Understanding the ecology of diseases requires the comprehension of pathogens in wild life-livestock interface. Feral pigs (Sus scrofa) are a health problem when countries work to prevent and control zoonotic diseases, as their populations raise environmental and health concerns due to infectious agents transmissible to domestic pigs and other animal species, including humans.  OBJECTIVE: To prioritize zoonotic diseases in the feral pigs, domestic animals and humans interface.  MATERIALS AND METHODS: The semi-quantitative prioritization method based on evidence included 27 criteria founded in recent publications. According to viral etiology we classified them in five categories: epidemiology (eight), prevention/control (three), economy/trade (four), public health (nine) and society (three). Each criterion had a coefficient of 0 to 7 according to their impact based on evidence (maximum sum of 189). Evidence on the criteria for the nine viral diseases analyzed came from the review of 81 sources published between 1977 and 2015.  RESULTS: The top three diseases with the highest score and zoonotic potential were swine influenza (133), hepatitis E (123), and hantavirus infection (103), whose highest scores were observed on epidemiology and public health criteria.  CONCLUSION: The semi-quantitative methods of prioritization impartially contribute to decision-making based on evidence; however, they are seldom used in developing countries due to the lack of data from public health surveillance. Control of shared diseases requires the development of strategies to reduce transmission of pathogens between wildlife and domestic animals and humans.",animal;health survey;hepatitis E;human;pathology;pig;public health;swine disease;virology;zoonosis,"Benavides-Arias, D.;Soler-Tovar, D.",2015,,10.7705/biomedica.v36i0.2950,0
160,Characterization of the surface proteins of influenza A (H5N1) viruses isolated from humans in 1997-1998,"Influenza A (H5N1) viruses infected humans in Hong Kong between May and December, 1997. Sixteen viruses, including 6 from fatal cases, were isolated during-this outbreak. Molecular analysis of the surface proteins genes encoding the hemagglutinin (HA) and neuraminidase (NA) of these H5N1 isolates, of a subtype not previously known to infect humans, are presented. The 16 human H5 HA sequences contain multiple basic amino acids adjacent to the cleavage site, a motif associated with highly pathogenic avian influenza A viruses. The phylogenetic relationship among both avian and human H5 hemagglutinins indicates that the human isolates are related directly to isolates that circulated among chickens in the five poultry markets in Hong Kong prior to and during the outbreak in humans. HA sequences from the human isolates and a recent chicken isolate represent a separate clade, within which there are two subgroups that are distinguishable antigenically and by the presence of a potential glycosylation site. Likewise the N1 neuraminidases of the human H5 isolates represent a clade that is evolutionarily distinct from previously characterized N1 neuraminidases. The recent human H5N1 virus NA genes are avian-like, indicating direct introduction from an avian source rather than evolution of a human N1 NA. All of the 16 human NA genes encode a shortened stalk due to a 19-amino acid deletion, also found n the recent avian H5N1 isolates from Hong Kong. Two unique amino acids were identified in the N1 NAs of the recent human isolates; however, it is not known if these residues influence host range. Neither the HA nor the NA genes of the human H5N1 virus isolates show evidence of adaptive changes during the outbreak. Although analyses of the surface protein genes of the HSN1 viruses from this outbreak did not provide immediate answers regarding the molecular basis for virulence, the analyses provided clues to potentially important areas of the genes worth further investigation.",hemagglutinin;membrane protein;sialidase;amino acid analysis;amino acid sequence;antigenicity;article;data analysis;enzyme activity;fowl;gene deletion;glycosylation;Hong Kong;human;Influenza A virus;phylogeny;priority journal;virus isolation;virus virulence,"Bender, C.;Hall, H.;Huang, J.;Klimov, A.;Cox, N.;Hay, A.;Gregory, V.;Cameron, K.;Lim, W.;Subbarao, K.",1999,,10.1006/viro.1998.9529,0
161,Analysis of the Variability in the Non-Coding Regions of Influenza A Viruses,"The genomes of influenza A viruses (IAVs) comprise eight negative-sense single-stranded RNA segments. In addition to the protein-coding region, each segment possesses 5' and 3' non-coding regions (NCR) that are important for transcription, replication and packaging. The NCRs contain both conserved and segment-specific sequences, and the impacts of variability in the NCRs are not completely understood. Full NCRs have been determined from some viruses, but a detailed analysis of potential variability in these regions among viruses from different host groups and locations has not been performed. To evaluate the degree of conservation in NCRs among different viruses, we sequenced the NCRs of IAVs isolated from different wild bird host groups (ducks, gulls and seabirds). We then extended our study to include NCRs available from the National Center for Biotechnology Information (NCBI) Influenza Virus Database, which allowed us to analyze a wider variety of host species and more HA and NA subtypes. We found that the amount of variability within the NCRs varies among segments, with the greatest variation found in the HA and NA and the least in the M and NS segments. Overall, variability in NCR sequences was correlated with the coding region phylogeny, suggesting vertical coevolution of the (coding sequence) CDS and NCR regions.",,"Benkaroun, J.;Robertson, G. J.;Whitney, H.;Lang, A. S.",2018,Aug 25,,0
162,Molecular techniques: new opportunities in the light of adenovirus research,"The author, through presenting their latest achievements obtained in the field of adenovirus research, summarizes the new possibilities residing in modern molecular techniques that have revolutionized the methods of virus research and diagnostics. Among the novel methods, the polymerase chain reaction (PCR) has the greatest significance. Because of the large and ever growing number of known virus serotypes, classical serological identification of new isolates has become exceptionally cumbersome nowadays. Moreover, reliable reference strain and serum collections are rarely available in the laboratories. PCR combined with sequencing provides a fast and efficient alternative. The new viruses identified and classified by such methods are called types instead of serotypes. In different veterinary laboratories, numerous adenovirus strains that have been isolated in different veterinary laboratories in the past couple of decades, are yet uncharacterized. Now these viruses can be typed and classified by the sequence analysis of certain genes. The other great advantage of the method is that it allows the molecular characterization of non-isolated viruses. This is especially valuable for the study of the adenoviruses of wild living animals when isolation of the virus is usually not a realistic option. The research group of the author was the first in the world to determine the complete genomic sequence of an adenovirus exclusively by PCRs from infected organ samples of diseased and dead birds without successful isolation of the virus. Organ samples from different vertebrate animals found dead in zoos, pet shops or in the wild are being screened by PCR continuously in the author's laboratory. Faecal samples are equally suitable for screening purposes. Besides birds and reptiles, high adenoviral infection rate was demonstrated recently among domestic bats.",DNA;AMPLIFICATION;SIADENOVIRUS;INFECTION;BATS;IDENTIFICATION;HYBRIDIZATION;EVOLUTION;CATTLE;PCR,"Benko, M.",2011,Aug,,0
163,A proposal for a new (third) genus within the family Adenoviridae,"This article presents a proposal for the establishment of a new adenovirus genus to accommodate certain bovine, ovine, and avian adenoviruses with special characteristics which differentiate them from members of the existing genera Mastadenovirus and Aviadenovirus. This proposal has been developed from earlier versions with advice from the Adenovirus Study Group of the International Committee on Taxonomy of Viruses (ICTV).",,"Benkö, M.;Harrach, B.",1998,,10.1007/s007050050335,0
164,Does common architecture reveal a viral lineage spanning all three domains of life?,"Our discovery that the major coat protein of bacteriophage PRD1 resembles that of human adenovirus raised the unexpected possibility that viruses infecting bacteria could be related by evolution to those infecting animal hosts. We first review the development of this idea. We then describe how we have used structure-based modeling to show that several other viruses with no detectable sequence similarity are likely to have coats constructed from similar proteins-the ""double-barrel trimer."" There is evidence that the group includes a diversity of viruses infecting very different hosts in all three domains of life: Eukarya; Bacteria; and Archaea that diverged billions of years ago. The current classification of viruses obscures such similarities. We propose that the occurrence of a double-barrel trimer coat protein in an icosahedral dsDNA virus with large facets, irrespective of its host, is a very strong indicator of its membership in a lineage of viruses with a common ancestor.",MAJOR CAPSID PROTEIN;SWINE-FEVER VIRUS;REFINED CRYSTAL-STRUCTURE;TUMOR NECROSIS FACTOR;BACTERIOPHAGE PRD1;ANGSTROM RESOLUTION;INTERNAL;MEMBRANE;RECEPTOR-BINDING;COAT PROTEIN;LENGTH DETERMINATION,"Benson, S. D.;Bamford, J. K. H.;Bamford, D. H.;Burnett, R. M.",2004,Dec,,0
165,"Crimean-Congo hemorrhagic fever: History, epidemiology, pathogenesis, clinical syndrome and genetic diversity","Crimean-Congo hemorrhagic fever (CCHF) is the most important tick-borne viral disease of humans, causing sporadic cases or outbreaks of severe illness across a huge geographic area, from western China to the Middle East and southeastern Europe and throughout most of Africa. CCHFV is maintained in vertical and horizontal transmission cycles involving ixodid ticks and a variety of wild and domestic vertebrates, which do not show signs of illness. The virus circulates in a number of tick genera, but Hyalomma ticks are the principal source of human infection, probably because both immature and adult forms actively seek hosts for the blood meals required at each stage of maturation. CCHF occurs most frequently among agricultural workers following the bite of an infected tick, and to a lesser extent among slaughterhouse workers exposed to the blood and tissues of infected livestock and medical personnel through contact with the body fluids of infected patients. CCHFV is the most genetically diverse of the arboviruses, with nucleotide sequence differences among isolates ranging from 20% for the viral S segment to 31% for the M segment. Viruses with diverse sequences can be found within the same geographic area, while closely related viruses have been isolated in far distant regions, suggesting that widespread dispersion of CCHFV has occurred at times in the past, possibly by ticks carried on migratory birds or through the international livestock trade. Reassortment among genome segments during co-infection of ticks or vertebrates appears to have played an important role in generating diversity, and represents a potential future source of novel viruses. In this article, we first review current knowledge of CCHFV, summarizing its molecular biology, maintenance and transmission, epidemiology and geographic range. We also include an extensive discussion of CCHFV genetic diversity, including maps of the range of the virus with superimposed phylogenetic trees. We then review the features of CCHF, including the clinical syndrome, diagnosis, treatment, pathogenesis, vaccine development and laboratory animal models of CCHF. The paper ends with a discussion of the possible future geographic range of the virus. For the benefit of researchers, we include a Supplementary Table listing all published reports of CCHF cases and outbreaks in the English-language literature, plus some principal articles in other languages, with total case numbers, case fatality rates and all CCHFV strains on GenBank. © 2013 Elsevier B.V. All rights reserved.",caspase 3;crimean congo hemorrhagic fever virus antibody;crimean congo hemorrhagic fever virus vaccine;DNA vaccine;fresh frozen plasma;hyperimmune globulin;immunoglobulin;infusion fluid;intercellular adhesion molecule 1;interferon;interleukin 6;interleukin 8;methylprednisolone;neopterin;neutralizing antibody;ribavirin;unclassified drug;vascular cell adhesion molecule 1;virus antibody;virus glycoprotein;virus vaccine;Africa;antiviral therapy;Asia;bird;bleeding;blood transfusion;clinical feature;Crimean Congo hemorrhagic fever;death;diagnostic accuracy;diagnostic test accuracy study;disease transmission;domestic animal;drug efficacy;drug megadose;ecchymosis;enzyme linked immunosorbent assay;Europe;experimental infection;fatality;genetic drift;genetic reassortment;genetic recombination;genetic variability;genome analysis;geographic distribution;hemorrhagic fever with renal syndrome;hepatitis C;histopathology;horizontal transmission;host;human;incidence;laboratory diagnosis;life cycle;lung edema;mammalian disease;medical history;Middle East;molecular biology;Nairovirus;nonhuman;phylogenetic tree;priority journal;real time polymerase chain reaction;respiratory syncytial virus infection;reverse transcription polymerase chain reaction;review;Rift Valley fever;Russian Federation;sensitivity and specificity;survival prediction;tick;tick borne encephalitis;unspecified side effect;USSR;vaccination;vertical transmission;virion;virus genome;virus morphology;virus pathogenesis;virus replication;virus transmission;virus virulence;wild animal,"Bente, D. A.;Forrester, N. L.;Watts, D. M.;McAuley, A. J.;Whitehouse, C. A.;Bray, M.",2013,,10.1016/j.antiviral.2013.07.006,0
166,Genetic characterization and phylogenetic analysis of host-range genes of Camelpox virus isolates from India,"Camelpox virus (CMLV), a close variant of variola virus (VARV) infects camels worldwide. The zoonotic infections reported from India signify the need to study the host-range genes—responsible for host tropism. We report sequence and phylogenetic analysis of five host-range genes: cytokine response modifier B (crmB), chemokine binding protein (ckbp), viral schlafen-like (v-slfn), myxomavirus T4-like (M-T4-like) and b5r of CMLVs isolated from outbreaks in India. Comparative analysis revealed that these genes are conserved among CMLVs and shared 94.5–100 % identity at both nucleotide (nt) and amino acid (aa) levels. All genes showed identity (59.3–98.4 %) with cowpox virus (CPXV) while three genes—crmB, ckbp and b5r showed similarity (92–96.5 %) with VARVs at both nt and aa levels. Interestingly, three consecutive serine residue insertions were observed in CKBP protein of CMLV-Delhi09 isolate which was similar to CPXV-BR and VACVs, besides five point mutations (K53Q, N67I, F84S, A127T and E182G) were also similar to zoonotic OPXVs. Further, few inconsistent point mutation(s) were also observed in other gene(s) among Indian CMLVs. These indicate that different strains of CMLVs are circulating in India and these mutations could play an important role in adaptation of CMLVs in humans. The phylogeny revealed clustering of all CMLVs together except CMLV-Delhi09 which grouped separately due to the presence of specific point mutations. However, the topology of the concatenated phylogeny showed close evolutionary relationship of CMLV with VARV and TATV followed by CPXV-RatGer09/1 from Germany. The availability of this genetic information will be useful in unveiling new strategies to control emerging zoonotic poxvirus infections.",amino acid;b5r protein;chemokine binding protein;cytokine response modifier B;myxomavirus T4 like protein;nucleotide;unclassified drug;viral schlafen like protein;viral protein;article;Camelpox virus;Camelpox virus infection;conservation genetics;Cowpox virus;epidemic;gene sequence;host range;India;nonhuman;phylogeny;point mutation;viral genetics;virus infection;virus isolation,"Bera, B. C.;Barua, S.;Shanmugasundaram, K.;Anand, T.;Riyesh, T.;Vaid, R. K.;Virmani, N.;Kundu, S.;Yadav, N. K.;Malik, P.;Singh, R. K.",2015,,10.1007/s13337-015-0266-8,0
167,"Sequence and phylogenetic analysis of host-range (E3L, K3L, and C7L) and structural protein (B5R) genes of buffalopox virus isolates from buffalo, cattle, and human in India","Buffalopox virus (BPXV), a close variant of vaccinia virus (VACV) has emerged as a zoonotic pathogen. The host tropism of poxviruses is governed by host-range genes. Among the host-range genes: E3L, K3L, and C7L are essential for virus replication by preventing interferon resistance, whereas B5R is essential for spread of the virus and evasion from the host's immune response as in VACV. We report sequence analysis of host-range genes: E3L, K3L, C7L, and membrane protein gene (B5R) of BPXVs from buffalo, cattle, and human from recent outbreaks in India - their phylogenetic relationship with reference strain (BP4) and other Orthopoxviruses. BPXVs revealed a sequence homology with VACVs including zoonotic Brazilian VACV-like viruses. The aa sequences of E3L and K3L genes were 100 % similar in buffalo, cattle, and human isolates. However, four significant point mutations (I11K; N12K and S36F in C7L gene and D249G in B5R gene) were observed specific to buffalo isolate only. This signifies that different strains of BPXV were circulated during the outbreak. The mutations in C7L and B5R could play an important role in adaptation of BPXV in human and cattle which needs further functional studies. The strain of BPXV isolated from buffalo may not be adopted in human and cow. Various point mutations were observed in the host-range genes of reference strain (BPXV-BP4) which may be due to several passages of virus in cell culture. The phylogeny constructed based on concatenated gene sequences revealed that BPXVs are not as closely related to vaccine strain (Lister and Lister-derived strain - LC16m8), as hypothesized earlier, rather they are more closely related to reference strain (BPXV-BP4) and other vaccinia and vaccinia-like viruses such as Passatempo and Aracatuba viruses. The availability of information regarding host tropism determinants would allow us to understand molecular mechanism of species tropism of poxviruses which would be useful in unveiling new strategies to control zoonotic poxviral infections. © 2012 Springer Science+Business Media, LLC.",membrane protein;article;B5R gene;buffalo;buffalopox virus;C7L gene;bovine;E3L gene;gene amplification;gene sequence;host range;host range gene;human;India;K3L gene;membrane protein gene;nonhuman;nucleotide sequence;phylogeny;point mutation;priority journal;sequence analysis;sequence homology;Vaccinia virus;viral tropism;virus gene;virus strain,"Bera, B. Ch;Shanmugasundaram, K.;Barua, S.;Anand, T.;Riyesh, T.;Vaid, R. K.;Virmani, N.;Bansal, M.;Shukla, B. N.;Malik, P.;Singh, R. K.",2012,,10.1007/s11262-012-0788-8,0
168,Analysis of the fusion protein gene of the porcine rubulavirus LPMV: Comparative analysis of paramyxovirus F proteins,"Complementary DNA clones representing the fusion (F) protein gene of the porcine rubulavirus LPMV were isolated and sequenced. The F gene was found to be 1845 nucleotides long containing one long open reading frame capable of encoding a protein of 541 amino acids. The cleavage motif for F0 into F1 and F2 is His-Arg-Lys-Lys-Arg. A sequence comparison and a phylogenetic analysis was performed in order to identify possible functional domains of paramyxovirus fusion proteins and also to classify the porcine rubulavirus. The F gene of LPMV is most closely related to the human mumps virus and simian virus type 5 F genes, and is therefore classified into the rubulavirus genus. A coding region for a small hydrophobic protein was however not found between the F and hemagglutinin-neuraminidase (HN) genes as previously found in both SV5 and mumps.",complementary DNA;glycoprotein;fusion protein;viral protein;article;gene isolation;gene sequence;molecular cloning;Mumps virus;nonhuman;nucleotide sequence;open reading frame;Paramyxoviridae;phylogeny;priority journal;protein analysis;simian virus;viral genetics;virus classification;virus gene,"Berg, M.;Bergvall, A. C.;Svenda, M.;Sundqvist, A.;Moreno-López, J.;Linné, T.",1997,,10.1023/a:1007987407250,0
169,Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome,"Viruses are the most abundant biological entities on the planet and play an important role in balancing microbes within an ecosystem and facilitating horizontal gene transfer. Although bacteriophages are abundant in rumen environments, little is known about the types of viruses present or their interaction with the rumen microbiome. We undertook random pyrosequencing of virus-enriched metagenomes (viromes) isolated from bovine rumen fluid and analysed the resulting data using comparative metagenomics. A high level of diversity was observed with up to 28000 different viral genotypes obtained from each environment. The majority (~78%) of sequences did not match any previously described virus. Prophages outnumbered lytic phages approximately 2:1 with the most abundant bacteriophage and prophage types being associated with members of the dominant rumen phyla (Firmicutes and Proteobacteria). Metabolic profiling based on SEED subsystems revealed an enrichment of sequences with putative functional roles in DNA and protein metabolism, but a surprisingly low proportion of sequences assigned to carbohydrate and amino acid metabolism. We expanded our analysis to include previously described metagenomic data and 14 reference genomes. Clustered regularly interspaced short palindromic repeats (CRISPR) were detected in most of the microbial genomes, suggesting previous interactions between viral and microbial communities. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.",bacterial DNA;virus DNA;animal;article;bacteriophage;bacterium;biodiversity;biology;bovine;DNA sequence;genetics;genotype;interspersed repeat;inverted repeat;isolation and purification;metabolism;metabolome;metagenome;microbiology;ruminant stomach;virology,"Berg Miller, M. E.;Yeoman, C. J.;Chia, N.;Tringe, S. G.;Angly, F. E.;Edwards, R. A.;Flint, H. J.;Lamed, R.;Bayer, E. A.;White, B. A.",2012,,10.1111/j.1462-2920.2011.02593.x,1
170,Using noninvasive metagenomics to characterize viral communities from wildlife,"Microbial communities play an important role in organismal and ecosystem health. While high-throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here, we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from noninvasively collected faecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in foetal bovine serum, we recommend storing swabs in RNAlater or another nonbiological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low-input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNase treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time.",article;clinical article;controlled study;Desmodus rotundus;domestic animal;extraction;feces;fetal bovine serum;human;human tissue;metagenomics;microbial community;nonhuman;Peru;storage;supernatant;viral contamination;virus detection;virus transmission;wildlife;deoxyribonuclease;endogenous compound;ribosome RNA;virus RNA,"Bergner, L. M.;Orton, R. J.;da Silva Filipe, A.;Shaw, A. E.;Becker, D. J.;Tello, C.;Biek, R.;Streicker, D. G.",2019,,10.1111/1755-0998.12946,0
171,Antigenic and genetic characterization of rabies viruses isolated from domestic and wild animals of Brazil identifies the hoary fox as a rabies reservoir,"Fifty Brazilian rabies viruses, collected from many different animal species and several regions of the country, were characterized by partial sequencing of the central, variable region of the P gene, a locus useful for sensitive molecular epidemiological studies. Phylogenetic analysis of the sequences, which included comparison with other rabies strains recovered from throughout the Americas, identified three main groups of Brazilian viruses, arbitrarily designated BRL-1 to BRL-3. BRL-1 was found in terrestrial carnivores and clusters with other American strains of the cosmopolitan lineage. BRL-2 comprised two distinct isolates, recovered from two species of non-haematophagous bats, that had evolutionary links to insectivorous-bat-derived strains of North America. BRL-3 consisted of isolates from vampire bats and from livestock species probably infected via contact with vampire bats. The terrestrial group was further subdivided into three subtypes: BRL-1a was associated exclusively with dogs and cats, while BRL-1b and BRL-1c were found exclusively in hoary foxes. These observations strongly support the role of the Brazilian hoary fox as a rabies reservoir. Screening of representative Brazilian rabies viruses against a collection of anti-rabies monoclonal antibodies (mAbs) identified a small panel of mAbs that could be used to discriminate between all Brazilian subgroups as defined by genetic classification in this study. © 2005 SGM.",monoclonal antibody;rabies immunoglobulin;virus antigen;antibody screening;article;bat;Brazil;carnivore;cat;cluster analysis;controlled study;dog;domestic animal;fox;gene locus;geographic distribution;livestock;molecular evolution;molecular phylogeny;nonhuman;North America;nucleotide sequence;priority journal;rabies;Rabies virus;sensitivity analysis;sequence analysis;species difference;strain difference;viral genetics;virus carrier;virus classification;virus isolation;wild type,"Bernardi, F.;Nadin-Davis, S. A.;Wandeler, A. I.;Armstrong, J.;Gomes, A. A. B.;Lima, F. S.;Nogueira, F. R. B.;Ito, F. H.",2005,,10.1099/vir.0.81223-0,0
172,"Human herpesvirus 7 is a T-lymphotropic virus and is related to, but significantly different from, human herpesvirus 6 and human cytomegalovirus","An independent strain (JI) of human herpesvirus 7 (HHV-7) was isolated from a patient with chronic fatigue syndrome (CFS). No significant association could be established by seroepidemiology between HHV-7 and CFS. HHV-7 is a T-lymphotropic virus, infecting CD4+ and CD8+ primary lymphocytes. HHV-7 can also infect SUP-T1, an immature T-cell line, with variable success. Southern blot analysis with DNA probes scanning 58.8% of the human herpesvirus 6 (HHV-6) genome and hybridizing to all HHV-6 strains tested so far revealed homology to HHV-7 with only 37.4% of the total probe length. HHV-7 contains the GGGTTA repetitive sequence, as do HHV-6 and Marek's disease chicken herpesvirus. DNA sequencing of a 186-base-pair fragment of HHV-7(JI) revealed an identify with HHV-6 and human cytomegalovirus of 57.5% and 36%, respectively. Oligonucleotide primers derived from this sequence (HV7/HV8, HV10/HV11) amplified HHV-7 DNA only and did not amplify DNA from other human herpesviruses, including 12 different HHV-6 strains. Southern blot analysis with the p43L3 probe containing the 186-base-pair HHV-7 DNA fragment hybridized to HHV-7 DNA only. The molecular divergence between human cytomegalovirus, on the one hand, and HHV-6 and HHV- 7, on the other, is greater than between HHV-6 and HHV-7, which, in turn, is greater than the difference between HHV-6 strains. This study supports the classification of HHV-7 as an additional member of the human β- herpesviruses.",CD4 antigen;CD8 antigen;DNA fragment;article;base pairing;chronic fatigue syndrome;disease association;DNA probe;DNA sequence;gene amplification;Human cytomegalovirus;Human herpesvirus 6;Human herpesvirus 7;immunofluorescence;molecular cloning;nonhuman;priority journal;sequence homology;seroepidemiology;Southern blotting;T lymphocyte;virus classification,"Berneman, Z. N.;Ablashi, D. V.;Li, G.;Eger-Fletcher, M.;Reitz Jr, M. S.;Hung, C. L.;Brus, I.;Komaroff, A. L.;Gallo, R. C.",1992,,10.1073/pnas.89.21.10552,0
173,"No evidence for viral sequences in five lepidic adenocarcinomas (former ""BAC"") by a high-throughput sequencing approach","BACKGROUND: The hypothesis of an infectious etiology of the formerly named bronchiolo-alveolar carcinoma (BAC) has raised controversy. We investigated tumor lung tissues from five patients with former BAC histology using high-throughput sequencing technologies to discover potential viruses present in this type of lung cancer. Around 180 million single reads of 100 bases were generated for each BAC sample. RESULTS: None of the reads showed a significant similarity for Jaagsiekte sheep retrovirus (JSRV) and no other viruses were found except for endogenous retroviruses. CONCLUSIONS: In conclusion, we have demonstrated the absence of JSRV and other known human viruses in five samples of well-characterized lepidic adenocarcinoma.",adenocarcinoma;aged;animal;endogenous retrovirus;female;genetics;high throughput sequencing;human;jaagsiekte;Jaagsiekte sheep retrovirus;lung;lung alveolus cell carcinoma;lung tumor;male;middle aged;pathology;physiology;procedures;sheep;virology,"Berthet, N.;Frangeul, L.;Olaussen, K. A.;Brambilla, E.;Dorvault, N.;Girard, P.;Validire, P.;Fadel, E.;Bouchier, C.;Gessain, A.;Soria, J. C.",2015,,10.1186/s13104-015-1669-8,0
174,Lack of Transmission of Foot-and-Mouth Disease Virus From Persistently Infected Cattle to Naive Cattle Under Field Conditions in Vietnam,"Foot-and-mouth disease (FMD), caused by FMD virus (FMDV; Aphthovirus, Picornaviridae), is a highly contagious and economically important disease of cloven-hoofed domestic livestock and wildlife species worldwide. Subsequent to the clinical phase of FMD, a large proportion of FMDV-infected ruminants become persistently infected carriers, defined by detection of FMDV in oropharyngeal fluid (OPF) samples 28 days or more post-infection. The goal of this prospective study was to characterize the FMD carrier state in cattle subsequent to natural infection under typical husbandry practices in Vietnam. Ten persistently infected cattle on eight farms in the Long An province in southern Vietnam were monitored by monthly screening of serum and oropharyngeal fluid samples for 12 months. To assess transmission from FMDV carriers, 16 naive cattle were intentionally brought into direct contact with the persistently infected animals for 6 months, and were monitored by clinical and laboratory methods. The restricted mean duration of the FMD carrier state was 27.7 months, and the rate of decrease of the proportion of carrier animals was 0.03 per month. There was no evidence of transmission to naive animals throughout the study period. Additionally, there was no detection of FMDV infection or seroconversion in three calves born to carrier animals during the study. The force of infection for carrier-to-contact transmission was 0 per month, with upper 95% confidence limit of 0.064 per month. Phylogenetic analysis of viral protein 1 (VP1) coding sequences obtained from carriers indicated that all viruses recovered in this study belonged to the O/ME-SA/PanAsia lineage, and grouped phylogenetically with temporally and geographically related viruses. Analysis of within-host evolution of FMDV, based upon full-length open reading frame sequences recovered from consecutive samples from one animal, indicated that most of the non-synonymous changes occurred in L<sub>pro</sub>, VP2, and VP3 protein coding regions. This study suggests that the duration of FMDV persistent infection in cattle may be longer than previously recognized, but the risk of transmission is low. Additional novel insights are provided into within-host viral evolution under natural conditions in an endemic setting.",,"Bertram, M. R.;Vu, L. T.;Pauszek, S. J.;Brito, B. P.;Hartwig, E. J.;Smoliga, G. R.;Hoang, B. H.;Phuong, N. T.;Stenfeldt, C.;Fish, I. H.;Hung, V. V.;Delgado, A.;VanderWaal, K.;Rodriguez, L. L.;Long, N. T.;Dung, D. H.;Arzt, J.",2018,,,0
175,Allergic vasculitis during ORF,"ORF is an infectious disease affecting sheep and goats caused by a parapoxvirus. It can be transmitted to humans, and is considered to be an occupational hazard for those handling sheep. The authors describe a case of ORF associated with allergic vasculitis, with an evolution that suggests a pathogenetic role of the virus. A 69-year-old woman presented erythematous plaques, target-like in appearance, suggesting an ORF. Ten days after the appearance of the first lesion, both non blanchable purpuric papules and necrotic purpura became evident on the legs, ankles and dorsa of the feet. The histological evaluation showed leucocytoclastic vasculitis. These latter lesions faded in ten days without therapy. At the same time, three weeks after their onset, the ORF lesions were also spontaneously resolved. After a six month follow-up, neither ORF lesions nor allergic vasculitis had recurred. Viral infections are well known as aetiological factors of vasculitis. Many elements prompted us to consider this case of allergic vasculitis to be correlated with the ORF virus infection: time of onset, duration, resolution related to the clinical course of ORF, no need of therapy for recovery and a six-month follow-up without relapses. This indicates the possibility of classifying the ORF virus within the group of virus responsible for allergic vasculitis.",aged;leukocytoclastic vasculitis;article;case report;disease transmission;female;goat;human;Parapoxvirus;sheep;virus infection,"Bettoli, V.;Trovato, C.;La Malfa, W.;Pazzaglia, M.",1997,,,0
176,Dynamics of acute Montipora white syndrome: bacterial communities of healthy and diseased M. capitata colonies during and after a disease outbreak,"Coral diseases contribute to the decline of coral reefs globally and threaten the health and future of coral reef communities. Acute Montipora white syndrome (aMWS) is a tissue loss disease that has led to the mortality of hundreds of Montipora capitata colonies in Kaneohe Bay, Hawai'i in recent years. This study describes the analysis of coral-associated bacterial communities using high-throughput sequencing generated by the PacBio RSII platform. Samples from three health states of M. capitata (healthy, healthy-diseased and diseased) were collected during an ongoing aMWS outbreak and a non-outbreak period and the bacterial communities were identified to determine whether a shift in community structure had occurred between the two periods. The bacterial communities associated with outbreak and non-outbreak samples were significantly different, and one major driver was a high abundance of operational taxonomic units (OTUs) identified as Escherichia spp. in the outbreak sequences. In silico bacterial source tracking suggested this OTU was likely from sewage contamination of livestock, rather than human, origin. The most abundant coliform OTU was a culturable E. fergusonii isolate, strain OCN300, however, it did not induce disease signs on healthy M. capitata colonies when used in laboratory infection trials. In addition, screening of the sequencing output found that the most abundant OTUs corresponded to previously described M. capitata pathogens. The synergistic combination of known coral pathogens, sewage contaminants and other stressors, such as fluctuating seawater temperatures and bacterial pathogens, have the potential to escalate the deterioration of coral reef ecosystems.",PacBio sequencing;fecal source tracking;coral disease;Montipora;capitata;VIRUS-LIKE PARTICLES;BLACK BAND DISEASE;KANEOHE BAY;ENVIRONMENTAL;WATERS;ESCHERICHIA-COLI;SEQUENCE DATA;CORAL;DIVERSITY;HAWAII;CONTAMINATION,"Beurmann, S.;Ushijima, B.;Videau, P.;Svoboda, C. M.;Chatterjee, A.;Aeby, G. S.;Callahan, S. M.",2018,Oct,,0
177,Prospects of control and eradication of capripox from the Indian subcontinent: A perspective,"Sheeppox and goatpox, two endemic capripox infections in India, pose a significant economic threat to small ruminant productivity in the subcontinent. Vaccination of all susceptible sheep and goats is the feasible and sustainable means of control. Availability of effective live attenuated vaccines that are inherently thermostable and development of improved diagnostics provide the opportunities to initiate effective control measures for capripox. All animals older than 4. months can be vaccinated with the current homologous vaccines using a single vaccination by intradermal or subcutaneous routes. The success of the control program needs to be monitored by active surveillance particularly for the presence of virus, as sero-monitoring does not enable the differentiation of infection and vaccination. And also the sero-conversion following capripox vaccination is not detectable enough by the available tools. Sustained control efforts call for socio-economic and political stability, adequate infrastructure and logistic support to store and transport vaccines for reaching out vaccines to the remote end users. Availability of veterinary services, improved extension services for increased awareness among farmers, contribute significantly to the control campaigns. Poor vaccination coverage and in-adequate infrastructure in major parts of the country are some of the major elements that come in the way of effective implementation of building herd immunity through immunization. © 2011 Elsevier B.V.",virus vaccine;agricultural worker;animal disease;antibody detection;antigen detection;Capripoxvirus;cost benefit analysis;differential diagnosis;disease control;disease surveillance;enzyme linked immunosorbent assay;feasibility study;goatpox;herd immunity;human;immunization;Indian;mass immunization;medical research;monitoring;nonhuman;nucleic acid analysis;political system;priority journal;review;sheeppox;socioeconomics;thermostability;vaccination;virus classification;virus transmission,"Bhanuprakash, V.;Hosamani, M.;Singh, R. K.",2011,,10.1016/j.antiviral.2011.06.004,0
178,The current status of sheep pox disease,"Sheep are the moving banks of shepherds and their economic contribution in terms of meat, wool and skin/hide is immense. Various infectious diseases jeopardize the optimum productivity; among which sheep pox is more important as the disease restricts the export of sheep and their products besides other economic losses. Although, clinical signs are indicative of the disease but a laboratory confirmation is necessary for unequivocal diagnosis and studying epidemiology. The causative agent, sheep pox virus (SPV), is antigenically and genetically closely related to goat pox virus (GPV) and lumpy skin disease virus (LSDV), the other members of the genus capripox virus. In some countries, SPV and GPV are cross infective to small ruminants posing problem in diagnosis and epidemiology. However, recent studies have showed that the viruses are phylogenetically distinct and can be differentiated by molecular tools. Prophylaxis using attenuated vaccines is the choice of control measure as the immunity is long lasting. Detailed information on isolation, identification, pathology, epidemiology, diagnosis and prophylaxis would not only help in updating the knowledge of scientific fraternity but will be useful to the policy makers in order to formulate appropriate measures for control and eradication of the disease. This synthesis is to present an up-to-date review of the disease and its control to provide the reader with an overview of the problem. © 2006 Elsevier Ltd. All rights reserved.","2 amino 7 [(1,3 dihydroxy 2 propoxy)methyl]purine;2,6 diamino 9 (3 hydroxy 2 phosphonomethoxypropyl)purine;6 (3 hydroxy 2 phosphonylmethoxypropyl)oxy 2,4 diaminopyrimidine;8 methyladenosine;aluminum hydroxide;anthrax vaccine;antibiotic agent;antiinfective agent;cidofovir;live vaccine;nucleoside analog;nucleotide derivative;unclassified drug;virus vaccine;bacterial infection;biosafety;Capripoxvirus;cell culture;clinical feature;cross reaction;differential diagnosis;economics;epidemiological data;epizootiology;eradication therapy;host pathogen interaction;in vivo study;infection control;laboratory test;meat;molecular dynamics;nonhuman;phylogeny;poxvirus infection;productivity;review;serology;sheep disease;species differentiation;virus strain;virus transmission;wool;s 2242","Bhanuprakash, V.;Indrani, B. K.;Hosamani, M.;Singh, R. K.",2006,,10.1016/j.cimid.2005.12.001,0
179,Fluorogenic RT-PCR assay (TaqMan) for detection and classification of bovine viral diarrhea virus,"A single tube fluorogenic RT-PCR-based 'TaqMan' assay was developed for detection and classification of bovine viral diarrhea virus (BVDV). TaqMan-PCR was optimized to quantify BVD virus using the ABI PRISM 7700 sequence detection system and dual-labeled fluorogenic probes. Two different gene specific labeled fluorogenic probes for the 5′ untranslated region (5′ UTR) were used to differentiate between BVD types I and II. Sensitivity of the single tube TaqMan assay was compared with two-tube TaqMan assay and standard RT-PCR using 10-fold dilutions of RNA. Single tube TaqMan assay was 10-100-fold more sensitive than the two-tube TaqMan assay and the standardized single tube RT-PCR. Specificity of the assay was evaluated by testing different BVD virus strains and other bovine viruses. A total of 106 BVD positive and negative pooled or single serum samples, field isolates and reference strains were tested. Quantitation of cRNA from types I and II BVD virus was accomplished by a standard curve plotting cycle threshold values (CT) versus copy number. Single tube TaqMan-PCR assay was sensitive, specific and rapid for detection, quantitation and classification of BVD virus. © 2001 Elsevier Science B.V. All rights reserved.",5' untranslated region;article;assay;Bovine viral diarrhea virus 1;controlled study;gene sequence;nonhuman;reverse transcription polymerase chain reaction;virus classification;virus detection;virus strain;virus titration;virus typing;TaqMan,"Bhudevi, B.;Weinstock, D.",2001,,10.1016/s0378-1135(01)00390-x,0
180,"Highly pathogenic avian influenza H5N1 Clade 2.3.2.1c virus in migratory birds, 2014–2015","A novel Clade 2.3.2.1c H5N1 reassortant virus caused several outbreaks in wild birds in some regions of China from late 2014 to 2015. Based on the genetic and phylogenetic analyses, the viruses possess a stable gene constellation with a Clade 2.3.2.1c HA, a H9N2-derived PB2 gene and the other six genes of Asian H5N1-origin. The Clade 2.3.2.1c H5N1 reassortants displayed a high genetic relationship to a human H5N1 strain (A/Alberta/01/2014). Further analysis showed that similar viruses have been circulating in wild birds in China, Russia, Dubai (Western Asia), Bulgaria and Romania (Europe), as well as domestic poultry in some regions of Africa. The affected areas include the Central Asian, East Asian-Australasian, West Asian-East African, and Black Sea/Mediterranean flyways. These results show that the novel Clade 2.3.2.1c reassortant viruses are circulating worldwide and may have gained a selective advantage in migratory birds, thus posing a serious threat to wild birds and potentially humans. [Figure not available: see fulltext.]",pb2 protein;unclassified drug;viral protein;Africa;animal experiment;article;Asian;Australia and New Zealand;avian influenza (H5N1);Black Sea;Bulgaria;Central Asian;China;cladistics;controlled study;domestic animal;Dubai;East African;East Asian;embryo;epidemic;evolutionary rate;genetic analysis;genetic reassortment;human;Influenza A virus (H5N1);Influenza A virus (H9N2);Mediterranean Sea;migrant bird;nonhuman;phylogenetic tree;phylogeny;Romania;Russian Federation;virus gene;virus isolation;virus load;virus strain;virus transmission;West Asian,"Bi, Y.;Chen, J.;Zhang, Z.;Li, M.;Cai, T.;Sharshov, K.;Susloparov, I.;Shestopalov, A.;Wong, G.;He, Y.;Xing, Z.;Sun, J.;Liu, D.;Liu, Y.;Liu, L.;Liu, W.;Lei, F.;Shi, W.;Gao, G. F.",2016,,10.1007/s12250-016-3750-4,0
181,"Atypical bovine spongiform encephalopathies, France, 2001-2007","In France, through exhaustive active surveillance, ≈17.1 million adult cattle were tested for bovine spongiform encephalopathy from July 2001 through July 2007; ≈3.6 million were >8 years of age. Our retrospective Western blot study of all 645 confirmed cases found that 7 were H-type and 6 were L-type.",antibody detection;article;bovine spongiform encephalopathy;bovine spongiform encephalopathy agent;bovine;disease transmission;epidemiological data;France;molecular weight;nonhuman;quantitative analysis;virus classification;virus examination;Western blotting,"Biacabe, A. G.;Morignat, E.;Vulin, J.;Calavas, D.;Baron, T. G. M.",2008,,,0
182,Genetic analysis of full-length genomes and subgenomic sequences of TT virus-like mini virus human isolates,"The phylogenetic relationship between the complete genomic sequences of ten Japanese and one French isolate of TT virus-like mini virus (TLMV) was investigated. Analysis of the variability of the nucleotide sequences and the detection of signature patterns for overlapping genes suggested that ORFs 1 and 2 are probably functional. However, this was not the case for a putative third ORF, ORF3. Throughout the viral genome, several nucleotide or amino acid motifs that are conserved in circoviruses such as TT virus (TTV) and chicken anaemia virus were identified. Phylogenetic analysis distinguished three main groups of TLMV and allowed the identification of putative recombination breakpoints in the untranslated region. TLMV genomes were detected by PCR in the plasma of 38/50 French blood donors tested and were also identified in peripheral blood mononuclear cells, faeces and saliva. A phylogenetic study of 37 TLMV strains originating from France, Japan and Brazil showed that groupings were not related to geographical origin.",amino acid;article;blood donor;Brazil;Circoviridae;controlled study;feces;France;gene sequence;genetic analysis;genetic variability;human;human cell;human tissue;Japan;nonhuman;nucleotide sequence;open reading frame;peripheral lymphocyte;phylogeny;plasma;polymerase chain reaction;priority journal;protein motif;saliva;Torque teno virus 1;TT virus like mini virus;virus characterization;virus genome;virus isolation;virus recombination;virus strain,"Biagini, P.;Gallian, P.;Attoui, H.;Touinssi, M.;Cantaloube, J. F.;de Micco, P.;de Lamballerie, X.",2001,,,0
183,The history and biology of Marek's disease virus,,Gallid alphaherpesvirus 2;bird disease;chick embryo;chicken;disease classification;embryo development;lymphoproliferative disease;nonhuman;priority journal;review;serotype;virogenesis;virus carcinogenesis;virus cell interaction;virus classification;virus culture;virus isolation;virus morphology;virus mutation;virus pathogenesis;virus recombinant;virus transmission,"Biggs, P. M.",2000,,,0
184,Polymerase errors accumulating during natural evolution of the glycoprotein gene of vesicular stomatitis virus Indiana serotype isolates,"We report the entire glycoprotein (G) gene nucleotide sequences of 26 vesicular stomatitis virus Indiana serotype (VSV IND) type 1 isolates from North and Central America. These sequences are also compared with partial G gene sequences of VSV IND type 2 (Cocal) and type 3 (Alagoas) viruses and the complete G gene sequences of the more distantly related VSV New Jersey (NJ) and Chandipura viruses. Phylogenetic analysis of the G gene sequences by maximum parsimony revealed four major lineages or subtypes within the classical VSV IND (type 1) viruses, each with a distinct geographic distribution. A high degree of VSV genetic diversity was found in Central America, with several virus subtypes of both VSV IND and NJ serotypes existing in this mainly enzootic disease region. Nineteen percent sequence variation but no deletions or insertions were evident within the 5' noncoding and the coding regions of the VSV IND type 1 G genes. In addition to numerous base substitutions, the 3' noncoding regions of these viruses also contained numerous base insertions and deletions. This resulted in striking variation in G gene sizes, with gene lengths ranging from 1,652 to 1,868 nucleotides. As the VSV IND type 1 subtypes have diverged from the common ancestor with the NJ subtypes, their G mRNAs have accumulated more 3' noncoding sequence inserts, ranging up to 303 nucleotides in length. These primarily consist of an imprecise reiteration of the sequence UUUUUAA, apparently generated by a unique polymerase stuttering error. Analysis of the deduced amino acid sequence differences among VSV IND type 1 viruses revealed numerous substitutions within defined antigenic epitopes, suggesting that immune selection may play a role in the evolution of these viruses.","Amino Acid Sequence;Animals;Base Sequence;*Biological Evolution;Cattle;*Genes, Viral;*Glycoproteins/ge [Genetics];Molecular Sequence Data;Phylogeny;RNA, Messenger/ge [Genetics];RNA, Viral/ge [Genetics];RNA, Viral/ip [Isolation & Purification];Sequence Homology, Nucleic Acid;Serotyping;Vesicular stomatitis Indiana virus/cl [Classification];*Vesicular stomatitis Indiana virus/ge [Genetics];Vesicular stomatitis Indiana virus/ip [Isolation & Purification];*Vesiculovirus;0 (Glycoproteins);0 (RNA, Messenger);0 (RNA, Viral)","Bilsel, P. A.;Nichol, S. T.",1990,Oct,,0
185,Physiological properties and classification of strains of Treponema sp. isolated from pigs in Poland,,fructose;animal experiment;biotypology;blood and hemopoietic system;classification;digestive system;dysentery;hemolysis;in vitro study;nonhuman;pig;Treponema;virus classification,"Binek, M.;Szynkiewicz, Z. M.",1984,,10.1016/0147-9571(84)90019-5,0
186,Different genotypes of nephropathogenic infectious bronchitis viruses co-circulating in chicken population in China,"Chicken nephropathogenic infectious bronchitis (IB) was prevalent in the most chicken farms during recent years, although the IB vaccination program has been widely performed in China. To characterize the S1 protein of infectious bronchitis virus (IBV) from China, five representative nephropathogenic IB viruses isolated from chickens in different provinces were genetically and phylogenetically analyzed. The results showed that the length of the S1 genes of the isolates were quite different (1,617, 1,620, 1,623, 1,629, and 1,632 nucleotides, respectively). The homology of the nucleotides and amino acids among the five isolates were 76.7% ∼ 92.1% and 73.9% ∼ 89.5%, respectively, indicating a great variation in S1 genes of the isolates. The variation in S1 genes might affect the antigenicity and pathogenicity of the viruses. Genetically, point mutations, insertions, and deletions in the S1 protein can be observed at many positions, especially at the first 150 amino acids in the N-terminal of the S1 protein. Two motif cleavage sites (R-R-X-R-R/S, H-R-R-R-R/S) were observed in the five sequenced strains. Phylogenetic analysis suggested that they belonged to different lineages. These findings indicated that different genotypes of nephropathogenic IB viruses were co-circulating in the chicken population in China. © 2007 Springer Science+Business Media, LLC.",antigenicity;article;Avian infectious bronchitis virus;chicken;China;controlled study;gene deletion;gene insertion;gene isolation;gene sequence;genetic analysis;genetic variability;genotype;kidney circulation;nonhuman;nucleotide sequence;pathogenicity;phylogeny;point mutation;priority journal;sequence homology;virus gene;virus isolation;virus strain,"Bing, G. X.;Liu, X.;Pu, J.;Liu, Q. F.;Wu, Q. M.;Liu, J. H.",2007,,10.1007/s11262-007-0100-5,0
187,Enterovirus serotypes in patients with central nervous system and respiratory infections in Viet Nam 1997-2010,"BACKGROUND: Enteroviruses are the most common causative agents of human illness. Enteroviruses have been associated with regional and global epidemics, recently, including with severe disease (Enterovirus A71 and D68), and are of interest as emerging viruses. Here, we typed Enterovirus A-D (EV) from central nervous system (CNS) and respiratory infections in Viet Nam. METHODS: Data and specimens from prospective observational clinical studies conducted between 1997 and 2010 were used. Species and serotypes were determined using type-specific RT-PCR and viral protein 1 or 4 (VP1, VP4) sequencing. RESULTS: Samples from patients with CNS infection (51 children - 10 CSF and 41 respiratory/rectal swabs) and 28 adults (28 CSF) and respiratory infection (124 children - 124 respiratory swabs) were analysed. Twenty-six different serotypes of the four Enterovirus species (A-D) were identified, including EV-A71 and EV-D68. Enterovirus B was associated with viral meningitis in children and adults. Hand, foot and mouth disease associated Enteroviruses A (EV-A71 and Coxsackievirus [CV] A10) were detected in children with encephalitis. Diverse serotypes of all four Enterovirus species were found in respiratory samples, including 2 polio-vaccine viruses, but also 8 CV-A24 and 8 EV-D68. With the exception of EV-D68, the relevance of these viruses in respiratory infection remains unknown. CONCLUSION: We describe the diverse spectrum of enteroviruses from patients with CNS and respiratory infections in Viet Nam between 1997 and 2010. These data confirm the global circulation of Enterovirus genera and their associations and are important for clinical diagnostics, patient management, and outbreak response.","Adolescent;Adult;Central Nervous System Infections/di [Diagnosis];*Central Nervous System Infections/ep [Epidemiology];Central Nervous System Infections/hi [History];*Central Nervous System Infections/vi [Virology];Child;Child, Preschool;*Enterovirus/cl [Classification];Enterovirus/ge [Genetics];Enterovirus/ip [Isolation & Purification];Enterovirus Infections/di [Diagnosis];*Enterovirus Infections/ep [Epidemiology];Enterovirus Infections/hi [History];*Enterovirus Infections/vi [Virology];Female;High-Throughput Nucleotide Sequencing;History, 20th Century;History, 21st Century;Humans;Infant;Male;Phylogeny;Population Surveillance;Respiratory Tract Infections/di [Diagnosis];*Respiratory Tract Infections/ep [Epidemiology];Respiratory Tract Infections/hi [History];*Respiratory Tract Infections/vi [Virology];Seasons;Sequence Analysis, DNA;Serogroup;Vietnam/ep [Epidemiology];Young Adult","B'Krong, N.;Minh, N. N. Q.;Qui, P. T.;Chau, T. T. H.;Nghia, H. D. T.;Do, L. A. H.;Nhung, N. N.;Van Vinh Chau, N.;Thwaites, G.;Van Tan, L.;van Doorn, H. R.;Thanh, T. T.",2018,04 12,,0
188,Adenovirus respiratory infection in turkey poults,"A virus from turkey poults with respiratory signs was isolated in specific-pathogen-free embryonated chicken eggs and subsequently adapted to chicken embryo fibroblast and turkey kidney cell cultures, where round cell formation was observed. The cloned virus was ether-resistant and incorporated tridiated thymidine. Intra-nuclear icosahedral virus particles of 80 nm were detected. These physicochemical characteristics place this isolant into the adenovirus group of viruses. The disease was experimentally reproduced by intratracheal inoculation of one-day-old turkey poults. Snicking occurred in 100% of the birds and mortality reached 50%. CELO (Phelps strain) antiserum neutralized uncloned and cloned CUA-2 in chicken embryos and uncloned virus in chicken embryo fibroblast cell cultures. Quail bronchitis virus antiserum neutralized cloned CUA-2 in TK cells. Agar-gel precipitin lines of identity were formed using CELO antiserum and postinoculation sera from experimentally infected turkeys. Serologically, this virus should be classified as a type-1 adenovirus.",Adenoviridae;animal;animal disease;article;bird disease;immunology;isolation and purification;microbiology;pathogenicity;respiratory tract infection;turkey (bird);virus infection,"Blalock, H. G.;Simmons, D. G.;Muse, K. E.;Gray, J. G.;Derieux, W. T.",1975,,,0
189,Variable and constant regions in African swine fever virus DNA,"An analysis of the SalI restriction pattern of African swine fever virus DNA showed that the SalI recognition sites did not change after more than 100 virus passages in porcine macrophages. The virus strain BA71V, obtained from the virus isolate BA71 by adaptation to grow in VERO cells, differed from the nonadapted virus in two deletions with a length of 2.5 and 7 kb located close to the DNA ends. A restriction analysis of several virus clones obtained from a naturally infected pig revealed length heterogeneity in both variable regions. A comparison of SalI restriction maps from 23 African swine fever virus field isolates (8 African, 11 European, and 4 American) has shown that the virus genome consists of a central region with a constant length of about 125 kb and two variable regions located close to the DNA ends with a length of 38-47 kb for the left DNA end, and 13-16 kb for the right DNA end. The total length of ASF virus DNA varied between 178 (BA71) and 189 (MOZ64) kb. The 23 African swine fever virus isolates were classified into five groups, according to the arrangement of the SalI sites in the central region. Four groups contained only African isolates, whereas all the European and American isolates belonged to the same group. This distribution of isolates suggests that all non-African virus field isolates have a common origin.","endodeoxyribonuclease SalI;type II site specific deoxyribonuclease;virus DNA;Africa;African swine fever virus;animal;article;cell culture;classification;Europe;genetic variability;genetics;growth, development and aging;Iridovirus;microbiology;monocyte;nucleic acid hybridization;restriction mapping;pig;swine disease;Vero cell line;virus gene;Western Hemisphere","Blasco, R.;Agüero, M.;Almendral, J. M.;Viñuela, E.",1989,,,0
190,Ledantevirus: A proposed new genus in the rhabdoviridae has a strong ecological association with bats,"The Le Dantec serogroup of rhabdoviruses comprises Le Dantec virus from a human with encephalitis and Keuriliba virus from rodents, each isolated in Senegal. The Kern Canyon serogroup comprises a loosely connected set of rhabdoviruses many of which have been isolated from bats, including Kern Canyon virus from California, Nkolbisson virus from Cameroon, Central African Republic, and Cote d'Ivoire, Kolente virus from Guinea, Mount Elgon bat and Fikirini viruses from Kenya, and Oita virus from Japan. Fukuoka virus isolated from mosquitoes, midges, and cattle in Japan, Barur virus from a rodent in India and Nishimuro virus from pigs in Japan have also been linked genetically or serologically to this group. Here, we analyze the genome sequences and phylogenetic relationships of this set of viruses. We show that they form three subgroups within a monophyletic group, which we propose should constitute the new genus Ledantevirus.",dihydrolipoamide dehydrogenase;article;bat;Cytorhabdovirus;ecological genetics;Ephemerovirus;gene sequence;genome analysis;Ledantevirus;Lyssavirus;monophyly;new genus;nonhuman;Novirhabdovirus;Nucleorhabdovirus;open reading frame;Perhabdovirus;phylogenetic tree;Rhabdoviridae;serotype;Sigmavirus;Sprivivirus;Tibrovirus;Tupavirus;Vesiculovirus;virus classification;virus genome;virus identification;virus isolation,"Blasdell, K. R.;Guzman, H.;Widen, S. G.;Firth, C.;Wood, T. G.;Holmes, E. C.;Tesh, R. B.;Vasilakis, N.;Walker, P. J.",2015,,10.4269/ajtmh.14-0606,0
191,Koolpinyah and Yata viruses: Two newly recognised ephemeroviruses from tropical regions of Australia and Africa,"Koolpinyah virus (KOOLV) isolated from healthy Australian cattle and Yata virus (YATV) isolated from a pool of Mansonia uniformis mosquitoes in the Central African Republic have been tentatively identified as rhabdoviruses. KOOLV was shown previously to be related antigenically to kotonkon virus, an ephemerovirus that has caused an ephemeral fever-like illness in cattle in Nigeria, but YATV failed to react antigenically with any other virus tested. Here we report the complete genome sequences of KOOLV (16,133 nt) and YATV (14,479 nt). Each has a complex genome organisation, with multiple genes, including a second non-structural glycoprotein (GNS) gene and a viroporin (α1) gene, between the G and L genes as is characteristic of ephemeroviruses. Based on an analysis of genome organisation, sequence identity and cross-neutralisation, we demonstrate that both KOOLV and YATV should be classified as two new species in the genus Ephemerovirus.",glycoprotein;Africa;amino acid sequence;article;Australia;bovine;carboxy terminal sequence;Central African Republic;cross reaction;Ephemerovirus;gene;gene sequence;genetic analysis;genome analysis;koolpinyah virus;Mansonia uniformis;mosquito;new species;nonhuman;nucleotide sequence;phylogeny;Rhabdoviridae;transcription initiation;transcription termination;viroporin gene;yata virus,"Blasdell, K. R.;Widen, S. G.;Diviney, S. M.;Firth, C.;Wood, T. G.;Guzman, H.;Holmes, E. C.;Tesh, R. B.;Vasilakis, N.;Walker, P. J.",2014,,10.1016/j.vetmic.2014.09.031,0
192,Fatal ulcerative and hemorrhagic typhlocolitis in a pregnant heifer associated with natural bovine enterovirus type-1 infection,"One 2-year-old, 7.5 months pregnant Aberdeen Angus out of a herd of 100 apparently healthy cows, died within 10 hours of hospitalization. At necropsy, multiple foci of mucosal hemorrhage and ulceration were observed in the spiral colon and cecum. Virus isolation from intestinal lesions yielded a cytopathic virus, which was revealed by electron microscopy to be an approximately 27 nm, nonenveloped virus. Further characterization by reverse transcription-polymerase chain reaction (RT-PCR), sequencing of the 5′UTR and partial VP1 coding region, and phylogenetic analysis classified the virus isolate as bovine enterovirus type 1 (BEV-1). No other significant pathogens were detected. This is the first report of BEV-1 isolated in the USA from an animal with fatal enteric disease in more than 20 years. Further investigation is required to determine the prevalence of BEV in North America and to establish the clinical relevance of this understudied virus.","virus RNA;animal;animal disease;article;bleeding;Bovine enterovirus;case report;bovine;cattle disease;chemistry;cytochemistry;electron microscopy;Enterovirus infection;fatality;female;genetics;growth, development and aging;pathology;pregnancy;pregnancy complication;reverse transcription polymerase chain reaction;small intestine;ulcerative colitis;ultrastructure;virology","Blas-Machado, U.;Saliki, J. T.;Boileau, M. J.;Goens, S. D.;Caseltine, S. L.;Duffy, J. C.;Welsh, R. D.",2007,,10.1354/vp.44-1-110,0
193,Bovine viral diarrhea virus type 2-induced meningoencephalitis in a heifer,"The brain from a 15-month-old, black female Angus, with a 48-hour history of central nervous system disease, was submitted to the Oklahoma Animal Disease Diagnostic Laboratory. Microscopic findings consisted of acute, multifocal meningoencephalitis, with neuronal degeneration and necrosis and gliosis. Viral isolation yielded noncytopathic bovine viral diarrhea virus (BVDV). Virus genotyping classified the virus as BVDV type 2. Immunohistochemical labeling for BVDV antigens with BVD MAb 3.12F1 clone was prominent in the cytoplasm of neurons, glial cells, ependymal epithelium, perivascular macrophages and spindle cells, smooth muscle cells, and intravascular monocytes of the cerebrum and brain stem. Laboratory results support that tissue alterations occurred as a result of BVDV type 2 infection. In the absence of other clinical signs related to BVDV infection and using the microscopic and laboratory evidence presented, we propose that the BVDV type 2 isolated from this case may represent a neurovirulent strain of the virus. To the best of our knowledge, this is the first report of brain lesions and neuronal viral antigen localization in BVDV genotype 2 viral infection, acquired either congenitally or postnatally.",monoclonal antibody;virus antigen;animal tissue;antibody labeling;antigen detection;article;Bovine viral diarrhea virus 1;brain;brain stem;cattle disease;cellular distribution;central nervous system disease;clinical feature;cytopathogenic effect;cytoplasm;ependyma;female;genotype;glia cell;gliosis;histopathology;immunohistochemistry;laboratory diagnosis;macrophage;meningoencephalitis;microscopy;monocyte;nerve cell;nerve cell necrosis;nerve degeneration;neuropathology;nonhuman;protein localization;smooth muscle cell;spindle cell;virus infection;virus isolation;virus strain;virus virulence,"Blas-Machado, U.;Saliki, J. T.;Duffy, J. C.;Caseltine, S. L.",2004,,10.1354/vp.41-2-190,0
194,Novel circular DNA viruses in stool samples of wild-living chimpanzees,"Viral particles in stool samples from wild-living chimpanzees were analysed using random PCR amplification and sequencing. Sequences encoding proteins distantly related to the replicase protein of single-stranded circular DNA viruses were identified. Inverse PCR was used to amplify and sequence multiple small circular DNA viral genomes. The viral genomes were related in size and genome organization to vertebrate circoviruses and plant geminiviruses but with a different location for the stem-loop structure involved in rolling circle DNA replication. The replicase genes of these viruses were most closely related to those of the much smaller (similar to 1 kb) plant nanovirus circular DNA chromosomes. Because the viruses have characteristics of both animal and plant viruses, we named them chimpanzee stool-associated circular viruses (ChiSCV). Further metagenomic studies of animal samples will greatly increase our knowledge of viral diversity and evolution.",SINGLE-STRANDED-DNA;FEATHER-DISEASE-VIRUS;NUCLEOTIDE-SEQUENCE;ANALYSIS;NECROTIC YELLOWS VIRUS;WASTING SYNDROME PMWS;SOUTH ASIAN;CHILDREN;PORCINE-CIRCOVIRUS;VIRAL METAGENOMICS;ENDONUCLEASE DOMAIN;PLANT CIRCOVIRUSES,"Blinkova, O.;Victoria, J.;Li, Y. Y.;Keele, B. F.;Sanz, C.;Ndjango, J. B. N.;Peeters, M.;Travis, D.;Lonsdorf, E. V.;Wilson, M. L.;Pusey, A. E.;Hahn, B. H.;Delwart, E. L.",2010,Jan,,0
195,Epitope-blocking enzyme-linked immunosorbent assays for the detection of serum antibodies to West Nile virus in multiple avian species,"We report the development of epitope-blocking enzyme-linked immunosorbent assays (ELISAs) for the rapid detection of serum antibodies to West Nile virus (WNV) in taxonomically diverse North American avian species. A panel of flavivirus-specific monoclonal antibodies (MAbs) was tested in blocking assays with serum samples from WNV-infected chickens and crows. Selected MAbs were further tested against serum samples from birds that represented 16 species and 10 families. Serum samples were collected from birds infected with WNV or Saint Louis encephalitis virus (SLEV) and from noninfected control birds. Serum samples from SLEV-infected birds were included in these experiments because WNV and SLEV are closely related antigenically, are maintained in similar transmission cycles, and have overlapping geographic distributions. The ELISA that utilized MAb 3.1112G potentially discriminated between WNV and SLEV infections, as all serum samples from WNV-infected birds and none from SLEV-infected birds were positive in this assay. Assays with MAbs 2B2 and 6B6C-1 readily detected serum antibodies in all birds infected with WNV and SLEV, respectively, and in most birds infected with the other virus. Two other MAbs partially discriminated between infections with these two viruses. Serum samples from most WNV-infected birds but no SLEV-infected birds were positive with MAb 3.67G, while almost all serum samples from SLEV-infected birds but few from WNV-infected birds were positive with MAb 6B5A-5. The blocking assays reported here provide a rapid, reliable, and inexpensive diagnostic and surveillance technique to monitor WNV activity in multiple avian species.",epitope;monoclonal antibody;monoclonal antibody 2b2;monoclonal antibody 3.1112g;monoclonal antibody 6b5a 5;monoclonal antibody 6b6c 1;unclassified drug;virus antibody;animal cell;antibody detection;antibody specificity;antigen binding;article;bird;bird disease;chicken;controlled study;cost control;enzyme linked immunosorbent assay;geographic distribution;nonhuman;priority journal;reliability;serodiagnosis;St. Louis encephalitis virus;virus detection;virus infection;virus transmission;West Nile virus,"Blitvich, B. J.;Marlenee, N. L.;Hall, R. A.;Calisher, C. H.;Bowen, R. A.;Roehrig, J. T.;Komar, N.;Langevin, S. A.;Beaty, B. J.",2003,,10.1128/jcm.41.3.1041-1047.2003,0
196,New Leaves in the Growing Tree of Pestiviruses,"Pestiviruses are a group of viruses of veterinary importance infecting livestock animals like pigs, cattle, and sheep, and also wildlife animals like wild boar and different deer species. While for decades only four classical species (Classical swine fever virus, Bovine viral diarrhea virus types 1 and 2, Border disease virus), and a few so-called atypical pestiviruses were known (e.g., Giraffe virus, Pronghorn virus, HoBi virus), a series of novel pestiviruses was identified in the last years (Bungowannah virus, Bat pestivirus, Norway rat pestivirus, Atypical porcine pestivirus, LINDA virus). The Australian Bungowannah virus could be isolated and further characterized by classical sequencing, but all the other latest novel pestiviruses were identified by metagenomics using next-generation sequencing technologies. Here, we describe these new viruses and their discovery and characterization. Differentiation is made between the occurrence of classical pestiviruses in new species and novel viruses or virus types.",animal;classification;high throughput sequencing;isolation and purification;metagenomics;Pestivirus;Pestivirus infection;procedures;veterinary medicine;virology,"Blome, S.;Beer, M.;Wernike, K.",2017,,10.1016/bs.aivir.2017.07.003,0
197,Detection of a novel porcine boca-like virus in the background of porcine circovirus type 2 induced postweaning multisystemic wasting syndrome,"Porcine circovirus type 2 (PCV-2) has been found to be the causative agent of postweaning multisystemic wasting syndrome (PMWS). However, PCV-2 is a ubiquitous virus in the swine population and a majority of pigs infected with PCV-2 do not develop the disease. Different factors such as age, maintenance, the genetics of PCV-2, other pathogens, etc. have been suggested to contribute to the development of PMWS. However, so far no proven connection between any of these factors and the disease development has been found. In this study we explored the possible presence of other so far unknown DNA containing infectious agents in lymph nodes collected from Swedish pigs with confirmed PMWS through random amplification and high-throughput sequencing. Although the vast majority of the amplified genetic sequences belonged to PCV-2, we also found genome sequences of Torque Teno virus (TTV) and of a novel parvovirus. The detection of TTV was expected since like PCV-2, TTV has been found to have high prevalence in pigs around the world. We were able to amplify a longer region of the parvovirus genome, consisting of the entire NP1 and partial VP1/2. By comparative analysis of the nucleotide sequences and phylogenetic studies we propose that this is a novel porcine parvovirus, with genetic relationship to bocaviruses. © 2009 Elsevier B.V. All rights reserved.",nuclear protein;protein VP1;protein VP2;animal tissue;article;Bocaparvovirus;Circoviridae;gene amplification;gene sequence;lymph node;nonhuman;nucleotide sequence;phylogeny;Porcine circovirus 2;postweaning multisystemic wasting syndrome;priority journal;pig;Torque teno virus 1;viral genetics;virus detection,"Blomström, A. L.;Belák, S.;Fossum, C.;McKillen, J.;Allan, G.;Wallgren, P.;Berg, M.",2009,,10.1016/j.virusres.2009.09.006,1
198,Viral metagenomic analysis displays the Co-infection situation in healthy and PMWS affected pigs,"The development of high-throughput sequencing technologies have allowed the possibility to investigate and characterise the entire microbiome of individuals, providing better insight to the complex interaction between different microorganisms. This will help to understand how the microbiome influence the susceptibility of secondary agents and development of disease. We have applied viral metagenomics to investigate the virome of lymph nodes from Swedish pigs suffering from the multifactorial disease postweaning multisystemic wasting syndrome (PMWS) as well as from healthy pigs. The aim is to increase knowledge of potential viruses, apart from porcine circovirus type 2 (PCV2), involved in PMWS development as well as to increase knowledge on the virome of healthy individuals. In healthy individuals, a diverse viral flora was seen with several different viruses present simultaneously. The majority of the identified viruses were small linear and circular DNA viruses, such as different circoviruses, anelloviruses and bocaviruses. In the pigs suffering from PMWS, PCV2 sequences were, as expected, detected to a high extent but other viruses were also identified in the background of PCV2. Apart from DNA viruses also RNA viruses were identified, among them were a porcine pestivirus showing high similarity to a recently (in 2015) discovered atypical porcine pestivirus in the US. Majority of the viruses identified in the background of PCV2 in PMWS pigs could also be identified in the healthy pigs. PCV2 sequences were also identified in the healthy pigs but to a much lower extent than in PMWS affected pigs. Although the method used here is not quantitative the very clear difference in amount of PCV2 sequences in PMWS affected pigs and healthy pigs most likely reflect the very strong replication of PCV2 known to be a hallmark of PMWS. Taken together, these findings illustrate that pigs appear to have a considerable viral flora consisting to a large extent of small single-stranded and circular DNA viruses. Future research on these types of viruses will help to better understand the role that these ubiquitous viruses may have on health and disease of pigs. We also demonstrate for the first time, in Europe, the presence of a novel porcine pestivirus.",single stranded DNA;virus DNA;animal experiment;animal model;article;controlled study;disease association;DNA determination;feces analysis;genome analysis;metagenomics;mixed infection;nonhuman;pig;Porcine circovirus 2;postweaning multisystemic wasting syndrome;sequence analysis;virus genome;virus transmission,"Blomström, A. L.;Fossum, C.;Wallgren, P.;Berg, M.",2016,,10.1371/journal.pone.0166863,1
199,A metagenomic analysis displays the diverse microbial community of a vermicomposting system in Uganda,"Background: Vermicomposting is a mesophilic process using earthworms to efficiently and at low cost process large volumes of organic waste. It has been suggested to not only increase soil fertility but also increase biomass of beneficial bacteriawhile reducing harmful bacteria. The aim of this study was to set up a strategy to investigate and characterise the viral as well as the bacterial composition of a vermicomposting system. Material and methods: The vermicomposting unit used in this study was placed at the Makerere University Agricultural Research Institute Kabanyolo on the outskirts of Kampala, Uganda, and was fed with 80% cattle manure and 20% food waste. On Day 172, the compost was terminated and compost samples werecollected from three layers of the unit: the top, the middle and the bottom layer. A metagenomic approach was then applied to characterise the viral and bacterial composition of the vermicomposting system. Results and discussion: A high abundance and diversity of bacteria were identified. Proteobacteria was the largest phyla in the compost (mainly Alpha-, Gamma- and Betaproteobacteria), constituting almost 65% of the bacterial reads in the data sets. DNA samples from several possible pathogenic bacteria, such as Salmonella spp., Escherichia coli, Enterobacter spp., Enterococcus spp. and Clostridium spp, were detected in the vermicompost, suggesting that there might still be harmful bacteria in the vermicast. Phages constituted the main viral group; apart from phages, mainly insect viruses were identified. The only animal or human virus identified was kobuvirus. In summary, metagenomic analysis was shown to be an efficient technology to characterise the microbial composition of vermicast. The data from this study contribute to a better understanding of the microbes present in this kind of composting system and can help determine measures necessary for safe manure handling.",animal experiment;animal virus;Betaproteobacteria;Clostridium;composting;Enterobacter;Escherichia coli;food waste;human versus animal comparison;insect virus;Kobuvirus;manure;metagenomics;microbial community;nonhuman;Salmonella;Uganda;university;vermicompost,"Blomström, A. L.;Lalander, C.;Komakech, A. J.;Vinnerås, B.;Boqvist, S.",2016,,10.3402/iee.V6.32453,0
200,Genome Sequence of a Bovine Rhinitis B Virus Identified in Cattle in Sweden,,,"Blomström, A. L.;Oma, V.;Khatri, M.;Hansen, H. H.",2017,,,1
201,Viral metagenomic analysis of bushpigs (Potamochoerus larvatus) in Uganda identifies novel variants of Porcine parvovirus 4 and Torque teno sus virus 1 and 2,"Background: As a result of rapidly growing human populations, intensification of livestock production and increasing exploitation of wildlife habitats for animal agriculture, the interface between wildlife, livestock and humans is expanding, with potential impacts on both domestic animal and human health. Wild animals serve as reservoirs for many viruses, which may occasionally result in novel infections of domestic animals and/or the human population. Given this background, we used metagenomics to investigate the presence of viral pathogens in sera collected from bushpigs (Potamochoerus larvatus), a nocturnal species of wild Suid known to move between national parks and farmland, in Uganda. Results: Application of 454 pyrosequencing demonstrated the presence of Torque teno sus virus (TTSuV), porcine parvovirus 4 (PPV4), porcine endogenous retrovirus (PERV), a GB Hepatitis C-like virus, and a Sclerotinia hypovirulence-associated-like virus in sera from the bushpigs. PCR assays for each specific virus combined with Sanger sequencing revealed two TTSuV-1 variants, one TTSuV-2 variant as well as PPV4 in the serum samples and thereby confirming the findings from the 454 sequencing. Conclusions: Using a viral metagenomic approach we have made an initial analysis of viruses present in bushpig sera and demonstrated for the first time the presence of PPV4 in a wild African Suid. In addition we identified novel variants of TTSuV-1 and 2 in bushpigs. © 2012 Blomström et al.; licensee BioMed Central Ltd.",agricultural land;article;blood sampling;endogenous retrovirus;Hepatitis C virus;metagenomics;national park;nonhuman;nucleotide sequence;polymerase chain reaction;Porcine parvovirus;Porcine parvovirus 4;Potamochoerus larvatus;pyrosequencing;Sclerotinia;pig;Torque teno sus virus 1;Torque teno sus virus 2;Torque teno virus 1;Uganda;unindexed sequence;virus identification,"Blomström, A. L.;Ståhl, K.;Masembe, C.;Okoth, E.;Okurut, A. R.;Atmnedi, P.;Kemp, S.;Bishop, R.;Belák, S.;Berg, M.",2012,,10.1186/1743-422x-9-192,0
202,Characterisation of the virome of tonsils from conventional pigs and from specific pathogen-free pigs,"Porcine respiratory disease is a multifactorial disease that can be influenced by a number of different microorganisms, as well as by non-infectious factors such as the management and environment of the animals. It is generally believed that the interaction between different infectious agents plays an important role in regard to respiratory diseases. Therefore, we used high-throughput sequencing combined with viral metagenomics to characterise the viral community of tonsil samples from pigs coming from a conventional herd with lesions in the respiratory tract at slaughter. In parallel, samples from specific pathogen-free pigs were also analysed. This study showed a variable co-infection rate in the different pigs. The differences were not seen at the group level but in individual pigs. Some viruses such as adenoviruses and certain picornaviruses could be found in most pigs, while others such as different parvoviruses and anelloviruses were only identified in a few pigs. In addition, the complete coding region of porcine parvovirus 7 was obtained, as were the complete genomes of two teschoviruses. The results from this study will aid in elucidating which viruses are circulating in both healthy pigs and in pigs associated with respiratory illness. This knowledge is needed for future investigations into the role of viral-viral interactions in relation to disease development.",Adenoviridae;Anelloviridae;article;controlled study;gene amplification;gene sequence;health status;high throughput sequencing;metagenomics;nonhuman;Parechovirus;Picornaviridae;pig;pneumonia;Porcine circovirus 2;respiratory tract injury;tonsil disease;viral respiratory tract infection,"Blomström, A. L.;Ye, X.;Fossum, C.;Wallgren, P.;Berg, M.",2018,,10.3390/v10070382,1
203,Phylogenetic analysis of partial S1 and N gene sequences of infectious bronchitis virus isolates from Italy revealed genetic diversity and recombination,"A total of ten infectious bronchitis virus (IBV) isolates collected from commercial chickens in Italy in 1999 were characterized by RT-PCR and sequencing of the S1 and N genes. Phylogenetic analysis based on partial S1 gene sequences showed that five field viruses clustered together with 793/B-type strains, having 91.3-98.5% nucleotide identity within the group, and one isolate had very close sequence relationship (94.6% identity) with 624/I strain. These two IBV types have been identified in Italy previously. The other three variant isolates formed novel genotype detected recently in many countries of Western Europe. For one of these variant viruses, Italy-02, which afterwards became the prototype strain, the entire S1 gene was sequenced to confirm its originality. In contrast, phylogenetic analysis of more conserved partial N gene sequences, comprising 1-300 nucleotides, revealed different clustering. Thus, three variant IBVs of novel Italy-02 genotype, which had 96.7-99.2% S1 gene nucleotide identity with each other, belonged to three separate subgroups based on N gene sequences. 624/I-type isolate Italy-06 together with Italy-03, which was undetectable using S1 gene primers, shared 97.7% and 99.3% identity, respectively, in N gene region with vaccine strain H120. Only one of the 793/B-type isolates, Italy-10, clustered with the 793/B strain sharing 99.3% partial N gene identity, whereas the other four isolates were genetically distant from them (only 87.7-89.7% identity) and formed separate homogenous subgroup. The results demonstrated that both mutations and recombination events could contribute to the genetic diversity of the Italian isolates. © 2006 Springer Science+Business Media, LLC.",nucleotide;primer DNA;vaccine;article;Avian infectious bronchitis virus;chicken;controlled study;gene cluster;gene N;gene sequence;genetic conservation;genetic distance;genetic recombination;genetic variability;genotype;Italy;nonhuman;nucleotide sequence;phylogeny;priority journal;reverse transcription polymerase chain reaction;s1 gene;virus gene;virus identification;virus isolation;virus mutation;virus recombinant;virus strain;virus typing;Western Europe,"Bochkov, Y. A.;Tosi, G.;Massi, P.;Drygin, V. V.",2007,,10.1007/s11262-006-0037-0,0
204,Basic research on BSE transmission to people,"Prion diseases of animal and man belong to neurological diseases with amyloidal deposition of the respective proteins. As to prion disease, the cellular prionprotein is in its abnormal isoform(s) an essential component of prionprotein aggregates found in affected tissue. In contrast to all neurodegenerative diseases like Morbus Alzheimer or Huntington's disease, prion diseases are transmissible. Therefore, prion diseases were designated Transmissible Spongiform Encephalopathies (TSE). The diseases are well known since decades. Scrapie was first described around 1750, a BSE case was reported in the 1850, most likely a misdiagnosis, and in 1920/1930 the human Creutzfeldt-Jakob disease (CJD) had been described. Transmission of CJD i.e. Kuru had been suspected in the early 1950s and erronously classified as slow virus disease. The CJD transmission posed a problem to humans when transplants from CJD cases were used for treatment. Fortunately, these iatrogenic transmissions remained limited. But with the advent of BSE and appearance of variant CJD cases in the UK and some places in Europe scientists suspected that transmission from cattle to man could have happened. From animal models we know of successful transmission via several routes. Species barriers do not completely prevent transmission. Rather transmission barriers might exist controlling individual susceptibility against prions. Modes of transmission, susceptibility for transmission, identification of receptor molecules as well as molecular mechanisms of the transmission process are intensely investigated. Current knowledge let us to assume that inapparent stages of prion infection pretend a (not existing) species barrier. This inapparent infection preceeds overt disease and, thus, most re-search focuses on the development of highly sensitive assay systems for detection of minute amounts of pathological prionprotein in suspected cases. Inapparence also should warn us to underestimate BSE or human vCJD cases; at present, 124 in Europe and one probable case in Hongkong (7 March 2002). Whether BSE had spread to other parts of the world by animal nutrition components or meat can neither be excluded nor confirmed at this time. New data on transmission and consequences of BSE for the human population are summarized in this review.",animal;bovine spongiform encephalopathy;bovine;Creutzfeldt Jakob disease;disease predisposition;disease transmission;food contamination;human;Huntington chorea;prion disease;review;scrapie;species difference;zoonosis,"Bodemer, W.;Kaup, F. J.",2002,,,0
205,Comments on present-day spread and epidemiology of BSE and prion diseases,"Prion diseases of animals and man are neurological diseases with amyloidal deposition of the respective proteins. As to prion disease, the cellular prion protein is in its abnormal isoform(s) an essential component of prion protein aggregates found in affected tissue. In contrast to all neurodegenerative diseases like Morbus Alzheimer or Huntington's disease, prion diseases are transmissible. Therefore, prion diseases were designated Transmissible Spongiform Encephalopathies (TSE). The diseases have been well known for decades. Scrapie was first described around 1750, a BSE case was reported in the 1850s most likely a misdiagnosis, and in 1920/1930 the human Creutzfeldt-Jakob disease (CJD) had been described. Transmission of CJD i.e. Kuru had been suspected in the early 1950 s and was erroneously classified as slow virus disease. The CJD transmission posed a problem to humans when transplants from CJD cases were used for treatment. Fortunately, these iatrogenic transmissons remained limited. But with the advent of BSE and appearance of variant CJD cases in the UK and some places in Europe scientists suspected that transmission from cattle to man could have happened. From animal models we know of successful transmission via several routes. Species barriers do not completely prevent transmission. Rather, transmission barriers might exist controlling individual susceptibilty against prions. Modes of transmission, susceptibility to transmission, identification of receptor molecules as well as molecular mechanisms of the transmission process are being investigated with great intensity. Current knowledge leads us to assume that inapparent stages of prion infection wrongly suggest a (non-existent) species barrier. This inapparent infection precedes overt disease, and, hence, most research focusses on the development of highly sensitive assay systems for detection of minute amounts of pathological prion protein in suspected cases. Inapparence also should warn us to underestimate BSE or human vCJD cases; at present, approx. 145 cases occurred in Europe and one probable case in Hongkong (June 2003). Whether BSE had spread to other parts of the world by animal nutrition components or meat can neither be excluded nor confirmed at this time. New data on transmission and consequences of BSE for the human population are summarised in this review. © Georg Thieme Verlag Stuttgart.",prion protein;conference paper;Creutzfeldt Jakob disease;degenerative disease;diagnostic error;disease predisposition;disease transmission;Europe;human;Huntington chorea;nonhuman;prion disease;scrapie;United Kingdom,"Bodemer, W.;Kaup, F. J.",2004,,10.1055/s-2004-812760,0
206,Novel viruses in birds: Flying through the roof or is a cage needed? Review,"Emerging viral diseases continue to have a major global impact on human beings and animals. To be able to take adequate measures in case of an outbreak of an emerging disease, rapid detection of the causative agent is a crucial first step. In this review, various aspects of virus discovery are discussed, with a special focus on recently discovered viruses in birds. Novel viruses with a potential major impact have been discovered in domestic and wild bird species in recent years using various virus discovery methods. Only a few studies report the detection of novel viruses in endangered bird species, although increased knowledge about viruses circulating in these species is important. Additional studies focusing on the exact role of a novel virus in disease and on the impact of a novel virus on bird populations are often lacking. Intensive collaboration between different disciplines is needed to obtain useful information about the role of these novel viruses.","Animals;Animals, Domestic/vi [Virology];Animals, Wild/vi [Virology];Bird Diseases/vi [Virology];*Birds/vi [Virology];Chickens/vi [Virology];Columbidae/vi [Virology];Ducks/vi [Virology];Endangered Species;Virus Diseases/ve [Veterinary];Viruses/ip [Isolation & Purification];Viruses/py [Pathogenicity]","Bodewes, R.",2018,03,,0
207,Viral metagenomic analysis of feces of wild small carnivores,"Background: Recent studies have clearly demonstrated the enormous virus diversity that exists among wild animals. This exemplifies the required expansion of our knowledge of the virus diversity present in wildlife, as well as the potential transmission of these viruses to domestic animals or humans. Methods. In the present study we evaluated the viral diversity of fecal samples (n = 42) collected from 10 different species of wild small carnivores inhabiting the northern part of Spain using random PCR in combination with next-generation sequencing. Samples were collected from American mink (Neovison vison), European mink (Mustela lutreola), European polecat (Mustela putorius), European pine marten (Martes martes), stone marten (Martes foina), Eurasian otter (Lutra lutra) and Eurasian badger (Meles meles) of the family of Mustelidae; common genet (Genetta genetta) of the family of Viverridae; red fox (Vulpes vulpes) of the family of Canidae and European wild cat (Felis silvestris) of the family of Felidae. Results: A number of sequences of possible novel viruses or virus variants were detected, including a theilovirus, phleboviruses, an amdovirus, a kobuvirus and picobirnaviruses. Conclusions: Using random PCR in combination with next generation sequencing, sequences of various novel viruses or virus variants were detected in fecal samples collected from Spanish carnivores. Detected novel viruses highlight the viral diversity that is present in fecal material of wild carnivores. © 2014 Bodewes et al.; licensee BioMed Central Ltd.",Aleutian mink disease virus;Neovison vison;article;Bunyaviridae;Canidae;carnivore;Encephalomyocarditis virus;Mustela lutreola;feces analysis;Felidae;Kobuvirus;Lutra lutra;Martes foina;Martes martes;Meles meles;metagenomics;microbial diversity;Theiler's murine encephalomyelitis virus;Mustela putorius;Mustelidae;nonhuman;nucleotide sequence;otter;Phlebovirus;Picobirnavirus;viral genetics;Viverridae;Vulpes vulpes,"Bodewes, R.;Ruiz-Gonzalez, A.;Schapendonk, C. M. E.;Van Den Brand, J. M. A.;Osterhaus, A. D. M. E.;Smits, S. L.",2014,,10.1186/1743-422x-11-89,0
208,"Identification of multiple novel viruses, including a parvovirus and a hepevirus, in feces of red foxes","Red foxes (Vulpes vulpes) are the most widespread members of the order of Carnivora. Since they often live in (peri)urban areas, they are a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. Here we evaluated the fecal viral microbiome of 13 red foxes by random PCR in combination with next-generation sequencing. Various novel viruses, including a parvovirus, bocavirus, adeno-associated virus, hepevirus, astroviruses, and picobirnaviruses, were identified.","Amino Acid Sequence;Animals;Astroviridae/ge [Genetics];Base Sequence;*Disease Reservoirs/ve [Veterinary];Disease Reservoirs/vi [Virology];*Feces/vi [Virology];*Foxes/vi [Virology];*Hepevirus/ge [Genetics];Likelihood Functions;*Metagenome/ge [Genetics];Models, Genetic;Molecular Sequence Data;*Parvovirus/ge [Genetics];Phylogeny;Picobirnavirus/ge [Genetics];Polymerase Chain Reaction/ve [Veterinary];Sequence Analysis, DNA;Species Specificity","Bodewes, R.;van der Giessen, J.;Haagmans, B. L.;Osterhaus, A. D.;Smits, S. L.",2013,Jul,,0
209,"Spatiotemporal Analysis of the Genetic Diversity of Seal Influenza A(H10N7) Virus, Northwestern Europe","UNLABELLED: Influenza A viruses are major pathogens for humans, domestic animals, and wildlife, and these viruses occasionally cross the species barrier. In spring 2014, increased mortality of harbor seals (Phoca vitulina), associated with infection with an influenza A(H10N7) virus, was reported in Sweden and Denmark. Within a few months, this virus spread to seals of the coastal waters of Germany and the Netherlands, causing the death of thousands of animals. Genetic analysis of the hemagglutinin (HA) and neuraminidase (NA) genes of this seal influenza A(H10N7) virus revealed that it was most closely related to various avian influenza A(H10N7) viruses. The collection of samples from infected seals during the course of the outbreak provided a unique opportunity to follow the adaptation of the avian virus to its new seal host. Sequence data for samples collected from 41 different seals from four different countries between April 2014 and January 2015 were obtained by Sanger sequencing and next-generation sequencing to describe the molecular epidemiology of the seal influenza A(H10N7) virus. The majority of sequence variation occurred in the HA gene, and some mutations corresponded to amino acid changes not found in H10 viruses isolated from Eurasian birds. Also, sequence variation in the HA gene was greater at the beginning than at the end of the epidemic, when a number of the mutations observed earlier had been fixed. These results imply that when an avian influenza virus jumps the species barrier from birds to seals, amino acid changes in HA may occur rapidly and are important for virus adaptation to its new mammalian host. IMPORTANCE: Influenza A viruses are major pathogens for humans, domestic animals, and wildlife. In addition to the continuous circulation of influenza A viruses among various host species, cross-species transmission of influenza A viruses occurs occasionally. Wild waterfowl and shorebirds are the main reservoir for most influenza A virus subtypes, and spillover of influenza A viruses from birds to humans or other mammalian species may result in major outbreaks. In the present study, various sequencing methods were used to elucidate the genetic changes that occurred after the introduction and subsequent spread of an avian influenza A(H10N7) virus among harbor seals of northwestern Europe by use of various samples collected during the outbreak. Such detailed knowledge of genetic changes necessary for introduction and adaptation of avian influenza A viruses to mammalian hosts is important for a rapid risk assessment of such viruses soon after they cross the species barrier.","Amino Acid Substitution;Animals;Computational Biology/mt [Methods];Europe/ep [Epidemiology];*Genetic Variation;Genome, Viral;Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];High-Throughput Nucleotide Sequencing;Influenza A Virus, H10N7 Subtype/cl [Classification];*Influenza A Virus, H10N7 Subtype/ge [Genetics];*Orthomyxoviridae Infections/ep [Epidemiology];*Orthomyxoviridae Infections/vi [Virology];*Phoca/vi [Virology];Phylogeny;Phylogeography;*Spatio-Temporal Analysis;0 (Hemagglutinin Glycoproteins, Influenza Virus)","Bodewes, R.;Zohari, S.;Krog, J. S.;Hall, M. D.;Harder, T. C.;Bestebroer, T. M.;van de Bildt, M. W. G.;Spronken, M. I.;Larsen, L. E.;Siebert, U.;Wohlsein, P.;Puff, C.;Seehusen, F.;Baumgartner, W.;Harkonen, T.;Smits, S. L.;Herfst, S.;Osterhaus, A.;Fouchier, R. A. M.;Koopmans, M. P.;Kuiken, T.",2016,May,,0
210,"Newcastle disease outbreaks in Kazakhstan and Kyrgyzstan during 1998, 2000, 2001, 2003, 2004, and 2005 were caused by viruses of the genotypes VIIb and VIId","Newcastle disease virus (NDV) infects domesticated and wild birds throughout the world, and infections with virulent NDV strains continue to cause disease outbreaks in poultry and wild birds. To assess the evolutionary characteristics of 28 NDV strains isolated from chickens in Kazakhstan and Kyrgyzstan during 1998, 2000, 2001, 2003, 2004, and 2005, we investigated the phylogenetic relationships among these viruses and viruses described previously. For genotyping, fusion (F) gene phylogenetic analysis (nucleotide number 47-421) was performed using sequences of Kazakhstanian and Kyrgyzstanian isolates as compared to sequences of selected NDV strains from GenBank. Phylogenetic analysis demonstrated that the 14 newly characterized strains from years 1998 to 2001 belong to the NDV genotype VIIb, whereas the 14 strains isolated during 2003-2005 were of genotype VIId. All strains possessed a virulent fusion protein cleavage site (R-R-Q-R/K-R-F) and had intracerebral pathogenicity indexes in day-old chickens that ranged from 1.05 to 1.87, both properties typical of NDV strains classified in the mesogenic or velogenic pathotype. © 2009 Springer Science+Business Media, LLC.",article;bird disease;chicken;controlled study;epidemic;fusion gene;genotype;Kazakhstan;Kyrgyzstan;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;priority journal;virus isolation;virus strain,"Bogoyavlenskiy, A.;Berezin, V.;Prilipov, A.;Usachev, E.;Lyapina, O.;Korotetskiy, I.;Zaitceva, I.;Asanova, S.;Kydyrmanov, A.;Daulbaeva, K.;Shakhvorostova, L.;Sayatov, M.;King, D.",2009,,10.1007/s11262-009-0370-1,0
211,Molecular characterization of virulent newcastle disease virus isolates from chickens during the 1998 NDV outbreak in Kazakhstan,"Newcastle disease virus (NDV) infects domesticated and wild birds throughout the world and has the possibility to cause outbreaks in chicken flocks in future. To assess the evolutionary characteristics of 10 NDV strains isolated from chickens in Kazakhstan during 1998 we investigated the phylogenetic relationships among these viruses and viruses described previously. For genotyping, fusion (F) gene phylogenetic analysis (nucleotide number 47-421) was performed using sequences of Kazakhstanian isolates as compared to sequences of selected NDV strains from GenBank. Phylogenetic analysis showed that all newly characterized strains belonged to the genetic group designated as VIIb. All strains possessed a virulent fusion cleavage site (RRQRR/F) belonging to velogenic or mesogenic pathotypes with intracerebral pathogenicity indexes (ICPI) varying from 1.05 to 1.87. © 2005 Springer Science+Business Media, Inc.",article;chicken;fusion gene;GenBank;genotype;Kazakhstan;Newcastle disease virus;nonhuman;nucleotide sequence;pathotype;phylogeny;priority journal;unindexed sequence;virus isolation;virus strain;virus virulence,"Bogoyavlenskiy, A.;Berezin, V.;Prilipov, A.;Usachev, E.;Lyapina, O.;Levandovskaya, S.;Korotetskiy, I.;Tolmacheva, V.;Makhmudova, N.;Khudyakova, S.;Tustikbaeva, G.;Zaitseva, I.;Omirtaeva, E.;Ermakova, O.;Daulbaeva, K.;Asanova, S.;Kydyrmanov, A.;Sayatov, M.;King, D.",2005,,10.1007/s11262-004-2195-2,0
212,"Phylogenetic analyses indicate little variation among reticuloendotheliosis viruses infecting avian species, including the endangered Attwater's prairie chicken","Reticuloendotheliosis virus infection, which typically causes systemic lymphomas and high mortality in the endangered Attwater's prairie chicken, has been described as a major obstacle in repopulation efforts of captive breeding facilities in Texas. Although antigenic relationships among reticuloendotheliosis virus (REV) strains have been previously determined, phylogenetic relationships have not been reported. The pol and env of REV proviral DNA from prairie chickens (PC-R92 and PC-2404), from poxvirus lesions in domestic chickens, the prototype poultry derived REV-A and chick syncytial virus (CSV), and duck derived spleen necrosis virus (SNV) were PCR amplified and sequenced. The 5032 bp, that included the pol and most of env genes, of the PC-R92 and REV-A were 98% identical, and nucleotide sequence identities of smaller regions within the pol and env from REV strains examined ranged from 95 to 99% and 93 to 99%, respectively. The putative amino acid sequences were 97-99% identical in the polymerase and 90-98% in the envelope. Phylogenetic analyses of the nucleotide and amino acid sequences indicated the closest relationship among the recent fowl pox-associated chicken isolates, the prairie chicken isolates and the prototype CSV while only the SNV appeared to be distinctly divergent. While the origin of the naturally occurring viruses is not known, the avian poxvirus may be a critical component of transmission of these ubiquitous oncogenic viruses. © 2006 Elsevier B.V. All rights reserved.",Pol protein;virus DNA;virus envelope protein;amino acid sequence;animal cell;animal experiment;animal model;article;chicken;controlled study;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;Poxviridae;prairie;priority journal;protein analysis;Human respiratory syncytial virus;reticuloendotheliosis;Reticuloendotheliosis virus;virus strain,"Bohls, R. L.;Linares, J. A.;Gross, S. L.;Ferro, P. J.;Silvy, N. J.;Collisson, E. W.",2006,,10.1016/j.virusres.2006.01.011,0
213,"Forécariah virus, a new representative of the Bhanja antigenic group, isolated in the Republic of Guinea","A new arbovirus named ""Forécariah"" has been isolated from ticks Boophylus geigy in Republic of Guinea (West Africa), district Forecariah. This virus is classified into Bhanja antigen group, due to its physico-chemical, biological and antigenic properties.",virus antibody;virus antigen;animal;Arbovirus;article;Bunyaviridae;bovine;cytopathogenic effect;female;Guinea-Bissau;human;immunology;isolation and purification;microbiology;mouse;tick,"Boiro, I.;Lomonossov, N. N.;Malenko, G. V.;Balde, C.;Bah, A.",1986,,,0
214,Shotgun Pyrosequencing Metagenomic Analyses of Dusts from Swine Confinement and Grain Facilities,"Inhalation of agricultural dusts causes inflammatory reactions and symptoms such as headache, fever, and malaise, which can progress to chronic airway inflammation and associated diseases, e. g. asthma, chronic bronchitis, chronic obstructive pulmonary disease, and hypersensitivity pneumonitis. Although in many agricultural environments feed particles are the major constituent of these dusts, the inflammatory responses that they provoke are likely attributable to particle-associated bacteria, archaebacteria, fungi, and viruses. In this study, we performed shotgun pyrosequencing metagenomic analyses of DNA from dusts from swine confinement facilities or grain elevators, with comparisons to dusts from pet-free households. DNA sequence alignment showed that 19% or 62% of shotgun pyrosequencing metagenomic DNA sequence reads from swine facility or household dusts, respectively, were of swine or human origin, respectively. In contrast only 2% of such reads from grain elevator dust were of mammalian origin. These metagenomic shotgun reads of mammalian origin were excluded from our analyses of agricultural dust microbiota. The ten most prevalent bacterial taxa identified in swine facility compared to grain elevator or household dust were comprised of 75%, 16%, and 42% gram-positive organisms, respectively. Four of the top five swine facility dust genera were assignable (Clostridium, Lactobacillus, Ruminococcus, and Eubacterium, ranging from 4% to 19% relative abundance). The relative abundances of these four genera were lower in dust from grain elevators or pet-free households. These analyses also highlighted the predominance in swine facility dust of Firmicutes (70%) at the phylum level, Clostridia (44%) at the Class level, and Clostridiales at the Order level (41%). In summary, shotgun pyrosequencing metagenomic analyses of agricultural dusts show that they differ qualitatively and quantitatively at the level of microbial taxa present, and that the bioinformatic analyses used for such studies must be carefully designed to avoid the potential contribution of non-microbial DNA, e.g. from resident mammals.",DOSE-RESPONSE RELATIONSHIPS;ENVIRONMENTAL EXPOSURES;RESPIRATORY;HEALTH;PULMONARY-FUNCTION;AIRBORNE DUST;LUNG-FUNCTION;FARM-WORKERS;BUILDINGS;MICROORGANISMS;PIG,"Boissy, R. J.;Romberger, D. J.;Roughead, W. A.;Weissenburger-Moser, L.;Poole, J. A.;LeVan, T. D.",2014,Apr,,0
215,Genetic characterization of bovine virai diarrhea viruses isolated from persistently infected calves born to dams vaccinated against bovine viral diarrhea virus before breeding,"Objective - To collect and partially characterize strains of bovine viral diarrhea viruses (BVDVs) isolated from persistently infected (PI) calves born to vaccinated dams, determine genetic diversity of the isolated viruses, and identify regional distribution of genetically similar virus subpopulations. Sample Population - 17 noncytopathic (NCP) BVDVs from PI calves from 11 herds of beef or dairy cattle. Procedures - Viral RNA was extracted from infected cell cultures, and BVDV-specific PCR primers were used to amplify > 1,000 bases of the viral genome. Derived sequences were used for molecular phylogenetic analyses to determine the viral genotype and viral genogroup and to assess genetic similarity among BVDVs. Results - Analysis of the 17 NCP strains of BVDV failed to detect a viral genotype or viral genogroup not already reported to exist in the United States. One virus was classified as genotype 1, genogroup 1b, and 16 viruses were classified as genotype 2, genogroup 2a. Genotype 2 strains were genetically diverse, and genetic similarities were not obvious among viruses from geographic regions larger than a small locale. Conclusions and Clinical Relevance - Viruses isolated from herds where a genotype 1, genogroup 1a BVDV vaccine was administered prior to breeding were primarily genetically diverse genotype 2, genogroup 2a BVDVs. Vaccination with multiple BVDV genotypes may be needed to improve protection. Methods used in this study to obtain and analyze field strains are applicable to assessing efficacy of current BVDV vaccines. Candidates for future vaccines are viruses that appear able to elude the immune response of cattle vaccinated against BVDV with existing vaccines.",bovi shield;Bovine viral diarrhea virus vaccine;unclassified drug;virus RNA;virus vaccine;article;beef cattle;Bovine viral diarrhea virus 1;breeding;calf (bovine);cattle disease;cell culture;controlled study;dairy cattle;female;Flavivirus;gene amplification;genetic similarity;genetic variability;genotype;geographic distribution;immune response;molecular phylogeny;nonhuman;persistent virus infection;polymerase chain reaction;RNA extraction;sequence analysis;United States;viral genetics;virus genome;virus isolation;virus strain,"Bolin, S. R.;Lim, A.;Grotelueschen, D. M.;McBeth, W. W.;Cortese, V. S.",2009,,10.2460/ajvr.70.1.86,0
216,Prevalence of bovine viral diarrhea virus genotypes and antibody against those viral genotypes in fetal bovine serum,One thousand lots of pooled fetal bovine serum (FBS) were tested for contamination with bovine viral diarrhea virus (BVDV) and/or for contamination with neutralizing antibody against BVDV. Noncytopathic or cytopathic BVDV was isolated from 203 lots of FBS. Analysis of the viral isolates identified 115 type 1 and 65 type 2 BVDV isolates. An additional 23 virus isolates were mixtures of > or = 2 BVDV isolates and were not classified to viral genotype. Further characterization of the type 1 viruses identified 51 subgenotype 1a and 64 subgenotype 1b BVDV isolates. Viral neutralizing antibody was detected in 113 lots of FBS. Differential viral neutralization indicated that type 1 BVDV induced the antibody detected in 48 lots of FBS and type 2 BVDV induced the antibody detected in 16 lots of FBS.,monoclonal antibody;primer DNA;virus antibody;animal;article;blood;bovine;cattle disease;fetus blood;genetics;genotype;isolation and purification;pathogenicity;Pestivirus;polymerase chain reaction;sensitivity and specificity;serodiagnosis;virology,"Bolin, S. R.;Ridpath, J. F.",1998,,,0
217,Unexpected diversity and expression of avian endogenous retroviruses,"Endogenous retroviruses (ERVs) were identified and characterized in three avian genomes to gain insight into early retroviral evolution. Using the computer program RetroTector to detect relatively intact ERVs, we identified 500 ERVs in the chicken genome, 150 in the turkey genome, and 1,200 in the zebra finch genome. Previous studies suggested that endogenous alpharetroviruses were present in chicken genomes. In this analysis, a small number of alpharetroviruses were seen in the chicken and turkey genomes; however, these were greatly outnumbered by beta-like, gamma-like, and alphabeta proviruses. While the avian ERVs belonged to the same major groups as mammalian ERVs, they were more heterogeneous. In particular, the beta-like viruses revealed an evolutionary continuum with the gradual acquisition and loss of betaretroviral markers and a transition from beta to alphabeta and then to alpharetroviruses. Thus, it appears that birds may resemble a melting pot for early ERV evolution. Many of the ERVs were integrated in clusters on chromosomes, often near centromeres. About 25% of the chicken ERVs were in or near cellular transcription units; this is nearly random. The majority of these integrations were in the sense orientation in introns. A higher-than-random number of integrations were >100 kb from the nearest gene. Deep-sequencing studies of chicken embryo fibroblasts revealed that about 20% of the 500 ERVs were transcribed and translated. A subset of these were also transcribed in vivo in chickens, showing tissue-specific patterns of expression. IMPORTANCE Studies of avian endogenous retroviruses (ERVs) have given us a glimpse of an earlier retroviral world. Three different classes of ERVs were observed with many features of mammalian retroviruses, as well as some important differences. Many avian ERVs were transcribed and translated.","Animals;*Birds/vi [Virology];Cluster Analysis;Computational Biology/mt [Methods];*Endogenous Retroviruses/cl [Classification];*Endogenous Retroviruses/ge [Genetics];Evolution, Molecular;Gene Expression Profiling;Gene Order;*Genetic Variation;*Genome;Genotype;High-Throughput Nucleotide Sequencing;Proviruses/cl [Classification];Proviruses/ge [Genetics];Transcription, Genetic;Virus Integration","Bolisetty, M.;Blomberg, J.;Benachenhou, F.;Sperber, G.;Beemon, K.",2012,Oct 16,,0
218,Avian host spectrum of avipoxviruses,"A review is given of the occurrence of poxviruses in different bird species. The first publications appeared in Europe around 1850. At that time, pox as a definite disease entity was diagnosed on the basis of clinical signs, while later the detection of Bollinger's inclusion bodies (1877) allowed an aetiological diagnosis by microscopically visible viral aggregates. Virus isolation in embryonated chicken eggs and direct electron microscopy gained importance as diagnostic tools in the 1950s. Also briefly described are avipoxvirus taxonomy, virus characteristics, clinical signs, modes of prevention and diagnostic procedures. Of the approximately 9000 bird species, about 232 species in 23 orders have been reported to have acquired a natural poxvirus infection. However, it is likely that many more birds are susceptible to avipoxviruses.",,"Bolte, A. L.;Meurer, J.;Kaleta, E. F.",1999,Oct,,0
219,"Porcine Epidemic Diarrhea Virus and Discovery of a Recombinant Swine Enteric Coronavirus, Italy",Porcine epidemic diarrhea virus (PEDV) has been detected sporadically in Italy since the 1990s. We report the phylogenetic relationship of swine enteric coronaviruses collected in Italy during 2007-2014 and identify a drastic shift in PEDV strain variability and a new swine enteric coronavirus generated by recombination of transmissible gastroenteritis virus and PEDV.,"Animals;*Coronaviridae/ge [Genetics];Coronaviridae/ip [Isolation & Purification];Coronavirus Infections/vi [Virology];Italy;Phylogeny;*Porcine epidemic diarrhea virus/ge [Genetics];*Porcine epidemic diarrhea virus/ip [Isolation & Purification];RNA, Viral/ge [Genetics];Swine;Swine Diseases/vi [Virology];*Transmissible gastroenteritis virus/ge [Genetics];Transmissible gastroenteritis virus/ip [Isolation & Purification];0 (RNA, Viral)","Boniotti, M. B.;Papetti, A.;Lavazza, A.;Alborali, G.;Sozzi, E.;Chiapponi, C.;Faccini, S.;Bonilauri, P.;Cordioli, P.;Marthaler, D.",2016,Jan,,0
220,Sequence comparison of the L2 and S10 genes of bluetongue viruses from the United States and the People's Republic of China,"Bluetongue virus (BTV) infection of ruminants is endemic throughout much of the US and China. The S10 and a portion of the L2 gene segments of Chinese prototype strains of BTV serotypes 1, 2, 3, 4, 12, 15, and 16 were sequenced and compared to the same genes of prototype and field strains of BTV from the US. Phylogenetic analysis of the S10 gene segregated the Chinese viruses into a monophyletic group distinct from the US viruses, whereas similar analysis of the L2 gene segregated strains of BTV according to serotype, regardless of geographic origin. Copyright (C) 1999 Elsevier Science B.V.",article;Bluetongue orbivirus;bovine;China;controlled study;gene sequence;nonhuman;phylogeny;priority journal;sequence analysis;sheep;United States;virus characterization;virus gene,"Bonneau, K. R.;Zhang, N.;Zhu, J.;Zhang, F.;Li, Z.;Zhang, K.;Xiao, L.;Xiang, W.;MacLachlan, N. J.",1999,,10.1016/s0168-1702(99)00034-9,0
221,"Identification and phylogenetic analysis of orf viruses isolated from outbreaks in goats of Assam, a northeastern state of India","Two outbreaks of orf virus (ORFV) (a parapoxvirus) infection in goats, which occurred in Golaghat and Kamrup districts of Assam, a northeastern part of India, were investigated. The disease was diagnosed by standard virological and molecular techniques. The entire protein-coding region of B2L gene of two isolates were cloned and sequenced. Phylogenetic analysis based on B2L amino acid sequences showed that the ORFVs identified in these outbreaks were closely related to each other and both were closer to ORFV-Shahjahanpur 82/04 isolate from north India. The present study revealed that the precise characterization of the genomic region (B2L gene) might provide evidence for the genetic variation and movement of circulating ORFV strains in India. © Springer Science+Business Media, LLC 2012.",amino acid sequence;animal cell;animal tissue;article;B2L gene;contagious ecthyma;DNA sequence;epidemic;gene function;genetic code;genetic variability;goat;India;male;molecular epidemiology;nonhuman;nucleotide sequence;phylogeny;Poxviridae;priority journal;virus gene;virus identification;virus isolation;virus transmission,"Bora, D. P.;Barman, N. N.;Das, S. K.;Bhanuprakash, V.;Yogisharadhya, R.;Venkatesan, G.;Kumar, A.;Rajbongshi, G.;Khatoon, E.;Chakraborty, A.;Bujarbaruah, K. M.",2012,,10.1007/s11262-012-0740-y,0
222,Isolation and molecular characterization of Orf virus from natural outbreaks in goats of Assam,"Outbreaks of contagious ecthyma (caused by a Parapox virus) in goats were investigated in 6 districts of Assam, a north eastern state of India. Diagnosis of the disease was carried out employing both standard virological as well as molecular methods. Four representative isolates from different places were selected for phylogenetic analysis. The major envelop protein (B2L) of Orf virus was targeted for molecular analysis. The sequencing and phylogenetic analysis of the selected sequences at nucleotide level revealed that the Orf virus isolates were closely related to each other (97.6–100 %) and showed highest similarity to the Orf virus isolate 82/04 (98.4 %), reported from Shahjahanpur, India. The data will provide an insight in transmission of the virus from northern to North eastern part of the country.",B2L protein;unclassified drug;virus envelope protein;animal tissue;article;clinical examination;contagious ecthyma;counter immunoelectrophoresis;epidemic;goat;molecular diagnosis;nonhuman;Orf virus;Parapoxvirus;phylogeny;strain identification;virology;virus isolation;virus strain,"Bora, M.;Bora, D. P.;Barman, N. N.;Borah, B.;Bora, P. L.;Talukdar, A.;Tamuly, S.",2015,,10.1007/s13337-015-0255-y,0
223,Physicochemical and morphological relationships of some arthropod-borne viruses to bluetongue virus--a new taxonomic group. Physiocochemical and serological studies,,antigen;bile acid;lipid;solvent;animal;Arbovirus;article;classification;complement fixation test;cross reaction;drug effect;heat;immunology;LD50;microbiology;mouse;parasite vector;pH;Picornaviridae;Reoviridae;RNA virus;sheep;sheep disease,"Borden, E. C.;Shope, R. E.;Murphy, F. A.",1971,,,0
224,"Outbreaks of Neuroinvasive Astrovirus Associated with Encephalomyelitis, Weakness, and Paralysis among Weaned Pigs, Hungary","A large, highly prolific swine farm in Hungary had a 2-year history of neurologic disease among newly weaned (25- to 35-day-old) pigs, with clinical signs of posterior paraplegia and a high mortality rate. Affected pigs that were necropsied had encephalomyelitis and neural necrosis. Porcine astrovirus type 3 was identified by reverse transcription PCR and in situ hybridization in brain and spinal cord samples in 6 animals from this farm. Among tissues tested by quantitative RTPCR, the highest viral loads were detected in brain stem and spinal cord. Similar porcine astrovirus type 3 was also detected in archived brain and spinal cord samples from another 2 geographically distant farms. Viral RNA was predominantly restricted to neurons, particularly in the brain stem, cerebellum (Purkinje cells), and cervical spinal cord. Astrovirus was generally undetectable in feces but present in respiratory samples, indicating a possible respiratory infection. Astrovirus could cause common, neuroinvasive epidemic disease.",ACUTE RESPIRATORY-DISEASE;SHAKING MINK SYNDROME;ENCEPHALITIS;INFECTION;IDENTIFICATION;CATTLE;METAGENOMICS;REPLICATION;VA1/HMO-C;GENOTYPE,"Boros, A.;Albert, M.;Pankovics, P.;Biro, H.;Pesavento, P. A.;Phan, T. G.;Delwart, E.;Reuter, G.",2017,Dec,,0
225,Identification and complete genome characterization of a novel picornavirus in Turkey (Meleagris gallopavo),"Members of the family Picornaviridae are important pathogens of humans and animals, although compared with the thousands of known bird species (>10 000), only a few (n = 11) picornaviruses have been identified from avian sources. This study reports the metagenomic detection and complete genome characterization of a novel turkey picornavirus from faecal samples collected from eight turkey farms in Hungary. Using RT-PCR, both healthy (two of three) and affected (seven of eight) commercial turkeys with enteric and/or stunting syndrome were shown to be shedding viruses in seven (88 %) of the eight farms. The viral genome sequence (turkey/M176/2011/HUN; GenBank accession no. JQ691613) shows a high degree of amino acid sequence identity (96 %) to the partial P3 genome region of a picornavirus reported recently in turkey and chickens from the USA and probably belongs to the same species. In the P1 and P2 regions, turkey/M176/2011/HUN is related most closely to, but distinct from, the kobuviruses and turdivirus 1. Complete genome analysis revealed the presence of characteristic picornaviral amino acid motifs, a potential type II-like 5′ UTR internal ribosome entry site (first identified among avian-origin picornaviruses) and a conserved, 48 nt long 'barbell-like' structure found at the 3′ UTR of turkey/M176/2011/HUN and members of the picornavirus genera Avihepatovirus and Kobuvirus. The general presence of turkey picornavirus - a novel picornavirus species - in faecal samples from healthy and affected turkeys in Hungary and in the USA suggests the worldwide occurrence and endemic circulation of this virus in turkey farms. Further studies are needed to investigate the aetiological role and pathogenic potential of this picornavirus in food animals. © 2012 SGM.",3' untranslated region;5' untranslated region;amino acid sequence;Aphthovirus;article;Cardiovirus;Enterovirus;Erbovirus;farm animal;feces analysis;gene sequence;genome analysis;Hepatitis A virus;Hungary;internal ribosome entry site;Kobuvirus;metagenome;nonhuman;nucleotide sequence;Parechovirus;Picornaviridae;priority journal;protein motif;reverse transcription polymerase chain reaction;stunting syndrome;Teschovirus;turkey (bird);unindexed sequence;virus characterization;virus genome;virus identification;virus shedding,"Boros, A.;Nemes, C.;Pankovics, P.;Kapusinszky, B.;Delwart, E.;Reuter, G.",2012,,10.1099/vir.0.043224-0,1
226,Genetic characterization of a novel picornavirus in turkeys (Meleagris gallopavo) distinct from turkey galliviruses and megriviruses and distantly related to the members of the genus Avihepatovirus,"This study reports the metagenomic detection and complete genome characterization of a novel turkey picornavirus from faecal samples of healthy (1/3) and affected (6/8) commercial turkeys with enteric and/or stunting syndrome in Hungary. The virus was detected at seven of the eight farms examined. The turkey/M176-TuASV/2011/HUN genome (KC465954) was genetically different from the currently known picornaviruses of turkey origin (megriviruses and galliviruses), and showed distant phylogenetic relationship and common genomic features (e.g. uncleaved VP0 and three predicted and unrelated 2A polypeptides) to duck hepatitis A virus (DHAV) of the genus Avihepatovirus. The complete genome analysis revealed multiple distinct genome features like the presence of two in-tandem aphthovirus 2A-like sequence repeats with DxExNPG/P 'ribosomeskipping' sites (76 %, 23/30 amino acids identical), with the first aphthovirus 2A-like sequence being located at the end of the VP1 capsid protein (VP1/2A1 'ribosome-skipping' site). The phylogenetic analyses, low sequence identity (33, 32 and 36% amino acid identity in P1, P2 and P3 regions) to DHAV, and the type II-like internal ribosome entry site suggests that this turkey picornavirus is related to, but distinct from the genus Avihepatovirus and it could be the founding member of a novel Avihepatovirus sister-clade genus. This is the third, taxonomically highly distinct picornavirus clade identified from turkeys exhibiting varied symptoms. © 2013 SGM.",amino acid;capsid protein;genomic RNA;polypeptide;protein VP1;Aphthovirus;article;Avihepatovirus;cladistics;duck;Duck hepatitis A virus;duck hepatitis B;feces analysis;gallivirus;genus;Hepatitis A virus;human;megrivirus;metagenomics;nonhuman;nucleotide sequence;phylogeny;Picornaviridae;priority journal;ribosome;simple sequence repeat;Turkey (republic);viral genetics;virus detection;virus genome;virus strain,"Boros, A.;Nemes, C.;Pankovics, P.;Kapusinszky, B.;Delwart, E.;Reuter, G.",2013,,10.1099/vir.0.051797-0,1
227,A diarrheic chicken simultaneously co-infected with multiple picornaviruses: Complete genome analysis of avian picornaviruses representing up to six genera,"In this study all currently known chicken picornaviruses including a novel one (chicken phacovirus 1, KT880670) were identified by viral metagenomic and RT-PCR methods from a single specimen of a diarrheic chicken suffering from a total of eight picornavirus co-infections, in Hungary. The complete genomes of six picornaviruses were determined and their genomic and phylogenetic characteristics and UTR RNA structural models analyzed in details. Picornaviruses belonged to genera Sicinivirus (the first complete genome), Gallivirus, Tremovirus, Avisivirus and ""Orivirus"" (two potential genotypes). In addition, the unassigned phacoviruses were also detected in multiple samples of chickens in the USA. Multiple co-infections promote and facilitate the recombination and evolution of picornaviruses and eventually could contribute to the severity of the diarrhea in chicken, in one of the most important food sources of humans.",article;Avisivirus;chicken;controlled study;diarrhea;Gallivirus;genome analysis;Hungary;metagenomics;mixed infection;nonhuman;nucleotide sequence;Orivirus;phacovirus 1;phylogeny;Picornaviridae;picornavirus infection;priority journal;reverse transcription polymerase chain reaction;Sicinivirus;Tremovirus;untranslated region;virus genome;virus strain,"Boros, Á;Pankovics, P.;Adonyi, Á;Fenyvesi, H.;Day, J. M.;Phan, T. G.;Delwart, E.;Reuter, G.",2016,,10.1016/j.virol.2015.12.002,0
228,Genome characterization of a novel chicken picornavirus distantly related to the members of genus Avihepatovirus with a single 2A protein and a megrivirus-like 3' UTR,"The members of the genus Avihepatovirus and related picornaviruses (""Aalivius"") of ducks, turkey and chickens possess identical 2A peptide composition including three functionally unrelated 2A peptides which is a characteristic genome feature of these monophyletic avian picornaviruses. The complete genome of a novel picornavirus provisionally named Orivirus A1 (KM203656) from a cloacal sample of a 4-week-old diarrheic chicken (Gallus gallus domesticus) distantly related to members of genus Avihepatovirus was characterized. The study strain contains a type-II-like IRES, a single 2A protein of unknown function unrelated to the 2A proteins of avihepatoviruses and a long 3' untranslated region (UTR) with multiple repeated sequence motifs followed by an AUG-rich region. The repeated sequences of the 3' UTR show significant identity to the ""Unit A"" sequences of the phylogenetically distant megriviruses. The presence of a novel single 2A and the megrivirus-like ""Unit A"" motifs suggest multiple recombination events in the evolution of this novel picornavirus.",viral protein;3' untranslated region;article;Avihepatovirus;chicken;cloaca;gene sequence;genetic association;genetic code;genetic conservation;metagenomics;nonhuman;nucleotide motif;nucleotide sequence;Orivirus A1;phylogeny;Picornaviridae;promoter region;strain identification;unindexed sequence;virus genome;virus identification;virus strain,"Boros, Á;Pankovics, P.;Adonyi, Á;Phan, T. G.;Delwart, E.;Reuter, G.",2014,,10.1016/j.meegid.2014.10.025,0
229,Comparative complete genome analysis of chicken and Turkey megriviruses (family picornaviridae): long 3' untranslated regions with a potential second open reading frame and evidence for possible recombination,"UNLABELLED: Members of the family Picornaviridae consist of small positive-sense single-stranded RNA (+ssRNA) viruses capable of infecting various vertebrate species, including birds. One of the recently identified avian picornaviruses, with a remarkably long (>9,040-nucleotide) but still incompletely sequenced genome, is turkey hepatitis virus 1 (THV-1; species Melegrivirus A, genus Megrivirus), a virus associated with liver necrosis and enteritis in commercial turkeys (Meleagris gallopavo). This report presents the results of the genetic analysis of three complete genomes of megriviruses from fecal samples of chickens (chicken/B21-CHV/2012/HUN, GenBank accession no. KF961186, and chicken/CHK-IV-CHV/2013/HUN, GenBank accession no. KF961187) (Gallus gallus domesticus) and turkey (turkey/B407-THV/2011/HUN, GenBank accession no. KF961188) (Meleagris gallopavo) with the largest picornavirus genome (up to 9,739 nucleotides) so far described. The close phylogenetic relationship to THV-1 in the nonstructural protein-coding genome region and possession of the same internal ribosomal entry site type (IVB-like) suggest that the study strains belong to the genus Megrivirus. However, the genome comparisons revealed numerous unique variations (e.g., different numbers of potential 2A peptides, unusually long 3' genome parts with various lengths of a potential second open reading frame, and multiple repeating sequence motifs in the 3' untranslated region) and heterogeneous sequence relationships between the structural and nonstructural genome regions. These differences suggest the classification of chicken megrivirus-like viruses into a candidate novel species in the genus Megrivirus. Based on the different phylogenetic positions of chicken megrivirus-like viruses at the structural and nonstructural genome regions, the recombinant nature of these viruses is plausible. IMPORTANCE: The comparative genome analysis of turkey and novel chicken megriviruses revealed numerous unique genome features, e.g., up to four potential 2A peptides, unusually long 3' genome parts with various lengths containing a potential second open reading frame, multiple repeating sequence motifs, and heterogeneous sequence relationships (possibly due to a recombination event) between the structural and nonstructural genome regions. Our results could help us to better understand the evolution and diversity (in terms of sequence and genome layout) of picornaviruses.","*3' Untranslated Regions/ge [Genetics];Animals;Base Sequence;*Chickens/vi [Virology];Cluster Analysis;Computational Biology;DNA Primers/ge [Genetics];Feces/vi [Virology];Genome Components;*Genome, Viral/ge [Genetics];Metagenome/ge [Genetics];Molecular Sequence Data;Open Reading Frames/ge [Genetics];*Phylogeny;Picornaviridae/cl [Classification];*Picornaviridae/ge [Genetics];Recombination, Genetic/ge [Genetics];Reverse Transcriptase Polymerase Chain Reaction;Sequence Analysis, DNA;Species Specificity;*Turkeys/vi [Virology];0 (3' Untranslated Regions);0 (DNA Primers)","Boros, A.;Pankovics, P.;Knowles, N. J.;Nemes, C.;Delwart, E.;Reuter, G.",2014,Jun,,1
230,"Genomic analysis of a novel picornavirus from a migratory waterfowl, greater white-fronted goose (Anser albifrons)","The complete genome of goose picornavirus 1 (GPV-1) strain goose/NLSZK2/HUN/2013 (MF358731) was determined by RT-PCR and next-generation sequencing from a cloacal sample of a migratory waterfowl, greater white-fronted goose (Anser albifrons) in Hungary. The genome of GPV-1 shows an L-3-3-4 organization pattern with a 5'-terminal origin of replication (ORI) region, a type-IV IRES, and an Hbox/NC-type 2A protein. This virus showed the highest overall sequence identity to the members of the genus Kobuvirus, although the phylogenetic position of GPV-1 is different in the analyzed P1, 2C and 3CD phylogenetic trees, which further increases the diversity of known avian picornaviruses.",viral protein;amino acid sequence;animal;bird disease;classification;genetics;genomics;goose;high throughput sequencing;Hungary;isolation and purification;nucleotide sequence;phylogeny;Picornaviridae;picornavirus infection;population migration;sequence alignment;sequence homology;veterinary medicine;virology;virus genome,"Boros, Á;Pankovics, P.;Simmonds, P.;Kiss, T.;Phan, T. G.;Delwart, E.;Reuter, G.",2018,,10.1007/s00705-017-3696-3,0
231,Multiple divergent picobirnaviruses with functional prokaryotic Shine-Dalgarno ribosome binding sites present in cloacal sample of a diarrheic chicken,"Picobirnaviruses (PBVs) of family Picobirnaviridae have bisegmented (S1 and S2 segments), double-stranded RNA genomes. In this study a total of N = 12 complete chicken PBVs (ChPBV) segments (N = 5 of S1 and N = 7 of S2, Acc. Nos.: MH425579-90) were determined using viral metagenomic and RT-PCR techniques from a single cloacal sample of a diarrheic chicken. The identified ChPBV segments are unrelated to each other and distant from all of the currently known PBVs. In silico sequence analyses revealed the presence of conserved prokaryotic Shine-Dalgarno-like (SD-like) sequences upstream of the three presumed open reading frames (ORFs) of the S1 and a single presumed ORF of the S2 segments. According to the results of expression analyses in E. coli using 6xHis-tagged recombinant ChPBV segment 1 construct and Western blot these SD-like sequences are functional in vivo suggesting that S1 of study PBVs can contain three ORFs and supporting the bacteriophage-nature of PBVs.",animal tissue;article;bacteriophage;binding site;chicken;cloaca;controlled study;gene expression;genetic variability;in vivo study;limit of quantitation;metagenomics;next generation sequencing;nonhuman;open reading frame;phylogeny;Picobirnavirus;priority journal;reverse transcription polymerase chain reaction;ribosome;virogenesis;Western blotting,"Boros, Á;Polgár, B.;Pankovics, P.;Fenyvesi, H.;Engelmann, P.;Phan, T. G.;Delwart, E.;Reuter, G.",2018,,10.1016/j.virol.2018.09.008,1
232,Characterization of neutralization sites on the circulating variant of swine vesicular disease virus (SVDV): A new site is shared by SVDV and the related coxsackie B5 virus,"Using a panel of new monoclonal antibodies (mAbs), five neutralizing, conformation-dependent sites have been identified on the antigenic variant of swine vesicular disease virus (SVDV) circulating currently. In studies on the antigenic conservation of these sites, the four antigenic/genetic groups of SVDV described showed distinguishable patterns, confirming this classification. By sequencing mAb-resistant mutants, the five sites have been mapped precisely and localized on a three-dimensional model of the SVDV capsid. All were found to be orientated, to a different extent, towards the external surface of the capsid. Three of the five sites, located in VP1, VP2 and VP3, correspond to epitopes identified previously in historic isolates as sites 1, 2a and 3b, respectively. Another site, site IV, which maps to position 258 of VP1, corresponds to an epitope reported recently and is described in this study to be specific for isolates of the most recent antigenic group of SVDV. A fifth site is described for the first time and corresponds to the unique neutralizing site that is common to both SVDV and coxsackie B5 virus; it maps to positions 95 and 98 of VP1, but may also include positions nearby that belong to site 1 on the BC-loop of VP1, suggesting the classification of site Ia. These results may have useful diagnostic and epidemiological applications, since mAbs to the new conserved site Ia provide universal reagents for SVDV detection systems, while the specificity of mAbs to site IV make them unique markers for the most recent strains of SVDV.",epitope;monoclonal antibody;protein VP1;virus antibody;virus antigen;viral protein;antigenic variation;article;conformational transition;controlled study;Enterovirus;diagnostic test;diagnostic value;disease marker;epitope mapping;gene sequence;nonhuman;Picornaviridae;priority journal;protein conformation;protein localization;pig;virus capsid;virus characterization;virus classification;virus detection;virus infection;virus isolation;virus mutant;virus neutralization;virus strain,"Borrego, B.;Carra, E.;García-Ranea, J. A.;Brocchi, E.",2002,,,0
233,The role of viral population diversity in adaptation of bovine coronavirus to new host environments,"The high mutation rate of RNA viruses enables a diverse genetic population of viral genotypes to exist within a single infected host. In-host genetic diversity could better position the virus population to respond and adapt to a diverse array of selective pressures such as host-switching events. Multiple new coronaviruses, including SARS, have been identified in human samples just within the last ten years, demonstrating the potential of coronaviruses as emergent human pathogens. Deep sequencing was used to characterize genomic changes in coronavirus quasispecies during simulated host-switching. Three bovine nasal samples infected with bovine coronavirus were used to infect human and bovine macrophage and lung cell lines. The virus reproduced relatively well in macrophages, but the lung cell lines were not infected efficiently enough to allow passage of non lab-adapted samples. Approximately 12 kb of the genome was amplified before and after passage and sequenced at average coverages of nearly 950x(454 sequencing) and 38,000x(Illumina). The consensus sequence of many of the passaged samples had a 12 nucleotide insert in the consensus sequence of the spike gene, and multiple point mutations were associated with the presence of the insert. Deep sequencing revealed that the insert was present but very rare in the unpassaged samples and could quickly shift to dominate the population when placed in a different environment. The insert coded for three arginine residues, occurred in a region associated with fusion entry into host cells, and may allow infection of new cell types via heparin sulfate binding. Analysis of the deep sequencing data indicated that two distinct genotypes circulated at different frequency levels in each sample, and support the hypothesis that the mutations present in passaged strains were ""selected"" from a pre-existing pool rather than through de novo mutation and subsequent population fixation.","Amino Acid Sequence;Animals;*Cattle/vi [Virology];Cell Line;Consensus Sequence;*Coronavirus Infections/ve [Veterinary];*Coronavirus Infections/vi [Virology];Coronavirus, Bovine/ch [Chemistry];*Coronavirus, Bovine/ge [Genetics];Coronavirus, Bovine/ph [Physiology];Genetic Variation;Genome, Viral;High-Throughput Nucleotide Sequencing;Humans;Models, Molecular;Molecular Sequence Data;Mutation Rate;Phylogeny;Point Mutation;Protein Structure, Tertiary;Sequence Alignment;Viral Proteins/ch [Chemistry];Viral Proteins/ge [Genetics];Virus Internalization;0 (Viral Proteins)","Borucki, M. K.;Allen, J. E.;Chen-Harris, H.;Zemla, A.;Vanier, G.;Mabery, S.;Torres, C.;Hullinger, P.;Slezak, T.",2013,,,0
234,Capripoxvirus-vectored vaccines against livestock diseases in Africa,"Five different viral diseases of livestock, lumpy skin disease (LSD), sheep pox (SPP), goat pox (GTP), Rift Valley fever (RVF) and peste des petits ruminants (PPR), circulate in the same regions of Africa, imposing a major burden on economic activity and public health. While commercial vaccines against these viruses are available, the cost of implementing regular vaccination regimens against multiple diseases is prohibitive for most African farmers. A single, affordable multivalent vaccine that simultaneously protects against all 5 diseases would therefore be of significant benefit to the livestock sector in Africa. It could also serve as a platform for the development of new vaccines of significance to other developing countries around the world. In this paper, we present an overview of the economic importance of livestock in Africa, the pathogens responsible for RVF, PPR, SPP, GTP and LSD and the vaccination strategies currently used to combat them. We then review experience with the development of attenuated capripoxviruses as vaccines against LSD, SPP and GTP and of recombinant capripoxvirus-vectored vaccines against RVF and PPR. We conclude the article by presenting the rationale for a single, multivalent capripoxvirus-vectored vaccine that would protect against all 5 diseases of livestock, and describe the approach being taken by a consortium of Canadian and South African researchers to develop such a vaccine. Crown Copyright © 2013 Published by Elsevier B.V. All rights reserved.",arasur 87 vaccine;av41 vaccine;clone 13 vaccine;coimbatore 97;gorgan vaccine;inactivated virulent RVFV vaccine;ks 1 vaccine;mysore vaccine;nigerian 71 vaccine;nigerian 75 vaccine;O240 vaccine;onderstepoort vaccine;recombinant vaccine;rm 65 vaccine;romanian vaccine;smithburn vaccine;sungri 96 vaccine;unclassified drug;virus vaccine;virus vector;Africa;agricultural worker;bluetongue;Bluetongue orbivirus;bovid;Capripoxvirus;Rinderpest virus;developing country;goatpox;immunogenicity;livestock;lumpy skin disease;Measles virus;nonhuman;peste des petits ruminants;priority journal;public health problem;review;Rift Valley fever;Rift Valley fever virus;rinderpest;sheeppox;vaccination;Vaccinia virus;virus classification;virus infection;virus recombinant,"Boshra, H.;Truong, T.;Nfon, C.;Gerdts, V.;Tikoo, S.;Babiuk, L. A.;Kara, P.;Mather, A.;Wallace, D.;Babiuk, S.",2013,,10.1016/j.antiviral.2013.02.016,0
235,Molecular genetics analyses of varicella-zoster clinical isolates (VZV),"Varicella-zoster virus (VZV) is classified into the alpha-herpesvirus subfamily. The VZV genome is extremely conserved. Molecular genetics brings more information about evolutionary processes of VZV, mechanisms of infectious processes of VZV and also about VZV pathogenesis. VZV causes chicken pox (varicella) in childhood and can also reactivate later in life causing shingles (herpes zoster) in the same individual. In both diseases it is the same kind of virus. In latest years the molecular genetic analysis methods (whole genome sequencing, microarray techniques) help to collect more detailed information about VZV genome, including information about genetic recombination.",chickenpox;childhood;gene sequence;genetic conservation;genetic recombination;human;microarray analysis;molecular genetics;nonhuman;review;Varicella zoster virus;virus genome;virus isolation;virus pathogenesis,"Boštíková, V.;Boštík, P.",2012,,,0
236,Indication of Cross-Species Transmission of Astrovirus Associated with Encephalitis in Sheep and Cattle,We report the identification of a neurotropic astrovirus associated with encephalitis in a sheep. This virus is genetically almost identical to an astrovirus recently described in neurologically diseased cattle. The similarity indicates that astroviruses of the same genotype may cause encephalitis in different species.,"Animals;Astroviridae/cl [Classification];*Astroviridae/ge [Genetics];Astroviridae/ip [Isolation & Purification];Astroviridae Infections/ep [Epidemiology];Astroviridae Infections/pa [Pathology];Astroviridae Infections/tm [Transmission];*Astroviridae Infections/ve [Veterinary];Brain/pa [Pathology];Brain/vi [Virology];Cattle;Cattle Diseases/ep [Epidemiology];Cattle Diseases/pa [Pathology];*Cattle Diseases/tm [Transmission];Encephalitis, Viral/ep [Epidemiology];Encephalitis, Viral/pa [Pathology];Encephalitis, Viral/tm [Transmission];*Encephalitis, Viral/ve [Veterinary];*Genome, Viral;Host Specificity;Humans;Immunohistochemistry;Phylogeny;Sheep;Sheep Diseases/ep [Epidemiology];Sheep Diseases/pa [Pathology];*Sheep Diseases/tm [Transmission];Switzerland/ep [Epidemiology]","Boujon, C. L.;Koch, M. C.;Wuthrich, D.;Werder, S.;Jakupovic, D.;Bruggmann, R.;Seuberlich, T.",2017,09,,1
237,"Genetic characterization and codon usage bias of full-length Hepatitis E virus sequences shed new lights on genotypic distribution, host restriction and genome evolution","Hepatitis E virus (HEV) is present in different species and ecological niches. It has been divided into 4 major mammalian genotypes. In this study, 3 new full-length genomes of swine HEV were sequenced and the results did not reveal any particular host determinant in comparison with human isolates belonging to the same genotype. Nucleotide composition and codon usage bias were determined to characterize HEV host restriction and genome evolution. Peculiar nucleotide bias was observed for A and C nucleotides in all HEV genotypes. Apart from the ORF1 hypervariable region and the ORF2/3 overlapping region, no nucleotide bias was observed between the 3 codon positions. CpG dinucleotides were also shown to be under-represented in HEV as in most RNA viruses. The effective number of codon used in HEV genome was high, indicating a lack of codon bias. Correspondence analysis of the relative synonymous codon usage was performed and demonstrated that evolution of HEV is not driven by geographical or host factors, but is representative of HEV phylogeny. These results confirm that HEV genome evolution is mainly based on mutational pressure. Natural selection, for instance involving fine-tuning translation kinetics and escape from the host immune system, may also play a role in shaping the HEV genome, particularly in the ORF1 hypervariable region and the ORF2/3 overlapping region. These regions might be involved in host restriction. Finally this study revealed the need to re-evaluate the possible subtyping classification. © 2012 Elsevier B.V.",CpG dinucleotide;dinucleotide;unclassified drug;article;codon usage;controlled study;gene sequence;genetic analysis;genotype;Hepatitis E virus;immune system;molecular evolution;natural selection;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;sequence analysis;pig;virus genome;virus isolation,"Bouquet, J.;Cherel, P.;Pavio, N.",2012,,10.1016/j.meegid.2012.07.021,0
238,Identical consensus sequence and conserved genomic polymorphism of hepatitis E virus during controlled interspecies transmission,"High-throughput sequencing of bile and feces from two pigs experimentally infected with human hepatitis E virus (HEV) of genotype 3f revealed the same full-length consensus sequence as in the human sample. Twenty-nine percent of polymorphic sites found in HEV from the human sample were conserved throughout the infection of the heterologous host. The interspecies transmission of HEV quasispecies is the result of a genomic negative-selection pressure on random mutations which can be deleterious to the viral population. HEV intrahost nucleotide diversity was found to be in the lower range of other human RNA viruses but correlated with values found for zoonotic viruses. HEV transmission between humans and pigs does not seem to be modulated by host-specific mutations, suggesting that adaptation is mainly regulated by ecological drivers. © 2012, American Society for Microbiology.",RNA polymerase;virus RNA;3' untranslated region;5' untranslated region;animal experiment;animal model;article;consensus sequence;controlled study;experimental pig;gene frequency;genetic association;genetic variability;genome analysis;Hepatitis E virus;high throughput sequencing;host pathogen interaction;human;Human immunodeficiency virus;mutational analysis;nonhuman;nucleotide sequence;open reading frame;priority journal;sequence analysis;single nucleotide polymorphism;virus genome;virus transmission;West Nile virus,"Bouquet, J.;Cheval, J.;Rogée, S.;Pavio, N.;Eloit, M.",2012,,10.1128/jvi.06843-11,0
239,"Whole-genome, deep pyrosequencing analysis of a duck influenza A virus evolution in swine cells","We studied the sub-population level evolution of a duck influenza A virus isolate during passage in swine tracheal cells. The complete genomes of the A/mallard/Netherlands/10-Nmkt/1999 strain and its swine cell-passaged descendent were analysed by 454 pyrosequencing with coverage depth ranging from several hundred to several thousand reads at any point. This allowed characterization of defined minority sub-populations of gene segments 2, 3, 4, 5, 7, and 8 present in the original isolate. These minority sub-populations ranged between 9.5% (for segment 2) and 46% (for segment 4) of their respective gene segments in the parental stock. They were likely contributed by one or more viruses circulating within the same area, at the same period and in the same or a sympatric host species. The minority sub-populations of segments 3, 4, and 5 became extinct upon viral passage in swine cells, whereas the minority sub-populations of segments 2, 7 and 8 completely replaced their majority counterparts. The swine cell-passaged virus was therefore a three-segment reassortant and also harboured point mutations in segments 3 and 4. The passaged virus was more homogenous than the parental stock, with only 17 minority single nucleotide polymorphisms present above 5% frequency across the whole genome. Though limited here to one sample, this deep sequencing approach highlights the evolutionary versatility of influenza viruses whereby they exploit their genetic diversity, predilection for mixed infection and reassortment to adapt to a new host environmental niche.","Animals;Animals, Wild;Cell Line;Coinfection/vi [Virology];Ducks;*Evolution, Molecular;High-Throughput Nucleotide Sequencing;Influenza A virus/cl [Classification];*Influenza A virus/ge [Genetics];*Influenza in Birds/vi [Virology];Polymorphism, Single Nucleotide;RNA, Viral/an [Analysis];RNA, Viral/ch [Chemistry];RNA, Viral/ge [Genetics];Reverse Transcriptase Polymerase Chain Reaction;*Sequence Analysis, DNA/mt [Methods];Swine;0 (RNA, Viral)","Bourret, V.;Croville, G.;Mariette, J.;Klopp, C.;Bouchez, O.;Tiley, L.;Guerin, J. L.",2013,Aug,,0
240,Full-genome basedmolecular characterization of encephalitis-associated bovine astroviruses,"Novel types of astrovirus have been identified recently in association with neurological disease in cattle. Among those viruses is bovine astrovirus CH13 (BoAstV CH13) that has been identified in Switzerland in a cow with encephalitis. Molecular testing by a combination of reverse transcription (RT-) PCR and in situ hybridization (ISH) indicated that astrovirus infection accounts for around one quarter of viral encephalitis cases of unknown etiology in cattle. Yet, it remained to be explored whether these animals were infected by BoAstV CH13 or other astrovirus species. In the present study we sequenced the entire astrovirus genome in brain tissues of eight RT-PCR and/or ISH positive cattle. Phylogenetic comparison of the genomic RNA and the encoded non-structural and structural proteins revealed that all these astrovirus strains were very similar to BoAstV CH13 as well as to a bovine encephalitis strain reported from the USA (BoAstV NeuroS1), and clearly distinct from other previously reported astroviruses. Conserved 5' and 3' untranslated regions (UTRs) were predicted to display distinct secondary RNA structures, which likely play a role in viral RNA replication and/or protein translation. Based on these data we propose that BoAstV CH13/NeuroS1 represents a new genotype species within the genus Mammastrovirus. The high degree of similarity between the strains and their relative distance to other genotype species suggest that during evolution some astroviruses acquired factors that specifically contribute to neuroinvasion. (C) 2016 The Authors. Published by Elsevier B.V.",Encephalitis;Cattle;Astrovirus;Epidemiology;Neurology;NONSUPPURATIVE ENCEPHALITIS;CATTLE;INFECTION;METAGENOMICS;VIRUSES,"Bouzalas, I. G.;Wuthrich, D.;Selimovic-Hamza, S.;Drogemuller, C.;Bruggmann, R.;Seuberlich, T.",2016,Oct,,1
241,Neurotropic astrovirus in cattle with nonsuppurative encephalitis in Europe,"Encephalitis is a frequently diagnosed condition in cattle with neurological diseases. Many affected animals present with a non-suppurative inflammatory reaction pattern in the brain. While this pattern supports a viral etiology, the causative pathogen remains unknown in a large proportion of cases. Using viral metagenomics, we identified an astrovirus (bovine astrovirus [BoAstV]-CH13) in the brain of a cow with nonsuppurative encephalitis. Additionally, BoAstV RNA was detected with reverse transcription-PCR and in situ hybridization in about one fourth (5/22 animals) of cattle with nonsuppurative encephalitis of unknown etiology. Viral RNA was found primarily in neurons and at the site of pathology. These findings support the notion that BoAstV infection is a common cause of encephalitis in cattle. Phylogenetically, BoAstV-CH13 was closely related to rare astrovirus isolates from encephalitis cases in animals and a human patient. Future research needs to be directed toward the pathogenic mechanisms, epidemiology, and potential cross-species transmission of these neurotropic astroviruses. Copyright © 2014, American Society for Microbiology. All Rights Reserved.",animal tissue;article;Astroviridae;astrovirus infection;bovine astrovirus CH13;cattle disease;controlled study;disease association;encephalitis;Europe;in situ hybridization;metagenomics;molecular pathology;nonhuman;nonsuppurative encephalitis;nucleotide sequence;phylogeny;priority journal;retrospective study;reverse transcription polymerase chain reaction;sequence analysis;virus detection;virus identification,"Bouzalas, I. G.;Wüthrich, D.;Walland, J.;Drögemüller, C.;Zurbriggen, A.;Vandevelde, M.;Oevermann, A.;Bruggmann, R.;Seuberlich, T.",2014,,10.1128/jcm.01195-14,1
242,A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine …,,,"Bovo, S.;Mazzoni, G.;Ribani, A.;Utzeri, V. J.;Bertolini, F.",2017,,,0
243,A viral metagenomic approach on a nonmetagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections,"Shot-gun next generation sequencing (NGS) on whole DNA extracted from specimens collected from mammals often produces reads that are not mapped (i.e. unmapped reads) on the host reference genome and that are usually discarded as by-products of the experiments. In this study, we mined Ion Torrent reads obtained by sequencing DNA isolated from archived blood samples collected from 100 performance tested Italian Large White pigs. Two reduced representation libraries were prepared from two DNA pools constructed each from 50 equimolar DNA samples. Bioinformatic analyses were carried out to mine unmapped reads on the reference pig genome that were obtained from the two NGS datasets. In silico analyses included read mapping and sequence assembly approaches for a viral metagenomic analysis using the NCBI Viral Genome Resource. Our approach identified sequences matching several viruses of the Parvoviridae family: porcine parvovirus 2 (PPV2), PPV4, PPV5 and PPV6 and porcine bocavirus 1-H18 isolate (PBoV1-H18). The presence of these viruses was confirmed by PCR and Sanger sequencing of individual DNA samples. PPV2, PPV4, PPV5, PPV6 and PBoV1-H18 were all identified in samples collected in 1998-2007, 1998-2000, 1997-2000, 1998-2004 and 2003, respectively. For most of these viruses (PPV4, PPV5, PPV6 and PBoV1-H18) previous studies reported their first occurrence much later (from 5 to more than 10 years) than our identification period and in different geographic areas. Our study provided a retrospective evaluation of apparently asymptomatic parvovirus infected pigs providing information that could be important to define occurrence and prevalence of different parvoviruses in South Europe. This study demonstrated the potential of mining NGS datasets non-originally derived by metagenomics experiments for viral metagenomics analyses in a livestock species.",article;bioinformatics;controlled study;limit of detection;limit of quantitation;metagenomics;next generation sequencing;nonhuman;nucleotide sequence;polymerase chain reaction;Porcine parvovirus;porcine parvovirus 1 H18;porcine parvovirus 2;porcine parvovirus 4;porcine parvovirus 5;porcine parvovirus 6;retrospective study;virus identification;virus isolation;virus strain,"Bovo, S.;Mazzoni, G.;Ribani, A.;Utzeri, V. J.;Bertolini, F.;Schiavo, G.;Fontanesi, L.",2017,,10.1371/journal.pone.0179462,0
244,"Molecular characterization of menangle virus, a novel paramyxovirus which infects pigs, fruit bats, and humans","Menangle virus (MenV), isolated in August 1997 following an outbreak of reproductive disease in a piggery in New South Wales, is the second previously unclassified member of the family Paramyxoviridae to be identified in Australia since 1994. Similar to Hendra virus (HeV), MenV appears to be a virus of fruit bats (flying foxes) in the genus Pteropus. No serological cross-reactivity was detected between MenV and other known paramyxoviruses and to facilitate virus classification a cDNA subtraction method was used to obtain viral-specific cDNA from MenV-infected cells. Cloning and sequencing of the products enabled the entire sequences of the NP, P/V, M, F, and HN genes to be determined. Comparison of the nucleotide and deduced amino acid sequences for each gene with members of the family Paramyxoviridae, determination of the P gene mRNA editing strategy, and phylogenetic analyses confirmed that MenV is a new member of the genus Rubulavirus. However the deduced protein sequence of MenV HN exhibited only limited sequence homology when compared with attachment proteins of other paramyxoviruses. Key differences within the amino acid residues considered important determinants of neuraminidase activity suggest MenV HN is unlikely to possess the same degree of neuraminidase activity characteristic of other rubulavirus and respirovirus HN proteins. © 2001 Academic Press.",complementary DNA;sialidase;virus DNA;article;Australia;bat;epidemic;Hendra virus;Menangle virus;molecular cloning;nonhuman;nucleotide sequence;Paramyxoviridae;phylogeny;priority journal;sequence analysis;virus genome,"Bowden, T. R.;Westenberg, M.;Wang, L. F.;Eaton, B. T.;Boyle, D. B.",2001,,10.1006/viro.2001.0893,0
245,Mechanism of Action of A238L: An Immune Evasion Protein of African Swine Fever Virus,,,"Bowick, G.",2004,,,0
246,Analysis of the differential host cell nuclear proteome induced by attenuated and virulent hemorrhagic arenavirus infection,"Arenaviruses are important emerging pathogens and include a number of hemorrhagic fever viruses classified as NIAID category A priority pathogens and CDC potential biothreat agents. Infection of guinea pigs with the New World arenavirus Pichindé virus (PICV) has been used as a biosafety level 2 model for the Lassa virus. Despite continuing research, little is known about the molecular basis of pathogenesis, and this has hindered the design of novel antiviral therapeutics. Modulation of the host response is a potential strategy for the treatment of infectious diseases. We have previously investigated the global host response to attenuated and lethal arenavirus infections by using high-throughput immunoblotting and kinomics approaches. In this report, we describe the differential nuclear proteomes of a murine cell line induced by mock infection and infection with attenuated and lethal variants of PICV, investigated by using two-dimensional gel electrophoresis. Spot identification using tandem mass spectrometry revealed the involvement of a number of proteins that regulate inflammation via potential modulation of NF-κB activity and of several heterogeneous nuclear ribonuclear proteins. Pathway analysis revealed a potential role for transcription factor XBP-1, a transcription factor involved in major histocompatibility complex II (MHC-II) expression; differential DNA-binding activity was revealed by electrophoretic mobility shift assay, and differences in surface MHC-II expression were seen following PICV infection. These data are consistent with the results of several previous studies and highlight potential differences between transcriptional and translational regulation. This study provides a number of differentially expressed targets for further research and suggests that key events in pathogenesis may be established early in infection. Copyright © 2009, American Society for Microbiology. All Rights Reserved.",immunoglobulin enhancer binding protein;major histocompatibility antigen class 2;nuclear protein;nuclear RNA;proteome;X box binding protein 1;animal cell;article;DNA binding;enzyme activity;gel mobility shift assay;inflammation;mouse;nonhuman;pathogenesis;Pichinde virus;priority journal;protein expression;tandem mass spectrometry;transcription regulation;translation regulation;two dimensional gel electrophoresis;virus infection,"Bowick, G. C.;Spratt, H. M.;Hogg, A. E.;Endsley, J. J.;Wiktorowicz, J. E.;Kurosky, A.;Luxon, B. A.;Gorenstein, D. G.;Herzog, N. K.",2009,,10.1128/jvi.01281-08,0
247,Genomic sequences of australian bluetongue virus prototype serotypes reveal global relationships and possible routes of entry into Australia,"Bluetongue virus (BTV) is transmitted by biting midges (Culicoides spp.). It causes disease mainly in sheep and occasionally in cattle and other species. BTV has spread into northern Europe, causing disease in sheep and cattle. The introduction of new serotypes, changes in vector species, and climate change have contributed to these changes. Ten BTV serotypes have been isolated in Australia without apparent associated disease. Simplified methods for preferential isolation of double-stranded RNA (dsRNA) and template preparation enabled high-throughput sequencing of the 10 genome segments of all Australian BTV prototype serotypes. Phylogenetic analysis reinforced the Western and Eastern topotypes previously characterized but revealed unique features of several Australian BTVs. Many of the Australian BTV genome segments (Seg-) were closely related, clustering together within the Eastern topotypes. A novel Australian topotype for Seg-5 (NS1) was identified, with taxa spread across several serotypes and over time. Seg-1, -2, -3, -4, -6, -7, -9, and -10 of BTV_2_AUS_2008 were most closely related to the cognate segments of viruses from Taiwan and Asia and not other Australian viruses, supporting the conclusion that BTV_2 entered Australia recently. The Australian BTV_15_AUS_1982 prototype was revealed to be unusual among the Australian BTV isolates, with Seg-3 and -8 distantly related to other BTV sequences from all serotypes. © 2012, American Society for Microbiology.",double stranded RNA;genomic DNA;nonstructural protein 1;nonstructural protein 2;nonstructural protein 3;protein VP1;protein VP2;protein VP3;protein VP4;protein VP5;protein VP6;protein VP7;unclassified drug;viral protein;animal cell;article;Australia;Bluetongue orbivirus;climate change;gene sequence;genome analysis;high throughput sequencing;molecular phylogeny;nonhuman;nucleotide sequence;priority journal;sequence analysis;sequence homology;serotype;virus genome;virus isolation;virus transmission,"Boyle, D. B.;Bulach, D. M.;Amos-Ritchie, R.;Adams, M. M.;Walker, P. J.;Weir, R.",2012,,10.1128/jvi.00182-12,0
248,The evolution of human influenza A viruses from 1999 to 2006: A complete genome study,"Background: Knowledge about the complete genome constellation of seasonal influenza A viruses from different countries is valuable for monitoring and understanding of the evolution and migration of strains. Few complete genome sequences of influenza A viruses from Europe are publicly available at the present time and there have been few longitudinal genome studies of human influenza A viruses. We have studied the evolution of circulating human H3N2, H1N1 and H1N2 influenza A viruses from 1999 to 2006, we analysed 234 Danish human influenza A viruses and characterised 24 complete genomes. Results: H3N2 was the prevalent strain in Denmark during the study period, but H1N1 dominated the 2000-2001 season. H1N2 viruses were first observed in Denmark in 2002-2003. After years of little genetic change in the H1N1 viruses the 2005-2006 season presented H1N1 of greater variability than before. This indicates that H1N1 viruses are evolving and that H1N1 soon is likely to be the prevalent strain again. Generally, the influenza A haemagglutinin (HA) of H3N2 viruses formed seasonal phylogenetic clusters. Different lineages co-circulating within the same season were also observed. The evolution has been stochastic, influenced by small ""jumps"" in genetic distance rather than constant drift, especially with the introduction of the Fujian-like viruses in 2002-2003. Also evolutionary stasis-periods were observed which might indicate well fit viruses. The evolution of H3N2 viruses have also been influenced by gene reassortments between lineages from different seasons. None of the influenza genes were influenced by strong positive selection pressure. The antigenic site B in H3N2 HA was the preferred site for genetic change during the study period probably because the site A has been masked by glycosylations. Substitutions at CTL-epitopes in the genes coding for the neuraminidase (NA), polymerase acidic protein (PA), matrix protein 1 (M1), non-structural protein 1 (NS1) and especially the nucleoprotein (NP) were observed. The N-linked glycosylation pattern varied during the study period and the H3N2 isolates from 2004 to 2006 were highly glycosylated with ten predicted sequons in HA, the highest amount of glycosylations observed in this study period. Conclusion: The present study is the first to our knowledge to characterise the evolution of complete genomes of influenza A H3N2, H1N1 and H1N2 isolates from Europe over a time period of seven years from 1999 to 2006. More precise knowledge about the circulating strains may have implications for predicting the following season strains and thereby better matching the vaccine composition.",EMBRYONATED CHICKEN EGGS;PEPTIDE BINDING MOTIF;AMINO-ACID SITES;T-CELL EPITOPES;H3N2 VIRUSES;ADAMANTANE RESISTANCE;REASSORTANT;VIRUSES;POSITIVE SELECTION;ANTIGENIC DRIFT;HEMAGGLUTININ,"Bragstad, K.;Nielsen, L. P.;Fomsgaard, A.",2008,Mar,,0
249,Genomic evolution of porcine reproductive and respiratory syndrome virus (PRRSV) isolates revealed by deep sequencing,"Most studies on PRRSV evolution have been limited to a particular region of the viral genome. A thorough genome-wide understanding of the impact of different mechanisms on shaping PRRSV genetic diversity is still lacking. To this end, deep sequencing was used to obtain genomic sequences of a diverse set of 16 isolates from a region of Hong Kong with a complex PRRSV epidemiological record. Genome assemblies and phylogenetic typing indicated the co-circulation of strains of both genotypes (type 1 and type 2) with varying Nsp2 deletion patterns and distinct evolutionary lineages (""High Fever""-like and local endemic type). Recombination analyses revealed genomic breakpoints in structural and non-structural regions of genomes of both genotypes with evidence of many recombination events originating from common ancestors. Additionally, the high fold of coverage per nucleotide allowed the characterization of minor variants arising from the quasispecies of each strain. Overall, 0.56-2.83% of sites were found to be polymorphic with respect to cognate consensus genomes. The distribution of minor variants across each genome was not uniform indicating the influence of selective forces. Proportion of variants capable of causing an amino acid change in their respective codons ranged between 25-67% with many predicted to be non-deleterious. Low frequency deletion variants were also detected providing one possible mechanism for their sudden emergence as cited in previous reports.","Animals;*Biological Evolution;*Genome, Viral;*Genomics;*High-Throughput Nucleotide Sequencing/mt [Methods];Phylogeny;*Porcine Reproductive and Respiratory Syndrome/ge [Genetics];*Porcine Reproductive and Respiratory Syndrome/vi [Virology];Porcine respiratory and reproductive syndrome virus/cl [Classification];Porcine respiratory and reproductive syndrome virus/ge [Genetics];*Porcine respiratory and reproductive syndrome virus/ip [Isolation & Purification];RNA, Messenger/ge [Genetics];Real-Time Polymerase Chain Reaction;Reverse Transcriptase Polymerase Chain Reaction;Swine;0 (RNA, Messenger)","Brar, M. S.;Shi, M.;Hui, R. K.;Leung, F. C.",2014,,,0
250,Border disease in cattle,"Within the family Flaviviridae, viruses within the genus Pestivirus, such as Border disease virus (BDV) of sheep, can cause great economic losses in farm animals. Originally, the taxonomic classification of pestiviruses was based on the host species they were isolated from, but today, it is known that many pestiviruses exhibit a broad species tropism. This review provides an overview of BDV infection in cattle. The clinical, hematological and pathological–anatomical findings in bovines that were transiently or persistently infected with BDV largely resemble those in cattle infected with the closely related pestivirus bovine viral diarrhoea virus (BVDV). Accordingly, the diagnosis of BDV infection can be challenging, as it must be differentiated from various pestiviruses in cattle. The latter is very relevant in countries with control programs to eradicate BVDV in Bovidae, as in most circumstances, pestivirus infections in sheep, which act as reservoir for BDV, are not included in the eradication scheme. Interspecies transmission of BDV between sheep and cattle occurs regularly, but BDV in cattle appears to be of minor general importance. Nevertheless, BDV outbreaks at farm or local level can be very costly.",virus vaccine;blood examination;border disease;Bovine viral diarrhea virus 1;cattle disease;cattle farming;clinical assessment;epidemic;epidemiology;Flaviviridae;health program;human;infection control;infection prevention;morphology;pathological anatomy;persistent virus infection;Pestivirus infection;review;viral clearance;virus carrier;virus classification;virus transmission,"Braun, U.;Hilbe, M.;Peterhans, E.;Schweizer, M.",2019,,10.1016/j.tvjl.2019.01.006,0
251,"Swine Influenza Virus (H1N2) Characterization and Transmission in Ferrets, Chile","Phylogenetic analysis of the influenza hemagglutinin gene (HA) has suggested that commercial pigs in Chile harbor unique human seasonal H1-like influenza viruses, but further information, including characterization of these viruses, was unavailable. We isolated influenza virus (H1N2) from a swine in a backyard production farm in Central Chile and demonstrated that the HA gene was identical to that in a previous report. Its HA and neuraminidase genes were most similar to human H1 and N2 viruses from the early 1990s and internal segments were similar to influenza A(H1N1)pdm09 virus. The virus replicated efficiently in vitro and in vivo and transmitted in ferrets by respiratory droplet. Antigenically, it was distinct from other swine viruses. Hemagglutination inhibition analysis suggested that antibody titers to the swine Chilean H1N2 virus were decreased in persons born after 1990. Further studies are needed to characterize the potential risk to humans, as well as the ecology of influenza in swine in South America.","Animal Diseases/ep [Epidemiology];*Animal Diseases/tm [Transmission];*Animal Diseases/vi [Virology];Animals;Antibodies, Viral/im [Immunology];Cell Line;Chile/ep [Epidemiology];Female;*Ferrets/vi [Virology];Geography, Medical;Hemagglutination Inhibition Tests;High-Throughput Nucleotide Sequencing;Humans;Influenza A Virus, H1N2 Subtype/cl [Classification];Influenza A Virus, H1N2 Subtype/ge [Genetics];Influenza A Virus, H1N2 Subtype/ip [Isolation & Purification];*Influenza A Virus, H1N2 Subtype;Influenza, Human/ep [Epidemiology];Influenza, Human/vi [Virology];*Orthomyxoviridae Infections/ve [Veterinary];Public Health Surveillance;RNA, Viral;Seasons;Seroepidemiologic Studies;Swine;*Swine Diseases/vi [Virology];Virus Replication;0 (Antibodies, Viral);0 (RNA, Viral)","Bravo-Vasquez, N.;Karlsson, E. A.;Jimenez-Bluhm, P.;Meliopoulos, V.;Kaplan, B.;Marvin, S.;Cortez, V.;Freiden, P.;Beck, M. A.;Hamilton-West, C.;Schultz-Cherry, S.",2017,02,,0
252,ICTV Virus Taxonomy Profile: Circoviridae,"The family Circoviridae comprises viruses with small, circular, single-stranded DNA (ssDNA) genomes, including the smallest known animal viruses. Members of this family are classified into two genera, Circovirus and Cyclovirus, which are distinguished by the position of the origin of replication relative to the coding regions and the length of the intergenic regions. Within each genus, the species demarcation threshold is 80% genome-wide nucleotide sequence identity. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Circoviridae, which is available at www.ictv.global/report/circoviridae.",Circoviridae;Circovirus;Cyclovirus;ICTV report;taxonomy;FEATHER-DISEASE-VIRUS;PORCINE-CIRCOVIRUS;DNA-REPLICATION;ORIGIN;PROTEIN;TYPE-1;BEAK;REP,"Breitbart, M.;Delwart, E.;Rosario, K.;Segales, J.;Varsani, A.",2017,Aug,,0
253,Shotgun metagenomics of biological stains using ultra-deep DNA sequencing,"A detailed molecular analysis of blood or other biological stains at a crime scene is often hampered by the low quantity and quality of the extractable DNA. However, the determination of the origin and composition of a stain is in most cases a prerequisite for the final elucidation of a criminal case. Standard methodologies, e.g. amplification of DNA followed by microsatellite typing or mitochondrial DNA sequencing, are often not sensitive enough to result in sufficient and conclusive data. We have applied ultra-deep DNA sequencing using the 454 pyrosequencing technology on a whole genome amplified (WGA) environmental biological stain, which was analysed unsuccessfully with standard methodologies following WGA. With the combination of WGA and 454 pyrosequencing, however, we were able to generate 7242 single sequences with an average length of 195 bp. A total of 1,441,971 bp DNA sequences were generated and compared with public DNA sequence databases. Using RepeatMasker and basic logical alignment search tool (BLAST) searches against known microbial and mammalian genomes it was possible to determine the metagenomic composition of the stain, i.e. 4.2% bacterial DNA, 0.3% viral DNA, 2.7% fungal DNA, 10.3% mammalian repetitive DNA, 0.9% porcine DNA, 0.13% human DNA and 81.5% DNA of unknown origin. Our data demonstrate that 454 pyrosequencing has the potential to become a powerful tool not only in basic research but also in the metagenomic analysis of biological trace materials for forensic genetics. © 2009 Elsevier Ireland Ltd. All rights reserved.",bacterial DNA;fungal DNA;microsatellite DNA;mitochondrial DNA;virus DNA;article;basic logical alignment search tool;blood stain;crime;DNA extraction;DNA isolation;DNA purification;DNA sequence;forensic genetics;gene amplification;genome;gunshot injury;human;metagenomics;methodology;microsatellite marker;nonhuman;priority journal;pyrosequencing;search engine;sequence database;ultra deep dna sequencing,"Brenig, B.;Beck, J.;Schütz, E.",2010,,10.1016/j.fsigen.2009.10.001,0
254,"A proposal for a common nomenclature for viral clades that form the species varicella-zoster virus: Summary of VZV Nomenclature Meeting 2008, Barts and the London School of Medicine and Dentistry, 24-25 July 2008","Varicella-zoster virus (VZV), the cause of chickenpox and zoster, was the first human herpesvirus to be sequenced fully and the first for which vaccines have been licensed and widely used. Three groups have published genotyping schemes based on single nucleotide polymorphisms (SNPs) and, between them, have identified five distinct phylogenetic clades, with an additional two putative clades. Sequencing of over 23 whole VZV genomes from around the world further refined the phylogenetic distinctions between SNP genotypes. Widespread surveillance in countries in which the varicella vaccine is now in use and the difficulties posed by three unique genotyping approaches prompted an international meeting, at which a common nomenclature based on phylogenetic clades was agreed upon. In this paper, we review the original genotyping schemes and discuss the basis for a novel common nomenclature for VZV strains. We propose a minimum set of SNPs that we recommend should be used to genotype these viruses. Finally, we suggest criteria by which novel clades can be recognized.",chickenpox vaccine;glycoprotein;amino acid substitution;gene sequence;genotype;nomenclature;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;review;single nucleotide polymorphism;tandem repeat;vaccination;Varicella zoster virus;virus classification;virus identification;virus strain,"Breuer, J.;Grose, C.;Norberg, P.;Tipples, G.;Schmid, D. S.",2010,,10.1099/vir.0.017814-0,0
255,Sequence determination of the nucleocapsid protein gene of the porcine epidemic diarrhoea virus confirms that this virus is a coronavirus related to human coronavirus 229E and porcine transmissible gastroenteritis virus,"The nucleotide sequence of 1.7 kbp cDNA, comprising the region nearest the 3' end of the genome of the porcine epidemic diarrhoea virus (PEDV), has been independently determined for two European isolates of PEDV. Almost identical results were obtained for the two isolates, which were derived from cases of PEDV infection in Belgium and Britain in 1977 and 1987, respectively. The sequences contained a 1323 nucleotide (nt) open reading frame (ORF), which showed moderate identity to the nucleocapsid (N) gene of other coronaviruses. The greatest similarity at both the nucleic acid and protein levels was to the human coronavirus 229E. The PEDV N gene was, however, notably larger than that of the human 229E and porcine transmissible gastroenteritis viruses. This reflects the presence of a putative insertion of approximately 135 nt located towards the middle of the N gene. A second 336 nt ORF, which might encode a leucine-rich protein similar to, but shorter than, the bovine coronavirus internal protein was found within the PEDV N gene. Several RNA motifs typical of coronaviruses were also observed. These results confirm the earlier provisional classification of PEDV as a coronavirus.",complementary DNA;leucine;viral protein;article;Coronavirinae;Enterovirus;gene sequence;nonhuman;nucleotide sequence;open reading frame;priority journal;sequence homology;virus classification;virus gene;virus genome;virus nucleocapsid,"Bridgen, A.;Duarte, M.;Tobler, K.;Laude, H.;Ackermann, M.",1993,,,0
256,WHO expert consultation on rabies,,alcohol;alpha interferon;antibiotic agent;antiinfective agent;antivirus agent;complementary DNA;inactivated vaccine;live vaccine;methisoprinol;povidone iodine;rabies immunoglobulin;rabies vaccine;recombinant vaccine;ribavirin;steroid;thymocyte antibody;vidarabine;virus RNA;antibody titer;antigen detection;autopsy;bat;brain biopsy;cadaver;carnivore;disabled person;disease transmission;dog;domestic animal;drug efficacy;drug potency;drug safety;enzyme linked immunosorbent assay;health care personnel;health care policy;health program;human;infection control;injection site erythema;injection site pruritus;laboratory diagnosis;law enforcement;livestock;mass immunization;nonhuman;organ transplantation;passive immunization;protective clothing;rabies;Rabies virus;review;rodent;vaccination;virus classification;virus identification;virus infection;virus strain;virus transmission;wildlife;World Health Organization;wound care;wound infection,"Briggs, D.;Bourhy, H.;Cleaveland, S.;Cliquet, F.;Ertl, H.;Fayaz, A.;Fooks, A.;Hemachudha, T.;Ichhpujani, R. L.;Kaboyo, W. R.;Koprowski, H.;Madhusudana, S. N.;Müller, T.;Nel, L.;Quiambao, B.;Rupprecht, C. E.;Salahuddin, N.;Sudarshan, M. K.;Tordo, N.;Wandeler, A. I.;Wilde, H.;Cliquet, F.;Spinola, F.;Belotto, A.;Bhatia, R.;Endo, H.;Ganter, B.;Gibert, R.;Grachev, V.;Knezevic, I.;Mc Adams, D.;Meslin, F. X.;Miranda, E.;Morgeaux, S.;Roungou, J. B.",2005,,,0
257,Review of the Global Distribution of Foot-and-Mouth Disease Virus from 2007 to 2014,"Foot-and-mouth disease (FMD) virus affects livestock worldwide. There are seven different serotypes, each with a diversity of topotypes, genetic lineages and strains. Some lineages have different properties that may contribute to sporadic spread beyond their recognized endemic areas. The objective of this study was to review the most significant FMD epidemiological events that took place worldwide between 2007 and 2014. Severe epidemics were caused by FMD virus (FMDV) lineage O/Asia/Mya-98 in Japan and South Korea in 2010, both previously free of disease. In India, where FMD is endemic, the most important event was the re-emergence of lineage O/ME-SA/Ind-2001 in 2008. Notably, this lineage, normally restricted to India, Bangladesh, Nepal and Bhutan, was also found in Saudi Arabia and Libya in 2013 and has caused several outbreaks in Tunisia and Algeria in 2014-2015. In January 2011, FMDV-positive wild boars were found in Bulgaria, where the disease last occurred in 1996, followed by 12 outbreaks in livestock infected with FMDV O/ME-SA/PanAsia2. In 2012, FMDV SAT2 caused outbreaks in Egypt and the Palestinian Autonomous Territories. Another significant event was the emergence of FMDV Asia1 Sindh-08 in the Middle East. In South America, one outbreak of FMDV serotype O, topotype Euro-SA was reported in Paraguay in 2011, which was recognized as FMD-free with vaccination at the time. Lessons learned from past events, point out the need for an integrated strategy that comprises coordinated global and regional efforts for FMDV control and surveillance. Specific local characteristics related to host, environment and virus that condition FMD occurrence should be carefully considered and incorporated to adapt appropriate strategies into local plans. In this review, we compiled relevant epidemiological FMD events to provide a global overview of the current situation. We further discussed current challenges present in different FMD areas.",animal;endemic disease;epidemic;Foot and mouth disease virus;foot and mouth disease;genetics;global health;serotype;vaccination;virology,"Brito, B. P.;Rodriguez, L. L.;Hammond, J. M.;Pinto, J.;Perez, A. M.",2017,,10.1111/tbed.12373,0
258,The enteric virome in inflammatory bowel disease,,,"Brooks, J.;Watson, A.",2015,,,0
259,Non-maternal transmission is the major mode of ovine lentivirus transmission in a ewe flock: A molecular epidemiology study,"Transmission of ovine progressive pneumonia virus (OPPV), a lentivirus of sheep, occurs through both maternal and non-maternal means. Currently, the contribution of each route to the overall flock OPPV prevalence is poorly understood since previous serological epidemiologic studies lacked the ability to accurately track routes of transmission within an infected flock. In this study, the amount of maternal OPP transmission was assessed in a naturally infected ewe flock by applying molecular analyses to proviral sequences derived from peripheral blood leukocytes of OPP positive dam-daughter pairs (N=40). Both proviral envelope (env) and long terminal repeat (LTR) sequences, separately and combined, were utilized in the following 2 sequence analysis methods: phylogenetic analysis and pairwise distance calculations. True maternal transmission events were defined as agreement in 2 out of the 2 sequence analysis methods. Using this criterion, proviral env sequences resulted in a 14.3% maternal transmission frequency, and proviral LTR sequences resulted in a 10% maternal transmission frequency. Both proportions of maternal transmission varied significantly from equality (P<0.0001). This indicates that the remaining 85.7-90% of daughters are infected via non-maternal transmission. This is also the first study to calculate the OPP proviral rate of change for the env gene and LTR promoter. Accurately defining the routes of OPPV transmission provides critical epidemiological data supporting management intended to reduce flock transmission and viral dose. © 2010.",article;controlled study;envelope gene;ewe;female;Lentivirus;Lentivirus infection;leukocyte;long terminal repeat;molecular epidemiology;nonhuman;nucleotide sequence;Ovine progressive pneumonia virus;phylogeny;priority journal;promoter region;sequence analysis;unindexed sequence;United States;vertical transmission;virus transmission,"Broughton-Neiswanger, L. E.;White, S. N.;Knowles, D. P.;Mousel, M. R.;Lewis, G. S.;Herndon, D. R.;Herrmann-Hoesing, L. M.",2010,,10.1016/j.meegid.2010.06.007,0
260,Antigenic and genetic analyses of H1N1 influenza A viruses from European pigs,"H1N1 influenza A viruses isolated from pigs in Europe since 1981 were examined both antigenically and genetically and compared with H1N1 viruses from other sources. H1N1 viruses from pigs and birds could be divided into three groups: avian, classical swine and 'avian-like' swine viruses. Low or no reactivity of 'avian-like' swine viruses in HI tests with monoclonal antibodies raised against classical swine viruses was associated with amino acid substitutions within antigenic sites of the haemagglutinin (HA). Phylogenetic analysis of the HA gene revealed that classical swine viruses from European pigs are most similar to each other and are closely related to North American swine strains, whilst the 'avian-like' swine viruses cluster with avian viruses. 'Avian-like' viruses introduced into pigs in the UK in 1992 apparently originated directly from strains in pigs in continental Europe at that time. The HA genes of the swine viruses examined had undergone limited variation in antigenic sites and also contained fewer potential glycosylation sites compared to human H1N1 viruses. The HA exhibited antigenic drift which was more marked in 'avian-like' swine viruses than in classical swine strains. Genetic analyses of two recent 'avian-like' swine viruses indicated that all the RNA segments are related most closely to those of avian influenza A viruses.",monoclonal antibody;virus antibody;virus antigen;virus hemagglutinin;virus RNA;amino acid substitution;antigenic variation;article;bird;comparative study;Influenza A virus;nonhuman;phylogeny;priority journal;protein glycosylation;pig;viral genetics;virus classification,"Brown, I. H.;Ludwig, S.;Olsen, C. W.;Hannoun, C.;Scholtissek, C.;Hinshaw, V. S.;Harris, P. A.;McCauley, J. W.;Strong, I.;Alexander, D. J.",1997,,,0
261,"Molecular comparisons of full length metapneumovirus (MPV) genomes, including newly determined french AMPV-C and -D isolates, further supports possible subclassification within the MPV genus","Four avian metapneumovirus (AMPV) subgroups (A-D) have been reported previously based on genetic and antigenic differences. However, until now full length sequences of the only known isolates of European subgroup C and subgroup D viruses (duck and turkey origin, respectively) have been unavailable. These full length sequences were determined and compared with other full length AMPV and human metapneumoviruses (HMPV) sequences reported previously, using phylogenetics, comparisons of nucleic and amino acid sequences and study of codon usage bias. Results confirmed that subgroup C viruses were more closely related to HMPV than they were to the other AMPV subgroups in the study. This was consistent with previous findings using partial genome sequences. Closer relationships between AMPV-A, B and D were also evident throughout the majority of results. Three metapneumovirus ""clusters"" HMPV, AMPV-C and AMPV-A, B and D were further supported by codon bias and phylogenetics. The data presented here together with those of previous studies describing antigenic relationships also between AMPV-A, B and D and between AMPV-C and HMPV may call for a subclassification of metapneumoviruses similar to that used for avian paramyxoviruses, grouping AMPV-A, B and D as type I metapneumoviruses and AMPV-C and HMPV as type II. © 2014 Brown et al.",matrix protein;membrane protein;protein M2;RNA directed RNA polymerase;small hydrophobic protein;unclassified drug;virus fusion protein;virus glycoprotein;virus nucleoprotein;virus phosphoprotein;article;Avian metapneumovirus subgroup A;Avian metapneumovirus subgroup B;Avian metapneumovirus subgroup C;Avian metapneumovirus subgroup D;Avian metapneumovirus;codon usage;consensus sequence;Human metapneumovirus;L gene;nonhuman;nucleotide sequence;open reading frame;phylogeny;virus classification;virus gene;virus genome,"Brown, P. A.;Lemaitre, E.;Briand, F. X.;Courtillon, C.;Guionie, O.;Allée, C.;Toquin, D.;Bayon-Auboyer, M. H.;Jestin, V.;Eterradossi, N.",2014,,10.1371/journal.pone.0102740,0
262,Bovine virus diarrhoea virus - Strategic decisions for diagnosis and control,"In the 15 years since the last In Practice article on bovine virus diarrhoea virus (BVDV), there has been an explosion in the understanding of the molecular mechanisms of viral replication and mutation, especially those related to biotypic variation. Hand in hand has come a greater understanding of the importance of BVDV as a primary pathogen of cattle, particularly as a cause of reproductive loss. A BVDV vaccine is now available in the UK, giving better prospects for protection against infection. However, for the veterinary clinician, the strategic decisions regarding diagnosis, control and vaccination continue to pose difficult dilemmas and it is on these issues that this article focuses.",virus antibody;viral protein;virus vaccine;antibody titer;Bovine viral diarrhea virus 1;cattle disease;infection control;nonhuman;review;vaccination;virus classification;virus mutation;virus replication,"Brownlie, J.;Thompson, I.;Curwen, A.",2000,,,0
263,"Viral meningitis epidemics and a single, recent, recombinant and anthroponotic origin of swine vesicular disease virus","Background and objectives: Swine vesicular disease virus (SVDV) is a close relative of the human Enterovirus B serotype, coxsackievirus B5. As the etiological agent of a significant emergent veterinary disease, several studies have attempted to explain its origin. However, several key questions remain, including the full biological ancestry of the virus, and its geographical and temporal origin. Methodology: We sequenced near-complete genomes of 27 SVDV and 13 coxsackievirus B5 samples, all originally isolated between 1966 and 2006, and analysed these in conjunction with existing sequences and historical information. Results: While analyses incorporating 24 additional near-complete SVDV genomic sequences indicate clear signs of within-SVDV recombination, all 51 SVDV isolates remain monophyletic. This supports a hypothesis of a single anthroponotic transfer origin. Analysis of individual coding and non-coding regions supports that SVDV has a recombinant origin between coxsackievirus B5 and another Enterovirus B serotype, most likely coxsackievirus A9. Extensive Bayesian sequence-based analysis of the time of the most recent common ancestor of all analysed sequences places this within a few years around 1961. Epidemiological evidence points to China as an origin, but there are no available samples to test this conclusively. Conclusions and implications: Historical investigation and the clinical aspects of the involved Enterovirus B serotypes, makes the current results consistent with a hypothesis stating that SVDV originated through co-infection, recombination, and a single anthroponotic event, during large viral meningitis epidemics around 1960/1961 involving the ancestral serotypes. The exact geographical origin of SVDV may remain untestable due to historical aspects.",article;China;controlled study;Coxsackievirus A9;Coxsackievirus B5;Enterovirus;Enterovirus B;epidemic;geographic origin;high throughput sequencing;mixed infection;monophyly;nonhuman;phylogeny;priority journal;sequence analysis;swine vesicular disease virus;virus genome;virus isolation;virus meningitis;virus recombinant;virus recombination;virus transmission,"Bruhn, C. A. W.;Abel Nielsen, S. C.;Samaniego, J. A.;Wadsworth, J.;Knowles, N. J.;Gilbert, M. T. P.",2015,,10.1093/emph/eov026,0
264,Role of Schmallenberg virus infection in congenital malformations in ruminants in Scotland in spring 2017,"Scotland's Rural College (SRUC), together with the Moredun Research Institute, carries out surveillance for Schmallenberg virus (SBV) infection in cattle and sheep. This article reports findings relating to diagnoses of fetopathy associated with SBV infection and other congenital malformations in these species made between January 1 and May 5, 2017.",virus RNA;arthrogryposis;autopsy;Border disease virus;Bovine viral diarrhea virus 1;congenital malformation;disease surveillance;enzyme linked immunosorbent assay;histology;metagenomics;nerve cell degeneration;neuropathology;nonhuman;Orthobunyavirus;real time polymerase chain reaction;reverse transcription polymerase chain reaction;review;ruminant;Schmallenberg virus;serology;teratogenesis;virus infection,"Brülisauer, F.;Scholes, S.;Caldow, G. L.;Rocchi, M.;Dagleish, M. P.;Chianini, F.",2017,,10.1136/vr.j4503,0
265,A genetic study of the interaction of Piry virus with drosophila. II. Classification of viral agD mutants and some preliminary characterizations,"Piry virus mutants selected for altered growth properties in Drosophila melanogaster have previously been designated agD mutants. This paper presents a classification scheme for grouping some of these mutants and also presents the characteristics of some members of each group. Analysis, for each agD clone, of the mean incubation time at 20°C relative to the time at 28°C (t̄20, t̄28), compared to the range of similar data for wild-type virus enabled us to define 4 classes of agD mutant: (1) mutants equally affected at both temperatures, (2) cold-sensitive mutants in drosophila (csD), (3) heat-sensitive mutants in drosophila (tsD) and (4) mutants whose mean incubation time could not be estimated at either 20 or 28°C. All agD mutants are listed. The majority of them were also ts in chicken embryo cells (CEC), and some were classified into complementation groups. Some correlations were noted. For example, the agD mutants that were ts+ in CEC were frequently (7 out of 12) weakly cold-sensitive in drosophila. Those tsD mutants which were also ts in CEC, all belonged to complementation group I (L protein). True csD mutants, whose divergence of incubation time with wt regularly increased, and which were also ts in CEC, all belonged to group I except for one which belonged to group V (G protein). Three mutants fell into a distinct sub-class of csD mutants, characterized by a defect in the CO2 sensitivity symptom expression below a definite temperature. One of these which was further characterized was shown to be in complementation group V. Some mutants of the fourth class were examined for their fly-invading capacity. This was found to be more-or-less strongly affected. Among these mutants, independent of this phenomenon, mutations were assigned to L, N and G proteins, suggesting that different physiological defects are involved. A comparison was made of the phenotypes in drosophila of some of the agD mutants with other members of the vesiculovirus family. The analogy of sigma rhabdovirus with tsD mutants is also reported.",article;Drosophila melanogaster;genetic analysis;insect;nonhuman;priority journal;taxonomy;virus cell interaction,"Brun, G.",1991,,10.1016/0923-2516(91)90018-x,0
266,"Rotavirus 993/83, isolated from calf faeces, closely resembles an avian rotavirus","Polypeptides from purified virions of the calf rotavirus (RV) isolate 993/83 and those from the pigeon RV isolate PO-13 comigrated on SDS-polyacrylamide gels. Two polypeptides of 45K and 47K were detected at the position of VP6. Both proteins behaved like authentic VP6 protein with EDTA and heat treatment. RV 993/83 and PO-13 showed identical one-dimensional peptide maps for VP2, and the 45K and 47K proteins. More than 70% of sera from German cattle older than 1 year showed neutralizing serum antibodies to RV 993/83 and RV PO-13.",edetic acid;neutralizing antibody;viral protein;animal cell;article;bird;bovine;feces;heating;nonhuman;peptide mapping;polyacrylamide gel electrophoresis;priority journal;protein purification;Rotavirus;virion;virus classification;virus isolation,"Brussow, H.;Nakagomi, O.;Minamoto, N.;Eichhorn, W.",1992,,,0
267,"Bovine herpesvirus 4 genome: Cloning, mapping and strain variation analysis","The restriction map of the bovine herpesvirus 4 (BHV-4) genome (V. Test strain) was established for the restriction enzymes EcoRI, BamHI and HindIII by analysis of clones from a lambda library (Sau3AI partial digestion) and from a plasmid library (EcoRI fragments). One genome unit was defined as the length of the unique central part, flanked at both ends by one of the terminal tandem repeats called polyrepetitive DNA (prDNA) and was estimated to be 113 ± 2 kbp. A restriction map of the prDNA of the V. Test strain showed internal 200 bp tandem repeats of different sequences. This region in the prDNA was highly polymorphic between BHV-4 strains, even in a viral DNA preparation from a plaque-purified strain. The right junction between the repeated and the unique sequence of the genome occurred at an almost constant site, but the left junction contained a modified prDNA and was variable between BHV-4 strains. The unique central part of the genome was very similar in the four strains under consideration, with a few variations due to the presence or absence of a restriction site and four length variations were observed, located at positions 0.006 to 0.034 (left end), 0.211 to 0.225, 0.864 to 0.881 and 0.962 to 0.984 (right end). The total length variation of 1 genome unit does not exceed 1 kbp.",animal cell;article;Bovine herpesvirus 1;cell culture;DNA probe;DNA replication;gene mapping;molecular cloning;nonhuman;priority journal;virus classification;virus strain,"Bublot, M.;Van Bressem, M. F.;Thiry, E.;Dubuisson, J.;Pastoret, P. P.",1990,,,0
268,The Ancient Evolutionary History of Polyomaviruses,"Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae.","Amino Acid Sequence;Animals;Base Sequence;*Biological Evolution;Fishes;*Host-Parasite Interactions/ge [Genetics];Models, Molecular;Molecular Sequence Data;Phylogeny;*Polyomavirus/ge [Genetics];Scorpions;Sheep","Buck, C. B.;Van Doorslaer, K.;Peretti, A.;Geoghegan, E. M.;Tisza, M. J.;An, P.;Katz, J. P.;Pipas, J. M.;McBride, A. A.;Camus, A. C.;McDermott, A. J.;Dill, J. A.;Delwart, E.;Ng, T. F.;Farkas, K.;Austin, C.;Kraberger, S.;Davison, W.;Pastrana, D. V.;Varsani, A.",2016,Apr,,0
269,Inflammation of the teats of cows due to a virus from the pox group,"Clinical and laboratory studies were carried out on the enzootic inflammation of cow teats. The isolated virus was classified as Pox group on the basis of its physico chemical and biological properties. It seems to be poxvirus officinale. Treatment of the teats with a 3.0% alcohol water solution of pyoctanine, plus milking (catheterization), led to recovery.",bovine;infection;microorganism;Poxviridae,"Buczek, J.;Krzyzanowski, J.;Majer, B.;Malinowski, E.",1973,,,0
270,"Rift Valley fever seroprevalence and abortion frequency among livestock of Kisoro district, South Western Uganda (2016): A prerequisite for zoonotic infection","Background: Rift Valley fever (RVF) is classified as viral hemorrhagic fever and is endemic in East and West Africa. RVF is caused by an arthropod borne virus (RVFV); the disease is zoonotic and affects human, animal health as well as international trade. In livestock it causes abortions, while human infection occurs through close contact with infected animals or animal products. Methods: A quantitative observational study using stratified sampling was conducted in the western region of Uganda. Blood samples and abortion events from 1000 livestock (goats, sheep and cattle) was collected and recorded. Serum was analyzed for RVFV IgG reacting antibodies using competitive ELISA test. Results: The overall RVFV seroprevalence was of 10.4% (104/1000). Cattle had the highest seroprevalence (7%) followed by Sheep (2.2%) then goats (1.2%). Species specific RVFV seroprevalence was highest in cattle (20.5%) followed by sheep (6.8%) then goats (3.6%). RVFV seroprevalence in northern highlands (21.8%) was significantly higher (p < 0.001) than in the southern lowlands (3.7%). Overall prevalence of abortion was (17.4%), sheep had the highest prevalence of abortion (7.8%) followed by goats (6.3%) and then cattle (3.3%). Species specific abortion prevalence was highest in Sheep (24.1%) followed by goats (18.8%) and then 9.7% in cattle. Conclusion: RVFV is endemic in Kisoro district and livestock in the highland areas are more likely to be exposed to RVFV infection compared to those in the southern lowlands. Out breaks in livestock most likely will lead to zoonotic infection in Kisoro district.",immunoglobulin G;abortion;article;controlled study;enzyme linked immunosorbent assay;laboratory test;livestock;nonhuman;observational study;prevalence;Rift Valley fever;sampling;seroprevalence;serum;stratified sample;study design;Uganda;zoonosis,"Budasha, N. H.;Gonzalez, J. P.;Sebhatu, T. T.;Arnold, E.",2018,,10.1186/s12917-018-1596-8,0
271,Molecular analysis of H7 avian influenza viruses from Australia and New Zealand: genetic diversity and relationships from 1976 to 2007,"Full-genome sequencing of 11 Australian and 1 New Zealand avian influenza A virus isolate (all subtype H7) has enabled comparison of the sequences of each of the genome segments to those of other subtype H7 avian influenza A viruses. The inference of phylogenetic relationships for each segment has been used to develop a model of the natural history of these viruses in Australia. Phylogenetic analysis of the hemagglutinin segment indicates that the Australian H7 isolates form a monophyletic clade. This pattern is consistent with the long-term, independent evolution that is, in this instance, associated with geographic regions. On the basis of the analysis of the other H7 hemagglutinin sequences, three other geographic regions for which similar monophyletic clades have been observed were confirmed. These regions are Eurasia plus Africa, North America, and South America. Analysis of the neuraminidase sequences from the H7N1, H7N3, and H7N7 genomes revealed the same region-based relationships. This pattern of independent evolution of Australian isolates is supported by the results of analysis of each of the six remaining genomic segments. These results, in conjunction with the occurrence of five different combinations of neuraminidase subtypes (H7N2, H7N3, H7N4, H7N6, H7N7) among the 11 Australian isolates, suggest that the maintenance host(s) is nearly exclusively associated with Australia. The single lineage of Australian H7 hemagglutinin sequences, despite the occurrence of multiple neuraminidase types, suggests the existence of a genetic pool from which a variety of reassortants arise rather than the presence of a small number of stable viral clones. This pattern of evolution is likely to occur in each of the regions mentioned above.","Amino Acid Sequence;Animal Migration;Animals;Australia/ep [Epidemiology];*Birds/vi [Virology];Genetic Variation;Genome, Viral;Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];Influenza A Virus, H7N7 Subtype/ge [Genetics];Influenza A Virus, H7N7 Subtype/ip [Isolation & Purification];*Influenza A virus/cl [Classification];*Influenza A virus/ge [Genetics];Influenza A virus/ip [Isolation & Purification];Influenza in Birds/ep [Epidemiology];*Influenza in Birds/vi [Virology];Molecular Biology;Molecular Epidemiology;Molecular Sequence Data;Neuraminidase/ge [Genetics];New Zealand/ep [Epidemiology];Phylogeny;Sequence Homology, Amino Acid;Time Factors;Viral Nonstructural Proteins/ge [Genetics];0 (Hemagglutinin Glycoproteins, Influenza Virus);0 (INS1 protein, influenza virus);0 (Viral Nonstructural Proteins)","Bulach, D.;Halpin, R.;Spiro, D.;Pomeroy, L.;Janies, D.;Boyle, D. B.",2010,Oct,,0
272,Influence of the hepatitis C virus 3′-untranslated region on IRES-dependent and cap-dependent translation initiation,"Translation of hepatitis C virus (HCV) genomic RNA is directed by an internal ribosome entry site (IRES) in the 5′-untranslated region (5′-UTR), and the HCV 3′-UTR enhances IRES activity. Since the HCV 3′-UTR has a unique structure among 3′-UTRs, we checked possible communication between the 5′- and the 3′-UTR of HCV during translation using chimeric reporter RNAs. We show that translation directed by the HCV IRES and by the HCV-like IRES of porcine teschovirus (PTV) which belongs to a quite distinct family of viruses (picornaviruses) or by the EMCV IRES is also enhanced by the HCV 3′-UTR or by a poly(A)-tail in different cell types. © 2010 Federation of European Biochemical Societies.",polyadenylated RNA;virus RNA;3' untranslated region;5' untranslated region;article;cells by body anatomy;controlled study;Encephalomyocarditis virus;Hepatitis C virus;human;human cell;internal ribosome entry site;nonhuman;priority journal;reporter gene;RNA analysis;Teschovirus;translation initiation;virus classification;virus transcription,"Bung, C.;Bochkaeva, Z.;Terenin, I.;Zinovkin, R.;Shatsky, I. N.;Niepmann, M.",2010,,10.1016/j.febslet.2010.01.015,0
273,Estimating population diversity with unreliable low frequency counts,"We consider the classical population diversity estimation scenario based on frequency count data (the number of classes or taxa represented once, twice, etc. in the sample), but with the proviso that the lowest frequency counts, especially the singletons, may not be reliably observed. This arises especially in data derived from modern high-throughput DNA sequencing, where errors may cause sequences to be incorrectly assigned to new taxa instead of being matched to existing, observed taxa. We look at a spectrum of methods for addressing this issue, focusing in particular on fitting a parametric mixture model and deleting the highest-diversity component; we also consider regarding the data as left-censored and effectively pooling two or more low frequency counts. We find that these purely statistical ""downstream"" corrections will depend strongly on their underlying assumptions, but that such methods can be useful nonetheless.",animal;article;Bayes theorem;biodiversity;biology;feces;genetics;high throughput sequencing;microflora;statistical model;pig;virology,"Bunge, J.;Böhning, D.;Allen, H.;Foster, J. A.",2012,,,0
274,Clinical and Pathologic Characterization of an Outbreak of Highly Pathogenic Avian Influenza H7N8 in Commercial Turkeys in Southern Indiana,"Highly pathogenic avian influenza (HPAI) is a systemic lethal disease of poultry caused by several subtypes of influenza A virus and classified on the basis of serologic reactions to hemagglutinin and neuraminidase surface glycoproteins. In January 2016, a novel subtype of HPAI-H7N8-was diagnosed in a commercial turkey (Meleagris gallopavo) flock in southern Indiana. Clinical signs and history included increased mortality, dyspnea, head tremors, recumbency, and somnolent or unaware birds. Postmortem examination of six recently dead birds showed red-tinged mucous in the choana and trachea and marked pulmonary edema. Histologic lesions in the brain included severe, multifocal lymphohistiocytic meningoencephalitis with foci of malacia, neuronal necrosis, and neuronophagia. All anatomic locations of the brain were affected, although histologic changes in the cerebellum were considered mild. Other histologic lesions included pulmonary congestion and edema, splenic congestion and lymphoid depletion, fibrinoid necrosis of vessels within the spleen, and multifocal pancreatic acinar necrosis. Immunohistochemistry (IHC) was weakly positive for influenza A in the brain; IHC was negative in other tissues tested. The clinical and pathologic characteristics of this case matched previously published material concerning HPAI and add to instances of known or suspected mutation of a low pathogenic virus to a highly pathogenic virus.",animal;avian influenza;bird disease;case report;classification;differential diagnosis;epidemic;Indiana;Influenza A virus;isolation and purification;male;pathology;physiology;turkey (bird);veterinary medicine;virology,"Burcham, G. N.;Ramos-Vara, J. A.;Murphy, D. A.",2017,,10.1637/11661-042717-CaseR,0
275,The Isolation of a Latent Adenolike Virus from Chicken Kidney Cell Cultures,,*Adenoviridae;*Adenoviridae Infections;Animals;*Chickens;*Classification;*Kidney;*Meat;*Poultry;*Research;*Tissue Culture Techniques;*Virus Cultivation,"Burke, C. N.;Luginbuhl, R. E.;Helmboldt, C. F.",1965,Feb,,0
276,Etiological classifiable virus infections in domestic animals: situation 1970,,animal;animal disease;bird disease;cat;cat disease;bovine;cattle disease;classification;dog;dog disease;goat;horse;horse disease;microbiology;review;sheep;sheep disease;pig;swine disease;virus;virus infection,"Bürki, F.",1970,,,0
277,Herpesvirus strigis: a new avian herpesvirus. I. Biological properties,"A virus isolated from dead owls displaying a syndrom called hepato splenitis infectiosa strigum (HSIS) killed chicken embryos following inoculation by various routes. Miliary necrotic foci and type A nuclear inclusion bodies were observed on CAM and in embryonic livers and spleens. In chicken embryo fibroblast tissue cultures syncytia, giant cells and type A nuclear bodies appeared. These features, as well as biochemical and biophysical properties described in another paper, allowed classification of HSIS virus as a herpesvirus. No serologic cross reaction was observed between HSIS virus on one hand, and infectious laryngotracheitis virus, Marek virus, and 5 non avian herpesviruses on the other hand. HSIS virus is therefore considered as a new avian herpesvirus. Herpesvirus strigis is proposed as an appropriate name, since owls of the order strigiformes are its natural host.",avian virus;bird;chicken;microorganism;theoretical study;virus inclusion,"Burki, F.;Burtscher, H.;Sibalin, M.",1973,,,0
278,Bovine adenoviruses. III. Subclassification into two subgroups by means of immunodiffusion-tests,"Bovine subgroup II adenoviruses, actually represented by the officially recognized serotypes 4 to 8, possess soluble antigens that in immunodiffusion tests neither cross-react with classical mastadenovirus (human or bovine subgroup I) nor aviadenovirus antigens or their respective antibodies. Earlier, by means of cross-complement fixation, small amounts of classical mastadenovirus group-reactive antigen were demonstrated in bovine subgroup II adenoviruses. No bovine subgroup II specific adenovirus antigen was, however, demonstrated in classical mastadenoviruses. Up to the present, serodiagnosis of bovine adenoviral infections has been severely hampered by not taking into account these facts, leading to great underestimation of the frequency of such infections. We propose a third genus, paramastadenovirus, within the family adenoviridae, including presently known and future strains containing mainly the novel group-reactive soluble antigen demonstrated here.",bovine;classification;Mastadenovirus;methodology;theoretical study;virus classification,"Burki, F.;Hinaidy, B.;Bockmann, J.",1979,,,0
279,Classification as a separate equine herpes virus of isolate 53/69 from equine coital exanthema,"On the occasion of an outbreak of equine coital exanthema (ECE) a virus strain designated ECE 53/69 was isolated from a vaginal swab. It induced plaques, polykaryotic giant cells and Cowdry type A nuclear inclusion bodies in equine cell cultures. Replication of ECE 53/69 was completely inhibited by IUDR. It proved sensitive to ether, trypsin, heat and low pH. All these features, as well as electron microscopic data described elsewhere, allowed classification of the strain as a herpesvirus. That it was an equine herpesvirus was substantiated by natural and experimental infections in horses and by replication occurring exclusively in equine cell cultures. Equine cytomegaloviruses also replicate solely in equine cells. They do so, however, at a much slower rate and remain cellbound. ECE 53/69, on the contrary, causes very rapid cpe and is liberated to high titer into the t.c. medium. Equine rhinopneumonitis virus, differs from ECE by replicating in a broad spectrum of heterologous cells as well as by lack of cross neutralization, cross complement fixation and by different clinical manifestations. ECE 53/69 is thus a separate equine herpesvirus species.",classification;electron microscopy;equine virus;Herpesviridae;horse;microorganism;rash;theoretical study;virus classification;virus isolation,"Burki, F.;Pichler, L.;Sibalin, M.",1973,,,0
280,Virus classification and nomenclature,,,"Burnet, S. M.",1953,,,0
281,Inactivation of viruses by aziridines,"Ethyleneimine (EI) and N-acetylethyleneimine (AEI) have been shown to inactivate viruses belonging to most of the families described by the International Committee for the Taxonomy of Viruses. The mechanism by which they inactivate the viruses has not been established. In this paper, experiments with foot-and-mouth disease virus (FMDV) and poliovirus are described which indicate that the inactivating lesion is on the RNA.",antivirus agent;aziridine derivative;animal;Aphthovirus;article;cell line;Cercopithecus;drug effect;genetics;hamster;human;Poliomyelitis virus;ultrastructure;Vero cell line,"Burrage, T.;Kramer, E.;Brown, F.",2000,,,0
282,"Hepatitis E Virus in Farmed Rabbits, Wild Rabbits and Petting Farm Rabbits in the Netherlands","Rabbits have been suggested as a zoonotic source of Hepatitis E virus. Phylogenetic analysis of HEV isolates from farmed, wild and pet rabbits in the Netherlands (23, 0, and 60 % respectively) showed them to be grouped amongst published rabbit HEV sequences and distinct from most human isolates. Dutch rabbits are unlikely to be a zoonotic source.",animal experiment;animal tissue;article;controlled study;Dutch belted (rabbit);farm animal;feces analysis;hepatitis E;Hepatitis E virus;Netherlands;nonhuman;pet animal;phylogeny;priority journal;virus transmission;zoonosis,"Burt, S. A.;Veltman, J.;Hakze-van der Honing, R.;Schmitt, H.;van der Poel, W. H. M.",2016,,10.1007/s12560-016-9239-3,0
283,Influenza A virus subtypes in wild birds in North-Eastern Spain (Catalonia),"Since the spread of H5N1 highly pathogenic avian influenza virus in 2005, many surveillance programmes have been initiated in poultry and wild birds worldwide. This study describes for the first time the detection of different subtypes of avian influenza viruses (AIV) in wild birds in the West Mediterranean area (Catalonia, North-Eastern Spain). During a 3-year period (from mid-2006 to mid-2009), 1374 birds from 16 different families were examined, and a total of 62 AIV were detected by means of a real-time reverse transcriptase PCR assay. AIV were more frequently detected in Anatidae, Phoenicopteridae, Rallidae and Laridae families. Of the 62 positive samples, 28 AIV could be isolated in embryonated eggs. All isolates were subtyped by haemagglutinin and neuraminidase inhibition techniques and 10 different haemagglutinins (HA) and 7 neuraminidases (NA) were found in 13 different subtype combinations. The most common combinations were H4N6 (22.2%) and H1N1 (18.5%). The HA and NA gene sequences of different AIV subtypes were compared and aligned with those available AIV strains from genome databases. Our studies on AIV phylogenetic analysis revealed that all AIV genes sequenced from wild birds in North-Eastern Spain clustered within Eurasian avian clades, including the sequences of H8, N4 and N5 genes analyzed for the first time in Europe. The results contribute to the understanding of AIV in the Mediterranean area and in Europe. © 2009 Elsevier B.V. All rights reserved.",Influenza virus hemagglutinin;virus sialidase;article;bird;bird disease;controlled study;waterfowl;enzyme inhibition;gene sequence;genetic database;Influenza A virus;Laridae;nonhuman;nucleotide sequence;Phoenicopteridae;phylogeny;priority journal;Rallidae;reverse transcription polymerase chain reaction;sequence alignment;Spain;virus characterization;virus detection;virus isolation;wild type;zygote,"Busquets, N.;Alba, A.;Napp, S.;Sánchez, A.;Serrano, E.;Rivas, R.;Núñez, J. I.;Majó, N.",2010,,10.1016/j.virusres.2009.12.005,0
284,Studies on the sialidase and the esterase of influenza viruses,"The main contributions of the author and collaborators about sialidase (EC 3.2.1.18) of influenza virus types A and B and O-acetylesterase (EC 3.1.1.53) of type C are summarized. After a short introduction on the topic, the negative results obtained by the author on inhibitors ar commented. Then, the peculiarities of the three procedures assayed, based on the NADH determination as a measurement for the silaidase activity, are discussed. The spectrofluorimetric measuremnt of NADH concentration is a more sensitive and convenient procedure than that by spectrophotometry, although it is less sensitive than that based on bioluminscence. Sialidase activity is generally higher in influenza virus type A than in type B; however, some differences have been found between the three sub-types A analysed. Further-more, thermal stability and stability against changes in the pH values are higher for influenza virus from ducks, followed by those from humans and, finally, by those from pigs. O-acetylerterase of influencza virus type C shows a broad specificity; it acts on O-acetyl-containing compounds which may not be sialic acids. It seems that this enzyme might contribute to facilitate the action of sialidase of influencza virus type A and B. The peculiarities of influenza virus type C suggest to include this type as a new genus in the future classification of viruses.",esterase;sialidase;Influenza virus;nonhuman;short survey,"Cabezas, J. A.",1991,,,0
285,"Circulation of the rabies virus in non-hematophagous bats in the City of Rio de Janeiro, Brazil, during 2001-2010","Introduction: Rabies is one of the most known lethal zoonosis, responsible for 55,000 human deaths per year. It is transmitted to humans mainly by the bite of domestic or wild animals infected with the virus. This paper shows the circulation of this virus in non-hematophagous bats in the City of Rio de Janeiro, Brazil. Methods: A survey was performed on the number of bats that had been sent for diagnosis by the Seção de Virologia of the Instituto Municipal de Medicina Veterinária Jorge Vaitsman and were positive for rabies. The positive animals were identified, and the isolated viruses were sent for antigenic typification with indirect immunofluorescence. The results were compared with the antigenic panel of the Centers for Disease Control and Prevention. Results: During 2001-2010, the laboratory received 555 non-hematophagous bats for rabies diagnosis, with 198 (35.7%) from Rio de Janeiro City. A total of 11 (5.5%) animals were positive for this disease. Antigenic typification revealed the predominance of variant 3 in 9 (81.8%) of the isolated viruses; 1 virus was classified as variant 4 and 1 variant was identified that segregated with the viruses in insectivorous bats. Conclusions: The data obtained in this study showed the presence of the rabies virus in synanthropic populations of non-hematophagous bats in the City of Rio de Janeiro. The circulation of this agent in these animals represents a serious risk to human and animal health and requires attention and control measures by the authorities.",antigen detection;antigen function;article;bat;Brazil;controlled study;female;insectivore;male;nonhuman;rabies;Rabies virus;seasonal variation;virus classification;virus detection;virus isolation;virus transmission,"Cabral, C. C.;de Morais, A. C. N.;Dias, A. V. A. B.;Araújo, M. G.;Moreira, W. C.;Mattos, G. L. M.",2012,,10.1590/s0037-86822012000200008,0
286,Molecular epidemiology of enterovirus and parechovirus infections according to patient age over a 4-year period in Spain,"The epidemiology and clinical association of enterovirus (EV) and parechovirus (HPeV) infections, as well as the type-distribution-according-to-age, were determined during a 4-year study period in Spain. During 2010-2013, a total of 21,832 clinical samples were screened for EV and the detection frequency was 6.5% (1,430). Of the total EV-negative samples, only 1,873 samples from 2011 to 2013 were available for HPeV testing. HPeV was detected in 42 (2%) of them. Positive samples were genotyped using PCR and sequencing. EV infections occurred in all age groups of patients: neonates (17%), children 28 days to 2 years (29%), children 2-14 years (40%), and adults (14%). Thirty-four different EV types were identified. HPeV infections were detected exclusively in infants <8 m (70% neonates, P < 0.05). All but one HPeV were HPeV-3. Differences in type frequency detection were found according to age and clinical manifestation. Coxsackievirus (CV)-B4 (61%), CV-B5 (83%), and HPeV-3 (64%) were more frequent in neonates than in older patients (P < 0.05). Echovirus (E)-3 (60%), E-18 (47%), E-25 (62%), CV-A6 (61%), CV-A16 (72%), and EV-71 (75%) were mainly detected in children 28 days to 2 years (P < 0.05), whereas, E-6 (79%), E-20 (88%), and E-30 (85%) were predominant in children >2 years and adults (P < 0.05). Clinically, meningitis was associated with EV (P < 0.01) whereas, encephalitis was more frequent in HPeV-infected patients. CV-B types were associated with myocarditis (90%; P < 0.05) and EV species A with hand-foot-mouth-disease/atypical exanthema (88%; P < 0.05). J. Med. Virol. 89:435-442, 2017. © 2016 Wiley Periodicals, Inc.","Adolescent;Adult;Age Factors;Aged;Aged, 80 and over;Child;Child, Preschool;*Enterovirus/cl [Classification];*Enterovirus/ge [Genetics];Enterovirus/ip [Isolation & Purification];*Enterovirus Infections/ep [Epidemiology];Enterovirus Infections/pa [Pathology];Enterovirus Infections/vi [Virology];Female;*Genotype;Genotyping Techniques;Humans;Infant;Infant, Newborn;Male;Middle Aged;Molecular Epidemiology;*Parechovirus/cl [Classification];*Parechovirus/ge [Genetics];Parechovirus/ip [Isolation & Purification];*Picornaviridae Infections/ep [Epidemiology];Picornaviridae Infections/pa [Pathology];Picornaviridae Infections/vi [Virology];Polymerase Chain Reaction;Prevalence;Sequence Analysis, DNA;Spain/ep [Epidemiology];Young Adult","Cabrerizo, M.;Diaz-Cerio, M.;Munoz-Almagro, C.;Rabella, N.;Tarrago, D.;Romero, M. P.;Pena, M. J.;Calvo, C.;Rey-Cao, S.;Moreno-Docon, A.;Martinez-Rienda, I.;Otero, A.;Trallero, G.",2017,03,,0
287,"Molecular evolution of H1N1 swine influenza in Guangdong, China, 2016–2017","Swine are the main host of the H1N1 swine influenza virus (SIV), however, H1N1 can also infect humans and occasionally cause serious respiratory disease. To trace the evolution of the SIV in Guangdong, China, we performed an epidemic investigation during the period of 2016–2017. Nine H1N1 influenza viruses were isolated from swine nasal swabs. Antigenic analysis revealed that these viruses belonged to two distinct antigenic groups, represented by A/Swine/Guangdong/101/2016 and A/Swine/Guangdong/52/2017. Additionally, three genotypes, known as GD52/17-like, GD493/17-like and GD101/16-like, were identified by phylogenetic analysis. Importantly, the genotypes including a minimum of 4 pdm/09-origin internal genes have become prevalent in China in recent years. A total of 2966 swine serum samples were used to perform hemagglutination inhibition (HI) tests, and the results showed that the seroprevalence values of SW/GD/101/16 (32.2% in 2016, 32.1% in 2017) were significantly higher than the seroprevalence values of SW/GD/52/17 (18.0% in 2016, 16.7% in 2017). Our study showed that the three reassortant genotypes of H1N1 SIV currently circulating in China are stable, but H1N1pdm09 poses challenges to human health by the introduction of internal genes into these reassortant genotypes. Strengthening SIV surveillance is therefore critical for SIV control and minimizing its potential threat to public health.",animal tissue;antigenicity;article;China;genotype;hemagglutination inhibition test;Influenza A virus (H1N1);molecular evolution;nonhuman;nose smear;phylogeny;priority journal;seroprevalence;swine influenza;swine influenza virus,"Cai, M.;Huang, J.;Bu, D.;Yu, Z.;Fu, X.;Ji, C.;Zhou, P.;Zhang, G.",2018,,10.1016/j.meegid.2018.02.029,0
288,Genetic characterization and evolutionary analysis of 4 Newcastle disease virus isolate full genomes from waterbirds in South China during 2003-2007,"Complete genomes of four Newcastle disease virus (NDV) strains, isolated from ducks and wild birds in Guangdong province of China from 2003 to 2007, were sequenced and analyzed in this study. Pathogenicity tests in chicken embryos and chickens illustrate that D3 and R8 are lentogenic, and W4 and P4 are mesogenic strains. Phylogenetic analysis using all six genes provides a high resolution profile for genotype designation as genotype I for D3 and R8 strains and genotype VI for W4 and P4 strains. In addition, molecular dating based on different genes suggests that D3 and R8 diverged from their common ancestor at around 1998; W4 and P4 diverged from their common ancestor at around 1999. Subsequent selective pressure analysis displayed specific traits of genes evolution in all 4 strains since their divergence from the recent common ancestor. Furthermore, the geographic origins of 4 strains were deduced to be from Europe via two independent introduction events by phylogeographical analysis. This provides insights to the potential influence of waterfowl migration on NDV epidemiology. © 2011 Elsevier B.V.",analysis;article;bird;chicken;China;duck;embryo;Europe;gene sequence;genetic trait;genome;genotype;molecular evolution;Newcastle disease virus;nonhuman;nucleotide sequence;pathogenicity;phylogeny;phylogeography;virus isolation;virus strain,"Cai, S.;Li, J.;Wong, M. T.;Jiao, P.;Fan, H.;Liu, D.;Liao, M.;Jiang, J.;Shi, M.;Lam, T. T. Y.;Ren, T.;Leung, F. C. C.",2011,,10.1016/j.vetmic.2011.04.014,0
289,Identification and analysis of differentially-expressed microRNAs in Japanese encephalitis virus-infected PK-15 cells with deep sequencing,"Japanese encephalitis virus (JEV), a mosquito-borne Flavivirus, causes acute viral encephalitis with high morbidity and mortality in humans and animals. MicroRNAs (miRNAs) are small noncoding RNAs that are important modulators of the intricate host-pathogen interaction networks. However, our knowledge of the changes that occur in miRNAs in host cells after JEV infection is still limited. To understand the molecular pathogenesis of JEV at the level of posttranscriptional regulation, we used Illumina deep sequencing to sequence two small RNA libraries prepared from PK-15 cells before and after JEV infection. We identified 522 and 427 miRNAs in the infected and uninfected cells, respectively. Overall, 132 miRNAs were expressed significantly differently after challenge with JEV: 78 were upregulated and 54 downregulated. The sequencing results for selected miRNAs were confirmed with RT-qPCR. GO analysis of the host target genes revealed that these dysregulated miRNAs are involved in complex cellular pathways, including the metabolic pathway, inflammatory response and immune response. To our knowledge, this is the first report of the comparative expression of miRNAs in PK-15 cells after JEV infection. Our findings will underpin further studies of miRNAs' roles in JEV replication and identify potential candidates for antiviral therapies against JEV.","Animals;Cell Line;Chromosomes, Mammalian/ge [Genetics];*Encephalitis Virus, Japanese/ph [Physiology];*Encephalitis, Japanese/ge [Genetics];*Encephalitis, Japanese/vi [Virology];*Gene Expression Profiling;*Gene Expression Regulation;Gene Ontology;*High-Throughput Nucleotide Sequencing/mt [Methods];*MicroRNAs/ge [Genetics];MicroRNAs/me [Metabolism];Molecular Sequence Annotation;Real-Time Polymerase Chain Reaction;Reproducibility of Results;Sus scrofa;0 (MicroRNAs)","Cai, Y.;Zhu, L.;Zhou, Y.;Liu, X.;Liu, X.;Li, X.;Lang, Q.;Qiao, X.;Xu, Z.",2015,Jan 20,,0
290,Tiny but mighty: The role of the rumen microbes in livestock production,,,"Cammack, K. M.;Austin, K. J.;Lamberson, W. R.",,,,0
291,RUMINNAT NUTRITION SYMPOSIUM: Tiny but mighty: the role of the rumen microbes in livestock production,"The microbes inhabiting the rumen convert low-quality, fibrous, plant material into useable energy for the host ruminant. Consisting of bacteria, protozoa, fungi, archaea, and viruses, the rumen microbiome composes a sophisticated network of symbiosis essential to maintenance, immune function, and overall production efficiency of the host ruminant. Robert Hungate laid the foundation for rumen microbiome research. This area of research has expanded immensely with advances in methodology and technology that have not only improved the ability to describe microbes in taxonomic and density terms but also characterize populations of microbes, their functions, and their interactions with each other and the host. The interplay between the rumen microbiome and the host contributes to variation in many phenotypic traits expressed by the host animal. A better understanding of how the rumen micro biome influences host health and performance may lead to novel strategies and treatments for trait improvement. Furthermore, elucidation of maternal, genetic, and environmental factors that influence rumen microbiome establishment and development may provide novel insights into possible mechanisms for manipulating the rumen microbial composition to enhance long-term host health and performance. The potential for these tiny but mighty rumen microbes to play a role in improving livestock production is appreciated despite being relatively obscure.",metagenomics;microbes;performance;production;rumen;RESIDUAL FEED-INTAKE;LACTATING DAIRY-COWS;GASTROINTESTINAL-TRACT;GUT;MICROBIOME;BACTERIAL COMMUNITY;METHANE EMISSIONS;BEEF-CATTLE;EARLY-LIFE;MEGASPHAERA-ELSDENII;ENTERIC METHANE,"Cammack, K. M.;Austin, K. J.;Lamberson, W. R.;Conant, G. C.;Cunningham, H. C.",2018,Feb,,0
292,Complete Genome Sequence of Porcine Parvovirus 2 Recovered from Swine Sera,"A complete genomic sequence of porcine parvovirus 2 (PPV-2) was detected by viral metagenome analysis on swine sera. A phylogenetic analysis of this genome reveals that it is highly similar to previously reported North American PPV-2 genomes. The complete PPV-2 sequence is 5,426 nucleotides long.",,"Campos, F. S.;Kluge, M.;Franco, A. C.;Giongo, A.;Valdez, F. P.;Saddi, T. M.;Brito, W. M.;Roehe, P. M.",2016,Jan 28,,1
293,First detection and molecular characterization of Nebovirus in Brazil,"Nebovirus is a new genus of viruses belonging to the Caliciviridae family recently characterized in cattle, and is associated with gastrointestinal disorders, such as diarrhoea, anorexia and intestinal lesions particularly in calves. The aim of this study was to investigate the prevalence of neboviruses in Brazilian cattle and analyse phylogenetically the virus strains detected. A prevalence of 4·8% of neboviruses in faecal samples from 62 head of cattle from different Brazilian states was detected. All positive animals were aged <20 days and had diarrhoea. Phylogenetic analysis clustered the virus sequences into the Newbury1 clade. There was >96·0% nt (100% aa) sequence identity between the virus sequences in this study and >88·8% nt (>94·4% aa) identity with Newbury1/UK. Our results indicate, for the first time, the occurrence of neboviruses in Brazil as well as in South America, and the first Newbury1-like nebovirus found outside the UK.",article;bovine;Brazil;Caliciviridae;controlled study;diarrhea;feces;female;male;Nebovirus;nonhuman;nucleotide sequence;phylogeny;prevalence;reverse transcription polymerase chain reaction;South America;virus detection;virus strain,"Candido, M.;Alencar, A. L. F.;Almeida-Queiroz, S. R.;Buzinaro, M. G.;Munin, F. S.;Godoy, S. H. S.;Livonesi, M. C.;Fernandes, A. M.;Sousa, R. L. M.",2016,,10.1017/s0950268816000029,0
294,Lambda display phage as a mucosal vaccine delivery vehicle for peptide antigens,"Bacteriophage are structurally stable in the gastro-intestinal tract and have favorable traits of safety, stability, ease of production, and immunogenicity. These attributes make them potential candidates as oral vaccine delivery vehicles but little is known about their capacity to induce mucosal immune responses in the small intestine. Whole body imaging of mice confirmed lambda bacteriophage (LP) were distributed throughout the gastro-intestinal tract 24 h after oral delivery. In newborn calves, targeted delivery of LP within the small intestine confirmed LP were immunogenic in a dose-dependent manner and were taken up by Peyer's patches. LP-specific IgA responses were induced within both Peyer's patches and draining mesenteric lymph nodes. A lambda display phage (LDP) was constructed to present three immunogenic disease specific epitopes (DSE) from cervid prion protein (amino acids 130-140 [YML]; 163-170 [YRR]; and 171-178[YRR]) fused to phage capsid head protein D (LDP-DSE). Targeted delivery of purified LDP-DSE to intestinal segments induced IgA responses to all three peptide epitopes. Further, delivery of bacteria expressing soluble D-DSE also induced epitope-specific IgA responses in the targeted Peyer's patches. These are the first studies to report use of LDP to induce epitope-specific IgA responses in the small intestine and confirm Peyer's patches function as a site for LP uptake. Furthermore, IgA responses to peptide epitopes on LDP were observed in the absence of a mucosal adjuvant. These observations confirm LDP have the capacity to function as a mucosal delivery vehicle with protein D as an effective carrier for peptide epitopes. (C) 2017 Elsevier Ltd. All rights reserved.",IgA;Lambda display phage;Mucosal immune responses;Peptide antigens;Peyer's patches;BACTERIOPHAGE-T4 CAPSID SURFACE;IN-VIVO;ESCHERICHIA-COLI;RESPONSES;VIROME;INDUCTION;VIRUSES;EPITOPE;CALVES;ILEAL,"Cano, P. G.;Gamage, L. N. A.;Marciniuk, K.;Hayes, C.;Napper, S.;Hayes, S.;Griebel, P. J.",2017,Dec,,0
295,Two novel parvoviruses in frugivorous new and old world bats,"Bats, a globally distributed group of mammals with high ecological importance, are increasingly recognized as natural reservoir hosts for viral agents of significance to human and animal health. In the present study, we evaluated pools of blood samples obtained from two phylogenetically distant bat families, in particular from flying foxes (Pteropodidae), Eidolon helvum in West Africa, and from two species of New World leaf-nosed fruit bats (Phyllostomidae), Artibeus jamaicensis and Artibeus lituratus in Central America. A sequence-independent virus discovery technique (VIDISCA) was used in combination with high throughput sequencing to detect two novel parvoviruses: a PARV4-like virus named Eh-BtPV-1 in Eidolon helvum from Ghana and the first member of a putative new genus in Artibeus jamaicensis from Panama (Aj-BtPV-1). Those viruses were circulating in the corresponding bat colony at rates of 7-8%. Aj-BtPV-1 was also found in Artibeus lituratus (5.5%). Both viruses were detected in the blood of infected animals at high concentrations: up to 10E8 and to 10E10 copies/ml for Aj-BtPV-1 and Eh-BtPV-1 respectively. Eh-BtPV-1 was additionally detected in all organs collected from bats (brain, lungs, liver, spleen, kidneys and intestine) and spleen and kidneys were identified as the most likely sites where viral replication takes place. Our study shows that bat parvoviruses share common ancestors with known parvoviruses of humans and livestock. We also provide evidence that a variety of Parvovirinae are able to cause active infection in bats and that they are widely distributed in these animals with different geographic origin, ecologies and climatic ranges. © 2011 Canuti et al.",Africa;animal tissue;Artibeus jamaicensis;Artibeus lituratus;article;bat;blood sampling;brain;Central America;controlled study;Eidolon helvum;frugivore;genome analysis;geographic origin;Ghana;high throughput sequencing;intestine;kidney;liver;lung;molecular phylogeny;new genus;nonhuman;nucleotide sequence;Panama;Parvoviridae;Phyllostomidae;flying fox;sequence analysis;species distribution;spleen;tissue distribution;unindexed sequence;virus detection;virus genome;virus identification;virus replication,"Canuti, M.;Eis-Huebinger, A. M.;Deijs, M.;de Vries, M.;Drexler, J. F.;Oppong, S. K.;Müller, M. A.;Klose, S. M.;Wellinghausen, N.;Cottontail, V. M.;Kalko, E. K. V.;Drosten, C.;van der Hoek, L.",2011,,10.1371/journal.pone.0029140,0
296,Outbreak of swine influenza in Argentina reveals a non-contemporary human H3N2 virus highly transmissible among pigs,"Sporadic outbreaks of human H3N2 influenza A virus (IAV) infections in swine populations have been reported in Asia, Europe and North America since 1970. In South America, serological surveys in pigs indicate that IAVs of the H3 and H1 subtypes are currently in circulation; however, neither virus isolation nor characterization has been reported. In November 2008, an outbreak of respiratory disease in pigs consistent with swine influenza virus (SIV) infection was detected in Argentina. The current study describes the clinical epidemiology, pathology, and molecular and biological characteristics of the virus. Phylogenetic analysis revealed that the virus isolate shared nucleotide identities of 96-98% with H3N2 IAVs that circulated in humans from 2000 to 2003. Antigenically, sera from experimentally inoculated animals cross-reacted mainly with noncontemporary human-origin H3N2 influenza viruses. In an experimental infection in a commercial swine breed, the virus was of low virulence but was transmitted efficiently to contact pigs and caused severe disease when an infected animal acquired a secondary bacterial infection. This is the first report of a wholly human H3N2 IAV associated with clinical disease in pigs in South America. These studies highlight the importance of two-way transmission of IAVs and SIVs between pigs and humans, and call for enhanced influenza surveillance in the pig population worldwide. © 2011 SGM.",nucleotide;animal tissue;Argentina;article;disease severity;epidemic;Influenza A virus (H3N2);nonhuman;nucleotide sequence;phylogeny;priority journal;randomized controlled trial;Simian immunodeficiency virus;pig;swine influenza;virus isolation;virus transmission;virus virulence,"Cappuccio, J. A.;Pena, L.;Dibárbora, M.;Rimondi, A.;Piñeyro, P.;Insarralde, L.;Quiroga, M. A.;Machuca, M.;Craig, M. I.;Olivera, V.;Chockalingam, A.;Perfumo, C. J.;Perez, D. R.;Pereda, A.",2011,,10.1099/vir.0.036590-0,0
297,Newcastle disease outbreaks in Italy during 2000,"Among the consequences of the epidemic of highly pathogenic avian influenza which affected Italy between 1999 and 2000 was an epidemic of Newcastle disease in northern and central Italy. It affected industrially reared poultry, dealer flocks and backyard flocks, with a total of 254 outbreaks notified up to December 31, 2000. Virological investigations yielded virulent isolates of Newcastle disease virus, which produced intracerebral pathogenicity indices ranging from 1-6 to 2-0 and which, on the basis of their monoclonal antibody binding patterns, could be classified as belonging to group C1. The clinical, gross and microscopical findings were typical of Newcastle disease, and different avian species were susceptible to different degrees. Chickens and guinea fowl appeared to be the most susceptible, followed by pheasants, turkeys and ostriches. The epidemiological inquiry highlighted the crucial role of a broiler hatchery in initiating the epidemic, and of dealers in perpetuating it. The control measures imposed by Directive 92/66/EEC are discussed with reference to the outbreaks in backyard flocks.",monoclonal antibody;antigen binding;article;bird disease;brain infection;chicken;control strategy;controlled study;disease predisposition;epidemic;herd;histopathology;Influenza virus;Italy;microbiological examination;Newcastle disease virus;nonhuman;ostrich;poultry;species difference;turkey (bird);virus classification;virus isolation;virus pathogenesis,"Capua, I.;Dalla Pozza, M.;Mutinelli, F.;Marangon, S.;Terregino, C.",2002,,,0
298,Isolation of an avian paramyxovirus type 9 from migratory waterfowl in Italy [3],,bird disease;duck;fowl;hemagglutination inhibition test;infection risk;Influenza virus;Italy;letter;nonhuman;Orthomyxoviridae;Paramyxoviridae;poultry;serotype;virus characterization;virus classification;virus isolation;virus transmission,"Capua, I.;De Nardi, R.;Beato, M. S.;Terregino, C.;Scremin, M.;Guberti, V.",2004,,,0
299,Neurovirulence of pseudorabies virus,"Virulence is defined as the relative capacity of a microorganism to overcome the defense mechanisms of the host organism and thereby cause disease. Virally induced virulence is usually quantitated by measuring the mean time to death or appearance of symptoms following viral inoculation. In this review we make a distinction between general virulence and neurovirulence. We define neurovirulence as the degree of pathogenesis in the nervous system, but intend it to be more encompassing than the simple ability of the virus to grow in the central nervous system (CNS). This distinction is made possible by recent advances that permit an integrated assessment of the degree of pathology, reactive gliosis, and inflammatory response to infection in the intact organism with specific antisera and molecular probes.",virus antibody;virus antigen;virus DNA;virus envelope protein;central nervous system;central nervous system infection;gliosis;Herpes simplex virus;human;inflammation;latent virus infection;neuropathology;neurotoxicity;nonhuman;pseudorabies;Pseudorabies virus;review;virus classification;virus genome;virus morphology;virus replication;virus virulence,"Card, J. P.;Enquist, L. W.",1995,,,0
300,"Fatal Outbreak in Tonkean Macaques Caused by Possibly Novel Orthopoxvirus, Italy, January 2015 <sup>1</sup>","In January 2015, during a 3-week period, 12 captive Tonkean macacques at a sanctuary in Italy died. An orthopoxvirus infection was suspected because of negative-staining electron microscopy results. The diagnosis was confirmed by histology, virus isolation, and molecular analysis performed on different organs from all animals. An epidemiologic investigation was unable to define the infection source in the surrounding area. Trapped rodents were negative by virologic testing, but specific IgG was detected in 27.27% of small rodents and 14.28% of rats. An attenuated live vaccine was administered to the susceptible monkey population, and no adverse reactions were observed; a detectable humoral immune response was induced in most of the vaccinated animals. We performed molecular characterization of the orthopoxvirus isolate by next-generation sequencing. According to the phylogenetic analysis of the 9 conserved genes, the virus could be part of a novel clade, lying between cowpox and ectromelia viruses.","Animals;Antibodies, Viral/bl [Blood];*Disease Outbreaks;Housing, Animal;Immunity, Humoral/de [Drug Effects];Immunoglobulin G/bl [Blood];Italy/ep [Epidemiology];Macaca;Male;*Monkey Diseases/ep [Epidemiology];Monkey Diseases/im [Immunology];Monkey Diseases/mo [Mortality];Monkey Diseases/pc [Prevention & Control];Orthopoxvirus/cl [Classification];*Orthopoxvirus/ge [Genetics];Orthopoxvirus/ip [Isolation & Purification];Orthopoxvirus/py [Pathogenicity];*Phylogeny;*Poxviridae Infections/ep [Epidemiology];Poxviridae Infections/mo [Mortality];Poxviridae Infections/pc [Prevention & Control];*Poxviridae Infections/ve [Veterinary];Rats;Rodentia/vi [Virology];Skin/pa [Pathology];Skin/vi [Virology];Survival Analysis;Vaccination;Viral Vaccines/ad [Administration & Dosage];0 (Antibodies, Viral);0 (Immunoglobulin G);0 (Viral Vaccines)","Cardeti, G.;Gruber, C. E. M.;Eleni, C.;Carletti, F.;Castilletti, C.;Manna, G.;Rosone, F.;Giombini, E.;Selleri, M.;Lapa, D.;Puro, V.;Di Caro, A.;Lorenzetti, R.;Scicluna, M. T.;Grifoni, G.;Rizzoli, A.;Tagliapietra, V.;De Marco, L.;Capobianchi, M. R.;Autorino, G. L.",2017,12,,0
301,Virological and phylogenetic characterization of attenuated small ruminant lentivirus isolates eluding efficient serological detection,"Three field isolates of small ruminant lentiviruses (SRLVs) were derived from a mixed flock of goats and sheep certified for many years as free of caprine arthritis encephalitis virus (CAEV). The phylogenetic analysis of pol sequences permitted to classify these isolates as A4 subtype. None of the animals showed clinical signs of SRLV infection, confirming previous observations which had suggested that this particular subtype is highly attenuated, at least for goats. A quantitative real time PCR strategy based on primers and probes derived from a highly variable env region permitted us to classify the animals as uninfected, singly or doubly infected. The performance of different serological tools based on this classification revealed their profound inadequacy in monitoring animals infected with this particular SRLV subtype. In vitro, the isolates showed differences in their cytopathicity and a tendency to replicate more efficiently in goat than sheep cells, especially in goat macrophages. By contrast, in vivo, these viruses reached significantly higher viral loads in sheep than in goats. Both env subtypes infected goats and sheep with equal efficiency. One of these, however, reached significantly higher viral loads in both species. In conclusion, we characterized three isolates of the SRLV subtype A4 that efficiently circulate in a mixed herd of goats and sheep in spite of their apparent attenuation and a strict physical separation between goats and sheep. The poor performance of the serological tools applied indicates that, to support an SRLV eradication campaign, it is imperative to develop novel, subtype specific tools. © 2012 Elsevier B.V.",animal cell;article;controlled study;cytopathology;in vitro study;in vivo study;Lentivirus;macrophage;nonhuman;phylogeny;real time polymerase chain reaction;serology;Ovine/caprine lentivirus;virus characterization;virus detection;virus isolation;virus load,"Cardinaux, L.;Zahno, M. L.;Deubelbeiss, M.;Zanoni, R.;Vogt, H. R.;Bertoni, G.",2013,,10.1016/j.vetmic.2012.11.017,0
302,An outbreak of pseudocowpox in fattening calves in southern Brazil,"Pseudocowpox virus is a parapoxvirus frequently associated with papulovesicular and scabby lesions on the teats and udders of milking cows and is often transmitted to human beings. An unusual outbreak of skin disease in fattening calves in southern Brazil is described. Fourteen of 17 male cattle (82%), aged 6-48 months, feeding on grass pastures were affected. Animals developed papules, vesicles, and scabby proliferative lesions on the muzzle in a clinical course of approximately 10-15 days. The scabby lesions often presented with exudation and bleeding. Histological examination of mucocutaneous tissue in detached scabs revealed acanthosis with thickening of the corneal layer and premature keratinization (parakeratotic hyperkeratosis). The dermis had multifocal lymphoplasmacytic infiltrates. Electron microscopic examination of scab specimens revealed typical parapoxvirus particles: oval shaped (260 nm × 160 nm), enveloped, and covered with a helical layer. Polymerase chain reaction using a set of pan-parapoxvirus primers for the B2L gene amplified a 590-bp product out of DNA extracted from scabs. Nucleotide sequencing of the amplicons revealed a nucleotide homology of 97% with Pseudocowpox virus and lower homology with other parapoxviruses: Bovine papular stomatitis virus (84%) and Orf virus (94%). A phylogenetic tree based on the B2L sequence was constructed, showing that the virus clustered with Pseudocowpox virus isolates. © 2012 American Association of Veterinary Laboratory Diagnosticians.",virus DNA;animal;animal disease;article;Brazil;bullous skin disease;case report;bovine;cattle disease;chemistry;cytochemistry;DNA sequence;electron microscopy;epidemic;genetics;isolation and purification;male;molecular genetics;nucleotide sequence;phylogeny;polymerase chain reaction;Poxviridae;poxvirus infection;sequence alignment;ultrastructure;virology,"Cargnelutti, J. F.;Flores, M. M.;Teixeira, F. R. M.;Weiblen, R.;Flores, E. F.",2012,,10.1177/1040638711435408,0
303,Diagnosis and Control of a LPAI H5N8 Outbreak in a Japanese Quail (Coturnix coturnix japonica) Commercial Flock in the Central Valley of California,"In April 2014 an outbreak of low pathogenic avian influenza H5N8 North American genetic lineage was diagnosed in a commercial quail operation in Stanislaus County, California. Sudden increase in mortality prompted the submission of 20 Japanese quail hens (Coturnix c. japonica) to the California Animal Health and Food Safety Laboratory, Turlock Branch. Oropharyngeal and cloacal swabs tested positive for influenza A virus H5N8 by real-time reverse transcription-polymerase chain reaction. The virus was subsequently isolated. In vivo assay and sequencing of the hemagglutinin protein cleavage site classified the virus as a North American genetic lineage of low pathogenicity for chickens. Following the diagnosis, a rapid and coordinated response took place to contain the outbreak. The affected premise was depopulated, cleaned, and disinfected. Three areas from the affected premises-a 3 kilometer (km) radius (High Risk Zone), a 3-10 km area (Buffer Zone), and a 10-20 km (Surveillance Zone)-were established for avian influenza testing of commercial and noncommercial poultry operations. Surveillance testing and rapid control measures were successful in the control and eradication of the outbreak and revealed no area of spread of the virus from the index flock. This report describes the history, diagnosis, surveillance, and control measures applied to manage this outbreak.",animal;California;classification;Coturnix;Influenza A virus;avian influenza;bird disease;virology,"Carnaccini, S.;Crossley, B.;Breitmeyer, R.;Charlton, B. R.;Bland, M.;Fowler, K.;De La Torre, F.;Torchetti, M. K.;Wong, S. S.;Wilson, D.;Jones, A.;Sentíes-Cué, C. G.",2015,,10.1637/11018-011515-Case,0
304,High throughput sequencing and comparative genomics of foot-and-mouth disease virus,"Despite a basic understanding of many aspects of FMD biology, much information regarding FMDV virulence, host range, and virus transmission remains poorly understood. Here we present how the use of high throughput sequencing for complete genome sequences of foot-and mouth disease virus (FMDV) led to a series of new insights into viral genome sequence conservation and variability, genetic diversity in nature and phylogenetic classification of isolates, including the first complete sequences of the South African Territories type 1 and 3 (SAT1 and SAT3) genomes. Comparative genomic analysis of full-length sequences of FMDV isolates did allow: (i) the identification of highly conserved regulatory or coding regions which are critical for aspects of virus biology as well as novel viral genomic motifs with likely biological relevance; (ii) characterization of the first complete sequences of the SAT1 and SAT3 genomes; (iii) identification of a novel SAT virus lineage genetically distinct from other SAT and Euro-Asiatic lineages; (iv) precise identification of strains circulating around the world for epidemiological and forensic attribution; (v) assessment of mutation and recombination processes as mechanisms equally involved in evolution; (vi) mutation rates, tolerance and constraints of genes and proteins during evolution of FMD viruses during in vivo replication and (vi) support for the hypothesis of a new evolutionary model.",animal;bovid;conference paper;foot and mouth disease;Foot and mouth disease virus;genetic reassortment;genetic recombination;genetics;genomics;methodology;mutation;phylogeny;physiology;pig;virology;virus genome;virus replication,"Carrillo, C.;Tulman, E. R.;Delhon, G.;Lu, Z.;Carreno, A.;Vagnozzi, A.;Kutish, G. F.;Rock, D. L.",2006,,,0
305,The global virome project,,,"Carroll, D.;Daszak, P.;Wolfe, N. D.;Gao, G. F.",2018,,,0
306,Chasing Jenner's vaccine: Revisiting Cowpox virus classification,"Cowpox virus (CPXV) is described as the source of the first vaccine used to prevent the onset and spread of an infectious disease. It is one of the earliest described members of the genus Orthopoxvirus, which includes the viruses that cause smallpox and monkeypox in humans. Both the historic and current literature describe ""cowpox"" as a disease with a single etiologic agent. Genotypic data presented herein indicate that CPXV is not a single species, but a composite of several (up to 5) species that can infect cows, humans, and other animals. The practice of naming agents after the host in which the resultant disease manifests obfuscates the true taxonomic relationships of ""cowpox"" isolates. These data support the elevation of as many as four new species within the traditional ""cowpox"" group and suggest that both wild and modern vaccine strains of Vaccinia virus are most closely related to CPXV of continental Europe rather than the United Kingdom, the homeland of the vaccine.",Chasing Jenner vaccine;Cowpox virus vaccine;unclassified drug;virus vaccine;article;controlled study;cow;Cowpox virus;Europe;genotype;host susceptibility;nonhuman;nucleotide sequence;phylogeny;taxonomy;United Kingdom;Vaccinia virus;virus isolation;virus strain,"Carroll, D. S.;Emerson, G. L.;Li, Y.;Sammons, S.;Olson, V.;Frace, M.;Nakazawa, Y.;Czerny, C. P.;Tryland, M.;Kolodziejek, J.;Nowotny, N.;Olsen-Rasmussen, M.;Khristova, M.;Govil, D.;Karem, K.;Damon, I. K.;Meyer, H.",2011,,10.1371/journal.pone.0023086,0
307,Vaccinia and other viruses with available vaccines show marked homology with the HIV-1 envelope glycoprotein: The prospect of using existing vaccines to stem the AIDS pandemic,"Cross-reactive immunity occurs when infection with or vaccination against one virus protects against another related family member. A search for homologues of the HIV-1 envelope glycoprotein revealed that it is composed of thousands of intercalating and overlapping viral matches of pentapeptide or longer gapped consensi, belonging to over 70% of the currently sequenced virome, infecting all kingdoms from bacteria to man. It was also highly homologous to proteins from the Visna/Maedi and other ovine viruses, while other proteins (nef/tat/gag/pol) were homologous to proteins from the equine infectious anaemia virus and HTLV-2/HTLV-3 viruses. This phenomenon suggests that horizontal gene transfer from coinfecting RNA and DNA viruses to retroviruses is extensive, providing a route for the subsequent insertion of non-retroviral genes into human and other genomes via retroviral integration. This homology includes all viruses for which vaccines already exist. Cross-reactive immunity may be operative in AIDS, as Vaccinia vaccination decreases viral replication in HIV-1 infected patients' cells, for the CCR5 tropic form. Measles, Dengue virus, or GB virus C infections also decrease the HIV-1 viral load. A resumption of Vaccinia/smallpox vaccination might be expected to have a significant effect on the AIDS pandemic, and a careful study of the potential uses of other existing viral and bacterial vaccines merits close attention. This phenomenon may also be relevant to other recalcitrant viruses, bacteria, and parasites for which no vaccine exists and the armory of existing vaccines may have a role to play in diseases other than those for which they were designed. © 2012 Informa Healthcare USA, Inc.",Human immunodeficiency virus vaccine;pentapeptide;virus glycoprotein;acquired immune deficiency syndrome;amino acid sequence;article;cross reaction;Dengue virus;Equine infectious anemia virus;gene insertion;gene transfer;Hepatitis A virus;Hepatitis B virus;Hepatitis G virus;human;Human immunodeficiency virus 1;Human immunodeficiency virus infected patient;Human T-lymphotropic virus 2;Influenza A virus;Japanese encephalitis virus;maedi visna;Measles virus;mixed infection;Mumps virus;nonhuman;pandemic;Papillomaviridae;Poliomyelitis virus;priority journal;Rabies virus;Retroviridae;Rotavirus;Rubella virus;sequence homology;Smallpox virus;vaccination;vaccinia;Vaccinia virus;Varicella zoster virus;virus envelope;virus load;virus replication;Yellow fever virus,"Carter, C. J. C.",2012,,10.3109/08923973.2011.596542,0
308,Hepatitis E Virus: A Cross-Sectional Serological and Virological Study in Pigs and Humans at Zoonotic Risk within a High-Density Pig Farming Area,"An increase in autochthonous hepatitis E virus (HEV) infections has been recorded in Italy suspected to be zoonotically transmitted from pigs; this study was carried out to determinate the seroprevalence and risk factors associated with hepatitis HEV exposition, both in swine and humans working in pig farms, located within a high-density pig farming area in Piedmont region, north-western Italy. The presence of viral RNA in human and swine samples was also evaluated, and phylogenetic analysis was performed on HEV-positive samples. Forty-two swine farms were sampled; 142 workers were enrolled in the study and classified into two groups: (i) 69 workers with occupational contact with swine (including veterinarians and farmers) recruited in the 42 sampled farms; (ii) 73 without occupational contact with swine. Forty-one of 42 (97%) swine farms resulted positive to enzyme-linked immunosorbent assay test for HEV antibodies (Abs). Overall seroprevalence in swine was 50% (441/879), with seropositivity rate higher in sows (333/469, 71%). HEV RNA in stool samples was detected in animals from 13 of 42 tested farms (31%), and a higher positivity resulted in weaners (40/246, 16.3%). Phylogenetic analysis classified all HEV isolates within genotype 3 (subtypes 3f, 3e, 3c). All humans were negative for HEV viral genome in blood. Five of 142 sera were positive for IgG anti-HEV with an overall prevalence of 3.52% with no statistically significant differences in prevalence rates between workers at zoonotic risk and the control group (5.7% versus 1.3%). In contrast, a significant difference (OR 10.1) was observed within the subgroup including subjects exposed for short periods (veterinarians) compared with those who worked for long periods (farmers) suggesting a correlation between the time of exposure and the likelihood of HEV infection. Reporting HEV infection is not mandatory in Italy, but a constant epidemiological surveillance should be ensured to clarify the epidemiology of this disease.",immunoglobulin G;virus RNA;adult;agricultural worker;article;cross-sectional study;enzyme linked immunosorbent assay;feces analysis;female;genotype;Hepatitis E virus;human;infection risk;major clinical study;male;middle aged;nonhuman;occupational disease;phylogeny;pig;pig farming;questionnaire;reverse transcription polymerase chain reaction;serology;seroprevalence;veterinarian;virology;zoonosis,"Caruso, C.;Peletto, S.;Rosamilia, A.;Modesto, P.;Chiavacci, L.;Sona, B.;Balsamelli, F.;Ghisetti, V.;Acutis, P. L.;Pezzoni, G.;Brocchi, E.;Vitale, N.;Masoero, L.",2017,,10.1111/tbed.12533,0
309,Bovine papillomavirus in Brazil: Detection of coinfection of unusual types by a PCR-RFLP method,"Bovine papillomavirus (BPV) is recognized as a causal agent of benign and malignant tumors in cattle. Thirteen types of BPV are currently characterized and classified into three distinct genera, associated with different pathological outcomes. The described BPV types as well as other putative ones have been demonstrated by molecular biology methods, mainly by the employment of degenerated PCR primers. Specifically, divergences in the nucleotide sequence of the L1 gene are useful for the identification and classification of new papillomavirus types. On the present work, a method based on the PCR-RFLP technique and DNA sequencing was evaluated as a screening tool, allowing for the detection of two relatively rare types of BPV in lesions samples from a six-year-old Holstein dairy cow, chronically affected with cutaneous papillomatosis. These findings point to the dissemination of BPVs with unclear pathogenic potential, since two relatively rare, new described BPV types, which were first characterized in Japan, were also detected in Brazil. © 2013 R. F. Carvalho et al.",virus DNA;article;Bovine papillomavirus;bovine papillomavirus infection;Brazil;cattle disease;controlled study;dairy cattle;DNA sequence;mixed infection;nonhuman;nucleotide sequence;Papillomaviridae;papillomatosis;papillomavirus infection;polymerase chain reaction;restriction fragment length polymorphism;virus classification;virus detection,"Carvalho, R. F.;Sakata, S. T.;Giovanni, D. N. S.;Mori, E.;Brandão, P. E.;Richtzenhain, L. J.;Pozzi, C. R.;Arcaro, J. R. P.;Miranda, M. S.;Mazzuchelli-De-Souza, J.;Melo, T. C.;Comenale, G.;Assaf, S. L. M. R.;Beçak, W.;Stocco, R. C.",2013,,10.1155/2013/270898,0
310,Two novel circo-like viruses detected in human feces: complete genome sequencing and electron microscopy analysis,"The application of viral metagenomic techniques and a series of PCRs in a human fecal sample enabled the detection of two novel circular unisense DNA viral genomes with 92% nucleotide similarity. The viruses were tentatively named circa-like virus-Brazil (CLV-BR) strains hs1 and hs2 and have genome lengths of 2526 and 2533 nucleotides, respectively. Four major open reading frames (ORFs) were identified in each of the genomes, and differences between the two genomes were primarily observed in ORF 2. Only ORF 3 showed significant amino acid similarities to a putative rolling circle replication initiator protein (Rep), although with low identity (36%). Our phylogenetic analysis, based on the Rep protein, demonstrated that the CLV-BRs do not cluster with members of the Circoviridae, Nanoviridae or Geminiviridae families and are more closely related to circo-like genomes previously identified in reclaimed water and feces of a wild rodent and of a bat. The CLV-BRs are members of a putative new family of circular Rep-encoding ssDNA viruses. Electron microscopy revealed icosahedral (similar to 23 nm) structures, likely reflecting the novel viruses, and rod-shaped viral particles (similar to 65-460 x 21 x 10 nm in length, diameter, and axial canal, respectively). Circo-like viruses have been detected in stool samples from humans and other mammals (bats, rodents, chimpanzees and bovines), cerebrospinal fluid and sera from humans, as well as samples from many other sources, e.g., insects, meat and the environment. Further studies are needed to classify all novel circular DNA viruses and elucidate their hosts, pathogenicity and evolutionary history. (C) 2013 Elsevier B.V. All rights reserved.",Metagenomics;Novel circo-like virus;Complete genome;Electron;microscopy;Rep gene;Circular Rep-encoding ssDNA virus;CIRCULAR SSDNA VIRUSES;VIRAL COMMUNITY;DNA VIRUSES;METAGENOMIC;ANALYSES;GENETIC DIVERSITY;MAMMALIAN VIRUSES;STOOL SAMPLES;IDENTIFICATION;CIRCOVIRUSES;REPLICATION,"Castrignano, S. B.;Nagasse-Sugahara, T. K.;Kisielius, J. J.;Ueda-Ito, M.;Brandao, P. E.;Curti, S. P.",2013,Dec,,0
311,Research of Torque Teno Virus (TTV) in Serum and Total Blood of Brazilian Non-Human Primates and in Chicken Plasma (Gallus gallus domesticus) by the PCR N22 Region,"Torque teno virus (TTV) is a recently discovered DNA virus that was originally isolated from a Japanese patient ( initials, TT) with post-transfusion hepatitis of unknown aetiology. TTV is an circular DNA virus classified recently together with related Torque teno minivirus, into a new genus called Anellovirus. Infection TTV has been detected in a range of non-human primates as well as domestic animals. The purpose of this study was to search TTV in the serum and total blood of Brazilian monkeys and in plasma of domestic chickens by seminested PCR of coding region (N22), followed by a genomic sequence and phylogenetic analysis. No serum sample was amplified. TTV DNA was detected in total blood from 3 (4%) out of 75 brown-capuchin ( Cebus apella) and from 1 (25%) out of 4 golden-headed lion-tamarin ( Leontopithecus chrysomelas). Phylogenetic analysis revealed that one sample showed similarity with one sequence of the cotton top tamarin ( Saguinus oedipus) (So-TTV2) and with one of the douroucoulis (Aotes trivirgatus) (At-TTV3). Two samples showed similarity with a human Torque Teno Mini Virus (TLMV). The other sample clustered with one sequence of the chimpanzee (Pt-TTV6) and with the human TTV strain TA278. The plasma chicken samples tested were all negative. The amino acid sequences reported in this study are the first obtained in Brazil from total blood of non-human primates naturally infected by TTV.",Torque teno virus;Non-humans primates;Coding region;Amino acid;sequencing;TRANSFUSION-TRANSMITTED VIRUS;INTRAVENOUS-DRUG-USERS;SPECIES-SPECIFIC;TTVS;CIRCULAR DNA GENOME;MINI VIRUS;NUCLEOTIDE-SEQUENCES;MIXED;INFECTIONS;HIGHLY PREVALENT;ANEMIA VIRUS;HUMANS,"Catroxo, M. H. B.;Nishiya, A.;Sabino, E.;Teixeira, P. S.;Petrella, S.;Milanelo, L.;Vieira, J. C. F.;Diaz, R. S.",2008,Jun,,0
312,Human hepatitis E virus circulation in Bulgaria: Deep Bayesian phylogenetic analysis for viral spread control in the country,"Hepatitis E virus (HEV) infection in Bulgaria is endemic, as demonstrated by the seroprevalence of antibody against the virus in the general population and by the high prevalence of clinical cases registered. In this study, a deep Bayesian phylogenetic analysis has been performed to provide information on the genetic diversity and the spread of HEV genotypes in Bulgaria. Three different data sets of HEV virus was built for genotyping by the maximum likelihood method, for evolutionary rate estimated by Bayesian Markov Chain Monte Carlo approach, for demographic history investigation and for selective pressure analysis. The evolutionary rate for genotype 3e, was 351 × 10−3 substitution/site/year (95% highest posterior density [95% HPD]: 145 × 10 −3-575 × 10 −3). The root of the time to the most recent common ancestor of the Bayesian maximum clade credibility tree of HEV 3e genotype corresponded to 1965 (HPD 95% 1949-1994). The Bulgarian sequences mainly clustered in the main clade (clade A). The monophyletic clade included all Bulgarian genotype 3e sequences. The demographic history showed a slight growth from 1995 to 2000, followed by a sort of bottleneck in 2010s, a peak in 2011 and a new growth to 2015. Selection pressure analysis did not show sites under positive pressure but 64 statistically significant sites under negative selection. Molecular epidemiological surveillance by Bayesian phylogeny of HEV virus can contribute to trace the way of human infection after contact with swine source directly or heating meat improving public health control.",animal experiment;article;Bulgaria;cladistics;controlled study;evolutionary rate;genetic variability;heating;Hepatitis E virus;Markov chain;maximum likelihood method;nonhuman;phylogeny;pig;public health,"Cella, E.;Golkocheva-Markova, E.;Sagnelli, C.;Scolamacchia, V.;Bruni, R.;Villano, U.;Ciccaglione, A. R.;Equestre, M.;Sagnelli, E.;Angeletti, S.;Ciccozzi, M.",2019,,10.1002/jmv.25296,0
313,First report of Cowpea mild mottle virus in chia (Salvia hispanica),"Chia (Salvia hispanica), a herbaceous plant of Lamiaceae family, has gained popularity due to its high concentrations of health-beneficial Omega-3 fatty acids. Plants showing different virus-like symptoms were observed in the principal chia production areas in Argentina. Some plants exhibited yellowing, mottled and blistering leaves, and others shortened internodes and leaf and stem deformation. The aim of this study was to identify the viruses infecting this crop. Forty symptomatic chia plants were collected from nine production fields in northeastern Argentina. The samples were tested for Alfalfa mosaic virus (AMV), Cowpea mild mottle virus (CPMMV), Cucumber mosaic virus (CMV), Tobacco mosaic virus (TMV) and Tospovirus group (I, II and III) by DAS-ELISA, for the genera Potyvirus by PTA-ELISA and for Begomovirus by PCR. CPMMV was detected in three plants with different kind of symptoms. In these plants, feather-like inclusions formed by virions were observed with transmission electron microscopy. ORF2 to ORF6 (2462 nucleotides) from the CPMMV viral genome was amplified by RT-PCR. Nucleotide (nt) sequence of the coat-protein gene (CP - ORF5) of the chia virus isolate was obtained and compared with 31 CPMMV sequences reported in GenBank. Results showed between 75.5% and 99.0% of nt identity, which is above the International Committee on Taxonomy of Viruses criteria for Carlavirus species differentiation. The phylogenetic analysis with the CP gene nt sequences revealed that the CPMMV chia isolate grouped with other CPMMV isolates from other plant species from Brazil, Ghana, India, Puerto Rico, Taiwan and USA, but were separated from four others from India. This is the first report of the presence of CPMMV in chia in the world. Although the other viruses were not detected in this work, it is possible that the different symptoms observed could be produced by a mixture of viruses because CPMMV was found in chia plants with different symptoms. (C) 2016 Elsevier Ltd. All rights reserved.",Carlavirus;CPMMV;Lamiaceae;Plant virus;VIGNA-UNGUICULATA,"Celli, M. G.;Perotto, M. C.;Merino, M. C.;Nome, C. F. D.;Flores, C. R.;Conci, V. C.",2016,Nov,,0
314,Taxon ordering in phylogenetic trees by means of evolutionary algorithms,"BACKGROUND: In in a typical ""left-to-right"" phylogenetic tree, the vertical order of taxa is meaningless, as only the branch path between them reflects their degree of similarity. To make unresolved trees more informative, here we propose an innovative Evolutionary Algorithm (EA) method to search the best graphical representation of unresolved trees, in order to give a biological meaning to the vertical order of taxa. METHODS: Starting from a West Nile virus phylogenetic tree, in a (1 + 1)-EA we evolved it by randomly rotating the internal nodes and selecting the tree with better fitness every generation. The fitness is a sum of genetic distances between the considered taxon and the r (radius) next taxa. After having set the radius to the best performance, we evolved the trees with (lambda + mu)-EAs to study the influence of population on the algorithm. RESULTS: The (1 + 1)-EA consistently outperformed a random search, and better results were obtained setting the radius to 8. The (lambda + mu)-EAs performed as well as the (1 + 1), except the larger population (1000 + 1000). CONCLUSIONS: The trees after the evolution showed an improvement both of the fitness (based on a genetic distance matrix, then close taxa are actually genetically close), and of the biological interpretation. Samples collected in the same state or year moved close each other, making the tree easier to interpret. Biological relationships between samples are also easier to observe.",,"Cerutti, F.;Bertolotti, L.;Goldberg, T. L.;Giacobini, M.",2011,Jul 01,,0
315,Phylogenetic characterization of classical swine fever viruses isolated in Korea between 1988 and 2003,"Twenty-four isolates of classical swine fever (CSF) virus which were obtained from CSF outbreaks during 1988 and 2003 in the Republic of Korea were genetically characterized for partial E2 gene (190 nucleotides) and compared with CSF viruses reported by other countries. Phylogenetic analyses classified Korean field isolates between1988 and 1999 into subgroup 3.2, forming an independent clade distinct from CSF viruses identified in other countries. In contrast, the viruses isolated during 2002-2003 CSF epidemics were classified into a different subgroup (2.1). The 2.1 viruses showed a close genetic relationship (92.1-100% nucleotide similarity) with CSF viruses reported from China and Taiwan in 1998-2001. As no evidence of CSF virus infection was detected in the wild boar (Sus scrofa coreanus) population that inhabits Korea, the results of molecular characterization strongly suggest that CSF epidemic outbreaks in Korean swine populations during 2002-2003 were attributed to the introduction of a new strain or strains, likely from neighboring countries. © 2007 Elsevier B.V. All rights reserved.",glycoprotein E2;nucleotide;article;China;epidemic;Korea;molecular phylogeny;nonhuman;nucleotide sequence;Pestivirus;phylogeny;priority journal;Taiwan;unindexed sequence;virus isolation;virus strain;European wild boar,"Cha, S. H.;Choi, E. J.;Park, J. H.;Yoon, S. R.;Kwon, J. H.;Yoon, K. J.;Song, J. Y.",2007,,10.1016/j.virusres.2007.01.017,0
316,Molecular characterization of bovine ephemeral fever virus in Thailand between 2013 and 2017,"Bovine ephemeral fever (BEF) is an arthropod-borne disease caused by bovine ephemeral fever virus (BEFV), a negative sense, single-stranded RNA virus. BEFV is endemic in tropical and sub-tropical regions including Thailand, a country in mainland Southeast Asia. However, there are few studies on BEFV and no available information regarding molecular characteristics of BEFV in Thailand. Therefore, the aims of this study were to genetically characterize Thai BEFVs and reveal their evolutions by phylogenetic analysis of G gene ectodomain sequences. From 2013 to 2017, blood samples were collected from bovine that matched with BEF case definition from three regions of Thailand. Thai BEFV G genes and a whole genome of an isolate, East Asia/TH/LRI0045/2016, were sequenced and characterized. Additionally, their phylogenies were constructed. This is the first report on genetics of BEFV in Southeast Asia. G ectodomain encoding region of Thai BEFV found during 2013–2017 are closely related to the second and third sub-clades of East Asia lineage. In addition, we observed mutation in the putative P’ ORF of all Thai BEFVs which generated a premature stop codon. Thai G gene sequences are closely related to those of mainland Chinese and Taiwanese isolates. The whole genomic sequences of Thai BEFV and East Asia/China/JT02 L/2002 possess common characteristics, suggesting shared evolutionary relationship between East and Southeast Asian strains. Further studies on relationship between animal translocation, circulation of BEFV in Greater Mekong subregion and acquisition of more G gene sequences may improve understanding of BEFV epidemiology in mainland Southeast Asia.",amino acid;cysteine;glycoprotein;nucleotide;amino acid sequence;amino acid substitution;article;blood sampling;Bovine ephemeral fever virus;gene sequence;genetic variation;maximum likelihood method;nonhuman;phylogenetic tree;phylogeny;stop codon;Thailand;transcription initiation;transcription termination;virus characterization,"Chaisirirat, T.;Sangthong, P.;Arunvipas, P.;Petcharat, N.;Thangthamniyom, N.;Chumsing, W.;Lekcharoensuk, P.",2018,,10.1016/j.vetmic.2018.10.013,0
317,Metagenomic analysis of antibiotic resistance genes in dairy cow feces following therapeutic administration of third generation cephalosporin,"Although dairy manure is widely applied to land, it is relatively understudied compared to other livestock as a potential source of antibiotic resistance genes (ARGs) to the environment and ultimately to human pathogens. Ceftiofur, the most widely used antibiotic used in U.S. dairy cows, is a 3rd generation cephalosporin, a critically important class of antibiotics to human health. The objective of this study was to evaluate the effect of typical ceftiofur antibiotic treatment on the prevalence of ARGs in the fecal microbiome of dairy cows using a metagenomics approach. β-lactam ARGs were found to be elevated in feces from Holstein cows administered ceftiofur (n = 3) relative to control cows (n = 3). However, total numbers of ARGs across all classes were not measurably affected by ceftiofur treatment, likely because of dominance of unaffected tetracycline ARGs in the metagenomics libraries. Functional analysis via MG-RAST further revealed that ceftiofur treatment resulted in increases in gene sequences associated with ""phages, prophages, transposable elements, and plasmids"", suggesting that this treatment also enriched the ability to horizontally transfer ARGs. Additional functional shifts were noted with ceftiofur treatment (e.g., increase in genes associated with stress, chemotaxis, and resistance to toxic compounds; decrease in genes associated with metabolism of aromatic compounds and cell division and cell cycle), along with measureable taxonomic shifts (increase in Bacterioidia and decrease in Actinobacteria). This study demonstrates that ceftiofur has a broad, measureable and immediate effect on the cow fecal metagenome. Given the importance of 3rd generation cephalospirins to human medicine, their continued use in dairy cattle should be carefully considered and waste treatment strategies to slow ARG dissemination from dairy cattle manure should be explored. Copyright:",ceftiofur;cephalosporin derivative;ribonuclease A;Actinobacteria;antibiotic resistance;ARG gene;article;bacterial virulence;centrifugation;chemotaxis;controlled study;dairy cattle;DNA extraction;feces analysis;functional assessment;gene;gene sequence;Holstein cattle;manure;metagenomics;microbiome;nitrogen metabolism;nonhuman;plasmid;polymerase chain reaction;prevalence;principal coordinate analysis;prophage;pyrosequencing;quantitative analysis;taxonomy;transposon,"Chambers, L.;Yang, Y.;Littier, H.;Ray, P.;Zhang, T.;Pruden, A.;Strickland, M.;Knowlton, K.",2015,,10.1371/journal.pone.0133764,0
318,Cross-species transmission and emergence of novel viruses from birds,"Birds, the only living member of the Dinosauria clade, are flying warm-blooded vertebrates displaying high species biodiversity, roosting and migratory behavior, and a unique adaptive immune system. Birds provide the natural reservoir for numerous viral species and therefore gene source for evolution, emergence and dissemination of novel viruses. The intrusions of human into natural habitats of wild birds, the domestication of wild birds as pets or racing birds, and the increasing poultry consumption by human have facilitated avian viruses to cross species barriers to cause zoonosis. Recently, a novel adenovirus was exclusively found in birds causing an outbreak of Chlamydophila psittaci infection among birds and humans. Instead of being the primary cause of an outbreak by jumping directly from bird to human, a novel avian virus can be an augmenter of another zoonotic agent causing the outbreak. A comprehensive avian virome will improve our understanding of birds' evolutionary dynamics.",Adenoviridae;article;avian influenza virus;bird;human;nonhuman;priority journal;virus;virus transmission,"Chan, J. F. W.;To, K. K. W.;Chen, H.;Yuen, K. Y.",2015,,10.1016/j.coviro.2015.01.006,0
319,Identification and phylogenetic analysis of orf virus from goats in Taiwan,"An outbreak of contagious ecthyma in goats in central Taiwan was investigated. The disease was diagnosed by physical and histopathologic examinations, and the etiology of the disease was identified as orf virus by electron microscopy and polymerase chain reaction (PCR) and sequence of major envelope protein (B2L) gene. The entire protein-coding region of B2L gene were cloned and sequenced. Phylogenetic analysis of B2L amino acid sequences showed that the orf virus identified in this outbreak was closer to the Indian ORFV-Mukteswar 59/05 isolate. This is the first report on the molecular characterization of orf virus in Taiwan. © 2007 Springer Science+Business Media, LLC.",amino acid sequence;article;ecthyma;electron microscopy;epidemic;gene sequence;goat;histopathology;nonhuman;nucleotide sequence;phylogeny;physical examination;polymerase chain reaction;Poxviridae;priority journal;Taiwan;virus identification,"Chan, K. W.;Lin, J. W.;Lee, S. H.;Liao, C. J.;Tsai, M. C.;Hsu, W. L.;Wong, M. L.;Shih, H. C.",2007,,10.1007/s11262-007-0144-6,0
320,"Analysis of genomic sequences of 95 papillomavirus types: Uniting typing, phylogeny, and taxonomy","Our aim was to study the phylogenetic relationships of all known papillomaviruses (PVs) and the possibility of establishing a supratype taxonomic classification based on this information. Of the many detectably homologous segments present in PV genomes, a 291-bp segment of the L1 gene is notable because it is flanked by the MY09 and MY11 consensus primers and contains highly conserved amino acid residues which simplify sequence alignment. We determined the MY09-MY11 sequences of human PV type 20 (HPV- 20), HPV-21, HPV-22, HPV-23, HPV-24, HPV-36, HPV-37, HPV-38, HPV-48, HPV-50, HPV-60, HPV-70, HPV-72, HPV-73, ovine (sheep) PV, bovine PV type 3 (BPV-3), BPV-5, and BPV-6 and created a database which now encompasses HPV-1 to HPV- 70, HPV-72, HPV-73, seven yet untyped HPV genomes, and 15 animal PV types. Three additional animal PVs were analyzed on the basis of other sequence data. We constructed phylogenies based on partial L1 and E6 gene sequences and distinguished five major clades that we call supergroups. One of them unites 54 genital PV types, which can be further divided into eleven groups. The second supergroup has 24 types and unites most PVs that are typically found in epidermodysplasia verruciformis patients but also includes several types typical of other cutaneous lesions, like HPV-4. The third supergroup unites the six known ungulate fibropapillomaviruses, the fourth includes the cutaneous ungulate PVs BPV-3, BPV-4, and BPV-6, and the fifth includes HPV- 1, HPV-41, HPV-63, the canine oral PV, and the cottontail rabbit PV. The chaffinch PV and two rodent PVs, Micromys minutus PV and Mastomys natalensis PV, are left ungrouped because of the relative isolation of each of their lineages. Within most supergroups, groups formed on the basis of cladistic principles unite phenotypically similar PV types. We discuss the basis of our classification, the concept of the PV type, speciation, PV-host evolution, and estimates of their rates of evolution.",virus DNA;animal cell;article;gene sequence;human;human cell;karyotype evolution;nonhuman;Papillomaviridae;phylogeny;priority journal;sequence analysis;species differentiation;taxonomy;virus classification;virus morphology;virus typing,"Chan, S. Y.;Delius, H.;Halpern, A. L.;Bernard, H. U.",1995,,,0
321,Full genome sequencing of the bluetongue virus-1 isolate MKD20/08/Ind from goat in India,"This communication reports full genome sequencing of the bluetongue virus-1 (BTV-1) isolate MKD20/08/Ind from goat in northern India. The total BTV-1 genome size was found to be 19,190bp. A comparison study between the Indian isolate and other global isolates revealed that it belongs to the 'Eastern' BTV topotype. The full genome sequence of BTV-1 will provide vital information on its geographical origin and it will also be proved useful for comparing the Indian isolate with global isolates from other host species.",animal;Bluetongue orbivirus;classification;DNA sequence;genetics;genomics;goat;high throughput sequencing;India;isolation and purification;phylogeny;serotype;virology;virus genome,"Chand, K.;Biswas, S. K.;Sharma, G.;Saxena, A.;Tewari, N.;Mahajan, S.;Pandey, A. B.",2016,,10.1016/j.bjm.2016.04.022,0
322,Genome sequence comparison of two United States live attenuated vaccines of infectious laryngotracheitis virus (ILTV),"This study was conducted to identify unique nucleotide differences in two U.S. chicken embryo origin (CEO) vaccines [LT Blen (GenBank accession: JQ083493) designated as vaccine 1; Laryngo-Vac® (GenBank accession: JQ083494) designated as vaccine 2] of infectious laryngotracheitis virus (ILTV) genomes compared to an Australian Serva vaccine reference ILTV genome sequence [Gallid herpesvirus 1 (GaHV-1); GenBank accession number: HQ630064]. Genomes of the two vaccine ILTV strains were sequenced using Illumina Genome Analyzer 2X of 36 cycles of single-end reads. Results revealed that few nucleotide differences (23 in vaccine 1; 31 in vaccine 2) were found and indicate that the US CEO strains are practically identical to the Australian Serva CEO strain, which is a European-origin vaccine. The sequence differences demonstrated the spectrum of variability among vaccine strains. Only eight amino acid differences were found in ILTV proteins including UL54, UL27, UL28, UL20, UL1, ICP4, and US8 in vaccine 1. Similarly, in vaccine 2, eight amino acid differences were found in UL54, UL27, UL28, UL36, UL1, ICP4, US10, and US8. Further comparison of US CEO vaccines to several ILTV genome sequences revealed that US CEO vaccines are genetically close to both the Serva vaccine and 63140/C/08/BR (GenBank accession: HM188407) and are distinct from the two Australian-origin CEO vaccines, SA2 (Gen-Bank accession: JN596962) and A20 (GenBank accession: JN596963), which showed close similarity to each other. These data demonstrate the potential of high-throughput sequencing technology to yield insight into the sequence variation of different ILTV strains. This information can be used to discriminate between vaccine ILTV strains and further, to identify newly emerging mutant strains of field isolates. © Springer Science+Business Media, LLC 2012.",Iltovirus vaccine;laryngo vac;live vaccine;lt blen;protein ICP4;protein UL1;protein UL20;protein UL27;protein UL28;protein UL36;protein UL54;protein US10;protein US8;unclassified drug;viral protein;virus vaccine;article;Australia;controlled study;gene sequence;ICP4 gene;Iltovirus;nonhuman;nucleotide sequence;priority journal;strain difference;UL1 gene;UL20 gene;UL27 gene;UL28 gene;UL36 gene;UL54 gene;United States;US10 gene;US8 gene;virus gene;virus genome;virus strain,"Chandra, Y. G.;Lee, J.;Kong, B. W.",2012,,10.1007/s11262-012-0728-7,0
323,"Virus isolation and molecular epidemiology of highly pathogenic avian influenza A(H5N8) from an outbreak in free-ranging wild birds, India 2016","We report the molecular epidemiology of highly pathogenic avian influenza (HPAI) virus involved in an outbreak causing death in free-ranging wild birds at Mysore, Karnataka state of India. The virus was typed as HPAI A(H5N8) by conventional and TaqMan probe based realtime PCR assays. Six isolates of HPAI virus were recovered in 9-day-old embryonated chicken eggs. Haemagglutinin gene-based phylogeny of virus isolates showed > 99.9% nucleotide sequence identity with HPAI A(H5N8) isolates from migratory birds and domestic poultry from China and Korea indicating either these wild birds have routed their migration through Korea and/or eastern China or these dead birds must have directly or indirectly contacted with wild birds migrating from Eastern China and/or Korean regions. The study emphasises the role of migratory wild birds in spread of HPAI across the globe.",Avian influenza;HPAI;HPAI A(H5N8);Free-ranging wild birds;Zoo;Mysore;Karnataka;India;2016,"Chandranaik, B. M.;Byregowda, S. M.;Venkatesha, M. D.;Ramesha, K. R.;Nandini, P.;Reddy, P.;Bindu, K. V. T.;Shivashankar, B. P.;Shankar, B. P.;Rani, M. S.",2018,Feb,,0
324,"Lessons from the Largest Epidemic of Avian Influenza Viruses in Taiwan, 2015","The largest epidemic of avian influenza (AI) in history attacked poultry and wild birds throughout Taiwan starting January 6, 2015. This study analyzed surveillance results, epidemiologic characteristics, and viral sequences by using government-released information, with the intention to provide recommendations to minimize future pandemic influenza. The H5 clade 2.3.4.4 highly pathogenic AI viruses (HPAIVs) had not been detected in Taiwan before 2015. During this epidemic, four types of etiologic agents were identified: the three novel subtypes H5N2, H5N8, and H5N3 clade 2.3.4.4 HPAIVs and one endemic chicken H5N2 subtype (Mexican-like lineage) of low pathogenic AI viruses. Cocirculation of mixed subtypes also occurred, with H5N2 clade 2.3.4.4 HPAIVs accompanied by the H5N8 and H5N3 subtypes or old H5N2 viruses in the same farm. More than 90% of domestic geese died from this AI epidemic; geese were affected the most at the early outbreaks. The epidemic peaked in mid-January for all three novel H5 subtypes. Spatial epidemiology found that most affected areas were located in southwestern coastal areas. In terrestrial poultry (mostly chickens), different geographic distributions of AI virus subtypes were detected, with hot spots of H5N2 clade 2.3.4.4 vs. past-endemic old H5N2 viruses in Changhwa (P = 0.03) and Yunlin (P = 0.007) counties, respectively, of central Taiwan. Phylogenetic and sequence analyses of all the early 10 Taiwan H5 clade 2.3.4.4 isolates covering the three subtypes showed that they were very different from the HA of the past local H5 viruses from domestic ducks (75%-80%) and chickens (70%-75%). However, they had the highest sequence identity percentages (99.53%-100%), with the HA of A/crane/Kagoshima/KU13/2014(H5N8) isolated on December 7, 2014, in Japan being higher than those of recent American and Korean H5 HPAIVs [A/Northern pintail/Washington/40964/2014 (H5N2) and A/gyrfalcon/Washington/41088-6/2014 (H5N8): 99.02%-99.54% and A/Baikal teal/Korea/Donglim3/2014 (H5N8): 98.61%-99.08%], implying a likely common ancestor of these H5 clade 2.3.4.4 viruses. The multiple subtypes of H5 clade 2.3.4.4 HPAIVs imply high viral reassortment. We recommend establishing an integrated surveillance system, involving clinical, virologic, and serologic surveillance in poultry and wild birds, swine and other mammals prevalent on multiple-animal mixed-type traditional farms, and high-risk human populations, as a crucially important step to minimize future pandemic influenza.",animal;chicken;classification;duck;epidemic;genetics;goose;Influenza A virus;avian influenza;isolation and purification;phylogeny;bird disease;Taiwan;virology;wild animal,"Chang, C. F.;King, C. C.;Wan, C. H.;Chang, Y. C.;Chan, T. C.;David Lee, C. C.;Chou, P. H. B.;Li, Z. R. T.;Li, Y. T.;Tseng, T. J.;Lee, P. F.;Chang, C. H.",2016,,10.1637/11168-051915-Reg,0
325,Dual infection of gnotobiotic calves with bovine strains of group a and porcine-like group C rotaviruses influences pathogenesis of the group C rotavirus,"There is serological evidence that bovine group C rotaviruses exist in the United States, but there are no reports of their isolation. Ninety fecal samples from calves with diarrhea, 81 samples from adult cows with diarrhea (winter dysentery), and 20 fecal samples from healthy adult cows were tested for group C rotaviruses by polyacrylamide gel electrophoresis, immune electron microscopy, and reverse transcription-PCR (RT-PCR). Three samples from adult cow diarrhea cases were positive only by RT-PCR, and a group C rotavirus was isolated from a positive sample in monkey kidney (MA104) cells (WD534tc/C). Genetically and serologically, the WD534tc/C strain was more closely related to the Cowden porcine group C strain than to the Shintoku bovine strain. Because the original cow feces also contained a group A rotavirus (detected after passage in cell culture), we hypothesized that such dual-rotavirus infections might play a-role in the pathogenesis and host adaptation of rotaviruses. Thus, we examined the pathogenesis of WD534tc/C alone or combined with virulent (IND/A) or attenuated (NCDV/A) bovine group A rotaviruses in gnotobiotic calves. WD534tc/C alone induced diarrhea without (or with limited) virus shedding in inoculated calves (n = 3). In contrast, all calves coinfected with WD534tc/C and IND/A (n = 2) developed diarrhea and shed both viruses, whereas calves coinfected with WD534tc/C and NCDV/A (n = 3) developed diarrhea but did not shed either virus. Infection with WD534tc/C or NCDV/A alone caused only mild villous atrophy (jejunum and/or ileum), whereas dual infection with both viruses induced lesions throughout the small intestine. Although IND/A alone caused villous atrophy, more-widespread small intestinal lesions occurred in calves coinfected with WD534tc/C and IND/A. In conclusion, coinfection of calves with group A rotaviruses enhanced fecal shedding of a bovine group C rotavirus and the extent of histopathological lesions in the small intestines. Thus, our findings suggest a potential novel hypothesis involving dual infections for the adaptation of heterologous rotaviruses to new host species.",article;bovine;controlled study;diarrhea;gnotobiotics;immunoelectron microscopy;intestine injury;nonhuman;nucleotide sequence;polyacrylamide gel electrophoresis;priority journal;reverse transcription polymerase chain reaction;Rotavirus;serology;United States;virus classification;virus isolation;virus pathogenesis;virus shedding,"Chang, K. O.;Nielsen, P. R.;Ward, L. A.;Saif, L. J.",1999,,,0
326,Nipah virus: Phylogeny and replication,"Phylogenetic analysis of Nipah virus isolates from Malaysia, Bangladesh and Cambodia suggested the presence of at least two different clusters of NiV strains. Based on the major glycoprotein (G) gene, the Nipah virus-Tambun isolate clustered with Nipah virus isolates from Cambodia and Bangladesh, whereas the remaining isolates from Malaysia clustered in a separate cluster. Sequence heterogeneity among the Nipah virus isolates from Malaysia was noted but the overall genomic sequence divergence value was small, suggesting a possible recent introduction of the virus. Nipah virus replicated well in porcine stable kidney cells and human lung fibroblast cells. Human monocytes, on the other hand were infected with Nipah virus but the cells did not support productive infection. Similarly, infection of human neuronal cells did not result in release of high infectious virus yield. The monocytes can serve to disseminate Nipah virus from site of infection including across the blood-brain barrier. And in the brain, Nipah virus is probably spread through cell-to-cell spread mechanism.",DNA polymerase;glycoprotein;matrix protein;nucleoprotein;phosphoprotein;Bangladesh;blood brain barrier;Cambodia;conference paper;gene sequence;genetic heterogeneity;human;kidney cell;lung fibroblast;Malaysia;microbial kinetics;monocyte;Nipah virus;nonhuman;nucleotide sequence;phylogeny;sequence analysis;vaccination;virus isolation;virus replication;virus strain;virus transmission,"Chang, L. Y.;AbuBakar, S.",2009,,,0
327,"Torque Teno Mini Virus Infection in Chronic Cervicitis and Cervical Tumors in Isfahan, Iran","Objectives: Torque teno mini virus (TTMV) is classified as the Betatorquevirus genus of Anelloviridoe. Little is known about the prevalence of TTMV in humans. Worldwide, cervical cancer is the second most common cancer affecting women. This study aimed to estimate the TTMV infection frequency in cervicitis cases and cervical tumors including intraepithelial neoplasia (CIN), squamous cell carcinoma (SCC) and adenocarcinoma, and the possible role of this virus in the etiology of them in an Isfahan population. Methods: 79 cervicitis cases and 42 tumors were collected from histopathological files of Al-Zahra Hospital in Isfahan, Iran. DNA was extracted and subjected to nested polymerase chain reaction. Results: Totally 62% of the tested samples were positive for TTMV. It was positive in 52.4% of adenocarcinoma, 68.4% of CIN and 100% SCC cases. In cervicitis, 48% of the cases were positive. In the phylogenetic construct two of the cervical tumor isolates and two of the cervicitis isolates were placed in the same cluster with already reported isolates from Japan (EF538880 and AB041962). Also, three of the cervical tumors isolated (JQ734980, JQ734981 and JQ734982) were placed in another cluster. Conclusion: The presence of the virus in cervical tissues suggests possible sexual transmission of the virus. Copyright (C) 2013 S. Karger AG, Basel",Torque teno mini virus;Cervical cancer;Adenocarcinoma;Squamous cell;carcinoma;Cervical intraepithelial neoplasia;Cervicitis;Nested;polymerase chain reaction;CHICKEN ANEMIA VIRUS;FRENCH BLOOD-DONORS;TT VIRUS;HUMAN-PAPILLOMAVIRUS;GENETIC-ANALYSIS;DNA;HPV;SEQUENCES;CANCERS,"Changani, L.;Bouzari, M.;Talebi, A.",2013,,,0
328,Isolation and characterisation of a feline syncytial virus,"A syncytium forming virus was isolated by trypsinization cultivation and serial passage of tissue kidney of an apparently normal kitten. The growth of virus in Crandell feline kidney cell line and a complete study of biological properties were performed. The morphogenesis and the morphology of this feline syncytial virus was examined by electron microscopy. The characteristics of the virus as demonstrated in this study warrant further effort to definitively classify it. It is concluded that feline syncytial virus, bovine syncytial virus and simian foamy agent all belong to the same virus group.",cat;classification;in vitro study;microorganism;theoretical study;virus classification;virus isolation,"Chappuis, G.;Tektoff, J.",1974,,,0
329,"Host specificity, pathogen exposure, and superinfections impact the distribution of Anaplasma phagocytophilum genotypes in ticks, roe deer, and livestock in a fragmented agricultural landscape","Anaplasma phagocytophilum is a bacterial pathogen mainly transmitted by Ixodes ricinus ticks in Europe. It infects wild mammals, livestock, and, occasionally, humans. Roe deer are considered to be the major reservoir, but the genotypes they carry differ from those that are found in livestock and humans. Here, we investigated whether roe deer were the main source of the A. phagocytophilum genotypes circulating in questing I. ricinus nymphs in a fragmented agricultural landscape in France. First, we assessed pathogen prevalence in 1837 I. ricinus nymphs (sampled along georeferenced transects) and 79 roe deer. Prevalence was dramatically different between ticks and roe deer: 1.9% versus 76%, respectively. Second, using high-throughput amplicon sequencing, we characterized the diversity of the A. phagocytophilum genotypes found in 22 infected ticks and 60 infected roe deer; the aim was to determine the frequency of co-infections. Only 22.7% of infected ticks carried genotypes associated with roe deer. This finding fits with others suggesting that cattle density is the major factor explaining infected tick density. To explore epidemiological scenarios capable of explaining these patterns, we constructed compartmental models that focused on how A. phagocytophilum exposure and infection dynamics affected pathogen prevalence in roe deer. At the exposure levels predicted by the results of this study and the literature, the high prevalence in roe deer was only seen in the model in which superinfections could occur during all infection phases and when the probability of infection post exposure was above 0.43. We then interpreted these results from the perspective of livestock and human health.",Agriculture;*Anaplasma phagocytophilum/cl [Classification];*Anaplasma phagocytophilum/ge [Genetics];Animal Diseases/ep [Epidemiology];*Animal Diseases/mi [Microbiology];Animal Diseases/tm [Transmission];Animals;Bacterial Typing Techniques;*Deer/mi [Microbiology];Disease Reservoirs;*Ehrlichiosis/ve [Veterinary];Environmental Exposure;Genotype;*Host Specificity;Humans;*Livestock/mi [Microbiology];Phylogeny;Prevalence;Superinfection;*Ticks/mi [Microbiology],"Chastagner, A.;Pion, A.;Verheyden, H.;Lourtet, B.;Cargnelutti, B.;Picot, D.;Poux, V.;Bard, E.;Plantard, O.;McCoy, K. D.;Leblond, A.;Vourc'h, G.;Bailly, X.",2017,11,,0
330,"Reassortant Avian Influenza A(H9N2) viruses in chickens in retail poultry shops, Pakistan, 2009-2010","Phylogenetic analysis of influenza viruses collected during December 2009-February 2010 from chickens in live poultry retail shops in Lahore, Pakistan, showed influenza A(H9N2) lineage polymerase and nonstructural genes generate through inter- and intrasubtypic reassortments. Many amino acid signatures observed were characteristic of human isolates; hence, their circulation could enhance inter- or intrasubtypic reassortment.","Amino Acid Substitution;Animals;*Chickens;Genes, Viral;Geography;History, 21st Century;*Influenza A Virus, H9N2 Subtype/ge [Genetics];*Influenza in Birds/ep [Epidemiology];Influenza in Birds/hi [History];*Influenza in Birds/vi [Virology];Molecular Sequence Data;Mutation;Pakistan/ep [Epidemiology];*Reassortant Viruses","Chaudhry, M.;Angot, A.;Rashid, H. B.;Cattoli, G.;Hussain, M.;Trovo, G.;Drago, A.;Valastro, V.;Thrusfield, M.;Welburn, S.;Eisler, M. C.;Capua, I.",2015,Apr,,0
331,Variations in lentiviral gene expression in monocyte-derived macrophages from naturally infected sheep,"Seventy-nine 1-year-old lambs from three individual farms and a feedlot were examined for natural lentivirus infection. We used three different methods to detect infection and to identify the stage of the ovine lentivirus life cycle in blood-derived macrophages. Cytopathic infectious virus was obtained from 14/14 Border Leicester animals obtained from a naturally infected flock. Neither virus particles, virus proteins, virus specific antibodies nor viral DNA were detected in samples from 34 lambs from two South Kansas City farms. However, among 31 feedlot lambs, we identified 11 infected animals. Specific viral proteins were immunoprecipitated from macrophages of one animal, but no infectious cytopathic virus was isolated from these cells. Cells from ten of the other feedlot animals harboured viral DNA but neither viral particles nor proteins could be detected by our techniques. Thus, in these naturally infected animals, the virus life cycle either proceeded to completion, subject to differentiation of infected precursor cells in blood, or remained arrested at the DNA stage despite maturation of monocytes to macrophages. Sequence analysis of the env gene of viral genomes from two of the ten feedlot sheep showed sequences distinct from those of known ovine and caprine lentiviruses. Surprisingly, these sequences have a higher identity (of nucleotide and derived amino acid sequences) to caprine arthritis-encephalitis virus than to the ovine prototype, maedi-visna virus. These data suggest that the ovine and caprine lentiviruses found in North American sheep may have a common ancestral genotype that is closely related to the caprine virus.",virus DNA;viral protein;amino acid sequence;animal cell;article;Caprine arthritis encephalitis virus;controlled study;envelope gene;gene expression;immunoprecipitation;lamb;Lentivirus;life cycle;macrophage;nonhuman;nucleotide sequence;priority journal;retrovirus infection;sequence homology;virus classification;virus gene;virus infectivity;Visna virus,"Chebloune, Y.;Karr, B.;Sheffer, D.;Leung, K.;Narayan, O.",1996,,,0
332,Inferring the Clonal Structure of Viral Populations from Time Series Sequencing,"RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We would like to identify the underlying evolutionary structures. We utilize two sources of information to attempt this; within segment linkage information, and mutation prevalence. We demonstrate that clone haplotypes, their prevalence, and maximum parsimony reticulate evolutionary structures can be identified, although the solutions may not be unique, even for complete sets of information. This is applied to a chain of influenza infection, where we infer evolutionary structures, including reassortment, and demonstrate some of the difficulties of interpretation that arise from deep sequencing due to artifacts such as template switching during PCR amplification.",EQUINE INFLUENZA-VIRUS;GENETIC DIVERSITY;GENERATION;RECONSTRUCTION;RECOMBINATION;DYNAMICS;SAMPLE;SWINE,"Chedom, D. F.;Murcia, P. R.;Greenman, C. D.",2015,Nov,,0
333,Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation,"Fecal microbiota transplantation (FMT) is a highly effective treatment for refractory Clostridium difficile infections. However, concerns persist about unwanted cotransfer of pathogenic microbes such as viruses. Here we studed FMT from a single healthy human donor to three pediatric ulcerative colitis patients, each of whom received a course of 22 to 30 FMT treatments. Viral particles were purified from donor and recipient stool samples and sequenced; the reads were then assembled into contigs corresponding to viral genomes or partial genomes. Transfer of selected viruses was confirmed by quantitative PCR. Viral contigs present in the donor could be readily detected in recipients, with up to 32 different donor viral contigs appearing in a recipient sample. Reassuringly, none of these were viruses are known to replicate on human cells. Instead, viral contigs either scored as bacteriophage or could not be attributed taxonomically, suggestive of unstudied phage. The two most frequently transferred gene types were associated with temperate-phage replication. In addition, members of Siphoviridae, the group of typically temperate phages that includes phage lambda, were found to be transferred with significantly greater efficiency than other groups. On the basis of these findings, we propose that the temperate-phage replication style may promote efficient phage transfer between human individuals. In summary, we documented transfer of multiple viral lineages between human individuals through FMT, but in this case series, none were from viral groups known to infect human cells. IMPORTANCE Transfer of whole communities of viruses between humans has rarely been studied but is of likely medical importance. Here we studied fecal microbiota transplantation (FMT), a highly successful treatment for relapsing Clostridium difficile infection and, potentially, other gastrointestinal (GI) diseases. We investigated the transfer of viral communities during FMT and documented transfer of multiple viral lineages between humans. None of these were viruses that replicated on animal cells or that are known to be pathogenic. We found that temperate bacteriophage, which form stable associations with their hosts, were significantly more likely to be transferred during FMT. This supports a model in which the viral temperate replication style may have evolved in part to support efficient viral transmission between environments.",HUMAN GUT VIROME;VIRUSES;DISEASE;INFECTION;FECES;HIV-1;DIET;CELL,"Chehoud, C.;Dryga, A.;Hwang, Y.;Nagy-Szakal, D.;Hollister, E. B.;Luna, R. A.;Versalovic, J.;Kellermayer, R.;Bushman, F. D.",2016,Mar-Apr,,0
334,Complete genome sequence of newcastle disease virus mesogenic vaccine strain R2B from India,"Mesogenic vaccine strains of Newcastle disease virus (NDV) are widely used in many countries of Asia and Africa to control the Newcastle disease of poultry. In India, the mesogenic strain R2B was introduced in 1945; it protects adult chickens that have been preimmunized with a lentogenic vaccine virus and provides long-lasting immunity. In this article, we report the complete genome sequence of the hitherto unsequenced Indian vaccine virus strain R2B. The viral genome is 15,186 nucleotides in length and contains the polybasic amino acid motif in the fusion protein cleavage site, indicating that this vaccine strain has evolved from a virulent virus. Phylogenetic analysis of this mesogenic vaccine virus classified it with the viruses belonging to genotype III of the class cluster II of NDV. © 2012, American Society for Microbiology.",fusion protein;amino acid sequence;chicken;embryo;gene cluster;gene sequence;genome analysis;genotype;India;molecular evolution;Newcastle disease virus;nonhuman;note;nucleotide sequence;phylogeny;priority journal;protein cleavage;protein motif;reverse transcription polymerase chain reaction;sequence analysis;virus classification;virus genome;virus identification;virus strain;virus virulence,"Chellappa, M. M.;Dey, S.;Gaikwad, S.;Kataria, J. M.;Vakharia, V. N.",2012,,10.1128/jvi.02552-12,0
335,Minimum core genome sequence typing of bacterial pathogens: a unified approach for clinical and public health microbiology,"Bacterial pathogens impose a heavy health burden worldwide. In the new era of high-throughput sequencing and online bioinformatics, real-time genome typing of infecting agents, and in particular those with potential severe clinical outcomes, holds promise for guiding clinical care to limit the detrimental effects of infections and to prevent potential local or global outbreaks. Here, we sequenced and compared 85 isolates of Streptococcus suis, a zoonotic human and swine pathogen, wherein we analyzed 32 recognized serotypes and 75 sequence types representing the diversity of the species and the human clinical isolates with high public health significance. We found that 1,077 of the 2,469 genes are shared by all isolates. Excluding 201 common but mobile genes, 876 genes were defined as the minimum core genome (MCG) of the species. Of 190,894 single-nucleotide polymorphisms (SNPs) identified, 58,501 were located in the MCG genes and were referred to as MCG SNPs. A population structure analysis of these MCG SNPs classified the 85 isolates into seven MCG groups, of which MCG group 1 includes all isolates from human infections and outbreaks. Our MCG typing system for S. suis provided a clear separation of groups containing human-associated isolates from those containing animal-associated isolates. It also separated the group containing outbreak isolates, including those causing life-threatening streptococcal toxic shock-like syndrome, from sporadic or less severe meningitis or bacteremia-only isolates. The typing system facilitates the application of genome data to the fields of clinical medicine and epidemiology and to the surveillance of S. suis. The MCG groups may also be used as the taxonomical units of S. suis to define bacterial subpopulations with the potential to cause severe clinical infections and large-scale outbreaks.","Animals;*Bacteriological Techniques/mt [Methods];Computational Biology/mt [Methods];Genes, Bacterial;Genome, Bacterial;*High-Throughput Nucleotide Sequencing/mt [Methods];Humans;*Molecular Epidemiology/mt [Methods];*Molecular Typing/mt [Methods];Streptococcal Infections/di [Diagnosis];*Streptococcal Infections/ep [Epidemiology];Streptococcal Infections/mi [Microbiology];Streptococcal Infections/ve [Veterinary];*Streptococcus suis/cl [Classification];*Streptococcus suis/ge [Genetics];Streptococcus suis/ip [Isolation & Purification];Swine;Swine Diseases/ep [Epidemiology];Swine Diseases/mi [Microbiology];Zoonoses/ep [Epidemiology];Zoonoses/mi [Microbiology]","Chen, C.;Zhang, W.;Zheng, H.;Lan, R.;Wang, H.;Du, P.;Bai, X.;Ji, S.;Meng, Q.;Jin, D.;Liu, K.;Jing, H.;Ye, C.;Gao, G. F.;Wang, L.;Gottschalk, M.;Xu, J.",2013,Aug,,0
336,Genetic analysis of virulence and antimicrobial-resistant plasmid pOU7519 in Salmonella enterica serovar Choleraesuis,"Background: Zoonotic Salmonella enterica serovar Choleraesuis (S. Choleraesuis), causing paratyphoid in pigs and bacteremia in humans, commonly carry a virulence plasmid and sometimes a separate antimicrobial-resistant plasmid or merging together. This study aimed to analyze the likely mechanism of how to form a virulence-resistance chimera of plasmid in S. Choleraesuis. Methods: Whole plasmid sequence of pOU7519 in S. Choleraesuis strain OU7519 was determined using shotgun cloning and sequencing. Sequence annotation and comparison were performed to determine the sequence responsible for the formation of a chimeric virulence-resistance pOU7519. Other chimeric plasmids among the collected strains of S. Choleraesuis were also confirmed. Results: The sequence of pOU719, 127,212 bp long, was identified to be a chimera of the virulence plasmid pSCV50 and a multidrug-resistant plasmid pSC138 that have been found in S. Choleraesuis strain SC-B67. The pOU7519 is a conjugative plasmid carrying various mobile DNAs, including prophages, insertion sequences, integrons and transposons, especially a Tn. 6088-like transposon. By dissecting the junction site of the pSCV50-pSC138 chimera in pOU7519, defective sequences at integrase gene scv50 (int) and its attachment site (att) were found, and that likely resulted in a stable chimera plasmid due to the failure of excision from the pSCV50-pSC138 chimera. Similar structure of chimera was also found in other large plasmids. Conclusion: The deletion of both the int and att sties could likely block chimera excision, and result in an irreversible, stable pSCV50-pSC138 chimera. The emergence of conjugative virulence and antimicrobial-resistant plasmids in S. Choleraesuis could pose a threat to health public.",chimera;drug resistance;excision;genetic analysis;human;integron;nonhuman;plasmid;prophage;Salmonella enterica serovar Choleraesuis;transposon;virulence;antiinfective agent;endogenous compound;integrase,"Chen, C. L.;Su, L. H.;Janapatla, R. P.;Lin, C. Y.;Chiu, C. H.",2017,,10.1016/j.jmii.2017.11.004,0
337,"Ordered shotgun sequencing of a 135 kb Xq25 YAC containing ANT2 and four possible genes, including three confirmed by EST matches","Ordered shotgun sequencing (OSS) has been successfully carried out with an Xq25 YAC substrate. yWXD703 DNA was subcloned into lambda phage and sequences of insert ends of the lambda subclones were used to generate a map to select a minimum tiling path of clones to be completely sequenced. The sequence of 135 038 nt contains the entire ANT2 cDNA as well as four other candidates suggested by computer-assisted analyses. One of the putative genes is homologous to a gene implicated in Graves' disease and it, ANT2 and two others are confirmed by EST matches. The results suggest that OSS can be applied to YACs in accord with earlier simulations and further indicate that the sequence of the YAC accurately reflects the sequence of uncloned human DNA.","Bacteriophage lambda/ge [Genetics];*Chromosomes, Artificial, Yeast/ge [Genetics];Cloning, Molecular;DNA Primers;Female;Humans;Molecular Sequence Data;Polymerase Chain Reaction;Repetitive Sequences, Nucleic Acid;*Sequence Analysis/mt [Methods];Sequence Tagged Sites;Software;*X Chromosome/ge [Genetics];0 (DNA Primers)","Chen, C. N.;Su, Y.;Baybayan, P.;Siruno, A.;Nagaraja, R.;Mazzarella, R.;Schlessinger, D.;Chen, E.",1996,Oct 15,,0
338,Complete genome characterization of a rotavirus B (RVB) strain identified in alpine goat kids with enteritis reveals inter-species transmission with RVB bovine strains,"Rotavirus B (RVB) has been associated with enteric disease in many animal species. An RVB strain was identified in pooled intestinal samples from Alpine caprine kids (between 2 and 3 days of age) experiencing high (>90%) morbidity, and the complete caprine RVB genome was characterized. Histology revealed villus atrophy, the samples tested positive for RVB by real-time RT-PCR and metagenomic next-generation sequencing identified only RVB and orf virus. In the VP4 gene segment, the caprine RVB strain had a higher percentage nucleotide identity to the Indian bovine RVB strains than to the Japanese bovine RVB strains, but the VP7, VP6, VP2, NSP1, NSP2 and NSP5 gene segments of the American caprine RVB strain were genetically related to the Japanese bovine RVB strains. The results indicate a lack of RVB sequences to understand reassortment or the evolutionary relationship of RVB strains from cattle and goats.",nucleotide;amino acid sequence;animal tissue;article;bovine;enteritis;genetic reassortment;goat;histology;histopathology;intestine villus atrophy;metagenomics;molecular evolution;morbidity;next generation sequencing;nonhuman;NSP1 gene;NSP2 gene;NSP5 gene;nucleotide sequence;phylogenetic tree;priority journal;real time polymerase chain reaction;Rotavirus B;virus gene;virus genome;virus strain;virus transmission;VP2 gene;VP4 gene;VP6 gene;VP7 gene,"Chen, F.;Knutson, T. P.;Ciarlet, M.;Sturos, M.;Marthaler, D. G.",2018,,10.1099/jgv.0.001022,1
339,Evolutionary relationships among large double-stranded DNA viruses that infect microalgae and other organisms as inferred from DNA polymerase genes,"In order to examine genetic relatedness among viruses that infect microalgae, DNA polymerase gene (DNA pol) fragments were amplified and sequenced from 13 virus clones that infect three genera of distantly related microalgae (Chlorella strains NC64A and Pbi, Micromonas pusilla and Chrysochromulina spp.). Phylogenetic trees d on DNA pol sequences and hybridization of total genomic DNA showed similar branching patterns. Genetic relatedness calculated from the hybridization and sequence data showed good concordance (r = 0.90), indicating that DNA pol sequences can be used to determine genetic relatedness and infer phylogenetic relationships among these viruses. The phylogenetic tree inferred from the deduced amino acid sequences of DNA pol from 24 dsDNA viruses, including phycodnaviruses, herpesviruses, poxviruses, baculoviruses, and African swine fever virus corresponded well with groupings based on the International Committee on Taxonomy of Viruses. Microalgal viruses are more closely related to each other than to the other dsDNA viruses and form a distinct phyletic group, suggesting that they share a common ancestor and belong to the Phycodnaviridae. Moreover, the Phycodnaviridae are more closely related to the Herpesviridae than to other virus families for which DNA pol sequences are available.",DNA polymerase;alga;article;DNA sequence;DNA virus;evolution;molecular cloning;nonhuman;polymerase chain reaction;priority journal,"Chen, F.;Suttle, C. A.",1996,,10.1006/viro.1996.0234,0
340,Identification of key genes fluctuated induced by avian leukemia virus (ALV-J) infection in chicken cells,"Avian leukemia subgroup J (ALV-J) is one of the most detrimental neoplastic diseases in poultry production. However, the differences between somatic cells and immune cells post-infection remain poorly understood. The aim of our study was to detect the different responses in chicken to infection with ALV-J in different cell lines. In this study, we detected transcriptome expression changes during infection with ALV-J in chicken embryo fibroblast (CEF) and HD11 cell lines. RNA-Seq was used to determine the expression levels of mRNA transcripts from the two cell types after infection with ALV-J at 1, 4, and 7 dpi, and gene ontology analyses were used to cluster differentially expressed genes into pathways. Quantitative real-time PCR confirmed the expression of 336 and 269 differentially expressed genes in CEF and HD11 lines, respectively, involved in innate immunity (OASL, CCL4), adaptive immunity (LYZ, CD72), apoptosis and autophagy (WISP2, COMP), inflammation (JSC, IL8), and tumorgenesis (PCNA, GPX3). The notable signal transduction pathways included the PPARs signaling pathway and ECM-receptor interactions in CEF, and the Toll-like receptor, NOD-like receptor, and RIG-I-like receptor signaling pathways in HD11. To our knowledge, this is the first study to use high-throughput sequencing methods to investigate viral infection in different cell types. The results of the present study form a foundation for developing potential biological markers for viral infection.",adaptive immunity;animal;apoptosis;autophagy;avian leukosis;Avian leukosis virus;cell line;chick embryo;chicken;gene expression regulation;gene ontology;genetics;host pathogen interaction;immunology;innate immunity;pathogenicity;signal transduction;virology;virus replication,"Chen, G.;Li, Z.;Su, S.;Chang, G.;Qiu, L.;Zhu, P.;Zhang, Y.;Xu, Q.",2018,,10.1007/s11626-017-0198-2,0
341,Identification and Survey of a Novel Avian Coronavirus in Ducks,"The rapid discovery of novel viruses using next generation sequencing (NGS) technologies including DNA-Seq and RNA-Seq, has greatly expanded our understanding of viral diversity in recent years. The timely identification of novel viruses using NGS technologies is also important for us to control emerging infectious diseases caused by novel viruses. In this study, we identified a novel duck coronavirus (CoV), distinct with chicken infectious bronchitis virus (IBV), using RNA-Seq. The novel duck-specific CoV was a potential novel species within the genus Gammacoronavirus, as indicated by sequences of three regions in the viral 1b gene. We also performed a survey of CoVs in domestic fowls in China using reverse-transcription polymerase chain reaction (RT-PCR), targeting the viral nucleocapsid (N) gene. A total of 102 CoV positives were identified through the survey. Phylogenetic analysis of the viral N sequences suggested that CoVs in domestic fowls have diverged into several region-specific or host-specific clades or subclades in the world, and IBVs can infect ducks, geese and pigeons, although they mainly circulate in chickens. Moreover, this study provided novel data supporting the notion that some host-specific CoVs other than IBVs circulate in ducks, geese and pigeons, and indicated that the novel duck-specific CoV identified through RNA-Seq in this study is genetically closer to some CoVs circulating in wild water fowls. Taken together, this study shed new insight into the diversity, distribution, evolution and control of avian CoVs. © 2013 Chen et al.",article;Avian infectious bronchitis virus;chicken;China;cladistics;Coronavirinae;domestic fowl;duck;goose;metagenomics;nonhuman;nucleotide sequence;phylogeny;Columbidae;reverse transcription polymerase chain reaction;RNA sequence;spike gene;unindexed sequence;viral 1b gene;virus gene;virus genome;virus nucleocapsid;virus nucleocapsid gene,"Chen, G. Q.;Zhuang, Q. Y.;Wang, K. C.;Liu, S.;Shao, J. Z.;Jiang, W. M.;Hou, G. Y.;Li, J. P.;Yu, J. M.;Li, Y. P.;Chen, J. M.",2013,,10.1371/journal.pone.0072918,1
342,"Evolution of the complete matrix and matrix1, matrix2 gene of H3N8 equine influenza virus","In our study, the M, Ml and M2 gene of H3N8 equine influenza virus (EIV) were phylogenetic analyzed. Also, the aa sequences of the Ml and M2 proteins were aligned and mapped. The result showed that the M, Ml and M2 gene of all the recent EIV strains of Florida-2 clade isolated after 2007 was under divergent evolution. It evolved into a different clade named Aisan clade, which was distinguished from EIV strains of Florida-2 clade isolated before 2007 and was more genetic similar to the European clade. This was also revealed by aa sequence analysis of Ml and M2 protein. In addition, the phylogenetic tree of M2 gene indicated that it evolved in different pattern from the complete M and Ml gene. The Ml and M2 gene of two horse-derived influenza viruses of A/Swine/Chibi/01/ 2005 and A/Swine/Anhui/01/2006 was confirmed under frozen evolution here. Our studies enrich our knowledge of the M, Ml and M2 gene of H3N8 EIV and will make foundation of further research on it.",matrix1 protein;protein M2;unclassified drug;viral protein;article;cladistics;equine influenza virus;gene mapping;gene sequence;Influenza A virus (H3N8);nonhuman;phylogenetic tree;sequence analysis;virus particle;virus strain,"Chen, J.;Guo, X.",2013,,,0
343,Genetic variation of Chinese PRRSV strains based on ORF5 sequence,"Thirteen isolates of porcine reproductive and respiratory syndrome virus (PRRSV) from different provinces of China were studied and compared with several PRRSV isolates from other countries. Phylogenetic analysis shows that all Chinese isolates of PRRSV in this study belong to the American genotype, except for one strain, B13, which clustered as a European genotype. Sequence analysis revealed that PRRSV Chinese isolates of the American genotype were highly similar in the ORF5 sequence and could be classified into two subclades. One contains PRRSV isolates that are more closely related to the American vaccine strain MLV Resp and its parent strain VR-2332, and the other contains ones only distantly related to them. Within the Chinese isolates slight genetic variation occurred, and some strains may originate directly from the vaccine virus. © 2006 Springer Science+Business Media, Inc.",animal cell;Arterivirus;article;Chinese;controlled study;gene;gene sequence;genetic variability;genotype;nonhuman;nucleotide sequence;orf5 gene;phylogeny;sequence analysis;virus classification,"Chen, J.;Liu, T.;Zhu, C. G.;Jin, Y. F.;Zhang, Y. Z.",2006,,10.1007/s10528-006-9039-9,0
344,Molecular epidemiology of porcine epidemic diarrhea virus in China,"Since early 2006, porcine epidemic diarrhea virus (PEDV) has been reemerging in immunized swine herds. Open reading frame 3 (ORF3) is the only accessory gene in the PEDV genome. The entire ORF3 genes of 12 PEDV field strains and one vaccine strain were sequenced. The ORF3 genes of Chinese PEDV field strains (excluding CH/GSJIII/07) contain a single 672- or 675-nucleotide (nt) ORF, which encodes a 223- or 224-aa-long peptide. However, the CV777 vaccine strain and CH/GSJIII/07 contain a 276-nt ORF because of a 49-nt deletion at nt 245-293. The Chinese PEDV field strains and PEDV reference strains are divided into three groups based on the phylogenetic relationship of their ORF3 genes. Chinese PEDV field strains (excluding CH/GSJIII/07) have a close phylogenetic relationship to Korean strains and are genetically different from the PEDV vaccine strains. However, CH/GSJIII/07 has a close phylogenetic relationship to two vaccine strains, suggesting that it might have evolved from a live vaccine strain. Chinese PEDV field strains (excluding CH/GSJIII/07) can be differentiated from PEDV vaccine strains by a nested RT-PCR method. © 2010 Springer-Verlag.",viral protein;animal;animal disease;article;chemistry;China;classification;Coronavirus infection;genetics;isolation and purification;molecular epidemiology;molecular genetics;nucleotide sequence;open reading frame;phylogeny;Porcine epidemic diarrhea virus;sequence alignment;sequence homology;pig;swine disease;virology;virus genome,"Chen, J.;Wang, C.;Shi, H.;Qiu, H.;Liu, S.;Chen, X.;Zhang, Z.;Feng, L.",2010,,10.1007/s00705-010-0720-2,0
345,Origin and future distribution of the new A (H1N1) influenza virus emerging in North America in 2009,"The origin of the new A (H1N1) influenza virus recently emerging in North America is a hot controversial topic of significance in disease control and risk assessment. Some experts claimed that it was an unusually mongrelized mix of human, avian and swine influenza viruses, while some others concluded that it was totally a simple re-assortment hybrid of two lineages of swine influenza viruses. Here the phylogenetic diversity of the viral PB1, PA and PB2 gene sequences using online web servers, and the results suggest that all the 8 genetic segments of the new virus were possibly from two lineages of swine influenza viruses, and one of the lineage was a mongrelized mix of human, avian and swine influenza viruses emerging in the world approximately 10 years ago. Considering the recent epidemiological trends of the new virus, we believe it will spread more widely in the world and persist long in human populations. It also could spread among swine populations. The future wide spreading of the new virus may coincide the disappearance of a subtype of previous human influenza A virus.",A (H1N1) influenza virus;origin;gene;swine influenza;epidemiology;A VIRUSES,"Chen, J. M.;Sun, Y. X.;Liu, S.;Jiang, W. M.;Chen, J.;Hou, G. Y.;Li, J. P.",2009,Jul,,0
346,"Reassortant Clade 2.3.4.4 of Highly Pathogenic Avian Influenza A(H5N6) Virus, Taiwan, 2017",A highly pathogenic avian influenza A(H5N6) virus of clade 2.3.4.4 was detected in a domestic duck found dead in Taiwan during February 2017. The endemic situation and continued evolution of various reassortant highly pathogenic avian influenza viruses in Taiwan warrant concern about further reassortment and a fifth wave of intercontinental spread.,,"Chen, L. H.;Lee, D. H.;Liu, Y. P.;Li, W. C.;Swayne, D. E.;Chang, J. C.;Chen, Y. P.;Lee, F.;Tu, W. J.;Lin, Y. J.",2018,06,,0
347,"Isolation, genome sequencing and functional analysis of two T7-like coliphages of avian pathogenic Escherichia coli","Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which results in significant economic losses to the poultry industry worldwide. Due to the drug residues and increased antibiotic resistance caused by antibiotic use, bacteriophages and other alternative therapeutic agents are expected to control APEC infection in poultry.Two APEC phages, named P483 and P694, were isolated from the feces from the farmers market in China. We then studied their biological properties, and carried out high-throughput genome sequencing and homology analyses of these phages. Assembly results of high-throughput sequencing showed that the structures of both P483 and P694 genomes consist of linear and double-stranded DNA. Results of the electron microscopy and homology analysis revealed that both P483 and P694 belong to T7-like virus which is a member of the Podoviridae family of the Caudovirales order.Comparative genomic analysis showed that most of the predicted proteins of these two phages showed strongest sequence similarity to the Enterobacteria phages BA14 and 285P, Erwinia phage FE44, and Kluyvera phage Kvp1; however, some proteins such as gp0.6a, gp1.7 and gp17 showed lower similarity (<. 85%) with the homologs of other phages in the T7 subgroup. We also found some unique characteristics of P483 and P694, such as the two types of the genes of P694 and no lytic activity of P694 against its host bacteria in liquid medium.Our results serve to further our understanding of phage evolution of T7-like coliphages and provide the potential application of the phages as therapeutic agents for the treatment of diseases.",double stranded DNA;agricultural worker;article;avian pathogenic Escherichia coli;Caudovirales;China;coliphage;Enterobacteriaceae;Erwinia;feces;gene function;gene isolation;genome analysis;high throughput sequencing;host range;liquid culture;nonhuman;pH;Podoviridae;priority journal;sequence homology;T7 like coliphage;thermostability;transmission electron microscopy;virogenesis;virus gene;virus genome;virus isolation;virus morphology;virus plaque,"Chen, M.;Xu, J.;Yao, H.;Lu, C.;Zhang, W.",2016,,10.1016/j.gene.2016.01.049,0
348,Deep Sequencing Details the Cross-over Map of Chimeric Genes in Two Porcine Reproductive and Respiratory Syndrome Virus Infectious Clones,"BACKGROUND: Recombination is an important contributor to the genetic diversity of most viruses. A reverse genetics system using green fluorescence protein (GFP)- and enhanced GFP (EGFP)-expressing infectious clones was developed to study the requirements for recombination. However, it is still unclear what types of cross-over events occurred to produce the viable offspring. OBJECTIVE: We utilized 454 sequencing to infer recombination events in this system. METHOD: Two porcine reproductive and respiratory syndrome virus (PRRSV) infectious clones, P129-EGFP-97C and P129-GFPm-d (2-6), were co-transfected into HEK-293T cells. P129-EGFP-97C is a fully functional virus that contains a non-fluorescent EGFP. P129-GFPm-d (2-6) is a defective virus but contains a fluorescent GFPm. Successful recombination was evident by the appearance of fully functional progeny virus that expresses fluorescence. Total RNA was extracted from infected cells expressing fluorescence, and the entire fluorescent gene was amplified to prepare an amplicon library for 454 sequencing. RESULTS: Deep sequencing showed that the nucleotide identities changed from ~37% (in the variable region from 21nt to 165nt) to 20% (T<sub>289</sub>C) to ~38% (456-651nt) then to 100% (672-696nt) when compared to EGFP. The results indicated that cross-over events occurred in three conserved regions (166-288nt, 290-455nt, 652-671nt), which were also supported by sequence alignments. Remarkably, the short conserved region (652-671nt) showed to be a cross-over hotspot. In addition, four cross-over patterns (two single and two double cross-over) might be used to produce viable recombinants. CONCLUSION: The reverse genetics system incorporating the use of high throughput sequencing creates a genetic platform to study the generation of viable recombinant viruses.",,"Chen, N.;Chand, R. J.;Rowland, R. R. R.",2017,,,0
349,Porcine reproductive and respiratory syndrome virus replication and quasispecies evolution in pigs that lack adaptive immunity,"The replication of porcine reproductive and respiratory syndrome virus (PRRSV) was studied in a line of pigs possessing a severe combined immunodeficiency (SCID). Real-time RT-PCR revealed a unique course of infection for the SCID group. During the course of infection, viremia was initially significantly lower than normal littermates, but by 21 days was significantly elevated. Deep sequencing of the viral structural genes at days 11 and 21 identified seven amino acid substitutions in both normal and SCID pigs. The most significant change was a W99R substitution in GP2, which was present in the inoculum at a frequency of 35%, but eventually disappeared from all pigs regardless of immune status. Therefore, amino acid substitutions that appear during acute infection are likely the result of the adaptation of the virus to replication in pigs and not immune selection.","Adaptive Immunity;Amino Acid Substitution;Animals;*Genetic Variation;High-Throughput Nucleotide Sequencing;Porcine respiratory and reproductive syndrome virus/cl [Classification];*Porcine respiratory and reproductive syndrome virus/ge [Genetics];*Porcine respiratory and reproductive syndrome virus/ph [Physiology];RNA, Viral/ge [Genetics];Real-Time Polymerase Chain Reaction;Reverse Transcriptase Polymerase Chain Reaction;*Severe Combined Immunodeficiency;Swine;Time Factors;Viral Load;Viremia;*Virus Replication;0 (RNA, Viral)","Chen, N.;Dekkers, J. C.;Ewen, C. L.;Rowland, R. R.",2015,Jan 02,,0
350,Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States,"Background: Emergence and re-emergence of porcine epidemic diarrhea virus (PEDV) in North America, Asia and Europe has caused severe economic loss to the global swine industry. However, the virome of PEDV infected pigs and its effect on disease severity remains unknown. The advancements of sequencing technology have made it possible to characterize the entire microbiome of different body sites for any host. Methods: The objective of this study was to characterize the RNA virome in PEDV-positive pigs using the hypothesis-free metagenomics approach based on next-generation sequencing. Specifically, 217 PEDV-positive swine fecal swab samples collected from diarrheic piglets over 17 US states during 2015-2016 were analyzed. Results: A Kraken algorithm-based bioinformatics analysis revealed the presence of up to 9 different RNA genera besides PEDV (Alphacoronavirus genus), including Mamastrovirus (52%, 113/217), Enterovirus (39%, 85/217), Sapelovirus (31%, 67/217), Posavirus (30%, 66/217), Kobuvirus (23%, 49/217), Sapovirus (13%, 28/217), Teschovirus (10%, 22/217), Pasivirus (9%, 20/217), and Deltacoronavirus (3%, 6/217). There were 58 out of 217 piglets (27%) have PEDV infection alone whereas the remaining 159 (73%) shed 2 up to 9 different viruses. Conclusion: These findings demonstrated that PEDV infected diarrheic pigs had an extensive RNA viral flora consisting of four different families: Astroviridae, Picornaviridae, Caliciviridae, and Coronaviridae.",algorithm;Alphacoronavirus;article;Astroviridae;bioinformatics;Caliciviridae;controlled study;Coronaviridae;Deltacoronavirus;Enterovirus;feces culture;Kobuvirus;Mamastrovirus;metagenomics;next generation sequencing;nonhuman;Pasivirus;Picornaviridae;piglet;porcine epidemic diarrhea;Porcine epidemic diarrhea virus;Posavirus;RNA virus;Sapelovirus;Sapovirus;Teschovirus;United States,"Chen, Q.;Wang, L.;Zheng, Y.;Zhang, J.;Guo, B.;Yoon, K. J.;Gauger, P. C.;Harmon, K. M.;Main, R. G.;Li, G.",2018,,10.1186/s12985-018-1001-z,1
351,"A novel astrovirus species in the gut of yaks with diarrhoea in the Qinghai-Tibetan plateau, 2013","The yak (Bos grunniens) is an iconic symbol in the high-altitude region of the Qinghai-Tibetan Plateau. Diarrhoea is a common disease in yaks, resulting in major economic losses. To investigate the diversity of viral species, we reported the metagenomics-derived virome in a pooled faecal sample of 20 diarrhoeic yaks. The nine viruses found in the pooled diarrhoeic samples, in order of abundance of nucleic acid sequence, were influenza A virus, bovine viral diarrhoea virus (BVDV), rotavirus, ungulate tetraparvovirus 1 (bovine hokovirus), astrovirus (AstV), bovine enterovirus, hepatitis E virus, kobuvirus and woodchuck hepatitis virus. Compared with healthy yaks, only AstV had a significantly higher prevalence rate in diarrhoeal samples, indicating a correlation with the clinical symptoms of diarrhoea in yaks. To further investigate the molecular characterization of yak AstV, a near-full genome was obtained from a diarrhoeic sample. It was 6243 bp in length and shared 46.4-66.2% similarity with other related bovine AstVs from faeces. Phylogenetic analysis of the genome demonstrated that the yak AstV fell within the bovine AstVs cluster, but was located in a unique lineage, suggesting a novel AstV species was identified in yaks. Interestingly, the ORF2 region of yak AstV had closer similarity and genetically relationship with deer AstV strain CcAstV-2 than that of the bovine AstVs. Further analysis showed that one possible interspecies recombination event occurred in ORF2. In summary, this study expanded our understanding of the viral communities of diarrhoeal yaks and identified a novel AstV that was associated with diarrhoea in yaks.",article;Astroviridae;Bovine enterovirus;bovine viral diarrhea;China;controlled study;diarrhea;genetic recombination;Hepatitis E virus;Influenza A virus;intestine;Kobuvirus;metagenomics;nonhuman;nucleotide sequence;open reading frame;Parvoviridae;prevalence;priority journal;Rotavirus;ungulate tetraparvovirus 1;virus detection;virus genome;virus strain;Woodchuck hepatitis virus;yak,"Chen, X.;Zhang, B.;Yue, H.;Wang, Y.;Zhou, F.;Zhang, Q.;Tang, C.",2015,,10.1099/jgv.0.000303,1
352,Cloning and molecular characterization of the ORF5 gene from a PRRSV-SN strain from Southwest China,"To monitor the genetic variation of PRRSV, the ORF5 gene of the PRRSV-SN strain found in Suining City, Sichuan Province, was cloned and sequenced. The results showed that the PRRSV-SN strain was a highly pathogenic PRRSV (HP-PRRSV) variant strain with the North American (NA) genotype. Homology analysis showed that the ORF5 gene of the PRRSV-SN isolate shared 89.4% (86.5%) nucleotide (amino acid) sequence similarity with the North American strain VR-2332, 98.8% (96%) similarity with JXA1, and 63.8% (57.7%) similarity with the European type representative strain Lelystad virus. Phylogenetic analysis showed that PRRSV-SN belongs to the NA genotype and has the same subtype as other highly pathogenic PRRSV strains. Amino acid sequence analysis showed that compared with the VR2332 strain, PRRSV-SN has different degrees of variation in the signal peptide, transmembrane region (TM), primary neutralizing epitope (PNE), non-neutral epitopes and N-glycosylation sites. Antigenicity analysis showed that the PRRSV-SN ORF5 gene products and JXA1 have similar antigenic characteristics, and the antigenic epitopes are mainly located in aa30-39, aa50-60, aa128-141, aa146-155 and aa161-183 regions. In contrast, the antigenic characteristics of PRRSV-SN are quite different from those of the VR2332 strain. The main differences were that the PRRSV-SN strain was significantly narrower than the VR2332 strain in the aa30-39 and the aa50-60 regions but was significantly wider in the aa136-141 region. The results of this study showed that the epidemic strains that cause PRRSV outbreaks in the farm are still mainly JXA1 variants, but due to the more frequent use of live vaccine immunizations, the genes of the PRRSV epidemic strain still show constant variation. Vaccination with live PRRSV should be reduced, and surveillance of PRRSV strains should be enhanced.","Amino Acid Sequence;Animals;Antigens, Viral/ge [Genetics];Antigens, Viral/im [Immunology];Base Sequence;China;*Genes, Viral/ge [Genetics];*Genetic Variation;Genetic Vectors;Genotype;Molecular Epidemiology;Phylogeny;Porcine Reproductive and Respiratory Syndrome/ep [Epidemiology];*Porcine Reproductive and Respiratory Syndrome/vi [Virology];*Porcine respiratory and reproductive syndrome virus/cl [Classification];*Porcine respiratory and reproductive syndrome virus/ge [Genetics];Porcine respiratory and reproductive syndrome virus/im [Immunology];*Porcine respiratory and reproductive syndrome virus/ip [Isolation & Purification];Porcine respiratory and reproductive syndrome virus/py [Pathogenicity];RNA, Viral/ge [Genetics];RNA-Binding Proteins/ge [Genetics];Sequence Alignment;Sequence Analysis;Sequence Homology, Amino Acid;Sequence Homology, Nucleic Acid;Swine;Vaccination;*Viral Envelope Proteins/ge [Genetics];Viral Nonstructural Proteins/ge [Genetics];Viral Proteins/ge [Genetics];0 (Antigens, Viral);0 (RNA, Viral);0 (RNA-Binding Proteins);0 (Viral Envelope Proteins);0 (Viral Nonstructural Proteins);0 (Viral Proteins);0 (glycoprotein 5, PRRSV)","Chen, X. W.;Li, L.;Yin, M.;Wang, Q.;Luo, W. T.;Ma, Y.;Pu, Z. H.;Zhou, J. L.",2017,Nov,,0
353,Phylogenetic analysis of human/swine/avian gene reassortant H1N2 influenza A virus isolated from a pig in China,"OBJECTIVE: Our aim in this study was to determine the genetic characterization and probable origin of the H1N2 swine influenza virus (A/Swine/Guangxi/13/2006) (Sw/GX/13/06) from lung tissue of a pig in Guangxi province, China. METHODS: Eight genes of Sw/GX/13/06 were cloned and genetically analyzed. RESULTS: The hemagglutinin (HA), nucleoprotein (NP), matrix (M) and non-structural (NS) genes of Sw/GX/13/06 were most closely related to genes from the classical swine H1N1 influenza virus lineage. The neuraminidase (NA) and PB1 genes were most closely related to the corresponding genes from the human influenza H3N2 virus lineage. The remaining two genes PA and PB2 polymerase genes were most closely related to the genes from avian influenza virus lineage. CONCLUSION: Phylogenetic analyses revealed that Sw/GX/13/06 was a human/swine/avian H1N2 virus, and closely related to H1N2 viruses isolated from pigs in United States (1999-2001) and Korea (2002). To our knowledge, Sw/GX/13/06 was the first triple-reassortant H1N2 influenza A virus isolated from a pig in China. Whether the Sw/GX/13/06 has a potential threat to breeding farm and human health remains to be further investigated.",animal;article;bird;China;classification;cytology;genetic reassortment;genetics;genotype;human;Influenza A virus;isolation and purification;lung;phylogeny;poultry;sequence homology;pig;virology;virus gene,"Chen, Y.;Meng, X.;Liu, Q.;Huang, X.;Huang, S.;Liu, C.;Shi, K.;Guo, J.;Chen, F.;Hu, L.",2008,,,0
354,Gene expression profile after activation of RIG-I in 5'ppp-dsRNA challenged DF1,"Retinoic acid inducible gene I (RIG-I) can recognize influenza viruses and evoke the innate immune response. RIG-I is absent in the chicken genome, but is conserved in the genome of ducks. Lack of RIG-I renders chickens more susceptible to avian influenza infection, and the clinical symptoms are more prominent than in other poultry. It is unknown whether introduction of duck RIG-I into chicken cells can establish the immunity as is seen in ducks and the role of RIG-I in established immunity is unknown. In this study, a chicken cell strain with stable expression of duRIG-I was established by lentiviral infection, giving DF1/LV5-RIG-I, and a control strain DF1/LV5 was established in parallel. To verify stable, high level expression of duRIG-I in DF1 cells, the levels of duRIG-I mRNA and protein were determined by real-time RT-PCR and Western blot, respectively. Further, 5'triphosphate double stranded RNA (5'ppp-dsRNA) was used to mimic an RNA virus infection and the infected DF1/LV5-RIG-I and DF1/LV5 cells were subjected to high-throughput RNA-sequencing, which yielded 193.46 M reads and 39.07 G bases. A total of 278 differentially expressed genes (DEGs), i.e., duRIG-I-mediated responsive genes, were identified by RNA-seq. Among the 278 genes, 120 DEGs are annotated in the KEGG database, and the most reliable KEGG pathways are likely to be the signaling pathways of RIG-I like receptors. Functional analysis by Gene ontology (GO) indicates that the functions of these DEGs are primarily related to Type I interferon (IFN) signaling, IFN-β-mediated cellular responses and up-regulation of the RIG-I signaling pathway. Based on the shared genes among different pathways, a network representing crosstalk between RIG-I and other signaling pathways was constructed using Cytoscape software. The network suggests that RIG-mediated pathway may crosstalk with the Jak-STAT signaling pathway, Toll-like receptor signaling pathway, Wnt signaling pathway, ubiquitin-mediated proteolysis and MAPK signaling pathway during the transduction of antiviral signals. After screening, a group of key responsive genes in RIG-I-mediated signaling pathways, such as ISG12-2, Mx1, IFIT5, TRIM25, USP18, STAT1, STAT2, IRF1, IRF7 and IRF8, were tested for differential expression by real-time RT-PCR. In summary, by combining our results and the current literature, we propose a RIG-I-mediated signaling network in chickens.",5' triphosphate double stranded RNA;beta interferon;interferon;interferon consensus sequence binding protein;interferon regulatory factor 1;interferon regulatory factor 7;Janus kinase;messenger RNA;mitogen activated protein kinase;retinoic acid inducible protein I;RNA;STAT protein;STAT1 protein;STAT2 protein;toll like receptor;ubiquitin;unclassified drug;animal cell;article;cell strain;cellular immunity;chicken;software;controlled study;fibroblast culture;gene expression;gene function;gene ontology;high throughput sequencing;Lentivirus infection;molecular interaction;nonhuman;priority journal;protein degradation;protein expression;real time polymerase chain reaction;RNA sequence;RNA virus infection;signal transduction;upregulation;Western blotting;Wnt signaling;Cytoscape software,"Chen, Y.;Xu, Q.;Li, Y.;Liu, R.;Huang, Z.;Wang, B.;Chen, G.",2016,,10.1016/j.dci.2016.07.009,0
355,Characterisation of a newly detected bacteriophage infecting Bordetella bronchiseptica in swine,"A novel virulent bacteriophage, vB_BbrM_PHB04, infecting Bordetella bronchiseptica was isolated from wastewater collected at a swine farm in China. Phage vB_BbrM_PHB04 exhibited growth over a wide range of temperature and pH conditions and showed different efficiency of plating values and lytic spectra within the same strains at 25 °C and 37 °C. High-throughput sequencing revealed that vB_BbrM_PHB04 has a linear double-stranded DNA genome with 124 putative open reading frames. Overall, the genome of vB_BbrM_PHB04 showed very low similarity (the highest nucleotide identity 82%, 1% coverage) to other phage sequences in the GenBank database. Phylogenetic analysis indicated that vB_BbrM_PHB04 is a new member of the family Myoviridae. In addition, polymerase chain reaction-based detection of phage genes in phage-resistant B. bronchiseptica variants revealed no evidence of lysogenic activity of phage vB_BbrM_PHB04.",animal;Bordetella bronchiseptica;genetics;isolation and purification;microbiology;Myoviridae;pH;phylogeny;pig;temperature;virology;virus genome,"Chen, Y.;Yang, L.;Sun, E.;Song, J.;Wu, B.",2019,,10.1007/s00705-018-4034-0,0
356,"Co-circulation of pandemic 2009 H1N1, classical swine H1N1 and avian-like swine H1N1 influenza viruses in pigs in China","The pandemic A/H1N1 influenza viruses emerged in both Mexico and the United States in March 2009, and were transmitted efficiently in the human population. They were transmitted occasionally from humans to other mammals including pigs, dogs and cats. In this study, we report the isolation and genetic analysis of novel viruses in pigs in China. These viruses were related phylogenetically to the pandemic 2009 H1N1 influenza viruses isolated from humans and pigs, which indicates that the pandemic virus is currently circulating in swine populations, and this hypothesis was further supported by serological surveillance of pig sera collected within the same period. Furthermore, we isolated another two H1N1 viruses belonging to the lineages of classical swine H1N1 virus and avian-like swine H1N1 virus, respectively. Multiple genetic lineages of H1N1 viruses are co-circulating in the swine population, which highlights the importance of intensive surveillance for swine influenza in China. © 2012 Elsevier B.V.",virus antigen;2009 H1N1 influenza;amino acid sequence;article;avian like swine H1N1 influenza A;China;classical swine H1N1 influenza A;controlled study;genetic analysis;HA gene;Influenza A virus (H1N1);nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;sequence analysis;sequence homology;pig;virus detection;virus gene;virus genome;virus identification;virus isolation,"Chen, Y.;Zhang, J.;Qiao, C.;Yang, H.;Zhang, Y.;Xin, X.;Chen, H.",2013,,10.1016/j.meegid.2012.09.021,0
357,"Japanese encephalitis virus genotype replacement, Taiwan, 2009-2010",Genotype I of Japanese encephalitis virus first appeared in Taiwan in 2008. Phylogenetic analysis of 37 viruses from pig farms in 2009-2010 classified these viruses into 2 unique subclusters of genotype I viruses and suggested multiple introductions and swift replacement of genotype III by genotype I virus in Taiwan.,article;E gene;farm animal;gene sequence;genotype;Japanese encephalitis virus;nonhuman;nucleotide sequence;phylogeny;seasonal variation;sequence homology;pig;Taiwan;virus gene;virus isolation;virus strain;virus transmission;winter,"Chen, Y. Y.;Fan, Y. C.;Tu, W. C.;Chang, R. Y.;Shih, C. C.;Lu, I. H.;Chien, M. S.;Lee, W. C.;Chen, T. H.;Chang, G. J.;Chiou, S. S.",2011,,10.3201/eid1712.110914,0
358,Genetic diversity in envelope genes of contemporary U.S. porcine reproductive and respiratory syndrome virus strains influences viral antigenicity,"Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically important diseases in swine caused by porcine reproductive and respiratory syndrome virus (PRRSV). Genome sequences of sixty-six PRRSV strains were obtained using metagenomic sequencing of serum samples collected in the U.S. in 2014 to explore contemporary genetic diversity. Phylogenetic analysis of the genes encoding the envelope proteins identified four to eight distinct lineages with > 87% intraclade identity. To explore the effect of the observed genetic diversity on antigenicity, the genome regions encoding either GP2a-GP3-GP4 or GP5-M in strain SD95-21 were replaced with alleles from each of eight distinct PRRSV strains using reverse genetics. The GP2a-GP3-GP4 region from only four of the eight strains yielded viable recombinant virus. When viable, both GP2a-GP3-GP4 and GP5-M variably affected antigenicity. A strain-dependent significant loss in cross reactivity was variably observed by indirect immunofluorescence assays using antisera from pigs vaccinated with commercial modified-live vaccines following replacement of GP2a-GP3-GP4 or GP5-M. Significantly reduced neutralization titers were similarly measured using antisera from naturally PRRSV-exposed pigs. These results illustrate the need to consider genomic regions besides GP5 for PRRSV epidemiology and vaccination.",neutralizing antibody;allele;animal cell;antibody detection;antibody titer;antigenicity;article;controlled study;cross reaction;envelope gene;gene sequence;genetic code;genetic variability;immunofluorescence;metagenomics;molecular phylogeny;nonhuman;nucleotide sequence;open reading frame;Porcine reproductive and respiratory syndrome virus;viral tropism;virus genome;virus strain,"Chen, Z.;Collin, E.;Peddireddi, L.;Clement, T.;Gauger, P.;Hause, B. M.",2017,,10.1016/j.rvsc.2017.07.027,1
359,Phylogenetic analysis of Indian rabies virus isolates targeting the complete glycoprotein gene,"Rabies a fatal viral zoonosis is endemic in India. There is no report on phylogenetic study of Indian rabies virus isolates based on the complete G gene. In the present study, a total of 25 rabies positive brain samples collected during 2001-2014 from North India (UP, MP, Delhi, Rajasthan), South India (Kerala and Karnataka) and Gujarat states belonging to six different host species were subjected to G gene amplification by RT-PCR as three overlapping fragments of 881. bp, 991. bp and 618. bp. Phylogenetic analysis revealed that all Indian rabies virus isolates are genetically closely related with Arctic-like 1a lineage viruses. However, two distinct clusters were identified namely, India South and India North. All the Indian rabies isolates had 95.5-100% homology related to geography, but not to host species. Deduced amino acids on comparison revealed two amino acid changes, aa 356 in ECTO; N. → K and aa 458; M. → I, which were found to distinguish between the India South and India North isolates.",virus glycoprotein;amino acid sequence;animal tissue;Arctic;article;black bear;bovine;cladistics;comparative study;controlled study;dog;G gene;gene amplification;gene cluster;gene identification;genetic similarity;geographic distribution;hyena;India;mongoose;nonhuman;phylogeny;priority journal;Rabies virus;sequence analysis;sequence homology;species differentiation;virus gene;wildlife,"Cherian, S.;Singh, R.;Singh, K. P.;Manjunatha Reddy, G. B.;Anjaneya;Ravi Kumar, G. V. P. P. S.;Sumithra, T. G.;Singh, R. P.",2015,,10.1016/j.meegid.2015.09.024,0
360,Evolution of Bovine viral diarrhea virus in Canada from 1997 to 2013,"Bovine viral diarrhea virus (BVDV) is a rapidly evolving, single-stranded RNA virus and a production limiting pathogen of cattle worldwide. 79 viral isolates collected between 1997 and 2013 in Canada were subjected to next-generation sequencing. Bayesian phylogenetics was used to assess the evolution of this virus. A mean substitution rate of 1.4×10−3 substitutions/site/year was found across both BVDV1 and BVDV2. Evolutionary rates in the E2 gene were slightly faster than other regions. We also identified population structures below the sub-genotype level that likely have phenotypic implications. Two distinct clusters within BVDV2a are present and can be differentiated, in part, by a tyrosine to isoleucine mutation at position 963 in the E2 protein, a position implicated in the antigenicity of BVDV1 isolates. Distinct clustering within all sub-genotypes, particularly BVDV2a, is apparent and could lead to new levels of genotypic classification. Continuous monitoring of emerging variants is therefore necessary.",glycoprotein E2;isoleucine;tyrosine;amino acid substitution;article;bovine;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;Canada;controlled study;E2 gene;envelope gene;evolutionary rate;next generation sequencing;nonhuman;phylogenetic tree;population structure;priority journal;sequence alignment,"Chernick, A.;van der Meer, F.",2017,,10.1016/j.virol.2017.06.024,0
361,Identification of several clades of novel single-stranded circular DNA viruses with conserved stem-loop structures in pig feces,"Metagenomic analysis of fecal samples collected from diarrheal swine detected sequences encoding a replication initiator protein (Rep). The genomes of ten novel single-stranded DNA viruses were determined, and they exhibited a similar genome organization. The two putative open reading frames (ORFs) encoding Rep and the capsid protein are bidirectionally transcribed and separated by two intergenic regions. Stem-loop structure(s) typical of genomes that undergo the rolling-circle DNA replication mechanism were observed. Phylogenetically, these ten genomes are in a monophyletic clade with the previously described porcine stool-associated virus (PoSCV) but are divergent enough to be further classified into to six distinct virus clades.",DNA virus;single stranded DNA;virus DNA;viral protein;amino acid sequence;animal;classification;diarrhea;feces;gene expression regulation;genetics;isolation and purification;metabolism;molecular genetics;nucleotide sequence;phylogeography;physiology;pig;swine disease;veterinary medicine;virology,"Cheung, A. K.;Ng, T. F.;Lager, K. M.;Alt, D. P.;Delwart, E.;Pogranichniy, R. M.",2015,,10.1007/s00705-014-2234-9,0
362,Unique circovirus-like genome detected in pig feces,"Using a metagenomic approach and molecular cloning methods, we identified, cloned, and sequenced the complete genome of a novel circular DNA virus, porcine stool-associated virus (PoSCV4), from pig feces. Phylogenetic analysis of the deduced replication initiator protein showed that PoSCV4 is most related to a fur seal feces-associated circular DNA virus.",,"Cheung, A. K.;Ng, T. F.;Lager, K. M.;Alt, D. P.;Delwart, E. L.;Pogranichniy, R. M.",2014,Apr 10,,1
363,A divergent clade of circular single-stranded DNA viruses from pig feces,"Using metagenomics and molecular cloning methods, we characterized five novel small, circular viral genomes from pig feces that are distantly related to chimpanzee and porcine stool-associated circular viruses, (ChiSCV and PoSCV1). Phylogenetic analysis placed these viruses into a highly divergent clade of this rapidly growing new viral family. This new clade of viruses, provisionally named porcine stool-associated circular virus 2 and 3 (PoSCV2 and PoSCV3), encodes a stem-loop structure (presumably the origin of DNA replication) in the small intergenic region and a replication initiator protein commonly found in other biological systems that replicate their genomes via the rolling-circle mechanism. Furthermore, these viruses also exhibit three additional overlapping open reading frames in the large intergenic region between the capsid and replication initiator protein genes. © 2013 Springer-Verlag Wien (outside the USA).",viral protein;amino acid sequence;animal;article;DNA virus;feces;genetic variability;genetics;isolation and purification;metabolism;molecular genetics;phylogeny;pig;swine disease;virology;virus genome,"Cheung, A. K.;Ng, T. F.;Lager, K. M.;Bayles, D. O.;Alt, D. P.;Delwart, E. L.;Pogranichniy, R. M.;Kehrli Jr, M. E.",2013,,10.1007/s00705-013-1701-z,1
364,Biology of influenza a virus,"The outbreaks of avian influenza A virus in poultry and humans over the last decade posed a pandemic threat to human. Here, we discuss the basic classification and the structure of influenza A virus. The viral genome contains eight RNA viral segments and the functions of viral proteins encoded by this genome are described. In addition, the RNA transcription and replication of this virus are reviewed. © 2007 New York Academy of Sciences.",acidic polymerase;basic polymerase protein 1;basic polymerase protein 2;hemagglutinin;matrix protein;nucleoprotein;protein m1;protein M2;nonstructural protein 1;nonstructural protein 2;ribonucleoprotein;sialidase;unclassified drug;viral protein;virus RNA;conference paper;Influenza A virus;nonhuman;Orthomyxoviridae;protein expression;protein function;protein transport;RNA replication;RNA transcription;virus classification;virus genome;virus morphology;virus replication,"Cheung, T. K. W.;Poon, L. L. M.",2007,,10.1196/annals.1408.001,0
365,Genome analysis of orf virus isolates from goats in the Fujian Province of southern China,"Orf virus (ORFV), a species of the genus Parapoxvirus of the family Poxviridae, causes non-systemic, highly contagious, and eruptive disease in sheep, goat, and other wild and domestic ruminants. Our previous work shows orf to be ubiquitous in the Fujian Province of China, a region where there is considerable heterogeneity among ORFVs. In this study, we sequenced full genomes of four Fujian goat ORFV strains (OV-GO, OV-YX, OV-NP, and OV-SJ1). The four strains were 132-139 kb in length, with each containing 124-132 genes and about 64% G+C content. The most notable differences between the four strains were found near the genome termini. OV-NP lacked seven and OV-SJ1 lacked three genes near the right terminus when compared against other ORFVs. We also investigated the skin-virulence of the four Fujian ORFVs in goats. The ORFVs with gene deletions showed low virulence while the ORFVs without gene deletions showed high virulence in goats suggesting gene deletion possibly leads to attenuation of ORFVs. Gene 134 was disrupted in OV-NP genome due to the lack of initial code. The phylogenetic tree based on complete Parapoxviruse genomes showed that sheep originated and goat originated ORFVs formed distinctly separate branches with 100% bootstrap. Based on the single gene phylogenetic tree of 132 genes of ORFVs, 47 genes can be easily distinguished as having originated from sheep or goats. In order to further reveal genetic variation presented in goat ORFVs and sheep ORFVs, we analyzed the deduced amino acid sequences of gene 008, multiple alignment of amino acid sequences of gene 008 from the genome of five goat ORFVs and four sheep ORFVs revealed 33 unique amino acids differentiating it as having sheep or goats as host. The availability of genomic sequences of four Fujian goat ORFVs aids in our understanding of the diversity of orf virus isolates in this region and can assist in distinguishing between orf strains that originate in sheep and goats.",amino acid sequence;animal experiment;article;China;controlled study;gene deletion;gene sequence;genetic analysis;goat;inoculation;nonhuman;nucleotide sequence;open reading frame;Orf virus;phylogenetic tree;phylogeny;polymerase chain reaction;sequence alignment;virus virulence,"Chi, X.;Zeng, X.;Li, W.;Hao, W.;Li, M.;Huang, X.;Huang, Y.;Rock, D. L.;Luo, S.;Wang, S.",2015,,10.3389/fmicb.2015.01135,0
366,"Diagnosis and phylogenetic analysis of a multifocal cutaneous orf virus with mixed bacterial infection outbreak in goats in Fujian province, China","Outbreaks of orf virus on goat farms are common in China. In this study, we investigated a severe multifocal cutaneous orf virus outbreak with a correlative mixed bacterial infection which persisted for up to 6 months, and which had a high morbidity (93.7%) and mortality (15%) among kids in a herd of crossbreed goats in Fujian province in China. The disease was diagnosed as an orf virus (ORFV XD strain) infection associating with Streptococcus pluranimalium and Staphylococcus, identified using standard virological and bacteriological techniques. Multiple sequence alignments and phylogenetic analyses of the whole ORFV 011 (B2L), 059 (F1L), 032 and 080 genes revealed that the even though the virus phylogeny was clustered in branches of conventional orf virus strains, it nonetheless evidenced high variation within this subset. Furthermore, the sequences from the ORFV 080 gene allowed us to distinguish between the different strains at a higher resolution and these observations afforded us a comparative view of the ORFV 080 gene. This is the first report describing an outbreak of severe multifocal cutaneous orf virus with associated bacterial infection in China.",animal;bacterial skin disease;China;complication;contagious ecthyma;epidemic;genetics;goat;goat disease;microbiology;Orf virus;pathology;phylogeny;veterinary medicine;virology,"Chi, X.;Zeng, X.;Luo, S.",2017,,10.1007/s00705-017-3424-z,0
367,Classification and putative origins of Brazilian porcine circovirus 2 inferred through phylogenetic and phylogeographical approaches,"Porcine circovirus 2 (PCV2) is the major causative agent of postweaning multisystemic wasting syndrome (PMWS) and is associated with different syndromes affecting pigs. The PCV2 genome has three main open reading frames (ORFs) among which the ORF2 encodes the capsid protein. In this study, the ORF2 nucleotide sequences of 30 Brazilian isolates were analyzed. The sequences were compared to other GenBank sequences using phylogenic and phylogeographic approaches. Our results show high sequence variability in Brazil, since, in this work, the Brazilian isolates were classified into subgroup 1AB, 2D and 2, which reveals that the virus was introduced in Brazil more than once. On the other hand, most of Brazilian isolates seem to be derived from only one introduction. According to the data from the Pig Breeders' Association, the multiple introductions of the virus probably occurred through the import of animals with the asymptomatic form of the virus or through the import of contaminated semen. The results point to the necessity of implementing programs aimed at selecting sows in order to avoid the import of animals infected by Group 1 PCV2. © 2008 Elsevier B.V. All rights reserved.",article;Brazil;Circoviridae;genetic variability;nonhuman;nucleotide sequence;open reading frame;phylogeny;phylogeography;Porcine circovirus 2;priority journal;sequence analysis;sperm;viral contamination;virus classification;virus transmission,"Chiarelli-Neto, O.;Yotoko, K. S. C.;Vidigal, P. M. P.;Silva, F. M. F.;Castro, L. A.;Fietto, J. L. R.;Silva Jr, A.;Almeida, M. R.",2009,,10.1016/j.virusres.2008.11.002,0
368,Ranaviruses and other members of the family Iridoviridae: Their place in the virosphere,"Members of the family Iridoviridae, collectively referred to as iridovirids, are large, double-stranded DNA-containing viruses that infect invertebrates and cold-blooded (ectothermic) vertebrates. Infections in the former often lead to massive levels of virus replication resulting in iridescence of the infected animal and ultimately death. Among the latter, infections target a variety of organs and are capable of causing high levels of morbidity and mortality among commercially and ecologically important fish and amphibian species. The viral replication strategy has been elucidated primarily through the study of frog virus 3 (FV3) with additional input from other iridovirids of ecological or commercial importance. Replication occurs within both nuclear and cytoplasmic compartments and involves synthesis of genome length and concatemeric DNA, extensive methylation of the viral genome (among vertebrate viruses only), coordinate expression of three classes of viral gene products, and formation of icosahedral virions within cytoplasmic viral assembly sites. Phylogenetic analyses delineate five genera within the family and suggest that members of the families Iridoviridae, Ascoviridae, and Marseilleviridae compromise a monophyletic lineage in which ascoviruses are most closely related to invertebrate iridoviruses.",Ranavirus;Iridovirus;Amphibian decline;Viral taxonomy;Nuclear;cytoplasmic large DNA viruses;FROG VIRUS 3;SINGAPORE GROUPER IRIDOVIRUS;CHILO IRIDESCENT VIRUS;MAJOR CAPSID PROTEIN;SWINE-FEVER VIRUS;LARGE DNA VIRUSES;INNATE;IMMUNE-RESPONSES;KIDNEY NECROSIS VIRUS;VIRAL MESSENGER-RNAS;MACROMOLECULAR-SYNTHESIS,"Chinchar, V. G.;Waltzek, T. B.;Subramaniam, K.",2017,Nov,,0
369,Genetic diversity of Crimean Congo hemorrhagic fever virus strains from Iran,"Background: Crimean Congo hemorrhagic fever virus (CCHFV) is a member of the Bunyaviridae family and Nairovirus genus. It has a negative-sense, single stranded RNA genome approximately 19.2 kb, containing the Small, Medium, and Large segments. CCHFVs are relatively divergent in their genome sequence and grouped in seven distinct clades based on S-segment sequence analysis and six clades based on M-segment sequences. Our aim was to obtain new insights into the molecular epidemiology of CCHFV in Iran. Methods: We analyzed partial and complete nucleotide sequences of the S and M segments derived from 50 Iranian patients. The extracted RNA was amplified using one-step RT-PCR and then sequenced. The sequences were analyzed using Mega5 software. Results: Phylogenetic analysis of partial S segment sequences demonstrated that clade IV-(Asia 1), clade IV-(Asia 2) and clade V-(Europe) accounted for 80 %, 4 % and 14 % of the circulating genomic variants of CCHFV in Iran respectively. However, one of the Iranian strains (Iran-Kerman/22) was associated with none of other sequences and formed a new clade (VII). The phylogenetic analysis of complete S-segment nucleotide sequences from selected Iranian CCHFV strains complemented with representative strains from GenBank revealed similar topology as partial sequences with eight major clusters. A partial M segment phylogeny positioned the Iranian strains in either association with clade III (Asia-Africa) or clade V (Europe). Conclusion: The phylogenetic analysis revealed subtle links between distant geographic locations, which we propose might originate either from international livestock trade or from long-distance carriage of CCHFV by infected ticks via bird migration.",Africa;Asia;bird;cladistics;clinical article;software;Crimean-Congo hemorrhagic fever virus;Europe;GenBank;gene amplification;genetic variability;geography;human;Iranian (citizen);livestock;molecular epidemiology;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;tick;virus strain,"Chinikar, S.;Bouzari, S.;Shokrgozar, M. A.;Mostafavi, E.;Jalali, T.;Khakifirouz, S.;Nowotny, N.;Fooks, A. R.;Shah-Hossein, N.",2016,,,0
370,Genetic diversity of porcine reproductive and respiratory syndrome virus in Korea,"The high genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV) has been an obstacle to developing an effective vaccine for porcine reproductive and respiratory syndrome (PRRS). This study was performed to assess the degree of genetic diversity among PRRSVs from Korean pig farms where wasting and respiratory syndrome was observed from 2005 to 2009. Samples from 786 farms were tested for the presence of PRRSV using reverse transcription PCR protocol. A total of 117 farms were positive for type 1 PRRSV while 198 farms were positive for type 2. Nucleotide sequences encoding the open reading frame (ORF) 5 were analyzed and compared to those of various published PRRSV isolates obtained worldwide. Sequence identity of the ORF 5 in the isolates was 81.6̃100% for type 1 viruses and 81.4̃100% for type 2 viruses. Phylogenetic analysis of the ORF 5 sequences showed that types 1 and 2 PRRSVs from Korea were mainly classified into three and four clusters, respectively. The analyzed isolates were distributed throughout the clusters independent of the isolation year or geographical origin. In conclusion, our results indicated that the genetic diversity of PRRSVs from Korean pig farms is high and has been increasing over time. © 2013 The Korean Society of Veterinary Science.",animal;animal disease;animal husbandry;Arterivirus;article;chemistry;classification;DNA sequence;genetic variability;genetics;isolation and purification;Korea;lung;lymph node;open reading frame;open reading frame 5;phylogeny;porcine reproductive and respiratory syndrome;reverse transcription polymerase chain reaction;sequence analysis;South Korea;pig;virology;virus gene,"Choi, E. J.;Lee, C. H.;Song, J. Y.;Song, H. J.;Park, C. K.;Kim, B.;Shin, Y. K.",2013,,10.4142/jvs.2013.14.2.115,0
371,Sequence analysis of old and new strains of porcine circovirus associated with congenital tremors in pigs and their comparison with strains involved with postweaning multisystemic wasting syndrome,"The entire genomes of 7 isolates of porcine circovirus (PCV) from pigs with congenital tremors (CT), type A2, or postweaning multisystemic wasting syndrome (PMWS) were cloned and sequenced. One isolate (CT-PCV-P7) originated from the late 1960s from a neonatal pig with CT, type A2. Two recent PCV isolates (CT-PCV-P5, CT-PCV-P6) were from 2 affected neonatal pigs, from different farms, with unrelated outbreaks of CT; type A2. Four isolates (PMWS-PCV-Pl, PMWS-PCV-P2, PMWS-PCV-P3, PMWS-PCV-P4) originated from pigs with PMWS from 4 different farms. A comparative analysis of these PMWS and PCV isolates demonstrated 99% sequence identity with each other, and over 96% sequence identity with previously sequenced PCV2 isolates. The CT-PCV-P5 and CT-PCV-P6 isolates, however, shared 99% of the same identity with each other, and inter-estingly also with PMWS PCV isolates. There were no consistent genomic differences between PMWS and recent CT isolates. The CT-PCV-P7 showed 98% identity similarity to PK-15-derived PCV1 and demonstrated only 72% identity similarity to either CT-PCV-P5 or CT-PCV-P6. Phylogenetic analysis confirmed that the old isolate (CT-PCV-P7), and the new isolates (CT-PCV-P5, CT-PCV-P6, PMWS-PCV-PI, PMWS-PCV-P2, PMWS-PCV-P3, PMWS-PCV-P4) were correctly classified as PCVI and PCV2, respectively.",article;Circoviridae;comparative study;controlled study;epidemic;female;gene sequence;molecular cloning;newborn;nonhuman;nucleotide sequence;phylogeny;pig farming;postweaning multisystemic wasting syndrome;sequence analysis;sequence homology;pig;swine disease;tremor;virus classification;virus genome;virus isolation;virus strain,"Choi, J.;Stevenson, G. W.;Kiupel, M.;Harrach, B.;Anothayanontha, L.;Kanitz, C. L.;Mittal, S. K.",2002,,,0
372,Molecular epidemiologic investigation of lentogenic newcastle disease virus from domestic birds at live bird markets in Korea,"A Newcastle disease surveillance program was conducted at live bird markets in Korea to expand our epidemiologic understanding of the disease in Korea. During the surveillance program, 10 lentogenic Newcastle disease viruses (NDVs) were isolated and identified from apparently healthy chickens and ducks at live bird markets. The lentogenic viruses had sequence motifs of either 112GKQGRL117 (n = 8) or 112GRQGRL117 (n = 2) at the F0 cleavage site. Sequencing and phylogenetic analyses of NDV isolates based on the hypervariable region of the F protein revealed two different genotypes: genotypes I (n = 8) and II (n = 2). Genotype I viruses were most closely related to the NDV V4 strain (n = 7) or the NDV Ulster 2C strain (n = 1). In contrast, genotype II viruses clustered with the NDV vaccine strains (LaSota and VG/GA) that are commonly used as live vaccines in Korea. The epidemiologic importance of NDV at live bird markets in Korea is discussed. © 2012 American Association of Avian Pathologists.",virus RNA;animal;article;chicken;classification;duck;genetics;isolation and purification;molecular genetics;Newcastle disease;Newcastle disease virus;phylogeny;reverse transcription polymerase chain reaction;South Korea;virology,"Choi, K. S.;Lee, E. K.;Jeon, W. J.;Kwon, J. H.;Lee, J. H.;Sung, H. W.",2012,,10.1637/9699-030311-ResNote.1,0
373,Epidemiological observations of bovine viral diarrhea virus in Korean indigenous calves,"Bovine viral diarrhea virus (BVDV) is an important worldwide disease in the livestock industry. To date, little research has been done on BVDV circulating in the Republic of Korea (ROK). The cases outlined in our research originated from rectal swabs taken from calves up to 80 days of age. Twenty-two of 99 Korean indigenous calves with diarrhea were identified as BVDV positive and 3 different 50-untranslated region (UTR) sequences were determined. The results indicated that BVDV infections in the ROK were found mostly in winter and when calves were less than 20 days old. Phylogenetic analysis based on the 50-UTR revealed that our cases from Korean indigenous calves belonged to BVDV-2a. Therefore, the result of this study will be useful to understand epidemiology and allow producers in the ROK to better protect their livestock. © Springer Science+Business Media, LLC 2010.",3' untranslated region;5' untranslated region;article;Bovine viral diarrhea virus 1;bovine viral diarrhea;calf (bovine);controlled study;incidence;livestock;molecular epidemiology;molecular phylogeny;native species;nonhuman;nucleotide sequence;observational study;priority journal;South Korea;virus classification;virus identification;virus strain;winter,"Choi, K. S.;Song, M. C.",2011,,10.1007/s11262-010-0542-z,0
374,Avian influenza viruses in Korean live poultry markets and their pathogenic potential,"We surveyed live-poultry markets in Korea in 2003 and isolated 9 H9N2, 6 H3N2, and 1 H6N1 influenza viruses. Antigenic and phylogenetic analyses showed that all 9 H9N2 isolates were of A/Chicken/Korea/25232-96006/96-like lineage (which caused disease in chickens in Korea in 1996) but were different from H9N2 viruses of southeastern China. They had at least 4 genotypes and replicated in chickens but not in mice. The H3N2 and H6N1 viruses were new to Korea and were probably reassortants of avian influenza viruses from southeastern China and recent Korean H9N2 viruses. All 8 segments of the H3N2 viruses formed a single phylogenetic cluster with 99.1 to 100% homology. The H3N2 viruses replicated in chickens and mice without preadaptation, but the H6N1 virus did not. Our results show an increasingly diverse pool of avian influenza viruses in Korea that are potential pandemic influenza agents. © 2004 Elsevier Inc. All rights reserved.",animal cell;animal tissue;antigen expression;avian influenza;chicken;China;controlled study;gene cluster;Influenza virus;Korea;nonhuman;phylogeny;priority journal;review;sequence homology,"Choi, Y. K.;Heui Seo, S.;Kim, J. A.;Webby, R. J.;Webster, R. G.",2005,,10.1016/j.virol.2004.12.002,0
375,Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique,"Background: Ticks are primary vectors for many well-known disease-causing agents that affect human and animal populations globally such as tick-borne encephalitis, Crimean-Congo hemorrhagic fever and African swine fever. In this study, viral metagenomics was used to identify what viruses are present in Rhipicephalus spp. ticks collected in the Zambezi Valley of Mozambique. Methods: The RNA was amplified with sequence-independent single primer amplification (SISPA) and high-throughput sequencing was performed on the Ion Torrent platform. The generated sequences were subjected to quality check and classfied by BLAST. CodonCode aligner and SeqMan were used to assemble the sequences. Results: The majority of viral sequences showed closest sequence identity to the Orthomyxoviridae family, although viruses similar to the Parvoviridae and Coronaviridae were also identified. Nearly complete sequences of five orthomyxoviral segments (HA, NP, PB1, PB2, and PA) were obtained and these showed an amino acid identity of 32–52% to known quaranjaviruses. The sequences were most closely related to the Wellfleet Bay virus, detected and isolated from common eider during a mortality event in the USA. Conclusions: In summary, this study has identified a highly divergent virus with in the Orthomyxoviridae family associated with Rhipicephalus ticks from Mozambique. Further genetic and biological studies are needed in order to investigate potential pathogenesis of the identified orthomyxovirus.",acid protein;hemagglutinin;nucleoprotein;polymerase acidic protein;polymerase basic 1 protein;polymerase basic 2 protein;unclassified drug;viral protein;virus RNA;adult;article;Coronaviridae;genetic association;high throughput sequencing;metagenomics;Mozambique;nonhuman;Orthomyxoviridae;orthomyxovirus infection;Parvoviridae;Rhipicephalus;RNA sequence;United States;virus identification;virus isolation,"Cholleti, H.;Hayer, J.;Mulandane, F. C.;Falk, K.;Fafetine, J.;Berg, M.;Blomström, A. L.",2018,,10.1080/20008686.2018.1478585,0
376,Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics,,,"Chong, R.;Shi, M.;Grueber, C. E.;Holmes, E. C.;Hogg, C.",2018,,,0
377,Effect of seasonal vaccination on the selection of influenza A/H3N2 epidemic variants,"The effect of vaccination on the dynamics of influenza virus variants remains largely unknown in humans, unlike in poultry. In this study, we compared influenza hemagglutinin (HA) gene sequences isolated from vaccinated and unvaccinated populations with the yearly vaccine strains. In total, 181 influenza A/H3N2 virus samples isolated from 82 vaccinated and 99 unvaccinated patients (2011-15, four Japanese influenza seasons) were genetically analyzed using a next-generation sequencer. Amino acid (AA) differences from corresponding vaccine strains were found in 74 of 329 HA1 sites. There was a maximum of four AA differences within the epitopes in the former three seasons (2011-14) and fifteen in the latter season (2014-15). Deviation to a greater number of AA differences was found more significantly in the isolates from vaccinated patients as compared to unvaccinated patients (P=0.0005 in 2011-14; P=0.0096 in 2014-15). AA difference rates within epitopes were also significantly higher in the isolates from vaccinated patients than from unvaccinated patients (2.64% vs. 2.14% for 2011-14, P=0.033; 7.78% vs. 6.59% for 2014-15, P=0.058). The AA differences at seven sites (48I-278K, 128A-142G, 145S, 158K, and 193S) became dominant in the following seasons. In all of these sites, the dominance was retained during the mismatch of isolates with the vaccine strains and was lost after vaccine match. Our data suggest that in humans, immune pressure induced by vaccination works to select influenza variants genetically distant from vaccine strains.","Adolescent;Adult;Amino Acid Substitution;Child;Child, Preschool;*Epidemics;Epitopes/ge [Genetics];Female;*Genotype;Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];High-Throughput Nucleotide Sequencing;Humans;Immune Evasion;Infant;Influenza A Virus, H3N2 Subtype/cl [Classification];Influenza A Virus, H3N2 Subtype/ge [Genetics];*Influenza A Virus, H3N2 Subtype/ip [Isolation & Purification];*Influenza Vaccines/ad [Administration & Dosage];*Influenza Vaccines/im [Immunology];*Influenza, Human/ep [Epidemiology];*Influenza, Human/vi [Virology];Male;Middle Aged;Mutation, Missense;RNA, Viral/ge [Genetics];Selection, Genetic;Young Adult;0 (Epitopes);0 (Hemagglutinin Glycoproteins, Influenza Virus);0 (Influenza Vaccines);0 (RNA, Viral)","Chong, Y.;Ikematsu, H.",2017,01 05,,0
378,The influence of viral and bacterial community diversity on pathogenic E. coli prevalence in pre-harvest cattle,,,"Chopyk, J.",2015,,,0
379,"Pathogenicity, sequence and phylogenetic analysis of Malaysian Chicken anaemia virus obtained after low and high passages in MSB-1 cells","Specific-pathogen-free (SPF) chickens inoculated with low passage Chicken anaemia virus (CAV), SMSC-1 and 3-1 isolates produced lesions suggestive of CAV infection. Repeated passages of the isolates in cell culture until passage 60 (P60) and passage 123 produced viruses that showed a significantly reduced level of pathogenicity in SPF chickens compared to the low passage isolates. Sequence comparison indicated that nucleotide changes in only the coding region of the P60 passage isolates were thought to contribute to virus attenuation. Phylogenetic analysis indicated that SMSC-1 and 3-1 were highly divergent, but their P60 passage derivatives shared significant homology to a Japanese isolate A2.","capsid protein;VP1 protein, Chicken anemia virus;animal;article;chemistry;chicken;Circoviridae;classification;genetics;molecular genetics;nucleotide sequence;pathogenicity;phylogeny","Chowdhury, S. M. Z. H.;Omar, A. R.;Aini, I.;Hair-Bejo, M.;Jamaluddin, A. A.;Md-Zain, B. M.;Kono, Y.",2003,,10.1007/s00705-003-0189-3,0
380,Characterization of H9N2 avian influenza viruses from the Middle East demonstrates heterogeneity at amino acid position 226 in the hemagglutinin and potential for transmission to mammals,"Next-generation sequencing (NGS) technologies are a valuable tool to monitor changes in viral genomes and determine the genetic heterogeneity of viruses. In this study, NGS was applied to clinical poultry samples from Jordan to detect eleven H9N2 low pathogenic avian influenza viruses (LPAIV). All of the viruses tested belonged to Middle East A genetic group of G1 lineage. Deep sequencing demonstrated a high degree of heterogeneity of glutamine and leucine residues at position 226 in the hemagglutinin (HA) gene, which increases specificity to either avian or mammalian-type receptors. Moreover, additional amino acid changes in PB1, PA, M1, M2, and NS1 were identified among the viruses tested. Compared to single gene amplification, application of NGS for surveillance and characterization of H9N2 LPAIV provides a complete genetic profile of emerging isolates and better understanding of the potential of zoonotic transmissions to mammals.","*Amino Acids/ge [Genetics];Animals;Disease Transmission, Infectious;*Genetic Variation;*Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];High-Throughput Nucleotide Sequencing;*Host Specificity;Influenza A Virus, H9N2 Subtype/cl [Classification];*Influenza A Virus, H9N2 Subtype/ge [Genetics];Influenza A Virus, H9N2 Subtype/ip [Isolation & Purification];*Influenza A Virus, H9N2 Subtype/ph [Physiology];Influenza in Birds/tm [Transmission];*Influenza in Birds/vi [Virology];Jordan;Mammals;Poultry;0 (Amino Acids);0 (Hemagglutinin Glycoproteins, Influenza Virus)","Chrzastek, K.;Lee, D. H.;Gharaibeh, S.;Zsak, A.;Kapczynski, D. R.",2018,05,,0
381,"Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses","Current technologies with next generation sequencing have revolutionized metagenomics analysis of clinical samples. To achieve the non-selective amplification and recovery of low abundance genetic sequences, a simplified Sequence-Independent, Single-Primer Amplification (SISPA) technique in combination with MiSeq platform was applied to target negative- and positive-sense single-stranded RNA viral sequences. This method allowed successful sequence assembly of full or near full length avian influenza virus (AIV), infectious bronchitis virus (IBV), and Newcastle disease virus (NDV) viral genome. Moreover, SISPA analysis applied to unknown clinical cases of mixed viral infections produced genome assemblies comprising 98% NDV and 99% of IBV genomes. Complete or near complete virus genome sequence was obtained with titers at or above 10<sup>4.5</sup> EID<sub>50</sub>/ml (50% embryo infectious dose), and virus identification could be detected with titers at or above 10<sup>3</sup> EID<sub>50</sub>/ml. Taken together, these studies demonstrate a simple template enrichment protocol for rapid detection and accurate characterization of avian RNA viruses.","Animals;*DNA Primers/ge [Genetics];Infectious bronchitis virus/ge [Genetics];*Infectious bronchitis virus/ip [Isolation & Purification];Influenza A virus/ge [Genetics];*Influenza A virus/ip [Isolation & Purification];*Metagenomics/mt [Methods];Newcastle disease virus/ge [Genetics];*Newcastle disease virus/ip [Isolation & Purification];*Nucleic Acid Amplification Techniques/mt [Methods];Poultry;Poultry Diseases/vi [Virology];*RNA Virus Infections/ve [Veterinary];RNA Virus Infections/vi [Virology];Sequence Analysis, DNA/mt [Methods];0 (DNA Primers)","Chrzastek, K.;Lee, D. H.;Smith, D.;Sharma, P.;Suarez, D. L.;Pantin-Jackwood, M.;Kapczynski, D. R.",2017,09,,0
382,Characterization of a novel gyrovirus in human stool and chicken meat,"Background: Sequence-independent amplification of clinical specimens can lead to the identification of novel pathogens. Objectives: To identify novel viruses in human stool specimens from patients with diarrhea and to investigate the ecology and clinical significance of such viruses. Study design: Nucleic acid extracted from stool specimens from patients with diarrhea with no known etiology were subjected to random PCR amplification and Roche/454 pyrosequencing. Novel viruses identified were genetically and epidemiologically characterized. Results: Four gyroviruses, chicken anemia virus (CAV), human gyrovirus (HGV)/avian gyrovirus 2 (AGV2), gyrovirus 3 (GyV3) and a novel gyrovirus (tentatively designated as gyrovirus 4 (GyV4)) were identified in human stool specimens. GyV4, as well as CAV and AGV2/HGV were also detected in chicken skin and meat used for human consumption. Conclusions: A novel gyrovirus (GyV4) was identified in human stool and in chicken meat sold for human consumption. This virus was phylogenetically distinct from previously reported gyroviruses in chicken and humans (chicken anemia virus, human gyrovirus, avian gyrovirus 2 and recently reported gyrovirus 3). The epidemiology and pathogenesis of this virus in humans and in chicken needs to be further investigated. © 2012 Elsevier B.V.",virus DNA;adolescent;adult;aged;article;chicken meat;child;diarrhea;feces analysis;Gyrovirus;high throughput screening;human;infant;newborn;phylogeny;polymerase chain reaction;preschool child;priority journal;pyrosequencing;school child;virus gene;virus identification,"Chu, D. K. W.;Poon, L. L. M.;Chiu, S. S. S.;Chan, K. H.;Ng, E. M.;Bauer, I.;Cheung, T. K.;Ng, I. H. Y.;Guan, Y.;Wang, D.;Peiris, J. S. M.",2012,,10.1016/j.jcv.2012.07.001,0
383,"Molecular detection of a mixed infection of goatpox virus, orf virus, and mycoplasma capricolum subsp. capripneumoniae in goats","The current study investigated an outbreak of mixed infection with Goatpox virus (GTPV), Orf virus (ORFV), and Mycoplasma capricolum subsp. capripneumoniae (MCCP) that occurred on a Chinese goat farm, with a case fatality rate of 60.2%. The observed clinical signs were ecthyma and accelerated respiration with frequent coughing. Specific fragments of the p32 gene of GTPV, B2L gene of ORFV, and 16S ribosomal RNA gene of MCCP were synchronously amplified by polymerase chain reaction (PCR) from the tissues of 12 dead goats. The PCR products were cloned, sequenced, and aligned with related reference sequences in GenBank for further identification of the pathogens. The present study reports a mixed infection with GTPV, ORFV, and MCCP in goats. © 2011 The Author(s).",animal;animal disease;article;Capripoxvirus;China;classification;contagious ecthyma;contagious pleuropneumonia;epidemic;genetics;goat;goat disease;isolation and purification;methodology;microbiology;Mycoplasma capricolum;phylogeny;polymerase chain reaction;Poxviridae;poxvirus infection;virology,"Chu, Y.;Yan, X.;Gao, P.;Zhao, P.;He, Y.;Liu, J.;Lu, Z.",2011,,10.1177/1040638711407883,0
384,Pathotyping and Phylogenetic Characterization of Newcastle Disease Viruses Isolated in Peru: Defining Two Novel Subgenotypes Within Genotype XII,"Infections of poultry with virulent strains of avian paramyxovirus 1 (APMV-1), also known as Newcastle disease viruses (NDVs), cause Newcastle disease (ND). This highly contagious disease affects poultry and many other species of birds worldwide. In countries where the disease is prevalent, constant monitoring and characterization of isolates causing outbreaks are necessary. In this study, we report the results of pathogenicity testing and phylogenetic analyses of seven NDVs isolated from several regions of Peru between 2004 and 2015. Six viruses had intracerebral pathogenicity indices (ICPIs) of between 1.75 and 1.88, corresponding to a velogenic pathotype. The remaining virus had an ICPI of 0.00, corresponding to a lentogenic pathotype. These results were consistent with amino acid sequences at the fusion protein (F) cleavage site. All velogenic isolates had the polybasic amino acid sequence 112RRQKR↓F117 at the F cleavage site. Phylogenetic analyses of complete F gene sequences showed that all isolates are classified in class II of APMV-1. The velogenic viruses are classified in genotype XII, while the lentogenic virus is classified in genotype II, closely related to the LaSota vaccine strain. Moreover, tree topology, bootstrap values, and genetic distances observed within genotype XII resulted in the identification of novel subgenotypes XIIa (in South America) and XIIb (in China) and possibly two clades within genotype XIIa. All velogenic Peruvian viruses belonged to subgenotype XIIa. Overall, our results confirm the presence of genotype XII in Peru and suggest that it is the prevalent genotype currently circulating in our country. The phylogenetic characterization of these isolates helps to characterize the evolution of NDV and may help with the development of vaccines specific to our regional necessities.",animal;chicken;classification;epidemic;genetics;genotype;isolation and purification;Newcastle disease;Newcastle disease virus;pathology;Peru;phylogeny;bird disease;virology,"Chumbe, A.;Izquierdo-Lara, R.;Tataje, L.;Gonzalez, R.;Cribillero, G.;González, A. E.;Fernández-Díaz, M.;Icochea, E.",2017,,10.1637/11456-062016-Reg,0
385,Introduction to ecology of arboviruses (Russian),"Arboviruses comprise the largest group of viruses of vertebrates. By 1972 approximately 400 arboviruses had been registered in the world, of which about 260 viruses were placed into 41 groups on the basis of their antigenic properties; 130 viruses are ungrouped as yet. In the Universal Classification System of viruses, arboviruses are included into 6 genea: Alfavirus, Flavivirus, Rhabdovirus, Reovirus, Arenavirus and Enterovirus. Members of these genera differ markedly in biology, morphology and biochemical and antigenic properties, indicating the heterogeneic character of the group of arboviruses. The heterogeneity of this group suggest that transmission of the viruses by arthropods as the mode of their spread originated independently in different systematically remote genera of viruses. All the known arboviruses are pathogenic only for vertebrates. They also multiply in arthropod tissue (in vivo and in vitro) but exert no pathogenic effect on them. It is noteworthy that specific viruses of arthropods do not multiply in tissues of vertebrates. Cycles of arbovirus circulation are determined essentially by trophic relations of hematophagous arthropods with vertebrates. These relations are most numerous with the group of mammals which are parasitized by approx. 2500 species of mosquitoes, midges, sand flies and Ixodid, Argasid and Gamasid ticks. Trophic relations of arbovirus vectors with birds are considerably inferior to those with mammals. Apparently no more than 500 species of hematophages of this category are associated with birds. Most numerous relations with this group of vertebrates are found in mosquitoes and Argasid ticks. Close trophic relations reptilia reptilla are shown by mosquitoes of the genus Deinocerites, some sand flies of the genus Sergentomyia and all Ixodid ticks of the genus Aponoma. The total number of species of arbovirus vectors parasitizing on reptilia does not exceed 50. Ecologically, 212 arboviruses can be called mammalian viruses, 39 avian viruses and 3 reptilian arboviruses. There is a close positive correlation (coefficient 0.90) between the number of vectors trophically related with one or another group of ground vertebrates and the number of arboviruses specific for this group. The majority of arboviruses occur in one continent but spread over two-three continents if they have mainland connections (Northern and Southern Americas, Africa and Eurasia). Arboviruses occurring in the Western and Eastern hemispheres are ecologically associated with man (Dengue 2 and 3, yellow fever), domestic animals (blue tongue of sheep, Wad Medani) or with migratory birds and their narrowly specific parasites (Tyuleniy virus). (453 references.)",Arbovirus;ecology;epidemiology;microorganism;review;virus,"Chunikhin, S. P.",1973,,,0
386,Genetic characterization of the rabies virus field isolates detected in russian federation within the period 2008-2011,"Sixty-three gene N fragments of rabies virus field isolates detected within the period 2008-2011 in different regions of Russian Federation were sequenced. The comparison with previously tested isolates and strains has shown that newly isolated isolates can be placed Into five previously described phylogenetic groups: Arctic group, Cen-ral Russian group, Eurasian group, Northern European group, and Caucasian group. The Arctic group isolates detected in Komi republic were identical to previously described rabies virus strain from Yakutia. This is the first reliable case of detecting Arctic group rabies virus in European part of Russia.",animal;Arctic;article;cat;bovine;genetics;human;isolation and purification;phylogeny;rabies;Rabies virus;Russian Federation;sequence analysis,"Chupin, S. A.;Chernyshova, E. V.;Metlin, A. E.",2013,,,0
387,"Genetic characterization of H1N1, H1N2 and H3N2 swine influenza virus in Thailand","Swine have been known to be a suitable host for influenza A virus. In Thailand, phylogenetic analysis on swine influenza virus (SIV) has as yet not been attempted. The present report presents molecular and phylogenetic analysis performed on SIV in Thailand. In this study, 12 SIV isolates from the central and eastern part of Thailand were subtyped and the molecular genetics of hemagglutinin and neuraminidase were elucidated. Three subtypes, H1N1, H1N2 and H3N2, are described. Phylogenetic analysis of the SIV hemagglutinin and neuraminidase genes shows individual clusters with swine, human or avian influenza virus at various global locations. Furthermore, amino acid substitutions were detected either at the receptor binding site or the antigenic sites of the hemagglutinin gene. © 2008 Springer-Verlag.",sialidase;virus hemagglutinin;viral protein;amino acid sequence;amino acid substitution;animal;article;classification;genetics;Influenza A virus;Influenza A virus (H1N1);Influenza A virus (H3N2);molecular genetics;orthomyxovirus infection;phylogeny;sequence alignment;pig;Thailand;virology;virus gene,"Chutinimitkul, S.;Thippamom, N.;Damrongwatanapokin, S.;Payungporn, S.;Thanawongnuwech, R.;Amonsin, A.;Boonsuk, P.;Sreta, D.;Bunpong, N.;Tantilertcharoen, R.;Chamnanpood, P.;Parchariyanon, S.;Theamboonlers, A.;Poovorawan, Y.",2008,,10.1007/s00705-008-0097-7,0
388,Ungulate copiparvovirus 1 (bovine parvovirus 2): characterization of a new genotype and associated viremia in different bovine age groups,"A novel bovine parvovirus 2 (BPV2) genotype comprising 5394 nt was identified by next generation sequencing from sera of healthy cattle at different age groups farmed in the state of Rio Grande do Sul, Brazil. The genome organization of new BPV2 genotype retains the two ORFs typical of members of the Parvovirinae with 86.4 % of overall nucleotide sequence identities in comparison to other members of the subfamily. Phylogenetic analysis revealed similar clustering with two previously described bovine BPV2 within the genus Copiparvovirus. No significant differences (P ≥ 0.05) were detected in the distribution of BPV2 infection in cattle at different age groups. This is the third complete or near complete genome sequence of BPV2 reported to date and may contribute to a better understanding of the biology of copiparvoviruses and its interactions with the host.",capsid protein;phospholipase A2;article;Bocaparvovirus;bovine parvovirus 2;bovine parvovirus 2 infection;Brazil;controlled study;DNA base composition;gene sequence;groups by age;high throughput sequencing;next generation sequencing;nonhuman;nucleotide sequence;open reading frame;parvovirus infection;polymerase chain reaction;priority journal;quantitative analysis;viremia;virus genome,"Cibulski, S. P.;Teixeira, T. F.;dos Santos, H. F.;de Sales Lima, F. E.;Scheffer, C. M.;Varela, A. P. M.;de Lima, D. A.;Schmidt, C.;Silveira, F.;de Almeida, L. L.;Roehe, P. M.",2016,,10.1007/s11262-015-1266-x,1
389,Phylogenesis and Clinical Aspects of Pandemic 2009 Influenza A (H1N1) Virus Infection,"During the spring of 2009, a new influenza A (H1N1) virus of swine origin emerged and spread worldwide causing a pandemic influenza. Here, 329 naso-pharyngeal swabs collected from patients with flu-like symptoms were analyzed by real-time PCR for the presence of H1N1 2009 pandemic virus. Twenty-five samples collected from immunocompetent and immunodepressed patients contained the H1N1 pandemic virus. Phylogenetic analysis of the hemagglutinin and neuraminidase genes showed no obvious differences in terms of similarity and/or homology between the sequences identified in immunocompetent individuals and those obtained from immunocompromised patients. Pre-existing clinical conditions may influence the outcome of H1N1 disease.",,"Ciccozzi, M.;Babakir-Mina, M.;Lo Presti, A.;Marcuccilli, F.;Perno, C. F.;Ciotti, M.",2011,,,0
390,Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community,"BACKGROUND: In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. RESULTS: By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre. CONCLUSIONS: As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis.","Animals;*Bacteriophages/me [Metabolism];Cattle;*Cell Surface Display Techniques;Cellulosomes/me [Metabolism];Databases, Protein;High-Throughput Nucleotide Sequencing;*Metagenome/ge [Genetics];*Metagenomics/mt [Methods];Open Reading Frames;*Rumen/mi [Microbiology];Sequence Analysis, DNA","Ciric, M.;Moon, C. D.;Leahy, S. C.;Creevey, C. J.;Altermann, E.;Attwood, G. T.;Rakonjac, J.;Gagic, D.",2014,May 12,,0
391,Genetic typing of bovine viral diarrhoea virus: Evidence of an increasing number of variants in Italy,"Bovine Viral Diarrhoea Virus (BVDV) is responsible worldwide for severe economic losses on cattle farms. BVDV is an RNA virus with a high genome variability having practical consequences on epidemiology, diagnosis and disease control. Genetic monitoring was suggested as the first step in BVDV control. Thirty-seven Bovine Viral Diarrhoea Viruses were identified in persistently infected cattle, mucosal disease-affected animals and in bulk milk, and were characterised genetically. The 5′UTR region was amplified and sequenced, and a phylogenetic analysis was carried out comparing all the Italian sequences of BVDV available from the Genbank database. An unusual number of persistent infected animals was evidenced on more than one farm. Phylogenetic analysis attributed all our viruses to BVDV type I and distinguished four different subgroups inside this genotype. Analysis of old and new viruses revealed the circulation of viruses classified in subgroups BVDV Ia and Ij never reported in Italy.",5' untranslated region;animal;article;Bovine viral diarrhea virus 1;bovine;cattle disease;classification;diarrhea;DNA sequence;epidemiology;feces;genetics;genotype;isolation and purification;Italy;milk;phylogeny;reverse transcription polymerase chain reaction;sequence homology;virology,"Ciulli, S.;Galletti, E.;Battilani, M.;Scagliarini, A.;Gentile, A.;Morganti, L.;Prosperi, S.",2008,,,0
392,Evidence for Tunisian-Like Pestiviruses Presence in Small Ruminants in Italy Since 2007,"The genus Pestivirus, which belongs to the Flaviviridae family, includes ssRNA+ viruses responsible for infectious diseases in pigs, cattle, sheep, goats and other domestic and wild ruminants. Like most of the RNA viruses, pestivirus has high genome variability with practical consequences on disease epidemiology, diagnosis and control. In addition to the officially recognized species in the genus Pestivirus, such as BVDV-1, BVDV-2, BDV and CSFV, other pestiviruses have been detected. Furthermore, most of the ruminant pestiviruses show low or absent species specificity observed in serological tests and are able to infect multiple species. Particularly, small ruminants are receptive hosts of the most heterogeneous group of pestiviruses. The aim of this study was to carry out the molecular characterization of pestiviruses isolated from sheep and goats in Sicily, Italy. Phylogenetic analysis of two viral genomic regions (a fragment of 5'-UTR and the whole Npro regions) revealed the presence of different pestivirus genotypes in the analysed goat and sheep herds. Two of five viral isolates were clustered with BVDV-1d viruses, a strain widespread in Italy, but never reported in Sicily. The other three isolates formed a distinct cluster with high similarity to Tunisian isolates, recently proposed as a new pestivirus species. This represents the first evidence for Tunisian-like pestivirus presence in small ruminants in Italy. Furthermore, one of the isolates was collected from a goat, representing the first isolation of Tunisian-like pestivirus from this species.",virus RNA;animal;Bovine viral diarrhea virus 1;classification;genetics;genotype;goat;goat disease;isolation and purification;Pestivirus;Pestivirus infection;phylogeny;sequence analysis;sheep;sheep disease;Sicily;veterinary medicine;virology;virus genome,"Ciulli, S.;Purpari, G.;Agnello, S.;Di Marco, P.;Di Bella, S.;Volpe, E.;Mira, F.;de Aguiar Saldanha Pinheiro, A. C.;Vullo, S.;Guercio, A.",2017,,10.1111/tbed.12498,0
393,Correlates of protection against human rotavirus disease and the factors influencing protection in low-income settings,"Rotaviruses (RV) are the leading cause of gastroenteritis in infants and children worldwide and are associated with high mortality predominately in low-income settings. The virus is classified into G and P serotypes and further into P genotypes based on differences in the surface-exposed proteins VP7 and VP4, respectively. Infection results in a variable level of protection from subsequent reinfection and disease. This protection is predominantly homotypic in some settings, whereas broader heterotypic protection is reported in other cohorts. Two antigenically distinct oral RV vaccines are licensed and are being rolled out widely, including in resource-poor setting, with funding provided by the GAVI alliance. First is a monovalent vaccine derived from a live-attenuated human RV strain, whereas the second is a pentavalent bovine-human reassortment vaccine. Both vaccines are highly efficacious in high-income settings, but greatly reduced levels of protection are reported in low-income countries. Here, the current challenges facing mucosal immunologists and vaccinologists aiming to define immunological correlates and to understand the variable levels of protection conferred by these vaccines in humans is considered. Such understanding is critical to maximize the public health impact of the current vaccines and also to the development of the next generation of RV vaccines, which are needed.",immunoglobulin A antibody;immunoglobulin G antibody;maternal antibody;neutralizing antibody;protein VP1;protein VP3;protein VP4;protein VP6;protein VP7;Rotavirus vaccine;adoptive transfer;antibody blood level;antibody production;antibody response;antibody titer;asymptomatic infection;breast feeding;cross protection;cytokine release;developing country;diarrhea;drug efficacy;hospitalization;human;intestine flora;intestine mucosa;lowest income group;mixed infection;mucosal immunity;nonhuman;priority journal;reinfection;review;Rotavirus infection;seroconversion;strain difference;viral gastroenteritis;viremia;virus attachment;virus strain;rotarix;rotateq,"Clarke, E.;Desselberger, U.",2015,,10.1038/mi.2014.114,0
394,Structural analysis of electrophoretic variation in the genome profiles of rotavirus field isolates,"Detailed structural studies were undertaken on five isolates of bovine rotavirus which showed variability in the migration patterns of their genome segments on electrophoresis in polyacrylamide gels. The individual genome segments of each isolate were characterized by partial digestion of terminally radiolabeled RNA with a base-specific nuclease. This analysis showed that whereas mobility variations were always associated with detectable changes in nucleotide sequence, sequence changes at least as great as those found in segments showing electrophoretic mobility variations were also detected in segments showing no mobility variation. Evidence for the occurrence of genome segment reassortment between viruses in the field was obtained from analyzing the species 11 RNAs from these five isolates. The overall conclusion from these results is that great care is required in the interpretation of simple genome profile analysis of different isolates for epidemiological purposes and that classification of these viruses solely on the basis of genome electropherotype could be misleading.",virus RNA;methodology;polyacrylamide gel electrophoresis;Rotavirus;theoretical study,"Clarke, I. N.;McCrae, M. M. A.",1982,,,0
395,Identification and analysis of the first 2009 pandemic H1N1 influenza virus from US feral swine,,,"Clavijo, A.;Nikooienejad, A.;Esfahani, M. S.",2013,,,0
396,Inactivation of the hemagglutinins of type A influenza viruses by physical and chemical means: an aid to classification,"The effects of temperature and treatment with sodium dodecyl sulfate, Tween 20, dithiothreitol, trypsin, or guanidine on the hemagglutinating capacity of six strains of type A influenza virus (A(0)/PR8/34, A(1)/CAME/46, A(2)/J305/57, A(2)/Bethesda/63, A(2)/HK/Aichi/68, and A(2)/HK/80/68), one strain of swine virus (A/Swine/76/?), and one equine strain (A/Equi-2/63) were determined. The two Hong Kong strains could be readily distinguished from the earlier A(2) strains by the resistance of their hemagglutinins to trypsin treatment and their inability to recover hemagglutinating capacity after removal of dithiothreitol from treated virus preparations. In these respects, the equine strain most closely resembled the Hong Kong variants. The pattern of hemagglutination inactivation also set the swine, PR8, and CAME strains apart from each other as well as from the other five strains. The results suggest that separation of type A viruses into groups by the pattern of inactivation of their hemagglutinins may be a valuable adjunct to standard serology for a more definite classification of these viruses.","Animals;Antibodies, Viral/ip [Isolation & Purification];Antigens, Viral;Chickens/im [Immunology];Chromatography;Cross Reactions;Dithiothreitol/pd [Pharmacology];Drug Stability;Guanidines/pd [Pharmacology];Guinea Pigs/im [Immunology];Hemagglutination Inhibition Tests;Hemagglutination Tests;Hemagglutination, Viral/de [Drug Effects];*Hemagglutinins, Viral/ai [Antagonists & Inhibitors];Hot Temperature;Immune Sera;*Orthomyxoviridae/cl [Classification];Orthomyxoviridae/im [Immunology];Sodium Dodecyl Sulfate/pd [Pharmacology];Surface-Active Agents/pd [Pharmacology];Trypsin/pd [Pharmacology];0 (Antibodies, Viral);0 (Antigens, Viral);0 (Guanidines);0 (Hemagglutinins, Viral);0 (Immune Sera);0 (Surface-Active Agents);368GB5141J (Sodium Dodecyl Sulfate)","Cleeland, R.;Grunberg, E.;Prince, H. N.",1972,Mar,,0
397,"A complex mosaic of enteroviruses shapes community-acquired hand, foot and mouth disease transmission and evolution within a single hospital","Human enteroviruses (EV) pose a major risk to public health. This is especially so in the Asia-Pacific region where increasing numbers of hand, foot and mouth disease (HFMD) cases and large outbreaks of severe neurological disease associated with EV-A71 have occurred. Despite their importance, key aspects of the emergence, epidemiology and evolution of EVs remain unclear, and most studies of EV evolution have focused on a limited number of genes. Here, we describe the genomic-scale evolution of EV-A viruses sampled from pediatric patients with mild disease attending a single hospital in western Sydney, Australia, over an 18-month period. This analysis revealed the presence of eight viral serotypes-Coxsackievirus (CV) A2, A4, A5, A6, A8, A10, A16 and EV-A71-with up to four different serotypes circulating in any 1 month. Despite an absence of large-scale outbreaks, high levels of geographical and temporal mixing of serotypes were identified. Phylogenetic analysis revealed that multiple strains of the same serotype were present in the community, and that this diversity was shaped by multiple introductions into the Sydney population, with only a single lineage of CV-A6 exhibiting in situ transmission over the entire study period. Genomic-scale analyses also revealed the presence of novel and historical EV recombinants. Notably, our analysis revealed no association between viral phylogeny, including serotype, and patient age, sex, nor disease severity (for uncomplicated disease). This study emphasizes the contribution of EV-A viruses other than EV-A71 to mild EV disease including HFMD in Australia and highlights the need for greater surveillance of these viruses to improve strategies for outbreak preparedness and vaccine design.",adolescent;age;article;Australia;child;community;controlled study;Coxsackievirus A10;Coxsackievirus A16;Coxsackievirus A2;Coxsackievirus A4;Coxsackievirus A5;Coxsackievirus A6;Coxsackievirus A8;disease severity;disease surveillance;Enterovirus;Enterovirus A;Enterovirus A71;epidemic;female;gender;genome analysis;geography;hand foot and mouth disease;hospital infection;human;infant;major clinical study;male;microbial diversity;molecular evolution;mosaicism;nonhuman;nucleotide sequence;pediatric patient;phylogeny;preschool child;priority journal;school child;serotype;virus genome;virus identification;virus recombination;virus strain;virus transmission,"Cobbin, J. C. A.;Britton, P. N.;Burrell, R.;Thosar, D.;Selvakumar, K.;Eden, J. S.;Jones, C. A.;Holmes, E. C.",2018,,10.1093/ve/vey020,0
398,Enhanced arbovirus surveillance with deep sequencing: Identification of novel rhabdoviruses and bunyaviruses in Australian mosquitoes,"Viral metagenomics characterizes known and identifies unknown viruses based on sequence similarities to any previously sequenced viral genomes. A metagenomics approach was used to identify virus sequences in Australian mosquitoes causing cytopathic effects in inoculated mammalian cell cultures. Sequence comparisons revealed strains of Liao Ning virus (Reovirus, Seadornavirus), previously detected only in China, livestock-infecting Stretch Lagoon virus (Reovirus, Orbivirus), two novel dimarhabdoviruses, named Beaumont and North Creek viruses, and two novel orthobunyaviruses, named Murrumbidgee and Salt Ash viruses. The novel virus proteomes diverged by ≥50% relative to their closest previously genetically characterized viral relatives. Deep sequencing also generated genomes of Warrego and Wallal viruses, orbiviruses linked to kangaroo blindness, whose genomes had not been fully characterized. This study highlights viral metagenomics in concert with traditional arbovirus surveillance to characterize known and new arboviruses in field-collected mosquitoes. Follow-up epidemiological studies are required to determine whether the novel viruses infect humans. © 2013 Elsevier Inc.",proteome;Arbovirus;article;Beaumont virus;blindness;Bunyaviridae;cell culture;cytopathogenic effect;deep sequencing;dimarhabdovirus;gene sequence;genetic strain;inoculation;kangaroo;Liao Ning virus;mammal cell;metagenomics;mosquito;Murrumbridgee virus;nonhuman;North Creek virus;nucleotide sequence;Orbivirus;Orthobunyavirus;priority journal;Reoviridae;Rhabdoviridae;Salt Ash virus;Stretch Lagoon virus;unindexed sequence;virus genome;virus identification;virus strain;Wallal virus;Warrego virus,"Coffey, L. L.;Page, B. L.;Greninger, A. L.;Herring, B. L.;Russell, R. C.;Doggett, S. L.;Haniotis, J.;Wang, C.;Deng, X.;Delwart, E. L.",2014,,10.1016/j.virol.2013.09.026,0
399,Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology,"ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses, and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring many years of testing to understand complicated RNA and protein gene relationships. High-throughput sequencing now offers the opportunity to characterize miRNAs, siRNAs, small nucleolar RNAs (snoRNAs), and long ncRNAs on a genomic scale, making it faster and easier to clarify how these ncRNAs contribute to the disease state. However, this technology is still relatively new, and ncRNA discovery is not an application of high priority for streamlined bioinformatics. Here we summarize background concepts and practical approaches for ncRNA analysis using high-throughput sequencing, and how it relates to understanding human disease. As a case study, we focus on the parasitic protists Giardia lamblia and Trichomonas vaginalis, where large evolutionary distance has meant difficulties in comparing ncRNAs with those from model eukaryotes. A combination of biological, computational, and sequencing approaches has enabled easier classification of ncRNA classes such as snoRNAs, but has also aided the identification of novel classes. It is hoped that a higher level of understanding of ncRNA expression and interaction may aid in the development of less harsh treatment for protist-based diseases.",,"Collins, L. J.",2011,,,0
400,The recently identified flavivirus Bamaga virus is transmitted horizontally by Culex mosquitoes and interferes with West Nile virus replication in vitro and transmission in vivo,"Arthropod-borne flaviviruses such as yellow fever (YFV), Zika and dengue viruses continue to cause significant human disease globally. These viruses are transmitted by mosquitoes when a female imbibes an infected blood-meal from a viremic vertebrate host and expectorates the virus into a subsequent host. Bamaga virus (BgV) is a flavivirus recently discovered in Culex sitiens subgroup mosquitoes collected from Cape York Peninsula, Australia. This virus phylogenetically clusters with the YFV group, but is potentially restricted in most vertebrates. However, high levels of replication in an opossum cell line (OK) indicate a potential association with marsupials. To ascertain whether BgV could be horizontally transmitted by mosquitoes, the vector competence of two members of the Cx. sitiens subgroup, Cx. annulirostris and Cx. sitiens, for BgV was investigated. Eleven to thirteen days after imbibing an infectious blood-meal, infection rates were 11.3% and 18.8% for Cx. annulirostris and Cx. sitiens, respectively. Cx. annulirostris transmitted the virus at low levels (5.6% had BgV-positive saliva overall); Cx. sitiens did not transmit the virus. When mosquitoes were injected intrathoracially with BgV, the infection and transmission rates were 100% and 82%, respectively, for both species. These results provided evidence for the first time that BgV can be transmitted horizontally by Cx. annulirostris, the primary vector of pathogenic zoonotic flaviviruses in Australia. We also assessed whether BgV could interfere with replication in vitro, and infection and transmission in vivo of super-infecting pathogenic Culex-associated flaviviruses. BgV significantly reduced growth of Murray Valley encephalitis and West Nile (WNV) viruses in vitro. While prior infection with BgV by injection did not inhibit WNV super-infection of Cx. annulirostris, significantly fewer BgV-infected mosquitoes could transmit WNV than mock-injected mosquitoes. Overall, these data contribute to our understanding of flavivirus ecology, modes of transmission by Australian mosquitoes and mechanisms for super-infection interference.",article;controlled study;Culex;disease transmission;egg laying;egg production;enzyme linked immunosorbent assay;epithelium cell;evidence based medicine;evolutionary adaptation;Flavivirus infection;harvesting;immunocompetence;immunofluorescence;immunohistochemistry;in vitro study;in vivo study;incubation temperature;interference microscopy;limit of quantitation;metastasis;Murray Valley encephalitis virus;nerve cell;nonhuman;phylogeny;progeny;reverse transcription polymerase chain reaction;risk assessment;RNA extraction;Ross River virus;salivary gland;spectrophotometry;virus culture;virus detection;virus replication;West Nile fever,"Colmant, A. M. G.;Hall-Mendelin, S.;Ritchie, S. A.;Bielefeldt-Ohmann, H.;Harrison, J. J.;Newton, N. D.;O’Brien, C. A.;Cazier, C.;Johansen, C. A.;Hobson-Peters, J.;Hall, R. A.;van den Hurk, A. F.",2018,,10.1371/journal.pntd.0006886,0
401,Viromes as genetic reservoir for the microbial communities in aquatic environments: A focus on antimicrobial-resistance genes,"Despite studies of viromes isolated from aquatic environments are becoming increasingly frequent, most of them are limited to the characterization of viral taxonomy. Bacterial reads in viromes are abundant but the extent to which this genetic material is playing a role in the ecology of aquatic microbiology remains unclear. To this aim, we developed of a useful approach for the characterization of viral and microbial communities of aquatic environments with a particular focus on the identification of microbial genes harbored in the viromes. Virus-like particles were isolated from water samples collected across the Lambro River, from the spring to the high urbanized Milan area. The derived viromes were analyzed by shotgun metagenomic sequencing looking for the presence, relative abundance of bacterial genes with particular focus on those genes involved in antimicrobial resistance mechanisms. Antibiotic and heavy metal resistance genes have been identified in all virome samples together with a high abundance of reads assigned to cellular processes and signaling. Virome data compared to those identified in the microbiome isolated from the same sample revealed differences in terms of functional categories and their relative abundance. To verify the role of aquatic viral population in bacterial gene transfer, water-based mesocosms were perturbed or not perturbed with a low dose of tetracycline. The results obtained by qPCR assays revealed variation in abundance of tet genes in the virome and microbiome highlighting a relevant role of viral populations in microbial gene mobilization.",tetracycline;unclassified drug;virome;virus DNA;antibiotic resistance;aquatic environment;aquatic species;article;bacterial gene;bacterium contamination;bacterium culture;bioinformatics;DNA extraction;gene identification;Lactococcus garvieae;mesocosm;metagenomics;microbial community;nonhuman;repressor gene;taxonomy;virus genome;virus like agent;whole genome sequencing,"Colombo, S.;Arioli, S.;Neri, E.;Della Scala, G.;Gargari, G.;Mora, D.",2017,,10.3389/fmicb.2017.01095,0
402,Beyond the gut bacterial microbiota: The gut virome,,,"Columpsi, P.;Sacchi, P.;Zuccaro, V.",2016,,,0
403,Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs,"Diarrhea outbreaks in pig farms have raised major concerns in Europe and USA, as they can lead to dramatic pig losses. During a suspected outbreak in Belgium of porcine epidemic diarrhea virus (PEDV), we performed viral metagenomics to assess other potential viral pathogens. Although PEDV was detected, its low abundance indicated that other viruses were involved in the outbreak. Interestingly, a porcine bocavirus and several enteroviruses were most abundant in the sample. We also observed the presence of a porcine enterovirus genome with a gene insertion, resembling a C28 peptidase gene found in toroviruses, which was confirmed using re-sequencing, bioinformatics, and proteomics approaches. Moreover, the predicted cleavage sites for the insertion suggest that this gene was being expressed as a single protein, rather than a fused protein. Recombination in enteroviruses has been reported as a major mechanism to generate genetic diversity, but gene insertions across viral families are rather uncommon. Although such inter-family recombinations are rare, our finding suggests that these events may significantly contribute to viral evolution.",,"Conceicao-Neto, N.;Theuns, S.;Cui, T.;Zeller, M.;Yinda, C. K.;Christiaens, I.;Heylen, E.;Van Ranst, M.;Carpentier, S.;Nauwynck, H. J.;Matthijnssens, J.",2017,Jul,,1
404,Fecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses,,,"Conceição-Neto, N.;Zeller, M.;Heylen, E.",2015,,,0
405,Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis,,,"Conceição-Neto, N.;Zeller, M.;Lefrère, H.;Bruyn, P. De",2015,,,0
406,Hepatitis E virus is prevalent in the pig population of Lao People's Democratic Republic and evidence exists for homogeneity with Chinese Genotype 4 human isolates,"The objective of this study was to determine the prevalence and genotypic range of Hepatitis E virus (HEV) in the pig population of northern Lao People's Democratic Republic (PDR). We collected 181 faecal samples from indigenous-breed pigs ≤6 months of age and the faeces was stored in RNA stabilisation buffer due to cold-chain and transport limitations. Twenty-one (11.6%) pigs had detectable HEV RNA and 43.5% of village pig herds were infected. Based on a 240 base pair-nucleotide sequence flanking the junction of open reading frames 1, 2 and 3 (ORF1, ORF2 and ORF3) the isolates were phylogenetically classified within genotype 4. Phylogenetic analyses revealed distinct genetic groupings of the Lao HEV isolates and two groups clustered with human and pig HEV isolates from China. This was the first study to demonstrate genotype 4 HEV in Lao PDR and indicates pigs are a potential reservoir for human HEV infection. © 2011 Elsevier B.V.",article;base pairing;Chinese;controlled study;DNA sequence;feces analysis;genetic variability;genotype;hepatitis E;Hepatitis E virus;human;Laos;nonhuman;nucleotide sequence;open reading frame;phylogenetic tree;priority journal;RNA stability;sequence homology;pig;virus carrier;virus classification;virus detection;virus isolation,"Conlan, J. V.;Jarman, R. G.;Vongxay, K.;Chinnawirotpisan, P.;Melendrez, M. C.;Fenwick, S.;Thompson, R. C. A.;Blacksell, S. D.",2011,,10.1016/j.meegid.2011.04.022,0
407,Highly divergent hepaciviruses from African cattle,"The hepatitis C virus (HCV; genus Hepacivirus) is a highly relevant human pathogen. Unique hepaciviruses (HV) were discovered recently in animal hosts. The direct ancestor of HCV has not been found, but the genetically most closely related animal HVs exist in horses. To investigate whether other peridomestic animals also carry HVs, we analyzed sera from Ghanaian cattle for HVs by reverse transcription-PCR (RT-PCR). Nine of 106 specimens from different sampling sites contained HV RNA (8.5%) at median viral loads of 1.6×105 copies/ml. Infection seemed unrelated to cattle age and gender. Near-full-genome sequencing of five representative viruses confirmed taxonomic classifications. Cattle HVs formed two distinct phylogenetic lineages that differed by up to 17.7% on the nucleotide level in the polyprotein-encoding region, suggesting cocirculation of different virus subtypes. A conserved microRNA122-binding site in the 5' internal ribosomal entry site suggested liver tropism of cattle HVs. Phylogenetic analyses suggested the circulation of HVs in cattle for several centuries. Cattle HVs were genetically highly divergent from all other HVs, including HCV. HVs from genetically related equine and bovine hosts were not monophyletic, corroborating host shifts during the evolution of the genus Hepacivirus. Similar to equine HVs, the genetic diversity of cattle HVs was low compared to that of HCV genotypes. This suggests an influence of the human-modified ecology of peridomestic animals on virus diversity. Further studies should investigate the occurrence of cattle HVs in other geographic areas and breeds, virus pathogenicity in cattle, and the potential exposure of human risk groups, such as farmers, butchers, and abattoir workers.",microRNA 122;virus RNA;article;binding site;bovine;controlled study;domestic animal;gene sequence;genetic association;genetic conservation;genetic variability;Hepacivirus;infection risk;nonhuman;phylogenetic tree;priority journal;reverse transcription polymerase chain reaction;species comparison;species diversity;viral tropism;virus detection;virus load;virus virulence,"Corman, V. M.;Grundhoff, A.;Baechlein, C.;Fischer, N.;Gmyl, A.;Wollny, R.;Dei, D.;Ritz, D.;Binger, T.;Adankwah, E.;Marfo, K. S.;Annison, L.;Annan, A.;Adu-Sarkodie, Y.;Oppong, S.;Becher, P.;Drosten, C.;Drexler, J. F.",2015,,10.1128/jvi.00393-15,0
408,Next-generation sequencing as a tool for the study of Porcine reproductive and respiratory syndrome virus (PRRSV) macro- and micro- molecular epidemiology Review,,"Animals;*Genetic Variation;*Genome, Viral/ge [Genetics];High-Throughput Nucleotide Sequencing/ve [Veterinary];Molecular Epidemiology;Mutation;*Porcine Reproductive and Respiratory Syndrome/ep [Epidemiology];Porcine Reproductive and Respiratory Syndrome/tm [Transmission];Porcine Reproductive and Respiratory Syndrome/vi [Virology];*Porcine respiratory and reproductive syndrome virus/ge [Genetics];Porcine respiratory and reproductive syndrome virus/ip [Isolation & Purification];Sequence Analysis, DNA/ve [Veterinary];Swine","Cortey, M.;Diaz, I.;Martin-Valls, G. E.;Mateu, E.",2017,09,,0
409,Heterosubtypic neutralizing antibodies are produced by individuals immunized with a seasonal influenza vaccine,"The target of neutralizing antibodies that protect against influenza virus infection is the viral protein HA. Genetic and antigenic variation in HA has been used to classify influenza viruses into subtypes (H1-H16). The neutralizing antibody response to influenza virus is thought to be specific for a few antigenically related isolates within a given subtype. However, while heterosubtypic antibodies capable of neutralizing multiple influenza virus subtypes have been recently isolated from phage display libraries, it is not known whether such antibodies are produced in the course of an immune response to influenza virus infection or vaccine. Here we report that, following vaccination with seasonal influenza vaccine containing H1 and H3 influenza virus subtypes, some individuals produce antibodies that cross-react with H5 HA. By immortalizing IgG-expressing B cells from 4 individuals, we isolated 20 heterosubtypic mAbs that bound and neutralized viruses belonging to several HA subtypes (H1, H2, H5, H6, and H9), including the pandemic A/California/07/09 H1N1 isolate. The mAbs used different VH genes and carried a high frequency of somatic mutations. With the exception of a mAb that bound to the HA globular head, all heterosubtypic mAbs bound to acid-sensitive epitopes in the HA stem region. Four mAbs were evaluated in vivo and protected mice from challenge with influenza viruses representative of different subtypes. These findings reveal that seasonal influenza vaccination can induce polyclonal heterosubtypic neutralizing antibodies that cross-react with the swine-origin pandemic H1N1 influenza virus and with the highly pathogenic H5N1 virus.",epitope;FB110 monoclonal antibody;FE17 monoclonal antibody;FE43 monoclonal antibody;immunoglobulin G;influenza vaccine;monoclonal antibody;neutralizing antibody;unclassified drug;animal cell;animal experiment;animal tissue;antibody production;antibody response;antigen antibody reaction;article;B lymphocyte;cell immortalization;controlled study;female;human;human cell;influenza;influenza vaccination;Influenza A virus (H1N1);Influenza A virus (H3N2);Influenza A virus (H5N1);Influenza A virus (H9N2);mouse;nonhuman;priority journal;somatic mutation,"Corti, D.;Suguitan Jr, A. L.;Pinna, D.;Silacci, C.;Fernandez-Rodriguez, B. M.;Vanzetta, F.;Santos, C.;Luke, C. J.;Torres-Velez, F. J.;Temperton, N. J.;Weiss, R. A.;Sallusto, F.;Subbarao, K.;Lanzavecchia, A.",2010,,10.1172/jci41902,0
410,Evaluation of the virulence of some strains of peste-des-petits-ruminants virus (PPRV) in experimentally infected West African dwarf goats,"Different isolates of peste-des-petits-ruminants virus (PPRV) from outbreaks in Africa and India were investigated for virulence in West African dwarf goats in the Ivory Coast. Six groups of five animals received a virulent suspension of various strains of virus at a concentration of 103 TCID50/mL and the goats were observed for 15 days after infection. The Côte-d'Ivoire 89 (CI89), Guinea Conakry and Bissau Guinea PPRV strains caused a peracute disease; the India-Calcutta strain caused acute disease; the Sudan-Sennar strain produced an acute to mild disease, while the Nigeria 75/1 wild-type strain caused a mild disease and the animals recovered. The viruses studied contained examples of PPRV from specific lineage groups based on their nucleoprotein PPRV gene. This experiment indicated that virulence characteristics might be a useful marker to help classify PPRV isolates. © 2005 Elsevier Ltd. All rights reserved.",nucleoprotein;acute disease;Africa;article;controlled study;Cote d'Ivoire;disease course;disease severity;experimental infection;goat;India;nonhuman;Paramyxoviridae;Peste-des-petits-ruminants virus;virus classification;virus concentration;virus gene;virus isolation;virus strain;virus virulence;wild type,"Couacy-Hymann, E.;Bodjo, C.;Danho, T.;Libeau, G.;Diallo, A.",2007,,10.1016/j.tvjl.2005.08.020,0
411,Genetic and antigenic variability in bovine viral diarrhea virus (BVDV) isolates from Belgium,"This report describes the genetic and antigenic variability of bovine viral diarrhea virus strains isolated in Belgium. Part of the 5′ untranslated region and the 5′ end of the gp53 (E2) coding sequence were amplified by PCR and sequenced. Phylogenetic analysis showed that most field isolates segregated into genotypes Ib or II. Only one out of 28 field isolates belonged to genotype Ia. Interestingly, some type I strains were equally divergent from types Ia and Ib strains and clustered into additional subtypes within genotype I. Immune sera from young calves experimentally inoculated with field isolates first identified on the basis of their sequences were used in two-way neutralisation experiments. The results clearly differentiated type I from type II strains although some degree of cross-neutralisation was observed. Within type I, the new clusters could not be antigenically differentiated from the more prevalent type Ib strains or from type Ia strain NADL, suggesting that BVDV genotype I is antigenically homogeneous. The isolation of BVDV types I and II strains from cell lines and from a bovine vaccine suggest that molecular epidemiology surveillance is warranted for BVDV. © 2002 Elsevier Science B.V. All rights reserved.",antiserum;glycopeptide;glycopeptide gp53;neutralizing antibody;unclassified drug;vaccine;5' untranslated region;animal cell;animal model;antigenic variation;article;Belgium;Bovine viral diarrhea virus 1;bovine;cattle disease;cell line;controlled study;diarrhea;gene amplification;gene sequence;genetic epidemiology;genetic variability;genotype;inoculation;nonhuman;phylogeny;polymerase chain reaction;priority journal;RNA virus;strain difference;virus isolation;virus strain,"Couvreur, B.;Letellier, C.;Collard, A.;Quenon, P.;Dehan, P.;Hamers, C.;Pastoret, P. P.;Kerkhofs, P.",2002,,10.1016/s0168-1702(02)00014-x,0
412,Animal genomics in natural reservoirs of infectious diseases,"Natural virus reservoirs such as wild bats, birds, rodents and non-human primates are generally non-model organisms that have, until recently, presented limited opportunities for in-depth study. Next-generation sequencing provides a way to partially circumvent this limitation, since the methods required for data acquisition and analysis are largely species-independent. Comparative genomics and other 'omics' provide new opportunities to study the structure and function of various biological systems of wild species that are otherwise out of reach. Genomes of natural reservoir hosts can help to identify dominant pathways of virus-host interaction and to reveal differences between susceptible and resistant organisms, populations and species. This is of great scientific interest and may also provide a resource for the rational design of treatments for viral diseases in humans and livestock. In this way, we will 'learn from nature' and one day apply this knowledge to create disease-resistant livestock or develop novel therapeutic and prevention strategies. Reservoir host genomics will also open up possibilities for developing novel vaccines for wildlife, aid in the development of new diagnostic platforms, and have broad implications for developmental and evolutionary biology. In this review, the authors focus on natural reservoir hosts of viral pathogens, although most of the discussion points should be equally applicable to natural reservoirs of pathogenic bacteria, fungi or other parasites.",animal;communicable disease;disease carrier;genetics;genomics;high throughput sequencing;procedures;veterinary medicine,"Cowled, C.;Wang, L. F.",2016,,10.20506/rst.35.1.2425,0
413,Pseudorabies virus infection in Oklahoma hunting dogs,"Pseudorabies is caused by Suid herpesvirus 1, a member of the Alphaherpesvirinae subfamily. Although pigs are the natural host of Pseudorabies virus (PRV), the virus has a broad host range and may cause fatal encephalitis in many species. The United States obtained PRV-free status in 2004 after the virus was eradicated from domestic swineherds, but the virus is still present in feral swine populations. The current report describes PRV infection in 3 dogs that were used to hunt feral swine. The dogs developed clinical signs including facial pruritus with facial abrasions, dyspnea, vomiting, diarrhea, ataxia, muscle stiffness, and death. Two were euthanized, and 1 died within approximately 48 hr after onset of clinical signs. The salient histologic changes consisted of neutrophilic trigeminal ganglioneuritis with neuronophagia and equivocal intranuclear inclusion bodies. Pseudorabies virus was isolated from fresh tissues from 2 of the dogs, and immunohistochemistry detected the virus in the third dog. Virus sequencing and phylogeny, based upon available GenBank sequences, revealed that the virus was likely a field strain that was closely related to a cluster of PRV strains previously identified in Illinois. Though eradicated from domestic swine in the United States, PRV is present in populations of feral swine, and should therefore continue to be considered a possible cause of disease in dogs and other domestic animals with compatible clinical history and signs. Continued surveillance is necessary to prevent reintroduction of PRV into domestic swine. © 2011 American Association of Veterinary Laboratory Diagnosticians.",animal;article;case report;disease transmission;dog;dog disease;fatality;isolation and purification;pseudorabies;Pseudorabies virus;pig;swine disease;United States;virology,"Cramer, S. D.;Campbell, G. A.;Njaa, B. L.;Morgan, S. E.;Smith, Ii S. K.;McLin, Iv W. R.;Brodersen, B. W.;Wise, A. G.;Scherba, G.;Langohr, I. M.;Maes, R. K.",2011,,10.1177/1040638711416628,0
414,Chronic arthritis in goats caused by a retrovirus,A virus was isolated from an adult goat with chronic arthritis and shown to belong to the retrovirus group by electron microscopy and biochemical methods. Inoculation of the virus into cesarean-derived specific-pathogen-free goats' kids produced arthritic lesions similar to those in the spontaneous disease. Virus was reisolated from the experimentally induced lesions.,case report;chronic arthritis;experimental infection;goat;joint;Retroviridae;virology;virus classification;virus infection;virus isolation;virus morphology,"Crawford, T. B.;Adams, D. S.;Cheevers, W. P.;Cork, L. C.",1980,,,0
415,"Highly pathogenic avian influenza a(h5n1) viruses at the animal-human interface in Vietnam, 2003-2010","Mutation and reassortment of highly pathogenic avian influenza A(H5N1) viruses at the animal-human interface remain a major concern for emergence of viruses with pandemic potential. To understand the relationship of H5N1 viruses circulating in poultry and those isolated from humans, comprehensive phylogenetic and molecular analyses of viruses ollected from both hosts in Vietnam between 2003 and 2010 were performed. We examined the temporal and spatial istribution of human cases relative to H5N1 poultry outbreaks and characterized the genetic lineages and amino acid substitutions in each gene segment identified in humans relative to closely related viruses from avian hosts. Six emagglutinin clades and 8 genotypes were identified in humans, all of which were initially identified in poultry. Several amino acid mutations throughout the genomes of viruses isolated from humans were identified, indicating the potential for poultry viruses infecting humans to rapidly acquire molecular markers associated with mammalian adaptation and antiviral resistance",oseltamivir;peramivir;zanamivir;amino acid substitution;antiviral susceptibility;article;genetic linkage;genetic variability;genotype;human;influenza A (H5N1);Influenza A virus (H5N1);molecular genetics;nonhuman;phylogeny;poultry;priority journal;Viet Nam;virus isolation;virus mutation,"Creanga, A.;Hang, N. L. K.;Cuong, V. D.;Nguyen, H. T.;Phuong, H. V. M.;Thanh, L. T.;Thach, N. C.;Hien, P. T.;Tung, N.;Jang, Y.;Balish, A.;Dang, N. H.;Duong, M. T.;Huong, N. T.;Hoa, D. N.;Tho, N. D.;Klimov, A.;Kapella, B. K.;Gubareva, L.;Kile, J. C.;Hien, N. T.;Mai, L. Q.;Davis, C. T.",2017,,10.1093/infdis/jix003,0
416,Emergence of multiple clade 2.3.2.1 influenza A (H5N1) virus subgroups in Vietnam and detection of novel reassortants,"Phylogenetic analyses of 169 influenza A(H5N1) virus genomes were conducted for samples collected through active surveillance and outbreak responses in Vietnam between September 2010 and September 2012. While clade 1.1 viruses persisted in southern regions, three genetically distinct subgroups of clade 2.3.2.1 were found in northern and central Vietnam. The identification of each subgroup corresponded with detection of novel reassortants, likely due to their overlapping circulation throughout the country. While the previously identified clade 1.1 and A/Hubei/1/2010-like 2.3.2.1 genotypes remained the predominant viruses detected, four viruses were found to be reassortants between A/Hubei/1/2010-like (HA, NA, PB2, PB1, PA, NP) and A/duck/Vietnam/NCVD-885/2010-like (M, NS) viruses and one virus was identified as having A/duck/Vietnam/NCVD-885/2010-like HA, NA, PB1, and NP with A/Hubei/1/2010-like PB2 and PA genes. Additionally, clade 2.3.2.1 A/Hong Kong/6841/2010-like viruses, first detected in mid-2012, were identified as reassortants comprised of A/Hubei/1/2010-like PB2 and PA and A/duck/Vietnam/NCVD-885/2010-like PB1, NP, NA, M, NS genes. © 2013.",hemagglutinin;sialidase;viral protein;amino acid sequence;amino acid substitution;animal tissue;article;cladistics;genetic reassortment;genome analysis;genotype;geographical variation (species);hemagglutinin gene;Influenza A virus (H5N1);molecular evolution;molecular phylogeny;neuraminidase gene;nonhuman;poultry;priority journal;Viet Nam;virus detection;virus gene;virus genome;virus identification,"Creanga, A.;Thi Nguyen, D.;Gerloff, N.;Thi Do, H.;Balish, A.;Dang Nguyen, H.;Jang, Y.;Thi Dam, V.;Thor, S.;Jones, J.;Simpson, N.;Shu, B.;Emery, S.;Berman, L.;Nguyen, H. T.;Bryant, J. E.;Lindstrom, S.;Klimov, A.;Donis, R. O.;Davis, C. T.;Nguyen, T.",2013,,10.1016/j.virol.2013.06.005,0
417,Main molecular aspects of human coronaviruses and homologies with animal coronavirus strains,"Starting in 1965 after the discovery of several new human respiratory pathogens, a group of viruses, which had been known since 1937, although not by the name of coronavirus, began to emerge. Avian infectious bronchitis virus (IBV), mouse hepatitis virus (MHV), and some newly described human respiratory viruses, named OC43 and 229E were noted to have similar appearances. These viruses displayed a characteristic fringe of large, distinctive, petal-shaped peplomers or spikes which resembled a crown. They were called 'coronaviruses' after this feature. Shortly thereafter, several new viruses causing diseases in pigs, rats, turkeys, dogs, cats, and cattle were added to the coronavirus group. The range of animal species infected and the multiplicity of organ systems involved have made Coronaviridae one of the most important viral family in veterinary medicine. The two human coronaviruses (HCV) HCV-OC43 and HCV-229E belong to distinct antigenic groups. HCV-OC43 shares antigenic correlation with neonatal calf diarrhea coronavirus (NCDCV), hemagglutinating encephalomyelitis virus of swine (HEV) and MHV. HCV-229E is antigenically related to porcine transmissible gastroenteritis virus (TGEV) and canine coronavirus (CCV). Coronaviruses, as a group, contain a single-stranded, positive-sense RNA genome of 27 to 31 kb with an estimated molecular weight of 6 x 106 to 8 x 106 daltons. In infected cells, the viral RNA genome is first transcribed into a full-length negative-strand RNA, which, in turn, is transcribed into a positive-sense genomic RNA and six to eight subgenomic mRNAs by a mechanism of leader-primed transcription.",virus antigen;virus RNA;animal disease;Avian infectious bronchitis virus;Coronavirinae;Murine hepatitis virus;nonhuman;review;RNA translation;virology;virus classification;virus genome,"Cristallo, A.;Gambaro, F.;Battaglia, M.;Cereda, P. M.",1996,,,0
418,Two loci controlling genetic cellular resistance to avian leukosis-sarcoma viruses,"Female chickens known to be heterozygous for resistance to subgroups A and B of the avian leukosis-sarcoma viruses were mated to males known to be homozygously resistant to both. The progeny were assayed both on the chorioallantoic membrane (CAM) and in tissue culture for resistance to representative viruses of the A, B, and tentatively defined C subgroups. Segregation ratios of resistance to A and B subgroup viruses agreed with the previously suggested hypothesis of single-autosomal-recessive genes controlling resistance to each subgroup. Mixed infection on the CAM and replicate plate infection in tissue culture with subgroup A and B viruses showed that resistance to the A and B subgroups was inherited independently. Assays with viruses tentatively classified as subgroup C indicated that they were largely composed of a mixture of subgroup A and B viruses or of particles possessing the host range specificity of both. However, virus stocks of the subgroup C category, as well as some stocks classified as subgroup B, produced small numbers of pocks or foci on individuals known to be resistant to subgroup A and B viruses. It is suggested that these Rous sarcoma virus stocks carry between 1 and 10% of a true subgroup C virus.","*Alpharetrovirus/im [Immunology];Animals;Chick Embryo;*Chickens/im [Immunology];Culture Techniques;Female;*Genes, Recessive;*Genetics;Genotype;Male;Phenotype","Crittenden, L. B.;Stone, H. A.;Reamer, R. H.;Okazaki, W.",1967,Oct,,0
419,Phylogenetic analysis and pathogenicity of H3 subtype avian influenza viruses isolated from live poultry markets in China,"H3 subtype influenza A virus is one of the main subtypes that threats both public and animal health. However, the evolution and pathogenicity of H3 avian influenza virus (AIV) circulating in domestic birds in China remain largely unclear. In this study, seven H3 AIVs (four H3N2 and three H3N8) were isolated from poultry in live poultry market (LPM) in China. Phylogenetic analyses of full genomes showed that all viruses were clustered into Eurasian lineage, except N8 genes of two H3N8 isolates fell into North American lineage. Intriguingly, the N8 gene of one H3N8 and PB2, PB1, NP and NS of two H3N2 isolates have close relationship with those of the highly pathogenic H5N8 viruses circulating in Korea and United States, suggesting that the H3-like AIV may contribute internal genes to the highly pathogenic H5N8 viruses. Phylogenetic tree of HA gene and antigenic cross-reactivity results indicated that two antigenically different H3 viruses are circulating in LPM in China. Most of the H3 viruses replicated in mice lung and nasal turbinate without prior adaptation, and the representative H3 viruses infected chickens without causing clinical signs. The reassortment of H3 subtype influenza viruses warrants continuous surveillance in LPM in China.",Influenza virus hemagglutinin;virus antibody;virus RNA;animal;avian influenza;China;classification;cluster analysis;cross reaction;disease model;DNA sequence;genetic variation;genetics;immunology;Influenza A virus (H3N2);Influenza A virus (H3N8);isolation and purification;mouse;orthomyxovirus infection;pathogenicity;pathology;phylogeny;poultry;virology;whole genome sequencing,"Cui, H.;Shi, Y.;Ruan, T.;Li, X.;Teng, Q.;Chen, H.;Yang, J.;Liu, Q.;Li, Z.",2016,,10.1038/srep27360,0
420,"Phylogeny, Pathogenicity, and Transmission of H5N1 Avian Influenza Viruses in Chickens","We analyzed five H5N1 avian influenza viruses (AIVs) isolated from different birds in 2012 in China. Based on whole-genome sequences, we divided the viruses into four genotypes. The DKE26, GSE43, and DKE53 viruses belonged to Genotypes 1–3, respectively. The CKE93 and CKE96 viruses were classified into Genotype 4. Genotypes 1–3 correspond to the viruses containing the HA gene of clade 2.3.2, and Genotype 4 is the virus that bears the HA gene of clade 7.2. To better understand the pathogenicity and transmission of the viruses, we infected chickens with 103 EID50 /0.1 ml GSE43 (clade 2.3.2) or CKE93 (clade 7.2) virus. Our results revealed that 6 of 7 specific-pathogen-free (SPF) chickens inoculated with GSE43 virus were dead before 7-day post-infection, but all the SPF chickens inoculated with CKE93 virus survived the infection. Both the GSE43 and CKE93 viruses replicated systemically in chickens. The virus titers of GSE43 virus in tested organs were obviously higher than those of CKE93 virus. Our results revealed that the pathogenicity and replication of GSE43 in chickens was much higher than those of CKE93. The GSE43 virus could transmit between chickens, but the CKE93 could not transmit between chickens by naïve contact. Therefore, different clades of H5N1 AIVs possessed variable pathogenicities and transmission abilities among chickens. Our study contributes to knowledge of pathogenic variations of prevalent H5N1 viruses.",article;avian influenza (H5N1);chicken;genotype;Influenza A virus (H5N1);nonhuman;phylogeny;polymerase chain reaction;sequence analysis;virus transmission;virus virulence,"Cui, J.;Qu, N.;Guo, Y.;Cao, L.;Wu, S.;Mei, K.;Sun, H.;Lu, Y.;Qin, Z.;Jiao, P.;Liao, M.",2017,,10.3389/fcimb.2017.00328,0
421,Identification and genetic characterization of a novel circular single-stranded DNA virus in a human upper respiratory tract sample,"Metagenomic analysis through high-throughput sequencing is a tool for detecting both known and novel viruses. Using this technique, a novel circular single-stranded DNA (ssDNA) virus genome was discovered in respiratory secretions from a febrile traveler. The virus, named human respiratory-associated PSCV-5-like virus (HRAPLV), has a genome comprising 3,018 bases, with two major putative ORFs inversely encoding capsid (Cap) and replicase (Rep) protein and separated by two intergenic regions. One stem-loop structure was predicted in the larger intergenic region (LIR). The predicted amino acid sequences of the Cap and Rep proteins of HRAPLV showed highest identity to those of porcine stool-associated circular virus 5 isolate CP3 (PoSCV 5) (53.0% and 48.9%, respectively). The host tropism of the virus is unknown, and further study is warranted to determine whether this novel virus is associated with human disease.",circular DNA;single stranded DNA;virus DNA;Circovirus;genetics;human;isolation and purification;male;middle aged;pharynx;phylogeny;virology;virus genome,"Cui, L.;Wu, B.;Zhu, X.;Guo, X.;Ge, Y.;Zhao, K.;Qi, X.;Shi, Z.;Zhu, F.;Sun, L.;Zhou, M.",2017,,10.1007/s00705-017-3481-3,0
422,Analysis of the microRNA expression profiles in DEF cells infected with duck Tembusu virus,"Duck Tembusu virus (DTMUV), belonging to the Flaviviridae family, is a single-stranded positive-sense RNA virus. Since April 2010, the outbreak of DTMUV in southeast provinces of China has caused great economic losses. MicroRNAs (miRNAs) play important regulatory roles in viral infection through binding to the host target genes or the viral genomes. To better understanding the molecular mechanisms of virus-host interaction, here we identified the miRNA expression profiles in DTMUV-infected and uninfected DEF cells by high-throughput sequencing. A total of 287 known and 63 novel miRNAs were identified. 48 miRNAs, including 26 known miRNAs and 22 novel miRNAs, were differentially expressed in response to DTMUV infection. Among these miRNAs, 37 miRNAs were up-regulated and 11 miRNAs were down-regulated. 9 miRNAs were randomly selected for validation by qRT-PCR experiment. The results of qRT-PCR experiment were consistent with the sequencing data. GO enrichment showed that the predicted targets of these differentially expressed miRNAs were mainly involved in the regulation of immune system, cellular process and metabolic process. KEGG pathways analysis showed that predicted target genes were involved in several signaling pathways such as Wnt signaling pathway, TGF-beta signaling pathway, mTOR signaling pathway and FoxO signaling pathway. This is the first study to evaluate changes of miRNA expression in DEF cells upon DTMUV infection. Our findings provide important clues for better understanding the DTMUV-host interaction.",microRNA;microRNA 133a 5p;microRNA 146b 5p;microRNA 148a 3p;microRNA 1a 3p;microRNA 206;microRNA 21 5p;microRNA 221;microRNA 222a;microRNA 29b 3p;microRNA 6516 3p;unclassified drug;virus envelope protein;animal cell;article;binding site;bioinformatics;controlled study;down regulation;duck;Duck Tembusu virus;embryo;embryo cell;fibroblast;Flaviviridae;gene expression profiling;gene ontology;high throughput sequencing;nonhuman;priority journal;protein expression;real time polymerase chain reaction;signal transduction;upregulation;virus genome;virus replication,"Cui, M.;Jia, R.;Huang, J.;Wu, X.;Hu, Z.;Zhang, X.;Wang, M.;Zhu, D.;Chen, S.;Liu, M.;Zhao, X.;Wu, Y.;Yang, Q.;Zhang, S.;Liu, Y.;Zhang, L.;Yin, Z.;Jing, B.;Cheng, A.",2018,,10.1016/j.meegid.2018.05.020,0
423,Precision surveillance for viral respiratory pathogens: virome capture sequencing for the detection and genomic characterization of severe acute respiratory …,,,"Cummings, M. J.;Tokarz, R.;Bakamutumaho, B.",2018,,,0
424,Precision surveillance for viral respiratory pathogens: virome capture sequencing for the detection and genomic characterization of severe acute respiratory infection in Uganda,"Background: Precision public health is a novel set of methods to target disease prevention and mitigation interventions to high-risk subpopulations. We applied a precision public health strategy to syndromic surveillance for severe acute respiratory infection (SARI) in Uganda by combining spatiotemporal analytics with genomic sequencing to detect and characterize viral respiratory pathogens with epidemic potential. Methods: Using a national surveillance network we identified patients with unexplained, influenza-negative SARI from 2010-2015. Spatiotemporal analyses were performed retrospectively to identify clusters of unexplained SARI. Within clusters, respiratory viruses were detected and characterized in naso- and oro-pharyngeal swab samples using a novel oligonucleotide probe capture (VirCapSeq-VERT) and high-throughput sequencing platform. Linkage to conventional epidemiologic strategies further characterized transmission dynamics of identified pathogens. Results: Among 2,901 unexplained SARI cases, 9 clusters were detected, accounting for 301 (10.4%) cases. Clusters were more likely to occur in urban areas and during biannual rainy seasons. Within detected clusters, we identified an unrecognized outbreak of measles-associated SARI; sequence analysis implicated co-circulation of endemic genotype B3 and genotype D4 likely imported from England. We also detected a likely nosocomial SARI cluster associated with a novel picobirnavirus most closely related to swine and dromedary viruses. Conclusions: Using a precision approach to public health surveillance, we detected and characterized the genomics of vaccine-preventable and zoonotic respiratory viruses associated with clusters of severe respiratory infections in Uganda. Future studies are needed to assess the feasibility, scalability, and impact of applying similar approaches during real-time public health surveillance in low-income settings.",,"Cummings, M. J.;Tokarz, R.;Bakamutumaho, B.;Kayiwa, J.;Byaruhanga, T.;Owor, N.;Namagambo, B.;Wolf, A.;Mathema, B.;Lutwama, J. J.;Schluger, N. W.;Lipkin, W. I.;O'Donnell, M. R.",2018,Aug 07,,0
425,One health-one medicine: Unifying human and animal medicine within an evolutionary paradigm,"One health is a concept since early civilization, which promoted the view that there was no major distinction between animal and human medicine. Although persisting through the 19th century, this common vision was then all but forgotten in the early 20th century. It is now experiencing a renaissance, coincident with an awakening of the role that evolutionary biology plays in human and animal health, including sexually transmitted infections (STIs). A number of STIs in humans have comparable infections in animals; likewise, both humans and animals have STIs unique to each mammalian camp. These similarities and differences offer opportunities for basic medical and public health studies, including evolutionary insights that can be gleaned from ongoing interdisciplinary investigation-especially with the molecular analytical tools available-in what can become a golden age of mutually helpful discovery. © 2011 New York Academy of Sciences.",antibiotic agent;Marek disease vaccine;veterinary drug;Wart virus vaccine;antibiotic therapy;article;disease transmission;environmental aspects and related phenomena;evolution;history;human;Human immunodeficiency virus 1;Human immunodeficiency virus 2;human versus animal comparison;Marek disease;medicine;metagenomics;molecular genetics;Mycobacterium bovis;nonhuman;scabies;sexual behavior;sexually transmitted disease;tuberculosis;uterine cervix cancer;vaccination;veterinary medicine;virus identification,"Currier, R. W.;Steele, J. H.",2011,,10.1111/j.1749-6632.2011.06138.x,0
426,Preliminary characterization of D'Aguilar virus and three Palyam group viruses new to Australia,"Between 1974 and 1980, 424 viruses were isolated at the Long Pocket Laboratories of the Division of Animal Health, CSIRO, either from insects or from the blood of sentinel cattle, and of these, 165 cross-reacted with D'Aguilar virus (an Australian Palyam group virus) in a complement fixation test. Neutralization tests were used to classify these viruses into four serotypes with the isolates D'Aguilar B8112, CSIRO 11, CSIRO 58 and CSIRO 82 as the type strains. The latter three were new to Australia. Like other orbiviruses, these four serotypes were partially sensitive to treatment with either or chloroform. Neutralizing antibodies against D'Aguilar, CSIRO 11 and CSIRO 58 viruses were detected in sera from cattle, buffalo, deer and sheep but not in sera from humans, horses, pigs or marsupials. Antibodies against CSIRO 82 virus were detected in 85% of 26 buffalo, and 0.4% of 495 cattle sera tested. The antibody distribution in Australia for D'Aguilar, CSIRO 11 and CSIRO 58 viruses fell within the distribution limits of Culicoides brevitarsis, the insect from which these viruses were most commonly recovered. The antibody distribution for CSIRO 82 virus, which was isolated from a pool containing C. schultzei and C. peregrinus, fell within the much more restricted distribution limits of these species. None of these viruses has been associated with disease.",virus antibody;animal;article;Australia;bovine;cell line;complement fixation test;geography;hamster;isolation and purification;kidney;mouse;serodiagnosis;species difference;virus,"Cybinski, D. H.;St George, T. D.",1982,,,0
427,Third genome size category of avian paramyxovirus serotype 1 (Newcastle disease virus) and evolutionary implications,"The goal of the study was to establish if there was a relationship between molecular patterns and virus evolution. Therefore the complete genome sequence of two distinct apathogenic Newcastle disease virus (NDV) strains was determined and a third genome size category, containing 15,198 nucleotides, was recognized. Phylogenetic analysis revealed that two major separations resulting in three genome size categories occurred during the history of NDV. An ancient division in the primordial reservoir (wild waterbird species) led to two basal sister clades, class I and II, with genome sizes 15,198 (due to a 12 nucleotide insert in the phosphoprotein gene) and 15,186 nucleotides, respectively. Ancestors of only class II viruses colonized chicken populations and subsequently converted to virulent forms. These took place more than once and resulted in an early lineage [including genotypes I-IV and H33(W)] with genome size of 15,186 nucleotides. A second division occurred in the 20th century in the secondary (chicken) host. This gave rise to the branching-off of a clade (including recent genotypes V-VIII consisting of only pathogenic viruses) with the concomitant insertion of six nucleotides into the 5′ non-coding region of the nucleoprotein gene thereby increasing the genome size to 15,192 nucleotides. © 2006 Elsevier B.V. All rights reserved.",nucleotide;phosphoprotein;article;chicken;cladistics;genetic code;genome size;host;molecular evolution;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;primordium;priority journal;separation technique;species identification,"Czeglédi, A.;Ujvári, D.;Somogyi, E.;Wehmann, E.;Werner, O.;Lomniczi, B.",2006,,10.1016/j.virusres.2005.11.009,0
428,Characterization of a cowpox-like orthopox virus which had caused a lethal infection in man,"In August 1990 an orthopox virus (OPV) had been isolated from a severe case of a generalized infection with lethal outcome in an immunosuppressed 18-year-old man. In this communication we present a detailed characterization of the causative virus strain. Based on distinct epitope configurations detected by various monoclonal antibodies the isolate could be differentiated from other OPV species and was classified as a cowpox virus (CP). This classification was confirmed by a species-specific PCR assay and by establishing physical maps for the restriction enzymes HindIII and XhoI. Based on serological data of neutralization assays, blocking-ELISAs and Western blotting analysis evidence is provided that the infection had been acquired from a stray cat.",virus antibody;virus antigen;adolescent;animal;article;case report;cat;cat disease;cell line;Cercopithecus;classification;Cowpox virus;disease transmission;fatality;genetics;human;immunology;isolation and purification;male;Orthopoxvirus;polymerase chain reaction;poxvirus infection;Leporidae;restriction mapping;species difference;virology;zoonosis,"Czerny, C. P.;Zeller-Lue, C.;Eis-Hübinger, A. M.;Kaaden, O. R.;Meyer, H.",1997,,,0
429,Zoonotic vaccinia virus outbreaks in Brazil,"The vaccinia virus (VACV) was used as a live vaccine during the WHO-led smallpox eradication campaign in the second half of the 20th century. The program culminated with the obliteration of the disease, one of the most important achievements in modern medicine. Interestingly, one of the key factors in the successful vaccination campaign - the VACV itself - is poorly understood in relation to its natural reservoirs, evolutionary history and origins, being frequently considered extinct as a naturally occurring virus. Nevertheless, orthopoxviruses other than variola virus have been known to circulate in Brazil since the early 1960s. More specifically, VACV has been associated with naturally acquired infections in humans, cattle and possibly other reservoirs since 1999, when bovine vaccinia outbreaks started to be consistently described year after year. In this article, we list and discuss the most important VACV outbreaks that have occurred in Brazil in the last 20 years. Phylogenetic issues are considered, as the latest studies point to large genetic variance among isolates. Clinical and epidemiological data, both published and new, are presented. © 2011 Future Medicine Ltd.",monkeypox vaccine;smallpox vaccine;vaccinia vaccine;Brazil;cattle disease;cattle farming;communicable disease;cowpox;disease surveillance;DNA polymorphism;epidemic;eradication therapy;genetic variability;human;livestock;monkeypox;nonhuman;phylogeny;priority journal;review;skin defect;smallpox;Smallpox virus;vaccination;vaccinia;Vaccinia virus;virus isolation,"Da Fonseca, F. G.;Kroon, E. G.;Nogueira, M. L.;De Souza Trindade, G.",2011,,10.2217/fvl.11.46,0
430,Novel bovine papillomavirus type discovered by rolling-circle amplification coupled with next-generation sequencing,"Currently, fifteen bovine papillomavirus (BPV) types have been identified and classified into four genera: Deltapapillomavirus, Epsilonpapillomavirus, Dyoxipapillomavirus, and Xipapillomavirus. Here, the complete genome sequence of a new BPV type (BPV 04AC14) recovered from a papillomatous lesion is reported. The genome is 7,282 bp in length and exhibits the classic genetic organization and motifs of the members of Papillomaviridae. Maximum likelihood phylogenetic analyses revealed that BPV 04AC14 clusters with members of the Xipapillomavirus genus. The nucleotide sequence of the L1 capsid protein of the novel BPV is closely related to its counterpart, BPV3, with which it shares 79% similarity. These findings suggest that this virus is a new BPV type of the Xipapillomavirus genus.",capsid protein L1;animal tissue;article;Deltapapillomavirus;Dyoxipapillomavirus;Epsilonpapillomavirus;gene amplification;gene cluster;gene structure;genetic analysis;high throughput sequencing;histopathology;next generation sequencing;nonhuman;nucleotide sequence;Papillomaviridae;phylogeny;sequence analysis;strain difference;virus characterization;virus genome;virus identification;virus strain;Xipapillomavirus,"Da Silva, F. R. C.;Cibulski, S. P.;Daudt, C.;Weber, M. N.;Guimarães, L. L. B.;Streck, A. F.;Mayer, F. Q.;Roehe, P. M.;Canal, C. W.",2016,,10.1371/journal.pone.0162345,0
431,"Zika virus: What do we know about the viral structure, mechanisms of transmission, and neurological outcomes?","The Zika virus epidemic that started in Brazil in 2014 has spread to >30 countries and territories in Latin America, leading to a rapid rise in the incidence of microcephalic newborns and adults with neurological complications. At the beginning of the outbreak, little was known about Zika virus morphology, genome structure, modes of transmission, and its potential to cause neurological malformations and disorders. With the advancement of basic science, discoveries of the mechanisms of strain variability, viral transfer to the fetus, and neurovirulence were published. These will certainly lead to the development of strategies to block vertical viral transmission, neuronal invasion, and pathogenesis in the near future. This paper reviews the current literature on Zika virus infections, with the aim of gaining a holistic insight into their etiology and pathogenesis. We discuss Zika virus history and epidemiology in Brazil, viral structure and taxonomy, old and newly identified transmission modes, and neurological consequences of infection.",arthrogryposis;Brazil;disease transmission;Flaviviridae infection;Flavivirus;gene sequence;glycosylation;Guillain Barre syndrome;head circumference;human;human tissue;immune response;immunocytochemistry;Japanese encephalitis virus;microcephaly;neurologic disease;neuropathology;pathogenesis;review;sexually transmitted disease;South and Central America;vector control;vertical transmission;virus morphology;virus strain;virus transmission;West Nile fever;Zika fever;Zika virus,"Da Silva, L. R. C.;De Souza, A. M.",2016,,10.1590/0037-8682-0150-2016,0
432,A Fatal Case of Louping-ill in a Dog: Immunolocalization and Full Genome Sequencing of the Virus,"Louping-ill (LI), caused by louping-ill virus (LIV), results in a frequently fatal encephalitis primarily affecting sheep and red grouse (Lagopus lagopus scotica), but it does occur in other species. An adult male Border collie dog was definitively diagnosed with fatal LI and the lesion profile, LIV antigen distribution and full genome sequence of the LIV responsible were investigated to determine if this differed significantly from sheep-derived LIV. No gross lesions were present. The histological lesions were confined to the central nervous system and comprised of lymphocytic perivascular cuffs, glial foci, neuronal necrosis and neuronophagia. Immunolocalization of viral antigen showed small amounts present in neurons only. These histological and immunohistochemical findings were similar to those reported in affected sheep. Compared with published full genome sequences of sheep-derived LIV, only very minor differences were present and phylogenetically the virus clustered individually between a subclade containing Scottish strains, LIV 369/T2 and G and another subclade containing an English isolate LIV A. The LIV isolated from the dog shares a common progenitor with LIV A. These findings suggest there is no canine-specific LIV strain, dogs are susceptible to sheep-associated strains of LI and with the increase in tick prevalence, and therefore exposure to LIV, a safe, effective vaccine for dogs may be required.",amoxicillin plus clavulanic acid;infusion fluid;Louping ill virus antigen;synulox rtu;unclassified drug;virus antigen;adult;animal cell;animal tissue;article;ataxia;border collie;controlled study;depression;histology;immunohistochemistry;immunolocalization;louping ill;Louping ill virus;male;next generation sequencing;nonhuman;phylogeny;priority journal;reverse transcription polymerase chain reaction;serology;tachypnea;thorax radiography;urinalysis;virus genome;virus strain,"Dagleish, M. P.;Clark, J. J.;Robson, C.;Tucker, M.;Orton, R. J.;Rocchi, M. S.",2018,,10.1016/j.jcpa.2018.09.004,0
433,Evolutionary analysis of Tembusu virus: Evidence for the emergence of a dominant genotype,"We recently identified Tembusu virus (TMUV) as a causative agent of duck infectious disease, which has spread in China since 2010. A recent study has indicated a potential case of human infection by TMUV, highlighting the need for further study of TMUV, especially its evolution. Because no information exists regarding the evolution of TMUV, we conducted comprehensive phylogenetic analyses using the largest collection of complete open reading frame (ORF) sequences of TMUV. Our results indicated that two lineages of viruses were associated with the 2010 outbreak in China, and lineage II, in particular sublineage II-c, has arisen as the dominant lineage currently circulating. We inferred that the most recent common ancestor (MRCA) of this TMUV was emerged around 1996. Evidence of natural recombination was also detected in TMUV. Molecular adaptation analyses revealed that strong negative selection shaped the evolution of TMUV, while a number of codons subjected to positive pressure were also identified. Our study, for the first time, illustrated the evolutionary history and character of TMUV and will be helpful for vaccine and diagnostic development.",article;codon;evolutionary adaptation;Flavivirus;genotype;molecular phylogeny;natural selection;nonhuman;open reading frame;priority journal;sequence analysis;Tembusu virus;virus mutation;virus recombination,"Dai, L.;Li, Z.;Tao, P.",2015,,10.1016/j.meegid.2015.03.004,0
434,Next-generation sequencing strategies for characterizing the turkey genome,"The turkey genome sequencing project was initiated in 2008 and has relied primarily on next-generation sequencing (NGS) technologies. Our first efforts used a synergistic combination of 2 NGS platforms (Roche/454 and Illumina GAII), detailed bacterial artificial chromosome (BAC) maps, and unique assembly tools to sequence and assemble the genome of the domesticated turkey, Meleagris gallopavo. Since the first release in 2010, efforts to improve the genome assembly, gene annotation, and genomic analyses continue. The initial assembly build (2.01) represented about 89% of the genome sequence with 17X coverage depth (931 Mb). Sequence contigs were assigned to 30 of the 40 chromosomes with approximately 10% of the assembled sequence corresponding to unassigned chromosomes (ChrUn). The sequence has been refined through both genome-wide and area-focused sequencing, including shotgun and paired-end sequencing, and targeted sequencing of chromosomal regions with low or incomplete coverage. These additional efforts have improved the sequence assembly resulting in 2 subsequent genome builds of higher genome coverage (25X/ Build3.0 and 30X/Build4.0) with a current sequence totaling 1,010 Mb. Further, BAC with end sequences assigned to the Z/W and MG18 (MHC) chromosomes, ChrUn, or not placed in the previous build were isolated, deeply sequenced (Hi-Seq), and incorporated into the latest build (5.0). To aid in the annotation and to generate a gene expression atlas of major tissues, a comprehensive set of RNA samples was collected at various developmental stages of female and male turkeys. Transcriptome sequencing data (using Illumina Hi-Seq) will provide information to enhance the final assembly and ultimately improve sequence annotation. The most current sequence covers more than 95% of the turkey genome and should yield a much improved gene level of annotation, making it a valuable resource for studying genetic variations underlying economically important traits in poultry.",turkey;genome;next-generation sequencing;transcriptome;COMPARATIVE GENETIC-MAP;MELEAGRIS-GALLOPAVO;EVOLUTION;DIVERSITY;REVEALS;INSIGHT;VIRUS,"Dalloul, R. A.;Zimin, A. V.;Settlage, R. E.;Kim, S.;Reed, K. M.",2014,Feb,,0
435,Characterization of Newcastle disease virus isolates obtained from outbreak cases in commercial chickens and wild pigeons in Ethiopia,"Newcastle disease (ND), caused by virulent avian paramyxovirus type 1, is one of the most important diseases responsible for devastating outbreaks in poultry flocks in Ethiopia. However, the information about genetic characteristics of the Newcastle disease viruses (NDVs) circulating in commercial chickens and wild birds is scarce. In this study, we characterized isolates obtained from ND suspected outbreaks during 2012-2014 from poultry farms (n = 8) and wild pigeons (n = 4). The NDVs isolated from pathological specimens, through inoculation in embryonated chicken eggs, were characterized biologically by conventional intracerebral pathogenicity indices (ICPI), and genetically on the basis of Phylogenic analysis of partial F-gene sequences (260 bp) encompassing the cleavage site. The ICPI values of isolates from chickens ranged from 0.9 to 1.8; whereas, the ICPI of pigeon isolates was 1.4. All isolates contained multiple basic amino acids at the deduced cleavage site of fusion protein, which is a typical feature of virulent viruses. Phylogenic analysis of the partial cleavage site of F-gene (260 bp) indicated that all the sequences of viruses obtained from pigeons were identical and clustered within the genotype VIh while the sequences of viruses obtained from chickens were clustered together within the genotype VIf. The similarity between the viruses obtained from chickens and those obtained from pigeons ranged from 82.5 to 85.6 %. This suggests that different sub genotypes of genotype VI are circulating in chicken and wild pigeon population in Ethiopia. This warrants further study to understand the role of wild birds in the epidemiology of NDV in Ethiopia and as well highlights the importance of continuous surveillances both in wild birds and domestic poultry.",,"Damena, D.;Fusaro, A.;Sombo, M.;Belaineh, R.;Heidari, A.;Kebede, A.;Kidane, M.;Chaka, H.",2016,,,0
436,Characterisation of Hungarian porcine circovirus 2 genomes associated with PMWS and PDNS cases,"The authors report the data of the first survey on the incidence of postweaning multisystemic wasting syndrome (PMWS) and porcine dermatitis and nephropathy syndrome (PDNS) in Hungary. A PCR method specific for the detection of porcine circovirus 2 (PCV-2) was developed, which proved to be suitable for diagnostic purposes. PCR screening of organ samples from pigs suspected to be affected with PMWS or PDNS revealed the presence of PCV-2 in 80% of the cases. Six PCV-2 genomes from Hungarian isolates were completely sequenced. Phylogenetic comparison with all the available PCV-2 sequences showed that porcine circoviruses circulating in Hungary are more variable than in several other European countries. Two Hungarian strains clustered together with the Spanish strains forming a distinct group; two others fell in a common group with the French, UK, and Dutch strains, whereas another two strains showed the closest relationship to two of the three known German PCV-2 sequences.",animal tissue;article;Circoviridae;comparative study;controlled study;dermatitis;diagnostic procedure;Europe;France;gene sequence;genetic screening;genome analysis;Hungary;kidney disease;Netherlands;nonhuman;phylogeny;polymerase chain reaction;Spain;pig;swine disease;United Kingdom;virus detection;virus genome;virus isolation;virus strain;wasting syndrome,"Dán, Á;Molnár, T.;Biksi, I.;Glávits, R.;Shaheim, M.;Harrach, B.",2003,,10.1556/AVet.51.2003.4.13,0
437,Application of the SureSelect target enrichment system for next-generation sequencing to obtain the complete genome sequence of bovine leukemia virus,"In this study, the SureSelect target enrichment system for Illumina Multiplexed Sequencing was applied to proviral DNA sequencing of bovine leukemia virus (BLV). The complete genomic DNA sequences of four Vietnamese BLV strains were successfully obtained with high read depth values and a genome coverage of 100% across all sequenced samples, in less than one week. This study provides the first complete Vietnamese BLV genome sequences. Their genetic variability and phylogenetic relationship were also analyzed and compared with those of 28 whole BLV genome sequences from different parts of the world. The results obtained provided new insights into the genetic diversity of the BLV tax gene, and further enabled us to identify nucleotide mutations in the gene that might not have been detected with the commercial detection kit that is currently available.",animal;bovine;Bovine leukemia virus;classification;DNA sequence;genetic variation;genetics;high throughput sequencing;isolation and purification;molecular genetics;nucleotide sequence;phylogeny;provirus;virus genome,"Dao, T. D.;Bui, V. N.;Omatsu, T.;Katayama, Y.;Mizutani, T.;Ogawa, H.;Imai, K.",2018,,10.1007/s00705-018-3957-9,0
438,Rift valley fever and a new paradigm of research and development for zoonotic disease control,"Although Rift Valley fever is a disease that, through its wider societal effects, disproportionately affects vulnerable communities with poor resilience to economic and environmental challenge, Rift Valley fever virus has since its discovery in 1931 been neglected by major global donors and disease control programs. We describe recent outbreaks affecting humans and animals and discuss the serious socioeconomic effects on the communities affected and the slow pace of development of new vaccines. We also discuss the mixed global response, which has largely been fueled by the classification of the virus as a potential bioterrorism agent and its potential to migrate beyond its traditional eastern African boundaries. We argue for a refocus of strategy with increased global collaboration and a greater sense of urgency and investment that focuses on an equity-based approach in which funding and research are prioritized by need, inspired by principles of equity and social justice.",rain;article;awareness;biological warfare;biosafety;disease control;disease surveillance;drug cost;epidemic;funding;geographic distribution;human;investment;livestock;medical research;nonhuman;Rift Valley fever;Rift Valley fever virus;socioeconomics;vaccination;vaccine production;zoonosis,"Dar, O.;McIntyre, S.;Hogarth, S.;Heymann, D.",2013,,10.3201/eid1902.120941,0
439,Development and validation of a highly sensitive real-time PCR assay for rapid detection of parapoxviruses,"Parapoxviruses (PaPVs) cause widespread infections in ruminants worldwide. All PaPVs are zoonotic and may infect humans after direct or indirect contact with infected animals. Herein we report the development and validation of a highly sensitive real-time PCR assay for rapid detection of PaPVs. The new assay (referred to as the RVSS assay) was specific for PaPVs only and had no cross-reactivity against other pox viruses. Using a recombinant plasmid as positive control, the analytical sensitivity of the assay was determined to be 16 genome copies of PaPV per assay. The amplification efficiency estimate (91–99%), the intra- and interassay variability estimate (standard deviation [SD]: 0.28–1.06 and 0.01–0.14, respectively), and the operator variability estimate (SD: 0.78 between laboratories and 0.28 between operators within a laboratory) were within the acceptable range. The diagnostic specificity was assessed on 100 specimens from healthy normal animals and all but 1 tested negative (99%). The diagnostic sensitivity (DSe) was assessed on 77 clinical specimens (skin/scab) from infected sheep, goats, and cattle, and all tested positive (100%). The assay was multiplexed with beta-actin as an internal positive control, and the multiplex assay exhibited the same DSe as the singleplex assay. Further characterization of the PaPV specimens by species-specific real-time PCR and nucleotide sequencing of the PCR products following conventional PCR showed the presence of Orf virus not only in sheep and goats but also in 1 bovid. The validated RVSS assay demonstrated high specificity, sensitivity, reproducibility, and ruggedness, which are critical for laboratory detection of PaPVs.",beta actin;analytic method;article;broth dilution;Capripoxvirus;controlled study;Foot and mouth disease virus;high throughput sequencing;limit of detection;measurement repeatability;multiplex polymerase chain reaction;nonhuman;Orthopoxvirus;Parapoxvirus;process development;real time polymerase chain reaction;reliability;reproducibility;sensitivity and specificity;sequence analysis;Swinepox virus;transmission electron microscopy;validation process;virus characterization;virus genome;virus infection,"Das, A.;Ward, G.;Lowe, A.;Xu, L.;Moran, K.;Renshaw, R.;Dubovi, E.;Reising, M.;Jia, W.",2017,,10.1177/1040638716680676,0
440,"Characterisation of the bovine enteric calici-like virus, Newbury agent 1","The bovine enteric calici-like virus, Newbury agent 1 (NA1) was characterised to determine if it is a member of the Caliciviridae and to establish its antigenic relationship to the established bovine enteric calicivirus Newbury agent 2 (NA2). Solid phase immune electron microscopy (SPIEM) allowed quantification of NA1 virions and identification of faecal samples with optimal virus levels. NA1 particles were 36.6 nm in diameter, had an indefinite surface structure resembling that of human small round structured viruses (SRSVs), and a buoyant density of 1.34 g ml-1. A single capsid protein of 49.4 kDa was detected by Western blotting in purified NA1 preparations prepared from post-infection but not pre-infection faecal samples and with post- but not pre-infection sera. NA1 was antigenically unrelated to the bovine enteric calicivirus NA2 by SPIEM. These properties were consistent with classification of NA1 within the Caliciviridae but demonstrated heterogeneity in the capsid composition of bovine enteric caliciviruses. Copyright (C) 2000 Federation of European Microbiological Societies.",capsid protein;virus capsid antigen;viral protein;article;Caliciviridae;bovine;controlled study;immunoelectron microscopy;molecular weight;nonhuman;priority journal;United Kingdom;virus classification;virus particle;Western blotting,"Dastjerdi, A. M.;Snodgrass, D. R.;Bridger, J. C.",2000,,10.1016/s0378-1097(00)00422-5,0
441,How many papillomavirus species can go undetected in papilloma lesions?,"A co-infection comprising to at least seven papillomavirus (PV) types was detected by next generation sequencing (NGS) of randomly primed rolling circle amplification (RCA) products of a bovine (Bos taurus) papilloma lesion from the Brazilian Amazon region. Six putative new PV types that could not be detected by commonly used PCR protocols were identified. Their overall L1 nucleotide identities were less than 90% compared to described PV species and types. L1 nucleotide BLAST sequence hits showed that each new type was related to Beta, Gamma, Dyokappa, Dyoeta, and Xipapillomavirus, as well as two likely new unclassified genera. Our results show that the employment of NGS is relevant to the detection and characterization of distantly related PV and is of major importance in co-infection studies. This knowledge will help us understand the biology and pathogenesis of PV, as well as contribute to disease control. Moreover, we can also conclude that there are many unknown circulating PVs.",virus DNA;animal;bovine;chemistry;classification;DNA sequence;genetics;high throughput sequencing;isolation and purification;metabolism;mixed infection;nucleic acid amplification;nucleotide sequence;open reading frame;papilloma;Papillomaviridae;pathology;phylogeny;polymerase chain reaction;veterinary medicine;virology;virus genome,"Daudt, C.;da Silva, F. R.;Streck, A. F.;Weber, M. N.;Mayer, F. Q.;Cibulski, S. P.;Canal, C. W.",2016,,10.1038/srep36480,0
442,Borna disease: Current knowledge and virus detection in France,"For over two centuries, Borna disease (BD) has been described as a sporadically occurring infectious meningoencephalomyelitis affecting horses and sheep in Central Europe. Over the last decade, the BD epidemiology has been discussed. Firstly, its geographical distribution seems larger than what was previously thought. Secondly, the disease can affect a large number of warm-blooded animal species, including humans. The aetiological agent is the Borna disease virus (BDV), an enveloped, nonsegmented negative-stranded RNA virus classified in the new virus family Bornaviridae (Mononegavirales order). It can induce severe clinical signs of encephalitis with striking behavioural disturbances and may cause death. BDV genome has recently been detected in France in the blood and brain of several animal species (horses, bovines, foxes).",article;behavior disorder;blood analysis;Borna disease;Borna disease virus;cause of death;clinical feature;controlled study;disease severity;encephalomyelitis;Europe;France;geographic distribution;horse disease;meningoencephalitis;Mononegavirales;nonhuman;RNA virus;sheep disease;species;virus classification;virus detection;virus envelope;virus genome,"Dauphin, G.;Legay, V.;Pitel, P. H.;Zientara, S.",2002,,,0
443,Diagnostic phylogenetics reveals a new Porcine circovirus 2 cluster,"Porcine circovirus 2 (PCV2) was prevalent in swine in the United States before PCV2-associated disease (PCVAD) appeared in 2006. Limited nucleotide sequencing of open reading frame 2 (ORF2) encoding capsid, the only structural protein, revealed the presence of two genotypes, PCV2a and PCV2b. Later, PCV2c and mutant PCV2b, or PCV2d, were also described. However, extensive PCV2 ORF2 sequence databases in veterinary diagnostic laboratories have not been analyzed systematically to determine the genetic diversity of field isolates. Here, we interrogated >1100 PCV2 ORF2 nucleotide sequences to assess population diversity and genetic variation. We detected a novel PCV2 genotype that is substantially different, primarily in ORF2, from all known PCV2. Notably, ORF2 contains a unique carboxyl terminal amino acid insertion resulting in a 238 amino acid ORF2. All other PCV2 ORF2 proteins are 233 or 234 aa in length. Phylogenetic analysis indicates that it is more ancient than other PCV2 genotypes. The findings demonstrate the value of analyzing routine diagnostic laboratory sequence databases in population genetic analyses of animal pathogens.",amino acid sequence;article;carboxy terminal sequence;genetic variability;genotype;nonhuman;nucleotide sequence;phylogeny;Porcine circovirus 2;priority journal;protein structure;virus classification,"Davies, B.;Wang, X.;Dvorak, C. M. T.;Marthaler, D.;Murtaugh, M. P.",2016,,10.1016/j.virusres.2016.02.010,0
444,The dilemma of rare events: Porcine epidemic diarrhea virus in North America,"Porcine epidemic diarrhea virus (PEDV) has been recognized as a swine pathogen for 40 years, but until 2013 had not been detected in the Western Hemisphere. From originally causing a relatively mild and sporadic disease, PEDV has been more recently associated with severe outbreaks of diarrheal disease in Asia, and subsequently North America. PEDV shares some important characteristics with two major pandemic viruses (porcine reproductive and respiratory virus; porcine circovirus type 2) of pigs that have high rates of mutation and high host specificity, and appear to have been present in the swine virome for decades prior to emerging to cause severe clinical disease. A unique feature of the PEDV in North America has been the implication of feed as a vehicle for transmission, with particular concerns related to ingredients of porcine origin. The importance of relatively rare events in contributing to both the emergence and transmission of PEDV is discussed in relation to approaches for managing the associated risks.",animal;animal food;communicable disease;Coronavirus infection;North America;physiology;pig;Porcine epidemic diarrhea virus;swine disease;transmission;veterinary medicine;virology,"Davies, P. R.",2015,,10.1016/j.prevetmed.2015.08.006,0
445,Experience in shotgun sequencing a 134 kilobase pair DNA molecule,"Until now, large DNA sequences have been obtained by cloning fragments of the target molecule into plasmid, cosmid or bacteriophage lambda vectors. The 134 kbp DNA sequence of channel catfish virus was determined with relative ease by shotgun cloning of random fragments of genomic DNA directly into a bacteriophage M13 vector, sequencing by dideoxynucleotide chain termination, and compilation of the data using Staden's database handling programs. Experience gained during this endeavour indicates that sequences substantially larger than 134 kbp may be obtained using this approach.",virus DNA;animal;article;bacteriophage;catfish;cell line;genetics;Herpesviridae;methodology;molecular cloning;nucleotide sequence,"Davison, A. J.",1991,,,0
446,DNA sequence of frog adenovirus,"The genome of frog adenovirus (FrAdV-1) was sequenced and found to be the smallest of all known adenovirus genomes. The sequence obtained was 26163 bp in size and contains a substantial direct repeat near the right terminus, implying that it was derived by recombination from a parental genome of only 25517 bp. The closest relative of FrAdV-1 proved to be turkey adenovirus 3, an avian adenovirus with no previously known near relative. Sequence comparisons showed that the two viruses have equivalent gene complements, including one gene the product of which is related to sialidases. Phylogenetic analyses supported the establishment of a fourth adenovirus genus containing these two viruses, in addition to the established genera Mastadenovirus and Aviadenovirus and the proposed genus Atadenovirus. Sixteen genes were identified as being conserved between these four lineages and were presumably inherited from an ancestral adenovirus.",DNA;gene product;nucleotide;sialidase;Adenoviridae;animal cell;article;Aviadenovirus;comparative study;controlled study;DNA sequence;Anura;genetic complementation;genetic conservation;genetic recombination;Mastadenovirus;nonhuman;nucleotide repeat;nucleotide sequence;phylogeny;priority journal;sequence analysis;turkey (bird);unindexed sequence;virus classification;virus genome,"Davison, A. J.;Wright, K. M.;Harrach, B.",2000,,,0
447,Metagenomic analysis of the turkey gut RNA virus community,"Viral enteric disease is an ongoing economic burden to poultry producers worldwide, and despite considerable research, no single virus has emerged as a likely causative agent and target for prevention and control efforts. Historically, electron microscopy has been used to identify suspect viruses, with many small, round viruses eluding classification based solely on morphology. National and regional surveys using molecular diagnostics have revealed that suspect viruses continuously circulate in United States poultry, with many viruses appearing concomitantly and in healthy birds. High-throughput nucleic acid pyrosequencing is a powerful diagnostic technology capable of determining the full genomic repertoire present in a complex environmental sample. We utilized the Roche/454 Life Sciences GS-FLX platform to compile an RNA virus metagenome from turkey flocks experiencing enteric disease. This approach yielded numerous sequences homologous to viruses in the BLAST nr protein database, many of which have not been described in turkeys. Our analysis of this turkey gut RNA metagenome focuses in particular on the turkey-origin members of the Picornavirales, the Caliciviridae, and the turkey Picobirnaviruses. © 2010 Dayet al licensee BioMed Central Ltd.",complementary DNA;double stranded RNA;virus RNA;amino acid substitution;animal tissue;article;bird disease;Caliciviridae;gastrointestinal tract;nonhuman;nucleotide sequence;Picobirnavirus;Picornaviridae;polymerase chain reaction;poult enteritis complex;poultry;RNA virus;stunting syndrome;turkey (bird);viral gastroenteritis;virus diagnosis;virus infection,"Day, J. M.;Ballard, L. L.;Duke, M. V.;Scheffler, B. E.;Zsak, L.",2010,,10.1186/1743-422x-7-313,1
448,Comparative analysis of the intestinal bacterial and RNA viral communities from sentinel birds placed on selected broiler chicken farms,"There is a great deal of interest in characterizing the complex microbial communities in the poultry gut, and in understanding the effects of these dynamic communities on poultry performance, disease status, animal welfare, and microbes with human health significance. Investigations characterizing the poultry enteric virome have identified novel poultry viruses, but the roles these viruses play in disease and performance problems have yet to be fully characterized. The complex bacterial community present in the poultry gut influences gut development, immune status, and animal health, each of which can be an indicator of overall performance. The present metagenomic investigation was undertaken to provide insight into the colonization of specific pathogen free chickens by enteric microorganisms under field conditions and to compare the pre-contact intestinal microbiome with the altered microbiome following contact with poultry raised in the field. Analysis of the intestinal virome from contact birds (""sentinels"") placed on farms revealed colonization by members of the Picornaviridae, Picobirnaviridae, Reoviridae, and Astroviridae that were not present in precontact birds or present in proportionally lower numbers. Analysis of the sentinel gut bacterial community revealed an altered community in the post-contact birds, notably by members of the Lachnospiracea/Clostridium and Lactobacillus families and genera. Members of the avian enteric Reoviridae and Astroviridae have been well-characterized and have historically been implicated in poultry enteric disease; members of the Picobirnaviridae and Picornaviridae have only relatively recently been described in the poultry and avian gut, and their roles in the recognized disease syndromes and in poultry performance in general have not been determined. This metagenomic analysis has provided insight into the colonization of the poultry gut by enteric microbes circulating in commercial broiler flocks, and has identified enteric viruses and virus communities that warrant further study in order to understand their role(s) in avian gut health and disease.",virus RNA;animal experiment;animal health;animal welfare;article;Astroviridae;bacterial colonization;bird;broiler;Clostridium;comparative study;controlled study;immune status;intestine flora;Lachnospiraceae;Lactobacillus;metagenomics;microbial community;microbiome;nonhuman;Picornaviridae;Reoviridae,"Day, J. M.;Oakley, B. B.;Seal, B. S.;Zsak, L.",2015,,10.1371/journal.pone.0117210,0
449,Molecular and phylogenetic analysis of a novel Turkey-origin Picobirnavirus,"A previous metagenomic analysis of the turkey gut RNA virus community identified novel enteric viruses that may play roles in poultry enteric diseases or in performance problems noted in the field. As part of the molecular characterization of these novel enteric viruses, a reverse transcriptase-PCR diagnostic assay was developed, targeting a novel turkey-origin picobirnavirus (PBV) initially identified in a pooled intestinal sample from turkey poults in North Carolina. Little detailed molecular information exists regarding the family Picobirnaviridae, particularly for the PBVs that have been described in avian species. This diagnostic assay targets the turkey PBV RNA-dependent RNA polymerase gene and produces an 1135-bp amplicon. This assay was validated using in vitro transcribed RNA and was tested using archived enteric samples collected from turkey flocks in the southeastern United States. Further, a phylogenetic analysis suggests the turkey PBV is unique because it does not group closely with the recognized PBV genogroups circulating in mammalian hosts. © American Association of Avian Pathologists.",RNA directed RNA polymerase;animal;animal disease;article;bird disease;enzymology;evaluation study;genetics;metabolism;methodology;molecular genetics;nucleotide sequence;phylogeny;Picobirnavirus;reverse transcription polymerase chain reaction;RNA virus infection;turkey (bird);virology;virus gene,"Day, J. M.;Zsak, L.",2014,,10.1637/10593-061313-ResNote.1,0
450,Investigating Turkey Enteric Picornavirus and Its Association with Enteric Disease in Poults,"Previous research into the viral community in the poultry gastrointestinal tract has revealed a number of novel and partially described enteric viruses. It is evident that the poultry gut viral community remains minimally characterized and incompletely understood. Investigations into the microbiome of the poultry gut have provided some insight into the geographical distribution and the rapidly evolving taxonomy of the avian enteric picornaviruses. The present investigation was undertaken to produce a comparative metagenomic analysis of the gut virome from a healthy turkey flock versus a flock placed in the field. This investigation revealed a number of enteric picornavirus sequences that were present in the commercial birds in the field that were completely absent in the healthy flock. A novel molecular diagnostic assay was used to track the shedding of field strains of turkey enteric picornavirus in commercial poults inoculated with picornavirus-positive intestinal homogenates prepared from turkeys that were experiencing moderate enteric disease. The propagation of this novel enteric picornavirus in commercial poults resulted in significant reduction in weight gain, and suggests that this common inhabitant of the turkey gut may result in performance problems or enteric disease in the field.",animal;classification;embryology;enteritis;genetics;metagenomics;Picornaviridae;picornavirus infection;reverse transcription polymerase chain reaction;turkey (bird);veterinary medicine;virology;virus culture;body weight loss,"Day, J. M.;Zsak, L.",2015,,,1
451,Molecular Characterization of Enteric Picornaviruses in Archived Turkey and Chicken Samples from the United States,"Recent metagenomic analyses of the enteric viromes in turkeys and chickens have revealed complex viral communities comprised of multiple viral families. Of particular significance are the novel avian picobirnaviruses (family Picobirnaviridae), multiple genera of tailed phages (family Siphoviridae), and undescribed avian enteric picornaviruses (family Picornaviridae). In addition to these largely undescribed-and therefore relatively poorly understood-poultry enteric viral families, these metagenomic analyses have also revealed the presence of well-known groups of enteric viruses such as the chicken and turkey astroviruses (family Astroviridae) and the avian rotaviruses and reoviruses (family Reoviridae). The order Picornavirales is a group of viruses in flux, particularly among the avian picornaviruses, since several new genera have been described recently based upon community analysis of enteric viromes from poultry and other avian species worldwide. Our previous investigation of the turkey enteric picornaviruses suggests the avian enteric picornaviruses may contribute to the enteric disease syndromes and performance problems often observed in turkeys in the Southeastern United States. This report describes our recent phylogenetic analysis of turkey and chicken enteric samples archived at the Southeast Poultry Research Laboratory from 2004 to present and is a first step in placing these novel avian picornaviruses within the larger Picornaviridae family.",animal;bird disease;chicken;classification;genetics;phylogeny;Picornaviridae;picornavirus infection;sequence analysis;turkey (bird);United States;veterinary medicine;virology,"Day, J. M.;Zsak, L.",2016,,10.1637/11289-092415-ResNote,0
452,High global diversity of cycloviruses amongst dragonflies,"Members of the family Circoviridae, specifically the genus Circovirus, were thought to infect only vertebrates; however, members of a sister group under the same family, the proposed genusCyclovirus, have been detected recently in insects. In an effort to explore the diversity of cycloviruses and better understand the evolution of these novel ssDNA viruses, here we present five cycloviruses isolated from three dragonfly species (Orthetrum sabina, Xanthocnemis zealandica and Rhionaeschna multicolor) collected in Australia, New Zealand and the USA, respectively. The genomes of these five viruses share similar genome structure to other cycloviruses, with a circular ~1.7 kb genome and two major bidirectionally transcribed ORFs. The genomic sequence data gathered during this study were combined with all cyclovirus genomes available in public databases to identify conserved motifs and regulatory elements in the intergenic regions, as well as determine diversity and recombinant regions within their genomes. The genomes reported here represent four different cyclovirus species, three of which are novel. Our results confirm that cycloviruses circulate widely in winged-insect populations; in eight different cyclovirus species identified in dragonflies to date, some of these exhibit a broad geographical distribution. Recombination analysis revealed both intra-and inter-species recombination events amongst cycloviruses, including genomes recovered from disparate sources (e.g. goat meat and human faeces). Similar to other well-characterized circular ssDNA viruses, recombination may play an important role in cyclovirus evolution. © 2013 SGM.",single stranded DNA;article;Australia;Circoviridae;cyclovirus;data base;dragonfly;gene structure;geographic distribution;New Zealand;nonhuman;nucleotide sequence;Orthetrum sabina;priority journal;Rhionaeschna multicolor;United States;virus classification;virus genome;Xanthocnemis zealandica,"Dayaram, A.;Potter, K. A.;Moline, A. B.;Rosenstein, D. D.;Marinov, M.;Thomas, J. E.;Breitbart, M.;Rosario, K.;Argüello-Astorga, G. R.;Varsani, A.",2013,,10.1099/vir.0.052654-0,0
453,"Detection of hepatitis E virus in liver, mesenteric lymph node, serum, bile and faeces of naturally infected pigs affected by different pathological conditions","The objective of the present study was to detect hepatitis E virus (HEV) in different samples from naturally infected pigs and to characterise genetically the detected strains. Serum, bile, liver, lymph nodes and faeces of 69 animals from 1 week to 4 months of age with different pathological conditions were collected. Reverse transcriptase-polymerase chain reaction (RT-PCR) to detect HEV and histopathology of tissues was conducted. Positive RT-PCR samples were sequenced and phylogenetically analysed. HEV was detected in at least one sample in 26 out of 69 animals (37.7%). Bile was the most frequently positive sample, followed by mesenteric lymph nodes, liver, faeces and serum. HEV was detected in pigs of 1 (n = 7), 2 (n = 8) and 3 (n = 11) months of age. A total of 22 of 69 (31.9%) pigs had mild to moderate hepatitis and 15 of them were HEV RT-PCR positive in at least one of the tested samples.The highest sensitivity of viral detection was achieved using samples that cannot be obtained from live pigs, such as liver, mesenteric lymph node and bile. Phylogenetic analyses confirmed that all Spanish swine HEV strains detected belonged to genotype III. Therefore, genotype III strains are present in a relative high proportion of pigs between 1 and 3 months of age. Through this study, it cannot be ruled out if concomitant infections may influence the distribution of HEV in infected pigs. © 2006 Elsevier B.V. All rights reserved.",animal cell;article;bile;disease severity;feces;genotype;Hepatitis E virus;histopathology;liver;mesentery lymph node;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;RNA extraction;sensitivity and specificity;serum;pig;virus detection;virus hepatitis;virus strain,"de Deus, N.;Seminati, C.;Pina, S.;Mateu, E.;Martín, M.;Segalés, J.",2007,,10.1016/j.vetmic.2006.08.027,0
454,Antigenic and molecular heterogeneity in recent swine influenza A(H1N1) virus isolates with possible implications for vaccination policy,"In order to explore the occurrence of antigenic drift in swine influenza A(H1N1) viruses and the match between epidemic and vaccine strains, 26 virus isolates from outbreaks of respiratory disease among finishing pigs in the Netherlands in the 1995/1996 season and reference strains from earlier outbreaks were examined using serological and molecular methods. In contrast to swine H3N2 viruses, no significant antigenic drift was observed in swine H1N1 viruses isolated from the late 1980s up to 1996 inclusive. However, a marked antigenic and genetic heterogeneity in haemagglutination inhibition tests and nucleotide sequence analyses was detected among the 26 recent swine H1N1 virus strains. Interestingly, the observed antigenic and molecular variants were not randomly distributed over the farms. This finding indicates independent introductions of different swine H1N1 virus variants at the various farms of the study and points to a marked difference between the epidemiologies of human and swine influenza viruses. The observed heterogeneity may hamper the control of swine influenza by vaccination and indicates that the efficacy of current swine influenza vaccines requires re-evaluation and that the antigenic reactivity of swine influenza viruses should be monitored on a regular basis. © 2001 Elsevier Science Ltd. All rights reserved.",article;genetic heterogeneity;hemagglutination inhibition test;infection prevention;nucleotide sequence;priority journal;sequence analysis;swine influenza virus;virus isolation;virus strain,"De Jong, J. C.;Heinen, P. P.;Loeffen, W. L. A.;Van Nieuwstadt, A. P.;Claas, E. C. J.;Bestebroer, T. M.;Bijlsma, K.;Verweij, C.;Osterhaus, A. D. M. E.;Rimmelzwaan, G. F.;Fouchier, R. A. M.;Kimman, T. G.",2001,,10.1016/s0264-410x(01)00190-6,0
455,Evolutionary origin of 2A-like sequences in Totiviridae genomes,"In recent years there has been a significant increase in the number of new species potentially belonging to the Totiviridae family. Most of these new viruses have not yet been covered by the Committee on Taxonomy of Viruses (ICTV) official classification. In this study, a phylogenetic analysis including new sequences of Totiviridae candidates revealed a clade including Giardiavirus and a great diversity of new totiviruses, which infect arthropods, protozoa and mollusc. This expanded Giardiavirus clade comprises two monophyletic groups, one of them including Giardia lamblia virus (GLV) grouped with viruses that infect arthropods and vertebrates (GLV-like group), and the other includes the previously proposed Artivirus group (IMNV-like group). A screening of the members of the GLV-like group in search of genomic elements already described in IMNV-like group revealed the existence of sites with a high propensity to become 2 A-like oligopeptides, mainly in a specific subgroup of arthropod viruses, suggesting that these viruses preserved ancestral characteristics. The existence of these “pseudo 2 A-sites” associated to phylogenetic reconstruction indicates that these sequences appear at a decisive stage for viral evolution. If they are changed to functional 2 A-like sequences, an irreversible route to increase the genome complexity will be initiated.",oligopeptide;amino acid sequence;article;cladistics;gene sequence;genome analysis;Giardia intestinalis;Giardiavirus;molecular evolution;monophyly;nonhuman;phylogeny;priority journal;sequence alignment;sequence analysis;Totiviridae;virus genome,"de Lima, J. G. S.;Teixeira, D. G.;Freitas, T. T.;Lima, J. P. M. S.;Lanza, D. C. F.",2019,,10.1016/j.virusres.2018.10.011,0
456,"Akabane, Aino and Schmallenberg virus — where do we stand and what do we know about the role of domestic ruminant hosts and Culicoides vectors in virus transmission and overwintering?","Akabane, Aino and Schmallenberg virus belong to the Simbu serogroup of Orthobunyaviruses and depend on Culicoides vectors for their spread between ruminant hosts. Infections of adults are mostly asymptomatic or associated with only mild symptoms, while transplacental crossing of these viruses to the developing fetus can have important teratogenic effects. Research mainly focused on congenital malformations has established a correlation between the developmental stage at which a fetus is infected and the outcome of an Akabane virus infection. Available data suggest that a similar correlation also applies to Schmallenberg virus infections but is not yet entirely conclusive. Experimental and field data furthermore suggest that Akabane virus is more efficient in inducing congenital malformations than Aino and Schmallenberg virus, certainly in cattle. The mechanism by which these Simbu viruses cross-pass yearly periods of very low vector abundance in temperate climate zones remains undefined. Yearly wind-borne reintroductions of infected midges from tropical endemic regions with year-round vector activity have been proposed, just as overwintering in long-lived adult midges. Experimental and field data however indicate that a role of vertical virus transmission in the ruminant host currently cannot be excluded as an overwintering mechanism. More studies on Culicoides biology and specific groups of transplacentally infected newborn ruminants without gross malformations are needed to shed light on this matter.",virus vector;Aino virus;Akabane virus;congenital disorder;congenital malformation;Culicoides;dam (animal);geographic distribution;infection;metagenomics;nonhuman;Orthobunyavirus;overwintering;placenta tissue;pregnancy;priority journal;progeny;review;ruminant;Schmallenberg virus;tropics;virus;virus infectivity;virus isolation;virus transmission,"De Regge, N.",2017,,10.1016/j.coviro.2017.10.004,0
457,Proposal for a new subtype of the zoonotic genotype 3 Hepatitis E virus: HEV-3l,"The near-complete genomic sequences of two hepatitis E virus (HEV) strains, detected from feces of infected pigs, were obtained. Phylogenetic analysis and p-distance comparisons of the complete coding regions showed a close relationship to the French swine strain FR-SHEV3c-like detected in 2006 (p-distance value 0.101), belonging to HEV-3 but not assigned to any known subtype. The three HEV sequences showed, relatively high nucleotide distances (p-distance >0.129) compared to the other defined HEV subtype references and unclassified strains. The HEV classification criteria and the high sequence similarity suggest that these strains can be assigned to a putative novel subtype of genotype 3, HEV-3l.","Animals;Genome, Viral;*Genotype;*Hepatitis E/vi [Virology];Hepatitis E virus/cl [Classification];*Hepatitis E virus/ge [Genetics];High-Throughput Nucleotide Sequencing;Humans;Phylogeny;RNA, Viral;Sequence Analysis, DNA;Swine;Swine Diseases/vi [Virology];*Zoonoses/vi [Virology];0 (RNA, Viral)","De Sabato, L.;Lemey, P.;Vrancken, B.;Bonfanti, L.;Ceglie, L.;Vaccari, G.;Di Bartolo, I.",2018,03 15,,0
458,Bovine papular stomatitis affecting dairy cows and milkers in midwestern Brazil,"Bovine papular stomatitis virus (BPSV) is a parapoxvirus associated with papular and erosive lesions on the muzzle, lips, and oral mucosa of cattle. Teats of milking cows are occasionally affected, and the infection is frequently transmitted to human beings. The present report describes an outbreak of BPSV infection affecting cows in midwestern Brazil, with human involvement. The disease was observed in neighboring small hand-milking farms, affecting 20 milking cows. The signs included painful reddish papules, ulcers, and scabby proliferative lesions on the teats, with a clinical course of 7-12 days. Affected cows presented severe local pain, not allowing the completion of milking. Histologically, acanthosis, spongiosis, and parakeratotic hyperkeratosis with adjacent focally extensive ulcers and multifocal inflammatory infiltrate were observed in the epidermis. Eosinophilic inclusion bodies were noted in the cytoplasm of epithelial cells. Personnel milking the affected cows developed lesions on the hands, painful papules that progressed to ulcerative and scabby lesions in 4-7 days. A polymerase chain reaction using a set of pan-parapoxvirus primers for the B2L gene performed on DNA extracted from scabs amplified a 590-bp product, which when sequenced, revealed similarities of 99%, 85%, and 84% with BPSV, Pseudocowpox virus, and Orf virus, respectively. A phylogenetic tree based on the B2L sequence was constructed, showing that the virus clustered with BPSV isolates. Although clinical cases compatible with BSPV infection have been frequently described in Brazil, the present report identifies the agent associated with cattle and human disease in the country. © 2012 American Association of Veterinary Laboratory Diagnosticians.",virus DNA;animal;animal disease;article;Brazil;case report;bovine;cattle disease;chemistry;cytochemistry;DNA sequence;epidemic;female;genetics;human;isolation and purification;molecular genetics;nucleotide sequence;Parapoxvirus;pathology;phylogeny;polymerase chain reaction;poxvirus infection;sequence alignment;virology;zoonosis,"de Sant'Ana, F. J. F.;Rabelo, R. E.;Vulcani, V. A. S.;Cargnelutti, J. F.;Flores, E. F.",2012,,10.1177/1040638711434799,0
459,Laboratory decision-making during the classical swine fever epidemic of 1997-1998 in the Netherlands,"The National Reference Laboratory for classical swine fever (CSF) virus in the Netherlands examined more than two million samples for CSF virus or serum antibody during the CSF epizootic of 1997-1998. The immense amount of samples and the prevalence of border disease (BD) virus and bovine viral diarrhoea (BVD) virus infections in Dutch pig herds necessitated the diagnostic efforts of the laboratory to be focused on generating CSF specific test results throughout the eradication campaign. Detection of 82% of the 429 outbreaks was achieved through the combined use of a direct immunofluorescence and peroxidase assay (FAT/IPA) with samples (tonsils) collected from clinically-suspected pigs. This suggests that in the majority of the outbreaks, the pigs had clinical signs that were recognised by the farmer and/or veterinarians, indicating the presence of CSF virus in a pig herd. A positive diagnosis of 74% of all the tissue samples (tonsils) collected at infected pig holdings was established by FAT. More than 140,000 heparinised blood samples were examined by virus isolation, resulting in the detection of 4.5% of the infected herds. CSF virus was isolated in approximately 29% of all the blood samples collected from pigs at infected or suspected farms. Several serological surveys - each done within a different framework led to the detection of 13.5% of the total number of outbreaks. The detection of CSF virus antibody in serum was carried out by semi-automated blocking ELISA. Approximately 28.5% of the sera which reacted in the ELISA were classified as CSF virus-neutralising antibody positive and 26.5% as positive for other pestiviruses following the virus neutralisation test (VNT). We concluded that two of the CSF laboratory diagnostic methods described were determinative in the eradication campaign: first, the FAT for the screening of diseased pigs; and second, the ELISA and VNT when millions of predominantly healthy pigs needed to be screened for the presence of CSF serum antibody. Decision-making on the basis of results generated by either method can, however, be seriously hindered when samples are examined from pig herds with a high prevalence of non-CSF pestiviruses.",animal;animal disease;article;bovine;cattle disease;decision making;differential diagnosis;enzyme linked immunosorbent assay;epidemic;fluorescent antibody technique;immunology;isolation and purification;Netherlands;Pestivirus;sheep disease;pig;swine disease,"De Smit, A. J.;Eble, P. L.;De Kluijver, E. P.;Bloemraad, M.;Bouma, A.",1999,,,0
460,Araçatuba virus: A vaccinialike virus associated with infection in humans and cattle,"We describe a vaccinialike virus, Araçatuba virus, associated with a cowpoxlike outbreak in a dairy herd and a related case of human infection. Diagnosis was based on virus growth characteristics, electron microscopy, and molecular biology techniques. Molecular characterization of the virus was done by using polymerase chain reaction amplification, cloning, and DNA sequencing of conserved orthopoxvirus genes such as the vaccinia growth factor (VGF), thymidine kinase (TK), and hemagglutinin. We used VGF-homologous and TK gene nucleotide sequences to construct a phylogenetic tree for comparison with other poxviruses. Gene sequences showed 99% homology with vaccinia virus genes and were clustered together with the isolated virus in the phylogenetic tree. Araçatuba virus is very similar to Cantagalo virus, showing the same signature deletion in the gene. Araçatuba virus could be a novel vaccinialike virus or could represent the spread of Cantagalo virus.",animal cell;Aracatuba virus;article;cattle disease;controlled study;cowpox;DNA sequence;DNA virus;gene amplification;gene cluster;gene deletion;gene sequence;molecular biology;molecular cloning;nonhuman;nucleotide sequence;Orthopoxvirus;phylogeny;polymerase chain reaction;sequence analysis;sequence homology;Vaccinia virus;Vero cell line;virogenesis;virus gene;virus identification;virus infection;virus isolation,"De Souza Trindade, G.;Da Fonseca, F. G.;Marques, J. T.;Nogueira, M. L.;Mendes, L. C. N.;Borges, A. S.;Peiró, J. R.;Pituco, E. M.;Bonjardim, C. A.;Ferreira, P. C. P.;Kroon, E. G.",2003,,,0
461,Novel parvoviruses from wild and domestic animals in Brazil provide new insights into parvovirus distribution and diversity,"Parvoviruses (family Parvoviridae) are small, single-stranded DNA viruses. Many parvoviral pathogens of medical, veterinary and ecological importance have been identified. In this study, we used high-throughput sequencing (HTS) to investigate the diversity of parvoviruses infecting wild and domestic animals in Brazil. We identified 21 parvovirus sequences (including twelve nearly complete genomes and nine partial genomes) in samples derived from rodents, bats, opossums, birds and cattle in Pernambuco, São Paulo, Paraná and Rio Grande do Sul states. These sequences were investigated using phylogenetic and distance-based approaches and were thereby classified into eight parvovirus species (six of which have not been described previously), representing six distinct genera in the subfamily Parvovirinae. Our findings extend the known biogeographic range of previously characterized parvovirus species and the known host range of three parvovirus genera (Dependovirus, Aveparvovirus and Tetraparvovirus). Moreover, our investigation provides a window into the ecological dynamics of parvovirus infections in vertebrates, revealing that many parvovirus genera contain well-defined sub-lineages that circulate widely throughout the world within particular taxonomic groups of hosts.",article;biogeography;Bocaparvovirus;Brazil;Dependoparvovirus;domestic animal;gene sequence;genome size;high throughput sequencing;maximum likelihood method;microbial diversity;nonhuman;nucleotide sequence;Parvoviridae;Passeriformes;phylogenetic tree;sequence analysis;single-stranded DNA virus;wild animal,"De Souza, W. M.;Dennis, T.;Fumagalli, M. J.;Araujo, J.;Sabino-Santos, G.;Maia, F. G. M.;Acrani, G. O.;Carrasco, A. O. T.;Romeiro, M. F.;Modha, S.;Vieira, L. C.;Ometto, T.;Queiroz, L. H.;Durigon, E. L.;Nunes, M. R. T.;Figueiredo, L. T. M.;Gifford, R. J.",2018,,10.3390/v10040143,1
462,Neurologic Clinical Signs in Cattle With Astrovirus‐Associated Encephalitis,,,"Deiss, R.;Selimovic‐Hamza, S.",2017,,,0
463,Neurologic Clinical Signs in Cattle With Astrovirus-Associated Encephalitis,"Background: Evidence of neurotropic astroviruses has been established using novel genetic methods in cattle suffering from viral encephalitis of previously unknown origin. Objectives: To describe the clinical signs observed in cattle with astrovirus-associated encephalitis. Animals: Eight cattle (4 cows, 3 heifers, and 1 bull of 4 different breeds) admitted to the Clinic for Ruminants for neurologic disease and 1 cow investigated in the field. Methods: Cases were selected based on neuropathologic diagnosis of nonsuppurative encephalitis, positive in situ hybridization result for astrovirus, and availability of the results of physical and neurologic evaluations. Laboratory results were evaluated if available. Results: The most frequently observed clinical signs were decreased awareness of surroundings (7), cranial nerve dysfunction (5), and recumbency (5). The cow seen in the field was the only animal that had severe behavioral changes. Cell counts in cerebrospinal fluid (CSF) were increased in 4 animals, and protein concentration was increased in 3 of 5 specimens. In 1 case, the presence of astrovirus could be identified in a CSF sample by reverse transcriptase polymerase chain reaction. Other laboratory abnormalities were nonspecific. Conclusions and Clinical Importance: Astrovirus infection may be an important differential diagnosis in cattle with clinical signs of brain disease and should be considered after exclusion of other causes. The clinical and epidemiological relevance of encephalitis associated with astrovirus infection should be further investigated.",Atypical;Bovine;Central nervous system;Viral;NONSUPPURATIVE ENCEPHALITIS;BOVINE ASTROVIRUSES;METAGENOMICS;INFECTION;SCOTLAND;DISEASE;MINK,"Deiss, R.;Selimovic-Hamza, S.;Seuberlich, T.;Meylan, M.",2017,Jul-Aug,,0
464,Swine vesicular disease: properties of the virus strain France 1/73,"The France 1/73 strain of swine vesicular disease has the biological and physicochemical properties of an Enterovirus. Single cycle growth on IBR'S2 cell can be detected as early as 2 hr 30 min and the maximum is reached in 5 hr. Multiplication takes place in the cytoplasm of the cell. By fluorescein immunofluorescence a specific green fluorescence in the cytoplasm can be shown within four hours after infection. Virions yielded by this cell system have been concentrated with PEG and analysed by ultracentrifugation in a sucrose gradient. Two populations of particles have been thus separated. The first has a sedimentation coefficient of 150S, the other 75S. After isopycnic centrifugation, a density of 1.34 g/cm3 is attributed to the heavier particles and 1.30 g/cm3 to the lighter particles. Electron microscopic examination shows that the particles have a diameter of between 30 and 32 nm. The particles having a density of 1.30 g/cm3 are all penetrated by stain and correspond to empty capsids. With these viral antigens, an effective specific antiserum has been prepared in pigs. It can be used for all serological reactions. It is thus used for differential diagnosis by complement fixation tests (classical reaction at 37°C) using vesicular fluid taken from sick pigs. An inactivated oil adjuvant vaccine has also been prepared. The protection rate of vaccinated animals is between 75% and 100% with 95% probability.",virus antibody;classification;Enterovirus;in vitro study;microorganism;Picornaviridae;prevention;pig;theoretical study;vaccination;virogenesis;virology;virus capsid;virus classification;virus inactivation;virus infection,"Delagneau, J. F.;Guerche, J.;Adamowicz Ph. andPrunet, P.",1974,,,0
465,Properties of a bovine Parvovirus (strain 86/Alger). Type of nucleic acid stability and one step growth,,bovine;classification;microorganism;Parvoviridae;virus classification,"Delagneau, J. F.;Vincent, J.",1971,,,0
466,Foamy viruses - A world apart,"Foamy viruses (FVs) or spumaviruses were described for the first time in the early 1950s in cell cultures derived from monkey kidneys. Later, FVs were isolated in several mammal species such as cats, cattle and horses. Highly prevalent in non-human primates they are not naturally present in humans, although several cases of simian-to-human transmissions have been described. Interestingly, the replication strategy of FVs differs in many aspects from that of other retroviruses, presenting features that are closely related to pararetroviruses, exemplified by the hepatitis B virus (HBV), but also characteristics that are closely related to yeast retrotransposons. These characteristics led to the creation of a distinct viral subfamily by the International Committee on Virus Taxonomy in 2002; the Spumaretrovirinae. © 2004 Elsevier Ltd. All rights reserved.",virus DNA;cell activity;cell culture;disease transmission;DNA synthesis;Hepatitis B virus;human;kidney;Haplorhini;nonhuman;retroposon;Retroviridae;review;Spumavirus;virus replication,"Delelis, O.;Lehmann-Che, J.;Saïb, A.",2004,,10.1016/j.mib.2004.06.009,0
467,Microbial diversity of a full‐scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun …,,,"Delforno, T. P.;Júnior, G. V. Lacerda;Noronha, M. F.",2017,,,0
468,Microbial diversity of a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing,"The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset. The virome characterization revealed the presence of two viral families with Bacteria and Archaea as host, Myoviridae, and Siphoviridae. A wide functional diversity was found with predominance of genes involved in the metabolism of acetone, butanol, and ethanol synthesis; and one-carbon metabolism (e.g., methanogenesis). Genes related to the acetotrophic methanogenesis pathways were more abundant than methylotrophic and hydrogenotrophic, corroborating the taxonomic results that showed the prevalence of the acetotrophic genus Methanosaeta. Moreover, the dataset indicated a variety of metabolic genes involved in sulfur, nitrogen, iron, and phosphorus cycles, with many genera able to act in all cycles. BLAST analysis against Antibiotic Resistance Genes Database (ARDB) revealed that microbial community contained 43 different types of antibiotic resistance genes, some of them were associated with growth chicken promotion (e.g., bacitracin, tetracycline, and polymyxin).",iron;nitrogen;RNA 16S;sulfur;amplicon;archaeon;article;Bacillus;carbon metabolism;Clostridium;Deinococcus;gene sequence;genetic variability;metagenomics;methanogenesis;Methanosaeta;microbial community;microbial diversity;Myoviridae;nitrogen cycle;nonhuman;Ornithobacterium;phosphorus cycle;phylogeny;Porphyromonas;poultry;priority journal;Pseudomonas;Psychrobacter;sequence analysis;Siphoviridae;slaughterhouse;Sporosarcina;sulfur cycle;Tannerella;waste water management,"Delforno, T. P.;Lacerda Júnior, G. V.;Noronha, M. F.;Sakamoto, I. K.;Varesche, M. B. A.;Oliveira, V. M.",2017,,10.1002/mbo3.443,0
469,The physico-chemical characterization of bovine ephemeral fever virus as a member of the family Rhabdoviridae,"This study of the physico-chemical properties of bovine ephemeral fever virus was initiated to establish whether or not it should be classified as a rhabdovirus. In contrast to the regular bullet-shaped morphology of some rhabdovirus the virus particles are often cone-shaped or slight variants from bullet-shaped. The virion contains single-stranded RNA sedimenting at 42S and six proteins with mol. wt. of 164, 101, 64, 53, 43 and 29 x 103. The protein P101 is located on the surface of the virus and is glycosylated. It is removed by treatment of the virus particles with trypsin. Protein P64, the nucleoprotein, was found to be a phosphoprotein, like the N protein of rabies virus, whereas in vesicular stomatitis virus NS is the phosphorylated protein. Virus harvests contain defective-interfering particles. The particles are short cone-shaped forms about one-third the length of the infectious virion and similar in morphology to defective-interfering particles of vesicular stomatitis virus. These particles interfere with the replication of bovine ephemeral fever virus but not with the Indiana serotype of vesicular stomatitis virus. They contain single-stranded RNA sedimenting at 18 to 20S. The particles appear to have a protein composition identical to that found in the virus particle. The physico-chemical properties of bovine ephemeral fever virus justify its inclusion in the family Rhabdoviridae. The protein composition differs in detail from that found for vesicular stomatitis and rabies viruses, but is similar to that found for Obodhiang and kotonkan, two rabies serogroup viruses isolated from insects in Africa.",viral protein;virus RNA;bovine;cattle disease;classification;virus classification,"Della-Porta, A. J.;Brown, F.",1979,,,0
470,ICTV virus taxonomy profile: Birnaviridae,"Birnaviridae is a family of viruses with bi-segmented dsRNA genomes totalling about 6 kbp forming icosahedral, nonenveloped virions. The family includes four genera, members of three of which (Aquabirnavirus, Avibirnavirus and Blosnavirus) infect vertebrates (excluding mammals), whereas members of the fourth genus (Entomobirnavirus) infect insects. Each genus includes 1-3 species. Infectious pancreatic necrosis virus of salmonids and infectious bursal disease virus of poultry are two economically important birnaviruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of Birnaviridae, which is available at www.ictv.global/report/birnaviridae.",Aquabirnavirus;article;Avibirnavirus;Birnaviridae;Entomobirnavirus;infectious bursal disease virus;infectious pancreatic necrosis virus;nonhuman;pathogenesis;priority journal;virus genome;virus replication,"Delmas, B.;Attoui, H.;Ghosh, S.;Malik, Y. S.;Mundt, E.;Vakharia, V. N.;Lefkowitz, E. J.;Davison, A. J.;Siddell, S. G.;Simmonds, P.;Sabanadzovic, S.;Smith, D. B.;Orton, R. J.;Kuhn, J. H.",2019,,10.1099/jgv.0.001185,0
471,"Animal virus discovery: Improving animal health, understanding zoonoses, and opportunities for vaccine development","The characterization of viral genomes has accelerated due to improvement in DNA sequencing technology. Sources of animal samples and molecular methods for the identification of novel viral pathogens and steps to determine their pathogenicity are listed. The difficulties for predicting future cross-species transmissions are highlighted by the wide diversity of known viral zoonoses. Recent surveys of viruses in wild and domesticated animals have characterized numerous viruses including some closely related to those infecting humans. The detection of multiple genetic lineages within viral families infecting a single host species, phylogenetically interspersed with viruses found in other host species, reflects past cross-species transmissions. Numerous opportunities for the generation of novel vaccines will arise from a better understanding of animal viromes. © 2012 Elsevier B.V. All rights reserved.",virus vaccine;analytic method;animal health;animal virus;disease association;metagenomics;molecular evolution;nonhuman;nucleotide sequence;priority journal;review;virus detection;virus genome;virus infection;virus load;virus transmission;virus virulence;zoonosis,"Delwart, E.",2012,,10.1016/j.coviro.2012.02.012,0
472,Monitoring the immune response to vaccination with an inactivated vaccine associated to bovine neonatal pancytopenia by deep sequencing transcriptome analysis in cattle,"Bovine neonatal pancytopenia (BNP) is a new fatal, alloimmune/alloantibody mediated disease of new-born calves induced by ingestion of colostrum from cows, which had been vaccinated with a specific vaccine against the Bovine Virus Diarrhoea Virus (BVDV). The hypothesis of pathogenic MHC class I molecules in the vaccine had been put up, but no formal proof of specific causal MHC class I alleles has been provided yet. However, the unique features of the vaccine obviously result in extremely high specific antibody titres in the vaccinated animals, but apparently also in further molecules inducing BNP. Thus, a comprehensive picture of the immune response to the vaccine is essential. Applying the novel approach of next generation RNA sequencing (RNAseq), our study provides a new holistic, comprehensive analysis of the blood transcriptome regulation after vaccination with the specific BVDV vaccine. Our RNAseq approach identified a novel cytokine-like gene in the bovine genome that is highly upregulated after vaccination. This gene has never been described before in any other species and might be specific to ruminant immune response. Furthermore, our data revealed a very coordinated immune response to double-stranded (ds) RNA or a dsRNA analogue after vaccination with the inactivated single-stranded (ss) RNA vaccine. This would suggest either a substantial contamination of the vaccine with dsRNA from host cells after virus culture or a dsRNA analogue applied to the vaccine. The first option would highlight the potential risks associated with virus culture on homologous cells during vaccine production; the latter option would emphasise the potential risks associated with immune stimulating adjuvants used in vaccine production.","Amino Acid Sequence;Animals;*Antibodies, Viral/bl [Blood];Cattle;Cattle Diseases/bl [Blood];*Cattle Diseases/im [Immunology];Cattle Diseases/vi [Virology];*Cytokines/ge [Genetics];Cytokines/me [Metabolism];*Diarrhea Virus 1, Bovine Viral/im [Immunology];Female;Gene Expression Profiling/ve [Veterinary];High-Throughput Nucleotide Sequencing/ve [Veterinary];*Immunity, Active;Isoantibodies/bl [Blood];Molecular Sequence Data;Pancytopenia/bl [Blood];Pancytopenia/im [Immunology];*Pancytopenia/ve [Veterinary];Pancytopenia/vi [Virology];Sequence Alignment/ve [Veterinary];Sequence Analysis, RNA/ve [Veterinary];*Up-Regulation;Vaccines, Inactivated/im [Immunology];*Viral Vaccines/im [Immunology];0 (Antibodies, Viral);0 (Cytokines);0 (Isoantibodies);0 (Vaccines, Inactivated);0 (Viral Vaccines)","Demasius, W.;Weikard, R.;Hadlich, F.;Muller, K. E.;Kuhn, C.",2013,Oct 07,,0
473,Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin,"Recent studies show that human skin at homeostasis is a complex ecosystem whose virome include circular DNA viruses, especially papillomaviruses and polyomaviruses. To determine the chicken skin virome in comparison with human skin virome, a chicken swabs pool sample from fifteen indoor healthy chickens of five genetic backgrounds was examined for the presence of DNA viruses by high-throughput sequencing (HTS). The results indicate a predominance of herpesviruses from the Mardivirus genus, coming from either vaccinal origin or presumably asymptomatic infection. Despite the high sensitivity of the HTS method used herein to detect small circular DNA viruses, we did not detect any papillomaviruses, polyomaviruses, or circoviruses, indicating that these viruses may not be resident of the chicken skin. The results suggest that the turkey herpesvirus is a resident of chicken skin in vaccinated chickens. This study indicates major differences between the skin viromes of chickens and humans. The origin of this difference remains to be further studied in relation with skin physiology, environment, or virus population dynamics.",adult;animal tissue;article;Avian leukosis virus;Avian leukosis virus type E;chicken;Circovirus;controlled study;high throughput sequencing;human versus animal comparison;Marek's disease virus 2;nonhuman;open reading frame;Papillomaviridae;polymerase chain reaction;Polyomavirus;priority journal;Reticuloendotheliosis virus;sequence analysis;Turkey herpesvirus;virome;virus detection;virus genome,"Denesvre, C.;Dumarest, M.;Rémy, S.;Gourichon, D.;Eloit, M.",2015,,10.1007/s11262-015-1231-8,1
474,Phylogenetic analysis of classical swine fever virus isolated from Taiwan,"By analyzing the E2 sequences of classical swine fever virus from field outbreaks in Taiwan during 1993-2001, three virus populations with distinct genotypes were determined including one historical (subgroup 3.4) and two exotic (subgroup 2.1) strains. The first subgroup 2.1 virus was isolated in 1994 and further sporadic outbreaks occurred after 1996. Phylogenetic analysis using the E2 region has segregated the Taiwanese strains of 2.1virus into two different genotypes (termed 2.1a and 2.1b). The 2.1b viruses were only isolated in 2001 and shared approximately 94.8% nucleotide identities to the 2.1a viruses in the total genomic sequences. The results suggest that the 2.1a and 2.1b viruses may be introduced from different origins. © 2005 Elsevier B.V. All rights reserved.",RNA;article;controlled study;genomics;genotype;nonhuman;nucleotide sequence;Pestivirus;phylogeny;pig;Taiwan;virus isolation,"Deng, M. C.;Huang, C. C.;Huang, T. S.;Chang, C. Y.;Lin, Y. J.;Chien, M. S.;Jong, M. H.",2005,,10.1016/j.vetmic.2004.12.014,0
475,"Phylogenetic and genetic characterization of a 2017 clinical isolate of H7N9 virus in Guangzhou, China during the fifth epidemic wave","Pathogenic H7N9 influenza viruses continue to pose a public health concern. The H7N9 virus has caused five outbreak waves of human infections in China since 2013. In the present study, a novel H7N9 strain (A/Guangdong/8H324/2017) was isolated from a female patient with severe respiratory illness during the fifth wave of the 2017 H7N9 epidemic. Phylogenetic analysis showed that the H7N9 viruses collected during the fifth wave belong to two different lineages: the Pearl River Delta lineage and the Yangtze River Delta lineage. The novel isolate is closely related to the Pearl River Delta H7N9 viruses, which were isolated from patients in Guangdong Province. The novel H7N9 isolate has an insertion of three basic amino acids in the cleavage site of hemagglutinin (HA), which may enhance virulence in poultry. The 2017 isolate also possesses an R292K substitution in the neuraminidase (NA) protein, which confers oseltamivir resistance. This study highlights the pandemic potential of the novel H7N9 virus in mammals; thus, future characterization and surveillance is warranted.",Influenza virus hemagglutinin;sialidase;viral protein;adult;amino acid substitution;animal;antiviral resistance;avian influenza;China;classification;epidemic;female;genetics;human;influenza;Influenza A virus (H7N9);isolation and purification;pathogenicity;phylogeny;poultry;sequence analysis;virology;virus genome,"Deng, Y.;Li, C.;Han, J.;Wen, Y.;Wang, J.;Hong, W.;Li, X.;Liu, Z.;Ye, Q.;Li, J.;Zhou, C.;Yu, L.;Qin, C.;Zhang, F.;Jiang, T.",2017,,10.1007/s11427-017-9152-1,0
476,High prevalence of bovine viral diarrhea virus 1 in Chinese swine herds,"Nested RT-PCR was used to investigate bovine viral diarrhea virus in 511 specimens collected from Chinese pigs exhibiting clinical symptoms between 2007 and 2010. Of these, 137 samples were BVDV-positive and the BVDV prevalence rate was 23.1% (9/39) in 2007, 27.7% (44/159) in 2008, 33.6% (34/101) in 2009, and 23.6% (50/212) in 2010. Twenty of 137 BVDV-positive samples were used for further genetic analysis of the 5'-UTR. Phylogenetic analysis revealed that they were BVDV-1 and subtyped into BVDV-1a, BVDV-1b, BVDV-1m, BVDV-1o and an unknown subgenotype. This study showed that BVDVs were highly prevalent in Chinese pig herds and appropriate measures should be taken to control BVDV prevalence in pig herds. © 2012 Elsevier B.V.",animal experiment;animal model;article;Bovine viral diarrhea virus 1;bovine viral diarrhea;controlled study;genetic analysis;genotype;nonhuman;nucleotide sequence;phylogeny;prevalence;reverse transcription polymerase chain reaction;pig,"Deng, Y.;Sun, C. Q.;Cao, S. J.;Lin, T.;Yuan, S. S.;Zhang, H. B.;Zhai, S. L.;Huang, L.;Shan, T. L.;Zheng, H.;Wen, X. T.;Tong, G. Z.",2012,,10.1016/j.vetmic.2012.04.023,0
477,Transmission of influenza A(H1N1) 2009 pandemic viruses in Australian swine,"Background Swine have receptors for both human and avian influenza viruses and are a natural host for influenza A viruses. The 2009 influenza A(H1N1) pandemic (H1N1pdm) virus that was derived from avian, human and swine influenza viruses has infected pigs in various countries. Objectives To investigate the relationship between the H1N1pdm viruses isolated from piggery outbreaks in Australia and human samples associated with one of the outbreaks by phylogenetic analysis, and to determine whether there was any reassortment event occurring during the human-pig interspecies transmission. Methods Real-time RT-PCR and full genome sequencing were carried out on RNA isolated from nasal swabs and/or virus cultures. Phylogenetic analysis was performed using the Geneious package. Results The influenza H1N1pdm outbreaks were detected in three pig farms located in three different states in Australia. Further analysis of the Queensland outbreak led to the identification of two distinct virus strains in the pigs. Two staff working in the same piggery were also infected with the same two strains found in the pigs. Full genome sequence analysis on the viruses isolated from pigs and humans did not identify any reassortment of these H1N1pdm viruses with seasonal or avian influenza A viruses. Conclusions This is the first report of swine infected with influenza in Australia and marked the end of the influenza-free era for the Australian swine industry. Although no reassortment was detected in these cases, the ability of these viruses to cross between pigs and humans highlights the importance of monitoring swine for novel influenza infections. © 2012 Blackwell Publishing Ltd.",2009 H1N1 influenza;article;Australia;gene sequence;human;nonhuman;phylogeny;priority journal;reverse transcription polymerase chain reaction;sequence analysis;pig;virus transmission,"Deng, Y. M.;Iannello, P.;Smith, I.;Watson, J.;Barr, I. G.;Daniels, P.;Komadina, N.;Harrower, B.;Wong, F. Y. K.",2012,,10.1111/j.1750-2659.2012.00337.x,0
478,The porcine virome and xenotransplantation,"The composition of the porcine virome includes viruses that infect pig cells, ancient virus-derived elements including endogenous retroviruses inserted in the pig chromosomes, and bacteriophages that infect a broad array of bacteria that inhabit pigs. Viruses infecting pigs, among them viruses also infecting human cells, as well as porcine endogenous retroviruses (PERVs) are of importance when evaluating the virus safety of xenotransplantation. Bacteriophages associated with bacteria mainly in the gut are not relevant in this context. Xenotransplantation using pig cells, tissues or organs is under development in order to alleviate the shortage of human transplants. Here for the first time published data describing the viromes in different pigs and their relevance for the virus safety of xenotransplantation is analysed. In conclusion, the analysis of the porcine virome has resulted in numerous new viruses being described, although their impact on xenotransplantation is unclear. Most importantly, viruses with known or suspected zoonotic potential were often not detected by next generation sequencing, but were revealed by more sensitive methods.",Adenoviridae;Anelloviridae;Astroviridae;Caliciviridae;Circoviridae;Circovirus;Coronaviridae;Cytomegalovirus;Hepatitis E virus;human;metagenomics;next generation sequencing;nonhuman;Parvoviridae;Picornaviridae;pig;Porcine endogenous retrovirus;porcine virome;public health;Reoviridae;review;virus;virus identification;xenotransplantation;zoonosis,"Denner, J.",2017,,10.1186/s12985-017-0836-z,0
479,Identification of novel Ghanaian G8P 6 human-bovine reassortant rotavirus strain by next generation sequencing,"Group A rotaviruses (RVAs) are the most important etiological agent of acute gastroenteritis in children <5 years of age worldwide. The monovalent rotavirus vaccine Rotarix was introduced into the national Expanded Programme on Immunization (EPI) in Ghana in May 2012. However, there is a paucity of genetic and phylogenetic data on the complete genomes of human RVAs in circulation pre-vaccine introduction. The common bovine rotavirus VP7 genotype G8 has been sporadically detected in Ghanaian children, usually in combination with the VP4 genotype P[6]. To investigate the genomic constellations and phylogeny of RVA strains in circulation prior to vaccine introduction, the full genomes of two unusual G8P[6] strains, GH018-08 and GH019-08, detected during burden of disease surveillance, were characterized by Illumina MiSeq sequencing. The Ghanaian isolates, GH018-08 and GH019-08, exhibited the unusual, previously unreported genotype constellation G8-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H3. Phylogenetic analyses confirmed that 10 out of the 11 genes of GH018-08 and GH019-08 were identical/nearly identical, with significant variation detected only in their VP1 genes, and clearly established the occurrence of multiple independent interspecies transmission and reassortment events between co-circulating bovine/ovine/caprine rotaviruses and human DS-1-like RVA strains. These findings highlight the contribution of reassortment and interspecies transmission events to the high rotavirus diversity in this region of Africa, and justify the need for simultaneous monitoring of animal and human rotavirus strains.","Animals;Base Sequence;Capsid Proteins/ge [Genetics];Cattle;Child;Gene Library;Genotype;Ghana;High-Throughput Nucleotide Sequencing;Humans;Molecular Sequence Data;Phylogeny;RNA, Viral/ip [Isolation & Purification];RNA, Viral/me [Metabolism];Reassortant Viruses/cl [Classification];*Reassortant Viruses/ge [Genetics];Reassortant Viruses/ip [Isolation & Purification];Rotavirus/cl [Classification];*Rotavirus/ge [Genetics];Rotavirus/ip [Isolation & Purification];Rotavirus Infections/vi [Virology];Sequence Analysis, DNA;Viral Nonstructural Proteins/ge [Genetics];0 (Capsid Proteins);0 (RNA, Viral);0 (Viral Nonstructural Proteins)","Dennis, F. E.;Fujii, Y.;Haga, K.;Damanka, S.;Lartey, B.;Agbemabiese, C. A.;Ohta, N.;Armah, G. E.;Katayama, K.",2014,,,0
480,Insights into circovirus host range from the genomic fossil record,"A diverse range of DNA sequences derived from circoviruses (family Circoviridae) has been identified in samples obtained from humans and domestic animals, often in association with pathological conditions. In the majority of cases, however, little is known about the natural biology of the viruses from which these sequences are derived. Endogenous circoviral elements (CVe) are DNA sequences derived from circoviruses that occur in animal genomes and provide a useful source of information about circovirushost relationships. In this study, we screened genome assemblies of 675 animal species and identified numerous circovirus-related sequences, including the first examples of CVe derived from cycloviruses. We confirmed the presence of these CVe in the germ line of the elongate twig ant (Pseudomyrmex gracilis), thereby establishing that cycloviruses infect insects. We examined the evolutionary relationships between CVe and contemporary circoviruses, showing that CVe from ants and mites group relatively closely with cycloviruses in phylogenies. Furthermore, the relatively random interspersion of CVe from insect genomes with cyclovirus sequences recovered from vertebrate samples suggested that contamination might be an important consideration in studies reporting these viruses. Our study demonstrates how endogenous viral sequences can inform metagenomics-based virus discovery. In addition, it raises doubts about the role of cycloviruses as pathogens of humans and other vertebrates.",animal cell;animal experiment;article;Circovirus;contamination;fossil;germ line;host range;infectious agent;insect genome;metagenomics;mite;nonhuman;phylogeny;vertebrate,"Dennis, T. P. W.;Flynn, P. J.;de Souza, W. M.;Singer, J. B.;Moreau, C. S.;Wilson, S. J.;Gifford, R. J.",2018,,10.1128/jvi.00145-18,0
481,Deep sequencing of viral genomes provides insight into the evolution and pathogenesis of varicella zoster virus and its vaccine in humans,"Immunization with the vOka vaccine prevents varicella (chickenpox) in children and susceptible adults. The vOka vaccine strain comprises a mixture of genotypes and, despite attenuation, causes rashes in small numbers of recipients. Like wild-type virus, the vaccine establishes latency in neuronal tissue and can later reactivate to cause Herpes zoster (shingles). Using hybridization-based methodologies, we have purified and sequenced vOka directly from skin lesions. We show that alleles present in the vaccine can be recovered from the lesions and demonstrate the presence of a severe bottleneck between inoculation and lesion formation. Genotypes in any one lesion appear to be descended from one to three vaccine-genotypes with a low frequency of novel mutations. No single vOka haplotype and no novel mutations are consistently present in rashes, indicating that neither new mutations nor recombination with wild type are critical to the evolution of vOka rashes. Instead, alleles arising from attenuation (i.e., not derived from free-living virus) are present at lower frequencies in rash genotypes. We identify 11 loci at which the ancestral allele is selected for in vOka rash formation and show genotypes in rashes that have reactivated from latency cannot be distinguished from rashes occurring immediately after inoculation. We conclude that the vOka vaccine, although heterogeneous, has not evolved to form rashes through positive selection in the mode of a quasispecies, but rather alleles that were essentially neutral during the vaccine production have been selected against in the human subjects, allowing us to identify key loci for rash formation.","Alleles;Evolution, Molecular;Exanthema/vi [Virology];*Genome, Viral;Genotype;*Herpesvirus 3, Human/ge [Genetics];*Herpesvirus 3, Human/py [Pathogenicity];High-Throughput Nucleotide Sequencing;Humans;Molecular Sequence Data;Mutation Rate;Phylogeny;Polymorphism, Single Nucleotide;Selection, Genetic;*Skin/vi [Virology];Viral Vaccines/ae [Adverse Effects];*Viral Vaccines/ge [Genetics];0 (Viral Vaccines)","Depledge, D. P.;Kundu, S.;Jensen, N. J.;Gray, E. R.;Jones, M.;Steinberg, S.;Gershon, A.;Kinchington, P. R.;Schmid, D. S.;Balloux, F.;Nichols, R. A.;Breuer, J.",2014,Feb,,0
482,Molecular Aspects of Varicella-Zoster Virus Latency Review,"Primary varicella-zoster virus (VZV) infection causes varicella (chickenpox) and the establishment of a lifelong latent infection in ganglionic neurons. VZV reactivates in about one-third of infected individuals to cause herpes zoster, often accompanied by neurological complications. The restricted host range of VZV and, until recently, a lack of suitable in vitro models have seriously hampered molecular studies of VZV latency. Nevertheless, recent technological advances facilitated a series of exciting studies that resulted in the discovery of a VZV latency-associated transcript (VLT) and provide novel insights into our understanding of VZV latency and factors that may initiate reactivation. Deducing the function(s) of VLT and the molecular mechanisms involved should now be considered a priority to improve our understanding of factors that govern VZV latency and reactivation. In this review, we summarize the implications of recent discoveries in the VZV latency field from both a virus and host perspective and provide a roadmap for future studies.","Adaptive Immunity;Animals;*Chickenpox/vi [Virology];Epigenesis, Genetic;Ganglion Cysts/vi [Virology];Gene Expression Regulation, Viral;Genome, Viral;Genomics/mt [Methods];*Herpesvirus 3, Human/ph [Physiology];High-Throughput Nucleotide Sequencing;Humans;Immediate-Early Proteins/ge [Genetics];Immunity, Innate;Neurons/vi [Virology];Viral Envelope Proteins/ge [Genetics];Virus Activation/ge [Genetics];*Virus Latency/ge [Genetics];0 (Immediate-Early Proteins);0 (Viral Envelope Proteins);0 (immediate early protein 63, Human herpesvirus 3)","Depledge, D. P.;Sadaoka, T.;Ouwendijk, W. J. D.",2018,06 28,,0
483,Deep Sequencing of Distinct Preparations of the Live Attenuated Varicella-Zoster Virus Vaccine Reveals a Conserved Core of Attenuating Single-Nucleotide Polymorphisms,"UNLABELLED: The continued success of the live attenuated varicella-zoster virus vaccine in preventing varicella-zoster and herpes zoster is well documented, as are many of the mutations that contribute to the attenuation of the vOka virus for replication in skin. At least three different preparations of vOka are marketed. Here, we show using deep sequencing of seven batches of vOka vaccine (including ZostaVax, VariVax, VarilRix, and the Oka/Biken working seed) from three different manufacturers (VariVax, GSK, and Biken) that 137 single-nucleotide polymorphism (SNP) mutations are present in all vaccine batches. This includes six sites at which the vaccine allele is fixed or near fixation, which we speculate are likely to be important for attenuation. We also show that despite differences in the vaccine populations between preparations, batch-to-batch variation is minimal, as is the number and frequency of mutations unique to individual batches. This suggests that the vaccine manufacturing processes are not introducing new mutations and that, notwithstanding the mixture of variants present, VZV live vaccines are extremely stable. IMPORTANCE: The continued success of vaccinations to prevent chickenpox and shingles, combined with the extremely low incidence of adverse reactions, indicates the quality of these vaccines. The vaccine itself is comprised of a heterogeneous live attenuated virus population and thus requires deep-sequencing technologies to explore the differences and similarities in the virus populations between different preparations and batches of the vaccines. Our data demonstrate minimal variation between batches, an important safety feature, and provide new insights into the extent of the mutations present in this attenuated virus.","*Chickenpox Vaccine/ge [Genetics];*Herpesvirus 3, Human/ge [Genetics];Herpesvirus 3, Human/py [Pathogenicity];High-Throughput Nucleotide Sequencing;*Polymorphism, Single Nucleotide;Vaccines, Attenuated/ge [Genetics];Virulence;0 (Chickenpox Vaccine);0 (Vaccines, Attenuated)","Depledge, D. P.;Yamanishi, K.;Gomi, Y.;Gershon, A. A.;Breuer, J.",2016,10 01,,0
484,Classification of rotaviruses: Report from the World Health Organization/Food and Agriculture Organization Comparative Virology Program,"The Reoviridae working team was established under the World Health Organization/Food and Agriculture Organization Comparative Virology Program in 1975. The generic name rotavirus has been adopted for the reovirus-like agents associated with diarrhea in man and animals, and the Nebraska calf diarrheal virus strain of bovine rotavirus has been selected as a candidate reference virus. Stocks of this virus and of gnotobiotic calf antiserum have been prepared. Antigenic differences among rotaviruses isolated from different species were recognized on the basis of virus-neutralization tests; a possible association between antigen specificity and variation in the RNA segments and structural proteins of rotaviruses was noticed.",classification;Rotavirus;virus classification,"Derbyshire, J. B.;Woode, G. N.",1978,,,0
485,Isolation of bovine viral diarrhoea viruses from bison,,article;Bovine viral diarrhea virus 1;buffalo;cattle disease;clinical feature;culture medium;Flavivirus;fluorescent antibody technique;gene sequence;nonhuman;Pestivirus;phylogenetic tree;phylogeny;polymerase chain reaction;virus classification;virus culture;virus gene;virus infection;virus isolation,"Deregt, D.;Tessaro, S. V.;Baxi, M. K.;Berezowski, J.;Ellis, J. A.;Wu, J. T. Y.;Gilbert, S. A.",2005,,,0
486,[New classification of enteroviruses of pigs: serological and molecular genetic aspects],"Due to changes in modern classification and nomenclature family Picornaviridae made by the International Committee of Taxonomy of Viruses, conducted genetic and serological reclassification of 36 industrial, typical and laboratory strains porcine enteroviruses isolated in Ukraine. The results of molecular genetic studies of 34 strains assigned to the family Picornaviridae, genus Teschovirus, species Porcine teschovirus, 2 strains of virus did not engage in polymerase chain reaction with species specific primer. In the neutralization reaction of the virus revealed that 23 strains belonging to 1 serotype Porcine teschovirus, 4 strain--PTV-3, 1--to PTV-6, 1 strain--to Porcine sapelovirus, three strains have between typical antigenic properties, and 4 strains--antigenically different from reference strains Porcine teschovirus, Enterovirus G and Porcine sapelovirus.",virus DNA;animal;article;classification;electron microscopy;Enterovirus;genetics;isolation and purification;polymerase chain reaction;prenatal development;serotyping;pig;Ukraine;ultrastructure;virology,"Derev'ianko, S. V.",2014,,,0
487,5'-UTR-based phylogenetic analysis of Classical swine fever virus isolates from India,"Classical swine fever (CSF) caused by Classical swine fever virus (CSFV) is a globally significant disease of pigs. Genetic typing of CSFV isolates can help in understanding the epidemiology of disease and trace down the source of outbreak. 5'-UTR sequence analysis and subsequent genetic classification of nine CSFV field isolates from India indicated that 3 isolates belonged to genotype 2.1 and were closely related to European CSFV strains. The remaining 6 isolates belonged to genotype 1 that contained old and new strains. However, the genotype 2.1 group consisted of recent field isolates only. The study showed circulation of both genotypes 1 and 2.1 in north-eastern part of India.",messenger RNA;virus RNA;5' untranslated region;animal cell;animal tissue;article;classical swine fever;genotype;India;molecular cloning;nonhuman;nucleotide sequence;Pestivirus;phylogeny;reverse transcription polymerase chain reaction;sequence analysis;virus classification;virus strain,"Desai, G. S.;Sharma, A.;Kataria, R. S.;Barman, N. N.;Tiwari, A. K.",2010,,10.4149/av_2010_01_79,0
488,Phylogenetic analysis of Newcastle disease virus isolates occurring in India during 1989–2013,"The study details characterization of Newcastle disease virus (NDV) isolates recovered from commercial poultry flocks (chicken) and wild birds (crane) of India during the time period from 1989 to 2013. Phylogenetic analysis revealed that most of the NDV isolates belongs to class II, genotype XIIIa and a chicken isolate (108/BAREILLY/AD-IVRI/91) was of genotype VI, where it showed diversity of 3 % from the other viruses belonging to same genotype. Another chicken isolate (75/RAMPUR/AD-IVRI/89) grouped in genotype III and showed 4 % diversity with viruses of genotype III. The crane origin NDV identified as of genotype II corresponding to the vaccine virus. This appears to be the first report about existence of genotype XIIIa and its ancestral viruses are circulating in India for the last two decades in different species of birds. Furthermore, genetically distinct viruses belonging to genotypes II, III and VI are also circulating in India.",article;chicken;crane (bird);genetic variability;genotype;herd;India;Newcastle disease;Newcastle disease virus;nonhuman;phylogeny;poultry;virus isolation,"Desingu, P. A.;Singh, S. D.;Dhama, K.;Karthik, K.;Vinodh Kumar, O. R.;Malik, Y. S.",2016,,10.1007/s13337-016-0320-1,0
489,Expression kinetics of the transcript and product of the UL28 homologue of bovine herpesvirus 1,"We report that the bovine herpesvirus 1 (BHV1) UL28 ORF, a homologue of the herpes simplex virus (HSV) UL28 gene, represents a functional gene encoding a viral specific protein. The BHV1 UL28 ORF, located at positions 53 058 → 55 538 of the viral genome, encodes a viral specific transcript of 3.4 kb detected at 6 h post-infection (p.i.) after which its levels accumulated up to 12 h p.i. and then remained constant up to 24 h p.i. Transcription of the BHV1 UL28 was determined to initiate 95 bases upstream from the ORF's initiating codon, which corresponds to 33 nucleotides downstream from a putative TATA box. A BHV1 UL28 specific antiserum, generated against a T7-Tag/UL28 fusion protein expressed in E. coli, specifically reacted with a 100 kDa protein in Western blots of BHV1-infected protein cell lysates. The expression kinetics of the protein was delayed by 6 h relative to that of its transcript suggesting that the gene is regulated at the translational level. In contrast to the HSV and pseudorabies virus UL28 genes, which belong to viral genes of the early (β) class, that of BHV1 was unambiguously classified as a γ2 gene. Further studies will be required to determine whether these kinetic differences have any functional implications. © 2001 Elsevier Science B.V. All rights reserved.",nucleotide;virus antibody;virus fusion protein;viral protein;animal cell;animal model;antigen antibody reaction;article;Bovine herpesvirus 1;cell lysate;controlled study;gene expression regulation;gene location;Herpes simplex virus;kinetics;molecular weight;nonhuman;open reading frame;priority journal;Pseudorabies virus;RNA translation;start codon;TATA box;time;transcription initiation;viral genetics;virus classification;virus detection;virus gene;virus genome;virus infection;virus transcription,"Desloges, N.;Simard, C.",2001,,10.1016/s0168-1702(01)00338-0,0
490,A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds,"Runting-stunting syndrome (RSS) in broiler chickens is an enteric disease that causes significant economic losses to poultry producers worldwide due to elevated feed conversion ratios, decreased body weight during growth, and excessive culling. Of specific interest are the viral agents associated with RSS which have been difficult to fully characterize to date. Past research into the aetiology of RSS has implicated a wide variety of RNA and DNA viruses however, to date, no individual virus has been identified as the main agent of RSS and the current opinion is that it may be caused by a community of viruses, collectively known as the virome. This paper attempts to characterize the viral pathogens associated with 2-3-week-old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Analysis of the viromes identified a total of 20 DNA and RNA viral families, along with 2 unidentified categories, comprised of 31 distinct viral genera and 7 unclassified genera. The most abundant viral families identified in this study were the Astroviridae, Caliciviridae, Picornaviridae, Parvoviridae, Coronaviridae, Siphoviridae, and Myoviridae. This study has identified historically significant viruses associated with the disease such as chicken astrovirus, avian nephritis virus, chicken parvovirus, and chicken calicivirus along with relatively novel viruses such as chicken megrivirus and sicinivirus 1 and will help expand the knowledge related to enteric disease in broiler chickens, provide insights into the viral constituents of a healthy avian gut, and identify a variety of enteric viruses and viral communities appropriate for further study.","virus DNA;virus RNA;animal;Avastrovirus;bird disease;chemistry;chicken;classification;cluster analysis;comparative study;DNA sequence;gene library;genetics;growth disorder;growth, development and aging;high throughput sequencing;metagenomics;Parvoviridae;pathology;veterinary medicine;virology;virus genome","Devaney, R.;Trudgett, J.;Trudgett, A.;Meharg, C.;Smyth, V.",2016,,,1
491,Enrichment of Viral Nucleic Acids by Solution Hybrid Selection with Genus Specific Oligonucleotides,"Despite recent advances, our knowledge of potential and rare human pathogens is far from exhaustive. Current molecular diagnostic tools mainly rely on the specific amplification of marker sequences and may overlook infections caused by unknown and rare pathogens. Using high-throughput sequencing (HTS) can solve this problem; but, due to the extremely low fraction of pathogen genetic material in clinical samples, its application is only cost-effective in special, rather than routine, cases. In this study, we present a method for the semi-specific enrichment of viral conservative sequences in a HTS library by hybridization in solution with genus-specific degenerate biotinylated oligonucleotides. Nucleic acids of the test viruses (yellow fever virus and Japanese encephalitis virus) were enriched by solution hybrid selection using pan-flavivirus oligonucleotides. Moreover, enterovirus (family: Picornaviridae, genus: Enterovirus) sequences were successfully enriched using foot-and-mouth disease virus (family: Picornaviridae, genus: Aphthovirus) oligonucleotide. The enrichment factor relative to the background nucleic acid was about 1,000-fold. As hybridization has less stringent oligonucleotide match requirements than PCR, few oligonucleotides are sufficient to cover the potential sequence variation in the whole genus and may even enrich nucleic acids of viruses of other related genera. Efficient enrichment of viral sequences makes its use in diagnostics cost-efficient.",,"Deviatkin, A. A.;Lukashev, A. N.;Markelov, M. M.;Gmyl, L. V.;Shipulin, G. A.",2017,Aug 29,,0
492,Megaphages infect Prevotella and variants are widespread in gut microbiomes,"Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.",adult;article;baboon;bacteriophage;Bangladesh;biology;cladistics;clustered regularly interspaced short palindromic repeat;controlled study;female;gastrointestinal tract;genetic code;genotype;homologous recombination;human;human experiment;intron;male;metagenome;microbiome;nonhuman;pig;Prevotella;protein expression;sampling;Tanzania;endogenous compound;transfer RNA,"Devoto, A. E.;Santini, J. M.;Olm, M. R.;Anantharaman, K.;Munk, P.;Tung, J.;Archie, E. A.;Turnbaugh, P. J.;Seed, K. D.;Blekhman, R.;Aarestrup, F. M.;Thomas, B. C.;Banfield, J. F.",2019,,10.1038/s41564-018-0338-9,0
493,Molecular and Antigenic Characterization of Piscine orthoreovirus (PRV) from Rainbow Trout (Oncorhynchus mykiss),"Piscine orthoreovirus (PRV-1) causes heart and skeletal muscle inflammation (HSMI) in farmed Atlantic salmon (Salmo salar). Recently, a novel PRV (formerly PRV-Om, here called PRV-3), was found in rainbow trout (Oncorhynchus mykiss) with HSMI-like disease. PRV is considered to be an emerging pathogen in farmed salmonids. In this study, molecular and antigenic characterization of PRV-3 was performed. Erythrocytes are the main target cells for PRV, and blood samples that were collected from experimentally challenged fish were used as source of virus. Virus particles were purified by gradient ultracentrifugation and the complete coding sequences of PRV-3 were obtained by Illumina sequencing. When compared to PRV-1, the nucleotide identity of the coding regions was 80.1%, and the amino acid identities of the predicted PRV-3 proteins varied from 96.7% (lambda1) to 79.1% (sigma3). Phylogenetic analysis showed that PRV-3 belongs to a separate cluster. The region encoding sigma3 were sequenced from PRV-3 isolates collected from rainbow trout in Europe. These sequences clustered together, but were distant from PRV-3 that was isolated from rainbow trout in Norway. Bioinformatic analyses of PRV-3 proteins revealed that predicted secondary structures and functional domains were conserved between PRV-3 and PRV-1. Rabbit antisera raised against purified virus or various recombinant virus proteins from PRV-1 all cross-reacted with PRV-3. Our findings indicate that despite different species preferences of the PRV subtypes, several genetic, antigenic, and structural properties are conserved between PRV-1 and-3.","Amino Acid Sequence;Animals;*Antigens, Viral/ge [Genetics];*Antigens, Viral/im [Immunology];Cross Reactions/im [Immunology];*Fish Diseases/vi [Virology];Genome, Viral;Genomics/mt [Methods];High-Throughput Nucleotide Sequencing;*Oncorhynchus mykiss/vi [Virology];Open Reading Frames;*Orthoreovirus/ge [Genetics];*Orthoreovirus/im [Immunology];Orthoreovirus/ip [Isolation & Purification];Orthoreovirus/ul [Ultrastructure];Phylogeny;RNA, Viral;Serogroup;Virion/ul [Ultrastructure];0 (Antigens, Viral);0 (RNA, Viral)","Dhamotharan, K.;Vendramin, N.;Markussen, T.;Wessel, O.;Cuenca, A.;Nyman, I. B.;Olsen, A. B.;Tengs, T.;Krudtaa Dahle, M.;Rimstad, E.",2018,04 02,,0
494,Recent epidemiology of peste des petits ruminants virus (PPRV),"Peste des petits ruminants (PPR) is an economically important viral disease of goats and sheep first described in west Africa in the 1940s. The virus has been circulating in parts of sub-Saharan Africa for several decades and in the Middle East and southern Asia since 1993, although the first description of the virus in India dates to 1987. To study the genetic relationship between isolates of distinct geographical origin, a selected region of the fusion (F) protein gene of the viruses was amplified using RT/PCR and the resulting DNA product sequenced for phylogenetic analysis. Viruses from 27 outbreaks in Asian and Middle Eastern countries, reported between 1993 and 2000, and two recent outbreaks from the African continent were compared with the prototype African strain. Of the four known lineages of PPR virus, lineage 1 and 2 viruses have been found exclusively in west Africa. Virus from an outbreak in Burkina Faso in 1999 fell into the lineage 1 group. Viruses of lineage 3 have been found in east Africa, where an outbreak in Ethiopia in 1996 was of this type, and also in Arabia and in southern India. However, there have been no further isolations of lineage 3 virus from India since the one reported in 1992 from Tamil Nadu. A virus of this lineage was found circulating in Yemen in 2001. In the past 8 years virus exclusively of the fourth lineage has spread across the Middle East and the Asian sub-continent, reaching east as far as Nepal and Bangladesh. This virus lineage was also reported from Kuwait in 1999. The geographical source of the new lineage 4 virus is unknown although it is most closely related to African lineage 1. The possibility that its earlier presence in northern India was masked by the circulation of Rinderpest virus, a related virus of cattle, is considered unlikely. © 2002 Published by Elsevier Science B.V.",DNA;fusion protein;Africa;article;Asia;Bangladesh;bovine;controlled study;DNA sequence;epidemic;epidemiological data;Ethiopia;gene amplification;genetic analysis;genetic association;geographic distribution;geography;India;Middle East;Nepal;nonhuman;Peste-des-petits-ruminants virus;phylogeny;reverse transcription polymerase chain reaction;virus;virus isolation;virus strain;Yemen,"Dhar, P.;Sreenivasa, B. P.;Barrett, T.;Corteyn, M.;Singh, R. P.;Bandyopadhyay, S. K.",2002,,10.1016/s0378-1135(02)00102-5,0
495,"Genetic characterization of clade 2.3.2.1 avian influenza A(H5N1) viruses, Indonesia, 2012","After reports of unusually high mortality rates among ducks on farms in Java Island, Indonesia, in September 2012, influenza A(H5N1) viruses were detected and characterized. Sequence analyses revealed all genes clustered with contemporary clade 2.3.2.1 viruses, rather than enzootic clade 2.1.3 viruses, indicating the introduction of an exotic H5N1 clade into Indonesia.","Animals;Ducks/vi [Virology];Indonesia;*Influenza A Virus, H5N1 Subtype/ge [Genetics];*Influenza in Birds/vi [Virology];Phylogeny;Poultry Diseases/vi [Virology];Sequence Analysis, DNA/mt [Methods]","Dharmayanti, N. L.;Hartawan, R.;Pudjiatmoko;Wibawa, H.;Hardiman;Balish, A.;Donis, R.;Davis, C. T.;Samaan, G.",2014,Apr,,0
496,Temperate coliphages: classification and correlation with habitats,"Temperate coliphages were recovered from sewage, mammalian feces, and lysogenic strains of Escherichia coli. A total of 32 phages of independent origin were divided into six groups by applying the criteria of host range, antigenic homology, and the ultraviolet inducibility of the prophage. The demonstration of genetic interactions in some cases has confirmed the classification scheme. Nine phages were assigned to the P2 family and 19 to the lambda family. The remaining four isolates may represent some novel phylogenetic types. Phages recovered from the lysogenic strains of E. coli were all found to the P2 related, whereas a majority of the phages recovered as cell-free plaque-forming units were assignable to the lambda family. It is proposed that the biological attributes of the phages belonging to the two principal families are reflected in the distribution patterns observed. The virions of phage HK256 show multiple tail fibers and may thus represent a 'new' virion form among the temperate coliphages.",animal experiment;bacteriophage;classification;ecology;Escherichia coli;in vitro study;taxonomy;temperate bacteriophage;virus classification,"Dhillon, E. K. S.;Dhillon, T. S.;Lam, Y. Y.;Tsang, A. H. C.",1980,,,0
497,Evidence for recombination in neboviruses,"Neboviruses are bovine enteric caliciviruses (genus Nebovirus) associated with enteric diseases in calves. By screening the stools of calves collected from Italian herds using primers targeted to a conserved stretch in calicivirus RNA-dependent RNA-polymerase (RdRp), nebovirus RNA was detected in calves with enteritis (13.1%) but not in overtly health animals. Upon sequence analysis of the RdRp fragment, the Italian viruses formed a tightly conserved group and resembled closely the nebovirus prototype Nebraska/80/US. The sequence of a 2.2. kb ORF1 fragment, spanning the 3' end of the RdRp and the full-length capsid coding region, of two nebovirus strains was determined, revealing marked genetic heterogeneity in the capsid protein, as the two Italian viruses were classified into two distinct capsid lineages, and suggesting a recombination event downstream the highly conserved shell (S) domain. © 2011 Elsevier B.V.",capsid protein;virus RNA;animal tissue;article;Bovine enterovirus;calf (bovine);coding;enteritis;feces;gene sequence;nonhuman;nucleotide sequence;RNA processing;sequence analysis;virus capsid;virus detection;virus strain,"Di Martino, B.;Di Profio, F.;Martella, V.;Ceci, C.;Marsilio, F.",2011,,10.1016/j.vetmic.2011.05.034,0
498,Genome plasticity of triple-reassortant H1N1 influenza A virus during infection of vaccinated pigs,"To gain insight into the evolution of influenza A viruses (IAVs) during infection of vaccinated pigs, we experimentally infected a 3-week-old naive pig with a triple-reassortant H1N1 IAV and placed the seeder pig in direct contact with a group of age-matched vaccinated pigs (n510), We indexed the genetic diversity and evolution of the virus at an intra-host level by deep sequencing the entire genome directly from nasal swabs collected at two separate samplings during infection, We obtained 13 IAV metagenomes from 13 samples, which included the virus inoculum and two samples from each of the six pigs that tested positive for IAV during the study, The infection produced a population of heterogeneous alleles (sequence variants) that was dynamic over time, Overall, 794 polymorphisms were identified amongst all samples, which yielded 327 alleles, 214 of which were unique sequences, A total of 43 distinct haemagglutinin proteins were translated, two of which were observed in multiple pigs, whereas the neuraminidase (NA) was conserved and only one dominant NA was found throughout the study, The genetic diversity of IAVs changed dynamically within and between pigs, However, most of the substitutions observed in the internal gene segments were synonymous, Our results demonstrated remarkable IAV diversity, and the complex, rapid and dynamic evolution of IAV during infection of vaccinated pigs that can only be appreciated with repeated sampling of individual animals and deep sequence analysis.",hemagglutinin;influenza vaccine;sialidase;allele;amino acid sequence;amino acid substitution;animal experiment;animal model;article;controlled study;DNA sequence;enzyme linked immunosorbent assay;experimental pig;gene frequency;genetic polymorphism;genetic reassortment;genetic variability;influenza A (H1N1);Influenza A virus (H1N1);metagenome;next generation sequencing;nonhuman;nose smear;plasticity;priority journal;real time polymerase chain reaction;reverse transcription polymerase chain reaction;sequence analysis;virus genome;flusure,"Diaz, A.;Enomoto, S.;Romagosa, A.;Sreevatsan, S.;Nelson, M.;Culhane, M.;Torremorell, M.",2015,,10.1099/jgv.0.000258,0
499,Molecular characteristics of the Nipah virus glycoproteins,"Nipah virus (NiV) is a highly pathogenic paramyxovirus, which emerged in 1998 from fruit bats in Malaysia and caused an outbreak of severe respiratory disease in pigs and fatal encephalitis in humans with high mortality rates. In contrast to most paramyxoviruses, NiV can infect a large variety of mammalian species. Due to this broad host range, its zoonotic potential, its high pathogenicity for humans, and the lack of effective vaccines or therapeutics, NiV was classified as a biosafety level 4 pathogen. This article provides an overview of the molecular characteristics of NiV focusing on the structure, functions, and unique biological properties of the two NiV surface glycoproteins, the receptor-binding G protein, and the fusion protein F. Since viral glycoproteins are major determinants for cell tropism and virus spread, a detailed knowledge of these proteins can help to understand the molecular basis of viral pathogenicity. © 2007 New York Academy of Sciences.",fusion protein f;guanine nucleotide binding protein;unclassified drug;virus glycoprotein;conference paper;Nipah virus;nonhuman;pathogenicity;protein function;protein glycosylation;protein structure;virus classification;virus genome;virus replication,"Diederich, S.;Maisner, A.",2007,,10.1196/annals.1408.003,0
500,Genetic analysis of avian paramyxovirus-1 (Newcastle disease virus) isolates obtained from swine populations in China related to commonly utilized commercial vaccine strains,"Newcastle disease virus (NDV) has been thought to only infect avian species. However, at least eight NDV strains were isolated from swine populations in China during 1999-2006, four of which were characterized genetically and phylogenetically. Genetic analysis revealed that JL106 and SP13 had a 112G-R-Q-G-R-L117 motif at the cleavage site of F protein, while JL01 and MP01 possessed a 112G-K-Q-G-R-L117 motif, which indicated that all of them were typical of low-virulence viruses. Phylogenetic analysis based on the full-length F gene sequences showed that JL106 and SP13 belonged to genotype II, similar to the commonly utilized commercial La Sota vaccine strain in China. While JL01 and MP01 clustered within genotype I, genetically identical to the V4 vaccine strain. The animal trials showed that JL106 can effectively infect chickens. The present results indicated that the use of live La Sota and V4 vaccines and close contact between avian and pigs maybe resulted in cross-species infection, therefore, it is necessary to further carry out swine NDV epidemiology surveillance. © 2010 Springer Science+Business Media, LLC.",F protein;HN protein;La Sota virus strain vaccine;unclassified drug;viral protein;virus vaccine;amino acid substitution;animal experiment;animal tissue;antigen detection;antigenicity;article;binding site;brain tissue;China;controlled study;cross infection;gene sequence;genetic analysis;genetic variability;genotype;immunohistochemistry;lung parenchyma;Newcastle disease;Newcastle disease virus;nonhuman;nucleic acid base substitution;nucleotide sequence;phylogenetic tree;phylogeny;priority journal;protein cleavage;protein motif;protein structure;receptor binding;sequence homology;spleen;strain difference;pig;synovial bursa;virus characterization;virus gene;virus isolation;virus strain;virus virulence,"Ding, Z.;Cong, Y. L.;Chang, S.;Wang, G. M.;Wang, Z.;Zhang, Q. P.;Wu, H.;Sun, Y. Z.",2010,,10.1007/s11262-010-0516-1,0
501,Modulation of microRNAs in two genetically disparate chicken lines showing different necrotic enteritis disease susceptibility,"MicroRNAs (miRNA) play a critical role in post-transcriptional regulation by influencing the 3'-UTR of target genes. Using two inbred White Leghorn chicken lines, line 6.3 and line 7.2 showing Marek's disease-resistant and -susceptible phenotypes, respectively, we used small RNA high-throughput sequencing (HTS) to investigate whether miRNAs are differently expressed in these two chicken lines after inducing necrotic enteritis (NE). The 12 miRNAs, selected from the most down-regulated or up-regulated miRNAs following NE induction, were confirmed by their expressions in real-time PCR. Among these miRNAs, miR-215, miR-217, miR-194, miR-200a, miR-200b, miR-216a, miR-216b, and miR-429 were highly expressed in intestine derived from line 7.2, whereas, miR-1782 and miR-499 were down-regulated. In spleen, miR-34b and miR-1684 were the most up-regulated miRNAs in line 6.3. Notably, five out of six target genes, CXCR5, BCL2, GJA1, TCF12, and TAB3 were differentially expressed between line 6.3 and line 7.2, and showed suppression in the MD-susceptible chicken line. Their expression levels were conversely correlated with those of miRNA obtained from both HTS and quantitative real-time PCR.These results suggest that some miRNAs are differentially altered in response to NE and they modulate the expression of their target genes in the two inbred lines. Collectively, HTS analysis of intestinal miRNAs from NE-afflicted inbred chickens showing different disease phenotypes led to the identification of host immunity genes regulated by miRNA. Future studies of the function of these miRNAs and their target genes in the host will lead to enhanced understanding of molecular mechanisms controlling host-pathogen interaction in NE. © 2014 Elsevier B.V.",microRNA;RNA;transcriptome;animal experiment;animal model;article;chicken;Clostridium perfringens;disease predisposition;Eimeria;gene expression;high throughput sequencing;Marek disease;necrotizing enteritis;nonhuman;nucleotide sequence;phenotype;reverse transcription polymerase chain reaction;RNA sequence;small intestine mucosa;spleen,"Dinh, H.;Hong, Y. H.;Lillehoj, H. S.",2014,,10.1016/j.vetimm.2014.02.003,0
502,Studies on Myxovirus Yucaipa: Its Classification as a Member of the Paramyxovirus Group,,"Animals;*Antigens;Cattle;*Classification;*DNA;*DNA, Viral;*Electrons;*Fluorescent Antibody Technique;*Haplorhini;*Hemagglutination;*Hemagglutination Inhibition Tests;*Hemagglutination Tests;*Hemolysin Proteins;*Hydroxylamines;*Immune Sera;*Kidney;*Microscopy;*Microscopy, Electron;*Newcastle Disease;*Orthomyxoviridae;*Orthomyxoviridae Infections;*Poultry;*rna;*RNA, Viral;*Research;*Respiratory Tract Infections;*Tissue Culture Techniques;*Trypsin;*Virus Cultivation;0 (Antigens);0 (DNA, Viral);0 (Hemolysin Proteins);0 (Hydroxylamines);0 (Immune Sera);0 (RNA, Viral);63231-63-0 (rna);9007-49-2 (DNA)","Dinter, Z.;Hermodsson, S.;Hermodsson, L.",1964,Mar,,0
503,The Properties and Classification of Bovine Viral Diarrhea Virus,"Examination of the C24V (Oregon) and MAC A (Ontario) strains of bovine viral diarrhea viruses have shown them to be ribonucleic acid containing viruses, with essential lipid and having compound helical symmetry with the diameter of the helix being in the neighbourhood of 180 A. Because of these properties it is suggested that the virus should be considered a member of the Myxovirus group. Hog cholera virus is related to bovine viral diarrhea virus by means of a ""soluble"" antigen, and also possesses essential lipid. It is therefore suggested that hog cholera virus represents still another veterinary myxovirus.",,"Ditchfield, J.;Doane, F. W.",1964,Jun,,0
504,Metagenomic analysis of RNA viruses in a fresh water lake,"Freshwater lakes and ponds present an ecological interface between humans and a variety of host organisms. They are a habitat for the larval stage of many insects and may serve as a medium for intraspecies and interspecies transmission of viruses such as avian influenza A virus. Furthermore, freshwater bodies are already known repositories for disease-causing viruses such as Norwalk Virus, Coxsackievirus, Echovirus, and Adenovirus. While RNA virus populations have been studied in marine environments, to this date there has been very limited analysis of the viral community in freshwater. Here we present a survey of RNA viruses in Lake Needwood, a freshwater lake in Maryland, USA. Our results indicate that just as in studies of other aquatic environments, the majority of nucleic acid sequences recovered did not show any significant similarity to known sequences. The remaining sequences are mainly from viral types with significant similarity to approximately 30 viral families. We speculate that these novel viruses may infect a variety of hosts including plants, insects, fish, domestic animals and humans. Among these viruses we have discovered a previously unknown dsRNA virus closely related to Banna Virus which is responsible for a febrile illness and is endemic to Southeast Asia. Moreover we found multiple viral sequences distantly related to Israeli Acute Paralysis virus which has been implicated in honeybee colony collapse disorder. Our data suggests that due to their direct contact with humans, domestic and wild animals, freshwater ecosystems might serve as repositories of a wide range of viruses (both pathogenic and non-pathogenic) and possibly be involved in the spread of emerging and pandemic diseases. © 2009 Djikeng et al.",article;controlled study;endemic disease;fever;honeybee;lake ecosystem;metagenomics;nonhuman;nucleotide sequence;RNA virus;United States;viral genetics;virus cell interaction;virus identification;virus infectivity;virus transmission,"Djikeng, A.;Kuzmickas, R.;Anderson, N. G.;Spiro, D. J.",2009,,10.1371/journal.pone.0007264,0
505,Genetic analysis of human rotavirus C: The appearance of Indian-Bangladeshi strain in Far East Asian countries,"Rotaviruses C (RVCs) circulate worldwide as an enteric pathogen in both humans and animals. Most studies of their genetic diversity focus on the VP7 and VP4 genes, but the complete genomes of 18 human RVCs have been described in independent studies. The genetic background of the Far East Asian RVCs is different than other human RVCs that were found in India and Bangladesh. Recently, a RVC detected in 2010 in South Korea had genetic background similar to the Indian-Bangladeshi RVCs. This study was undertaken to determine the whole genome of eight Japanese RVCs detected in 2005-2012, and to compare them with other human and animal global RVCs to better understand the genetic background of contemporary Far East Asian RVC. By phylogenetic analysis, the human RVCs appeared to be distinct from animal RVCs. Among human RVCs, three lineage constellations had prolonged circulation. The genetic background of the Far East Asian RVC was distinguished from Indian-Bangladeshi RVC as reported earlier. However, we found one Japanese RVC in 2012 that carried the genetic background of Indian-Bangladeshi RVC, whereas the remaining seven Japanese RVCs carried the typical genetic background of Far East Asian RVC. This is the first report of the Indian-Bangladeshi RVC in Japan. With that observation and the reassortment event of human RVCs in Hungary, our study indicates that the RVCs are spreading from one region to another.","Animals;Capsid Proteins/ge [Genetics];Cattle;Dogs;Europe, Eastern/ep [Epidemiology];Far East/ep [Epidemiology];Gene Library;Genetic Variation;*Genome, Viral;Genotype;High-Throughput Nucleotide Sequencing;Humans;*Phylogeny;*RNA, Viral/ge [Genetics];Rotavirus/cl [Classification];*Rotavirus/ge [Genetics];Rotavirus/ip [Isolation & Purification];*Rotavirus Infections/ep [Epidemiology];Rotavirus Infections/tm [Transmission];Rotavirus Infections/vi [Virology];Swine/vi [Virology];*Swine Diseases/ep [Epidemiology];Swine Diseases/tm [Transmission];Swine Diseases/vi [Virology];Viral Nonstructural Proteins/ge [Genetics];0 (Capsid Proteins);0 (RNA, Viral);0 (Viral Nonstructural Proteins)","Doan, Y. H.;Haga, K.;Fujimoto, A.;Fujii, Y.;Takai-Todaka, R.;Oka, T.;Kimura, H.;Yoshizumi, S.;Shigemoto, N.;Okamoto-Nakagawa, R.;Shirabe, K.;Shinomiya, H.;Sakon, N.;Katayama, K.",2016,07,,0
506,"Zoonotic hepatitis E virus: Classification, animal reservoirs and transmission routes",,,"Doceul, V.;Bagdassarian, E.;Demange, A.;Pavio, N.",2016,,,0
507,Sequence analysis of a porcine enterovirus serotype 1 isolate: Relationships with other picornaviruses,The majority of the genomic sequence of a porcine enterovirus serotype 1 (PEV-1) isolate was determined. The genome was found to contain a large open reading frame which encoded a leader protein prior to the capsid protein region. This showed no sequence identity to other picornavirus leader regions and the sequence data suggested that it does not possess proteolytic activity. The 2A protease was small and showed considerable sequence identity to the aphthoviruses and to equine rhinovirus serotype 2. The 2A/2B junction possessed the typical cleavage site (NPG/P) exhibited by these viruses. The other proteins shared less than 40% sequence identity with equivalent proteins from other picornavirus genera. Phylogenetic analyses of the P1 and 3D sequences indicated that this virus forms a distinct branch of the family Picornaviridae. On the basis of results presented in this paper PEV-1 has been assigned to a new picornavirus genus. The phylogeny of the virus in relation to other picornaviruses is discussed.,proteinase;virus enzyme;Aphthovirus;article;Enterovirus;nucleotide sequence;open reading frame;phylogeny;Picornaviridae;priority journal;Rhinovirus;sequence analysis;sequence homology;virus genome,"Doherty, M.;Todd, D.;McFerran, N.;Hoey, E. M.",1999,,,0
508,Functional characterization of a monoclonal antibody epitope using a lambda phage display-deep sequencing platform,"We have recently described a method, named PROFILER, for the identification of antigenic regions preferentially targeted by polyclonal antibody responses after vaccination. To test the ability of the technique to provide insights into the functional properties of monoclonal antibody (mAb) epitopes, we used here a well-characterized epitope of meningococcal factor H binding protein (fHbp), which is recognized by mAb 12C1. An fHbp library, engineered on a lambda phage vector enabling surface expression of polypeptides of widely different length, was subjected to massive parallel sequencing of the phage inserts after affinity selection with the 12C1 mAb. We detected dozens of unique antibody-selected sequences, the most enriched of which (designated as FrC) could largely recapitulate the ability of fHbp to bind mAb 12C1. Computational analysis of the cumulative enrichment of single amino acids in the antibody-selected fragments identified two overrepresented stretches of residues (H248-K254 and S140-G154), whose presence was subsequently found to be required for binding of FrC to mAb 12C1. Collectively, these results suggest that the PROFILER technology can rapidly and reliably identify, in the context of complex conformational epitopes, discrete ""hot spots"" with a crucial role in antigen-antibody interactions, thereby providing useful clues for the functional characterization of the epitope.",epitope;monoclonal antibody;animal;chemistry;Enterobacteria phage lambda;genetics;high throughput sequencing;mouse;peptide library,"Domina, M.;Lanza Cariccio, V.;Benfatto, S.;Venza, M.;Venza, I.;Borgogni, E.;Castellino, F.;Midiri, A.;Galbo, R.;Romeo, L.;Biondo, C.;Masignani, V.;Teti, G.;Felici, F.;Beninati, C.",2016,,10.1038/srep31458,0
509,The broad host range and genetic diversity of mammalian and avian astroviruses,"Astroviruses are a diverse family of viruses that infect a wide range of mammalian and avian hosts. Here we describe the phylogenetic diversity and current classification methodology of astroviruses based on the ORF1b and ORF2 genes, highlighting the propensity of astroviruses to undergo interspecies transmission and genetic recombination which greatly increase diversity and complicate attempts at a unified and comprehensive classification strategy.",RNA directed RNA polymerase;Astroviridae;astrovirus infection;autoimmune disease;avian colibacillosis;Avian nephritis virus;bird;classification;disease transmission;duck;gastrointestinal disease;genetic recombination;genetic variability;host range;human;Mamastrovirus;mammal;maximum likelihood method;metagenomics;next generation sequencing;nonhuman;phylogeny;prevalence;review,"Donato, C.;Vijaykrishna, D.",2017,,10.3390/v9050102,0
510,"Identification of Peste des Petits Ruminants Virus, Georgia, 2016",A phylogenetic analysis of samples taken from reported outbreaks of peste des petits ruminants virus (PPRV) in Georgia revealed a closer relationship to viruses from northern and eastern Africa than to viruses from countries closer to Georgia. This finding has crucial implications for the control of PPRV in the region.,,"Donduashvili, M.;Goginashvili, K.;Toklikishvili, N.;Tigilauri, T.;Gelashvili, L.;Avaliani, L.;Khartskhia, N.;Loitsch, A.;Bataille, A.;Libeau, G.;Diallo, A.;Dundon, W. G.",2018,08,,0
511,Detecting transmission and reassortment events for influenza A viruses with genotype profile method,"Evolutionary events of transmission and reassortment for influenza A viruses were traditionally detected by phylogenetic analysis for influenza viruses' eight gene segments. Because the phylogenetic analysis can be complex, we developed genotype profile method which packaged the phylogenetic algorithms to analyze combination patterns of gene segments and integrated epidemiology knowledge. With the method, the analysis of reassortment and transmission becomes a simple and reliable process that combines genotypes, which is identical for the biological process of the virus. An application called IVEE that implements the method is available for all academic users to apply the method http://snptransformer.sourceforge.net. Furthermore, we found that a previous summary of the reassortment events in swine influenza A viruses may be inaccurate. © 2011 Dong et al; licensee BioMed Central Ltd.",article;avian influenza virus;cell lineage;fowl;genetic reassortment;genotype;human;Influenza virus;Influenza A virus;nonhuman;pig;swine influenza virus;virus strain;virus transmission,"Dong, C.;Ying, L.;Yuan, D.",2011,,10.1186/1743-422x-8-395,0
512,Phylogenetic diversity and genotypical complexity of H9N2 influenza A viruses revealed by genomic sequence analysis,"H9N2 influenza A viruses have become established worldwide in terrestrial poultry and wild birds, and are occasionally transmitted to mammals including humans and pigs. To comprehensively elucidate the genetic and evolutionary characteristics of H9N2 influenza viruses, we performed a large-scale sequence analysis of 571 viral genomes from the NCBI Influenza Virus Resource Database, representing the spectrum of H9N2 influenza viruses isolated from 1966 to 2009. Our study provides a panoramic framework for better understanding the genesis and evolution of H9N2 influenza viruses, and for describing the history of H9N2 viruses circulating in diverse hosts. Panorama phylogenetic analysis of the eight viral gene segments revealed the complexity and diversity of H9N2 influenza viruses. The 571 H9N2 viral genomes were classified into 74 separate lineages, which had marked host and geographical differences in phylogeny. Panorama genotypical analysis also revealed that H9N2 viruses include at least 98 genotypes, which were further divided according to their HA lineages into seven series (A-G). Phylogenetic analysis of the internal genes showed that H9N2 viruses are closely related to H3, H4, H5, H7, H10, and H14 subtype influenza viruses. Our results indicate that H9N2 viruses have undergone extensive reassortments to generate multiple reassortants and genotypes, suggesting that the continued circulation of multiple genotypical H9N2 viruses throughout the world in diverse hosts has the potential to cause future influenza outbreaks in poultry and epidemics in humans. We propose a nomenclature system for identifying and unifying all lineages and genotypes of H9N2 influenza viruses in order to facilitate international communication on the evolution, ecology and epidemiology of H9N2 influenza viruses. © 2011 Dong et al.",Influenza virus hemagglutinin;article;controlled study;genetic reassortment;genetic variability;genome analysis;genotype;geographic distribution;Influenza A virus;Influenza virus A H10N2;Influenza virus A H14N2;Influenza A virus (H3N2);Influenza virus A H4N2;Influenza A virus (H5N2);Influenza A virus (H7N2);Influenza A virus (H9N2);molecular evolution;molecular phylogeny;nonhuman;sequence analysis;sequence database;virus cell interaction;virus gene;virus genome;virus isolation;virus nomenclature,"Dong, G.;Luo, J.;Zhang, H.;Wang, C.;Duan, M.;Deliberto, T. J.;Nolte, D. L.;Ji, G.;He, H.",2011,,10.1371/journal.pone.0017212,0
513,Reassortant H9N2 influenza viruses containing H5N1-like PB1 genes isolated from black-billed magpies in Southern China,"H9N2 influenza A viruses have become endemic in different types of terrestrial poultry and wild birds in Asia, and are occasionally transmitted to humans and pigs. To evaluate the role of black-billed magpies (Pica pica) in the evolution of influenza A virus, we conducted two epidemic surveys on avian influenza viruses in wild black-billed magpies in Guangxi, China in 2005 and characterized three isolated black-billed magpie H9N2 viruses (BbM viruses). Phylogenetic analysis indicated that three BbM viruses were almost identical with 99.7 to 100% nucleotide homology in their whole genomes, and were reassortants containing BJ94-like (Ck/BJ/1/94) HA, NA, M, and NS genes, SH/F/98-like (Ck/SH/F/98) PB2, PA, and NP genes, and H5N1-like (Ck/YN/1252/03, clade 1) PB1 genes. Genetic analysis showed that BbM viruses were most likely the result of multiple reassortments between co-circulating H9N2-like and H5N1-like viruses, and were genetically different from other H9N2 viruses because of the existence of H5N1-like PB1 genes. Genotypical analysis revealed that BbM viruses evolved from diverse sources and belonged to a novel genotype (B46) discovered in our recent study. Molecular analysis suggested that BbM viruses were likely low pathogenic reassortants. However, results of our pathogenicity study demonstrated that BbM viruses replicated efficiently in chickens and a mammalian mouse model but were not lethal for infected chickens and mice. Antigenic analysis showed that BbM viruses were antigenic heterologous with the H9N2 vaccine strain. Our study is probably the first report to document and characterize H9N2 influenza viruses isolated from black-billed magpies in southern China. Our results suggest that black-billed magpies were susceptible to H9N2 influenza viruses, which raise concerns over possible transmissions of reassortant H9N2 viruses among poultry and wild birds. © 2011 Dong et al.",influenza vaccine;animal experiment;animal model;animal tissue;antigenicity;article;bird;black billed magpie;China;controlled study;embryo;genetic analysis;genetic difference;genetic reassortment;genotype;influenza A;Influenza A virus (H5N1);Influenza A virus (H9N2);molecular evolution;molecular genetics;mouse;nonhuman;nucleotide sequence;PB1 gene;phylogeny;sequence homology;virus gene;virus replication;virus virulence,"Dong, G.;Xu, C.;Wang, C.;Wu, B.;Luo, J.;Zhang, H.;Nolte, D. L.;Deliberto, T. J.;Duan, M.;Ji, G.;He, H.",2011,,10.1371/journal.pone.0025808,0
514,"Characteristics of influenza H13N8 subtype virus firstly isolated from Qinghai Lake Region, China","Background: Since the highly pathogenic H5N1 influenza caused thousands of deaths of wild bird in this area in 2005, Qinghai Lake in China has become a hot spot for study of the influence of avian influenza to migratory wild birds. However, the ecology and evolution of low pathogenic avian influenza virus in this region are limited. This project-based avian influenza surveillance in Qinghai lake region was initiated in year 2012. Method: Samples of wild bird feces and lake surface water were collected in Qinghai Lake in year 2012.Virus isolation was conducted on embryonated chicken eggs. The influenza A virus was determined by rRT-PCR. Virus sequences were acquired by deep sequencing. The phylogenetic correlation and molecular characteristics of the viruses were analyzed. The virus growth and infection features, receptor binding preference were studied, and pathogenicity in vitro as well as. Results: Two H13N8 subtype influenza viruses were isolated. The viruses are phylogenetically belong to Eurasian lineage. Most of the genes are associated with gull origin influenza virus except PB1 gene, which is most probably derived from Anseriformes virus. The evidence of interspecies reassortment was presented. The two viruses have limited growth capacity on MDCK and A549 cells while grow well in embryonated eggs. The dual receptor binding features of the two viruses was shown up. The low pathogenic features were determined by trypsin dependence plaque formation assay. Conclusions: The two H13N8 subtype influenza viruses are highly associated with gull origin. The interspecies reassortment of H13 subtype virus among Anseriforme sand Charadriiformes wild birds emphasizes the importance of strengthening avian influenza surveillance in this region. This study is helpful to understand the ecology, evolution and transmission pattern of H13 subtype influenza virus globally.",A-549 cell line;animal cell;article;avian influenza virus;avian influenza virus H12N8;Charadriiformes;China;genetic reassortment;human;human cell;MDCK cell line;nonhuman;phylogenetic tree;receptor binding;reverse transcription polymerase chain reaction;virogenesis;virus isolation;virus titration;virus virulence,"Dong, J.;Bo, H.;Zhang, Y.;Dong, L.;Zou, S.;Huang, W.;Liu, J.;Wang, D.;Shu, Y.",2017,,10.1186/s12985-017-0842-1,0
515,Polymorphisms affecting the gE and gI proteins partly contribute to the virulence of a newly-emergent highly virulent Chinese pseudorabies virus,"An outbreak of a highly virulent pseudorabies virus strain, ZJ01, occurred in PRV-vaccinated pigs in China in 2011. In this study, ZJ01 caused fatal diseases, while the Chinese prototypic PRV strain LA caused mild respiratory disorders. Full-genome sequencing results indicate the two viruses can be classified into two sub-clusters that distinct from traditional European and US strains. To examine the potential role of the gE and gI proteins in ZJ01 virulence, we generated several recombinant viruses. In two chimeric viruses (rZJ01-LA/gEI and rLA-ZJ01/gEI), the gE and gI genes were swapped using corresponding genes from ZJ01 and LA. rZJ01-LA/gEI and the parental virus rZJ01 retained high virulence in piglets, although the survival time for rZJ01-LA/gEI infected piglets was obviously prolonged. In contrast, rLA-ZJ01/gEI exhibited higher virulence than its parental virus rLA. We conclude that changes in gE and gI proteins partly contribute to the enhanced virulence of ZJ01 strain.",gE protein;gI proteins;unclassified drug;viral protein;animal tissue;article;China;controlled study;disease severity;European;female;gE gene;gI gene;male;nonhuman;piglet;priority journal;protein assembly;protein polymorphism;Pseudorabies virus;respiratory tract disease;survival time;United States;virogenesis;virus gene;virus genome;virus recombinant;virus strain;virus virulence;whole genome sequencing,"Dong, J.;Gu, Z.;Jin, L.;Lv, L.;Wang, J.;Sun, T.;Bai, J.;Sun, H.;Wang, X.;Jiang, P.",2018,,10.1016/j.virol.2018.03.024,0
516,A new recombined porcine reproductive and respiratory syndrome virus virulent strain in China,"Porcine reproductive and respiratory syndrome (PRRS) is one of the most important swine diseases worldwide. In the present study, a new virulent strain of PRRS virus (PRRSV), GDsg, was isolated in Guangdong province, China, and caused high fever, high morbidity, and high mortality in sows and piglets. The genome of this new strain was 15,413 nucleotides (nt) long, and comparative analysis revealed that GDsg shared 82.4% to 94% identity with type 2 PRRSV strains, but only 61.5% identity with type 1 PRRSV Lelystad virus strain. Phylogenetic analysis indicated that type 2 PRRSV isolates include five subgenotypes (I, II, III, IV, and V), which are represented by NADC30, VR-2332, GM2, CH-1a, and HuN4, respectively. Moreover, GDsg belongs to a newly emerging type 2 PRRSV subgenotype III. More interestingly, the newly isolated GDsg strain has multiple discontinuous nt deletions, 131 (19 + 18 + 94) at position 1404-1540 and a 107 nt insertion in the NSP2 region. Most importantly, the GDsg strain was identified as a virus recombined between low pathogenic field strain QYYZ and vaccine strain JXA1-P80. In conclusion, a new independent subgenotype and recombinant PRRSV strain has emerged in China and could be a new threat to the swine industry of China.",amino acid sequence;animal;China;genetics;genotype;nucleotide sequence;phylogeny;pig;porcine reproductive and respiratory syndrome;Porcine reproductive and respiratory syndrome virus;sequence alignment;veterinary medicine;virology,"Dong, J. G.;Yu, L. Y.;Wang, P. P.;Zhang, L. Y.;Liu, Y. L.;Liang, P. S.;Song, C. X.",2018,,10.4142/jvs.2018.19.1.89,0
517,Dynamic co-evolution and interaction of avian leukosis virus genetic variants and host immune responses,"Subgroup J avian leukosis virus (ALV-J), a typical retrovirus, is characterized of existence of a cloud of diverse variants and considerable genetic diversity. Previous studies describing the evolutionary dynamics of ALV-J genetic variants mainly focused on the early infection period or few randomly selected clones. Here, we inoculated 30 specific-pathogen-free chickens with the same founder ALV-J stock of known genetic background. Six (three antibody positive and three antibody negative) chickens were selected among 15 chickens with viremia. Viruses were serially isolated in 36 weeks and then sequenced using MiSeq high-throughput sequencing platform. This produced the largest ALV-J dataset to date, composed of more than three million clean reads. Our results showed that host humoral immunity could greatly enhance the genetic diversity of ALV-J genetic variants. In particular, selection pressures promoted a dynamic proportional changes in ALV-J genetic variants frequency. Cross-neutralization experiment showed that along with the change of the dominant variant, the antibody titers specific to infectious clones corresponding to the most dominant variants in weeks 12 and 28 have also changed significantly in sera collected in weeks 16 and 32. In contrast, no shift of dominant variant was observed in antibody-negative chickens. Moreover, we identified a novel hypervariable region in the gp85 gene. Our study reveals the interaction between ALV-J and the host, which could facilitate the development of vaccines and antiviral drugs.",virus antibody;antibody titer;article;Avian leukosis virus;blood sampling;coevolution;controlled study;entropy;gene sequence;genetic variability;high throughput sequencing;ID50 (median infectious dose);immune response;molecular cloning;nonhuman;nucleotide sequence;polymerase chain reaction;sequence analysis;virus isolation;virus neutralization,"Dong, X.;Meng, F.;Hu, T.;Ju, S.;Li, Y.;Sun, P.;Wang, Y.;Chen, W.;Zhang, F.;Su, H.;Li, S.;Cui, H.;Chen, J.;Xu, S.;Fang, L.;Luan, H.;Zhang, Z.;Chang, S.;Li, J.;Wang, L.;Zhao, P.;Shi, W.;Cui, Z.",2017,,10.3389/fmicb.2017.01168,0
518,"First report of Porcine teschovirus (PTV), Porcine sapelovirus (PSV) and Enterovirus G (EV-G) in pig herds of Brazil",,,"Donin, D. G.;Leme, R. de Arruda;Alfieri, A. F.",2014,,,0
519,Phylogenetic analysis of rotavirus A NSP2 gene sequences and evidence of intragenic recombination,"The rotavirus non-structural protein NSP2 is one of the earliest and most abundant viral proteins produced during infection. This protein has multiple essential roles in the replication cycle involving RNA binding, viroplasm formation, helicase and can hydrolyse the γ-phosphate of RNA and NTPs acting as an RTPase and NTPase. In studying sequences from rotavirus strains isolated in Australia between 1984 and 2009, the NSP2 gene was seen to be highly conserved and clustered with defined NSP2 genotypes N1 and N2 according to the full genome based rotavirus classification system. Phylogenetic analysis indicated that NSP2 gene sequences isolated from Australian rotavirus strains formed four distinct lineages. Temporal variation was observed in several clusters during the 26 year period, with lineage D identified throughout the entire study period and lineage A only detected since 1999. Phylogenetic analysis and dendrograms identified NSP2 genes that exhibited reassortment between different virus VP7 genotypes, as well as a sequence from a human strain that grouped closely with the NSP2 genes of bovine rotavirus strains. This study also identified a sequence that fell between lineages and exhibited evidence of recombination, the first time that intergenic recombination has been detected in a NSP2 gene sequence. This study increases the understanding of the evolution mechanisms of NSP2 in view of improved vaccine design. © 2011 Elsevier B.V.",nonstructural protein 2;RNA helicase;article;controlled study;gene sequence;genetic reassortment;genetic recombination;genotype;hydrolysis;molecular evolution;nonhuman;NSP2 gene;nucleotide sequence;phylogeny;priority journal;protein function;protein RNA binding;RNA replication;Rotavirus;virus classification;virus gene,"Donker, N. C.;Boniface, K.;Kirkwood, C. D.",2011,,10.1016/j.meegid.2011.05.024,0
520,Identification of fungi in shotgun metagenomics datasets,"Metagenomics uses nucleic acid sequencing to characterize species diversity in different niches such as environmental biomes or the human microbiome. Most studies have used 16S rRNA amplicon sequencing to identify bacteria. However, the decreasing cost of sequencing has resulted in a gradual shift away from amplicon analyses and towards shotgun metagenomic sequencing. Shotgun metagenomic data can be used to identify a wide range of species, but have rarely been applied to fungal identification. Here, we develop a sequence classification pipeline, FindFungi, and use it to identify fungal sequences in public metagenome datasets. We focus primarily on animal metagenomes, especially those from pig and mouse microbiomes. We identified fungi in 39 of 70 datasets comprising 71 fungal species. At least 11 pathogenic species with zoonotic potential were identified, including Candida tropicalis. We identified Pseudogymnoascus species from 13 Antarctic soil samples initially analyzed for the presence of bacteria capable of degrading diesel oil. We also show that Candida tropicalis and Candida loboi are likely the same species. In addition, we identify several examples where contaminating DNA was erroneously included in fungal genome assemblies.","Animals;Antarctic Regions;Ascomycota/cl [Classification];Ascomycota/ge [Genetics];Ascomycota/ip [Isolation & Purification];Candida tropicalis/ge [Genetics];Candida tropicalis/py [Pathogenicity];Databases, Genetic;Fungi/cl [Classification];*Fungi/ge [Genetics];Fungi/py [Pathogenicity];Humans;Metagenome;*Metagenomics;Mice;Microbiota/ge [Genetics];Phylogeny;Soil Microbiology;Swine;Zoonoses/mi [Microbiology]","Donovan, P. D.;Gonzalez, G.;Higgins, D. G.;Butler, G.;Ito, K.",2018,,,0
521,The art of culture: Developing cell lines,,telomerase reverse transcriptase;animal cell;animal disease;arenavirus infection;article;bat;cell culture;cell immortalization;cell isolation;Coronavirus infection;Epstein Barr virus;funding;human;human cell;immortalized cell line;inclusion body disease;influenza;lymphoblast;medical research;metagenomics;Middle East respiratory syndrome;Mycoplasma;nonhuman;oncogene;paramyxovirus infection;pluripotent stem cell;primary cell;primary culture;scientist;severe acute respiratory syndrome;snake;somatic cell;pig;tissue culture technique,"Dove, A.",2014,,10.1126/science.opms.p1400090,0
522,Assessing the Diversity of Rodent-Borne Viruses: Exploring of High-Throughput Sequencing and Classical Amplification/Sequencing Approaches,"Rodents are distributed throughout the world and interact with humans in many ways. They provide vital ecosystem services, some species are useful models in biomedical research and some are held as pet animals. However, many rodent species can have adverse effects such as damage to crops and stored produce, and they are of health concern because of the transmission of pathogens to humans and livestock. The first rodent viruses were discovered by isolation approaches and resulted in break-through knowledge in immunology, molecular and cell biology, and cancer research. In addition to rodent-specific viruses, rodent-borne viruses are causing a large number of zoonotic diseases. Most prominent examples are reemerging outbreaks of human hemorrhagic fever disease cases caused by arena- and hantaviruses. In addition, rodents are reservoirs for vector-borne pathogens, such as tick-borne encephalitis virus and Borrelia spp., and may carry human pathogenic agents, but likely are not involved in their transmission to human. In our days, next-generation sequencing or high-throughput sequencing (HTS) is revolutionizing the speed of the discovery of novel viruses, but other molecular approaches, such as generic RT-PCR/PCR and rolling circle amplification techniques, contribute significantly to the rapidly ongoing process. However, the current knowledge still represents only the tip of the iceberg, when comparing the known human viruses to those known for rodents, the mammalian taxon with the largest species number. The diagnostic potential of HTS-based metagenomic approaches is illustrated by their use in the discovery and complete genome determination of novel borna- and adenoviruses as causative disease agents in squirrels. In conclusion, HTS, in combination with conventional RT-PCR/PCR-based approaches, resulted in a drastically increased knowledge of the diversity of rodent viruses. Future improvements of the used workflows, including bioinformatics analysis, will further enhance our knowledge and preparedness in case of the emergence of novel viruses. Classical virological and additional molecular approaches are needed for genome annotation and functional characterization of novel viruses, discovered by these technologies, and evaluation of their zoonotic potential.",animal;classification;genetics;high throughput sequencing;isolation and purification;metagenomics;molecular diagnosis;nucleic acid amplification;procedures;rodent;veterinary medicine;virology;virus;virus infection;zoonosis,"Drewes, S.;Straková, P.;Drexler, J. F.;Jacob, J.;Ulrich, R. G.",2017,,10.1016/bs.aivir.2017.08.002,0
523,Bats host major mammalian paramyxoviruses,"The large virus family Paramyxoviridae includes some of the most significant human and livestock viruses, such as measles-, distemper-, mumps-, parainfluenza-, Newcastle disease-, respiratory syncytial virus and metapneumoviruses. Here we identify an estimated 66 new paramyxoviruses in a worldwide sample of 119 bat and rodent species (9,278 individuals). Major discoveries include evidence of an origin of Hendra- and Nipah virus in Africa, identification of a bat virus conspecific with the human mumps virus, detection of close relatives of respiratory syncytial virus, mouse pneumonia- and canine distemper virus in bats, as well as direct evidence of Sendai virus in rodents. Phylogenetic reconstruction of host associations suggests a predominance of host switches from bats to other mammals and birds. Hypothesis tests in a maximum likelihood framework permit the phylogenetic placement of bats as tentative hosts at ancestral nodes to both the major Paramyxoviridae subfamilies (Paramyxovirinae and Pneumovirinae). Future attempts to predict the emergence of novel paramyxoviruses in humans and livestock will have to rely fundamentally on these data. © 2012 Macmillan Publishers Limited. All rights reserved.",Africa;article;bat;bird;Canine distemper virus;Hendra virus;human;mammal;Mumps virus;Murine pneumonia virus;Nipah virus;nonhuman;Paramyxoviridae;paramyxovirus infection;phylogeny;Pneumovirinae;Human respiratory syncytial virus;rodent;Sendai virus;virus cell interaction;virus identification;virus strain,"Drexler, J. F.;Corman, V. M.;Müller, M. A.;Maganga, G. D.;Vallo, P.;Binger, T.;Gloza-Rausch, F.;Rasche, A.;Yordanov, S.;Seebens, A.;Oppong, S.;Sarkodie, Y. A.;Pongombo, C.;Lukashev, A. N.;Schmidt-Chanasit, J.;Stöcker, A.;Carneiro, A. J. B.;Erbar, S.;Maisner, A.;Fronhoffs, F.;Buettner, R.;Kalko, E. K. V.;Kruppa, T.;Franke, C. R.;Kallies, R.;Yandoko, E. R. N.;Herrler, G.;Reusken, C.;Hassanin, A.;Krüger, D. H.;Matthee, S.;Ulrich, R. G.;Leroy, E. M.;Drosten, C.",2012,,10.1038/ncomms1796,0
524,Bats worldwide carry hepatitis E virus-related viruses that form a putative novel genus within the family Hepeviridae,"Hepatitis E virus (HEV) is one of the most common causes of acute hepatitis in tropical and temperate climates. Tropical genotypes 1 and 2 are associated with food-borne and waterborne transmission. Zoonotic reservoirs (mainly pigs, wild boar, and deer) are considered for genotypes 3 and 4, which exist in temperate climates. In view of the association of several zoonotic viruses with bats, we analyzed 3,869 bat specimens from 85 different species and from five continents for hepevirus RNA. HEVs were detected in African, Central American, and European bats, forming a novel phylogenetic clade in the family Hepeviridae. Bat hepeviruses were highly diversified and comparable to human HEV in sequence variation. No evidence for the transmission of bat hepeviruses to humans was found in over 90,000 human blood donations and individual patient sera. Full-genome analysis of one representative virus confirmed formal classification within the family Hepeviridae. Sequence-and distance-based taxonomic evaluations suggested that bat hepeviruses constitute a distinct genus within the family Hepeviridae and that at least three other genera comprising human, rodent, and avian hepeviruses can be designated. This may imply that hepeviruses invaded mammalian hosts nonrecently and underwent speciation according to their host restrictions. Human HEV-related viruses in farmed and peridomestic animals might represent secondary acquisitions of human viruses, rather than animal precursors causally involved in the evolution of human HEV. © 2012, American Society for Microbiology.",article;avian hepevirus;bat hepevirus;cladistics;controlled study;embryo;genetic distance;genetic variability;genome analysis;Hepatitis E virus;Hepevirus;human;human cell;human hepevirus;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;rodent hepevirus;sequence analysis;species differentiation;virus carrier;virus cell interaction;virus detection;virus genome;virus particle,"Drexler, J. F.;Seelen, A.;Corman, V. M.;Tateno, A. F.;Cottontail, V.;Zerbinati, R. M.;Gloza-Rausch, F.;Klose, S. M.;Adu-Sarkodie, Y.;Oppong, S. K.;Kalko, E. K. V.;Osterman, A.;Rasche, A.;Adam, A.;Müller, M. A.;Ulrich, R. G.;Leroy, E. M.;Lukashev, A. N.;Drosten, C.",2012,,10.1128/jvi.00800-12,0
525,Next-generation sequencing shows West Nile virus quasispecies diversification after a single passage in a carrion crow (Corvus corone) in vivo infection model,"West Nile virus (WNV) occurs as a population of genetic variants (quasispecies) infecting a single animal. Previous low-resolution viral genetic diversity estimates in sampled wild birds and mosquitoes, and in multiple-passage adaptation studies in vivo or in cell culture, suggest that WNV genetic diversification is mostly limited to the mosquito vector. This study investigated genetic diversification of WNV in avian hosts during a single passage using next-generation sequencing. Wild-captured carrion crows were subcutaneously infected using a clonal Middle-East WNV. Blood samples were collected 2 and 4 days post-infection. A reverse-transcription (RT)-PCR approach was used to amplify the WNV genome directly from serum samples prior to next-generation sequencing resulting in an average depth of at least 700 x in each sample. Appropriate controls were sequenced to discriminate biologically relevant low-frequency variants from experimentally introduced errors. The WNV populations in the wild crows showed significant diversification away from the inoculum virus quasispecies structure. By contrast, WNV populations in intracerebrally infected day-old chickens did not diversify from that of the inoculum. Where previous studies concluded that WNV genetic diversification is only experimentally demonstrated in its permissive insect vector species, we have experimentally shown significant diversification of WNV populations in a wild bird reservoir species.","Animals;Chickens;*Crows/vi [Virology];Disease Models, Animal;*Genetic Variation;High-Throughput Nucleotide Sequencing;Molecular Sequence Data;RNA, Viral/ge [Genetics];Reverse Transcription;Sequence Analysis, DNA;*West Nile Fever/vi [Virology];*West Nile virus/cl [Classification];West Nile virus/ge [Genetics];*West Nile virus/ip [Isolation & Purification];0 (RNA, Viral)","Dridi, M.;Rosseel, T.;Orton, R.;Johnson, P.;Lecollinet, S.;Muylkens, B.;Lambrecht, B.;Van Borm, S.",2015,Oct,,0
526,Complete nucleotide sequence of a Chinese serotype Asia1 vaccine strain of foot-and-mouth disease virus,"The full-length nucleotide sequence of the Chinese vaccine strain Asia1/YNBS/58 of foot-and-mouth disease virus (FMDV) was determined. The results showed that the complete genome of YNBS/58 is 8,164 nucleotides (nt) in length including a 1,061-nt 5′ untranslated region (UTR), a 6,990-nt open reading frame (ORF), and a 113-nt 3′ UTR. Genome sequences of Asia1/YNBS/58 and other known FMDV strains were compared. The homology analysis indicated that non-structural proteins are more conserved than structural proteins in FMDV and that the 5′ UTR is more conserved than the 3′ UTR. Phylogenetic analysis revealed that Asia1/YNBS/58 is clustered in the Asia1 serotype and is linked to three other isolates, Asia1/IND/63/72, Asia1/3kimron/63, and Asia1/2ISRL/63, suggesting that they have a close genetic relationship. The VP1-, VP2-, and VP3-based phylogenetic trees divided into distinct clusters according to the different serotypes, while other gene-based phylogenetic trees exhibited some degree of intercrossing among serotypes. According to the nucleotide similarities between Asia1/YNBS/58 and two recent Chinese Asia1 isolates, Asia1/HKN/05, and Asia1/JS/05, each forms a distinct genotype. This study is the first description of the full-length genomic sequence of FMDV Chinese serotype Asia1. © 2007 Springer Science+Business Media, LLC.",foot and mouth disease vaccine;protein VP1;protein VP2;protein VP3;structural protein;5' untranslated region;article;controlled study;foot and mouth disease;Foot and mouth disease virus;molecular phylogeny;nonhuman;nucleotide sequence;phylogeny;priority journal;serotype;virus strain,"Du, J.;Chang, H.;Cong, G.;Shao, J.;Lin, T.;Shang, Y.;Liu, Z.;Liu, X.;Cai, X.;Xie, Q.",2007,,10.1007/s11262-007-0126-8,0
527,MicroRNA expression profiling of primary sheep testicular cells in response to bluetongue virus infection,"Bluetongue virus (BTV) is a member of the genus Orbivirus within the family Reoviridae and causes a non-contagious, insect-transmitted disease in domestic and wild ruminants, mainly in sheep and occasionally in cattle and some species of deer. Virus infection can trigger the changes of the cellular microRNA (miRNA) expression profile, which play important post-transcriptional regulatory roles in gene expression and can greatly influence viral replication and pathogenesis. Here, we employed deep sequencing technology to determine which cellular miRNAs were differentially expressed in primary sheep testicular (ST) cells infected with BTV. A total of 25 known miRNAs and 240 novel miRNA candidates that were differentially expressed in BTV-infected and uninfected ST cells were identified, and 251 and 8428 predicted target genes were annotated, respectively. Nine differentially expressed miRNAs and their mRNA targets were validated by quantitative reverse transcription-polymerase chain reaction. Targets prediction and functional analysis of these regulated miRNAs revealed significant enrichment for several signaling pathways including MAPK, PI3K-Akt, endocytosis, Hippo, NF-kB, viral carcinogenesis, FoxO, and JAK-STAT signaling pathways. This study provides a valuable basis for further investigation on the roles of miRNAs in BTV replication and pathogenesis.","Animals;*Bluetongue/ge [Genetics];Bluetongue/me [Metabolism];Bluetongue/pa [Pathology];Bluetongue/vi [Virology];*Bluetongue virus/gd [Growth & Development];Bluetongue virus/py [Pathogenicity];Forkhead Transcription Factors/ge [Genetics];Forkhead Transcription Factors/me [Metabolism];Gene Expression Profiling;*Gene Expression Regulation;Gene Ontology;High-Throughput Nucleotide Sequencing;*Host-Pathogen Interactions;Janus Kinases/ge [Genetics];Janus Kinases/me [Metabolism];Male;*MicroRNAs/ge [Genetics];MicroRNAs/me [Metabolism];Mitogen-Activated Protein Kinases/ge [Genetics];Mitogen-Activated Protein Kinases/me [Metabolism];Molecular Sequence Annotation;Phosphatidylinositol 3-Kinases/ge [Genetics];Phosphatidylinositol 3-Kinases/me [Metabolism];Primary Cell Culture;Proto-Oncogene Proteins c-akt/ge [Genetics];Proto-Oncogene Proteins c-akt/me [Metabolism];Reverse Transcriptase Polymerase Chain Reaction;STAT Transcription Factors/ge [Genetics];STAT Transcription Factors/me [Metabolism];Sheep, Domestic;Signal Transduction;*Testis/me [Metabolism];Testis/pa [Pathology];Testis/vi [Virology];0 (Forkhead Transcription Factors);0 (MicroRNAs);0 (STAT Transcription Factors)","Du, J.;Gao, S.;Tian, Z.;Xing, S.;Huang, D.;Zhang, G.;Zheng, Y.;Liu, G.;Luo, J.;Chang, H.;Yin, H.",2017,04,,0
528,Distribution and characteristics of rodent picornaviruses in China,"Rodents are important reservoir hosts of many important zoonotic viruses. The family Picornaviridae contains clinically important pathogens that infect humans and animals, and increasing numbers of rodent picornaviruses have recently been associated with zoonoses. We collected 574 pharyngeal and anal swab specimens from 287 rodents of 10 different species from eight representative regions of China from October 2013 to July 2015. Seven representative sequences identified from six rodent species were amplified as full genomes and classified into four lineages. Three lineage 1 viruses belonged to a novel genus of picornaviruses and was more closely related to Hepatovirus than to others genera of picornaviruses based on aa homology. Lineage 2, lineage 3, and lineage 4 viruses belonged to the genera Rosavirus, Hunnivirus, and Enterovirus, respectively, representing new species. According to both phylogenetic and identity analyses, Lineage 2 viruses had a close relationship with rosavirus 2 which was recovered from the feces of a child in Gambia and Lineage 3 viruses had a close relationship with domestic animal Hunnivirus. Lineage 4 viruses provide the first evidence of these enteroviruses and their evolution in rodent hosts in China.",ACUTE RESPIRATORY ILLNESS;STRAND RNA VIRUSES;IDENTIFICATION;INFECTION;DISTINCT;PROTEIN;VIROME;GENUS;SUPERFAMILY;ARENAVIRUS,"Du, J.;Lu, L.;Liu, F.;Su, H. X.;Dong, J.;Sun, L. L.;Zhu, Y. F.;Ren, X. W.;Yang, F.;Guo, F.;Liu, Q. Y.;Wu, Z. Q.;Jin, Q.",2016,Sep,,0
529,Molecular evolution and emergence of H5N6 avian influenza virus in central China,"H5N6 avian influenza virus (AIV) has posed a potential threat to public health since its emergence in China in 2013. To understand the evolution and emergence of H5N6 AIV in the avian population, we performed molecular surveillance of live poultry markets (LPMs) in Wugang Prefecture, Hunan Province, in central China, during 2014 and 2015. Wugang Prefecture is located on the Eastern Asian-Australian migratory bird flyway, and a human death due to an H5N6 virus was reported in the prefecture on 21 November 2016. In total, we sampled and sequenced the complete genomes of 175 H5N6 AIVs. Notably, our analysis revealed that H5N6 AIVs contain at least six genotypes arising from segment reassortment, including a rare variant that possesses an HA gene derived from H5N1 clade 2.3.2 and a novel NP gene that has its origins with H7N3 viruses. In addition, phylogenetic analysis revealed that genetically similar H5N6 AIVs tend to cluster according to their geographic regions of origin. These results help to reveal the evolutionary behavior of influenza viruses prior to their emergence in humans.",article;bird;China;cladistics;evolution;genetic analysis;genetic reassortment;genetic similarity;genetic variability;genotype;geographic origin;HA gene;Influenza A virus;Influenza A virus (H5N6);Influenza A virus (H7N3);migrant bird;molecular evolution;nonhuman;NP gene;phylogeny;poultry;priority journal;reverse transcription polymerase chain reaction;sequence analysis;virus gene;virus genome,"Du, Y.;Chen, M.;Yang, J.;Jia, Y.;Han, S.;Holmes, E. C.;Cui, J.",2017,,10.1128/jvi.00143-17,0
530,"Identification, phylogenetic evolutionary analysis of GDQY orf virus isolated from Qingyuan City, Guangdong Province, southern China","Infection with the orf virus (ORFV) leads to contagious ecthyma, also called contagious pustular dermatitis, which usually affects sheep, goats and other small ruminants. It has a great distribution throughout the world and has also been reported to infect humans. Though many strains have been isolated from differing parts of mainland China, rarely has any strain been reported from the southern provinces of China. We studied a case of orf virus infection that occurred at Qingyuan City, Guangdong Province in southern China. An orf virus strain, GDQY, was successfully isolated and identified through cell culture techniques and transmission electron microscopy. Complete genes of ORFV011, ORFV059, ORFV106 and ORFV107 were amplified for the sequence analysis based on their nucleotide or amino acid level. In order to discuss the genetic variation, precise sequences were used to compare to other reference strains isolated from different districts or countries. Phylogenetic trees based on those strains were built up and evolutionary distances were calculated based on the alignment of their complete sequences. The typical structure of the orf virus was observed in cell-culture suspensions inoculated with GDQY, and the full-length of four genes was amplified and sequenced. Phylogenetic analysis indicated that GDQY is homologous to FJ-DS and CQ/WZ on ORFV011 nucleotides. ORFV059 may be more variable than ORFV011 based on the comparison between GDQY and other isolates. Genetic studies of ORFV106 and 107 are reported for the first time in the presented study.",animal tissue;article;China;controlled study;genetic variability;geographic distribution;goat;nonhuman;nucleotide sequence;Orf virus;phylogenetic tree;polymerase chain reaction;poxvirus infection;sequence analysis;transmission electron microscopy;virus identification;virus isolation;virus particle,"Duan, C.;Liao, M.;Wang, H.;Luo, X.;Shao, J.;Xu, Y.;Li, W.;Hao, W.;Luo, S.",2015,,10.1016/j.gene.2014.11.016,0
531,Isolation and characterization of influenza A virus (subtype H5N1) that caused the first highly pathogenic avian influenza outbreak in chicken in Bhutan,"We characterized Influenza A/H5N1 virus that caused the first outbreak of highly pathogenic avian influenza (HPAI) in chickens in Bhutan in 2010. The virus was highly virulent to chicken, killing them within two days of the experimental inoculation with an intravenous pathogenicity index (IVPI) of 2.88. For genetic and phylogenetic analyses, complete genome sequencing of 4 viral isolates was carried out. The isolates revealed multiple basic amino acids at their hemagglutinin (HA) cleavage site, similar to other "" Qinghai-like"" H5N1 isolates. The receptor-binding site of HA molecule contained avian-like amino acids (222Q and 224G). The isolates also contained amino acid residue K at position 627 of the PB2 protein, and other markers in NS 1 and PB1 proteins, highlighting the risk to mammals. However, the isolates were sensitive to influenza drugs presently available in the market. The sequence analysis indicated that the Bhutan viruses shared 99.1-100% nucleotide homology in all the eight genes among themselves and 2010 chicken isolate from Bangladesh (A/chicken/Bangladesh/1151-11/2010) indicating common progenitor virus. The phylogenetic analysis indicated that the Bhutan isolates belonged to sub-clade 2.2.3 (EMA 3) and shared common progenitor virus with the 2010 Bangladesh virus. Based on the evidence of phylogeny and molecular markers, it could be concluded that the outbreaks in Bhutan and Bangladesh in 2010 were due to independent introductions of the virus probably through migratory birds. © 2011 Elsevier B.V.",amino acid;hemagglutinin;molecular marker;nonstructural protein 1;article;avian influenza;Bhutan;chicken;epidemic;Influenza A virus (H5N1);nonhuman;phylogeny;protein cleavage;sequence analysis;virus characterization;virus isolation;virus virulence,"Dubey, S. C.;Dahal, N.;Nagarajan, S.;Tosh, C.;Murugkar, H. V.;Rinzin, K.;Sharma, B.;Jain, R.;Katare, M.;Patil, S.;Khandia, R.;Syed, Z.;Tripathi, S.;Behera, P.;Kumar, M.;Kulkarni, D. D.;Krishna, L.",2012,,10.1016/j.vetmic.2011.08.002,0
532,Identification of a novel coronavirus from guinea fowl using metagenomics,"While classical virology techniques such as virus culture, electron microscopy, or classical PCR had been unsuccessful in identifying the causative agent responsible for the fulminating disease of guinea fowl, we identified a novel avian gammacoronavirus associated with the disease using metagenomics. Next-generation sequencing is an unbiased approach that allows the sequencing of virtually all the genetic material present in a given sample.","Animals;*Coronavirus/ge [Genetics];Coronavirus/ip [Isolation & Purification];*Coronavirus Infections/ve [Veterinary];Coronavirus Infections/vi [Virology];High-Throughput Nucleotide Sequencing;Metagenome;Metagenomics;Poultry/vi [Virology];*Poultry Diseases/vi [Virology];Sequence Analysis, DNA","Ducatez, M. F.;Guerin, J. L.",2015,,,0
533,Characterization of a new genotype and serotype of infectious bronchitis virus in Western Africa,"Between 2002 and 2007, more than 1000 chickens from commercial farms, live bird markets and backyard farms in Nigeria and Niger were tested for the presence of the infectious bronchitis virus (IBV) genome. Phylogenetic analysis of full-length sequences of the spike 1 (S1) gene revealed a new genotype of IBV that we refer to as 'IBADAN'. The minimum genetic distance to the closest 'non-IBADAN' strains (UK/7/93 at the nucleotide level; H120 and M41 at the amino acid level) reached 24 and 32% at the nucleotide and amino acid levels, respectively. The full genome of the IBADAN reference strain (NGA/A116E7/2006) had a genetic distance of 9.7-16.4% at the nucleotide level with all available fully sequenced strains. As IBV S1 plays a major role in antigenicity, the antigenic relatedness of NGA/A116E7/2006 was compared with strains of other serotypes. NGA/A116E7/2006 did not cross-react with antisera against IT02, M41, D274, Connecticut or 793/B strains in virus neutralization assays. NGA/A116E7/2006 cross-reacted with the QX-like strain ITA/90254/2005 but only to a low level (antigenic relatedness of 33 %), suggesting that IBADAN also represents a new serotype. A comparison of S1 sequences identified several amino acids that may play a role in IBV antigenicity. Despite the absence of obvious clinical signs in poultry infected by IBADAN strains, it is important to test the cross-protection of current vaccine strains. © 2009 SGM.",Africa;amino acid sequence;antigenicity;article;Avian infectious bronchitis virus;chicken;cross reaction;genotype;nonhuman;nucleotide sequence;phylogeny;poultry;priority journal;sequence analysis;seroprevalence;serotype;strain difference;virus detection;virus neutralization;virus strain,"Ducatez, M. F.;Martin, A. M.;Owoade, A. A.;Olatoye, I. O.;Alkali, B. R.;Maikano, I.;Snoeck, C. J.;Sausy, A.;Cordioli, P.;Muller, C. P.",2009,,10.1099/vir.0.012476-0,0
534,"Phylogenetic analysis of low pathogenicity H5N1 and H7N3 influenza A virus isolates recovered from sentinel, free flying, wild mallards at one study site during 2006","From August 2 to October 11, 2006, clusters of low pathogenicity (LP) North American lineage H5N1 and H7N3 avian influenza A viruses (AIV), and other subtypes, were recovered from free-flying, resident, wild mallards used as sentinels at one site. The antigenic subtypes, pathogenicity potential, and Sanger sequencing of the isolates determined the H5N1 and H7N3 isolates were only recovered from samples collected on 8/2/2006 and 9/8/2006, respectively. However, subsequent efforts using next-generation sequencing (NGS) and additional Sanger sequencing found partial H7 segments in other HA-NA virus combinations on 8/2/2006, 9/8/2006 and 10/11/2006. It is well established that over larger geographic areas and years AIVs form transient genomic constellations; this sequential sampling data revealed that over a short period of time the dynamics of AIVs can be active and newer sequencing platforms increase recognition of mixed infections. Both findings provide further insight into the natural history of AIVs in natural reservoirs. © 2011 Elsevier Inc.",virus antigen;article;bird;controlled study;genome analysis;geographic distribution;Influenza A virus (H5N1);Influenza A virus (H7N3);Anas platyrhynchos;nonhuman;nucleotide sequence;phylogeny;priority journal;sequence analysis;virus genome;virus strain;virus typing;virus virulence;wild animal,"Dugan, V. G.;Dunham, E. J.;Jin, G.;Sheng, Z. M.;Kaser, E.;Nolting, J. M.;Alexander, H. L.;Slemons, R. D.;Taubenberger, J. K.",2011,,10.1016/j.virol.2011.05.004,0
535,Viral diversity in swine intestinal mucus used for the manufacture of heparin as analyzed by high-throughput sequencing,"Heparin is one of the main pharmaceutical products manufactured from raw animal material. In order to describe the viral burden associated with this raw material, we performed high-throughput sequencing (HTS) on mucus samples destined for heparin manufacturing, which were collected from European pigs. We identified Circoviridae and Parvoviridae members as the most prevalent contaminating viruses, together with viruses from the Picornaviridae, Astroviridae, Reoviridae, Caliciviridae, Adenoviridae, Birnaviridae, and Anelloviridae families. Putative new viral species were also identified. The load of several known or novel small non-enveloped viruses, which are particularly difficult to inactivate or eliminate during heparin processing, was quantified by qPCR. Analysis of the combined HTS and specific qPCR results will influence the refining and validation of inactivation procedures, as well as aiding in risk analysis of viral heparin contamination.",heparin;Adenoviridae;Anelloviridae;article;Astroviridae;Birnaviridae;Caliciviridae;Circoviridae;drug contamination;drug manufacture;high throughput sequencing;intestinal mucus;microbial diversity;mucus;nonhuman;Parvoviridae;Picornaviridae;polymerase chain reaction;Reoviridae;pig;virus;virus load,"Dumarest, M.;Muth, E.;Cheval, J.;Gratigny, M.;Hébert, C.;Gagnieur, L.;Eloit, M.",2015,,10.1016/j.biologicals.2014.10.004,1
536,Impacts of poultry house environment on poultry litter bacterial community composition,"Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly Gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens. © 2011 Dumas et al.",RNA 16S;agricultural waste;Arcobacter;article;bacterial virulence;Clostridiales;cluster analysis;controlled study;dermatitis;gangrenous dermatitis;gene cluster;gene sequence;genetic variability;high throughput sequencing;microbial community;nonhuman;population abundance;poultry farming;poultry litter;Staphylococcus,"Dumas, M. D.;Polson, S. W.;Ritter, D.;Ravel, J.;Gelb Jr, J.;Morgan, R.;Wommack, K. E.",2011,,10.1371/journal.pone.0024785,0
537,Molecular and microscopic evidence of viruses in marine copepods,"As dominant members of marine mesozooplankton communities, copepods play critical roles in oceanic food webs and biogeochemical cycling. Despite the ecological significance of copepods, little is known regarding the causes of copepod mortality, and up to 35% of total copepod mortality cannot be accounted for by predation alone. Viruses have been established as ecologically important infectious agents in the oceans; however, viral infection has not been investigated in mesozooplankton communities. Here we used molecular and microscopic techniques to document viral infection in natural populations of the calanoid copepods Acartia tonsa (Dana) and Labidocera aestiva (Wheeler) in Tampa Bay, FL. Viral metagenomics revealed previously undocumented viruses in each species, named Acartia tonsa copepod circo-like virus (AtCopCV) and Labidocera aestiva copepod circo-like virus (LaCopCV). LaCopCV was found to be extremely prevalent and abundant in L. aestiva populations, with up to 100% prevalence in some samples and average viral loads of 1.13 x 10(5) copies per individual. LaCopCV transcription was also detected in the majority of L. aestiva individuals, indicating viral activity. AtCopCV was sporadically detected in A. tonsa populations year-round, suggesting temporal variability in viral infection dynamics. Finally, virus-like particles of unknown identity were observed in the connective tissues of A. tonsa and L. aestiva by transmission electron microscopy, demonstrating that viruses were actively proliferating in copepod connective tissue as opposed to infecting gut contents, parasites, or symbionts. Taken together, these results provide strong independent lines of evidence for active viral infection in dominant copepod species, indicating that viruses may significantly influence mesozooplankton ecology.",circovirus;zooplankton;crustacea;ssDNA virus;PORCINE CIRCOVIRUS TYPE-2;CIRCULAR SSDNA VIRUSES;ACARTIA-TONSA DANA;REAL-TIME PCR;NUCLEAR-LOCALIZATION;FOOD CONCENTRATION;CHESAPEAKE BAY;DNA VIRUSES;PROTEIN;REPLICATION,"Dunlap, D. S.;Ng, T. F. F.;Rosario, K.;Barbosa, J. G.;Greco, A. M.;Breitbart, M.;Hewson, I.",2013,Jan,,0
538,"Bovine enteroviruses in the calf: An attempt at serologic, biologic, and pathologic classification","Bovine enteroviruses were classified into 8 serotypes to provide a basis for pathogenicity studies. Oral and subcutaneous inoculation of virus into 1 day old to 8 week old calves generally resulted in leukopenia and fever. Of 6 colostrum deprived calves inoculated before they received their first milk, 3 died; however, a comparable proportion (9/17) of uninoculated colostrum deprived calves also died. In 4 to 8 week old calves exposed to the virus, fever and leukopenia developed but less than half of the calves developed diarrhea and few died. None of the colostrum fed, uninoculated calves died. Infection of the fetus in utero seemed to be of common occurrence, as judged by the finding of antibodies to one or more bovine enteroviruses in fetuses aborted at 4 months or more of gestation. The antibodies were believed to be of fetal origin. It was postulated that in utero infection may contribute to the early death or lack of resistance of the newborn calf to bacterial infection.",Bovine enterovirus;bovine;Enterovirus;microorganism;theoretical study;virus classification;virus infection,"Dunne, H. W.;Huang, C. M.;Lin, W. J.",1974,,,0
539,Characterization of novel Bovine Leukemia Virus (BLV) antisense transcripts by deep sequencing reveals constitutive expression in tumors and transcriptional interaction with viral microRNAs,"Background: Bovine Leukemia Virus (BLV) is a deltaretrovirus closely related to the Human T cell leukemia virus-1 (HTLV-1). Cattle are the natural host of BLV where it integrates into B-cells, producing a lifelong infection. Most infected animals remain asymptomatic but following a protracted latency period about 5% develop an aggressive leukemia/lymphoma, mirroring the disease trajectory of HTLV-1. The mechanisms by which these viruses provoke cellular transformation remain opaque. In both viruses little or no transcription is observed from the 5'LTR in tumors, however the proviruses are not transcriptionally silent. In the case of BLV a cluster of RNA polymerase III transcribed microRNAs are highly expressed, while the HTLV-1 antisense transcript HBZ is consistently found in all tumors examined. Results: Here, using RNA-seq, we demonstrate that the BLV provirus also constitutively expresses antisense transcripts in all leukemic and asymptomatic samples examined. The first transcript (AS1) can be alternately polyadenylated, generating a transcript of ~600bp (AS1-S) and a less abundant transcript of ~2200bp (AS1-L). Alternative splicing creates a second transcript of ~400bp (AS2). The coding potential of AS1-S/L is ambiguous, with a small open reading frame of 264bp, however the transcripts are primarily retained in the nucleus, hinting at a lncRNA-like role. The AS1-L transcript overlaps the BLV microRNAs and using high throughput sequencing of RNA-ligase-mediated (RLM) 5'RACE, we show that the RNA-induced silencing complex (RISC) cleaves AS1-L. Furthermore, experiments using altered BLV proviruses with the microRNAs either deleted or inverted point to additional transcriptional interference between the two viral RNA species. Conclusions: The identification of novel viral antisense transcripts shows the BLV provirus to be far from silent in tumors. Furthermore, the consistent expression of these transcripts in both leukemic and nonmalignant clones points to a vital role in the life cycle of the virus and its tumorigenic potential. Additionally, the cleavage of the AS1-L transcript by the BLV encoded microRNAs and the transcriptional interference between the two viral RNA species suggest a shared role in the regulation of BLV.",DNA directed RNA polymerase III;microRNA;RNA induced silencing complex;RNA ligase;unclassified drug;viral microRNA;3' long terminal repeat;3' rapid amplification of cDNA end;5' long terminal repeat;5' rapid amplification of cDNA end;antisense transcript;article;Bovine leukemia virus;cellular distribution;coding potential;controlled study;deep sequencing;DNA structure;gene deletion;gene interaction;gene sequence;gene silencing;general aspects of disease;genetic parameters;genetic transfection;HeLa cell line;high throughput sequencing;long terminal repeat;molecular cloning;molecular genetics;mutational analysis;nonhuman;open reading frame;polyadenylation;protein cleavage;RNA sequence;RNA splicing;structure activity relation;transcription regulation;transcriptional interaction;transcriptional interference;tumorigenic potential;virus genome;virus load,"Durkin, K.;Rosewick, N.;Artesi, M.;Hahaut, V.;Griebel, P.;Arsic, N.;Burny, A.;Georges, M.;Van den Broeke, A.",2016,,10.1186/s12977-016-0267-8,0
540,Phylogenetic analysis of beak and feather disease virus across a host ring-species complex,"Pathogens have been hypothesized to play a major role in host diversity and speciation. Susceptibility of hybrid hosts to pathogens is thought to be a common phenomenon that could promote host population divergence and subsequently speciation. However, few studies have tested for pathogen infection across animal hybrid zones while testing for codivergence of the pathogens in the hybridizing host complex. Over 8 y, we studied natural infection by a rapidly evolving single-strand DNA virus, beak and feather diseases virus (BFDV), which infects parrots, exploiting a host-ring species complex (Platycercus elegans) in Australia. We found that host subspecies and their hybrids varied strikingly in both BFDV prevalence and load: both hybrid and phenotypically intermediate subspecies had lower prevalence and load compared with parental subspecies, while controlling for host age, sex, longitude and latitude, as well as temporal effects. We sequenced viral isolates throughout the range, which revealed patterns of genomic variation analogous to Mayr's ring-species hypothesis, to our knowledge for the first time in any host-pathogen system. Viral phylogeny, geographic location, intraspecific host density, and parrot community diversity and composition did not explain the differences in BFDV prevalence or load between subpopulations. Overall, our analyses suggest that functional host responses to infection, or force of infection, differ between subspecies and hybrids. Our findings highlight the role of host hybridization and clines in altering host-pathogen interactions, dynamics that can have important implications for models of speciation with gene flow, and offer insights into how pathogens may adapt to diverging host populations.",virus DNA;animal;Australia;biological model;bird disease;Circoviridae infection;Circovirus;classification;female;gene flow;genetics;host pathogen interaction;host range;hybridization;male;molecular evolution;molecular genetics;nucleotide sequence;parrot;pathogenicity;phylogeny;species differentiation;veterinary medicine;virology;virulence;virus genome;virus load,"Eastwood, J. R.;Berg, M. L.;Ribot, R. F.;Raidal, S. R.;Buchanan, K. L.;Walder, K. R.;Bennett, A. T.",2014,,10.1073/pnas.1403255111,0
541,Novel Atlantic bottlenose dolphin parainfluenza virus TtPIV-1 clusters with bovine PIV-3 genotype B strains,"Parainfluenza virus 3 (PIV-3) is a common viral infection not only in humans, but also in many other species. Serological evidence suggests that nearly 100 % of children in the United States have been infected with PIV-3 by 5 years of age. Similarly, in cattle, PIV-3 is commonly associated with bovine respiratory disease complex. A novel dolphin PIV-3 (TtPIV-1) was described by Nollens et al. in 2008 from a dolphin that was diagnosed with an unknown respiratory illness. At that time, TtPIV-1 was found to be most similar to, but distinct from, bovine PIV-3 (BPIV-3). In the present study, similar viral growth kinetics and pro-inflammatory cytokine (IL-1β, IL-6, and CXCL8) production were seen between BPIV-3 and TtPIV-1 in BEAS-2B, MDBK, and Vero cell lines. Initial nomenclature of TtPIV-1 was based on partial sequence of the fusion and RNA polymerase genes. Based on the similarities we saw with the in vitro work, it was important to examine the TtPIV-1 genome in more detail. Full genome sequencing and subsequent phylogenetic analysis revealed that all six viral genes of TtPIV-1 clustered within the recently described BPIV-3 genotype B strains, and it is proposed that TtPIV-1 be re-classified with BPIV-3 genotype B strains.",interleukin 1beta;interleukin 6;interleukin 8;messenger RNA;amino acid sequence;amino acid substitution;amino terminal sequence;article;BEAS-2B cell line;bottlenose dolphin;Bovine parainfluenza virus 3;carboxy terminal sequence;cell line;classification;comparative study;controlled study;cytokine production;gene cluster;gene fusion;genetic conservation;genotype;Human parainfluenza virus 3;in vitro study;MDBK cell line;nonhuman;parainfluenza virus TtPIV 1;Paramyxovirinae;phylogenetic tree;priority journal;protein expression;sequence alignment;Vero cell line;viral growth kinetics;viral phenomena and functions;virus gene;virus genome;virus strain,"Eberle, K. C.;Neill, J. D.;Venn-Watson, S. K.;McGill, J. L.;Sacco, R. E.",2015,,10.1007/s11262-015-1224-7,0
542,"Characterization of the structural proteins of porcine epizootic diarrhea virus, strain CV777","Pig epizootic diarrhea virus cannot be grown in cell culture; for its characterization, intestinal perfusate material from a pig infected with the strain CV777 had to be used. In isopyknic sucrose gradients, a peak of virus-specific ELISA activity was detected at a density of 1.17 g/ml. Using immunoprecipitation of radioiodinated-purified virus material followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, 3 proteins of low molecular weight (20,000 to 32,000 daltons [D]) were found; after blotting nitrocellulose and glycoprotein identification with concanavalin A and horseradish peroxidase, 1 of the proteins (23,000 D) gave a signal. Another protein of 58,000 D was encountered, which was the only protein binding an RNA probe. Finally, a protein of 85,000 D was visible, associated with minor bands of about 110,000 and 135,000 D in most experiments. Using the concanavalin A-blotting technique, the same bands were visualized. The demonstration of a polydisperse cluster of proteins from 20,000 to 32,000 D (of which at least 1 is glycosylated), of glycosylated proteins from 85,000 to 135,000 D, and of an RNA-binding protein of 58,000 D is taken as structural evidence that pig epizootic diarrhea virus should be classified with the Coronaviridae, irrespective of the apparent lack of an antigenic relationship with other members of that family.",carrier protein;glycoprotein;RNA binding protein;viral protein;animal;article;classification;Coronavirinae;enzyme linked immunosorbent assay;isolation and purification;microbiology;molecular weight;pig,"Egberink, H. F.;Ederveen, J.;Callebaut, P.;Horzinek, M. C.",1988,,,0
543,Detection and Molecular Characterization of Foot and Mouth Disease Viruses from Outbreaks in Some States of Northern Nigeria 2013–2015,"Control measures for foot and mouth disease (FMD) in Nigeria have not been implemented due to the absence of locally produced vaccines and risk-based analysis resulting from insufficient data on the circulating FMD virus (FMDV) serotypes/strains. In 2013-2015, blood and epithelial samples were collected from reported FMD outbreaks in four states (Kaduna, Kwara, Plateau and Bauchi) in northern Nigeria. FMDV non-structural protein (NSP) seroprevalence for the outbreaks was estimated at 80% (72 of 90) and 70% (131 of 188) post-outbreak. Antibodies against FMDV serotypes O, A, SAT1, SAT2 and SAT3 were detected across the states using solid-phase competitive ELISA. FMDV genome was detected in 99% (73 of 74) of the samples from FMD-affected animals using rRT-PCR, and cytopathic effect was found in cell culture by 59% (44 of 74) of these samples. Three FMDV serotypes O, A and SAT2 were isolated and characterized. The phylogenetic assessments of the virus isolates showed that two topotypes of FMDV serotype O, East Africa-3 (EA-3) and West Africa (WA) topotypes were circulating, as well as FMDV strains belonging to the Africa genotype (G-IV) of serotype A and FMDV SAT2 topotype VII strains. While the serotype O (EA-3) strains from Nigeria were most closely related to a 1999 virus strain from Sudan, the WA strain in Nigeria shares genetic relationship with three 1988 viruses in Niger. The FMDV serotype A strains were closely related to a known virus from Cameroon, and the SAT2 strains were most closely related to virus subtypes in Libya. This study provides evidence of co-occurrence of FMDV serotypes and topotypes in West, Central, East and North Africa, and this has implication for control. The findings help filling the knowledge gap of FMDV dynamics in Nigeria and West Africa subregion to support local and regional development of vaccination-based control plans and international risk assessment.",nonstructural protein;unclassified drug;viral protein;virus RNA;animal tissue;antibody detection;article;bovine;cytopathogenic effect;enzyme linked immunosorbent assay;epidemic;Foot and mouth disease virus;gene sequence;genotype;molecular phylogeny;Nigeria;nonhuman;phylogenetic tree;real time polymerase chain reaction;reverse transcription polymerase chain reaction;sequence analysis;serotype;sheep;virus characterization;virus isolation,"Ehizibolo, D. O.;Haegeman, A.;De Vleeschauwer, A. R.;Umoh, J. U.;Kazeem, H. M.;Okolocha, E. C.;Van Borm, S.;De Clercq, K.",2017,,10.1111/tbed.12602,0
544,Bovine herpesvirus type 2 is closely related to the primate alphaherpesviruses,"Bovine herpesvirus type 2 (BoHV-2), also known as bovine mammillitis virus, is classified in the Family Herpesviridae, Subfamily Alphaherpesvirinae, and Genus Simplexvirus us along with herpes simplex viruses type 1 and 2 (HSV-1 and HSV-2) and other primate simplexviruses on the basis of similarities in 4 genes within the 15 kb U(L) 23-29 cluster. This could be explained either by a global similarity or a recombination event that brought primate herpesviral sequences into a bovine virus. Our sequences for DNA polymerase (U(L)30), a large gene adjacent to the previously identified conserved cluster, and glycoprotein G (U(S)4), a gene as distant from the cluster as possible on the circularized genome, confirm the close relationship between BoHV-2 and the primate simplexviruses, and argue for a global similarity and probably a close evolutionary relationship. Thus one can speculate that BoHV-2 may represent a greater hazard to humans than has been appreciated previously.",DNA polymerase;thrombospondin;article;Bovine herpesvirus 1;DNA sequence;gene sequence;Herpes simplex virus;nonhuman;nucleotide sequence;priority journal;sequence homology;structural gene;virus classification;virus genome,"Ehlers, B.;Goltz, M.;Ejercito, M. P.;Dasika, G. K.;Letchworth, G. J.",1999,,10.1023/a:1008184630066,0
545,First outbreaks and phylogenetic analyses of avian influenza H9N2 viruses isolated from poultry flocks in Morocco,"Background: H9N2 avian influenza viruses continue to spread in poultry and wild birds worldwide. Morocco just faced its first H9N2 influenza virus outbreaks early 2016 affecting different types of poultry production. After its introduction, the virus spread very rapidly throughout the country. Methods: Samples were collected from 11 chicken flocks with high morbidity and mortality rates. Four viruses were successfully isolated from broiler chickens and one from broiler breeders and fully sequenced. Results: Phylogenetic and molecular markers analyses showed the Moroccan viruses belonged to the G1 lineage and likely originated from the Middle East. As known for H9N2 viruses, the Moroccanisolates possess several genetic markers that enhance virulence in poultry and transmission to humans. Conclusion: The present study demonstrated that under field conditions H9N2 could have a devastating effect on egg production and mortalities and highlighted a lack of surveillance data on the pathogen in the region.",animal experiment;animal tissue;article;chicken;controlled study;epidemic;genetic marker;Influenza A virus (H9N2);molecular phylogeny;morbidity;Morocco;mortality;nonhuman;virus identification;virus isolation;virus transmission;virus virulence,"El Houadfi, M.;Fellahi, S.;Nassik, S.;Guérin, J. L.;Ducatez, M. F.",2016,,10.1186/s12985-016-0596-1,0
546,"Highly Pathogenic Avian Influenza H5N1 Clade 2.3.2.1c Virus in Lebanon, 2016",We report the phylogenetic analysis of the first outbreak of H5N1 highly pathogenic avian influenza virus detected in Lebanon from poultry in April 2016. Our whole-genome sequencing analysis revealed that the Lebanese H5N1 virus belongs to genetic clade 2.3.2.1c and clusters with viruses from Europe and West Africa.,animal;chicken;classification;epidemic;genetics;Influenza A virus (H5N1);avian influenza;isolation and purification;Lebanon;pathogenicity;phylogeny;bird disease;virology,"El Romeh, A.;Zecchin, B.;Fusaro, A.;Ibrahim, E.;El Bazzal, B.;El Hage, J.;Milani, A.;Zamperin, G.;Monne, I.",2017,,10.1637/11544-113016-Case.1,0
547,Detection of the first G6P[14] human rotavirus strain from a child with diarrhea in Egypt,"We report the first detection of a G6P[14] rotavirus strain in Egypt from the stool of a child participating in a hospital-based diarrhea surveillance study conducted throughout the year 2004. Rotavirus infection was initially detected using a rotavirus group A VP6 enzyme immunoassay; the P (VP4) and G (VP7) genotypes of the strain were identified by RT-PCR. We sequenced the VP7 gene and the VP8* portion of the VP4 gene and the strain displayed the strongest identity to the VP7 [>94% nucleotides (nt), >97% amino acids (aa)] and VP4 (>93% nt, >98% aa) sequences of PA169, a novel G6P[14] strain first isolated from a child in Italy during the winter of 1987. Additional sequencing and analysis of the other remaining structural (VP1-VP3, VP6) and non-structural (NSP1-NSP5) proteins support this animal-to-human reassortment theory. According to the full genome classification system, the G6P[14] strain (EGY3399) was assigned to G6-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3 genotypes. The greatest similarity of EGY3399 NSP4 and NSP5 gene sequences were to those of ovine and simian origin, respectively. Coupled with other observations, our results suggest G6P[14] isolates rarely cause severe diarrhea in Egyptian children, and support other studies that indicate animal rotavirus contribute to the genetic diversity of rotavirus detected from humans through interspecies transmission and single or multiple segments reassortment. © 2011.",glucose 6 phosphate;nonstructural protein 1;nonstructural protein 2;nonstructural protein 3;nonstructural protein 4;nonstructural protein 5;protein VP1;protein VP2;protein VP3;protein VP4;protein VP6;protein VP7;virus antigen;virus RNA;animal cell;article;biological monitoring;child;child health;controlled study;Egypt;feces analysis;gene sequence;genetic association;genetic identification;genetic variability;human;Human rotavirus;infectious diarrhea;male;molecular evolution;molecular phylogeny;nonhuman;nonstructural protein 1 gene;nonstructural protein 2 gene;nonstructural protein 3 gene;nonstructural protein 4 gene;nonstructural protein 5 gene;nucleotide sequence;phylogenetic tree;preschool child;priority journal;protein VP1 gene;protein VP2 gene;protein VP3 gene;protein VP4 gene;protein VP6 gene;protein VP7 gene;sequence analysis;virus detection;virus gene;virus strain,"El Sherif, M.;Esona, M. D.;Wang, Y.;Gentsch, J. R.;Jiang, B.;Glass, R. I.;Baker, S. A.;Klena, J. D.",2011,,10.1016/j.meegid.2011.05.012,0
548,"Avian influenza: Virology, diagnosis and surveillance","Avian influenza virus (AIV) is the causative agent of a zoonotic disease that affects populations worldwide with often devastating economic and health consequences. Most AIV subtypes cause little or no disease in waterfowl, but outbreaks in poultry can be associated with high mortality. Although transmission of AIV to humans occurs rarely and is strain dependent, the virus has the ability to mutate or reassort into a form that triggers a life-threatening infection. The constant emergence of new influenza strains makes it particularly challenging to predict the behavior, spread, virulence or potential for human-to-human transmission. Because it is difficult to anticipate which viral strain or what location will initiate the next pandemic, it is difficult to prepare for that event. However, rigorous implementation of biosecurity, vaccination and education programs can minimize the threat of AIV. Global surveillance programs help record and identify newly evolving and potentially pandemic strains harbored by the reservoir host. © 2013 Future Medicine Ltd.",antivirus agent;complementary DNA;DNA vaccine;influenza vaccine;messenger RNA;naked DNA;amnion fluid;antigen expression;antiviral therapy;avian influenza;avian influenza virus;Avulavirus;base pairing;Charadriiformes;chemical structure;complement fixation;cytopathogenic effect;disease surveillance;DNA immunization;education program;gene gun;Hong Kong influenza;human;immunofluorescence;influenza vaccination;Influenza A virus (H1N1);Influenza A virus (H2N2);Influenza A virus (H3N2);Influenza A virus (H5N1);morbidity;mortality;Newcastle disease virus;nonhuman;nonviral gene delivery system;pandemic influenza;poultry;priority journal;protein secondary structure;reverse transcription polymerase chain reaction;review;Salmonella enterica serovar Typhimurium;seasonal influenza;seroepidemiology;Spanish influenza;type III secretion system;virion;virology;virus classification;virus envelope;virus genome;virus isolation;virus neutralization;virus replication;virus strain;virus transmission;virus virulence,"El Zowalaty, M. E.;Bustin, S. A.;Husseiny, M. I.;Ashour, H. M.",2013,,10.2217/fmb.13.81,0
549,The ovine respiratory syncytial virus F gene sequence and its diagnostic application,"Ruminant respiratory syncytial viruses (RSVs) are classified into 2 subgroups, ovine RSV and bovine RSV. Although ovine RSV infects cattle, its contribution to bovine respiratory tract disease has not been established, which is an important issue for vaccine development in cattle. Diagnosis by virus isolation or serology has low or variable sensitivity and/or specificity and polymerase chain reaction (PCR) has been recommended as a rapid and sensitive technique for RSV detection. A simple procedure has been developed to detect and identify bovine and ovine RSVs. First, the nucleotide sequence of the ovine RSV fusion (F) gene was determined and compared with representative strains of bovine RSV and human RSV subgroups A and B. The ovine RSV F gene has 85 and 72-73% nucleotide identity with those of bovine RSV and human RSV, respectively. The predicted amino acid sequence of the ovine RSV F gene has 94 and 83-84% amino acid identity with those of bovine RSV and human RSV, respectively. Then PCR primers targeting a specific F gene fragment of bovine and ovine RSV were designed. The primers represented bases 85-103 and the complementary sequence to bases 510-493 of the ovine RSV F gene. A similar PCR product (426 bp) was obtained on agarose gel electrophoresis from bovine RSV and from ovine RSV. The products, however, were unique to the parent virus and could be distinguished by EcoRI or MspI restriction endonuclease cleavage. EcoRI cleaved the ovine product into 2 bands (285 and 141 bp) but failed to affect the bovine RSV PCR product. However, MspI cleaved the bovine product into 2 bands (229 and 197 bp) but had no effect on the ovine product. Also, this assay did not amplify any PCR product with human RSV. The reverse transcription-polymerase chain reaction (RT-PCR) followed by restriction enzyme digestion is a useful and practical approach for detection and differentiation of ruminant respiratory syncytial viruses.",primer DNA;agar gel electrophoresis;animal;animal disease;article;bovine;cattle disease;DNA sequence;gene fusion;genetics;molecular genetics;nucleotide sequence;Human respiratory syncytial virus;reverse transcription polymerase chain reaction;sensitivity and specificity;sheep;sheep disease;virology;virus infection,"Eleraky, N. Z.;Kania, S. A.;Potgieter, L. N.",2001,,,0
550,Accurate classification and hemagglutinin amino acid signatures for influenza A virus host-origin association and subtyping,"Host-origin classification and signatures of influenza A viruses were investigated based on the HA protein for tracking of the HA host of origin. Hidden Markov models (HMMs), decision trees and associative classification for each influenza A virus subtype and its major hosts (human, avian, swine) were generated. Features of the HA protein signatures that were host-and subtype-specific were sought. Host-associated signatures that occurred in different subtypes of the virus were identified. Evaluation of the classification models based on ROC curves and support and confidence ratings for the amino acid class-association rules was performed. Host classification based on the HA subtype achieved accuracies between 91.2% and 100% using decision trees after feature selection. Host-specific class association rules for avian-host origins gave better support and confidence ratings, followed by human and finally swine origin. This finding indicated the lower specificity of the swine host, perhaps pointing to its ability to mix different strains.© 2013 Elsevier Inc.",amino acid;virus hemagglutinin;accuracy;article;bird;decision tree;hidden Markov model;human;Influenza A virus;nonhuman;priority journal;rating scale;receiver operating characteristic;species difference;pig;virus cell interaction;virus classification;virus typing,"ElHefnawi, M.;Sherif, F. F.",2014,,10.1016/j.virol.2013.11.010,0
551,Close linkage of genes encoding receptors for subgroups A and C of avian sarcoma/leucosis virus on chicken chromosome 28,"Avian sarcoma and leucosis viruses (ASLV) are classified into six major subgroups (A to E and J) according to the properties of the viral envelope proteins and the usage of cellular receptors for virus entry. Subgroup A and B receptors are identified molecularly and their genomic positions TVA and TVB are mapped. The subgroup C receptor is unknown, its genomic locus TVC is reported to be genetically linked to TVA, which resides on chicken chromosome 28. In this study, we used two chicken inbred lines that carry different alleles coding for resistance (TVCR) and sensitivity (TFCS) to infection by subgroup C viruses. A backross population of these lines was tested for susceptibility to subgroup C infection and genotyped for markers from chicken chromosome 28. We confirmed the close linkage between TVA and TVC loci. Further, we have described the position of TVC on chromosome 28 relative to markers from the consensus map of the chicken genome.",microsatellite DNA;primer DNA;virus envelope protein;virus receptor;allele;animal;article;Avian sarcoma virus;chicken;chromosome map;classification;comparative study;cross breeding;genetics;phenotype;virology,"Elleder, D.;Plachý, J.;Hejnar, J.;Geryk, J.;Svoboda, J.",2004,,10.1111/j.1365-2052.2004.01118.x,0
552,Identification and genetic characterization of rabies virus from Egyptian water buffaloes (Bubalus bubalis) bitten by a fox,"Rabies is caused by negative strand RNA-virus classified in the genus Lyssavirus, family Rhabdoviridae of the order Mononegavirales. The aim of the present study was to identify and analyze nucleotides sequence of nucleoprotein (N) gene of rabies virus (RABV) from two cases of water buffaloes (Bubalus bubalis) bitten by a fox in Egypt, 2013. The diseased buffaloes showed nervous manifestations with fever. Specimens from brains of the buffaloes with suspected rabies were collected. RABV in collected samples was identified using direct fluorescent antibody (dFA) technique, histopathological examination and reverse transcription-polymerase chain reaction (RT-PCR). Also, nucleotides sequence of partially amplified nucleoprotein (N) gene was compared with the other street strains of RABV available on GenBank. The results revealed that RABV antigen was identified in the brains of diseased buffaloes by dFA technique and the characteristic intracytoplasmic inclusions (Negri bodies) and RABV nucleic acid were detected by histopathology and RT-PCR, respectively. The identified virus showed close genetic relationship with street strains identified previously from dogs in different Governorates in Egypt and with strains identified in Israel and Jordan indicating transmission of the virus between Egyptian Governorates with a potential transmission from and/or to our neighboring countries.",nucleoprotein;rabies virus antigen;unclassified drug;virus antigen;animal tissue;article;controlled study;Egypt;fever;fluorescent antibody technique;fox;gene sequence;histopathology;molecular phylogeny;nonhuman;nucleotide sequence;Rabies virus;reverse transcription polymerase chain reaction;viral genetics;virus identification;water buffalo,"El-Tholoth, M.;El-Beskawy, M.;Hamed, M. F.",2015,,10.1007/s13337-015-0263-y,0
553,Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses,,,"Enault, F.;Briet, A.;Bouteille, L.;Roux, S.;Sullivan, M. B.",2017,,,0
554,The genome of bovine herpesvirus 1 (BHV-1) strains exhibiting a neuropathogenic potential compared to known BHV-1 strains by restriction site mapping and cross-hybridization,,monoclonal antibody;radioisotope;virus DNA;viral protein;Bovine herpesvirus 1;classification;electron microscopy;gene structure;genetic engineering;heredity;nonhuman;nucleic acid hybridization;priority journal;restriction mapping;virus classification,"Engels, M.;Giuliani, C.;Wild, P.",1986,,10.1016/0168-1702(86)90057-2,0
555,Genetic and virulence characterization of classical swine fever viruses isolated in Mongolia from 2007 to 2015,"Classical swine fever (CSF), a highly contagious viral disease affecting domestic and wild pigs in many developing countries, is now considered endemic in Mongolia, with 14 recent outbreaks in 2007, 2008, 2011, 2012, 2014, and 2015. For the first time, CSF viruses isolated from these 14 outbreaks were analyzed to assess their molecular epidemiology and pathogenicity in pigs. Based on the nucleotide sequences of their 5′-untranslated region, isolates were phylogenetically classified as either sub-genotypes 2.1b or 2.2, and the 2014 and 2015 isolates, which were classified as 2.1b, were closely related to isolates from China and Korea. In addition, at least three different viruses classified as 2.1b circulated in Mongolia. Experimental infection of the representative isolate in 2014 demonstrated moderate pathogenicity in 4-week-old pigs, with relatively mild clinical signs. Understanding the diversity of circulating CSF viruses gleans insight into disease dynamics and evolution, and may inform the design of effective CSF control strategies in Mongolia.",5' untranslated region;animal cell;animal experiment;animal model;animal tissue;article;China;classical swine fever;Classical swine fever virus;controlled study;Korea;molecular epidemiology;molecular phylogeny;Mongolia;nonhuman;nucleotide sequence;sequence analysis;viral genetics;virus isolation;virus virulence,"Enkhbold, B.;Shatar, M.;Wakamori, S.;Tamura, T.;Hiono, T.;Matsuno, K.;Okamatsu, M.;Umemura, T.;Damdinjav, B.;Sakoda, Y.",2017,,10.1007/s11262-017-1442-2,0
556,Virology in the 21st century,,gene product;Rotavirus vaccine;virus DNA;viral protein;virus RNA;Wart virus vaccine;acquired immune deficiency syndrome;biological warfare;bovine spongiform encephalopathy;Chikungunya virus;climate change;Creutzfeldt Jakob disease;DNA modification;DNA replication;epidemic;Foot and mouth disease virus;funding;gene sequence;genetic analysis;human;Human immunodeficiency virus infection;immunopathology;influenza;Influenza virus;information processing;medical education;metagenomics;microbial community;molecular biology;nonhuman;oncogene;pandemic;Papillomaviridae;politics;priority journal;public health;risk assessment;RNA interference;RNA sequence;Rotavirus;severe acute respiratory syndrome;short survey;smallpox;somatic cell genetics;vaccination;viral genetics;virology;virus gene;virus genome;virus immunity;virus infection;virus load;virus pathogenesis;virus replication;virus transmission;virus virulence;West Nile virus;zoonosis,"Enquist, L. W.",2009,,10.1128/jvi.00151-09,0
557,Structural similarities of hog cholera virus with togaviruses,,viral protein;arthropod;cell culture;classification;in vitro study;methodology;Pestivirus;pig;virus classification;virus infection;virus purification,"Enzmann, P. J.;Weiland, F.",1978,,,0
558,Viral discovery as a tool for pandemic preparedness,"Emerging diseases are frequently caused by novel or previously unrecognised zoonotic viral pathogens, which tend to originate in and emerge from wildlife. When human or animal cases are first recognised, molecular or serological diagnostic assays specific to them do not yet exist, causing a delay in the identification of an outbreak's aetiologic agent as well as its source. Preparing for the next virus to emerge is a major public health challenge, impeded by a poor understanding of the diversity of potential candidates that exist in wildlife reservoirs. Characterising the diversity of viruses in key wildlife species will help to reduce the time between detection and response in an outbreak situation, and inform public health strategies that reduce the risk of spillover from animal reservoirs. Pathogen discovery techniques such as consensus polymerase chain reaction (cPCR) and next-generation sequencing (NGS) have been used to identify known and novel viruses in animals and humans, but have not been widely used in surveillance programmes. Metagenomic studies have identified novel viruses, new strains of known viruses, and have characterised host microbiomes. While NGS represents an unbiased approach to viral sequence detection, it is constrained by lower sensitivity than conventional PCR, requires substantial bioinformatics capabilities, and is cost prohibitive and therefore not widely available in the regions of the world that are most vulnerable to zoonotic disease emergence. In contrast, consensus PCR uses standard and widely available technologies, has greater sensitivity than NGS, and has also been used to identify novel viruses in wildlife, livestock and humans, though it is limited to detecting target genetic sequences conserved across known groups of viruses. The use of cPCR, in combination, if possible, with NGS and serology, can offer a powerful approach to rapidly identifying aetiologic agents in an outbreak and characterising the virome of key wildlife known to carry zoonotic viruses. Here, the authors review pathogen discovery techniques currently being used in human and animal surveillance programmes and the challenges of using viral discovery to identify novel zoonotic pathogens.",animal;health survey;high throughput sequencing;human;international cooperation;isolation and purification;pandemic;procedures;risk factor;veterinary medicine;virology;virus;virus infection;zoonosis,"Epstein, J. H.;Anthony, S. J.",2017,,10.20506/rst.36.2.2669,0
559,Major transitions in human evolution revisited: A tribute to ancient DNA,"The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this similar to 200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. These approaches promise to soon solve many pending controversies about our own origins that are indecipherable from modern patterns of genetic variation alone, and therefore provide an extremely powerful toolkit for a new generation of molecular anthropologists. (c) 2014 Elsevier Ltd. All rights reserved.",Paleogenomics;Archaic hominins;Neolithic transition;Admixture;Migration;Paleodemography;Selection;Epidemics;Epigenomics;Metagenomics;SPANISH INFLUENZA-VIRUS;MITOCHONDRIAL GENOME SEQUENCE;CLOVIS HUMAN;COPROLITES;HUNTER-GATHERERS;LATE PLEISTOCENE;YERSINIA-PESTIS;LACTASE-PERSISTENCE;PIG DOMESTICATION;MYCOBACTERIUM-TUBERCULOSIS;HORSE DOMESTICATION,"Ermini, L.;Sarkissian, C. D.;Willerslev, E.;Orlando, L.",2015,Feb,,0
560,Viral Communities Among Sympatric Vampire Bats and Cattle,"Vampire bats are the only mammals known to feed exclusively on blood from other animals, often from domestic cattle. We tested the hypothesis that the adaptation of vampire bats to hematophagy would have resulted in shared viral communities among vampire bats and cattle, as a direct result of historic spillover events occurring due to hematophagy. We analyzed the presence of different viruses in sample populations of sympatric bat and prey populations and searched for shared viruses between taxa. A limited number of DNA viral groups were detected within each species. However, there was no evidence for a shared viral community among the vampire bat and cattle populations tested.",animal;bat;bovine;sympatry;virology,"Escalera-Zamudio, M.;Taboada, B.;Rojas-Anaya, E.;Löber, U.;Loza-Rubio, E.;Arias, C. F.;Greenwood, A. D.",2018,,10.1007/s10393-017-1297-y,1
561,Large deletions in the 5'-untranslated region of foot-and-mouth disease virus of serotype C,"Nucleotide sequences of the 5'-untranslated region (5'-UTR), at the 3'-side of the poly C tract, have been compared for 21 isolates of foot-and-mouth disease virus (FMDV) of serotype C from Europe, South America and The Philippines. A deletion of 43 nucleotides is present in the European isolates as compared with most American isolates. A larger deletion of 86 nucleotides is present in some viruses from South America and The Philippines, These deletions include the loss of one or two pseudoknot structures predicted in this region of the 5'-UTR. In addition, multiple point mutations have allowed the derivation of a phylogenetic tree which defines a grouping of isolates very similar to that derived from the capsid gene sequences of the same viruses. The study provides evidence that deletion (or addition) events must be very frequent during evolution of FMDV type C, since viruses which are phylogenetically very closely related (they belong to the same tree branch) may differ in the presence or absence of these deletions. Implications for FMDV evolution are discussed.",article;controlled study;deletion mutant;evolution;Foot and mouth disease virus;nonhuman;phylogeny;Picornaviridae;polymerase chain reaction;priority journal;serotype,"Escarmis, C.;Dopazo, J.;Davila, M.;Palma, E. L.;Domingo, E.",1995,,10.1016/0168-1702(94)00091-p,0
562,Impact of antigenic and genetic drift on the serologic surveillance of H5N2 avian influenza viruses,"Serologic surveillance of Avian Influenza (AI) viruses is carried out by the hemagglutination inhibition (HI) test using reference reagents. This method is recommended by animal health organizations as a standard test to detect antigenic differences (subtypes) between circulating influenza virus, vaccine- and/or reference- strains. However, significant discrepancies between reference antisera and field isolates have been observed during serosurveillance of influenza A viruses in pig and poultry farms. The objective of this study was to examine the effects of influenza virus genetic and antigenic drift on serologic testing using standard HI assays and reference reagents. Low pathogenic AI H5N2 viruses isolated in Mexico between 1994 and 2008 were used for phylogenetic analysis of AI hemagglutinin genes and for serologic testing using antisera produced with year-specific AI virus isolates. Phylogenetic analysis revealed significant divergence between early LPAI H5N2 viruses (1994 - 1998) and more recent virus field isolates (2002 - 2008). Results of the HI test were markedly influenced by the selection of the AI H5N2 virus (year of isolation) used as reference antigen for the assay. These analyses indicate that LPAI H5N2 viruses in Mexico are constantly undergoing genetic drift and that serosurveillance of AI viruses is significantly influenced by the antigen or antisera used for the HI test. Reference viral antigens and/or antisera need to be replaced constantly during surveillance of AI viruses to keep pace with the AI antigenic drift. This strategy should improve the estimation of antigenic differences between circulating AI viruses and the selection of suitable vaccine strains.",influenza vaccine;virus antigen;animal;animal disease;article;avian influenza;epidemiology;genetic drift;genetics;hemagglutination inhibition test;immunology;Influenza A virus (H5N2);isolation and purification;Mexico;molecular genetics;phylogeny;poultry;time;virology,"Escorcia, M.;Carrillo-Sánchez, K.;March-Mifsut, S.;Chapa, J.;Lucio, E.;Nava, G. M.",2010,,10.1186/1746-6148-6-57,0
563,Identification of novel Newcastle disease virus sub-genotype VII-(j) based on the fusion protein,"Newcastle disease virus (NDV) is believed to be the cause of fatal poultry disease worldwide. The fusion (F) protein plays a key role in virus pathogenesis, and it is also used for Newcastle disease virus classification. In this study, we determined the complete coding sequence of the F gene in new velogenic NDV isolates with an intravenous pathogenicity index (IVPI) of 1.8 and a mean death time (MDT) of 72 or 48 h. Complete sequences of the F genes of new Iranian isolates were amplified and sequenced in both directions. These isolates were compared to 195 nucleotide sequences from GenBank (available as of 07/17/2016). A phylogenetic tree was constructed for the F gene, using MEGA6 software with statistical analysis based on 500 bootstrap replicates. Evolutionary distances revealed that the new virulent isolates from Iran belonged to genotype VII in a new distinct sub-genotype named VII-(j). This new sub-genotype showed 3% divergence from genotype VIId. Recombination analysis showed that these new isolates were not recombinant NDVs.",virus fusion protein;animal;bird disease;chicken;classification;genetics;genotype;Iran;isolation and purification;Newcastle disease;Newcastle disease virus;phylogeny;virology,"Esmaelizad, M.;Mayahi, V.;Pashaei, M.;Goudarzi, H.",2017,,10.1007/s00705-016-3189-9,0
564,Equination (inoculation of horsepox): An early alternative to vaccination (inoculation of cowpox) and the potential role of horsepox virus in the origin of the smallpox vaccine Review,"For almost 150years after Edward Jenner had published the ""Inquiry"" in 1798, it was generally assumed that the cowpox virus was the vaccine against smallpox. It was not until 1939 when it was shown that vaccinia, the smallpox vaccine virus, was serologically related but different from the cowpox virus. In the absence of a known natural host, vaccinia has been considered to be a laboratory virus that may have originated from mutational or recombinational events involving cowpox virus, variola viruses or some unknown ancestral Orthopoxvirus. A favorite candidate for a vaccinia ancestor has been the horsepox virus. Edward Jenner himself suspected that cowpox derived from horsepox and he also believed that ""matter"" obtained from either disease could be used as preventative of smallpox. During the 19th century, inoculation with cowpox (vaccination) was used in Europe alongside with inoculation with horsepox (equination) to prevent smallpox. Vaccine-manufacturing practices during the 19th century may have resulted in the use of virus mixtures, leading to different genetic modifications that resulted in present-day vaccinia strains. Horsepox, a disease previously reported only in Europe, has been disappearing on that continent since the beginning of the 20th century and now seems to have become extinct, although the virus perhaps remains circulating in an unknown reservoir. Genomic sequencing of a horsepox virus isolated in Mongolia in 1976 indicated that, while closely related to vaccinia, this horsepox virus contained additional, potentially ancestral sequences absent in vaccinia. Recent genetic analyses of extant vaccinia viruses have revealed that some strains contain ancestral horsepox virus genes or are phylogenetically related to horsepox virus. We have recently reported that a commercially produced smallpox vaccine, manufactured in the United States in 1902, is genetically highly similar to horsepox virus, providing a missing link in this 200-year-old mystery.","Animals;*Cowpox/im [Immunology];Genome, Viral;High-Throughput Nucleotide Sequencing;History, 18th Century;History, 19th Century;History, 20th Century;History, 21st Century;Humans;Orthopoxvirus/ge [Genetics];*Orthopoxvirus/im [Immunology];Phylogeny;Smallpox/pc [Prevention & Control];Smallpox Vaccine/ad [Administration & Dosage];Smallpox Vaccine/hi [History];*Smallpox Vaccine/im [Immunology];Vaccination/hi [History];Vaccinia virus/ge [Genetics];Vaccinia virus/im [Immunology];Vaccinia virus/ip [Isolation & Purification];Variola virus/im [Immunology];0 (Smallpox Vaccine)","Esparza, J.;Schrick, L.;Damaso, C. R.;Nitsche, A.",2017,12 19,,0
565,Orthopoxvirus DNA: Strain differentiation by electrophoresis of restriction endonuclease fragmented virion DNA,"Procedures were developed for purifying intact intracytoplasmic poxvirus particles from infected cells and for isolatig DNA from virions by equilibrium centrifugation in sodium diatrizoate density gradients. The buoyant density of twelve closely related orthopoxviruses purified in these gradients was determined to be 1.25 g/ml, and that of the isolated virion DNAs was 1.1 g/ml. Virion DNA from each of the 12 selected prototype and wild-type viruses was cleaved with three separate site-specific restriction endonucleases, Hin d III, Sal I, and Bam HI, and the fragments (molecular weights 0.5 x 106 to 20 x 106) were separated by agarose gel electrophoresis. Characteristic DNA frgment migration patterns observed in the gels permitted classification of the viruses. By comparting profiles of Hin d III cleaved DNAs we were able to group the viruses into 4 species: cowpox, vaccinia, monkeypox (2 isolates), and variola (8 isolates). Viruses from variola major infection could be differentiated from viruses from variola minor infection. Isolates within species (strains) were also differentiated, mainly by comparing the gel electrophoresis profiles of Sal I digested DNA from the viruses.",radioisotope;virus DNA;methodology;Poxviridae;theoretical study,"Esposito, J. J.;Obijeski, J. F.;Nakano, J. H.",1978,,,0
566,Zoonotic poxviruses,"Poxviruses compromise a group of long known important pathogens including some zoonotic members affecting lifestock animals and humans. While whole genome sequence analysis started to shed light into the molecular mechanisms underlying host cell infection, viral replication as well as virulence, our understanding of poxvirus maintenance in nature and their transmission to humans is still poor. During the last two decades, reports on emerging human monkeypox outbreaks in Africa and North America, the increasing number of cowpox virus infections in cats, exotic animals and humans and cases of vaccinia virus infections in humans in South America and India reminded us that - beside the eradicated smallpox virus - there are other poxviruses that can cause harm to men. We start to learn that the host range of some poxviruses is way broader than initially thought and that mainly rodents seem to function as virus reservoir. The following review is aiming to provide an up-to-date overview on the epidemiology of zoonotic poxviruses, emphasizing orthopoxviruses. By outlining the current knowledge of poxvirus transmission, we hope to raise the awareness about modes of acquisition of infections and their proper diagnosis. © 2009 Elsevier B.V. All rights reserved.",smallpox vaccine;animal disease;biological warfare;chickenpox;Chordopoxvirinae;Cowpox virus;differential diagnosis;electron microscopy;host range;human;infection control;infection risk;monkeypox;Monkeypox virus;nonhuman;Parapoxvirus;poxvirus infection;real time polymerase chain reaction;review;smallpox;Vaccinia virus;viral genetics;virus cell interaction;virus classification;virus replication;virus transmission;virus virulence;zoonosis,"Essbauer, S.;Pfeffer, M.;Meyer, H.",2010,,10.1016/j.vetmic.2009.08.026,0
567,Antigenic and genetic relationships between European very virulent infectious bursal disease viruses and an early West African isolate,"The antigenic and genetic relationships between very virulent (vv) infectious bursal disease viruses (IBDV) from different countries were investigated. Antigenic characterization was performed using an antigen-capture ELISA based on a panel of seven neutralizing monoclonal antibodies (Mabs), which probe at least three VP2-located antigenic domains. All these domains are reactive in the Faragher 52/70 (F52/70) reference strain for European classical serotype 1 IBDV, Genomic characterization was achieved by reverse transcription, amplification and direct sequencing of a genome fragment encoding the VP2 variable domain. Eleven vv isolates from France were compared to the British, Dutch and Belgian UK661, DV86 and 849VB viruses, and to an early vv isolate obtained from the Ivory Coast in 1988, All viruses exhibited antigenic profiles characterized by no binding of Mabs 3 and 4, Lack of binding of Mabs 3 and 4 might thus be helpful for differentiating classical and vvIBDVs, None of the non-French strains resembled the 91168 and 94432 French isolates, which did not bind Mabs 6, 7 or 8, The genetic analysis revealed close relationships between all the European viruses, which differed from one another by no more than 12 nucleotides and 3 amino acids. The African isolate was markedly different, with at least 22 nucleotide and six amino acid differences to all the European viruses, including the F52/70 virus. Phylogenetic analysis based on the neighbour-joining and parsimony methods suggest that the African virus may belong to a genetically distinct lineage of highly pathogenic IBDVs.",MONOCLONAL-ANTIBODIES;MOLECULAR-BASIS;SEQUENCE;STRAINS;EXPRESSION;POULTRY;FRANCE,"Eterradossi, N.;Arnauld, C.;Tekaia, F.;Toquin, D.;Le Coq, H.;Rivallan, G.;Guittet, M.;Domenech, J.;van den Berg, T. P.;Skinner, M. A.",1999,Feb,,0
568,Tracing the origin and co-phylogeny of the caliciviruses,"Caliciviruses infect a wide range of mammalian hosts and include the genus Norovirus, the major cause of food-borne viral gastroenteritis in humans. Using publicly available sequence data and phylogenetic analysis tools, the origins and virus-host co-phylogeny of these viruses were investigated. Here, evidence is presented in support of host switching by caliciviruses, but showing that zoonotic transfer does not appear to have occurred in the history of these viruses. The age or demography of the caliciviruses cannot yet be estimated with any firm degree of support, but further studies of this family, as new dated sequences become available, could provide key information of importance to human health and in understanding the emergence of food-borne disease.","Animals;*Caliciviridae/ge [Genetics];Cats/ge [Genetics];Cattle/ge [Genetics];Database Management Systems;Female;Genome;Genome, Viral;Hares/ge [Genetics];Humans/ge [Genetics];Norovirus/ge [Genetics];*Phylogeny;Rabbits/ge [Genetics];Sea Lions/ge [Genetics];Species Specificity;Swine/ge [Genetics]","Etherington, G. J.;Ring, S. M.;Charleston, M. A.;Dicks, J.;Rayward-Smith, V. J.;Roberts, I. N.",2006,May,,0
569,Antigenic characterization of the inclusion body hepatitis virus,"Proof that inclusion body hepatitis of chickens (IBHC) is caused by a virus (IBHV) was established in 1973. Characterization of IBHV has been conducted by employing the standard criteria for virus classification. The results have indicated that IBHV is a member of the avian adenovirus group. However, no antigenic relationship was found between IBHV and two other avian adenovirus isolates (CELO and Indiana C) as observed by hemagglutination (HA) and virus serum neutralization tests. Another adenovirus isolate was found to be serologically different from IBHV (Tipton strain) but it incited typical IBHV. This antigen was able to give a specific precipitin reaction with serums from chickens previously exposed to IBHV. Repeated embryo passage of IBHV lowered its pathogenicity for susceptible chickens. Protection of chickens against IBHV challenge was obtained by vaccination with high embryo passage IBHV (Tipton strain). It was also found that subcutaneous administration of the vaccine virus induced a better immune response than the eye drop route as observed by the virus serum neutralization index obtained.",protective agent;virus antigen;Adenoviridae;antibody production;avian virus;bird;Chick embryo lethal orphan virus;hemagglutination;liver;methodology;theoretical study;vaccination;virus characterization;virus inhibition,"Fadly, A. M.;Winterfield, R. W.",1975,,,0
570,Re-emergence of Peste des Petits Ruminants virus in 2015 in Morocco: Molecular characterization and experimental infection in Alpine goats,"Peste des Petits Ruminants (PPR) is a transboundary viral disease of small ruminants that causes huge economic losses in Africa, The Middle East and Asia. In Morocco, the first PPR outbreak was notified in 2008. Since then no cases were reported for seven years, probably due to three successive vaccination campaigns during 2008–2011 and close surveillance at the border areas. In June 2015, the disease re-emerged in Morocco, raising questions about the origin of the virus. The PPR virus was confirmed by qRT-PCR and virus was isolated from clinical samples on VeroNectin-4 cells. The disease was experimentally reproduced in Alpine goats using both sheep and goat derived outbreak isolates. Molecular characterization of the 2015 Moroccan PPR isolate confirmed the identity of the virus as lineage IV, closely related to the 2012 Algerian (KP793696) and 2012 Tunisian (KM068121) isolates and significantly distinct from the previous PPRV Morocco 2008 strain (HQ131927). Therefore this study confirms a new incursion of PPR virus in Morocco during 2015 and highlights the urgency of implementation of a common control strategy to combat PPR in Maghreb region in North Africa.",animal experiment;animal model;article;controlled study;experimental infection;gene sequence;goat;Morocco;nonhuman;nucleotide sequence;Peste-des-petits-ruminants virus;phylogeny;real time polymerase chain reaction;virus identification;virus isolation;virus load,"Fakri, F.;Embarki, T.;Parida, S.;Bamouh, Z.;Jazouli, M.;Mahapatra, M.;Tadlaoui, K.;Fassi-Fihri, O.;Richardson, C. D.;Elharrak, M.",2016,,10.1016/j.vetmic.2016.11.006,0
571,Genetic heterogeneity of bovine viral diarrhoea virus in Italy,"The genetic characteristics, of 38 field isolates of bovine viral diarrhoea virus (BVDV) collected in 1999 from sick or healthy and persistently infected cattle of dairy farms situated in northern Italy, were investigated. A partial 5′-untranslated region (5′-UTR) sequence of each isolate was determined and a phylogenetic analysis was performed. All the isolates were classified as belonging to the BVDV-1 genotype and could be assigned to different BVDV-1 groups, namely BVDV-1b (n = 20), BVDV-1d (n = 6) and BVDV-1e (n = 10). Two remaining isolates could be classified as BVDV-1f and BVDV-1h, respectively. These results provided evidence for genetic heterogeneity of BVDV in Italy, and contribute to a better knowledge of the circulation of BVDV strains, and to their classification.",5' untranslated region;article;Bovine viral diarrhea virus 1;cattle disease;controlled study;dairying;Flavivirus;gene sequence;genetic heterogeneity;genetic trait;genotype;Italy;nonhuman;nucleotide sequence;Pestivirus;phylogeny;sequence analysis;unindexed sequence;virus classification;virus isolation;virus strain,"Falcone, E.;Cordioli, P.;Tarantino, M.;Muscillo, M.;La Rosa, G.;Tollis, M.",2003,,10.1023/a:1025793708771,0
572,Frequency of bovine viral diarrhea virus detected in subpopulations of peripheral blood mononuclear cells in persistently infected animals and health outcome,"Bovine viral diarrhea viruses (BVDV) cause acute and persistent infections. Acute infection results in generalized immunosuppression characterized by a decrease in circulating lymphocytes as a result of depletion of CD4+ and CD8 + T cell populations. Persistent infection with BVDV is the result of immune tolerance and is generally not associated with lymphocytopenia. The health outcome of persistently infected (PI) calves varies widely; some die of mucosal disease, some succumb to ill thrift and others appear normal and survive to adulthood. Detection of BVDV at the single lymphoid cell level is important to the study of subpopulations of peripheral blood mononuclear cells (PBMC) during BVDV infections, however there are few methods available for the detection and quantification of BVDV at this level. To circumvent this difficulty, a novel flow cytometry-based PrimeFlow RNA assay using in-situ detection of BVDV was developed. This assay was used to evaluate differences in viral distribution within subpopulations of PBMC over time in PI calves carrying one of two different species of BVDV (type 1 and type 2). Calves were sampled at 3 different time points approximately one month apart. During the course of the study, a subset of the calves died from ill thrift. Mucosal disease was not indicated in any of the deaths. Using RNA probes specific for the BVDV N<sup>pro</sup>-E<sup>rns</sup> coding regions for each respective virus, BVDV RNA was detected in all PBMC of PI that appeared clinically healthy. Calves that succumbed to ill thrift were found to have no or little virus in T cells. The clearance of virus from T cells suggests a breakdown in immune tolerance in these calves. This is the first report of a pattern observed in the viral load in the T cell subpopulations and survival in PI calves.","Animals;*Bovine Virus Diarrhea-Mucosal Disease/im [Immunology];Cattle;Chronic Disease/ve [Veterinary];Diarrhea Virus 1, Bovine Viral/ge [Genetics];Diarrhea Virus 2, Bovine Viral/ge [Genetics];Diarrhea Viruses, Bovine Viral/ge [Genetics];*Diarrhea Viruses, Bovine Viral;Female;Flow Cytometry/ve [Veterinary];High-Throughput Nucleotide Sequencing/ve [Veterinary];*Leukocytes, Mononuclear/vi [Virology];Lymphocyte Count/ve [Veterinary]","Falkenberg, S. M.;Dassanayake, R. P.;Walz, P.;Casas, E.;Neill, J. D.;Ridpath, J. F.",2019,Jan,,0
573,Molecular characterization and phylogenetic analysis of pseudorabies virus variants isolated from Guangdong province of southern China during 2013-2014,"Outbreaks of pseudorabies (PR) have occurred in southern China since late 2011, resulting in significant economic impacts on the swine industry. To identify the cause of PR outbreaks, especially among vaccinated pigs, 11 pseudorabies virus (PRV) field strains were isolated from Guangdong province during 2013-2014. Their major viral genes (gE, TK, gI, PK, gD, 11K, and 28K) were analyzed in this study. Insertions or deletions were observed in gD, gE, gI and PK genes compared with other PRV isolates from all over the world. Furthermore, sequence alignment showed that insertions in gD and gE were unique molecular characteristics of the new prevalent PRV strains in China. Phylogenetic analysis showed that our isolates were clustered in an independent branch together with other strains isolated from China in recent years, and that they showed a closer genetic relationship with earlier isolates from Asia. Our results suggest that these isolates are novel PRV variants with unique molecular signatures.",viral protein;animal;China;classification;epidemic;genetics;metabolism;nucleotide sequence;phylogeny;physiology;pig;pseudorabies;Pseudorabies virus;sequence alignment;swine disease;veterinary medicine;virology,"Fan, J.;Zeng, X.;Zhang, G.;Wu, Q.;Niu, J.;Sun, B.;Xie, Q.;Ma, J.",2016,,10.4142/jvs.2016.17.3.369,0
574,"Identification and characterization of porcine kobuvirus variant isolated from suckling piglet in Gansu province, China",,,"Fan, S.;Sun, H.;Ying, Y.;Gao, X.;Wang, Z.;Yu, Y.;Li, Y.",2013,,,0
575,"Analysis of Egg-adapted Mutations in Influenza A H1N1pdm09 Viruses in Hubei Province of China, 2013-2014","Influenza A H1N1pdm09 Virus; Chicken embryo; Phylogenetic tree; Egg-adaptation; Antigenic site; Drug-resistance site; Abstract: To investigate egg-adapted mutation in influenza A H1N1pdm09 viruses isolated from the Hubei influenza surveillance network, a comparative analysis was performed of three influenza A H1N1pdm09 viruses isolated in chicken embryo and the corresponding MDCK cell-derived viruses. Analyses included examination of the phylogenetic tree, evolutionary rates, amino acid substitutions, egg-adapted mutation and homology modeling. We found differences between the egg-adapted viruses and MDCK cell-derived viruses based on phylogenetic trees and evolutionary rates; the viruses showed a trend of "" NA>HA>MP"". Four amino acid substitutions(Q223R,V527 I,M19Iand H275Y)were found in three egg-adapted viruses.Q223 Rand V527Iwere present in the haemagglutinin protein, while M19I and H275Y were detected in neuraminidase.The Q223R mutation changed the structure of antigenic sites between Sb and Ca2. H275Y is a classic neuraminidase resistance mutation. The results suggest that the egg-adapted mutations were introduced when influenza viruses were isolated in chicken embryos from the Hubei influenza surveillance network. These mutations may affect the selection of vaccine candidates and vaccine efficacy; therefore, monitoring of egg-adapted mutations should be strengthened in the influenza surveillance network.",viral protein;adaptation;animal;chemistry;chick embryo;China;classification;genetics;human;influenza;Influenza A virus (H1N1);isolation and purification;metabolism;mutation;ovum;phylogeny;physiology;virology,"Fang, B.;Liu, L.;Ye, G.;Li, X.;Yu, X.;Jiang, Y.",2016,,,0
576,Influenza A virus neuraminidase: regions of the protein potentially involved in virus-host interactions,"Phylogenetically informative amino acid positions (PIPs) were identified in influenza A neuraminidases of subtypes N1 and N2. Neuraminidase evolves in a lineage-specific way as the virus adapts to a new host or changes to evade the host's immune system. Thus, many PIPs undoubtedly identify positions involved in virus-host interactions. Phylogenetically important regions (PIRs) are defined as several PIPs near one another. There are 15 PIRs on N1 and 12 on N2, seven of which are shared between the two subtypes. Many PIRs are coincident with antigenic or glycosylation sites. Other PIRs may represent additional antigenic sites or may be involved in other aspects of virus-host biology.","Amino Acids/me [Metabolism];Animals;Antigens, Viral/me [Metabolism];Binding Sites;Birds;Humans;Influenza A virus/cl [Classification];*Influenza A virus/en [Enzymology];Influenza A virus/ph [Physiology];Neuraminidase/cl [Classification];*Neuraminidase/me [Metabolism];Phylogeny;Swine;0 (Amino Acids);0 (Antigens, Viral)","Fanning, T. G.;Reid, A. H.;Taubenberger, J. K.",2000,Oct 25,,0
577,Selection of vaccine strains of foot and mouth disease virus for use in southern Africa,"In the countries of Southern Africa, types SAT 1, SAT 2 and SAT 3 (SAT: Southern African Territories) of foot and mouth disease (FMD) virus are the most widely represented, especially the SAT 2 virus. Since 1982, examinations have been conducted on 139 isolates of these virus types. Other viruses, types O and A, have been detected in the north of this area. The typing and sub-typing of viruses with the complement fixation (CF) test can be improved by using panels of monoclonal antibodies (MAbs), which provide an accurate antigenic profile of a new strain. A total of 33 SAT 2 strains have been investigated using MAbs, and the results enable the classification of viruses into groups presenting the same profile. The author presents comparisons of isolates and vaccine viruses using conventional methods of serotyping--CF and virus neutralisation (VN) tests--as well as profiling the isolates using MAbs. Both manners of analysis provide information on the relationships between the viruses. The CF and VN tests give details on how animals responded against a particular isolate and how this antibody response would recognise another isolate; from this, the serological relationships can be proposed with respect to how different isolates might induce a humoral immune response. With MAb profiling, details of antigenic relationships between the isolates are obtained, enabling the identification of individual epitopic variations. These analyses can provide the potential to place different isolates into 'antigenic' groups. When compared with vaccine viruses, one can attempt to identify the vaccine virus with the closest profile to the isolate group. Immunological analysis (e.g. using the CF tests employed in this paper) can provide further information on the relationship between a particular vaccine and an antigenic group identified by MAb profiling. Of course, this MAb profiling can provide essential information in a very short time, which is of particular benefit in an emergency situation. Confirmation of the conclusions from the profiling would then be forthcoming through the serological analyses. Such combined analyses offer a more extensive identification of antigenic and immunogenic relationships between FMD virus isolates, as well as between isolates and vaccine viruses.",monoclonal antibody;virus antibody;virus antigen;virus vaccine;Africa;animal;animal disease;antibody specificity;Aphthovirus;article;cell line;classification;comparative study;complement fixation test;cytology;enzyme linked immunosorbent assay;epidemic;foot and mouth disease;hybridoma;immunology;kidney;mouse;serodiagnosis;serotyping;sheep;pig;virology,"Fargeaud, D.",1995,,,0
578,Intra-epidemic genome variation in highly pathogenic African swine fever virus (ASFV) from the country of Georgia,"BACKGROUND: African swine fever virus (ASFV) causes an acute hemorrhagic infection in suids with a mortality rate of up to 100%. No vaccine is available and the potential for catastrophic disease in Europe remains elevated due to the ongoing ASF epidemic in Russia and Baltic countries. To date, intra-epidemic whole-genome variation for ASFV has not been reported. To provide a more comprehensive baseline for genetic variation early in the ASF outbreak, we sequenced two Georgian ASFV samples, G-2008/1 and G-2008/2, derived from domestic porcine blood collected in 2008. METHODS: Genomic DNA was extracted directly from low-volume ASFV PCR-positive porcine blood samples and subjected to next generation sequencing on the Illumina Miseq platform. De novo and mapped sequence assemblies were performed using CLCBio software. Genomic illustrations, sequence alignments and assembly figures were generated using Geneious v10.2.4. Sequence repeat architecture was analyzed using DNASTAR GeneQuest 14.1.0. RESULTS: The G-2008/1 and G-2008/2 genomes were distinguished from each other by coding changes in seven genes, including MGF 110-1 L, X69R, MGF 505-10R, EP364R, H233R, E199L, and MGF 360-21R in addition to eight homopolymer tract variations. The 2008/2 genome possessed a novel allele state at a previously undescribed intergenic repeat locus between genes C315R and C147L. The C315R/C147L locus represents the earliest observed variable repeat sequence polymorphism reported among isolates from this epidemic. No sequence variation was observed in conventional ASFV subtyping markers. The two genomes exhibited complete collinearity and identical gene content with the Georgia 2007/1 reference genome. Approximately 56 unique homopolymer A/T-tract variations were identified that were unique to the Georgia 2007/1 genome. In both 2008 genomes, within-sample sequence read heterogeneity was evident at six homopolymeric G/C-tracts confined to the known hypervariable ~ 7 kb region in the left terminal region of the genome. CONCLUSIONS: This is the first intra-epidemic comparative genomic analysis reported for ASFV and provides insight into the intra-epidemic microevolution of ASFV. The genomes reported here, in addition to the G-2007/1 genome, provide an early baseline for future genome-level comparisons and epidemiological tracing efforts.","*African Swine Fever/ep [Epidemiology];*African Swine Fever Virus/ge [Genetics];Animals;Base Sequence;*DNA, Viral/bl [Blood];DNA, Viral/ge [Genetics];Disease Outbreaks;*Genome, Viral/ge [Genetics];Georgia (Republic)/ep [Epidemiology];High-Throughput Nucleotide Sequencing;*Polymorphism, Genetic/ge [Genetics];Sequence Alignment;Sequence Analysis, DNA;Swine;Viral Proteins/ge [Genetics];0 (DNA, Viral);0 (Viral Proteins)","Farlow, J.;Donduashvili, M.;Kokhreidze, M.;Kotorashvili, A.;Vepkhvadze, N. G.;Kotaria, N.;Gulbani, A.",2018,12 14,,1
579,Extraneous agent detection in vaccines - A review of technical aspects,"The quality and safety of commercial vaccines have a profound importance. Contrary to all precautions and efforts the use of biological material in vaccine development and production may lead to potential contamination of the vaccines with known and unknown extraneous agents (EAs).In veterinary field official lists of EAs have been compiled as legal framework to describe the potential agents, which must be tested during manufacture of vaccines. Nevertheless, detection of known and unknown contaminants in vaccines is a common duty for manufacturers and authorities of both veterinary and human field sharing similar needs of special technical approaches. State-of-art molecular methods such as randomly primed PCR combined with massive parallel sequencing (MPS) or microarrays may open new perspectives in extraneous agent testing. The robustness and efficacy of this technical approach in vaccine control was clearly demonstrated on a human vaccine example when porcine circovirus type 1 (PCV1) contamination was revealed in Rotarix, a human rotavirus vaccine. The consequences and implications are reviewed hereby from a veterinary regulatory point of view. © 2012 The International Alliance for Biological Standardization.",chickenpox vaccine;inactivated vaccine;live vaccine;measles mumps rubella vaccine;measles vaccine;Newcastle disease vaccine;poliomyelitis vaccine;Rotavirus vaccine;rubella vaccine;yellow fever vaccine;Circoviridae infection;diarrhea;drug determination;drug fatality;drug legislation;drug purity;drug quality;drug safety;drug screening;drug sensitivity;high throughput screening;human;metagenomics;microarray analysis;nonhuman;postweaning multisystemic wasting syndrome;priority journal;real time polymerase chain reaction;review;sensitivity analysis;sensitivity and specificity;vaccine production;virus detection;rotarix;rotateq,"Farsang, A.;Kulcsár, G.",2012,,10.1016/j.biologicals.2012.04.004,0
580,Xenosurveillance reflects traditional sampling techniques for the identification of human pathogens: A comparative study in West Africa,"Background Novel surveillance strategies are needed to detect the rapid and continuous emergence of infectious disease agents. Ideally, new sampling strategies should be simple to implement, technologically uncomplicated, and applicable to areas where emergence events are known to occur. To this end, xenosurveillance is a technique that makes use of blood collected by hematophagous arthropods to monitor and identify vertebrate pathogens. Mosquitoes are largely ubiquitous animals that often exist in sizable populations. As well, many domestic or peridomestic species of mosquitoes will preferentially take blood-meals from humans, making them a unique and largely untapped reservoir to collect human blood. Methodology/Principal findings We sought to take advantage of this phenomenon by systematically collecting blood-fed mosquitoes during a field trail in Northern Liberia to determine whether pathogen sequences from blood engorged mosquitoes accurately mirror those obtained directly from humans. Specifically, blood was collected from humans via finger-stick and by aspirating bloodfed mosquitoes from the inside of houses. Shotgun metagenomic sequencing of RNA and DNA derived from these specimens was performed to detect pathogen sequences. Samples obtained from xenosurveillance and from finger-stick blood collection produced a similar number and quality of reads aligning to two human viruses, GB virus C and hepatitis B virus. Conclusions/Significance This study represents the first systematic comparison between xenosurveillance and more traditional sampling methodologies, while also demonstrating the viability of xenosurveillance as a tool to sample human blood for circulating pathogens.",HEPATITIS-B-VIRUS;PUBLIC-HEALTH SURVEILLANCE;INFECTED POULTRY FARM;REAL-TIME;SEQUENCING PROJECTS;DISEASE OUTBREAK;HOST PREFERENCE;ZIKA;VIRUS;EMERGENCE;INFLUENZA,"Fauver, J. R.;Weger-Lucarelli, J.;Fakoli, L. S.;Bolay, K.;Bolay, F. K.;Diclaro, J. W.;Brackney, D. E.;Foy, B. D.;Stenglein, M. D.;Ebel, G. D.",2018,Mar,,0
581,Duck gut viral metagenome analysis captures snapshot of viral diversity,"BACKGROUND: Ducks (Anas platyrhynchos) an economically important waterfowl for meat, eggs and feathers; is also a natural reservoir for influenza A viruses. The emergence of novel viruses is attributed to the status of co-existence of multiple types and subtypes of viruses in the reservoir hosts. For effective prediction of future viral epidemic or pandemic an in-depth understanding of the virome status in the key reservoir species is highly essential. METHODS: To obtain an unbiased measure of viral diversity in the enteric tract of ducks by viral metagenomic approach, we deep sequenced the viral nucleic acid extracted from cloacal swabs collected from the flock of 23 ducks which shared the water bodies with wild migratory birds. RESULT: In total 7,455,180 reads with average length of 146 bases were generated of which 7,354,300 reads were de novo assembled into 24,945 contigs with an average length of 220 bases and the remaining 100,880 reads were singletons. The duck virome were identified by sequence similarity comparisons of contigs and singletons (BLASTx E score, <10(-3)) against viral reference database. Numerous duck virome sequences were homologous to the animal virus of the Papillomaviridae family; and phages of the Caudovirales, Inoviridae, Tectiviridae, Microviridae families and unclassified phages. Further, several duck virome sequences had homologous with the insect viruses of the Poxviridae, Alphatetraviridae, Baculoviridae, Densovirinae, Iflaviridae and Dicistroviridae families; and plant viruses of the Secoviridae, Virgaviridae, Tombusviridae and Partitiviridae families, which reflects the diet and habitation of ducks. CONCLUSION: This study increases our understanding of the viral diversity and expands the knowledge about the spectrum of viruses harboured in the enteric tract of ducks.",,"Fawaz, M.;Vijayakumar, P.;Mishra, A.;Gandhale, P. N.;Dutta, R.;Kamble, N. M.;Sudhakar, S. B.;Roychoudhary, P.;Kumar, H.;Kulkarni, D. D.;Raut, A. A.",2016,,,0
582,Inactivation of viruses of different taxonomic groups by cuprous sulphate,"Study results of inactivated effects exerted by cuprous sulphate on viruses of different taxonomy groups are summarized in the paper. Cuprous sulphate is a simple and reliable agent in inactivation of viruses of classical porcine fever, Aujeszky's disease and bovine infectious rhinotracheitis. Its inactivation action is based on the ability to reduce the viral genome to low-molecular fragment. Apart from inactivation of the virus material, a decreased level of protective antibody determinants is observed when cuprous sulphate is used in case of sheep catarrhal fever.",copper sulfate;virus antibody;virus DNA;virus RNA;virus vaccine;animal;article;blood;Bluetongue orbivirus;comparative study;drug effect;genetics;immunology;Bovine herpesvirus 1;metabolism;Pestivirus;Pseudorabies virus;sheep;sheep disease;temperature;time;virus inactivation,"Fedorov, D. G.;Balysheva, V. I.;Zhesterev, V. I.;Tsybanov, S. Z.;Zakutskii, N. I.;Slivko, V. V.",2004,,,0
583,"Role of the mosquitoes Culex pipienis f. pipiens and Cx. pipiens f. molestus (Diptera, Culicidae) in the spread of West Nile virus in the south of Russia","Cx. pipiens is one of the major vectors of West Nile virus in the south of Russia and it is represented by the autogenic form, molestus, and the non-autogenic form, pipiens. The spatial distribution of its larvae and food preferences of females was investigated to assess the potential role of each form in the spread of the virus. The taxonomic status of the mosquitoes was determined from their capacity for autogenicity (543 specimens) and the type of mitochondrial DNA (348 specimens). The mosquitoes of the pipiens form were shown to develop in the open urban and rural reservoirs and the females were non-autogenic. Cx. pipiens form molestus was found only in the urban biotopes, mainly in the flooded basements and, in some years, also in the open reservoirs where it formed a mixed population with Cx. pipiens form pipiens. Both autogenic (85-95.2%) and non-autogenic specimens were identified among the females with the mitotype in form molestus. Genetic analysis of Cx. pipiens females collected under the Berezantsev bell and in the trap with a bird showed that both forms were attracted to man and the bird. The findings suggest that Cx. pipiens form pipiens can transmit West Nile virus to humans both in the town and in its suburb and Cx. pipiens form molestus can only in urban areas.",mitochondrial DNA;animal;animal dispersal;bird;classification;Culex;disease carrier;female;genetics;genotype;human;larva;male;physiology;Russian Federation;species difference;transmission;virology;West Nile fever;West Nile virus,"Fedorova, M. V.;Shaĭkevich, E. V.",2013,,,0
584,Molecular detection and characterization of human gyroviruses identified in the ferret fecal virome,"The recently described novel gyroviruses may infect chickens and/or humans; however, their pathogenic potential is unknown. In our metagenomic investigation, we detected many of the novel gyroviruses in the fecal viromes of ferrets with lymph node and organ enlargement. The complete genomic sequences of selected gyrovirus strains showed 90.7-99.4 % similarity to homologous reference gyrovirus strains. This study did not demonstrate an association between gyrovirus shedding from ferrets and the observed background disease; however, it provides evidence for genetic diversity among gyroviruses and raises the possibility that pet ferrets may transmit gyroviruses to heterologous hosts, e.g., humans.",virus DNA;animal;chemistry;classification;DNA sequence;feces;Mustela putorius furo;genetic variability;genetics;Gyrovirus;isolation and purification;sequence homology;virology;virus genome,"Fehér, E.;Pazár, P.;Kovács, E.;Farkas, S. L.;Lengyel, G.;Jakab, F.;Martella, V.;Bányai, K.",2014,,10.1007/s00705-014-2203-3,0
585,Genome sequence analysis of a distinctive Italian infectious bursal disease virus,"In a recent study, an emerging infectious bursal disease virus (IBDV) genotype (ITA) was detected in IBDV-live vaccinated broilers without clinical signs of infectious bursal disease (IBD). VP2 sequence analysis showed that strains of the ITA genotype clustered separately from vaccine strains and from other IBDV reference strains, either classic or very virulent. In order to obtain a more exhaustive molecular characterization of the IBDV ITA genotype and speculate on its origin, genome sequencing of the field isolate IBDV/Italy/1829/2011, previously assigned to the ITA genotype, was performed, and the sequences obtained were compared to the currently available corresponding sequences. In addition, phylogenetic and recombination analyses were performed. Interestingly, multiple amino acid (AA) sequence alignments revealed that the IBDV/Italy/1829/2011 strain shared several AA residues with very virulent IBDV strains as well as some virulence markers, especially in the VP1 protein. Nevertheless, sequence analysis demonstrated the presence of several residues typical of IBDV strains at a low degree of virulence in the IBDV/Italy/1829/2011 strain. Although homologous recombination and reassortant phenomena may occur naturally among different IBDV strains, no evidence of those events was found in the genome of the IBDV/Italy/1829/2011 strain, which was confirmed to be a genetically distinctive IBDV genotype.",virus RNA;animal;bird disease;birnavirus infection;bursa Fabricii;chicken;genetics;genotype;infectious bursal disease virus;Italy;metabolism;phylogeny;physiology;sequence alignment;sequence analysis;veterinary medicine;virology,"Felice, V.;Franzo, G.;Catelli, E.;Di Francesco, A.;Bonci, M.;Cecchinato, M.;Mescolini, G.;Giovanardi, D.;Pesente, P.;Lupini, C.",2017,,10.3382/ps/pex278,0
586,First assessment of classical swine fever marker vaccine candidate CP7_E2alf for oral immunization of wild boar under field conditions,"Oral vaccination against classical swine fever (CSF) is a potent tool to control disease outbreaks in wild boar. So far, vaccination campaigns have been carried out using live attenuated vaccines that do not allow serological differentiation of infected from vaccinated animals (DIVA). Although this drawback is acceptable for wild boar, the use of marker vaccines would facilitate studies on disease and vaccination dynamics. Recently, the CSF marker vaccine candidate CP7_E2alf was assessed for oral immunization under laboratory conditions. Promising results prompted efforts to study the vaccine candidate under field conditions and in bait formulation. In this context, two oral vaccination campaigns were carried out with CP7_E2alf bait vaccines in two areas called 'faunistic-hunting farms' in the region of Umbria, Italy. One campaign was conducted using single vaccination, the second with the routinely employed double vaccination strategy. Both campaigns were carried out before concerted hunting actions were performed. Bait uptake, vaccine virus detection and antibody responses were assessed along with inspections upon gutting. As a comparator, seven wild boar were hand-fed with baits under laboratory conditions. In the field, bait uptake ranged from 63.7% to 98.7%, whereas antibody prevalence reached only 33.3-35.1%. The marker serology showed a strong influence of sample quality on the test outcome with a total of 85% of samples being classified correctly. Vaccine virus was not detectable. Under hand feeding conditions, six out of seven wild boar took up at least one bait, and five of them showed detectable antibody levels seven weeks after vaccination. These results were supplemented by stability tests. Appropriate stability of vaccine virus was shown both under field and laboratory conditions. In total, most results were in line with our expectations. However, optimization of the DIVA assay has to be attempted in the future. © 2014.",CP7_E2alf virus vaccine;iophenoxic acid;live vaccine;marker vaccine;neutralizing antibody;octopamine;oxytetracycline;unclassified drug;virus RNA;virus vaccine;animal experiment;animal hunting;animal model;antibody detection;antibody response;antibody titer;article;cattle farming;controlled study;environmental temperature;enzyme linked immunosorbent assay;feeding;female;good manufacturing practice;incubator;laboratory diagnosis;limit of detection;male;nonhuman;outcome assessment;Pestivirus;pleura fluid;priority journal;reverse transcription polymerase chain reaction;room temperature;seroconversion;seroprevalence;tonsil;transgenic organism;vaccination;viral disease ELISA kit;virus detection;virus titration;European wild boar;HerdChek CSFV Ab ELISA;PrioCHECK Erns ELISA,"Feliziani, F.;Blome, S.;Petrini, S.;Giammarioli, M.;Iscaro, C.;Severi, G.;Convito, L.;Pietschmann, J.;Beer, M.;De Mia, G. M.",2014,,10.1016/j.vaccine.2014.02.006,0
587,Co-localization of and interaction between duck enteritis virus glycoprotein H and L,"Background: Duck Enteritis Virus (DEV), belonging to the α-herpesvirus subfamily, is a linear double-stranded DNA virus. Glycoprotein H and L (gH and gL), encoded by UL22 and UL1, are conserved in the family of herpesviruses. They play important roles as gH/gL dimers during viral entry into host cells through cell-cell fusion. The interaction between gH and gL has been confirmed in several human herpesviruses, such as Herpes Simplex Virus (HSV), Epstein-Barr virus (EBV) and Human Cytomegalovirus (HCMV). In this paper, we studied the interaction between DEV gH and gL. Results: Recombinant plasmids pEGFP-N-gH and pDsRED-N-gL were constructed successfully. Expressions of both DEV gH and gL were observed after incubation of COS-7 cells transfected with pEGFP-N-gH and pDsRED-N-gL plasmids after 12 h, respectively. Also, the co-localization of a proportion of the gH and gL was detected in the cytoplasm of COS-7 cells after co-transfection for 24 h. Then, pCMV-Flag-gL and pCMV-Myc-gH recombinant plasmids were constructed and co-transfected into COS-7 cells. It was showed that both gH and gL were tested with positive results through co-immunoprecipitation and Western-blotting. Conclusions: Our results demonstrated not only the co-localization of DEV gH and gL in COS-7 cells, but also the interaction between them. It will provide an insight for the further studies in terms of protein-protein interaction in DEV.",DNA polymerase;glycoprotein L;article;bioinformatics;cytopathogenic effect;fluorescence microscopy;gene;high throughput sequencing;human;Human cytomegalovirus;immunofluorescence;immunoprecipitation;mouse;nonhuman;polyacrylamide gel electrophoresis;polymerase chain reaction;protein protein interaction;Turkey coronavirus;UL22 gene;Western blotting,"Feng, D.;Cui, M.;Jia, R.;Liu, S.;Wang, M.;Zhu, D.;Chen, S.;Liu, M.;Zhao, X.;Wu, Y.;Yang, Q.;Yin, Z.;Cheng, A.",2018,,10.1186/s12917-018-1553-6,0
588,Analysis of S1 gene of avian infectious bronchitis virus isolated in southern China during 2011-2012,"Sixty-two strains of avian infectious bronchitis virus (IBV) were isolated from diseased chickens at different farms in southern China during 2011-2012, and 66.1 % of the isolated strains were associated with typical nephritis. Analysis of the S1 gene sequences amplified from the 62 isolated strains together with 40 reference strains published in Genbank showed nucleotide homologies ranging from 63.5 to 99.9 % and amino acid homologies ranging from 57.9 to 100 %. Phylogenetic analysis revealed that all Chinese IBV strains were clustered into six distinct genetic groups (I-VI). Most of the isolated strains belonged to group I, and the isolation of group V strains was increased compared with an earlier period of surveillance. Current vaccine strains used in China (H120, H52, W93, and Ma5) formed the group Mass which is evolutionarily distant from Chinese isolates. Alignment of S1 amino acid sequences revealed polymorphic and diverse substitutions, insertions, and deletions, and the S1 protein of major pandemic strains contained 540 amino acids with a cleavage site sequence of HRRRR or RRF(L/S)RR. Further analysis showed that recombination events formed a new subgroup. Taken together, these findings suggest that various IBV variants were co-circulating and undergoing genetic evolution in southern China during the observation period. Therefore, long-term continuing surveillance is significantly important for prevention and control of IBV infection. © 2014 Springer Science+Business Media New York.",amino acid;vaccine;nucleotide;protein;Avian infectious bronchitis virus;gene;sequence analysis;China;phylogeny;nephritis;gene sequence;chicken;GenBank;implantable cardioverter defibrillator;commercial phenomena;prevention and control;amino acid sequence;indel mutation;pandemic;infection;United States,"Feng, K.;Xue, Y.;Wang, F.;Chen, F.;Shu, D.;Xie, Q.",2014,,10.1007/s11262-014-1097-1,0
589,Induction and suppression of innate antiviral responses by picornaviruses,"The family Picornaviridae comprises of small, non-enveloped, positive-strand RNA viruses and contains many human and animal pathogens including enteroviruses (e.g. poliovirus, coxsackievirus, enterovirus 71 and rhinovirus), cardioviruses (e.g. encephalomyocarditis virus), hepatitis A virus and foot-and-mouth disease virus. Picornavirus infections activate a cytosolic RNA sensor, MDA5, which in turn, induces a type I interferon response, a crucial component of antiviral immunity. Moreover, picornaviruses activate the formation of stress granules (SGs), large aggregates of preassembled mRNPs (messenger ribonucleoprotein particles) to temporarily store these molecules upon cellular stress. Meanwhile, picornaviruses actively suppress these antiviral responses to ensure efficient replication. In this review we provide an overview of the induction and suppression of the MDA5-mediated IFN-α/β response and the cellular stress pathway by picornaviruses.",alpha interferon;beta interferon;dihydrolipoamide dehydrogenase;messenger ribonucleoprotein particle;interferon induced helicase C domain containing protein 1;retinoic acid inducible protein I;ribonucleoprotein;RIG I like receptor;unclassified drug;virus RNA;antiviral activity;Cardiovirus;cellular stress response;cytokine production;Enterovirus;human;innate immunity;life cycle;molecular interaction;molecular recognition;nonhuman;nucleocytoplasmic transport;picornavirus infection;short survey;viral genetics;virus cell interaction;virus classification;virus replication;virus virulence,"Feng, Q.;Langereis, M. A.;van Kuppeveld, F. J. M.",2014,,10.1016/j.cytogfr.2014.07.003,0
590,"A novel recombinant lineage's contribution to the outbreak of coxsackievirus A6-associated hand, foot and mouth disease in Shanghai, China, 2012-2013","Since late 2012, coxsackievirus A6 (CVA6) has gradually become the predominant pathogen responsible for hand-foot-mouth disease (HFMD) in several provinces of China. A total of 626 patients diagnosed with HFMD in Shanghai, China from January 2012 to September 2013 were enrolled in this study. Of these, 292 CVA6 infected cases were subjected to clinical analyses. Whole-genome sequencing, recombination and phylogenetic analyses were also performed. A recombinant CVA6 monophyletic lineage was found during an outbreak of CVA6-associated HFMDs in Shanghai, China in November 2012, and accounted for 21.9% (64/292) of the CVA6 strains during the study period. Recombination analyses showed that the 2C gene of the novel CVA6 virus was probably derived from a coxsackievirus A4 (CVA4) strain circulating in the population. Clinical observation showed that this recombinant CVA6 virus led to a more generalized rash than did the non-recombinant CVA6 virus. This newly emerged CVA6 lineage was associated with a considerable proportion of HFMD cases from 2012 to 2013 in Shanghai, and poses a potential threat to public health.",viral protein;virus RNA;chemistry;China;classification;Enterovirus B;epidemic;genetic recombination;genetics;hand foot and mouth disease;high throughput sequencing;human;isolation and purification;metabolism;phylogeny;prevalence;real time polymerase chain reaction;sequence analysis;serotype;virology,"Feng, X.;Guan, W.;Guo, Y.;Yu, H.;Zhang, X.;Cheng, R.;Wang, Z.;Zhang, Z.;Zhang, J.;Li, H.;Zhuang, Y.;Zhang, H.;Lu, Z.;Li, M.;Yu, H.;Bao, Y.;Hu, Y.;Yao, Z.",2015,,10.1038/srep11700,0
591,Disease outbreaks caused by steppe-type rabies viruses in China,"While rabies is a significant public health concern in China, the epidemiology of animal rabies in the north and northwest border provinces remains unknown. From February 2013 to March 2014, seven outbreaks of domestic animal rabies caused by wild carnivores in Xinjiang (XJ) and Inner Mongolia (IM) Autonomous Regions, China were reported and diagnosed in brain samples of infected animals by the fluorescent antibody test (FAT) and RT-PCR. Ten field rabies viruses were obtained. Sequence comparison and phylogenetic analysis based on the complete N gene (1353 bp) amplified directly from the original brain tissues showed that these ten strains were steppe-type viruses, closely related to strains reported in Russia and Mongolia. None had been identified previously in China. The viruses from XJ and IM clustered separately into two lineages showing their different geographical distribution. This study emphasizes the importance of wildlife surveillance and of cross-departmental cooperation in the control of transboundary rabies transmission.",animal disease;animal tissue;article;China;epidemic;fluorescent antibody technique;gene;gene amplification;geographical variation (species);N gene;nonhuman;phylogeny;rabies;reverse transcription polymerase chain reaction;sequence analysis;virus classification,"Feng, Y.;Wang, W.;Guo, J.;Alatengheli;Li, Y.;Yang, G.;Su, N.;Zhang, L.;Xu, W.;Sheng, Z.;Ma, L.;Gui, J.;Dejide;Lin, H.;Tu, C.",2015,,10.1017/s0950268814001952,0
592,Next-generation sequencing of five new avian paramyxoviruses 8 isolates from Kazakhstan indicates a low genetic evolution rate over four decades,"Five avian paramyxoviruses of serotype 8 (APMV-8) were isolated during a study monitoring wild birds in Kazakhstan in 2013 and each was further characterized. The viruses were isolated from three White-fronted geese (Anser albifrons), one Whooper swan (Cygnus cygnus), and one Little stint (Calidris minuta). Before our study, only two complete APMV-8 sequences had been reported worldwide since their discovery in the USA and Japan in the 1970s. We report the complete genome sequences of the newly detected viruses and analyze the genetic evolution of the APMV-8 viruses over four decades.",animal;Avulavirus;Avulavirus infection;bird disease;classification;duck;genetics;goose;high throughput sequencing;isolation and purification;Kazakhstan;molecular evolution;phylogeny;serotype;veterinary medicine;virology;wild animal,"Fereidouni, S.;Jenckel, M.;Seidalina, A.;Karamendin, K.;Beer, M.;Starick, E.;Asanova, S.;Kasymbekov, E.;Sayatov, M.;Kydyrmanov, A.",2018,,10.1007/s00705-017-3593-9,0
593,Pathogenesis of Influenza D Virus in Cattle,"UNLABELLED: Cattle have been proposed as the natural reservoir of a novel member of the virus family Orthomyxoviridae, which has been tentatively classified as influenza D virus (IDV). Although isolated from sick animals, it is unclear whether IDV causes any clinical disease in cattle. To address this aspect of Koch's postulates, three dairy calves (treatment animals) held in individual pens were inoculated intranasally with IDV strain D/bovine/Mississippi/C00046N/2014. At 1 day postinoculation, a seronegative calf (contact animal) was added to each of the treatment animal pens. The cattle in both treatment and contact groups seroconverted, and virus was detected in their respiratory tracts. Histologically, there was a significant increase in neutrophil tracking in tracheal epithelia of the treatment calves compared to control animals. While infected and contact animals demonstrated various symptoms of respiratory tract infection, they were mild, and the calves in the treatment group did not differ from the controls in terms of heart rate, respiratory rate, or rectal temperature. To mimic zoonotic transmission, two ferrets were exposed to a plastic toy fomite soaked with infected nasal discharge from the treatment calves. These ferrets did not shed the virus or seroconvert. In summary, this study demonstrates that IDV causes a mild respiratory disease upon experimental infection of cattle and can be transmitted effectively among cattle by in-pen contact, but not from cattle to ferrets through fomite exposure. These findings support the hypothesis that cattle are a natural reservoir for the virus. IMPORTANCE: A novel influenza virus, tentatively classified as influenza D virus (IDV), was identified in swine, cattle, sheep, and goats. Among these hosts, cattle have been proposed as the natural reservoir. In this study, we show that cattle experimentally infected with IDV can shed virus and transmit it to other cattle through direct contact, but not to ferrets through fomite routes. IDV caused minor clinical signs in the infected cattle, fulfilling another of Koch's postulates for this novel agent, although other objective clinical endpoints were not different from those of control animals. Although the disease observed was mild, IDV induced neutrophil tracking and epithelial attenuation in cattle trachea, which could facilitate coinfection with other pathogens, and in doing so, predispose animals to bovine respiratory disease.",Animals;Cattle;*Cattle Diseases/vi [Virology];*Disease Reservoirs/vi [Virology];Ferrets;Orthomyxoviridae Infections/pp [Physiopathology];Orthomyxoviridae Infections/tm [Transmission];*Orthomyxoviridae Infections/ve [Veterinary];Orthomyxoviridae Infections/vi [Virology];Respiratory System/vi [Virology];*Respiratory Tract Infections/ve [Veterinary];Respiratory Tract Infections/vi [Virology];Seroconversion;Thogotovirus/ip [Isolation & Purification];*Thogotovirus/py [Pathogenicity];Trachea/cy [Cytology];Trachea/pa [Pathology];Trachea/vi [Virology];Virus Shedding,"Ferguson, L.;Olivier, A. K.;Genova, S.;Epperson, W. B.;Smith, D. R.;Schneider, L.;Barton, K.;McCuan, K.;Webby, R. J.;Wan, X. F.",2016,06 15,,0
594,Molecular and phylogenetic characterization based on the complete genome of a virulent pathotype of Newcastle disease virus isolated in the 1970s in Brazil,"Newcastle disease (ND) is caused by the avian paramyxovirus type 1 (APMV-1) or Newcastle disease virus (NDV) that comprises a diverse group of viruses with a single-stranded, negative-sense RNA genome. ND is one of the most important diseases of chickens, because it severely affects poultry production worldwide. In the 1970s, outbreaks of virulent ND were recorded in Brazil, and the strain APMV-1/Chicken/Brazil/SJM/75 (SJM) of NDV was isolated. This strain was characterized as highly pathogenic for chickens but not pathogenic for other bird species. Here we present the complete genome of NDV strain SJM and investigate the phylogenetic relationships of this virus with other NDV strains in terms of genome and proteins composition, as well as characterizing its evolution process. The NDV strain SJM is categorized as a velogenic virus and the complete genome is 15,192 nucleotides in length, consisting of six genes in the order 3'-NP-P-M-F-HN-L-5'. The presence of the major pathogenic determinant of NDV strains (112R-R-Q-K-R↓F117) was identified in the Fusion protein of the NDV strain SJM. In addition, phylogenetic analysis classified the NDV strain SJM as a member of class II, genotype V, and indicates that this virus help us in the understanding of the evolutionary process of strains belonging to this genotype. This study contributes to the growing interest involving the characterization of NDV isolates to improve our current understanding about the epidemiology, surveillance and evolution of the pathogenic strains. © 2014 The Authors.",fusion protein;amino acid sequence;article;controlled study;epidemic;evolution;genetic similarity;genotype;HN gene;molecular biology;Newcastle disease;Newcastle disease virus;nonhuman;nucleotide sequence;pathogenesis;phylogeny;priority journal;protein analysis;protein content;unindexed sequence;virus gene;virus genome;virus isolation;virus strain;virus virulence,"Fernandes, C. C.;Varani, A. M.;Lemos, E. G. M.;de Miranda, V. F. O.;Silva, K. R.;Fernando, F. S.;Montassier, M. F. S.;Montassier, H. J.",2014,,10.1016/j.meegid.2014.05.014,0
595,Molecular detection of bovine Noroviruses in Argentinean dairy calves: Circulation of a tentative new genotype,"Bovine noroviruses are enteric pathogens detected in fecal samples of both diarrheic and non-diarrheic calves from several countries worldwide. However, epidemiological information regarding bovine noroviruses is still lacking for many important cattle producing countries from South America. In this study, three bovine norovirus genogroup III sequences were determined by conventional RT-PCR and Sanger sequencing in feces from diarrheic dairy calves from Argentina (B4836, B4848, and B4881, all collected in 2012). Phylogenetic studies based on a partial coding region for the RNA-dependent RNA polymerase (RdRp, 503 nucleotides) of these three samples suggested that two of them (B4836 and B4881) belong to genotype 2 (GIII.2) while the third one (B4848) was more closely related to genotype 1 (GIII.1) strains. By deep sequencing, the capsid region from two of these strains could be determined. This confirmed the circulation of genotype 1 (B4848) together with the presence of another sequence (B4881) sharing its highest genetic relatedness with genotype 1, but sufficiently distant to constitute a new genotype. This latter strain was shown in silico to be a recombinant: phylogenetic divergence was detected between its RNA-dependent RNA polymerase coding sequence (genotype GIII.2) and its capsid protein coding sequence (genotype GIII.1 or a potential norovirus genotype). According to this data, this strain could be the second genotype GIII.2_GIII.1 bovine norovirus recombinant described in literature worldwide. Further analysis suggested that this strain could even be a potential norovirus GIII genotype, tentatively named GIII.4. The data provides important epidemiological and evolutionary information on bovine noroviruses circulating in South America.","Animals;Argentina/ep [Epidemiology];*Caliciviridae Infections/ep [Epidemiology];Capsid Proteins/ge [Genetics];Cattle;Cattle Diseases/ep [Epidemiology];*Cattle Diseases/vi [Virology];Genotype;*High-Throughput Nucleotide Sequencing/mt [Methods];*Norovirus/cl [Classification];Norovirus/ge [Genetics];Norovirus/ip [Isolation & Purification];Phylogeny;RNA Replicase/ge [Genetics];*Sequence Analysis, RNA/mt [Methods];Viral Proteins/ge [Genetics];0 (Capsid Proteins);0 (Viral Proteins)","Ferragut, F.;Vega, C. G.;Mauroy, A.;Conceicao-Neto, N.;Zeller, M.;Heylen, E.;Uriarte, E. L.;Bilbao, G.;Bok, M.;Matthijnssens, J.;Thiry, E.;Badaracco, A.;Parreno, V.",2016,06,,1
596,Oligonucleotide microchip for subtyping of influenza A virus,"BACKGROUND: Influenza A viruses are classified into subtypes depending on the antigenic properties of their two outer glycoproteins, hemagglutinin (HA) and neuraminidase (NA). Sixteen subtypes of HA and nine of NA are known. Lately, the circulation of some subtypes (H7N7, H5N1) has been closely watched because of the epidemiological threat they present. OBJECTIVES: This study assesses the potential of using gel-based microchip technology for fast and sensitive molecular subtyping of the influenza A virus. METHODS: The method employs a microchip of 3D gel-based elements containing immobilized probes. Segments of the HA and NA genes are amplified using multiplex RT-PCR and then hybridized with the microchip. RESULTS: The developed microchip was validated using a panel of 21 known reference strains of influenza virus. Selected strains represented different HA and NA subtypes derived from avian, swine and human hosts. The whole procedure takes 10 hours and enables one to identify 15 subtypes of HA and two subtypes of NA. Forty-one clinical samples isolated during the poultry fall in Novosibirsk (Russia, 2005) were successfully identified using the proposed technique. The sensitivity and specificity of the method were 76% and 100%, respectively, compared with the 'gold standard' techniques (virus isolation with following characterization by immunoassay). CONCLUSIONS: We conclude that the method of subtyping using gel-based microchips is a promising approach for fast detection and identification of influenza A, which may greatly improve its monitoring.","hemagglutinin fusogenic peptide, influenza virus;NA protein, influenza A virus;sialidase;virus hemagglutinin;viral protein;animal;article;avian influenza;bird;classification;DNA microarray;epidemic;evaluation study;gel;genetics;human;influenza;Influenza A virus;isolation and purification;methodology;nucleic acid hybridization;reverse transcription polymerase chain reaction;Russian Federation;sensitivity and specificity;pig;virology","Fesenko, E. E.;Kireyev, D. E.;Gryadunov, D. A.;Mikhailovich, V. M.;Grebennikova, T. V.;L'Vov D, K.;Zasedatelev, A. S.",2007,,10.1111/j.1750-2659.2007.00018.x,0
597,"Epidemiological investigation and analysis of the NS5B gene and protein variability of non-primate hepacivirus in several horse cohorts in Rio de Janeiro state, Brazil","Among the hepacivirus species recently described, the non-primate hepacivirus/hepacivirus A found in horses and donkeys is closely related to the human hepatitis C virus (HCV). Therefore, the equine is an attractive surrogate large animal model for the study of HCV therapy, pathogenesis and prophylaxis. Despite global efforts, epidemiological and genetic studies have not elucidated the risk factors, virus distribution or genetic variability of the hepacivirus A, which are also important issues for the equine welfare. Little information about this background scenery is available in Brazil. The aims of this study were to investigate potential risk factors associated with hepacivirus A infection among different horse cohorts throughout the state of Rio de Janeiro and to evaluate the diversity of the viral NS5B gene and protein. Hepacivirus A RNA was detected in horse cohorts from all geographical mesoregions, independent of horse activity or breed investigated. Statewide prevalence ranged from 4.0% to 27.5%. Potential risk factors such as geographical location and age of female horses were significantly associated with the presence of virus RNA. Phylogenetic analysis revealed the circulation of subtype 2 in all mesoregions. NS5B gene sequences clustered according to geographical origin, while the NS5B fragments did not allow discriminant analysis. The predicted NS5B protein showed marked conservation, especially in the thumb domain. In conclusion, the higher frequency of hepacivirus A RNA detection in horses bred for re-production purposes as well as in young females suggests a direct link between reproduction practices and the virus's spread. Additional studies are necessary to understand the distribution of this genetically conserved hepacivirus.",Equine hepacivirus;Horse;Prevalence;Risk factors;NS5B;Brazil;HEPATITIS-C VIRUS;EQUINE HEPACIVIRUS;IDENTIFICATION;TRANSMISSION;INFECTIONS;DISEASE;UPDATE;CATTLE,"Figueiredo, A. S.;Lampe, E.;de Albuquerque, Pplf;Chalhoub, F. L. V.;de Filippis, A. M. B.;Villar, L. M.;Cruz, O. G.;Pinto, M. A.;de Oliveira, J. M.",2018,Apr,,0
598,Bat astroviruses: Towards understanding the transmission dynamics of a neglected virus family,"Bats belong to the order Chiroptera that represents the second largest order of mammals with more than 1200 species and an almost global distribution. Environmental changes and deforestation have severely influenced many ecosystems, intensifying the contact between wildlife and humans. In recent years, bats have been found to harbor a number of different viruses with zoonotic potential, as well as a great diversity of astroviruses, for which the question of zoonotic potential remains unanswered to date. Human astroviruses have been identified as the causative agent for diarrhea in children and immunocompromised patients. For a long time, astroviruses have been considered to be strictly species-specific. However, a great genetic diversity has recently been discovered among animal and human astroviruses that might indicate the potential of these viruses to cross species barriers. Furthermore, our knowledge about the tissue tropism of astroviruses has been expanded to some neurotropic strains that have recently been shown to be responsible for encephalitis in humans and livestock. This review gives an overview on what is known about astroviruses in bats, humans and livestock, especially bovines and pigs. Future research activities are suggested to unravel astrovirus infection dynamics in bat populations to further assess the zoonotic potential of these viruses.",Astroviridae;deforestation;diarrhea;dynamics;encephalitis;flaccid paralysis;flying fox;hibernation;immunocompromised patient;immunoelectron microscopy;metagenomics;Myotis myotis;nonhuman;open reading frame;phylogeny;reverse transcription polymerase chain reaction;review;risk assessment;Vespertilionidae,"Fischer, K.;dos Reis, V. P.;Balkema-Buschmann, A.",2017,,10.3390/v9020034,0
599,A mutation 'Hot Spot' in the Schmallenberg virus M segment,"In the autumn of 2011, Schmallenberg virus (SBV), a novel orthobunyavirus of the Simbu serogroup, was identified by metagenomic analysis in Germany. SBV has since been detected in ruminants all over Europe, and investigations on phylogenetic relationships, clinical signs and epidemiology have been conducted. However, until now, only comparative sequence analysis of SBV genome segments with other species of the Simbu serogroup have been performed, and detailed data on the S and M segments, relevant for virus-host-cell interaction, have been missing. In this study, we investigated the S- and M-segment sequences obtained from 24 SBVpositive field samples from sheep, cattle and a goat collected from all over Germany. The results obtained indicated that the overall genome variability of SBV is neither regionally nor host species dependent. Nevertheless, we characterized for the first time a region of high sequence variability (a mutation 'hot spot') within the glycoprotein Gc encoded by the M segment. © 2013 SGM.",glycoprotein Gc;unclassified drug;virus glycoprotein;article;bovine;genome analysis;Germany;goat;nucleotide sequence;Orthobunyavirus;priority journal;Schmallenberg virus;sequence analysis;sheep;virus cell interaction;virus genome;virus mutation,"Fischer, M.;Hoffmann, B.;Goller, K. V.;Höper, D.;Wernike, K.;Beer, M.",2013,,10.1099/vir.0.049908-0,0
600,Rapid metagenomic diagnostics for suspected outbreak of severe pneumonia,,contig;RNA 16S;adult respiratory distress syndrome;Anelloviridae;antimicrobial therapy;Chlamydia psittaci;death;DNA sequence;epidemic;human;Influenza A virus (H3N2);letter;lung lavage;metagenomics;multiple organ failure;nonhuman;ornithosis;rapid test;RNA sequence;sequence analysis,"Fischer, N.;Rohde, H.;Indenbirken, D.;Günther, T.;Reumann, K.;Lütgehetmann, M.;Meyer, T.;Kluge, S.;Aepfelbacher, M.;Alawi, M.;Grundhoff, A.",2014,,10.3201/eid2006.131526,0
601,A55 Foot-and-mouth disease virus undergoes abundant viral genomic changes at distinct stages of infection of cattle,,,"Fish, I.;Stenfeldt, C.;Pauszek, S. J.;Brito, B. P.",2018,,,0
602,Rift Valley fever virus,"Rift Valley fever is considered to be one of the most important viral zoonoses in Africa. In 2000, the Rift valley fever virus spread to the Arabian Peninsula and caused two simultaneous outbreaks in Yemen and Saudi Arabia. It is transmitted to ruminants and to humans by mosquitoes. The viral agent is an arbovirus, which belongs to the Phlebovirus genus in the Bunyaviridae family. This family of viruses comprises more than 300 members grouped into five genera: Orthobunyavirus, Phlebovirus, Hantavirus, Nairovirus, and Tospovirus. Several members of the Bunyaviridae family are responsible for fatal hemorrhagic fevers: Rift Valley fever virus (Phlebovirus), Crimean-Congo hemorrhagic fever virus (Nairovirus), Hantaan, Sin Nombre and related viruses (Hantavirus), and recently Garissa, now identified as Ngari virus (Orthobunyavirus). Here are reviewed recent advances in Rift Valley fever virus, its epidemiology, molecular biology and focus on recent data on the interactions between viral and cellular proteins, which help to understand the molecular mechanisms utilized by the virus to circumvent the host cellular response. © 2005 Bentham Science Publishers Ltd.",antibody;interferon;interferon inducing agent;live vaccine;nucleoside analog;ribavirin;virus vaccine;Africa;Arbovirus;bovid;Bunyaviridae;epidemic;genus;Hantavirus;hemorrhagic fever;human;immune response;mosquito;Nairovirus;nonhuman;Phlebovirus;review;Rift Valley fever virus;Saudi Arabia;Sin Nombre virus;Tospovirus;virus cell interaction;virus classification;virus transmission;Yemen;zoonosis,"Flick, R.;Bouloy, M.",2005,,10.2174/156652405774962263,0
603,"Letter to the Editor refuting ""Epidemiological pattern of classical Borna disease and regional genetic clustering of Borna disease viruses point towards the existence of to-date unknown endemic reservoir host populations"" by Ralf Dürrwald, Jolanta Kolodziejek, Aemero Muluneh, Sibylle Herzog and Norbert Nowotny, Microbes and Infection 8 (2006) 917-929",,amino acid sequence;Australia;Borna disease;Borna disease virus;endemic disease;gene cluster;geographic distribution;human;letter;nonhuman;nucleotide sequence;open reading frame;phylogenetic tree;priority journal;reverse transcription polymerase chain reaction;virus classification;virus genome;virus isolation;virus strain,"Flower, R.;Kamhieh, S.",2006,,10.1016/j.micinf.2006.02.001,0
604,Torquetenovirus: the human virome from bench to bedside,,,"Focosi, D.;Antonelli, G.;Pistello, M.;Maggi, F.",2016,,,0
605,Crane hepatitis herpesviruses,"Comparative studies were performed on crane herpesviruses obtained from two different enzootics in Austria and France. The examined viruses appear to be identical in their physico-chemical properties, morphology and biological reactions in ovo. The crane viruses are tentatively classified as beta-herpesviruses. Crane herpesvirus antisera produced in rabbits reacted in cross neutralization tests with each other and with a herpesvirus obtained from a bobwhite quail. No reactivity was observed with other avian herpesviruses and with human herpes simplex virus type 1 and 2.",animal;animal disease;article;bird;bird disease;cell line;chick embryo;classification;comparative study;epidemic;Herpesviridae;herpes virus infection;microbiology;serodiagnosis,"Foerster, S.;Chastel, C.;Kaleta, E. F.",1989,,,0
606,Primate immunodeficiency virus classification and nomenclature,,,"Foley, B. T.;Leitner, T.;Paraskevis, D.;Peeters, M.",2016,,,0
607,Influenza D in Italy: towards a better understanding of an emerging viral infection in swine,,,"Foni, E.;Chiapponi, C.;Baioni, L.;Zanni, I.;Merenda, M.",2017,,,0
608,Pseudorabies virus can be classified into five genotypes using partial sequences of UL44,"Suid herpesvirus 1 (SuHV-1) is the causative agent of pseudorabies (PR), a disease of great importance due to the huge losses it causes in the swine industry. The aim of this study was to determine a method for genotyping SuHV-1 based on partial sequences of the gene coding for glycoprotein C (gC) and to elucidate the possible reasons for the variability of this region. A total of 109 gCsequences collected from GenBank were divided into five major groups after reconstruction of a phylogenetic tree by Bayesian inference. The analysis showed that a portion of gC (approximately 671 bp) is under selective pressure at various points that coincide with regions of protein disorder. It was also possible to divide SuHV-1 into five genotypes that evolved under different selective pressures. These genotypes are not specific to countries or continents, perhaps due to multiple introduction events related to the importation of swine.",,"Fonseca, A. A., Jr.;Camargos, M. F.;Sales, M. L.;Heinemann, M. B.;Leite, R. C.;Reis, J. K.",2012,Oct,,0
609,Genomic analysis of the multi-host pathogen Erysipelothrix rhusiopathiae reveals extensive recombination as well as the existence of three generalist clades with wide geographic distribution,"BACKGROUND: Knowledge about how bacterial populations are structured is an important prerequisite for studying their ecology and evolutionary history and facilitates inquiry into host specificity, pathogenicity, geographic dispersal and molecular epidemiology. Erysipelothrix rhusiopathiae is an opportunistic pathogen that is currently reemerging in both the swine and poultry industries globally. This bacterium sporadically causes mortalities in captive marine mammals, and has recently been implicated in large-scale wildlife die-offs. However, despite its economic relevance and broad geographic and host distribution, including zoonotic potential, the global diversity, recombination rates, and population structure of this bacterium remain poorly characterized. In this study, we conducted a broad-scale genomic comparison of E. rhusiopathiae based on a diverse collection of isolates in order to address these knowledge gaps. RESULTS: Eighty-three E. rhusiopathiae isolates from a range of host species and geographic origins, isolated between 1958 and 2014, were sequenced and assembled using both reference-based mapping and de novo assembly. We found that a high proportion of the core genome (58 %) had undergone recombination. Therefore, we used three independent methods robust to the presence of recombination to define the population structure of this species: a phylogenetic tree based on a set of conserved protein sequences, in silico chromosome painting, and network analysis. All three methods were broadly concordant and supported the existence of three distinct clades within the species E. rhusiopathiae. Although we found some evidence of host and geographical clustering, each clade included isolates from diverse host species and from multiple continents. CONCLUSIONS: Using whole genome sequence data, we confirm recent suggestions that E. rhusiopathiae is a weakly clonal species that has been shaped extensively by homologous recombination. Despite frequent recombination, we can reliably identify three distinct clades that do not clearly segregate by host species or geographic origin. Our results provide an essential baseline for future molecular epidemiological, ecological and evolutionary studies of E. rhusiopathiae and facilitate comparisons to other recombinogenic, multi-host bacteria.","Animals;Bacteriophages/ph [Physiology];Cluster Analysis;*Erysipelothrix/cl [Classification];*Erysipelothrix/ge [Genetics];Erysipelothrix/vi [Virology];Genetics, Population;*Genome, Bacterial;Genomics/mt [Methods];*Genomics;High-Throughput Nucleotide Sequencing;Host-Pathogen Interactions;Phylogeny;Plasmids/ge [Genetics];*Recombination, Genetic;Swine","Forde, T.;Biek, R.;Zadoks, R.;Workentine, M. L.;De Buck, J.;Kutz, S.;Opriessnig, T.;Trewby, H.;van der Meer, F.;Orsel, K.",2016,06 14,,0
610,Genetic diversity among pandemic 2009 influenza viruses isolated from a transmission chain,"BACKGROUND: Influenza viruses such as swine-origin influenza A(H1N1) virus (A(H1N1)pdm09) generate genetic diversity due to the high error rate of their RNA polymerase, often resulting in mixed genotype populations (intra-host variants) within a single infection. This variation helps influenza to rapidly respond to selection pressures, such as those imposed by the immunological host response and antiviral therapy. We have applied deep sequencing to characterize influenza intra-host variation in a transmission chain consisting of three cases due to oseltamivir-sensitive viruses, and one derived oseltamivir-resistant case. METHODS: Following detection of the A(H1N1)pdm09 infections, we deep-sequenced the complete NA gene from two of the oseltamivir-sensitive virus-infected cases, and all eight gene segments of the viruses causing the remaining two cases. RESULTS: No evidence for the resistance-causing mutation (resulting in NA H275Y substitution) was observed in the oseltamivir-sensitive cases. Furthermore, deep sequencing revealed a subpopulation of oseltamivir-sensitive viruses in the case carrying resistant viruses. We detected higher levels of intra-host variation in the case carrying oseltamivir-resistant viruses than in those infected with oseltamivir-sensitive viruses. CONCLUSIONS: Oseltamivir-resistance was only detected after prophylaxis with oseltamivir, suggesting that the mutation was selected for as a result of antiviral intervention. The persisting oseltamivir-sensitive virus population in the case carrying resistant viruses suggests either that a small proportion survive the treatment, or that the oseltamivir-sensitive virus rapidly re-establishes itself in the virus population after the bottleneck. Moreover, the increased intra-host variation in the oseltamivir-resistant case is consistent with the hypothesis that the population diversity of a RNA virus can increase rapidly following a population bottleneck.","Antiviral Agents/pd [Pharmacology];Drug Resistance, Viral;*Genetic Variation;High-Throughput Nucleotide Sequencing;Humans;*Influenza A Virus, H1N1 Subtype/cl [Classification];*Influenza A Virus, H1N1 Subtype/ge [Genetics];Influenza A Virus, H1N1 Subtype/ip [Isolation & Purification];*Influenza, Human/vi [Virology];*Neuraminidase/ge [Genetics];Oseltamivir/pd [Pharmacology];RNA, Viral/ge [Genetics];Selection, Genetic;*Viral Proteins/ge [Genetics];0 (Antiviral Agents);0 (RNA, Viral);0 (Viral Proteins);20O93L6F9H (Oseltamivir)","Fordyce, S. L.;Bragstad, K.;Pedersen, S. S.;Jensen, T. G.;Gahrn-Hansen, B.;Daniels, R.;Hay, A.;Kampmann, M. L.;Bruhn, C. A.;Moreno-Mayar, J. V.;Avila-Arcos, M. C.;Gilbert, M. T.;Nielsen, L. P.",2013,Apr 12,,0
611,Detection of Hepatitis E virus in samples of animal origin collected in Hungary,"Hepatitis E virus (HEV) is an enterically transmitted human pathogen. HEV infections are mainly associated with acute, self-limited, icteric hepatitis with an average mortality rate of 1%. Animal reservoirs are considered to play an important role in the maintenance of the virus and in the spread of HEV to humans. HEV-induced seroconversion was described in several species, however clinical hepatitis in animals has not been observed to date. HEV strains from animals are genetically closely related to human HEV isolates, which supports the opinions on the zoonotic transmission of the virus.In this expansive study the occurrence of HEV was investigated in Hungarian wild and domesticated animal samples. HEV RNA was detected by reverse transcription-polymerase chain reaction in liver samples of wild boars, roe deer, and deer. The investigations of domestic swine samples detected HEV in 39% of the investigated Hungarian pig farms. Simultaneous investigation revealed no definite difference between liver and faeces samples of domestic pigs in the frequency of HEV positivity. The highest (36%) incidence of HEV infection was found among the 11-16-week-old pigs. Samples from domestic cattle and rodents collected in pig farms, forests and meadows were tested negative for HEV RNA.Phylogenetic analysis of partial sequences amplified within the ORF1 and ORF2 regions of selected strains revealed that the detected viruses belong to three subgroups of the third genogroup of HEV, and are closely related to human and swine HEV strains detected in different countries. The investigations revealed widespread distribution of HEV in Hungarian wild ungulate and domesticated swine populations, with considerable genetic diversity among the strains. © 2009 Elsevier B.V.",virus RNA;animal tissue;article;bovine;controlled study;deer;doe (deer);domestic animal;domestic pig;genetic variability;geographic origin;hepatitis E;Hepatitis E virus;Hungary;mouse;nonhuman;nucleotide sequence;open reading frame;phylogeny;rat;reverse transcription polymerase chain reaction;rodent;sequence analysis;sequence homology;virus detection;virus strain;wild animal;European wild boar;zoonosis,"Forgách, P.;Nowotny, N.;Erdélyi, K.;Boncz, A.;Zentai, J.;Szucs, G.;Reuter, G.;Bakonyi, T.",2010,,10.1016/j.vetmic.2009.11.004,0
612,A Real-Time Reverse-Transcription Polymerase Chain Reaction for Differentiation of Massachusetts Vaccine and Brazilian Field Genotypes of Avian Infectious Bronchitis Virus,"The avian infectious bronchitis virus is classified into serotypes or genotypes (or both) in different poultry-producing countries of the world. In Brazil, Massachusetts type (Mass), used as a live vaccine, and local field Brazilian variants (genotypes; BR) predominate in the commercial poultry flocks. This study describes the development and validation of two real-time reverse-transcription polymerase chain reactions (RT-qPCR) for the specific detection of Mass and BR genotypes in allantoic fluids and clinical samples. Genotype-specific primers, combined with a generic probe targeted to the S1 gene, originated Mass RT-qPCR and BR RT-qPCR-specific assays. Analytical sensitivity and linearity of these assays were determined in comparison with an IBV generic real-time RT-PCR based on the 5' untranslated region (5'UTR RT-qPCR). Mass RT-qPCR detected five Mass field isolates, three vaccine samples, and one coinfected sample (BR and Mass) while BR RT-qPCR detected 16 BR field isolates. Both assays were linear (R(2) > 0.98), reproducible, and as sensitive as the classical 5'UTR RT-qPCR used to detect IBV. In the analysis of 141 IBV clinical samples, 8 were positive for Mass RT-qPCR, 76 for BR RT-qPCR, and 2 for both assays. In the remaining 55 samples, 25 were positive only for 5'UTR RT-qPCR and 30 were negative for the three assays. In conclusion, both assays were able to detect Mass and BR genotypes, allowing rapid and easy IBV molecular typing from allantoic fluids and clinical samples.",live vaccine;virus vaccine;animal;Avian infectious bronchitis virus;Brazil;chicken;Coronavirus infection;DNA sequence;genetics;genotype;immunology;polymerase chain reaction;bird disease;veterinary medicine;virology,"Fraga, A. P.;Ikuta, N.;Fonseca, A. S.;Spilki, F. R.;Balestrin, E.;Rodrigues, C. D.;Canal, C. W.;Lunge, V. R.",2016,,10.1637/11262-081815-RegR.1,0
613,Discovery of parvovirus-related sequences in an unexpected broad range of animals,"Our knowledge of the genetic diversity and host ranges of viruses is fragmentary. This is particularly true for the Parvoviridae family. Genetic diversity studies of single stranded DNA viruses within this family have been largely focused on arthropod- and vertebrate-infecting species that cause diseases of humans and our domesticated animals: a focus that has biased our perception of parvovirus diversity. While metagenomics approaches could help rectify this bias, so too could transcriptomics studies. Large amounts of transcriptomic data are available for a diverse array of animal species and whenever this data has inadvertently been gathered from virus-infected individuals, it could contain detectable viral transcripts. We therefore performed a systematic search for parvovirus-related sequences (PRSs) within publicly available transcript, genome and protein databases and eleven new transcriptome datasets. This revealed 463 PRSs in the transcript databases of 118 animals. At least 41 of these PRSs are likely integrated within animal genomes in that they were also found within genomic sequence databases. Besides illuminating the ubiquity of parvoviruses, the number of parvoviral sequences discovered within public databases revealed numerous previously unknown parvovirus-host combinations; particularly in invertebrates. Our findings suggest that the host-ranges of extant parvoviruses might span the entire animal kingdom.",virus RNA;animal;gene expression profiling;genetic database;genetic variation;genetics;metagenomics;Parvoviridae;phylogeny;procedures;sequence analysis,"François, S.;Filloux, D.;Roumagnac, P.;Bigot, D.;Gayral, P.;Martin, D. P.;Froissart, R.;Ogliastro, M.",2016,,10.1038/srep30880,0
614,Classification of cowpox viruses into several distinct clades and identification of a novel lineage,"Cowpox virus (CPXV) was considered as uniform species within the genus Orthopoxvirus (OPV). Previous phylogenetic analysis indicated that CPXV is polyphyletic and isolates may cluster into different clades with two of these clades showing genetic similarities to either variola (VARV) or vaccinia viruses (VACV). Further analyses were initiated to assess both the genetic diversity and the evolutionary background of circulating CPXVs. Here we report the full-length sequences of 20 CPXV strains isolated from different animal species and humans in Germany. A phylogenetic analysis of altogether 83 full-length OPV genomes confirmed the polyphyletic character of the species CPXV and suggested at least four different clades. The German isolates from this study mainly clustered into two CPXV-like clades, and VARV- and VACV-like strains were not observed. A single strain, isolated from a cotton-top tamarin, clustered distantly from all other CPXVs and might represent a novel and unique evolutionary lineage. The classification of CPXV strains into clades roughly followed their geographic origin, with the highest clade diversity so far observed for Germany. Furthermore, we found evidence for recombination between OPV clades without significant disruption of the observed clustering. In conclusion, this analysis markedly expands the number of available CPXV full-length sequences and confirms the co-circulation of several CPXV clades in Germany, and provides the first data about a new evolutionary CPXV lineage.",article;Callitrichinae;cladistics;cowpox;Cowpox virus;DNA extraction;genetic variability;genome analysis;geographic distribution;Germany;high throughput sequencing;nonhuman;phylogenetic tree;polymerase chain reaction;virus classification;virus genome;virus identification;virus isolation;virus recombination,"Franke, A.;Pfaff, F.;Jenckel, M.;Hoffmann, B.;Höper, D.;Antwerpen, M.;Meyer, H.;Beer, M.;Hoffmann, D.",2017,,10.3390/v9060142,0
615,Exploratory metagenomic analyses of periweaning failure-to-thrive syndrome-affected pigs,"Modern pig farming is characterised by the emergence of several syndromes whose aetiology is unclear or has a multifactorial origin, including periweaning failure-to-thrive syndrome (PFTS). In fact, its specific aetiology remains elusive, although several causes have been investigated over time. The present study aimed to investigate the potential role of viral agents in PFTS-affected and healthy animals by evaluating the virome composition of different organs using a metagenomic approach. This analysis allowed demonstrating a higher abundance of Porcine parvovirus 6 (PPV6) in healthy subjects while Ungulate bocaparvovirus 2 (BoPV2), Ungulate protoparvovirus 1 (PPV) and Porcine circovirus 3 (PCV-3) were increased in pigs with PFTS. No differential abundance of RNA viruses was found between PFTS-affected and control pigs. Remarkably, this is the first molecular characterisation of PPV6 and BoPV2 in Spain and one of the few all around the world, supporting their apparent widespread circulation. Interestingly, PCV-3 has been recently identified in several clinical-pathological conditions as well as in healthy pigs, while BoPV2 pathogenic potential is unknown. Although obtained results must be taken as preliminary, they open the door for further studies on the potential role of these viruses or their combination as predisposing factor/s for PFTS occurrence.",animal tissue;article;Bocaparvovirus;Circovirus;controlled study;failure to thrive;female;male;metagenomics;next generation sequencing;nonhuman;periweaning failure to thrive syndrome;pig;Porcine circovirus 3;Porcine parvovirus;Porcine parvovirus 6;Protoparvovirus;RNA virus;sequence alignment;Spain;Ungulate bocaparvovirus 2;Ungulate protoparvovirus 1,"Franzo, G.;Kekarainen, T.;Llorens, A.;Correa-Fiz, F.;Segalés, J.",2019,,10.1136/vr.105125,0
616,Subpopulations in aMPV vaccines are unlikely to be the only cause of reversion to virulence,"Avian metapneumovirus (aMPV) infects respiratory and reproductive tracts of domestic poultry, often involving secondary infections, and leads to serious economic losses in most parts of the world. While in general disease is effectively controlled by live vaccines, reversion to virulence of those vaccines has been demonstrated on several occasions. Consensus sequence mutations involved in the process have been identified in more than one instance. In one previous subtype A aMPV candidate vaccine study, small subpopulations were implicated. In the current study, the presence of subpopulations in a subtype B vaccine was investigated by deep sequencing. Of the 19 positions where vaccine (strain VCO3/50) and progenitor (strain VCO3/60616) consensus sequences differed, subpopulations were found to have sequence matching progenitor sequence in 4 positions. However none of these mutations occurred in a virulent revertant of that vaccine, thereby demonstrating that the majority progenitor virus population had not survived the attenuation process, hence was not obviously involved in any return to virulence. However within the vaccine, a single nucleotide variation was found which agreed with consensus sequence of a derived virulent revertant virus, hence this and other undetected, potentially virulent subpopulations, can be involved in reversion. Much deeper sequencing of progenitor, vaccine and revertant may clarify whether problematic virulent subpopulations are present and therefore whether these need to be routinely removed during aMPV vaccine preparation prior to registration and release.","Animals;Genetic Variation;High-Throughput Nucleotide Sequencing;Metapneumovirus/cl [Classification];Metapneumovirus/ge [Genetics];Metapneumovirus/ip [Isolation & Purification];*Metapneumovirus/ph [Physiology];Mutation;RNA, Viral/ge [Genetics];Vaccines, Attenuated/ad [Administration & Dosage];Vaccines, Attenuated/ae [Adverse Effects];Vaccines, Attenuated/ge [Genetics];Viral Vaccines/ad [Administration & Dosage];Viral Vaccines/ae [Adverse Effects];*Viral Vaccines/ge [Genetics];Virulence;0 (RNA, Viral);0 (Vaccines, Attenuated);0 (Viral Vaccines)","Franzo, G.;Naylor, C. J.;Drigo, M.;Croville, G.;Ducatez, M. F.;Catelli, E.;Laconi, A.;Cecchinato, M.",2015,May 15,,0
617,The actinic keratosis virome: can we prevent squamous cell carcinoma with a vaccine?,,,"Frazer, I. H.",2015,,,0
618,Quack leptin,"Background: A LEP transcript up-regulated in lungs of ducks (Anas platyrhynchos) infected by avian influenza A virus was recently described in the Nature Genetics manuscript that reported the duck genome. In vertebrates, LEP gene symbol is reserved for leptin, the key regulator of energy balance in mammals.Results: Launching an extensive search for this gene in the genome data that was submitted to the public databases along with duck genome manuscript and extending this search to all avian genomes in the whole-genome shotgun-sequencing database, we were able to report the first identification of coding sequences capable of encoding the full leptin protein precursor in wild birds. Gene structure, synteny and sequence-similarity (up to 54% identity and 68% similarity) to reptilian leptin evident in falcons (Falco peregrinus and cherrug), tits (Pseudopodoces humilis), finches (Taeniopygia guttata) and doves (Columba livia) confirmed that the bird leptin was a true ortholog of its mammalian form. Nevertheless, in duck, like other domestic fowls the LEP gene was not identifiable.Conclusion: Lack of the LEP gene in poultry suggests that birds that have lost it are particularly suited to domestication. Identification of an intact avian gene for leptin in wild birds might explain in part the evolutionary conservation of its receptor in leptin-less fowls. © 2014 Friedman-Einat and Seroussi; licensee BioMed Central Ltd.",leptin;avian genetics;bird;Columba livia;duck;Falco cherrug;Falco peregrinus;gene identification;gene sequence;gene structure;LEP gene;letter;nonhuman;nucleotide sequence;orthology;Pseudopodoces humilis;synteny;Taeniopygia guttata,"Friedman-Einat, M.;Seroussi, E.",2014,,10.1186/1471-2164-15-551,0
619,Crystal structure of swine vesicular disease virus and implications for host adaptation,"Swine vesicular disease virus (SVDV) is an Enterovirus of the family Picornaviridae that causes symptoms indistinguishable from those of foot-and-mouth disease virus. Phylogenetic studies suggest that it is a recently evolved genetic sublineage of the important human pathogen coxsackievirus B5 (CBV5), and in agreement with this, it has been shown to utilize the coxsackie and adenovirus receptor (CAR) for cell entry. The 3.0-Å crystal structure of strain UK/27/72 SVDV (highly virulent) reveals the expected similarity in core structure to those of other picornaviruses, showing most similarity to the closest available structure to CBV5, that of coxsackievirus B3 (CBV3). Features that help to cement together and rigidify the protein subunits are extended in this virus, perhaps explaining its extreme tolerance of environmental factors. Using the large number of capsid sequences available for both SVDV and CBV5, we have mapped the amino acid substitutions that may have occurred during the supposed adaptation of SVDV to a new host onto the structure of SVDV and a model of the SVDV/CAR complex generated by reference to the cryo-electron microscopy-visualized complex of CBV3 and CAR. The changes fall into three clusters as follows: one lines the fivefold pore, a second maps to the CAR-binding site and partially overlaps the site for decay accelerating factor (DAF) to bind to echovirus 7 (ECHO7), and the third lies close to the fivefold axis, where the low-density lipoprotein receptor binds to the minor group of rhinoviruses. Later changes in SVDV (post-1971) map to the first two clusters and may, by optimizing recognition of a pig CAR and/or DAF homologue, have improved the adaptation of the virus to pigs.",decay accelerating factor;low density lipoprotein receptor;protein VP1;protein VP2;protein VP3;protein VP4;unclassified drug;viral protein;adaptation;amino acid substitution;article;controlled study;Coxsackievirus B3;cryoelectron microscopy;crystal structure;Enterovirus B;Enterovirus;environmental factor;host;nonhuman;priority journal;protein analysis;protein structure;receptor binding;Rhinovirus;swine vesicular disease virus;virus capsid,"Fry, E. E.;Knowles, N. J.;Newman, J. W. I.;Wilsden, G.;Rao, Z.;King, A. M. Q.;Stuart, D. I.",2003,,10.1128/jvi.77.9.5475-5486.2003,0
620,Molecular detection and typing of duck hepatitis A virus directly from clinical specimens,"To develop a new approach for the detection and typing of duck hepatitis A virus (DHAV), a pair of non-degenerate primers was designed to amplify a ∼250-bp genomic region in the 5′UTR. 3 reference strains and 6 duck embryo-derived isolates from various regions in China, involving 2 serotypes, were successfully amplified with the primer set. By determining the nucleotide sequence of the amplicon, a molecular typing method was developed. If isolate sequences were compared to DHAV 5′UTR sequences available in public databases, nucleotide identity was ≥94% with homologous serotype and ≤73% with heterologous serotypes. Phylogenetic analysis revealed monophyletic clustering of 5′UTR sequences of a homologous serotype, confirming the new classification of DHAV (serotype 1 and the two new serotypes recently described in Taiwan and South Korea, respectively) into three genotypes (A, B and C) defined by the capsid coding region. Analysis of the results showed that the primer pair should aid in the detection of DHAV, and that the amplicon sequence contains type-specific information and can be used for effective and rapid molecular typing. The molecular methods proved their utility through the detection and typing of DHAV directly from 28 liver specimens collected from dead ducklings during duck viral hepatitis outbreaks in different regions of China between 2001 and 2007. The results confirmed the presence of DHAV in all of the 28 samples and demonstrated that genotypes A (13/28) and C (15/28) of DHAV are co-circulating in China. © 2008 Elsevier B.V. All rights reserved.",5' untranslated region;amplicon;animal tissue;article;China;data base;duck;embryo;epidemic;gene amplification;gene cluster;gene sequence;genotype;Hepatitis A virus;Hepatitis C virus;heterologous expression;molecular typing;nonhuman;nucleotide sequence;phylogeny;sequence homology;serotype;South Korea;Taiwan;unindexed sequence;virus capsid;virus classification;virus detection;virus genome;virus hepatitis;virus isolation;virus strain;virus typing,"Fu, Y.;Pan, M.;Wang, X.;Xu, Y.;Yang, H.;Zhang, D.",2008,,10.1016/j.vetmic.2008.03.011,0
621,Comparative transcriptome analyses indicate enhanced cellular protection against FMDV in PK15 cells pretreated with IFN-γ,"Interferon gamma (IFN-γ) can induce a host antiviral response to foot and mouth disease virus (FMDV) in vivo and in vitro. To elucidate the mechanism of IFN-γ anti FMDV infection in host cells, high-throughput RNA sequencing was analyzed for systemic changes in gene expression profiles in PK15 cells infected by FMDV with or without IFN-γ pretreatment. More than 25 million reads, covering 1.2–1.5 Gb, were analyzed from each experiment panel. FMDV challenge altered the transcription of genes involved in positively and negatively regulating cell death or apoptosis; however, the expected immune suppression response was not obvious. IFN-γ pretreatment combined with FMDV infection normalized the increase in apoptosis. Furthermore, the transcription factors required for IFN-γ functioning, STAT1 and IRF1 were up-regulated by IFN-γ pretreatment and stimulated downstream IFN-stimulated genes (ISGs). These induced ISGs are mainly responsible for antigen processing, antigen presentation or antiviral defense. Interestingly, a synergistic effect on some ISGs, including OAS1, OAS2, MX1, MX2, RIG-I and IFIT1, was observed in the combined treatment compared to the IFN-γ treatment alone. The suggested effects identified by RNA sequencing were consistent with cellular morphology changes and confirmed by related protein markers. This is the first report exploring transcriptome alterations introduced by FMDV infection with or without IFN-γ pretreatment. The identified key host genes that control cell survival in vitro broaden our comprehensive understanding of how IFN-γ inhibits FMDV infection and may shed light on developing improved FMD control approaches.",gamma interferon;histone H2AX;interferon regulatory factor 1;nicotinamide adenine dinucleotide adenosine diphosphate ribosyltransferase 1;protein Bax;protein bcl 2;STAT1 protein;toll like receptor 1;toll like receptor 6;transcriptome;animal cell;antigen presentation;apoptosis;article;cell death;cell protection;cell structure;cell survival;controlled study;foot and mouth disease;Foot and mouth disease virus;gene expression profiling;genetic transcription;high throughput sequencing;host cell;immunosuppressive treatment;in vitro study;natural killer cell mediated cytotoxicity;nonhuman;priority journal;RNA sequence;upregulation,"Fu, Y.;Zhu, Z.;Chang, H.;Liu, Z.;Liu, J.;Chen, H.",2016,,10.1016/j.gene.2016.03.027,0
622,"Molecular characterization of novel P[14],G8 bovine group A rotavirus, Sun9, isolated in Japan","In this study, a novel bovine group A rotavirus (RV-A), Sun9, isolated from calf diarrhea in the Tochigi Prefecture, Japan, was characterized genetically by the sequence analysis of the genome segments encoding VP4 and VP7. The nucleotide and deduced amino acid sequences of the genome segments encoding VP4 and VP7 of Sun9 revealed high homology with P[14] human and lapine RV-As (80.2-88.7% and 90.9-94.8%) and G8 bovine and human RV-As (83.1-95.5% and 92.3-98.2%). Sun9 was also classified into P[14] and G8 in the phylogenetic analysis of the nucleotide sequences of the genome segments encoding VP4 and VP7. Although previous reports have suggested that P[14],G8 human RV-As isolated until now were obtained from the reassortment between human and bovine RV-As, or the interspecies transmission of bovine RV-A to human, no P[14],G8 bovine RV-A has yet been reported. Sun9 may be initial direct evidence of the above hypothesis. © 2004 Elsevier B.V. All rights reserved.",amino acid;nucleotide;amino acid sequence;article;Bovine viral diarrhea virus 1;controlled study;genetic analysis;genetic trait;Human rotavirus;Japan;molecular biology;nonhuman;nucleotide sequence;phylogeny;priority journal;Rotavirus;sequence analysis;sequence homology;species comparison;unindexed sequence;virus classification;virus genome;virus isolation;virus transmission;virus typing,"Fukai, K.;Saito, T.;Inoue, K.;Sato, M.",2004,,10.1016/j.virusres.2004.04.016,0
623,Bovine herpesvirus-1: Comparison and differentiation of vaccine and field strains based on genomic sequence variation,"Bovine herpesvirus-1 (BoHV-1) causes significant disease in cattle including respiratory, fetal diseases, and reproductive tract infections. Control programs usually include vaccination with a modified live viral (MLV) vaccine. On occasion BoHV-1 strains are isolated from diseased animals or fetuses postvaccination. Currently there are no markers for differentiating MLV strains from field strains of BoHV-1. In this study several BoHV-1 strains were sequenced using whole-genome sequencing technologies and the data analyzed to identify single nucleotide polymorphisms (SNPs). Strains sequenced included the reference BoHV-1 Cooper strain (GenBank Accession JX898220), eight commercial MLV vaccine strains, and 14 field strains from cases presented for diagnosis. Based on SNP analyses, the viruses could be classified into groups having similar SNP patterns. The eight MLV strains could be differentiated from one another although some were closely related to each other. A number of field strains isolated from animals with a history of prior vaccination had SNP patterns similar to specific MLV viruses, while other field isolates were very distinct from all vaccine strains. The results indicate that some BoHV-1 isolates from clinically ill cattle/fetuses can be associated with a prior MLV vaccination history, but more information is needed on the rate of BoHV-1 genome sequence change before irrefutable associations can be drawn. © 2013 Elsevier Ltd.",live vaccine;modified live viral vaccine;unclassified drug;virus vaccine;article;Bovine herpesvirus 1;comparative study;DNA extraction;DNA sequence;genetic variability;nucleotide sequence;polymerase chain reaction;priority journal;Rhadinovirus;single nucleotide polymorphism;vaccination;virus classification;virus genome;virus identification;virus isolation;virus strain,"Fulton, R. W.;d'Offay, J. M.;Eberle, R.",2013,,10.1016/j.vaccine.2013.01.013,0
624,Evolutionary analyses on the HA gene ofpandemic H1N1/09: early findings,"The HA protein is responsible for influenza virus attachment and the subsequent fusion of viral and cellular membranes. Antigenic drift is driven by an accumulation of point mutations in the HA. And, the receptor-binding specificity of HA is responsible for the host range restriction of the virus. In April 2009, large outbreaks of novel H1N1 influenza in human population were reported from North America. The pandemic H1N1 virus originated from swine influenza virus. Evolutionary process of the pandemic virus after its introduction to human population remains to be clarified. We conducted phylogenetic analyses constructing a phylogenetic tree for and calculating site-by-site selective pressures in the HA gene. Phylogenetic tree showed that pandemic viruses were not clustered clearly by their geographical location or isolation time in the phylogenetic tree. The virus has been circulating the globe extensively with multiple introductions into most geographical areas. We found 3 sites positively selected in the HA gene for pandemic H1N1 virus. Among them, position 206 is located in an antigenic site. We did not find significant negative selection on any of the receptor binding sites. The virus has been evolving under unique selective pressure.",,"Furuse, Y.;Suzuki, A.;Oshitani, H.",2010,Jun 15,,0
625,Gene segment reassortment between Eurasian and American clades of avian influenza virus in Italy,"All genes of avian influenza A viruses are phylogenetically distinguished into two large clades, namely the American and Eurasian clade. Reassortments among the gene segments of influenza viruses belonging to the two distinct clades are rare events and have never been described in poultry in Europe and Asia before. This study presents the genetic characterization of two influenza viruses isolated from domestic mallards in Italy in 2004 and 2005. Phylogenetic analysis of the entire genome showed that these viruses contain mixed gene segments belonging to the American and Eurasian clades. © Springer-Verlag 2009.",animal;article;Asia;avian influenza;classification;waterfowl;Europe;genetic reassortment;genetic recombination;genetics;Influenza A virus;isolation and purification;Italy;molecular genetics;phylogeny;virology,"Fusaro, A.;Monne, I.;Cattoli, G.;de Nardi, R.;Salviato, A.;Martin, A. M.;Capua, I.;Terregino, C.",2010,,10.1007/s00705-009-0550-2,0
626,"Genetic Diversity of Highly Pathogenic Avian Influenza A(H5N8/H5N5) Viruses in Italy, 2016-17","In winter 2016-17, highly pathogenic avian influenza A(H5N8) and A(H5N5) viruses of clade 2.3.4.4 were identified in wild and domestic birds in Italy. We report the occurrence of multiple introductions and describe the identification in Europe of 2 novel genotypes, generated through multiple reassortment events.","Animals;Animals, Wild/vi [Virology];Birds/vi [Virology];*Genetic Variation;Genotype;Influenza A Virus, H5N8 Subtype/ge [Genetics];Influenza A Virus, H5N8 Subtype/py [Pathogenicity];Influenza A virus/cl [Classification];*Influenza A virus/ge [Genetics];*Influenza A virus/py [Pathogenicity];*Influenza in Birds/vi [Virology];Italy;Phylogeny;Reassortant Viruses/ge [Genetics];Reassortant Viruses/py [Pathogenicity];Turkeys","Fusaro, A.;Monne, I.;Mulatti, P.;Zecchin, B.;Bonfanti, L.;Ormelli, S.;Milani, A.;Cecchettin, K.;Lemey, P.;Moreno, A.;Massi, P.;Dorotea, T.;Marangon, S.;Terregino, C.",2017,09,,0
627,Unexpected Interfarm Transmission Dynamics during a Highly Pathogenic Avian Influenza Epidemic,"UNLABELLED: Next-generation sequencing technology is now being increasingly applied to study the within- and between-host population dynamics of viruses. However, information on avian influenza virus evolution and transmission during a naturally occurring epidemic is still limited. Here, we use deep-sequencing data obtained from clinical samples collected from five industrial holdings and a backyard farm infected during the 2013 highly pathogenic avian influenza (HPAI) H7N7 epidemic in Italy to unravel (i) the epidemic virus population diversity, (ii) the evolution of virus pathogenicity, and (iii) the pathways of viral transmission between different holdings and sheds. We show a high level of genetic diversity of the HPAI H7N7 viruses within a single farm as a consequence of separate bottlenecks and founder effects. In particular, we identified the cocirculation in the index case of two viral strains showing a different insertion at the hemagglutinin cleavage site, as well as nine nucleotide differences at the consensus level and 92 minority variants. To assess interfarm transmission, we combined epidemiological and genetic data and identified the index case as the major source of the virus, suggesting the spread of different viral haplotypes from the index farm to the other industrial holdings, probably at different time points. Our results revealed interfarm transmission dynamics that the epidemiological data alone could not unravel and demonstrated that delay in the disease detection and stamping out was the major cause of the emergence and the spread of the HPAI strain. IMPORTANCE: The within- and between-host evolutionary dynamics of a highly pathogenic avian influenza (HPAI) strain during a naturally occurring epidemic is currently poorly understood. Here, we perform for the first time an in-depth sequence analysis of all the samples collected during a HPAI epidemic and demonstrate the importance to complement outbreak investigations with genetic data to reconstruct the transmission dynamics of the viruses and to evaluate the within- and between-farm genetic diversity of the viral population. We show that the evolutionary transition from the low pathogenic form to the highly pathogenic form occurred within the first infected flock, where we identified haplotypes with hemagglutinin cleavage site of different lengths. We also identify the index case as the major source of virus, indicating that prompt application of depopulation measures is essential to limit virus spread to other farms.","Animals;*Biological Evolution;Chickens/ge [Genetics];*Chickens/vi [Virology];*Epidemics/ve [Veterinary];*Genetic Variation/ge [Genetics];High-Throughput Nucleotide Sequencing;*Influenza A Virus, H7N7 Subtype/ge [Genetics];*Influenza in Birds/ep [Epidemiology];*Influenza in Birds/tm [Transmission];Influenza in Birds/vi [Virology];Italy/ep [Epidemiology];Phylogeny","Fusaro, A.;Tassoni, L.;Milani, A.;Hughes, J.;Salviato, A.;Murcia, P. R.;Massi, P.;Zamperin, G.;Bonfanti, L.;Marangon, S.;Cattoli, G.;Monne, I.",2016,07 15,,0
628,Development of a pyrosequencing assay for the typing of alphaherpesviruses,"Identification of herpesvirus in biological material is usually carried out by real-time PCR. With the aim to classify the strain of virus identified, real-time PCR must be often supported by time-consuming capillary electrophoresis sequencing analysis. Here we provide a protocol for the rapid and reliable identification of 5 closely related herpesviruses by PyroMark Q24 sequencing system. PyroMark performs DNA sequencing analysis using pyrosequencing, a technology based on the detection of released pyrophosphate during DNA elongation [1]. PyroMark is designed to detect changes in specified variable positions of the DNA. It can efficiently detect single nucleotide differences in sequences [2]. In the present paper we describe a protocol to pyrosequence a small polymorphic segment of the US8 gene. On the basis of the differences identified in the nucleotide sequence we could readily classify the herpesvirus as Bovine herpesvirus 1.1, Bovine herpesvirus 1.2, Bovine herpesvirus 5, Bubaline herpesvirus 1 or Caprine herpesvirus. The protocol set up offers several advantages with respect to the techniques commonly used: it requires less than one working day to be carried;it gives the possibility to analyze, at reasonable costs, up to 24 samples at a time; andit allows to detect with great reliability and specificity strongly genetically correlated organisms like the herpesviruses named above. The procedure can be easily applied to other families of viruses, with opportune modifications.",DNA;nucleic acid;virus RNA;agar gel electrophoresis;article;capillary electrophoresis;DNA sequence;Herpesviridae;immobilization;nonhuman;nucleotide sequence;pyrosequencing;real time polymerase chain reaction;virus classification,"Fusco, G.;Amoroso, M. G.;Gesualdi Montesano, N.;Viscardi, M.",2015,,10.1016/j.mex.2015.01.001,0
629,Temperature-sensitive mutants of Chandipura virus. II. Phenotypic characteristics of the six complementation groups,"Fifty temperature-sensitive (ts) mutants of the rhabdovirus Chandipura virus have been classified into six complementation groups designated ChI to ChVI. Group ChI contains 44 mutants, group ChII contains 2 mutants, and the remaining groups have 1 mutant each. Mutants in groups ChI, ChIII, ChIV, and ChVI had RNA-negative phenotypes in experiments measuring amplification of RNA synthesis at restrictive temperature. The two mutants in group ChII had RNA-positive phenotypes, and the virions were thermolabile. Mutant ts Ch851 of group ChV was also RNA positive, and the M polypeptide of this mutant appeared to be unstable in cells incubated at restrictive temperature. It is likely, therefore, that complementation groups ChII and ChV represent the genes coding for the two viral proteins of the virion envelope. No precise assignment can be made in the case of the four RNA-negative groups, since all the mutants examined showed some polymerase activity in vitro at restrictive temperature. An attempt to obtain polymerase mutants by screening for sensitivity to rifampin was not successful. Six temperature-dependent host range mutants (the tdCE phenotype) of Chandipura virus failed to multiply in chicken embryo cells at restrictive temperature, but otherwise they differed in their host range properties from similar mutants of vesicular stomatitis virus.","Animals;Cell Line;Cell-Free System;Cricetinae;DNA-Directed RNA Polymerases/me [Metabolism];Haplorhini;Humans;Kidney;*Mutation;Peptide Biosynthesis;Phenotype;*RNA, Viral/ge [Genetics];*Rhabdoviridae/ge [Genetics];Rhabdoviridae/me [Metabolism];Temperature;Viral Proteins/bi [Biosynthesis];0 (RNA, Viral);0 (Viral Proteins)","Gadkari, D. A.;Pringle, C. R.",1980,Jan,,0
630,Analysis by high throughput sequencing of Specific Pathogen Free eggs,"Specific Pathogen Free (SPF) embryonated eggs are used for the production of many veterinary and human vaccines. We have used High Throughput Sequencing to screen allantoic fluids and embryos for the presence of encapsidated viral genomes and viral transcripts, respectively. SPF eggs from two different producers were tested. We evidenced sequences corresponding to known endogenous retroviruses and sequences of Avian Leukosis Virus, but no sequence that might suggest a productive infection of eggs with a virus even distant from known viruses. Our results strongly suggest that SPF eggs such as those used for this study represent a safe substrate for the production of vaccines. (C) 2014 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.",Chicken;Egg;Specific Pathogen Free;High throughput sequencing;Virus;safety;Vaccines;AVIAN-LEUKOSIS VIRUSES;VACCINES;CELLS,"Gagnieur, L.;Cheval, J.;Cochet, M.;Breard, E.;Gratigny, M.;Hebert, C.;Muth, E.;Viarouge, C.;Dumarest, M.;Coulpier, M.;Eloit, M.",2014,Jul,,0
631,Unbiased analysis by high throughput sequencing of the viral diversity in fetal bovine serum and trypsin used in cell culture,"Fetal bovine serum (FBS) and trypsin are reagents used in cell culture and have been the source of viral contamination of pharmaceutical products. We performed high throughput sequencing (HTS) of two pools of commercial batches of FBS and three commercial batches of trypsin. Taxonomies were assigned by comparing sequences of contigs and singletons to the entire NCBI nucleic acid and protein databases. The same major viral species were evidenced between batches of a given reagent but the proportion of viral reads among total reads varied markedly between samples (from 0.002% to 22.7%). In FBS, the sequences found were mainly from bovine viral diarrhea virus (BVDV) 1 to 3 and bovine parvovirus 3 (BPV3). The BVDV sequences derived from FBS showed only minor discrepancies with primers generally used for the screening of BVDV. Viral sequences in trypsin were mainly from porcine circovirus type 2. Other known viral sequences at lower read counts and potential new viral species (bovine parvovirus and bovine pegivirus) were evidenced. The load of some known and new viruses detected by HTS could be quantified by qPCR. Results of HTS provide a framework for evaluating the pertinence of control measures including the design of PCRs, bioassays and inactivation procedures. © 2014 The International Alliance for Biological Standardization.",contig;fetal bovine serum;reagent;trypsin;unclassified drug;5' untranslated region;article;bioinformatics;Bocaparvovirus;bovine Parvovirus 3;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;Bovine viral diarrhea virus 3;cell culture;Circovirus;comparative study;controlled study;high throughput sequencing;nonhuman;nucleic acid database;nucleotide sequence;Pestivirus;polymerase chain reaction;Porcine circovirus 2;priority journal;protein database;quality control;sequence analysis;species diversity;taxonomy;validation process;viral diversity;viral phenomena and functions;virus identification;virus load;virus strain,"Gagnieur, L.;Cheval, J.;Gratigny, M.;Hébert, C.;Muth, E.;Dumarest, M.;Eloit, M.",2014,,10.1016/j.biologicals.2014.02.002,0
632,Genetic characterization and evolutionary analysis of Newcastle disease virus isolated from domestic duck in South Korea,"Domestic ducks are considered a potential reservoir of Newcastle disease virus. In the study, a Newcastle disease virus (NDV) isolated from a domestic duck during surveillance in South Korea was characterized. The complete genome of the NDV isolate was sequenced, and the phylogenetic relationship to reference strains was studied. Phylogenetic analysis revealed that the strain clustered in genotype I of Class II ND viruses, has highly phylogenetic similarity to NDV strains isolated from waterfowl in China, but was distant from the viruses isolated in chickens and vaccine strains used in South Korea. Pathogenicity experiment in chickens revealed it to be a lentogenic virus. The deduced amino acid sequence of the cleavage site of the fusion (F) protein confirmed that the isolate contained the avirulent motif 112GKQGRL117 at the cleavage site and caused no apparent disease in chickens and ducks. With phylogeographic analysis based on fusion gene, we estimate the origin of an ancestral virus of the isolate and its sister strain located in China around 1998. It highlights the need of continuous surveillance to enhance current understanding of the molecular epidemiology and evolution of the pathogenic strains.",amino acid sequence;Anas platyrhynchos;article;fusion gene;gene sequence;genome analysis;genotype;glycosylation;molecular phylogeny;Newcastle disease virus;nonhuman;nucleotide sequence;pathogenicity;phylogeny;phylogeography;priority journal;South Korea;viral genetics;virus genome;virus isolation;virus virulence;waterfowl,"Gaikwad, S.;Kim, J. Y.;Lee, H. J.;Jung, S. C.;Choi, K. S.",2016,,10.1016/j.gene.2015.12.040,0
633,Antiviral activity of tetrahydro-2(1H)-pyrimidinones and related compounds,"24 derivatives of tetrahydro-2(1 H)-pyrimidinone and related compounds were tested in vitro for antiviral activity against representatives of six viral taxonomic groups. The screening was carried out by a two-stage procedure including the agar-diffusion plaque-inhibition test and the one-step growth cycle setup. A distinct activity of three mono- and bis-morpholinomethyl derivatives of tetrahydro-2(1H)-pyrimidinone (THP), 1,3-bis(piperidinomethyl)- THP, the 1-morpholinomethyl derivative of tetrahydro-2(1H)-pyrimidinethione (THPT) and the related N,N'-bis(morpholinomethyl)-urea against the fowl plague virus was established. In the one-step growth cycle setup these compounds inhibited 87.5-99.6% of the infectious virus yield. Two of the compounds, namely 1-morpholinomethyl derivatives of THP and THPT, manifested a strong inhibitory effect on the reproduction of Semliki Forest virus as well, exceeding 99.9% in the one-step growth cycle test. A borderline effect was observed in some derivatives against vaccinia virus and Newcastle disease virus. The structure-activity relationship of this group of compounds is discussed.",amantadine;antivirus agent;new drug;ribavirin;rimantadine;tetrahydro 2(1h) pyrimidinone derivative;unclassified drug;article;bird disease;cell culture;dose response;drug comparison;drug efficacy;drug response;drug screening;Fowl plague virus;in vitro study;Newcastle disease virus;nonhuman;Semliki Forest virus;structure activity relation;Vaccinia virus,"Galabov, A. S.;Velichkova, E.;Karparov, A.",1984,,,0
634,Genotyping of African swine fever virus (ASFV) isolates associated with disease outbreaks in Uganda in 2007,"Samples from infected domestic pigs associated with an outbreak of African swine fever (ASF) in three districts of central Uganda in 2007 were confirmed as being infected with African swine fever virus (ASFV) using a P72 gene-based polymerase chain reaction amplification (PCR) assay combined with restriction analysis. None of the sera collected from pigs with clinical symptoms were positive using the OIE serological prescribed tests. However, seven haemadsorbing viruses were isolated in macrophage culture and genotyped by partial p72 and full length p54-gene sequencing. Four of these viruses were isolated directly from serum samples. All the viruses were classified within the domesticpig cycle-associated p72 and p54 genotype IX which also includes viruses responsible for ASF outbreaks in Kenya in 2006 and 2007 and Uganda in 2003. To define virus relationships at higher resolution, typing was performed by analysis of tetrameric amino acid repeat regions within the central variable region (CVR) of the B602L gene. Ugandan isolates sequences exhibited 100% identity to viruses isolated from outbreaks in Kenya in 2007. The identity was greater than the viruses obtained from an earlier outbreak in Kenya in 2006. This provides further evidence that genetically similar ASFV virus within p72 Genotype IX may be circulating between Kenya and Uganda. © 2011 Academic Journals.",protein p54;protein p72;African swine fever;African swine fever virus;animal cell;animal tissue;article;controlled study;domestic pig;epidemic;gene sequence;genetic epidemiology;genetic similarity;genetic variability;genotype;Kenya;molecular phylogeny;nonhuman;nucleotide sequence;polymerase chain reaction;promoter region;restriction mapping;sequence homology;serodiagnosis;Uganda;variable number of tandem repeat;virus classification;virus gene;virus identification;virus isolation;virus transmission,"Gallardo, C.;Ademun, A. R.;Nieto, R.;Nantima, N.;Arias, M.;Martín, E.;Pelayo, V.;Bishop, R. P.",2011,,,0
635,Nanovirus-alphasatellite complex identified in Vicia cracca in the Rhone delta region of France,"Nanoviruses are multi-component plant-infecting single-stranded DNA viruses. Using a viral metagenomics-informed approach, a new nanovirus and two associated alphasatellite molecules have been identified in an uncultivated asymptomatic Vicia cracca plant in the Rhne region of France. This novel nanovirus genome includes eight genomic components (named DNA-R, DNA-S, DNA-M, DNA-C, DNA-N, DNA-U1, DNA-U2 and DNA-U4) and, across all components, shares < 66% pairwise sequence identity with other nanovirus genomes. The two associated alphasatellites share 62% identity with each other and < 81% identity will all other nanovirus-associated alphasatellites.",Nanoviridae;ssDNA virus;cow vetch,"Gallet, R.;Kraberger, S.;Filloux, D.;Galzi, S.;Fontes, H.;Martin, D. P.;Varsani, A.;Roumagnac, P.",2018,Mar,,0
636,Genetic information of mycobacteriophages DNAIII and its anti-tuberculosis potential,"Objective: To understand the genetic information of mycobacteriophage DNAIII, and explore its anti-tuberculosis potential. Methods: Mycobacteriophage DNAIII DNA was isolated and purified using lambda DNA extraction protocol. The shotgun sequences were assembled with Phred and PhraD and edited with Consed, then gaps were filled by sequencing PCR fragments. The general characteristics of genome were analysed using EditSeq software of DNAStar software package. The genome was scanned for open reading frames using Glimmer 3.0. The genetic information of mycobacteriophage DNAIII genome was further explored by colinearity analysis and phylogenetic tree construction. The ability of DNAIII to lyse M. tuberculosis was investigated in vitro, and the effects of temperature, alcohol, pH values on DNAIII survival was determined. Results: The genome of DNAIII possessed 39 520 bp in size, and was linear double-stranded DNA, with G+C content of 66.83%. DNAIII contained 60 predicted protein-coding genes, and did not encode any tRNAs. There was no tandem repeat sequence in the genome of DNAIII. DNAIII gene 32 encoded integrase, and there was also no gene encoding a repressor. DNAIII was highly similar and colinear in nucleotide acid level to Angel and BPs. At three different time points (1 d, 2 d and 3 d), the numbers of M. tuberculosis in DNAIII group were significantly smaller than those in control group (P<0.05). DNAIII was unstable to temperature, alcohol and pH values. Conclusion: DNAIII, which belongs to cluster G, is a mycobacteriophage capable of lysing M.tuberculosis.",alcohol;bacteriophage DNA;cytosine;DNA fragment;double stranded DNA;guanine;integrase;tuberculostatic agent;article;software;concentration (parameter);DNA extraction;DNA isolation;DNA purification;genetic analysis;mycobacteriophage;open reading frame;pH;phylogeny;polymerase chain reaction;sequence analysis;tandem repeat;temperature,"Gan, Y. L.;Liu, P.;Wu, T. T.;Guo, S. L.",2013,,10.3969/j.issn.1674-8115.2013.10.002,0
637,Newcastle disease virus: current status and our understanding Review,"Newcastle disease (ND) is one of the highly pathogenic viral diseases of avian species. ND is economically significant because of the huge mortality and morbidity associated with it. The disease is endemic in many third world countries where agriculture serves as the primary source of national income. Newcastle disease virus (NDV) belongs to the family Paramyxoviridae and is well characterized member among the avian paramyxovirus serotypes. In recent years, NDV has lured the virologists not only because of its pathogenic potential, but also for its oncolytic activity and its use as a vaccine vector for both humans and animals. The NDV based recombinant vaccine offers a pertinent choice for the construction of live attenuated vaccine due to its modular nature of transcription, minimum recombination frequency, and lack of DNA phase during replication. Our current understanding about the NDV biology is expanding rapidly because of the availability of modern molecular biology tools and high-throughput complete genome sequencing.",Animals;Biological Therapy/mt [Methods];*Bird Diseases/vi [Virology];Birds;Drug Carriers;Genetic Vectors;Humans;Newcastle disease virus/ge [Genetics];*Newcastle disease virus/ph [Physiology];Oncolytic Viruses/ge [Genetics];*Oncolytic Viruses/ph [Physiology];0 (Drug Carriers),"Ganar, K.;Das, M.;Sinha, S.;Kumar, S.",2014,May 12,,0
638,A REVIEW ARTICLE ON SWINE ORIGIN INFLUENZA VIRUS A (S-OIV) INFECTION,,,"Ganguly, S.;Giri, S.;Aseri, G. K.;Yadav, P.;Khare, N. K.",,,,0
639,Analysis of alternative splicing in chicken embryo fibroblasts in response to reticuloendotheliosis virus infection,"Alternative splicing (AS) plays a significant role in regulation of genomic expression at the transcriptional level and is involved in many important biological functions of cells, thus a gene can be spliced into distinct transcript variants then translated to many different kinds of protein. Reticuloendotheliosis virus (REV) is a kind of retrovirus that can infect multiple avian species, leading to runting syndrome, immunosuppression and oncogenesis. In this present study, we analyzed AS in REV-infected chicken embryo fibroblasts (CEFs) which were inoculated with the second generation of REV (group VB) and compared with normal CEFs (group C) by high-throughput RNA sequencing technology. A total of 6,939 genes which were alternatively spliced were detected, among them, skipped exon (SE) was the most common pattern. Moreover, 5,607 AS genes were detected as differentially expressed; compared with group C, group VB has 2,825 genes upregulated significantly and 2,782 genes downregulated significantly. These 5,607 differentially expressed AS genes are involved in many important biological processes. Many of them are involved in apoptosis and tumourigenesis. We also proved, by agarose gel electrophoresis, that AS events predicted by our study are authentic and AS is closely related with apoptosis and tumourigenesis in REV-infected CEFs. Our study provides the best analysis to date of the potential link between AS and CEFs in response to REV infection. Research highlights Transcriptomics analysis of REV-infected CEFs using high-throughput sequencing. Potential link between alternative splicing and CEFs in response to REV infection. Skipped exon is the most common spliced pattern in REV-infected CEFs. Differentially expressed genes mainly involved in apoptosis and tumourigenesis.",messenger RNA;transcriptome;agar gel electrophoresis;alternative RNA splicing;animal experiment;apoptosis;article;avian reticuloendotheliosis;biological phenomena and functions concerning the entire organism;carcinogenesis;chicken;down regulation;fibroblast;gene;gene expression;graft versus host reaction;high throughput screening;nonhuman;Reticuloendotheliosis virus;RNA extraction;RNA sequence;signal transduction;upregulation;virus genome,"Gao, C.;Zhai, J.;Dang, S.;Zheng, S.",2018,,10.1080/03079457.2018.1511047,0
640,"Classification of a new member of the TBE flavivirus subgroup by its immunological, pathogenetic and molecular characteristics: Identification of subgroup-specific pentapeptides","The antigenic, pathogenic and molecular characteristics of Turkish sheep encephalitis (TSE) virus, strain TTE80, were compared with other members of the tick-borne encephalitis (TBE) virus complex. Monoclonal antibodies with defined specificity for the flavivirus envelope glycoprotein distinguished TSE virus from louping ill (LI), western or far eastern TBE, Langat and Powassan virus in indirect immunofluorescence, haemagglutination-inhibition and neutralization tests. On the other hand, TSE virus, which produces an LI-like disease in sheep, resembled LI virus in mouse neurovirulence tests. Molecular homology data of all the structural genes of TSE virus compared with other tick-borne flaviviruses demonstrated that TSE virus is a distinct member in the TBE virus subgroup. The data are consistent with the conclusion that TSE virus has evolved by a separate evolutionary pathway as compared with the close antigenic relatives, western European, far eastern TBE viruses and LI virus. By aligning the encoded amino acids in the viral envelope glycoprotein of mosquito- and tick-borne flaviviruses, we have also identified subgroup-specific pentapeptide motifs for the tick-borne encephalitis, Japanese encephalitis and dengue subgroup viruses of the genus Flavivirus. These pentapeptides have important implications for the evolution, classification and diagnosis of flaviviruses.",monoclonal antibody;pentapeptide;antigenicity;article;controlled study;nonhuman;nucleotide sequence;priority journal;Tick borne encephalitis virus;Turkey (republic);virus characterization;virus classification,"Gao, G. F.;Hussain, M. H.;Reid, H. W.;Gould, E. A.",1993,,10.1016/0168-1702(93)90002-5,0
641,"Viral genome and antiviral drug sensitivity analysis of two patients from a family cluster caused by the influenza A(H7N9) virus in Zhejiang, China, 2013","Objectives: In the winter of 2013, people were facing the risk of human-to-human transmission of the re-emerging influenza A(H7N9) virus. We report herein information on the clinical features of two patients from the same family infected with this virus, the genomic sequences of the viruses harbored, and antiviral drug sensitivity. Methods: Clinical and epidemiological data of two patients from the same family were collected and analyzed. Sequencing was done for the viruses isolated from these two patients and one epidemiologically related chicken, and the sequences of the eight gene segments of the viruses were analyzed phylogenetically. The sensitivity of the viruses to antiviral drug treatment was determined by neuraminidase inhibitor susceptibility test. Results: The two patients from one family cluster shared the same symptoms but had different outcomes, and had a strong epidemiological link. Three strains, two from these two patients and one from the chicken, were isolated. Genome sequencing and analyses of phylogenetic trees demonstrated that the two viruses were almost identical. We noted the presence of the PB2 E627K amino acid substitution that was not present in isolates from the first wave, as well as two new mutations in the NA gene and six in the PB2 gene. Drug sensitivity testing showed that the new isolates were resistant to oseltamivir but sensitive to peramivir. Conclusions: The two patients from one family cluster were probable human-to-human transmission cases. The new isolates were sensitive to peramivir but showed reduced sensitivity to oseltamivir.",C reactive protein;creatine kinase;lactate dehydrogenase;oseltamivir;peramivir;adult;amino acid substitution;antiviral susceptibility;antiviral therapy;article;case report;China;clinical feature;human;IC50;influenza A (H7N9);influenza A;Influenza A virus (H7N9);male;middle aged;phylogenetic tree;viral clearance;virus genome,"Gao, H. N.;Yao, H. P.;Liang, W. F.;Wu, X. X.;Wu, H. B.;Wu, N. P.;Yang, S. G.;Zhang, Q.;Su, K. K.;Guo, J.;Zheng, S. F.;Zhu, Y. X.;Chen, H. L.;Yuen, K. Y.;Li, L. J.",2014,,10.1016/j.ijid.2014.10.029,0
642,Integrated analysis of microRNA-mRNA expression in A549 cells infected with influenza A viruses (IAVs) from different host species,"Although several miRNAs have been demonstrated to be involved in the influenza virus replication cycle, the identification of miRNAs and mRNAs that are expressed in A549 cells infected with influenza A viruses (IAVs) from different host species has remained poorly studied. To investigate the molecular mechanisms associated with the differential expression of miRNAs during influenza A virus infection, we performed global miRNA and mRNA expression profiling in A549 cells infected with human-origin seasonal influenza A virus H3N2 (Human_Br07), swine-origin influenza A virus H1N1 (SW_3861) or avian-origin influenza A virus H3N2 (AVI_9990). The miRNA and mRNA expression profiles were obtained by microarray and high-throughput sequencing analyses, respectively. The integrated analysis of differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs) was performed using bioinformatics tools, and the expression of miRNAs and mRNAs was validated by real-time quantitative polymerase chain reaction (RT-qPCR). We identified 20 miRNAs (6 upregulated and 14 downregulated) and 1286 mRNAs (935 upregulated and 351 downregulated) exhibiting the same differential expression trends in three infected groups of cells compared with an uninfected control. An integrated analysis of these expression profiles identified 79 miRNA-mRNA pairs associated with the influenza A reference pathway, and 107 miRNA-mRNA interactions were correlated with the defense of the virus. Additionally, the obtained results were supported by an RT-qPCR analysis of 8 differentially expressed miRNAs (hsa-miR-210-3p, hsa-miR-296-5p, hsa-miR-371a-5p, hsa-miR-762, hsa-miR-937-5p, hsa-miR-1915-3p, hsa-miR-3665, and hsa-miR-1290) and 13 differentially expressed mRNAs (IFNL1, CXCL10, RSAD2, MX1, OAS2, IFIT2, IFI44 L, MX2, XAF1, NDRG1, FGA, EGLN3, and TFRC). Our findings indicate that dysregulated miRNA expression plays a crucial role in infection caused by IAVs originating from different species and provide a foundation for further investigations of the molecular regulatory mechanisms of miRNAs involved in influenza A virus infection.",messenger RNA;microRNA;A-549 cell line;article;bioinformatics;controlled study;down regulation;gene expression profiling;gene identification;high throughput sequencing;host;human;human cell;in vitro study;influenza A;Influenza A virus (H1N1);Influenza A virus (H3N2);nonhuman;priority journal;real time polymerase chain reaction;upregulation;virus cell interaction,"Gao, J.;Gao, L.;Li, R.;Lai, Z.;Zhang, Z.;Fan, X.",2019,,10.1016/j.virusres.2018.12.016,0
643,De novo assembly and functional annotations of the transcriptome of Metorchis orientalis (trematoda: Opisthorchiidae),"Metorchis orientalis is a neglected zoonotic parasite, living in the gallbladder and bile duct of poultry and some mammals as well as humans. In spite of its economic and medical importance, the information known about the transcriptome and genome of M. orientalis is limited. In this study, we performed de novo sequencing, transcriptome assembly and functional annotations of the adult M. orientalis, obtained about 77.4 million high-quality clean reads, among which the length of the transcript contigs ranged from 100 to 11,249 nt with mean length of 373 nt and N50 length of 919 nt. We then assembled 31,943 unigenes, of which 20,009 (62.6%) were annotated by BLASTn and BLASTx searches against the available database. Among these unigenes, 19,795 (62.0%), 3407 (10.7%), 10,620 (33.2%) of them had significant similarity in the NR, NT and Swiss-Prot databases, respectively; 5744 (18.0%) and 4678 (14.6%) unigenes were assigned to GO and COG, respectively; and 9099 (28.5%) unigenes were identified and mapped onto 256 pathways in the KEGG Pathway database. Furthermore, we found that 98 (1.08%) unigenes were related to bile secretion and 5 (0.05%) to primary bile acid biosynthesis pathways category. The characterization of these transcriptomic data has implications for the better understanding of the biology of M. orientalis, and will facilitate the development of intervention agents for this and other pathogenic flukes of human and animal health significance.","Animals;Bile Ducts/ps [Parasitology];Computational Biology;DNA, Complementary/bi [Biosynthesis];Ducks/ps [Parasitology];Fish Diseases/ps [Parasitology];Fish Diseases/tm [Transmission];Fishes;Gallbladder/ps [Parasitology];High-Throughput Nucleotide Sequencing;Humans;*Neglected Diseases/ps [Parasitology];Opisthorchidae/ge [Genetics];*Opisthorchidae/ph [Physiology];Poultry Diseases/ps [Parasitology];RNA, Helminth/ge [Genetics];RNA, Helminth/ip [Isolation & Purification];RNA, Messenger/ge [Genetics];RNA, Messenger/ip [Isolation & Purification];*Transcriptome;*Trematode Infections/ps [Parasitology];Whole Exome Sequencing;*Zoonoses/ps [Parasitology];0 (DNA, Complementary);0 (RNA, Helminth);0 (RNA, Messenger)","Gao, J. F.;Gao, Y.;Qiu, J. H.;Chang, Q. C.;Zhang, Y.;Fang, M.;Wang, C. R.",2018,Jan,,0
644,"Biological heterogeneity, including systemic replication in mice, of H5N1 influenza A virus isolates from humans in Hong Kong","An H5N1 avian influenza A virus was transmitted to humans in Hong Kong in 1997. Although the virus causes systemic infection and is highly lethal in chickens because of the susceptibility of the hemagglutinin to furin and PC6 proteases, it is not known whether it also causes systemic infection in humans. The clinical outcomes of infection in Hong Kong residents ranged widely, from mild respiratory disease to multiple organ failure leading to death. Therefore, to understand the pathogenesis of influenza due to these H5N1 isolates, we investigated their virulence in mice. The results identified two distinct groups of viruses: group 1, for which the dose lethal for 50% of mice (MLD50) was between 0.3 and 11 PFU, and group 2, for which the MLD50 was more than 103 PFU. One day after intranasal inoculation of mice with 100 PFU of group 1 viruses, the virus titer in Lungs was 107 PFU/g or 3 log units higher than that for group 2 viruses. Both types of viruses had replicated to high titers (> 106 PFU/g) in the lungs by day 3 and maintained these titers through day 6. More importantly, only the group 1 viruses caused systemic infection, replicating in nonrespiratory organs, including the brain. Immunohistochemical analysis demonstrated the replication of a group 1 virus in brain neurons and glial cells and in cardiac myofibers. Phylogenetic analysis of all viral genes showed that both groups of Hong Kong H5N1 viruses had formed a lineage distinct from those of other viruses and that genetic reassortment between H5N1 and H1 or H3 human viruses had not occurred. Since mice and humans harbor both the furin and the PC6 proteases, we suggest that the virulence mechanism responsible for the lethality of influenza viruses in birds also operates in mammalian hosts. The failure of some H5N1 viruses to produce systemic infection in our model indicates that multiple, still-to-be-identified, factors contribute to the severity of H5N1 infection in mammals. In addition, the ability of these viruses to produce systemic infection in mice and the clear differences in pathogenicity among the isolates studied here indicate that this system provides a useful model for studying the pathogenesis of avian influenza virus infection in mammals.",furin;hemagglutinin;proteinase;animal tissue;article;female;Hong Kong;influenza;Influenza A virus;mouse;nonhuman;priority journal;virus characterization;virus classification;virus hemagglutination;virus isolation;virus pathogenesis;virus replication;virus titration;virus transmission;virus typing;virus virulence,"Gao, P.;Watanabe, S.;Ito, T.;Goto, H.;Wells, K.;McGregor, M.;James Cooley, A.;Kawaoka, Y.",1999,,,0
645,Deep-Sequencing Analysis of DF-1 Cell Transcriptome Response to Infection with Newcastle Disease Virus of Duck,"Newcastle Disease (ND) is caused by Newcastle Disease Virus (NDV) with a respiratory and digestive mucosal bleeding for typical symptoms. It is an acute highly contacting disease. NDV could multiplicate in DF-1 cells. NDV from waterfowl is different from former NDV from chicken, it lead waterfowl dead. But the molecular mechanisms of waterfowl NDV infected still are poorly understood. In this study researchers employed the illumina genome analyzer platform to perform genome-wide Digital Gene Expression (DGE), a tagbased high-throughput transcriptome sequencing method analysis of DF-1 cells infected NDV-YC. Researchers could reach a sequencing depth of 5.0-6.1 million tags per library and found >8000 genes to be differentially expressed during NDV-YC infection processes. NDV-YC notably identified genes involved I-kappaB kinase/NF-kappaB and TGF-beta signaling pathway. Further analysis employed Gene Ontology (GO) analysis cell part, binding and biological regulation terms are main items, respectively. The data benefit for better understanding the molecular mechanism of NDV-YC infected and provide a basis for further in vivo study and clinical trials.",Digital Gene Expression (DGE);NDV-YC;pathway;GO analysis;symptoms;SINGLE-NUCLEOTIDE RESOLUTION;ANTIBODIES;ISOLATE;TOOL,"Gao, S. M.;Sun, M. H.;Wang, Z. X.;Li, X. W.;Fan, H. Y.;Ren, T.",2012,,,0
646,Whole genome shotgun sequencing revealed highly polymorphic genome regions and genes in Escherichia coli O157:H7 isolates collected from a single feedlot,"Escherichia coli serotype O157:H7 continues to pose a serious health threat to human beings. Cattle, a major reservoir of the pathogen, harbor E. coli O157:H7 in their gastrointestinal tract and shed variable concentrations of E. coli O157:H7 into the environment. Genetic characterization of cattle-shed E. coli O157 strains is of interest to the livestock industry, food business, and public health community. The present study applied whole genome shotgun sequencing (WGS) and single nucleotide variant (SNV) calling to characterize 279 cattle-shed E. coli O157:H7 strains isolated from a single feedlot located in southwestern region of the US. More than 4,000 SNVs were identified among the strains and the resultant phylogenomic tree revealed three major groups. Using the Sakai strain genome as reference, more than 2,000 SNVs were annotated and a detailed SNV map generated. Results clearly revealed highly polymorphic loci along the E. coli O157:H7 genome that aligned with the prophage regions and highly variant genes involved in processing bacterial genetic information. The WGS data were further profiled against a comprehensive virulence factor database (VFDB) for virulence gene identification. Among the total 285 virulence genes identified, only 132 were present in all the strains. There were six virulence genes unique to single isolates. Our findings suggested that the genome variations of the E. coli O157:H7 were mainly attributable to dynamics of certain phages, and the bacterial strains have variable virulence gene profiles, even though they came from a single cattle population, which may explain the differences in pathogenicity, host prevalence, and transmissibility by E. coli O157:H7.",article;bacterial genome;bacterial strain;bacterial transmission;bacterial virulence;bacteriophage;bacterium isolate;bacterium isolation;bovine;controlled study;data base;dynamics;Escherichia coli O157;gene expression profiling;gene locus;genetic identification;genetic variation;genotype;nonhuman;phylogenomics;prevalence;promoter region;sequence alignment;sequence analysis;single feedlot;single nucleotide polymorphism;United States;virulence factor database;virulence gene;whole genome sequencing;whole genome shotgun sequencing,"Gao, X.;Yang, X.;Noll, L.;Shi, X.;Worley, J.;Allard, M.;Brown, E.;Nagaraja, T. G.;Meng, J.",2018,,10.1371/journal.pone.0202775,0
647,Koolpinyah: A virus related to kotonkan from cattle in Northern Australia,"Two closely related viruses were isolated from the blood of bovines near Darwin, Northern Territory, Australia. When studies of virus morphology indicated that these were rhabdoviruses, serologic studies were done. These isolates are closely related or identical and are related to, but distinct from, the rabies-related kotonkan virus. Other serologic studies showed that these are two isolates of a newly recognized virus, for which the name Koolpinyah virus is proposed.",animal cell;article;Australia;blood;bovine;nonhuman;priority journal;Rhabdoviridae;serology;virus classification;virus isolation;virus morphology,"Gard, G. P.;Melville, L. F.;Calisher, C. H.;Karabatsos, N.",1993,,,0
648,"Genomic characterisation of vinegar hill virus, an Australian nairovirus isolated in 1983 from Argas robertsi ticks collected from cattle egrets","This report describes the near complete genomic sequence and subsequent analysis of Vinegar Hill virus (VINHV; tentative member of the genus Orthonairovirus, family Nairoviridae, order Bunyavirales). VINHV is the second nairovirus reported to be isolated on mainland Australia and the first to be sequenced and analysed. Our genetic analysis shows that VINHV belongs to the Dera Ghazi Khan genogroup, a group of viruses previously isolated in other parts of the world including Asia, South Africa, and the USA. We discuss possible routes of entry for nairoviruses into Australia and the need to understand the virome of Australian ticks in the context of new and emerging disease.",dihydrolipoamide dehydrogenase;guanine nucleotide binding protein;article;bioinformatics;gene sequence;genetic analysis;glycosylation;high throughput sequencing;human;Nairovirus infection;nonhuman;open reading frame;phylogeny;sequence analysis;tick borne disease;virus isolation,"Gauci, P. J.;McAllister, J.;Mitchell, I. R.;Cybinski, D.;St George, T.;Gubala, A. J.",2017,,10.3390/v9120373,0
649,Whole genome sequencing and phylogenetic analysis of Bluetongue virus serotype 2 strains isolated in the Americas including a novel strain from the western United States,"Bluetongue is a potentially fatal arboviral disease of domestic and wild ruminants that is characterized by widespread edema and tissue necrosis. Bluetongue virus (BTV) serotypes 10, 11, 13, and 17 occur throughout much of the United States, whereas serotype 2 (BTV-2) was previously only detected in the southeastern United States. Since 1998, 10 other BTV serotypes have also been isolated from ruminants in the southeastern United States. In 2010, BTV-2 was identified in California for the first time, and preliminary sequence analysis indicated that the virus isolate was closely related to BTV strains circulating in the southeastern United States. In the current study, the whole genome sequence of the California strain of BTV-2 was compared with those of other BTV-2 strains in the Americas. The results of the analysis suggest co-circulation of genetically distinct viruses in the southeastern United States, and further suggest that the 2010 western isolate is closely related to southeastern strains of BTV. Although it remains uncertain as to how this novel virus was translocated to California, the findings of the current study underscore the need for ongoing surveillance of this economically important livestock disease.",animal;bluetongue;Bluetongue orbivirus;bovine;California;cattle disease;classification;genetics;isolation and purification;veterinary medicine;virology;virus genome;whole genome sequencing,"Gaudreault, N. N.;Mayo, C. E.;Jasperson, D. C.;Crossley, B. M.;Breitmeyer, R. E.;Johnson, D. J.;Ostlund, E. N.;MacLachlan, N. J.;Wilson, W. C.",2014,,10.1177/1040638714536902,0
650,Antigenic relationships among some animal rotaviruses: Virus neutralization in vitro and cross-protection in piglets,"The serotype, RNA electropherotype, and cross-protection properties of rota-viruses isolated from canine, simian porcine, and human species were compared. The bovine strain B:USA:78:1A and the canine strain C:USA:81:2 were adapted to cell culture and cloned in this study. The other viruses, i.e., simian strain S:USA:79:2, porcine Ohio State University strain P:USA:77:1, and human strain WA, were already cell culture adapted, although they were further cloned for this work. The serum neutralization test was used to classify the viruses into serotype groups. Viruses which exhibited a difference of 20-fold or greater in neutralization titer were separated into different serotype groups. In this study, four major serotype groups were found, and these groups were represented by bovine, human, porcine, and canine-simian strains. From cross-protection studies, these serotype groups were found to be significantly different. With the exception of the porcine strain, none of the viruses used as vaccines protected gnotobiotic piglets from challenge with the virulent porcine Ohio State University strain of rotavirus. Furthermore, the canine virus protected piglets from challenge with the simian virus. The RNA electropherotype confirmed that the canine and simian strains were different in eight RNA segments and eliminated the possibility that they were the same virus. From these findings, it was concluded that only viruses belonging to the same serotype group can be expected to confer cross-protection, and thus, vaccines should be made with the serotypes to which the animal is likely to be exposed.",electrophoresis;in vitro study;methodology;Rotavirus;theoretical study;virus isolation,"Gaul, A. K.;Simpson, T. F.;Woode, G. N.;Fulton, R. W.",1982,,,0
651,Haematological parameters in blood of maedi-visna virus-infected and uninfected sheep,"The maedi-visna virus (MVV) classified as a lentivirus of the retroviridae family, causes a very common economically important disease in sheep, in many parts of the worlds. Presences of the infection in Turkey have been shown by researches in previous studies. In this study all blood samples were examined by ELISA and PCR to detect MVV antibody and antigen responses, respectively. Hematological findings were monitored and comparing antibody and antigen positive naturally infected (n=5), antibody positive and antigen negative (n=20), antibody and antigen negative (n=20) in sheep was done. When infected sheep were compared with control sheep, Hgb and MPV parameters were shown statistically different (P <= 0.001). These findings suggested that MVV infections should be considered as an important health risk for sheep flock and Hgb and MPV blood parameters may be helpful to diagnosis of MVV.",ELISA;hematology;lentivirus;PCR;sheep;SMALL RUMINANT LENTIVIRUSES;TESTS,"Gazyagci, S.;Azkur, A. K.;Aslan, M. E.",2011,Jul,,0
652,An overview of Influenza A virus receptors,"Influenza A viruses are spherical particles that attach to cells through bonds between hemagglutinin and specific cellular receptors. Numerous studies performed have recently revealed that Sialic acid (SA) is a crucial component of influenza A virus receptors. This brief review summarizes recent advances in our understanding of influenza A virus receptors. The introduction describes the classification of influenza A virus receptors and the review continues with a survey of the distribution of SA in different tissue and host. This is followed by research applications of influenza A virus receptors, and explanation of why receptor studies are so important on a world-wide scale. © 2011 Informa Healthcare USA, Inc.",amantadine;oseltamivir;rimantadine;sialic acid;virus hemagglutinin;virus receptor;zanamivir;animal disease;ape;cat;chicken;Chlorocebus;dog;duck;Mustela putorius furo;horse;human;influenza A;Influenza A virus;nonhuman;priority journal;quail;review;rodent;pig;virus classification,"Ge, S.;Wang, Z.",2011,,10.3109/1040841x.2010.536523,0
653,Genetic diversity of novel circular ssDNA viruses in bats in China,"Novel circular ssDNA genomes have recently been detected in animals and in the environment using metagenomic and high-throughput sequencing approaches. In this study, five full-length circular ssDNA genomes were recovered from bat faecal samples using inverse PCR with sequences designed based on circovirus-related sequences obtained from Solexa sequencing data derived from a random amplification method. These five sequences shared a similar genomic organization to circovirus or the recently proposed cyclovirus of the family Circoviridae. The newly obtained circovirus/cyclovirus-like genomes ranged from 1 741 to 21 77 bp, and each consisted of two major ORFs, ORF1 and ORF2, encoding putative replicase (Rep) and capsid (Cap) proteins, respectively. The potential stem-loop region was predicted in all five genomes, and three of them had the typical conserved nonanucleotide motif of cycloviruses. A set of primers targeting the conserved Rep region was designed and used to detect the prevalence of circovirus/cyclovirus sequences in individual bats. Among 199 samples tested, 47 were positive (23.6 %) for the circovirus genome and two (1.0 %) were positive for the cyclovirus genome. In total, 48 partial Rep sequences plus the five full-length genomes were obtained in this study. Detailed analysis indicated that these sequences are distantly related to known circovirus/cyclovirus genomes and may represent 22 novel species that belong to the family Circoviridae.",CHICKEN ANEMIA VIRUS;MULTISYSTEMIC WASTING SYNDROME;PORCINE;CIRCOVIRUS;METAGENOMIC ANALYSIS;FEATHER DISEASE;GENOME;IDENTIFICATION;DNA,"Ge, X. Y.;Li, J. L.;Peng, C.;Wu, L. J.;Yang, X. L.;Wu, Y. Q.;Zhang, Y. Z.;Shi, Z. L.",2011,Nov,,0
654,"Epidemic of wild-origin H1NX avian influenza viruses in Anhui, China","Background: As the natural hosts of avian influenza viruses (AIVs), aquatic and migratory birds provide a gene pool for genetic transfer among species and across species, forming transient ""genome constellations."" This work describes the phylogenetic dynamics of H1NX based on the complete molecular characterization of eight genes of viruses that were collected from 2014 to 2015 in Anhui Province, China. Methods: Hemagglutination and hemagglutination inhibition tests were used to determine the hemagglutination (HA) activity of the HA subtypes. The entire genomes of the viruses were sequenced on an ABI PRISM 3500xl DNA Analyzer. The sequences were genetically analysed to study their genetic evolution using DNASTAR and MEGA 6. The pathogenic effects of the viruses were evaluated using mouse infection models. Results: Seven strains of the H1 subtype avian influenza virus were isolated. Phylogenetic analysis indicated natural recombination of the H1 influenza viruses between the Eurasian lineage and the North American lineage. Some genes had high sequence identity with A/bean goose/Korea/220/2011(H9N2), which is a typical case involving viral reassortment between the Eurasian lineage and the North American lineage. The results of infection experiments in mice showed that the viruses could acquire the ability to multiply in mouse respiratory organs without adaptation. Conclusions: These findings suggest that continued surveillance of wild birds, particularly migratory birds, is important to provide early warning of possible H1 influenza epidemics and to understand the ecology of the virus.",complementary DNA;animal experiment;animal model;article;avian influenza;avian influenza virus;chicken;China;controlled study;DNA sequence;duck;epidemic;female;genetic reassortment;genotype;goose;hemagglutination inhibition test;Influenza A virus (H1N1);Influenza A virus (H1N2);Influenza A virus (H9N2);maximum likelihood method;mouse;nonhuman;priority journal;reverse transcription polymerase chain reaction;virus genome;virus identification;waterfowl,"Ge, Y.;Yao, Q. C.;Wang, X. F.;Fan, Z. Q.;Deng, G. H.;Chai, H. L.;Chen, H. L.;Hua, Y. P.",2017,,10.1186/s40249-017-0304-4,0
655,Genetically diverse low pathogenicity avian influenza A virus subtypes co-circulate among poultry in Bangladesh,"Influenza virus surveillance, poultry outbreak investigations and genomic sequencing were assessed to understand the ecology and evolution of low pathogenicity avian influenza (LPAI) A viruses in Bangladesh from 2007 to 2013. We analyzed 506 avian specimens collected from poultry in live bird markets and backyard flocks to identify influenza A viruses. Virus isolation-positive specimens (n = 50) were subtyped and their coding-complete genomes were sequenced. The most frequently identified subtypes among LPAI isolates were H9N2, H11N3, H4N6, and H1N1. Less frequently detected subtypes included H1N3, H2N4, H3N2, H3N6, H3N8, H4N2, H5N2, H6N1, H6N7, and H7N9. Gene sequences were compared to publicly available sequences using phylogenetic inference approaches. Among the 14 subtypes identified, the majority of viral gene segments were most closely related to poultry or wild bird viruses commonly found in Southeast Asia, Europe, and/or northern Africa. LPAI subtypes were distributed over several geographic locations in Bangladesh, and surface and internal protein gene segments clustered phylogenetically with a diverse number of viral subtypes suggesting extensive reassortment among these LPAI viruses. H9N2 subtype viruses differed from other LPAI subtypes because genes from these viruses consistently clustered together, indicating this subtype is enzootic in Bangladesh. The H9N2 strains identified in Bangladesh were phylogenetically and antigenically related to previous human-derived H9N2 viruses detected in Bangladesh representing a potential source for human infection. In contrast, the circulating LPAI H5N2 and H7N9 viruses were both phylogenetically and antigenically unrelated to H5 viruses identified previously in humans in Bangladesh and H7N9 strains isolated from humans in China. In Bangladesh, domestic poultry sold in live bird markets carried a wide range of LPAI virus subtypes and a high diversity of genotypes. These findings, combined with the seven year timeframe of sampling, indicate a continuous circulation of these viruses in the country.",Africa;animal experiment;article;avian influenza virus;Bangladesh;bird;China;controlled study;Europe;gene cluster;gene sequence;genetic code;genetic variability;genotype;Influenza A virus (H11N3);Influenza A virus (H1N1);Influenza A virus (H1N3);Influenza A virus (H2N4);Influenza A virus (H3N2);Influenza A virus (H3N6);Influenza A virus (H3N8);Influenza A virus (H4N2);Influenza A virus (H4N6);Influenza A virus (H5N2);Influenza A virus (H6N1);Influenza A virus (H6N7);Influenza A virus (H7N9);Influenza A virus (H9N2);Influenza virus;low pathogenic avian influenza virus;nonhuman;phylogeny;poultry;Southeast Asia;virus strain,"Gerloff, N. A.;Khan, S. U.;Zanders, N.;Balish, A.;Haider, N.;Islam, A.;Chowdhury, S.;Rahman, M. Z.;Haque, A.;Hosseini, P.;Gurley, E. S.;Luby, S. P.;Wentworth, D. E.;Donis, R. O.;Sturm-Ramirez, K.;Davis, C. T.",2016,,10.1371/journal.pone.0152131,0
656,Microarray resources for genetic and genomic studies in chicken: A review,"Advent of microarray technologies revolutionized the nature and scope of genetic and genomic research in human and other species by allowing massively parallel analysis of thousands of genomic sites. They have been used for diverse purposes such as for transcriptome analysis, CNV detection, SNP and CNV genotyping, studying DNA-protein interaction, and detection of genome methylation. Microarrays have also made invaluable contributions to research in chicken which is an important model organism for studying embryology, immunology, oncology, virology, evolution, genetics, and genomics and also for other avian species. Despite their huge contributions in life science research, the future of microarrays is now being questioned with the advent of massively parallel next generation sequencing (NGS) technologies, which promise to overcome some of the limitations of microarray platforms. In this article we review the various microarray resources developed for chicken and their past and potential future applications. We also discuss about the future of microarrays in the NGS era particularly in the context of livestock genetics. We argue that even though NGS promises some major advantages-in particular, offers the opportunity to discover novel elements in the genome-microarrays will continue to be major tools for research and practice in the field of livestock genetics/genomics due to their affordability, high throughput nature, mature established technologies and ease of application. Moreover, with advent of new microarray technologies like capture arrays, the NGS and microarrays are expected to complement each other in future research in life science. © 2013 Wiley Periodicals, Inc.",algorithm;alternative RNA splicing;animal genetics;body weight;chicken;chromosome 1;chromosome 4;chromosome 5;comparative genomic hybridization;domestication;embryo;functional genomics;gene expression;gene frequency;gene linkage disequilibrium;genetic association;genetic improvement;genetic linkage;genetic variability;genotype;haplotype;haplotype map;high throughput sequencing;human genome;immune response;lipid metabolism;livestock;metaphase chromosome;microarray analysis;mitochondrion;nonhuman;phenotype;population structure;priority journal;protein DNA interaction;quantitative trait;quantitative trait locus;review;RNA sequence;sex chromosome;signal noise ratio;thermostability,"Gheyas, A. A.;Burt, D. W.",2013,,10.1002/dvg.22387,0
657,Transformation of animal genomics by next-generation sequencing technologies: a decade of challenges and their impact on genetic architecture,"For more than a quarter of a century, sequencing technologies from Sanger’s method to next-generation high-throughput techniques have provided fascinating opportunities in the life sciences. The continuing upward trajectory of sequencing technologies will improve livestock research and expedite the development of various new genomic and technological studies with farm animals. The use of high-throughput technologies in livestock research has increased interest in metagenomics, epigenetics, genome-wide association studies, and identification of single nucleotide polymorphisms and copy number variations. Such studies are beginning to provide revolutionary insights into biological and evolutionary processes. Farm animals, such as cattle, swine, and horses, have played a dual role as economically and agriculturally important animals as well as biomedical research models. The first part of this study explores the current state of sequencing methods, many of which are already used in animal genomic studies, and the second part summarizes the state of cattle, swine, horse, and chicken genome sequencing and illustrates its achievements during the last few years. Finally, we describe several high-throughput sequencing approaches for the improved detection of known, unknown, and emerging infectious agents, leading to better diagnosis of infectious diseases. The insights from viral metagenomics and the advancement of next-generation sequencing will strongly support specific and efficient vaccine development and provide strategies for controlling infectious disease transmission among animal populations and/or between animals and humans. However, prospective sequencing technologies will require further research and in-field testing before reaching the marketplace.",genetic analyzer;bovine;copy number variation;epigenetics;farm animal;Gallus gallus;genome-wide association study;genomics;horse;metagenomics;next generation sequencing;nonhuman;pig;priority journal;pyrosequencing;review;Sanger sequencing;single nucleotide polymorphism;zoonosis,"Ghosh, M.;Sharma, N.;Singh, A. K.;Gera, M.;Pulicherla, K. K.;Jeong, D. K.",2018,,10.1080/07388551.2018.1451819,0
658,Genetic detection and characterization of emerging HoBi-like viruses in archival foetal bovine serum batches,"Bovine viral diarrhea viruses (BVDV) are members of the Pestivirus genus within the family Flaviviridae. Based on antigenic and nucleotide differences, BVDV are classified into two recognized species, BVDV-1 and BVDV-2. More recently, a new putative pestivirus species, tentatively called ""HoBi-like"", has been associated with bovine viral diarrhea. HoBi-like viruses were first identified in fetal bovine serum (FBS) imported from Brazil. Subsequently, a number of HoBi-like viruses have been detected as contaminants in FBS or cell culture and in live ruminants. To further investigate the possible pestivirus contamination in commercially available FBS batches, 26 batches of FBS with various countries of origin, were tested in this study for the presence of bovine pestiviruses. All the 26 batches were positive by RT-PCR for at least one species of bovine pestiviruses. HoBi-like viruses were detected in 15 batches. Analysis of the 5'UTR and Npro sequences of 15 newly identified HoBi-like viruses combined with analysis of additional sequences from GenBank, identified 4 genetic groups tentatively named 3a-3d. The current study confirmed the presence of the emerging HoBi-like viruses in FBS products labeled with different geographic origins. This finding has obvious implications for the safety of biological products, such cell lines and vaccines.",5' untranslated region;article;Bangladesh;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;Brazil;Europe;gene sequence;genetic variability;HoBi like virus;new species;nonhuman;nucleotide sequence;Pestivirus;phylogeny;priority journal;South America;virus culture;virus genome;virus identification;virus isolation,"Giammarioli, M.;Ridpath, J. F.;Rossi, E.;Bazzucchi, M.;Casciari, C.;De Mia, G. M.",2015,,10.1016/j.biologicals.2015.05.009,0
659,Bovine viral diarrhea virus type 1 current taxonomy according to palindromic nucleotide substitutions method,"Pestivirus bovine viral diarrhea virus type 1 species is responsible for cosmopolitan diseases affecting cattle and other ruminants, presenting a wide range of clinical manifestations, with relevant impact on zootechnic production. Understanding genomic characteristic and virus taxonomy is fundamental in order to sustain control and prophylactic programs. Given the recent various studies reporting a relatively high number of new strains, in particular from Asian countries, in the present study, four hundred-eighty-two genomic sequences have been evaluated applying the palindromic nucleotide substitutions method for genotyping. Based on the secondary structure alignment and computing genetic distance among strains in the 5′ untranslated region of Pestivirus RNA, the current taxonomy of the species was reviewed. Twenty-two genotypes have been identified, applying a nomenclature based on divergence in the genus.",glycoprotein E2;virus RNA;5' untranslated region;article;base pairing;Bovine viral diarrhea virus 1;controlled study;domestic goat;domestic pig;domestic sheep;E2 glycoprotein gene;gene sequence;genetic distance;genetic similarity;genetic variability;genotype;genotyping technique;nonhuman;nucleic acid base substitution;Pestivirus;phylogenetic tree;phylogeny;priority journal;sequence alignment;sequence analysis;taurine cattle;taxonomy;water buffalo;zebu,"Giangaspero, M.;Apicella, C.",2018,,10.1016/j.jviromet.2018.02.003,0
660,Classification of peste des petits ruminants virus as the fourth member of the genus Morbillivirus,"Peste des petits ruminants (PPR) is a virus disease of sheep and goats in West Africa. When first described, the virus was considered a variant of rinderpest virus. The biological and physicochemical characteristics of the virus indicate that it is closely related to measles, rinderpest and canine distemper viruses. These three viruses form the genus Morbillivirus of the Paramyxoviridae. PPR virus is sufficiently distinct from these 3 viruses to justify considering it as the fourth member of the Morbillivirus genus.",classification;epidemiology;geographic distribution;goat;Measles virus;sheep;virus classification;virus infection,"Gibbs, E. P. J.;Taylor, W. P.;Lawman, M. J. P.;Bryant, J.",1979,,,0
661,Virome characterization of# Culex pipiens# in France through metagenomic analysis: a new virus discovered. P3,,,"Gil, P.;Rakotoarivony, I.;Ambert, G. L';Marie, A.;Francés, B.",2016,,,0
662,Phage therapy in livestock methane amelioration,,,"Gilbert, R. A.;Ouwerkerk, D.;Klieve, A. V.",2015,,,0
663,Whole-genome sequencing in outbreak analysis,"In addition to the ever-present concern of medical professionals about epidemics of infectious diseases, the relative ease of access and low cost of obtaining, producing, and disseminating pathogenic organisms or biological toxins mean that bioterrorism activity should also be considered when facing a disease outbreak. Utilization of whole-genome sequencing (WGS) in outbreak analysis facilitates the rapid and accurate identification of virulence factors of the pathogen and can be used to identify the path of disease transmission within a population and provide information on the probable source. Molecular tools such as WGS are being refined and advanced at a rapid pace to provide robust and higher-resolution methods for identifying, comparing, and classifying pathogenic organisms. If these methods of pathogen characterization are properly applied, they will enable an improved public health response whether a disease outbreak was initiated by natural events or by accidental or deliberate human activity. The current application of next-generation sequencing (NGS) technology to microbial WGS and microbial forensics is reviewed.",virulence factor;anthrax;article;bacterium culture;biological warfare;biosurveillance;disease transmission;DNA sequence;Ebolavirus;enterohemorrhagic Escherichia coli;epidemic;foot and mouth disease;forensic genetics;genome analysis;human;matrix assisted laser desorption ionization time of flight mass spectrometry;metagenomics;methicillin resistant Staphylococcus aureus;microbial genetics;multilocus sequence typing;Mycobacterium tuberculosis;next generation sequencing;nonhuman;polymerase chain reaction;public health,"Gilchrist, C. A.;Turner, S. D.;Riley, M. F.;Petri, W. A.;Hewlett, E. L.",2015,,10.1128/cmr.00075-13,0
664,Massive Depletion of Bovine Leukemia Virus Proviral Clones Located in Genomic Transcriptionally Active Sites during Primary Infection,"Deltaretroviruses such as human T-lymphotropic virus type 1 (HTLV-1) and bovine leukemia virus (BLV) induce a persistent infection that remains generally asymptomatic but can also lead to leukemia or lymphoma. These viruses replicate by infecting new lymphocytes (i.e. the infectious cycle) or via clonal expansion of the infected cells (mitotic cycle). The relative importance of these two cycles in viral replication varies during infection. The majority of infected clones are created early before the onset of an efficient immune response. Later on, the main replication route is mitotic expansion of pre-existing infected clones. Due to the paucity of available samples and for ethical reasons, only scarce data is available on early infection by HTLV-1. Therefore, we addressed this question in a comparative BLV model. We used high-throughput sequencing to map and quantify the insertion sites of the provirus in order to monitor the clonality of the BLV-infected cells population (i.e. the number of distinct clones and abundance of each clone). We found that BLV propagation shifts from cell neoinfection to clonal proliferation in about 2 months from inoculation. Initially, BLV proviral integration significantly favors transcribed regions of the genome. Negative selection then eliminates 97% of the clones detected at seroconversion and disfavors BLV-infected cells carrying a provirus located close to a promoter or a gene. Nevertheless, among the surviving proviruses, clone abundance positively correlates with proximity of the provirus to a transcribed region. Two opposite forces thus operate during primary infection and dictate the fate of long term clonal composition: (1) initial integration inside genes or promoters and (2) host negative selection disfavoring proviruses located next to transcribed regions. The result of this initial response will contribute to the proviral load set point value as clonal abundance will benefit from carrying a provirus in transcribed regions. © 2013 Gillet et al.",animal experiment;antibody response;article;Bovine leukemia virus;cell proliferation;clonal variation;clone;cow (mammal);enzyme linked immunosorbent assay;genome;high throughput sequencing;Human T-lymphotropic virus 1;humoral immunity;nonhuman;primary infection;promoter region;provirus;seroconversion;virus load,"Gillet, N. A.;Gutiérrez, G.;Rodriguez, S. M.;de Brogniez, A.;Renotte, N.;Alvarez, I.;Trono, K.;Willems, L.",2013,,10.1371/journal.ppat.1003687,0
665,Bovine Leukemia Virus Small Noncoding RNAs Are Functional Elements That Regulate Replication and Contribute to Oncogenesis In Vivo,"Retroviruses are not expected to encode miRNAs because of the potential problem of self-cleavage of their genomic RNAs. This assumption has recently been challenged by experiments showing that bovine leukemia virus (BLV) encodes miRNAs from intragenomic Pol III promoters. The BLV miRNAs are abundantly expressed in B-cell tumors in the absence of significant levels of genomic and subgenomic viral RNAs. Using deep RNA sequencing and functional reporter assays, we show that miRNAs mediate the expression of genes involved in cell signaling, cancer and immunity. We further demonstrate that BLV miRNAs are essential to induce B-cell tumors in an experimental model and to promote efficient viral replication in the natural host.","Animals;*Carcinogenesis/ge [Genetics];Cattle;Cell Transformation, Neoplastic/ge [Genetics];Enzootic Bovine Leukosis;Gene Expression Profiling;*Gene Expression Regulation, Viral/ge [Genetics];High-Throughput Nucleotide Sequencing;*Leukemia Virus, Bovine/ge [Genetics];*MicroRNAs/ge [Genetics];Polymerase Chain Reaction;RNA, Viral/ge [Genetics];Sheep;*Virus Replication/ge [Genetics];0 (MicroRNAs);0 (RNA, Viral)","Gillet, N. A.;Hamaidia, M.;de Brogniez, A.;Gutierrez, G.;Renotte, N.;Reichert, M.;Trono, K.;Willems, L.",2016,04,,0
666,Sequence analysis of the alpha trans-inducing factor of bovine herpesvirus type 5 (BHV-5),"Bovine herpesvirus (BHV), a member of the subfamily Alphaherpesvirinae, is classified into neurovirulent and non-neurovirulent subtypes on a basis of differential neuropathogenicities. Transcription of viral immediate early (IE) genes during alphaherpesvirus gene expression, is mediated by a multi-component immediate early complex (IEC) integrated by the viral tegument protein alpha trans-inducing factor (α-tif), a host cell protein (HCF), and a host Octamer protein (Oct). In this paper, we present a sequence analysis of the α-tif of the encephalitic BHV subtype, bovine herpesvirus type 5 (BHV-5). Bovine herpesvirus type 1 (BHV-1) and BHV-5 α-tifs share 98% amino acid sequence homology. However, BHV-5 α-tif is 23 residues shorter at the amino terminus than BHV-1 α-tif. Amino acid alignment of the α-tifs of BHV-1 and BHV-5 with other alphaherpesviruses indicates areas of conserved motifs but also important differences located mainly at the amino and carboxyl termini.",alpha trans inducing factor;cell protein;octamer protein;unclassified drug;viral protein;amino acid sequence;amino terminal sequence;article;Bovine herpesvirus 1;Bovine herpes virus 5;carboxy terminal sequence;gene expression regulation;gene sequence;immediate early gene;neuropathology;nonhuman;nucleotide sequence;priority journal;protein expression;protein localization;protein motif;residue analysis;sequence analysis;sequence homology;transcription regulation;virus classification;virus encephalitis;virus gene;virus morphology;virus typing;virus virulence,"Gillette, K.;Misra, V.;Bratanich, A.",2002,,10.1023/a:1014520616362,0
667,Neuropathotyping: a new system to classify Marek's disease virus,"A statistical approach was used to establish a new classification system of Marek's disease virus (MDV) on the basis of neurologic responses. To develop the system, neurologic response data from 15x7 chickens inoculated with 30 strains of serotype 1 MDV were statistically analyzed by a cluster analysis. The goal was to identify a statistical system that would verify if three neurovirulence groups correlated with the three pathotypes previously described. The system was also validated in two additional strains of specific-pathogen-free (SPF) chickens, SPAFAS and line SC (Hy-Vac). The proposed system is based on analysis of three variables: 1) frequency of birds showing transient paralysis between 9 and 11 days postinoculation (dpi), (2) mortality before 15 dpi, and (3) frequency of birds showing persistent neurologic disease between 21 and 23 dpi. By use of this system, a MDV may be classified in one of three groups, designated neuropathotypes A, B, and C, which roughly correspond to the virulent, very virulent, and very virulent plus pathotypes, respectively. However, correlation between neuropathotype and pathotype was not absolute, and neuropathotyping is more a complement to the current pathotyping system than a replacement for it. Our results showed that neuropathotyping studies can be conducted in two types of commercial SPF chickens by the use of the same variables, although the system would first have to be standardized by the use of prototype viruses. Neuropathotypes can also be estimated with our statistical analysis with reasonable accuracy. By use of this analysis, we established that MDV strains within the very virulent pathotype may be subdivided into neuropathotypes B and C, thus establishing a previously unrecognized pathotypic classification. This finding illustrates how neuropathotyping may extend important information not identified by conventional pathotyping.","Animals;Chickens;*Herpesvirus 2, Gallid/cl [Classification];Herpesvirus 2, Gallid/py [Pathogenicity];*Marek Disease/pa [Pathology];*Nervous System/pa [Pathology];Poultry","Gimeno, I. M.;Witter, R. L.;Neumann, U.",2002,Oct-Dec,,0
668,Natural transmission and comparative analysis of small ruminant lentiviruses in the Norwegian sheep and goat populations,"Serological surveys for small ruminant lentivirus (SRLV) infections have revealed seropositive sheep in several mixed herds, where sheep are kept together with seropositive goats. Here we have examined the genetic relationships in LTR, pol and env surface unit (SU) and the growth patterns in goat (GSM) and sheep (FOS) synovial membrane cell cultures of SRLV isolates obtained from both mixed and single species herds. Phylogenetic analyses of pol and env SU revealed that Norwegian SRLVs derived from both goat and sheep in mixed herds are distributed into group C, while isolates obtained from unmixed sheep flocks cluster in group A, together with maedi-visna-like representatives of the A1 subtype. In this study, the direction of group C virus transmission is proposed to be from goat to sheep. The replication efficiency in GSM and FOS cultures and the cytopathic phenotype induced by the SRLV isolates gave no indication of any species-specific characteristics. No particular nucleotide sequences of the LTR-U3 region or env SU were identified that could be related to cytopathic phenotype. This study shows that sheep in Norway harbour SRLVs belonging to phylogenetic groups A and C, and this provides further evidence for cross-species infection being a regular characteristic of SRLVs, which may represent an important source for viral persistence. © 2007 Elsevier B.V. All rights reserved.",complementary DNA;virus RNA;3' untranslated region;amino acid sequence;article;Caprine arthritis encephalitis virus;genetic distance;goat;Lentivirus;long terminal repeat;molecular evolution;nonhuman;Norway;nucleotide sequence;phylogenetic tree;phylogeny;priority journal;reverse transcription polymerase chain reaction;sheep;Ovine/caprine lentivirus;virus culture;virus genome;virus infection;virus isolation;virus transmission;virus typing;Visna virus,"Gjerset, B.;Jonassen, C. M.;Rimstad, E.",2007,,10.1016/j.virusres.2006.12.014,0
669,Characterization of microRNAs encoded by the bovine herpesvirus 1 genome,"Bovine herpesvirus 1 (BoHV-1) is a ubiquitous and important pathogen of cattle worldwide. This study reports the identification of 10 microRNA (miRNA) genes, Bhv1-mir-B1-Bhv1-mir-B10, encoded by the BoHV-1 genome that were processed into 12 detectable mature miRNAs as determined by ultra-high throughput sequencing bioinformatics analyses of small RNA libraries and expression studies. We found that four of the miRNA genes were present as two copies in the BoHV-1 genome, resulting in a total of 14 miRNA encoding loci. Unique features of the BoHV-1 miRNAs include evidence of bidirectional transcription and a close association of two miRNA genes with the origin of replication, including one miRNA that is encoded within the origin of replication. The miRNA gene Bhv1-mir-B5 was encoded on the opposite DNA strand to the latency associated transcript, potentially giving rise to antisense transcripts originating from this locus. The association of herpesvirus miRNAs with latency appears to be a common feature in the alphaherpesviruses. Analyses of the BoHV-5 genome for putative miRNA gene orthologues identified a high degree of evolutionary conservation for nine of the BoHV-1 miRNA genes. The possible roles for BoHV-1 miRNAs in the regulation of known BoHV-1 transcription units and the genetics of the BoHV-1 genotypes are also discussed. © 2010 The State of Queensland acting through the Department of Employment, Economic Development and Innovation.",microRNA;virus RNA;animal cell;article;Bovine herpesvirus 1;controlled study;DNA strand;gene expression;gene locus;genetic conservation;genome analysis;Herpesviridae;molecular evolution;nonhuman;nucleotide sequence;orthology;priority journal;RNA analysis;RNA sequence;structural bioinformatics;virus characterization;virus gene;virus genome;virus replication;virus transcription,"Glazov, E. A.;Horwood, P. F.;Assavalapsakul, W.;Kongsuwan, K.;Mitchell, R. W.;Mitter, N.;Mahony, T. J.",2010,,10.1099/vir.0.014290-0,0
670,Epidemiological and Molecular Analysis of an Outbreak of Highly Pathogenic Avian Influenza H5N8 clade 2.3.4.4 in a German Zoo: Effective Disease Control with Minimal Culling,"Outbreaks of highly pathogenic avian influenza A virus (HPAIV) subtype H5N8, clade 2.3.4.4, were first reported in January 2014 from South Korea. These viruses spread rapidly to Europe and the North American continent during autumn 2014 and caused, in Germany, five outbreaks in poultry holdings until February 2015. In addition, birds kept in a zoo in north-eastern Germany were affected. Only a few individual white storks (Ciconia ciconia) showed clinical symptoms and eventually died in the course of the infection, although subsequent in-depth diagnostic investigations showed that other birds kept in the same compound of the white storks were acutely positive for or had undergone asymptomatic infection with HPAIV H5N8. An exception from culling all of the 500 remaining zoo birds was granted by the competent authority. Restriction measures included grouping the zoo birds into eight epidemiological units in which 60 birds of each unit tested repeatedly negative for H5N8. Epidemiological and phylogenetical investigations revealed that the most likely source of introduction was direct or indirect contact with infected wild birds as the white storks had access to a small pond frequented by wild mallards and other aquatic wild birds during a period of 10 days in December 2014. Median network analysis showed that the zoo bird viruses segregated into a distinct cluster of clade 2.3.4.4 with closest ties to H5N8 isolates obtained from mute swans (Cygnus olor) in Sweden in April 2015. This case demonstrates that alternatives to culling exist to rescue valuable avifaunistic collections after incursions of HPAIV.",animal;animal culling;avian influenza;bird;DNA sequence;epidemic;genetics;Germany;high throughput sequencing;immunology;Influenza A virus (H5N8);isolation and purification;pathogenicity;pathology;phylogeny;veterinary medicine;virology;zoo animal,"Globig, A.;Starick, E.;Homeier, T.;Pohlmann, A.;Grund, C.;Wolf, P.;Zimmermann, A.;Wolf, C.;Heim, D.;Schlößer, H.;Zander, S.;Beer, M.;Conraths, F. J.;Harder, T. C.",2017,,10.1111/tbed.12570,0
671,Subtyping of swine influenza viruses using a high-throughput real-time PCR platform,"Influenza A viruses (IAVs) are important human and animal pathogens with high impact on human and animal health. In Denmark, a passive surveillance program for IAV in pigs has been performed since 2011, where screening tests and subsequent subtyping are performed by reverse transcription quantitative real-time PCR (RT-qPCR). A disadvantage of the current subtyping system is that several assays are needed to cover the wide range of circulating subtypes, which makes the system expensive and time-consuming. Therefore, the aim of the present study was to develop a high-throughput method, which could improve surveillance of swine influenza viruses (swIAVs) and lower the costs of virus subtyping. Twelve qPCR assays specific for various hemagglutinin and neuraminidase gene lineages relevant for swIAV and six assays specific for the internal genes of IAV were developed and optimized for the high-throughput qPCR platform BioMark (Fluidigm). The qPCR assays were validated and optimized to run under the same reaction conditions using a 48.48 dynamic array (48.48DA). The sensitivity and specificity was assessed by testing virus isolates and field samples with known subtypes. The results revealed a performance of the swIAV 48.48DA similar to conventional real-time analysis, and furthermore, the specificity of swIAV 48.48DA was very high and without cross reactions between the assays. This high-throughput system provides a cost-effective alternative for subtyping of swIAVs.",hemagglutinin;histamine H3 receptor;sialidase;accuracy;acute respiratory tract disease;analytical parameters;animal cell;animal experiment;animal health;animal model;animal tissue;article;cell lineage;comparative study;controlled study;cost effectiveness analysis;disorders of DNA synthesis and repair;dynamics;gene amplification;gene expression;high throughput screening;high throughput sequencing;immune adherence;lung parenchyma;nonhuman;nose smear;observational study;performance;real time polymerase chain reaction;reverse transcription polymerase chain reaction;RNA extraction;sensitivity analysis;sensitivity and specificity;sequence analysis;signal transduction;swine influenza virus;validation process;virus typing,"Goecke, N. B.;Krog, J. S.;Hjulsager, C. K.;Skovgaard, K.;Harder, T. C.;Breum, S. Ø;Larsen, L. E.",2018,,10.3389/fcimb.2018.00165,0
672,"Potential for co-infection of a mosquito-specific flavivirus, nhumirim virus, to block west nile virus transmission in mosquitoes","Nhumirim virus (NHUV) is an insect-specific virus that phylogenetically affiliates with dual-host mosquito-borne flaviviruses. Previous in vitro co-infection experiments demonstrated prior or concurrent infection of Aedes albopictus C6/36 mosquito cells with NHUV resulted in a 10,000-fold reduction in viral production of West Nile virus (WNV). This interference between WNV and NHUV was observed herein in an additional Ae. albopictus mosquito cell line, C7-10. A WNV 2K peptide (V9M) mutant capable of superinfection with a pre-established WNV infection demonstrated a comparable level of interference from NHUV as the parental WNV strain in C6/36 and C7-10 cells. Culex quinquefasciatus and Culex pipiens mosquitoes intrathoracically inoculated with NHUVandWNV, or solely withWNVas a control, were allowed to extrinsically incubate the viruses up to nine and 14 days, respectively, and transmissibility and replication of WNV was determined. The proportion of Cx. quinquefasciatus mosquitoes capable of transmitting WNV was significantly lower for the WNV/NHUV group than the WNV control at seven and nine days post inoculation (dpi), while no differences were observed in the Cx. pipiens inoculation group. By dpi nine, a 40% reduction in transmissibility in mosquitoes from the dual inoculation group was observed compared to the WNV-only control. These data indicate the potential that infection of some Culex spp. vectors with NHUV could serve as a barrier for efficient transmissibility of flaviviruses associated with human disease.",Aedes albopictus;article;controlled study;Culex pipiens;Culex quinquefasciatus;Flavivirus;immunofluorescence;mixed infection;Nhumirim virus;nonhuman;reverse transcription polymerase chain reaction;vertical transmission;virus interference;virus transmission;West Nile fever;West Nile virus,"Goenaga, S.;Kenney, J. L.;Duggal, N. K.;Delorey, M.;Ebel, G. D.;Zhang, B.;Levis, S. C.;Enria, D. A.;Brault, A. C.",2015,,10.3390/v7112911,0
673,The interplay between MDV and HVT affects viral miRNA expression,"It is well established that herpesviruses encode numerous microRNAs (miRNAs) and that these virally encoded small RNAs play multiple roles in infection. The present study was undertaken to determine how co-infection of a pathogenic MDV serotype one (MDV1) strain (MD5) and a vaccine strain (herpesvirus of turkeys [HVT]) alters viral miRNA expression in vivo. We first used small RNA deep sequencing to identify MDV1-encoded miRNAs that are expressed in tumorigenic spleens of MDV1-infected birds. The expression patterns of these miRNAs were then further assessed at an early time point (7 days postinfection [dpi]) and a late time point (42 dpi) in birds with and without HVT vaccination using real-time PCR (RT-PCR). Additionally, the effect of MDV1 co-infection on HVT-encoded miRNAs was determined using RT-PCR. A diverse population of miRNAs was expressed in MDV-induced tumorigenic spleens at 42 dpi, with 18 of the 26 known mature miRNAs represented. Of these, both mdv1-miR-M4-5p and mdv1-miR-M2-3p were the most highly expressed miRNAs. RT-PCR analysis further revealed that nine MDV miRNAs were differentially expressed between 7 dpi and 42 dpi infected spleens. At 7 dpi, three miRNAs were differentially expressed between the spleens of birds co-infected with HVT and MD5 compared with birds singly infected with MD5, whereas at 42 dpi, nine miRNAs were differentially expressed. At 7 dpi, the expression of seven HVT-encoded miRNAs was affected in the spleens of co-infected birds compared with birds only receiving the HVT vaccine. At 42 dpi, six HVT-encoded miRNAs were differentially expressed between the two groups. Target prediction analysis suggests that these differentially expressed viral miRNAs are involved in regulating several cellular processes, including cell proliferation and the adaptive immune response. © American Association of Avian Pathologists.",Marek disease vaccine;microRNA;virus RNA;animal;animal disease;article;bird disease;chicken;genetics;germfree animal;high throughput sequencing;Mardivirus;Marek disease;metabolism;mixed infection;real time polymerase chain reaction;sequence analysis;spleen;virology,"Goher, M.;Hicks, J. A.;Liu, H. C.",2013,,10.1637/10440-110112-Reg.1,0
674,Application of phylogeny reconstruction and character-evolution analysis to inferring patterns of directional microbial transmission,"I used phylogenetic analyses to reconstruct patterns of directional interspecific transmission during a pseudorabies virus outbreak in Illinois, USA, in 1989. Isolates were recovered from five species: cattle, sheep, goats, pigs, and raccoons (Procyon lotor). I generated DNA sequences for 16 isolates of pseudorabies virus at the glycoprotein C gene, from which I constructed phylogenetic trees. I then used these trees, in combination with parsimony-based analyses of character evolution, to infer the frequency and direction of interspecific transmission events. Comparing inferred frequencies and directions of transmission to null expectations based on 10,000 random trees indicated a significant excess of transmission events from pigs to pigs and a corresponding lack of transmission events from non-porcine species. These results are concordant with the know biology and natural history of pseudorabies virus, and they demonstrate that retrospective phylogeny reconstruction and analyses of character evolution can be used to investigate the transmission ecology of pathogens. © 2003 Elsevier B.V. All rights reserved.",virus DNA;animal;animal disease;article;bovine;disease transmission;epidemic;genetics;goat;isolation and purification;phylogeny;pseudorabies;Pseudorabies virus;raccoon;sheep;pig;United States;virology,"Goldberg, T. L.",2003,,10.1016/s0167-5877(03)00161-2,0
675,Bluetongue virus serotype 24 (BTV-24) in Israel: phylogenetic characterization and clinical manifestation of the disease,"Bluetongue (BT), an arthropod-borne viral disease of ruminants, a ects sheep most severely than other domestic animals. Bluetongue virus serotype 24 (BTV-24) is one of 26 known Bluetongue virus (BTV) serotypes. In this article, we present data of phylogenetic analysis of 9 viral genes (Seg1, Seg2, Seg3, Seg4, Seg5, Seg6, Seg8, Seg9, and Seg10) from 8 Israeli BTV-24 isolates and relate the genotype of the BTV-24 isolates to their phenotype with regard to clinical manifestations. The high level of genetic identity (> 99.6%) between Seg2, Seg4 and Seg5 in all 8 BTV-24 isolates indicated that these segments shared the same viral ancestor. Phylogenetic analysis of Seg1, Seg3, Seg5, Seg8, Seg9, and Seg10 revealed that the Israeli BTV-24 strains comprised 4 variants. Five of the viruses revealed high identity among all 9 segments, and represented variant 1. A second variant (BTV24/3027/6/10), isolated in 2010, showed signi cant variation from variant 1 in 3 gene segments (VP-1, VP-3, and NS-3 genes). A third variant (BTV24/3027/1/10) showed signi cant variation from variant 1 in 6 segments (VP-1, VP-3, VP-6 and NS-1, NS-2 and NS-3 genes), while a fourth variant (BTV24/2214/1/10) showed signi cant variation from variant 1 in 4 segments (VP-1, NS-1, NS-2 and NS-3 genes). These marked di erences in sequence identity indicate that a high level of genetic reassortment is occurring between co-circulating BTV strains in Israel.",animal;bluetongue;Bluetongue orbivirus;classification;genetics;isolation and purification;Israel;phylogeny;serotype;sheep;virology,"Golender, N.;Panshin, A.;Brenner, J.;Rotenberg, D.;Oura, C.;Khinich, E.;Bumbarov, V.",2016,,10.12834/VetIt.643.3163.3,0
676,Biological and molecular aspects of bovine herpesvirus 4 (BHV-4),"This review summarizes most recent information on the bovine cytomegalovirus BHV-4. The virus is not associated with clearly defined clinical entities in cattle. It can easily be isolated in tissue culture and has a broad host range. BHV-4 strains are rather similar in restriction enzyme analysis of their DNAs, the size of the pr DNAs, however, differs. The genome represents a γ-herpesvirus. Because of its uniqueness BHV-4 is discussed as an appropriate vector.",neutralizing antibody;repetitive DNA;virus DNA;Bovine herpesvirus 1;Cytomegalovirus;cytopathology;gene structure;host susceptibility;restriction mapping;review;sequence homology;tissue culture;virogenesis;virus classification;virus genome;virus strain,"Goltz, M.;Ludwig, H.",1991,,10.1016/0147-9571(91)90131-v,0
677,Review article compte rendu viral enteritis in calves,"A complex community of bacteria, viruses, fungi, protists, and other microorganisms inhabit the gastrointestinal tract of calves and play important roles in gut health and disease. The viral component of the microbiome (the virome) is receiving increasing attention for its role in neonatal calf diarrhea (NCD). Rotavirus and coronavirus have for a long time been associated with NCD and commercial vaccines have been produced against these agents. Recently, several other viruses which may play a role in diarrhea have been discovered in calf fecal samples, mostly by sequence-based methods. These viruses include torovirus, norovirus, nebovirus, astrovirus, kobuvirus, and enterovirus. Most studies have involved epidemiologic investigations seeking to show association with diarrhea for each virus alone or in combination with potential pathogens. However, determining the contribution of these viruses to calf diarrhea has been challenging and much uncertainty remains concerning their roles as primary pathogens, co-infection agents, or commensals.",anorexia;Astroviridae;calf (mammal);commensal;Coronavirinae;depression;diarrhea;enteritis;Enterovirus;enzyme linked immunosorbent assay;fever;gastrointestinal tract;immunoassay;infectious agent;microbiome;mixed infection;nonhuman;polymerase chain reaction;protist;review;Rotavirus;Torovirus;viral enteritis,"Gomez, D. E.;Weese, J. S.",2017,,,0
678,Genetic diversity of bovine viral diarrhea virus in cattle from Mexico,"Bovine viral diarrhea virus (BVDV) infects cattle populations worldwide, causing significant economic losses though its impact on animal health. Previous studies have reported the prevalence of BVDV species and subgenotypes in cattle from the United States and Canada. We investigated the genetic diversity of BVDV strains detected in bovine serum samples from 6 different Mexican regions. Sixty-two BVDV isolates from Mexico were genetically typed based on comparison of sequences from the 5′ untranslated region (5′-UTR) of the viral genome. Phylogenetic reconstruction indicated that 60 of the samples belonged to the BVDV-1 genotype and 2 to the BVDV-2 genotype. Comparison of partial 5′-UTR sequences clustered 49 samples within BVDV-1c, 8 samples within BVDV-1a, 3 samples within BVDV-1b, and 2 samples clustered with the BVDV-2a subgenotypes. Our study, combined with information previously published on BVDV field strain diversity in the United States and Canada, benefits the development of effective detection assays, vaccines, and control programs for North America.",Bovine viral diarrhea virus vaccine;article;bovine viral diarrhea;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;controlled study;genetic analysis;genetic variability;genotype;nonhuman;phylogenetic tree;phylogeny;reverse transcription polymerase chain reaction;RNA purification;viral genetics,"Gómez-Romero, N.;Basurto-Alcántara, F. J.;Verdugo-Rodríguez, A.;Bauermann, F. V.;Ridpath, J. F.",2017,,10.1177/1040638717690187,0
679,Detection of border disease virus in Mexican cattle,"The genus Pestivirus within Flaviviridae is comprised of four recognized species, namely, bovine viral diarrhoea virus 1 (BVDV-1), bovine viral diarrhoea virus 2 (BVDV-2), border disease virus (BDV) and classical swine fever virus (CSFV). BDV, while primarily infecting sheep and goats, has also been reported in cattle and wild animals. Infections of sheep and goats result in economic loss due to abortions and the birth of persistently infected animals that have poor production and reduced life expectancy. In this study, we report the detection of BDV in cattle serum collected as part of pestivirus surveillance programme from six regions of Mexico, where a 67.1% of BVDV seroprevalence was calculated previously. Phylogenetic analyses based on comparison of the 5′UTR region typed the Mexican strains as BDV-1. Border disease (BD) is listed as an exotic disease in Mexico, and the origin of BDV found in these cattle is unclear. This is the first identification of BDV in Mexican cattle.",5' untranslated region;animal experiment;animal model;article;border disease;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;cattle disease;Classical swine fever virus;comparative study;controlled study;disease surveillance;economic aspect;genetic analysis;genotyping technique;goat;health program;life expectancy;Mexican;nonhuman;phylogenetic tree;reverse transcription polymerase chain reaction;RNA extraction;sequence analysis;seroprevalence;sheep,"Gómez-Romero, N.;Basurto-Alcántara, F. J.;Verdugo-Rodríguez, A.;Lagunes-Quintanilla, R.;Bauermann, F. V.;Ridpath, J. F.",2018,,10.1111/tbed.12641,0
680,A pathological study of the perisinusoidal unit of the liver in acute African swine fever,"African swine fever is an acute haemorrhagic disease of pigs which may serve as a model for the study of the pathogenesis of other viral haemorrhagic fevers. This paper describes an ultrastructural study of the sequence of lesions produced in the perisinusoidal functional unit of the liver of pigs inoculated with the Malawi '83 strain of African swine fever virus, which is classified as haemadsorbing and highly virulent. Virus replication was observed in Kupffer cells and monocytes from three days after inoculation, in hepatocytes and fat-storing cells at five and seven days after inoculation, and in sinusoidal endothelial cells at seven days after inoculation. Further observations included intravascular coagulation, which peaked at five days after inoculation, and fibroblast and myofibroblast transformation of fat-storing cells at seven days after inoculation. These results suggest that activated cells of the mononuclear phagocyte system may play a major role in this sequence of lesions and the possible role of the cytokines that may be released by these cells is discussed.",acute disease;animal;article;comparative study;electron microscopy;female;liver;male;monocyte;pathology;reference value;pig;swine disease;time;ultrastructure,"Gómez-Villamandos, J. C.;Hervás, J.;Méndez, A.;Carrasco, L.;Villeda, C. J.;Sierra, M. A.;Wilkonson, P. J.",1995,,,0
681,"Molecular investigation of bovine viral diarrhea virus infection in yaks (Bos gruniens) from Qinghai, China","Background: Bovine viral diarrhea virus (BVDV) is a pestivirus which infects both domestic animals and wildlife species worldwide. In China, cattle are often infected with BVDV of different genotypes, but there is very limited knowledge regarding BVDV infection in Chinese yaks and the genetic diversity of the virus. The objectives of this study were to detect viral infection in yaks in Qinghai, China and to determine the genotypes of BVDV based on analysis of the 5′untranslated region (5′UTR) and N-terminal protease (N <sup>pro</sup>) region. Results: Between 2010 and 2012, 407 blood samples were collected from yaks with or without clinical signs in six counties of Qinghai Province. Ninety-eight samples (24%) were found to be positive by reverse transcription polymerase chain reaction (RT-PCR) targeting a conserved region of BVDV-1 and BVDV-2. The nucleotide sequences of the 5′UTR and complete N<sup>pro</sup> region were determined for 16 positive samples. Phylogenetic reconstructions demonstrated that all 16 samples belong to subgenotypes BVDV-1b, BVDV-1d and BVDV-1q. Conclusions: This study provides, for the first time, molecular evidence for BVDV infection in yaks in Qinghai involving multiple subgenotypes of BVDV-1. This may have occurred under three possible scenarios: interspecies transmission, natural infection, and the use of vaccines contaminated with BVDV. The results have important implications for yak production and management in China, and specifically indicate that unscientific vaccination practices should be stopped and bio-security increased. © 2014 Gong et al.; licensee BioMed Central Ltd.",proteinase;5' untranslated region;amino terminal sequence;article;blood sampling;bovine viral diarrhea;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;China;disease transmission;genotype;infection control;molecular phylogeny;nonhuman;nucleotide sequence;reverse transcription polymerase chain reaction;vaccination;virus strain;yak,"Gong, X.;Liu, L.;Zheng, F.;Chen, Q.;Li, Z.;Cao, X.;Yin, H.;Zhou, J.;Cai, X.",2014,,10.1186/1743-422x-11-29,0
682,Insect retroelements provide novel insights into the origin of hepatitis B viruses,"The origin of hepadnaviruses (Hepadnaviridae), a group of reverse-transcribing DNA viruses that infect vertebrates, remains mysterious. All the known retrotransposons are only distantly related to hepadnaviruses. Here, we report the discovery of two novel lineages of retroelements, which we designate hepadnavirus-like retroelement (HEART1 and HEART2), within the insect genomes through screening 1, 095 eukaryotic genomes. Both phylogenetic and similarity analyses suggest that the HEART retroelements represent the closest nonviral relatives of hepadnaviruses so far. The discovery of HEART retroelements narrows down the evolutionary gap between hepadnaviruses and retrotransposons and might thus provide unique insights into the origin and evolution of hepadnaviruses.",ribonuclease H;RNA directed DNA polymerase;telomerase reverse transcriptase;Anguilla anguilla;Anser caerulescens;Anura;article;Avihepadnavirus;bat;Bovine immunodeficiency like virus;Bovine leukemia virus;Cauliflower mosaic virus;Cetacea;cichlid;consensus sequence;crane (bird);DNA flanking region;Duck hepatitis B virus;endogenous retrovirus;Equine infectious anemia virus;Feline foamy virus;Gambusia affinis;genetic similarity;goose;Hepatitis B virus;Human immunodeficiency virus 1;insect;insect genome;Isoperla grammatica;Ixodes ricinus;Ixodes scapularis;killifish;Ladona fulva;lizard;long terminal repeat;molecular phylogeny;Murine leukemia virus;nonhuman;Oncorhynchus kisutch;parrot;Petunia;phylogenetic tree;Plecoptera;protein domain;Reticuloendotheliosis virus;retroposon;Rice tungro bacilliform virus;Rous sarcoma virus;Sciuridae;sheep;Simian foamy virus;stickleback;Visna virus;Woodchuck hepatitis virus;woolly monkey;Xenopus laevis;zebra fish,"Gong, Z.;Han, G. Z.",2018,,10.1093/molbev/msy129,0
683,Global spread of hemorrhagic fever viruses: Predicting pandemics,"As successive epidemics have swept the world, the scientific community has quickly learned from them about the emergence and transmission of communicable diseases. Epidemics usually occur when health systems are unprepared. During an unexpected epidemic, health authorities engage in damage control, fear drives action, and the desire to understand the threat is greatest. As humanity recovers, policy-makers seek scientific expertise to improve their “preparedness” to face future events. Global spread of disease is exemplified by the spread of yellow fever from Africa to the Americas, by the spread of dengue fever through transcontinental migration of mosquitos, by the relentless influenza virus pandemics, and, most recently, by the unexpected emergence of Ebola virus, spread by motorbike and long haul carriers. Other pathogens that are remarkable for their epidemic expansions include the arenavirus hemorrhagic fevers and hantavirus diseases carried by rodents over great geographic distances and the arthropod-borne viruses (West Nile, chikungunya and Zika) enabled by ecology and vector adaptations. Did we learn from the past epidemics? Are we prepared for the worst? The ultimate goal is to develop a resilient global health infrastructure. Besides acquiring treatments, vaccines, and other preventive medicine, bio-surveillance is critical to preventing disease emergence and to counteracting its spread. So far, only the western hemisphere has a large and established monitoring system; however, diseases continue to emerge sporadically, in particular in Southeast Asia and South America, illuminating the imperfections of our surveillance. Epidemics destabilize fragile governments, ravage the most vulnerable populations, and threaten the global community. Pandemic risk calculations employ new technologies like computerized maintenance of geographical and historical datasets, Geographic Information Systems (GIS), Next Generation sequencing, and Metagenomics to trace the molecular changes in pathogens during their emergence, and mathematical models to assess risk. Predictions help to pinpoint the hot spots of emergence, the populations at risk, and the pathogens under genetic evolution. Preparedness anticipates the risks, the needs of the population, the capacities of infrastructure, the sources of emergency funding, and finally, the international partnerships needed to manage a disaster before it occurs. At present, the world is in an intermediate phase of trying to reduce health disparities despite exponential population growth, political conflicts, migration, global trade, urbanization, and major environmental changes due to global warming. For the sake of humanity, we must focus on developing the necessary capacities for health surveillance, epidemic preparedness, and pandemic response.",Africa;Arenaviridae;biosurveillance;chikungunya;Chikungunya virus;Crimean Congo hemorrhagic fever;Crimean-Congo hemorrhagic fever virus;dengue hemorrhagic fever;Dengue virus;disease surveillance;disease transmission;DNA sequence;Ebolavirus;emergency care;environmental factor;epidemic;funding;geographic information system;Hantaan virus;Hantavirus infection;health care policy;hemorrhagic fever;Hendra virus;human;infection risk;Influenza virus;Junin virus;Kyasanur Forest disease;Lymphocytic choriomeningitis virus;Marburgvirus;next generation sequencing;Nipah virus;nonhuman;Omsk hemorrhagic fever;pandemic;prediction;preventive medicine;Puumala virus;Rift Valley fever;Rift Valley fever virus;risk assessment;severe acute respiratory syndrome;Tick borne encephalitis virus;virus;virus transmission;West Nile fever;West Nile virus;Western Hemisphere;yellow fever;Yellow fever virus;Zika fever,"Gonzalez, J. P.;Souris, M.;Valdivia-Granda, W.",2018,,10.1007/978-1-4939-6981-4_1,0
684,"Origin, distribution, and potential risk factors associated with influenza A virus in swine in two production systems in Guatemala","Background: Guatemala is the country with the largest swine production in Central America; however, evidence of influenza A virus (IAV) in pigs has not been clearly delineated. Objectives: In this study, we analyzed the presence and spatial distribution of IAV in commercial and backyard swine populations. Methods: Samples from two nationwide surveys conducted in 2010 and 2011 were tested using virological (rRT-PCR and virus isolation) and serological (ELISA and hemagglutination inhibition) assays to detect IAV. Results: Influenza A virus was detected in 15.7% of the sampled pigs (30.6% of herds) in 2010 and in 11.7% (24.2% of herds) in 2011. The percentage of seropositive pigs was 10.6% (16.1% of herds) and 1.4% (3.1% of herds) for each year, respectively. Three pandemic H1N1 and one seasonal human-like H3N2 viruses were isolated. Antibodies against viruses from different genetic clusters were detected. No reassortant strains with swine viruses were detected. The H3N2 virus was closely related to human viruses that circulated in Central America in 2010, distinct to the most recent human seasonal vaccine lineages. Spatial clusters of rRT-PCR positive herds were detected each year by scan statistics. Conclusions: Our results demonstrate circulation of IAV throughout Guatemala and identify commercial farms, animal health status, and age as potential risk factors associated with IAV infection and exposure. Detection of human-origin viruses in pigs suggests a role for humans in the molecular epidemiology of IAV in swine in Guatemala and evidences gaps in local animal and human surveillance.",virus antibody;age;animal experiment;animal model;article;backyard unit;cell lineage;Central America;commercial farm;controlled study;enzyme linked immunosorbent assay;farming system;female;gene cluster;Guatemala;health status;health survey;hemagglutination inhibition test;herd;human;influenza A;Influenza A virus (H1N1);Influenza A virus (H3N2);Influenza A virus;male;nonhuman;phylogeny;pig;reverse transcription polymerase chain reaction;risk factor;serology;spatial analysis;species comparison;species distribution;virogenesis;virology;virus diagnosis;virus isolation;virus strain,"Gonzalez-Reiche, A. S.;Ramírez, A. L.;Müller, M. L.;Orellana, D.;Sosa, S. M.;Ola, P.;Paniagua, J.;Ortíz, L.;Hernandez, J.;Cordón-Rosales, C.;Perez, D. R.",2017,,10.1111/irv.12437,0
685,"Marseillevirus, blood safety, and the human virome",,,"Goodman, J. L.",2013,,,0
686,Similarity of the outer capsid protein VP4 of the Gottfried strain of porcine rotavirus to that of asymptomatic human rotavirus strains,"Genomic segment 4 of the porcine Gottfried strain (serotype 4) of porcine rotavirus, which encodes the outer capsid protein VP4, was sequenced, and its deduced amino acid sequence was analyzed. Amino acid homology of the porcine rotavirus VP4 to the corresponding protein of asymptomatic or symptomatic human rotaviruses representing serotypes 1 to 4 ranged from 87.1 to 88.1% for asymptomatic strains and from 77.5 to 77.8% for symptomatic strains. Amino acid homology of the Gottfried strain to simian rhesus rotavirus, simian SA11 virus, bovine Nebraska calf diarrhea virus, and porcine OSU strains ranged from 71.5 to 74.3%. Antigenic similarities of VP4 epitopes between the Gottfried strain and human rotaviruses were detected by a plaque reduction neutralization test with hyperimmune antisera produced against the Gottfried strain or a Gottfried (10 genes) x human DS-1 rotavirus (VP7 gene) reassortant which exhibited serotype 2 neutralization specificity. In addition, a panel of six anti-VP4 monoclonal antibodies capable of neutralizing human rotaviruses belonging to serotype 1, 3, or 4 was able to neutralize the Gottfried strain. These observations suggest that the VP4 outer capsid protein of the Gottfried rotavirus is more closely related to human rotaviruses than to animal rotaviruses.",viral protein;article;classification;nonhuman;nucleotide sequence;priority journal;Rotavirus;virus capsid;virus classification;virus gene;virus strain,"Gorziglia, M.;Nishikawa, K.;Hoshino, Y.;Taniguchi, K.",1990,,,0
687,Molecular phylogenetics of Newcastle disease viruses isolated from vaccinated flocks during outbreaks in Southern India reveals circulation of a novel sub-genotype,"Newcastle disease (ND) is an economically important, contagious poultry viral disease reported across the globe. In India, ND is endemic and episodes of ND outbreaks despite strict vaccinations are not uncommon. We isolated and characterized seven ND viruses from vaccinated commercial poultry farms during severe disease outbreaks in Tamil Nadu, in Southern India, between April 2015 and June 2016. All the seven isolates were categorized as virulent by mean death time (48–54 hr) in embryonated chicken eggs. Also, their sequences carried the virulence signature of multi-basic amino acid residues in their fusion protein cleavage site (RRQ/RR/KRF). Phylogenetic and evolutionary distance analyses revealed circulation of a novel sub-genotype of genotype XIII, class II ND viruses, herein proposed as sub-genotype XIIIe. The genetic divergence between the circulating virulent strains and the vaccine strains could possibly explain the disease outbreak in the vaccinated flocks. Further, our study signifies the need to implement routine epidemiological surveillance and to revisit the current vaccination program.",amino acid sequence;animal tissue;article;gene amplification;gene sequence;genetic variability;genotype;herd;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;RNA isolation;Sanger sequencing;sequence analysis;vaccination;virus isolation,"Gowthaman, V.;Ganesan, V.;Gopala Krishna Murthy, T. R.;Nair, S.;Yegavinti, N.;Saraswathy, P. V.;Suresh Kumar, G.;Udhayavel, S.;Senthilvel, K.;Subbiah, M.",2019,,10.1111/tbed.13030,0
688,Update on information regarding hepatitis E virus,"Hepatitis E infection has been considered from its first description as a disease with an epidemiologic pattern related to the consumption of waste water and contaminated food, similarly to hepatitis A infection. Hepatitis E prevalence is higher in poor sanitary conditioned areas. The use of molecular techniques has contributed to obtain valuable information about the epidemiology of hepatitis E in developed countries. In these areas, hepatitis E virus infection shows a different pattern, and it has been linked to the contact with domestic animals, especially pigs. The role of hepatitis E in industrialized countries as a possible zoonosis implies a new and interesting approach of this disease. This review summarizes the current knowledge of the biology, structure and transmission of the virus as well as the diagnosis of the infection. Additionally, this review describes the current status of HE infection in areas with a low incidence of acute hepatitis E and the role of animals as potential reservoirs for HEV.",acute hepatitis;developed country;diagnostic test;disease association;domestic animal;food contamination;gene expression;hepatitis A;hepatitis E;Hepatitis E virus;human;industrialization;laboratory diagnosis;medical information;molecular biology;morbidity;nonhuman;phylogeny;prevalence;review;sanitation;pig;virus carrier;virus classification;virus morphology;virus transmission;waste water;water contamination;zoonosis,"Gracia, M. T. P.",2007,,,0
689,Detection and genome characterization of bovine polyomaviruses in beef muscle and ground beef samples from Germany,"Polyomaviruses are small, non-enveloped, circular double-stranded DNA viruses. Some polyomaviruses can induce tumors and cancer under certain circumstances. The bovine polyomaviruses (BPyV) 1-3 have been only scarcely analyzed so far. It was hypothesized that the consumption of beef meat containing polyomaviruses could contribute to the development of cancer in humans. In order to assess the distribution of the BPyV genome in meat from Germany, 101 beef muscle samples and 10 ground beef samples were analyzed here. A specific sample preparation method combined with or without rolling circle amplification (RCA), and BPyV-specific PCRs were developed and applied. BPyV-1 DNA was detected in 1/101 (1%) samples from beef meat and in 2/10 (20%) ground beef samples. BPyV-2 DNA was detected in 3/10 (30%) ground beef samples, whereas BPyV-3 was not detected in the samples. Application of RCA did not increase the detection rate in ground beef samples. Sequence analysis of the PCR products indicated the presence of BPyV-1, BPyV-2a and BPyV-2b. The whole genome of a BPyV-1 strain from ground beef meat showed 97.8% sequence identity to the BPyV-1 reference strain and that of a BPyV-2a strain from ground beef meet showed 99.9% sequence identity to strain 2aS11. It can be concluded that BPyV genomes can be frequently detected in ground beef samples, although higher sample numbers should be investigated in future to confirm this finding. Further studies should focus on the infectivity, tumorigenicity and heat resistance of the contained viruses in order to assess the risk of cancer induction through consumption of BPyVs present in beef products. (C) 2016 Elsevier B.V. All rights reserved.",Bovine polyomavirus;Beef meat;PCR detection;Genome characterization;Tumor induction;POLYMERASE-CHAIN-REACTION;PCR ASSAY;IDENTIFICATION;CONTAMINATION;METAGENOMICS;CHICKEN;VIRUS;SERA;PORK;MEAT,"Grafe, D.;Ehlers, B.;Made, D.;Ellerbroek, L.;Seidler, T.;Johne, R.",2017,Jan,,0
690,Advances in antiviral vaccine development,"Antiviral vaccines have been the most successful biomedical intervention for preventing epidemic viral disease. Vaccination for smallpox in humans and rinderpest in cattle was the basis for disease eradication, and recent progress in polio eradication is promising. Although early vaccines were developed empirically by passage in live animals or eggs, more recent vaccines have been developed because of the advent of new technologies, particularly cell culture and molecular biology. Recent technological advances in gene delivery and expression, nanoparticles, protein manufacturing, and adjuvants have created the potential for new vaccine platforms that may provide solutions for vaccines against viral pathogens for which no interventions currently exist. In addition, the technological convergence of human monoclonal antibody isolation, structural biology, and high-throughput sequencing is providing new opportunities for atomic-level immunogen design. Selection of human monoclonal antibodies can identify immunodominant antigenic sites associated with neutralization and provide reagents for stabilizing and solving the structure of viral surface proteins. Understanding the structural basis for neutralization can guide selection of vaccine targets. Deep sequencing of the antibody repertoire and defining the ontogeny of the desired antibody responses can reveal the junctional recombination and somatic mutation requirements for B-cell recognition and affinity maturation. Collectively, this information will provide new strategic approaches for selecting vaccine antigens, formulations, and regimens. Moreover, it creates the potential for rational vaccine design and establishing a catalogue of vaccine technology platforms that would be effective against any given family or class of viral pathogens and improve our readiness to address new emerging viral threats. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.",adenovirus vaccine;chickenpox vaccine;hepatitis B vaccine;hepatitis vaccine;Human immunodeficiency virus vaccine;human monoclonal antibody;immunological adjuvant;influenza vaccine;Japanese encephalitis vaccine;measles vaccine;mumps vaccine;nanoparticle;neutralizing antibody;poliomyelitis vaccine;rabies vaccine;Rotavirus vaccine;rubella vaccine;smallpox vaccine;virus vaccine;yellow fever vaccine;antibody isolation;antibody response;CD8+ T lymphocyte;cell culture;disease eradication;drug efficacy;gene expression;gene targeting;high throughput sequencing;human;medical technology;molecular recognition;nonhuman;ontogeny;poliomyelitis;priority journal;review;somatic mutation;vaccination,"Graham, B. S.",2013,,10.1111/imr.12098,0
691,Genital Zoster Infection: the Great Imposter,"Herpes simplex virus 1 (HSV-1), herpes simplex virus 2 (HSV-2), and varicella-zoster virus (VZV) are taxonomically closely related viruses that produce clinically distinct diseases but share common features of infection. HSV-1 and HSV-2 both produce cutaneous and mucocutaneous primary infections followed by reactivation disease occurring at the same or a nearby anatomic site. Primary VZV infection, also known as chickenpox, is usually a childhood disease that produces pox-like cutaneous lesions distributed over the entire body. Reactivation VZV infection, often called herpes zoster, generally occurs later in life but, unlike HSV disease, produces pox-like lesions at a different anatomic location, typically along dermatomes. As such, the clinical differential diagnosis of reactivation HSV infection and zoster is generally based upon the anatomic location and the appearance of the lesion(s). The recent availability of molecular assays has resulted in the unexpected diagnosis of zoster infections in male and female patients who presented with genital lesions. The purpose of this article is to present a brief overview of HSV and VZV infections and to relate a laboratory experience that resulted in the diagnosis of zoster infections using a molecular assay in which almost 10% of the 282 positive VZV specimens were from genital sites.",article;chickenpox;genital tract infection;herpes simplex;Herpes simplex virus 2;herpes zoster;human;Human alphaherpesvirus 1;immunofluorescence test;laboratory diagnosis;multiplex polymerase chain reaction;nonhuman;Varicella zoster virus;virus culture;virus detection,"Granato, P. A.",2018,,10.1016/j.clinmicnews.2018.09.001,0
692,"Metagenomic Detection of Viral Pathogens in Spanish Honeybees: Co-Infection by Aphid Lethal Paralysis, Israel Acute Paralysis and Lake Sinai Viruses","The situation in Europe concerning honeybees has in recent years become increasingly aggravated with steady decline in populations and/or catastrophic winter losses. This has largely been attributed to the occurrence of a variety of known and ""unknown"", emerging novel diseases. Previous studies have demonstrated that colonies often can harbour more than one pathogen, making identification of etiological agents with classical methods difficult. By employing an unbiased metagenomic approach, which allows the detection of both unexpected and previously unknown infectious agents, the detection of three viruses, Aphid Lethal Paralysis Virus (ALPV), Israel Acute Paralysis Virus (IAPV), and Lake Sinai Virus (LSV), in honeybees from Spain is reported in this article. The existence of a subgroup of ALPV with the ability to infect bees was only recently reported and this is the first identification of such a strain in Europe. Similarly, LSV appear to be a still unclassified group of viruses with unclear impact on colony health and these viruses have not previously been identified outside of the United States. Furthermore, our study also reveals that these bees carried a plant virus, Turnip Ringspot Virus (TuRSV), potentially serving as important vector organisms. Taken together, these results demonstrate the new possibilities opened up by high-throughput sequencing and metagenomic analysis to study emerging new diseases in domestic and wild animal populations, including honeybees. © 2013 Granberg et al.",aphid;Aphid Lethal Paralysis Virus;article;bee disease;high throughput sequencing;Israel Acute Paralysis Virus;Lake Sinai Virus;metagenomics;mixed infection;nonhuman;nucleotide sequence;plant virus;Spain;Turnip Ringspot Virus;virus;virus classification;virus detection;virus genome;virus infection;virus strain;virus typing,"Granberg, F.;Vicente-Rubiano, M.;Rubio-Guerri, C.;Karlsson, O. E.;Kukielka, D.;Belák, S.;Sánchez-Vizcaíno, J. M.",2013,,10.1371/journal.pone.0057459,0
693,Whole genome sequence comparison of vtx2-converting phages from Enteroaggregative Haemorrhagic Escherichia coli strains,"BACKGROUND: Enteroaggregative Haemorrhagic E. coli (EAHEC) is a new pathogenic group of E. coli characterized by the presence of a vtx2-phage integrated in the genomic backbone of Enteroaggregative E. coli (EAggEC). So far, four distinct EAHEC serotypes have been described that caused, beside the large outbreak of infection occurred in Germany in 2011, a small outbreak and six sporadic cases of HUS in the time span 1992-2012. In the present work we determined the whole genome sequence of the vtx2-phage, termed Phi-191, present in the first described EAHEC O111:H2 isolated in France in 1992 and compared it with those of the vtx-phages whose sequences were available. RESULTS: The whole genome sequence of the Phi-191 phage was identical to that of the vtx2-phage P13374 present in the EAHEC O104:H4 strain isolated during the German outbreak 20 years later. Moreover, it was also almost identical to those of the other vtx2-phages of EAHEC O104:H4 strains described so far. Conversely, the Phi-191 phage appeared to be different from the vtx2-phage carried by the EAHEC O111:H21 isolated in the Northern Ireland in 2012.The comparison of the vtx2-phages sequences from EAHEC strains with those from the vtx-phages of typical Verocytotoxin-producing E. coli strains showed the presence of a 900 bp sequence uniquely associated with EAHEC phages and encoding a tail fiber. CONCLUSIONS: At least two different vtx2-phages, both characterized by the presence of a peculiar tail fiber-coding gene, intervened in the emergence of EAHEC. The finding of an identical vtx2-phage in two EAggEC strains isolated after 20 years in spite of the high variability described for vtx-phages is unexpected and suggests that such vtx2-phages are kept under a strong selective pressure.The observation that different EAHEC infections have been traced back to countries where EAggEC infections are endemic and the treatment of human sewage is often ineffective suggests that such countries may represent the cradle for the emergence of the EAHEC pathotype. In these regions, EAggEC of human origin can extensively contaminate the environment where they can meet free vtx-phages likely spread by ruminants excreta.","*Bacteriophages/ge [Genetics];Databases, Genetic;*Escherichia coli/vi [Virology];*Genome, Viral;High-Throughput Nucleotide Sequencing;Sequence Alignment;Sequence Analysis, DNA","Grande, L.;Michelacci, V.;Tozzoli, R.;Ranieri, P.;Maugliani, A.;Caprioli, A.;Morabito, S.",2014,Jul 08,,0
694,"Genetic characterization of tick-borne flaviviruses: New insights into evolution, pathogenetic determinants and taxonomy","Here, we analyze the complete coding sequences of all recognized tick-borne flavivirus species, including Gadgets Gully, Royal Farm and Karshi virus, seabird-associated flaviviruses, Kadam virus and previously uncharacterized isolates of Kyasanur Forest disease virus and Omsk hemorrhagic fever virus. Significant taxonomic improvements are proposed, e.g. the identification of three major groups (mammalian, seabird and Kadam tick-borne flavivirus groups), the creation of a new species (Karshi virus) and the assignment of Tick-borne encephalitis and Louping ill viruses to a unique species (Tick-borne encephalitis virus) including four viral types (i.e. Western Tick-borne encephalitis virus, Eastern Tick-borne encephalitis virus, Turkish sheep Tick-borne encephalitis virus and Louping ill Tick-borne encephalitis virus). The analyses also suggest a complex relationship between viruses infecting birds and those infecting mammals. Ticks that feed on both categories of vertebrates may constitute the evolutionary bridge between the three distinct identified lineages. © 2006 Elsevier Inc. All rights reserved.",article;gene sequence;genetic trait;Kadam tick borne flavivirus;phylogeny;priority journal;sheep disease;taxonomy;tick borne encephalitis;Tick borne encephalitis virus;Tick borne flavivirus;virus isolation,"Grard, G.;Moureau, G.;Charrel, R. N.;Lemasson, J. J.;Gonzalez, J. P.;Gallian, P.;Gritsun, T. S.;Holmes, E. C.;Gould, E. A.;de Lamballerie, X.",2007,,10.1016/j.virol.2006.09.015,0
695,Taxonomy of the caliciviruses,"The International Committee on Taxonomy of Viruses (ICTV) has recently approved several proposals submitted by the present Caliciviridae study group. These proposals include the division of the family into 4 new genera designated Lagovirus, Vesivirus, 'Norwalk-like viruses' (NLVs), and 'Sapporo- like viruses' (SLVs); the latter 2 genera were assigned temporary names until acceptable names can be determined by the scientific community. The genera have been further divided into the following species: Feline calicivirus and vesicular exanthema of swine virus (genus Vesivirus), rabbit hemorrhagic disease virus and European brown hare syndrome virus (genus Lagovirus), Norwalk virus (genus NLV), and Sapporo virus (genus SLV). In addition, the ICTV approved a proposal to remove the hepatitis E virus from the Caliciviridae into an 'unassigned' classification status.",Caliciviridae;conference paper;Hepatitis E virus;nonhuman;Norwalk virus;priority journal;taxonomy;virus classification,"Green, K. Y.;Ando, T.;Balayan, M. S.;Berke, T.;Clarke, I. N.;Estes, M. K.;Matson, D. O.;Nakata, S.;Neill, J. D.;Studdert, M. J.;Thiel, H. J.",2000,,10.1086/315591,0
696,"Next-generation sequence analysis of the genome of RFHVMn, the macaque homolog of Kaposi's sarcoma (KS)-associated herpesvirus, from a KS-like tumor of a pig-tailed macaque","The complete sequence of retroperitoneal fibromatosis-associated herpesvirus Macaca nemestrina (RFHVMn), the pig-tailed macaque homolog of Kaposi's sarcoma-associated herpesvirus (KSHV), was determined by next-generation sequence analysis of a Kaposi's sarcoma (KS)-like macaque tumor. Colinearity of genes was observed with the KSHV genome, and the core herpesvirus genes had strong sequence homology to the corresponding KSHV genes. RFHVMn lacked homologs of open reading frame 11 (ORF11) and KSHV ORFs K5 and K6, which appear to have been generated by duplication of ORFs K3 and K4 after the divergence of KSHV and RFHV. RFHVMn contained positional homologs of all other unique KSHV genes, although some showed limited sequence similarity. RFHVMn contained a number of candidate microRNA genes. Although there was little sequence similarity with KSHV microRNAs, one candidate contained the same seed sequence as the positional homolog, kshv-miR-K12- 10a, suggesting functional overlap. RNA transcript splicing was highly conserved between RFHVMn and KSHV, and strong sequence conservation was noted in specific promoters and putative origins of replication, predicting important functional similarities. Sequence comparisons indicated that RFHVMn and KSHV developed in long-term synchrony with the evolution of their hosts, and both viruses phylogenetically group within the RV1 lineage of Old World primate rhadinoviruses. RFHVMn is the closest homolog of KSHV to be completely sequenced and the first sequenced RV1 rhadinovirus homolog of KSHV from a nonhuman Old World primate. The strong genetic and sequence similarity between RFHVMn and KSHV, coupled with similarities in biology and pathology, demonstrate that RFHVMn infection in macaques offers an important and relevant model for the study of KSHV in humans. © 2013, American Society for Microbiology.",microRNA;virus RNA;animal tissue;article;controlled study;gene duplication;gene number;gene replication;gene sequence;genetic conservation;Herpesviridae;Human herpesvirus 8;Kaposi sarcoma;Macaca;molecular evolution;next generation sequence analysis;nonhuman;nucleotide sequence;open reading frame;phylogeny;prediction;priority journal;promoter region;retroperitoneal fibromatosis associated herpesvirus Macaca nemestrina;Rhadinovirus;RNA sequence;RNA transcription;sequence analysis;sequence homology;virus gene;virus genome,"Gregory Bruce, A.;Ryan, J. T.;Thomas, M. J.;Peng, X.;Grundhoff, A.;Tsai, C. C.;Rose, T. M.",2013,,10.1128/jvi.02331-13,0
697,A metagenomic analysis of pandemic influenza a (2009 H1N1) infection in patients from North America,"Although metagenomics has been previously employed for pathogen discovery, its cost and complexity have prevented its use as a practical front-line diagnostic for unknown infectious diseases. Here we demonstrate the utility of two metagenomics-based strategies, a pan-viral microarray (Virochip) and deep sequencing, for the identification and characterization of 2009 pandemic H1N1 influenza A virus. Using nasopharyngeal swabs collected during the earliest stages of the pandemic in Mexico, Canada, and the United States (n = 17), the Virochip was able to detect a novel virus most closely related to swine influenza viruses without a priori information. Deep sequencing yielded reads corresponding to 2009 H1N1 influenza in each sample (percentage of aligned sequences corresponding to 2009 H1N1 ranging from 0.0011% to 10.9%), with up to 97% coverage of the influenza genome in one sample. Detection of 2009 H1N1 by deep sequencing was possible even at titers near the limits of detection for specific RT-PCR, and the percentage of sequence reads was linearly correlated with virus titer. Deep sequencing also provided insights into the upper respiratory microbiota and host gene expression in response to 2009 H1N1 infection. An unbiased analysis combining sequence data from all 17 outbreak samples revealed that 90% of the 2009 H1N1 genome could be assembled de novo without the use of any reference sequence, including assembly of several near full-length genomic segments. These results indicate that a streamlined metagenomics detection strategy can potentially replace the multiple conventional diagnostic tests required to investigate an outbreak of a novel pathogen, and provide a blueprint for comprehensive diagnosis of unexplained acute illnesses or outbreaks in clinical and public health settings. © 2010 Greninger et al.",adolescent;adult;article;Canada;child;clinical article;controlled study;diagnostic value;female;flu like syndrome;gene expression;gene sequence;human;human tissue;infant;influenza A (H1N1);Influenza A virus (H1N1);male;metagenomics;Mexico;microarray analysis;nose smear;nucleotide sequence;pandemic influenza;reverse transcription polymerase chain reaction;school child;United States;virus detection;virus genome;virus identification;virus titration,"Greninger, A. L.;Chen, E. C.;Sittler, T.;Scheinerman, A.;Roubinian, N.;Yu, G.;Kim, E.;Pillai, D. R.;Guyard, C.;Mazzulli, T.;Isa, P.;Arias, C. F.;Hackett Jr, J.;Schochetman, G.;Miller, S.;Tang, P.;Chiu, C. Y.",2010,,10.1371/journal.pone.0013381,0
698,The complete genome of klassevirus - a novel picornavirus in pediatric stool,"Background: Diarrhea kills 2 million children worldwide each year, yet an etiological agent is not found in approximately 30-50% of cases. Picornaviral genera such as enterovirus, kobuvirus, cosavirus, parechovirus, hepatovirus, teschovirus, and cardiovirus have all been found in human and animal diarrhea. Modern technologies, especially deep sequencing, allow rapid, high-throughput screening of clinical samples such as stool for new infectious agents associated with human disease. Results: A pool of 141 pediatric gastroenteritis samples that were previously found to be negative for known diarrheal viruses was subjected to pyrosequencing. From a total of 937,935 sequence reads, a collection of 849 reads distantly related to Aichi virus were assembled and found to comprise 75% of a novel picornavirus genome. The complete genome was subsequently cloned and found to share 52.3% nucleotide pairwise identity and 38.9% amino acid identity to Aichi virus. The low level of sequence identity suggests a novel picornavirus genus which we have designated klassevirus. Blinded screening of 751 stool specimens from both symptomatic and asymptomatic individuals revealed a second positive case of klassevirus infection, which was subsequently found to be from the index case's 11-month old twin. Conclusion: We report the discovery of human klassevirus 1, a member of a novel picornavirus genus, in stool from two infants from Northern California. Further characterization and epidemiological studies will be required to establish whether klasseviruses are significant causes of human infection.",AICHI-VIRUS;GASTROENTERITIS;PREVALENCE;SEQUENCE;5'-END;CATTLE,"Greninger, A. L.;Runckel, C.;Chiu, C. Y.;Haggerty, T.;Parsonnet, J.;Ganem, D.;DeRisi, J. L.",2009,Jun,,0
699,Isolation of a virus strain from Argas persicus ticks,A previously undescribed virus was isolated from Argas persicus ticks collected on sentinel chicken in western Slovakia. The strain was lethal for suckling mice only after intracerebral inoculation. No symptoms were induced in adult mice. The virus strain was insensitive to sodium deoxycholate and resistant to ether treatment. An antigen prepared from the virus did not agglutinate goose or human 0 erythrocytes. The single strain obtained in 1976 appeared to be unrelated to a large number of known arboviruses when tested by the complement-fixation reaction.,animal experiment;arthropod;central nervous system;complement fixation;experimental infection;histology;in vitro study;mouse;Togaviridae;virus classification;virus infection;virus isolation,"Gresikova, M.;Nosek, J.;Sekeyova, M.",1979,,,0
700,Molecular characterization of H3N2 influenza A viruses isolated from Ontario swine in 2011 and 2012,"Background: Data about molecular diversity of commonly circulating type A influenza viruses in Ontario swine are scarce. Yet, this information is essential for surveillance of animal and public health, vaccine updates, and for understanding virus evolution and its large-scale spread. Methods: The study population consisted of 21 swine herds with clinical problems due to respiratory disease. Nasal swabs from individual pigs were collected and tested by virus isolation in MDCK cells and by rtRT-PCR. All eight segments of 10 H3N2 viruses were sequenced using high-throughput sequencing and molecularly characterized. Results: Within-herd prevalence ranged between 2 and 100%. Structurally, Ontario H3N2 viruses could be classified into three different groups. Group 1 was the most similar to the original trH3N2 virus from 2005. Group 2 was the most similar to the Ontario turkey H3N2 isolates with PB1 and NS genes originating from trH3N2 virus and M, PB2, PA and NP genes originating from the A(H1N1)pdm09 virus. All Group 3 internal genes were genetically related to A(H1N1)pdm09. Analysis of antigenic sites of HA1 showed that Group 1 had 8 aa changes within 4 antigenic sites, A(1), B(3), C(2) and E(2). The Group 2 viruses had 8 aa changes within 3 antigenic sites A(3), B(3) and C(2), while Group 3 viruses had 4 aa changes within 3 antigenic sites, B(1), D(1) and E(2), when compared to the cluster IV H3N2 virus [A/swine/Ontario/33853/2005/(H3N2)]. Conclusions: The characterization of the Ontario H3N2 viruses clearly indicates reassortment of gene segments between the North American swine trH3N2 from cluster IV and the A(H1N1)pdm09 virus.",animal cell;article;genetic association;genetic reassortment;herd;high throughput sequencing;Influenza A virus (H1N1);Influenza A virus (H3N2);MDCK cell line;molecular phylogeny;nonhuman;nose smear;phylogenetic tree;pig;real time polymerase chain reaction;respiratory tract disease;reverse transcription polymerase chain reaction;trend study;virus gene;virus identification;virus isolation,"Grgić, H.;Costa, M.;Friendship, R. M.;Carman, S.;Nagy, É;Wideman, G.;Weese, S.;Poljak, Z.",2014,,10.1186/s12985-014-0194-z,0
701,"Prevalence of Hepatitis E Virus Infection in Pigs at the Time of Slaughter, United Kingdom, 2013","Since 2010, reports of infection with hepatitis E virus (HEV) have increased in England and Wales. Despite mounting evidence regarding the zoonotic potential of porcine HEV, there are limited data on its prevalence in pigs in the United Kingdom. We investigated antibody prevalence, active infection, and virus variation in serum and cecal content samples from 629 pigs at slaughter. Prevalence of antibodies to HEV was 92.8% (584/629), and HEV RNA was detected in 15% of cecal contents (93/629), 3% of plasma samples (22/629), and 2% of both (14/629). However, although HEV is prevalent in pigs in the United Kingdom and viremic pigs are entering the food chain, most (22/23) viral sequences clustered separately from the dominant type seen in humans. Thus, pigs raised in the United Kingdom are unlikely to be the main source of human HEV infections in the United Kingdom. Further research is needed to identify the source of these infections.","Abattoirs;Animals;Antibodies, Viral/bl [Blood];Cross-Sectional Studies;*Hepatitis E/ep [Epidemiology];Hepatitis E/vi [Virology];*Hepatitis E virus/py [Pathogenicity];Infection/ep [Epidemiology];Infection/pa [Pathology];*Swine/im [Immunology];Swine/vi [Virology];*Swine Diseases/ep [Epidemiology];United Kingdom/ep [Epidemiology];0 (Antibodies, Viral)","Grierson, S.;Heaney, J.;Cheney, T.;Morgan, D.;Wyllie, S.;Powell, L.;Smith, D.;Ijaz, S.;Steinbach, F.;Choudhury, B.;Tedder, R. S.",2015,Aug,,0
702,Molecular and in vitro characterisation of hepatitis E virus from UK pigs,"Hepatitis E virus (HEV) infection is widespread in the global pig population. Although clinically inapparent in pigs, HEV infection is the cause of Hepatitis E in humans and transmission via the food chain has been established. Following a 2013 study that investigated prevalence of HEV infection in UK slaughter-age pigs samples indicating highest viral load were selected for further characterisation. High throughput sequencing was used to obtain the complete coding sequence from five samples. An in-frame insertion was observed within the HEV hypervariable region in two samples. To interrogate whether this mutation may be the cause of high-level viraemia and faecal shedding as observed in the sampled pigs virus isolation and culture was conducted. Based on viral growth kinetics there was no evidence that these insertions affected replication efficiency in vitro, suggesting as yet undetermined host factors may affect the course of infection and consequently the risk of foodborne transmission.",article;controlled study;feces;Hepatitis E virus;high throughput sequencing;in vitro study;nonhuman;pig;priority journal;United Kingdom;virogenesis;virus characterization;virus culture;virus isolation;virus load;virus mutation;virus replication;virus shedding,"Grierson, S. S.;McGowan, S.;Cook, C.;Steinbach, F.;Choudhury, B.",2019,,10.1016/j.virol.2018.10.018,1
703,Genomic epidemiology of methicillin-susceptible Staphylococcus aureus across colonisation and skin and soft tissue infection,"OBJECTIVES: Staphylococcus aureus skin and soft tissue infection (Sa-SSTI) places a significant burden on healthcare systems. New Zealand has a high incidence of Sa-SSTI, and here most morbidity is caused by a polyclonal methicillin-susceptible (MSSA) bacterial population. However, MSSA also colonise asymptomatically the cornified epithelia of approximately 20% of the population, and their divide between commensalism and pathogenicity is poorly understood. We aimed to see whether MSSA are genetically differentiated across colonisation and SSTI; and given the close interactions between people and pets, whether strains isolated from pets differ from human strains. METHODS: We compared the genomes of contemporaneous colonisation and clinical MSSA isolates obtained in New Zealand from humans and pets. RESULTS: Core and accessory genome comparisons revealed a homogeneous bacterial population across colonisation, disease, humans, and pets. The rate of MSSA colonisation in dogs was comparatively low (5.4%). CONCLUSIONS: In New Zealand, most Sa-SSTI morbidity is caused by a random sample of the colonising MSSA population, consistent with the opportunistic infection model rather than the paradigm distinguishing strains according to their pathogenicity. Thus, studies of the factors determining colonisation and immune-escape may be more beneficial than comparative virulence studies. Contact with house-hold pets may pose low zoonotic risk.","Animals;*Anti-Bacterial Agents/pd [Pharmacology];Carrier State/mi [Microbiology];DNA, Bacterial;Dogs;Genome, Bacterial;Genomics;High-Throughput Nucleotide Sequencing;Humans;Incidence;*Methicillin/pd [Pharmacology];Methicillin Resistance;Methicillin-Resistant Staphylococcus aureus/ge [Genetics];Microbial Sensitivity Tests;New Zealand/ep [Epidemiology];Pets/mi [Microbiology];*Skin/mi [Microbiology];Soft Tissue Infections/ep [Epidemiology];*Soft Tissue Infections/mi [Microbiology];Staphylococcal Infections/ep [Epidemiology];*Staphylococcal Infections/mi [Microbiology];Staphylococcus aureus/de [Drug Effects];*Staphylococcus aureus/ge [Genetics];Staphylococcus aureus/gd [Growth & Development];Staphylococcus aureus/py [Pathogenicity];Symbiosis;Virulence Factors;Zoonoses;0 (Anti-Bacterial Agents);0 (DNA, Bacterial);0 (Virulence Factors);Q91FH1328A (Methicillin)","Grinberg, A.;Biggs, P. J.;Zhang, J.;Ritchie, S.;Oneroa, Z.;O'Neill, C.;Karkaba, A.;Velathanthiri, N. S.;Coombs, G. W.",2017,10,,0
704,Identification of potyviruses infecting vanilla by direct sequencing of a short RT-PCR amplicon,"A simple one-tube one-step RT-PCR assay with degenerate primers followed by direct sequencing of a 327 bp coat protein gene fragment was used to identify the potyviruses infecting vanilla. With this technique, unambiguous species allocation was achieved for 34 potyvirus-infected vanilla samples collected in the Indian Ocean and the Pacific areas between 1997 and 2005. Virus identification relied on BLAST homology and nucleotide identities of 162 to 327 nt fragments with known potyvirus sequences. Species allocation was confirmed by neighbour-joining of the 149 nt common to 32 vanilla sequences and 51 known potyviruses. Subject to further identification, these data revealed four additional Potyvirus species that may infect vanilla: Bean yellow mosaic virus, Cowpea aphid-borne mosaic virus, Ornithogalum mosaic virus and Wisteria vein mosaic virus. The procedure was rapid, cost-effective, easy to use and showed a good taxonomic discriminating value. It also enabled the identification of potyviruses in adjacent weeds and should thus aid the understanding of outbreaks of potyviruses occurring in varied epidemiological circumstances.",bean common mosaic virus subgroup;degenerate primers;Vanilla;planifolia;Vanilla tahitensis;virus taxonomy;POLYMERASE-CHAIN-REACTION;MOSAIC-VIRUS;NUCLEOTIDE-SEQUENCE;NECROSIS;POTYVIRUS;FRENCH-POLYNESIA;DIFFERENTIATION;SYMPTOMATOLOGY;GENOME;FAMILY;PRIMER,"Grisoni, M.;Moles, M.;Farreyrol, K.;Rassaby, L.;Davis, R.;Pearson, M.",2006,Aug,,0
705,"On the identity of Ootheca bennigseni Weise, O-mutabilis (Schonherr) and O-meridiana sp n. (Chrysomelidae : Galerucinae), bean and cowpea pests in the Afrotropical Region","Ootheca mutabilis (Schonherr) and O. bennigseni Weise are recognized as two prominent pest species on beans (Phaseolus vulgaris (L.), Fabaceae), in Central and East Africa. These beetles destroy root tissue and seedlings, skeletonize the leaves of plants and feed on inflorescences, causing serious crop losses. Both species also feed on cowpeas (Vigna unguiculata (L.) Walp. (Fabaceae). Ootheca mutabilis is known to be a vector of several plant viruses. The current taxonomic status of the African genus Ootheca is discussed, and the following species are transferred from the genus Ergana Chapuis to Ootheca Dejean as new combinations: O. bifrons (Laboissiere), O. bourquii (Laboissiere), O. caerulea (Jacoby), O. fulvipes (Jacoby), O. chapuisi (Jacoby), O. minuta (Laboissi re), O. nigrilabris (Laboissiere), O. podagrica (Laboissiere), O. proteus (Chapuis), O. semicaerulea (Jacoby), O. variabilis (Laboissiere), and O. vittata (Laboissiere). Ootheca vexa nom. n. is proposed as the replacement name for Ootheca apicicornis (Laboissiere) comb. n. (from Ergana), a junior homonym of O. apicicornis Laboissi re. Ootheca mutabilis and O. bennigseni have been studied to provide information and illustrations to facilitate their identification. Ootheca meridiana sp. n. is described as a new pest species of beans and cowpeas from southern Africa.",taxonomy;new combinations;new species;host plant damage;morphology;INSECT PESTS;COLEOPTERA;AFRICA,"Grobbelaar, E.",2008,Mar,,0
706,Varicella-Zoster virus-specific gp140: A highly immunogenic and disulfide-linked structural glycoprotein,"A 140,000-dalton disulfide-linked glycoprotein (gp140) specified by varicella-zoster virus (VZV) in infected cultured cells was identified and precipitated by two murine monoclonal antibodies (VZ-151 and VZ-158). When analyzed under reducing conditions by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, gp140 was cleaved predominantly into a 66,000 lower-molecular-weight product (gp66). This protein was classified as a viral structural component, since it was observed in the polypeptide profile of metrizamide gradient-purified enveloped virions. By immunofluorescence analyses with a monoclonal antibody probe, gp140 expression was documented to be highly conserved both within cultured cells inoculated with homologous (VZV-Oka) and heterologous (VZV-32) strains and in infected human tissues from chicken pox and zoster patients. That the glycoprotein was highly immunogenic was confirmed by the presence of high-titer anti-gp140 antibody in the sera of both hyperimmunized laboratory animals and naturally infected humans. Temporally, the humoral response to gp140 following primary VZV infection preceded that against the other viral glycoproteins. These studies describe, therefore, an immunogenic, disulfide-linked viral structural glycoprotein, which must be included among the other five previously described VZV-specific fucosylated species - gp118, gp98, gp88, gp62, and gp45.",monoclonal antibody;radioisotope;virus antigen;virus glycoprotein;cell culture;human;in vitro study;Varicella zoster virus;virus infection,"Grose, C.;Edwards, D. P.;Weigle, K. A.",1984,,,0
707,Epidemic late abortion in swine--status of research,"This article briefly describes the PRRS (Porcine Reproductive and Respiratory Syndrome), which arose in the winter of 1990 in Germany and other European countries. The data are accumulated from the literature and own experiences. The clinical picture of this new disease, which led to important economical losses is dominated by 1. an increased rate of reduced length of pregnancy with late abortion before day 110 or an increased length of pregnancy; 2. an increase of stillborn piglets; 3. a larger scale of preweaning mortality combined with a higher frequency of secondary infections. Pathological findings in piglets are subcutaneous edema, accumulation of fluids in the body cavities and sometimes interstitial pneumonia is observed. In sows originating from affected farms examined before partus a mononuclear placentitis is present. At present a non-classified virus, isolated by Dutch researchers is proposed to be the causative agent and named Lelystad virus.",animal;animal disease;female;fetus death;pregnancy;research;respiratory tract disease;review;pig;swine disease;syndrome;veterinary abortion;virus infection,"grosse Beilage, E.;Stockhofe-Zurwieden, N.;Schöttker-Wegner, H. H.",1992,,,0
708,A Next-Generation Sequencing Approach Uncovers Viral Transcripts Incorporated in Poxvirus Virions,"Transcripts are known to be incorporated in particles of DNA viruses belonging to the families of Herpesviridae and Mimiviridae, but the presence of transcripts in other DNA viruses, such as poxviruses, has not been analyzed yet. Therefore, we first established a next-generation-sequencing (NGS)-based protocol, enabling the unbiased identification of transcripts in virus particles. Subsequently, we applied our protocol to analyze RNA in an emerging zoonotic member of the Poxviridae family, namely Cowpox virus. Our results revealed the incorporation of 19 viral transcripts, while host identifications were restricted to ribosomal and mitochondrial RNA. Most viral transcripts had an unknown and immunomodulatory function, suggesting that transcript incorporation may be beneficial for poxvirus immune evasion. Notably, the most abundant transcript originated from the D5L/I1R gene that encodes a viral inhibitor of the host cytoplasmic DNA sensing machinery.","Animals;*Cowpox virus/ge [Genetics];Cowpox virus/im [Immunology];*High-Throughput Nucleotide Sequencing/mt [Methods];Host-Pathogen Interactions;Humans;Immunomodulation;Phylogeny;RNA/ge [Genetics];RNA, Mitochondrial;Transcription, Genetic;*Virion/ge [Genetics];0 (RNA, Mitochondrial);63231-63-0 (rna)","Grossegesse, M.;Doellinger, J.;Haldemann, B.;Schaade, L.;Nitsche, A.",2017,10 13,,0
709,Combined Proteomics/Genomics Approach Reveals Proteomic Changes of Mature Virions as a Novel Poxvirus Adaptation Mechanism,"DNA viruses, like poxviruses, possess a highly stable genome, suggesting that adaptation of virus particles to specific cell types is not restricted to genomic changes. Cowpox viruses are zoonotic poxviruses with an extraordinarily broad host range, demonstrating their adaptive potential in vivo. To elucidate adaptation mechanisms of poxviruses, we isolated cowpox virus particles from a rat and passaged them five times in a human and a rat cell line. Subsequently, we analyzed the proteome and genome of the non-passaged virions and each passage. While the overall viral genome sequence was stable during passaging, proteomics revealed multiple changes in the virion composition. Interestingly, an increased viral fitness in human cells was observed in the presence of increased immunomodulatory protein amounts. As the only minor variant with increasing frequency during passaging was located in a viral RNA polymerase subunit and, moreover, most minor variants were found in transcription-associated genes, protein amounts were presumably regulated at transcription level. This study is the first comparative proteome analysis of virus particles before and after cell culture propagation, revealing proteomic changes as a novel poxvirus adaptation mechanism.","*Adaptation, Physiological/ge [Genetics];Amino Acid Sequence;Animals;Cell Line;Cowpox virus/ch [Chemistry];*Cowpox virus/ge [Genetics];DNA-Directed RNA Polymerases;Gene Expression Regulation;Genetic Fitness;*Genome, Viral/ge [Genetics];High-Throughput Nucleotide Sequencing;Host Specificity;Immunomodulation;*Proteome/ge [Genetics];Rats;Rats, Wistar;Sequence Analysis, DNA;Viral Proteins/an [Analysis];Viral Proteins/ge [Genetics];*Virion/ch [Chemistry];Virus Cultivation;Virus Replication;0 (Proteome);0 (Viral Proteins)","Grossegesse, M.;Doellinger, J.;Tyshaieva, A.;Schaade, L.;Nitsche, A.",2017,11 10,,0
710,Bacteriophage strain typing by rapid single molecule analysis,"Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a DNA methyltransferase. Due to the diffraction limit of light, the dense distribution of labels results in a continuous fluorescent signal along the DNA. The amplitude modulations (AM) of the fluorescence intensity along the stretched DNA molecules exhibit a unique molecular fingerprint that can be used for identification. We show that this labelling scheme is highly informative, allowing accurate genotyping. We demonstrate the method by labelling the genomes of lambda and T7 bacteriophages, resulting in a consistent, unique AM profile for each genome. These profiles are also successfully used for identification of the phages from a background phage library. Our method may provide a facile route for screening and typing of various organisms and has potential applications in metagenomics studies of various ecosystems.","*Bacteriophage Typing/mt [Methods];Bacteriophages/cl [Classification];Bacteriophages/ge [Genetics];DNA Barcoding, Taxonomic;Fluorescent Dyes;Genome, Viral;Molecular Typing/mt [Methods];Site-Specific DNA-Methyltransferase (Adenine-Specific);0 (Fluorescent Dyes)","Grunwald, A.;Dahan, M.;Giesbertz, A.;Nilsson, A.;Nyberg, L. K.;Weinhold, E.;Ambjornsson, T.;Westerlund, F.;Ebenstein, Y.",2015,Oct 15,,0
711,Epidemiological investigation of pseudorabies in Shandong Province from 2013 to 2016,"In late 2011, a variant pseudorabies virus (vPRV) emerged in Bartha-K61-vaccinated pig herds, resulting in high morbidity and mortality of piglets in China. Since 2013, the autopsy lesions, histological examinations, virus isolation, phylogenetic analysis and selection pressure analysis of the gE gene of vPRV were recorded for 395 clinical cases, and 5,033 pig serum samples were detected by PRV gE-coated enzyme-linked immunosorbent assay. The major clinical symptoms were abortion in pregnant sows, fatal neurological signs in piglets and respiratory disease in growing pigs. Necrotic splenitis, hepatitis and lymphadenitis, haemorrhagic nephritis and non-suppurative encephalitis were observed by histopathological examination. Typical eosinophilic inclusion bodies were found in the nuclei of liver cells. Using PCR, 110 samples among 395 clinical cases tested positive for the gE gene. Fifteen vPRV strains were isolated and confirmed by sequencing and phylogenetic analysis of the gE gene. The strains shared 97.1%–99.9% nucleotide (nt) and 96.6%–99.5% amino acid (aa) homology with PRV reference strains. Selection pressure analysis showed that one site in the codons of glycoprotein E was under positive selection. Of the 5,033 serum samples, 2,909 were positive by ELISA for a positive rate of 57.8%. These results showed that vPRV was still prevalent in Shandong Province, indicating severe PRV infectious pressure. The preparation of new vaccines against PRV is extremely urgent.",glycoprotein E;virus DNA;virus RNA;animal cell;animal tissue;article;autopsy;China;comparative study;encephalitis;enzyme linked immunosorbent assay;gene expression;gene sequence;genetic transfection;hepatitis;histopathology;lymphadenitis;morbidity;mortality;nephritis;neurologic disease;nonhuman;phylogeny;piglet;polymerase chain reaction;pseudorabies;Pseudorabies virus;respiratory tract disease;virus detection,"Gu, J.;Hu, D.;Peng, T.;Wang, Y.;Ma, Z.;Liu, Z.;Meng, F.;Shang, Y.;Liu, S.;Xiao, Y.",2018,,10.1111/tbed.12827,0
712,Genome sequencing and genetic analysis of a natural reassortant H5N1 subtype avian influenza virus possessing H9N2 internal genes,"Abstract:One H5N1 subtype avian influenza virus, A/duck/Shandong/009/2008 (Dk/SD/009/08), was isolated from apparently healthy domestic ducks in some live bird market in East China during our epidemiological surveillance. To investigate the genetic composition, Dk/SD/009/08 was subjected to genome sequencing. The amino acid motif of cleavage site was ""PLRERRRK-R/GL"", which was consistent with the characterization of the HPAIV. According to the newest unified nomenclature system of H5N1, Dk/SD/ 009/08 was classified into Clade 2.3.4. The BLAST results showed that four gene segments (HA, NA, NP and NS) had the highest nucleotide identities with H5N1 subtype AIVs whereas the remaining four (PB2, PB1, PA and M) displayed the closest relationship with H9N2 subtype. Therefore, Dk/SD/009/08 might be a natural reassortant virus. The phylogenetic analysis further indicated that G1-like H9N2 subtype AIVs which was prevalent mainly in quails of Southern China might provide the internal genes for Dk/ SD/009/08.",viral protein;animal;article;chick embryo;classification;genetic reassortment;genetic recombination;genetics;human;influenza;Influenza A virus (H5N1);Influenza A virus (H9N2);isolation and purification;molecular genetics;phylogeny;virology;virus genome,"Gu, M.;Liu, W. B.;Cao, J. P.;Cao, Y. Z.;Zhang, X. R.;Peng, D. X.;Liu, X. F.",2010,,,0
713,"Novel variants of clade 2.3.4 highly pathogenic avian influenza A(H5N1) viruses, China",We characterized 7 highly pathogenic avian influenza A(H5N1) viruses isolated from poultry in China during 2009-2012 and found that they belong to clade 2.3.4 but do not fit within the 3 defined subclades. Antigenic drift in subtype H5N1 variants may reduce the efficacy of vaccines designed to control these viruses in poultry.,"Animals;Chickens;China/ep [Epidemiology];*Genotype;Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];*Influenza A Virus, H5N1 Subtype/cl [Classification];*Influenza A Virus, H5N1 Subtype/ge [Genetics];*Influenza in Birds/ep [Epidemiology];*Influenza in Birds/vi [Virology];Phylogeny;Poultry/vi [Virology];Poultry Diseases/ep [Epidemiology];Poultry Diseases/vi [Virology];0 (Hemagglutinin Glycoproteins, Influenza Virus)","Gu, M.;Zhao, G.;Zhao, K.;Zhong, L.;Huang, J.;Wan, H.;Wang, X.;Liu, W.;Liu, H.;Peng, D.;Liu, X.",2013,Dec,,0
714,Identification and Phylogenetic Analysis of an Orf Virus Isolated from an Outbreak in Boer Goat in Shanxi Province,"To identify and analyze the Orf virus in Shanxi Province, China, an Orf virus strain was successfully isolated from crust materials of boer goat with clinical sore mouth symptom from a goat farm of Shanxi Province by passaging in lamb testis (LT). The Orf virus was identified by enzyme linked immunosorbent assay (ELISA) test, recurrent infection test, transmission electron microscopy, and PCR. The nucleotide and amino acid sequences of two genes of the Orf virus were analyzed. The results showed that under the electron microscopy the virus had a presence of typical parapoxvirus virions and there were many eosinophilic intracytoplasmic inclusions observed by hematoxylin-eosin (H&E) stain. In ELISA test, optical density (OD) readings of the sample showed a positive result, and the rabbits infected with the virus showed a typically Orf virus-infected appearance. All these findings proved that the sample was an Orf virus. The phylogenetic studies of Orf B2L and Orf F1L genes showed that the virus clustered in different branches and were closer to the Orf virus Nantou (DQ904351) and the OV-SA00 isolates (AY386264). Furthermore, the above results may provide some insight into the genotype of the etiological agent responsible for the Orf outbreak in Shanxi Province, and could also provide a comparative view of the B2L and F1L genes of parapoxvirus.",Orf virus;boer goat;identification;phylogenetic analysis;B2L;F1L;PARAPOXVIRUS;GENE;SEQUENCE;PROTEIN;LESIONS;MEMBER;LAMBS;SHEEP;DNA,"Gu, S. P.;Shi, X. T.;Shi, Z. Y.;Wang, Z. B.;Zheng, M. X.",2011,Jun,,0
715,Metagenomic analysis of Sichuan takin fecal sample viromes reveals novel enterovirus and astrovirus,"The Sichuan takin inhabits the bamboo forests in the Eastern Himalayas and is considered as a national treasure of China with the highest legal protection and conservation status considered as vulnerable according to The IUCN Red List of Threatened Species. In this study, fecal samples of 71 Sichuan takins were pooled and deep sequenced. Among the 103,553 viral sequences, 21,961 were assigned to mammalian viruses. De novo assembly revealed genomes of an enterovirus and an astrovirus and contigs of circoviruses and genogroup I picobirnaviruses. Complete genome sequencing and phylogenetic analysis showed that Sichuan takin enterovirus is a novel serotype/genotype of the species Enterovirus G, with evidence of recombination. Sichuan takin astrovirus is a new subtype of bovine astrovirus, probably belonging to a new genogroup in the genus Mamastrovirus. Further studies will reveal whether these viruses can also be found in Mishmi takin and Shaanxi takin and their pathogenic potentials.",article;Astroviridae;China;Enterovirus;Enterovirus G;feces analysis;gene sequence;genetic recombination;genotype;Mamastrovirus;metagenomics;new species;nonhuman;nucleotide sequence;priority journal;Sichuan takin;takin;virus genome,"Guan, T. P.;Teng, J. L. L.;Yeong, K. Y.;You, Z. Q.;Liu, H.;Wong, S. S. Y.;Lau, S. K. P.;Woo, P. C. Y.",2018,,10.1016/j.virol.2018.05.027,0
716,Expression of pseudorabies virus-encoded long noncoding RNAs in epithelial cells and neurons,"Long noncoding RNAs (lncRNAs) play important roles in regulating eukaryotic genome replication and gene expression in diverse biological systems. Here, we identified lncRNAs transcribed from pseudorabies virus (PRV)-infected PK-15 cells. Based on high-throughput sequencing data, we obtained 87,263,926 and 93,947,628 clean reads from mock-infected and PRV-infected PK-15 cells, respectively. Through a normalized analytic protocol, we identified three novel viral lncRNAs. According to an analysis of differential expression between the mock-infected and PRV-infected cells, 4151 host lncRNAs were significantly upregulated and 2327 host lncRNAs were significantly downregulated in the latter group. Viral lncRNAs and several host lncRNAs were verified by northern blotting and real-time PCR. The findings showed that the viral lncRNA LDI might regulate the expression of IE180, a potent transcriptional activator of viral genes. Furthermore, we characterized the expression of viral lncRNAs in a culture of infected primary chicken dorsal root ganglia (DRG). Collectively, the obtained data suggest that PRV generates lncRNAs in both epithelial cells and chick DRG neurons.",long untranslated RNA;animal cell;article;controlled study;down regulation;epithelium cell;gene expression;high throughput sequencing;IE180 gene;nerve cell;nerve cell culture;nonhuman;Northern blotting;PK-15 cell line;priority journal;Pseudorabies virus;real time polymerase chain reaction;sensory nerve cell;upregulation;virus gene,"Guan, X.;Liu, J.;Jiang, H.;Wu, C. X.;Chen, H. C.;Liu, Z. F.",2018,,10.1007/s13365-018-0651-3,0
717,Genetic characterization of an H2N2 influenza virus isolated from a muskrat in Western Siberia,"Thirty-two muskrats (Ondatra zibethicus) were captured for surveillance of avian influenza virus in wild waterfowl and mammals near Lake Chany, Western Siberia, Russia. A/muskrat/Russia/63/2014 (H2N2) was isolated from an apparently healthy muskrat using chicken embryos. Based on phylogenetic analysis, the hemagglutinin and neuraminidase genes of this isolate were classified into the Eurasian avian-like influenza virus clade and closely related to low pathogenic avian influenza viruses (LPAIVs) isolated from wild water birds in Italy and Sweden, respectively. Other internal genes were also closely related to LPAIVs isolated from Eurasian wild water birds. Results suggest that interspecies transmission of LPAIVs from wild water birds to semiaquatic mammals occurs, facilitating the spread and evolution of LPAIVs in wetland areas of Western Siberia.",animal;Arvicolinae;genetics;Influenza A virus (H2N2);isolation and purification;orthomyxovirus infection;phylogeny;Russian Federation;veterinary medicine;virology,"Gulyaeva, M.;Sharshov, K.;Suzuki, M.;Sobolev, I.;Sakoda, Y.;Alekseev, A.;Sivay, M.;Shestopalova, L.;Shchelkanov, M.;Shestopalov, A.",2017,,10.1292/jvms.17-0048,0
718,Detection and characterisation of novel bocavirus (genus Bocaparvovirus) and gastroenteritis viruses from asymptomatic pigs in Ireland,"BACKGROUND: Livestock animals have been the assumed source of several human epidemics in recent years, for example, influenza H1N1, rotavirus G8/G9, and MERS-CoV. Surveillance of novel viruses in animals is essential to evaluate the risk to human and animal health and to determine any economic impact, for example, failure to thrive. There is a paucity of data regarding detection and characterisation of gastroenteritis viruses, particularly novel viruses, in porcines in Ireland. Recently, a number of small novel porcine DNA viruses have emerged globally, for example, torque teno sus virus, porcine bocavirus, and parvoviruses 2 & 4, and little is known about the biology and potential pathogenicity of these viruses. Bocaparvovirus is a genetically distinct group of viruses which has been recently detected in humans and animals. METHODS: In this study, the presence of gastroenteritis viruses (rotavirus A, porcine circovirus, adenovirus, and porcine bocavirus) was investigated in a selection of archived faecal samples from asymptomatic piglets from a commercial farm in Ireland. A total of 104 specimens were pooled and screened using conventional molecular techniques (PCR and RT-PCR), a subset of specimens (n=44) were then examined individually. Viral diversity was then investigated using statistical and phylogenetic techniques. RESULTS: Initial screening showed a high prevalence of PBoV in this farm, with the formation of three distinct groups in phylogenetic analysis. Other viruses were also investigated in this study with the first report of PCV, PAdV and lineage I G5 RVA in Ireland. Some specimens contained >1 virus, with statistical analysis indicating a strong correlation for mixed infections of PBoV and PAdV on this farm. CONCLUSION: Investigating the diversity of circulating enteric viruses on Irish porcine farms is important to improve the prophylactic tools available and to facilitate the early detection of changes in circulating viruses.",,"Gunn, L.;Collins, P. J.;Fanning, S.;McKillen, J.;Morgan, J.;Staines, A.;O'Shea, H.",2015,,,0
719,H1N1 influenza virus epitopes classified by monoclonal antibodies,"Epitopes serve an important role in influenza infection. It may be useful to screen universal influenza virus vaccines, analyzing the epitopes of multiple subtypes of the hemagglutinin (HA) protein. A total of 40 monoclonal antibodies (mAbs) previously obtained from flu virus HA antigens (development and characterization of 40 mAbs generated using H1N1 influenza virus split vaccines were previously published) were used to detect and classify mAbs into distinct flu virus sub-categories using the ELISA method. Following this, the common continuous amino acid sequences were identified by multiple sequence alignment analysis with the GenBank database and DNAMAN software, for use in predicting the epitopes of the HA protein. Synthesized peptides of these common sequences were prepared, and used to verify and determine the predicted linear epitopes through localization and distribution analyses. With these methods, nine HA linear epitopes distributed among different strains of influenza virus were identified, which included three from influenza A, four from 2009 H1N1 and seasonal influenza, and two from H1. The present study showed that considering a combination of the antigen-antibody reaction specificity, variation in the influenza virus HA protein and linear epitopes may present a useful approach for designing effective multi-epitope vaccines. Furthermore, the study aimed to clarify the cause and pathogenic mechanism of influenza virus HA-induced flu, and presents a novel idea for identifying the epitopes of other pathogenic microorganisms.",H1N1 influenza virus;monoclonal antibodies;epitope;classified;VACCINE DESIGN;A VIRUS;IDENTIFICATION;PROTEINS;IMMUNOINFORMATICS;GENE;PIGS,"Guo, C. Y.;Zhang, H. X.;Xie, X.;Liu, Y.;Sun, L. J.;Li, H. J.;Yu, P. B.;Hu, H. Y.;Sun, J. Y.;Li, Y.;Feng, Q.;Zhao, X. R.;Liang, D. Y.;Wang, Z.;Hu, J.",2018,Sep,,0
720,Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity,"Emergence and intercontinental spread of highly pathogenic avian influenza A(H5Nx) virus clade 2.3.4.4 is unprecedented. H5N8 and H5N2 viruses have caused major economic losses in the poultry industry in Europe and North America, and lethal human infections with H5N6 virus have occurred in Asia. Knowledge of the evolution of receptor-binding specificity of these viruses, which might affect host range, is urgently needed. We report that emergence of these viruses is accompanied by a change in receptor-binding specificity. In contrast to ancestral clade 2.3.4 H5 proteins, novel clade 2.3.4.4 H5 proteins bind to fucosylated sialosides because of substitutions K222Q and S227R, which are unique for highly pathogenic influenza virus H5 proteins. North American clade 2.3.4.4 virus isolates have retained only the K222Q substitution but still bind fucosylated sialosides. Altered receptor-binding specificity of virus clade 2.3.4.4 H5 proteins might have contributed to emergence and spread of H5Nx viruses.","Alleles;Amino Acid Substitution;Animals;Ducks;Genotype;Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];Humans;*Influenza A virus/cl [Classification];Influenza A virus/ip [Isolation & Purification];Influenza A virus/py [Pathogenicity];*Influenza A virus/ph [Physiology];Influenza in Birds/ep [Epidemiology];Influenza in Birds/pa [Pathology];Influenza in Birds/vi [Virology];*Influenza, Human/ep [Epidemiology];*Influenza, Human/vi [Virology];Mutation;Phylogeny;Reassortant Viruses;Receptors, Virus/ch [Chemistry];*Receptors, Virus/me [Metabolism];Structure-Activity Relationship;*Viral Tropism;*Virus Attachment;0 (Hemagglutinin Glycoproteins, Influenza Virus);0 (Receptors, Virus)","Guo, H.;de Vries, E.;McBride, R.;Dekkers, J.;Peng, W.;Bouwman, K. M.;Nycholat, C.;Verheije, M. H.;Paulson, J. C.;van Kuppeveld, F. J.;de Haan, C. A.",2017,02,,0
721,Target discovery for precision medicine using high-throughput genome engineering,"Over the past few years, programmable RNA-guided nucleases such as the CRISPR/Cas9 system have ushered in a new era of precision genome editing in diverse model systems and in human cells. Functional screens using large libraries of RNA guides can interrogate a large hypothesis space to pinpoint particular genes and genetic elements involved in fundamental biological processes and disease-relevant phenotypes. Here, we review recent high-throughput CRISPR screens (e.g. loss-of-function, gain-of-function, and targeting noncoding elements) and highlight their potential for uncovering novel therapeutic targets, such as those involved in cancer resistance to small molecular drugs and immunotherapies, tumor evolution, infectious disease, inborn genetic disorders, and other therapeutic challenges.",alpha hemolysin;Clostridium toxin;cytarabine;etoposide;lipopolysaccharide;tioguanine;tumor necrosis factor;vemurafenib;accuracy;apicomplexan infection;beta thalassemia;breast cancer;cancer resistance;Clostridium infection;clustered regularly interspaced short palindromic repeat;colon cancer;CRISPR Cas system;dengue;disorders of mitochondrial functions;drug resistance;evolution;gain of function mutation;gene activation;gene editing;gene expression;gene pool;gene repression;genetic code;genetic disorder;genetic screening;genome-wide association study;Gram negative infection;hematologic disease;hepatitis C;high throughput sequencing;human;Human immunodeficiency virus;immunotherapy;infection;lethality;liver cell carcinoma;loss of function mutation;lung adenocarcinoma;melanoma;mutagenesis;myeloid leukemia;neoplasm;neuroblastoma;nonhodgkin lymphoma;ovary cancer;pancreas cancer;priority journal;sarcoma;sickle cell anemia;Staphylococcus infection;Vibrio parahaemolyticus infection;virus cell interaction;virus infection;West Nile fever,"Guo, X.;Chitale, P.;Sanjana, N. E.",2017,,10.1007/978-3-319-63904-8_7,0
722,Identification and genomic characterization of a novel CRESS DNA virus from a calf with severe hemorrhagic enteritis in China,"In this study, a novel circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA virus was discovered in diarrheic sample of a calf with severe hemorrhagic enteritis. The virus, named Bo-Circo-like virus CH, has a circular genome with 3909 nucleotides (nt). Six putative open reading frames (ORFs) were identified, including Rep, capsid (Cap) and four proteins of unknown function. Both the genome size and the number as well as the organization of encoded ORFs, Bo-Circo-like virus CH is most closely related to Po-Circo-like virus 21 detected in pig faeces. A preliminary survey using specific primers for the Rep region showed that 5.3% (4/75) of diarrheic samples were positive for Bo-Circo-like virus, and all 42 healthy samples were negative. In conclusion, our results indicate that Bo-Circo-like virus CH may represent a new virus in bovine. Further investigation is needed to determine the relationship between the virus infection and diarrhea.",amino acid sequence;amplicon;animal experiment;animal model;article;calf (bovine);China;controlled study;diarrhea;disease severity;DNA virus;enteritis;genome analysis;genome size;intestinal bleeding;maximum likelihood method;metagenomics;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;sequence alignment;virus capsid;virus genome;virus identification;virus strain,"Guo, Z.;He, Q.;Tang, C.;Zhang, B.;Yue, H.",2018,,10.1016/j.virusres.2018.07.015,1
723,Detection and molecular characteristics of neboviruses in dairy cows in China,"In this study, 98 diarrhoeic and 70 non-diarrhoeic samples were collected from 13 dairy farms located across 5 provinces in China from April 2017 to May 2018. Approximately 41.8 % (41/98) of diarrhoeic samples and 5.7 % (4/70) of non-diarrhoeic samples were nebovirus-positive based on RT-PCR results, and some diarrhoeic samples were co-infected with bovine rotavirus (73.2 %), bovine coronavirus (36.6 %) and/or bovine viral diarrhoea virus (31.7 %). A phylogenetic analysis of 23 nebovirus RdRp fragments showed that these strains were closely related to Nebraska-like (NB-like) strains but were all located in a unique large branch. Moreover, a phylogenetic analysis of the 18 complete VP1 sequences from this study revealed that 14 strains belonged to lineage 1 and 4 strains belonged to lineage 3. Notably, all four lineage 3 strains shared the same recombination event, with a breakpoint located within the P1A domain. The complete genome of one nebovirus strain, Bo/YLA-2/17/CH, which had a recombination event within the P1A domain of its VP1, was successfully sequenced and was found to be 7453 nt in length, and this may represent a novel nebovirus strain based on the phylogenetic analysis of its complete genome sequence. In conclusion, this study reveals that neboviruses circulate widely in dairy cows in China and exhibit a unique evolution of RdRp. To the best of our knowledge, this is the first reported recombination event located within the P1A domain of nebovirus VP1.",,"Guo, Z.;He, Q.;Zhang, B.;Yue, H.;Tang, C.",2019,Jan,,0
724,Sequence analysis of Meq oncogene among Indian isolates of Marek's disease herpesvirus,"Marek's disease (MD), caused by Marek's disease virus (MDV), is a highly contagious neoplastic disease of chicken that can be prevented by vaccination. However, in recent years many cases of vaccine failure have been reported worldwide as chickens develop symptoms of MD in spite of proper vaccination. Distinct polymorphism and point mutations in Meq gene of MDV have been reported to be associated with virulence and oncogenicity. The present study was carried out with the objective to isolate and characterize field isolates of MDV on the basis of Meq gene. Twenty five samples of suspected cases of MD were collected and processed for virus isolation in duck embryo fibroblast (DEF) primary culture where 28% (7 of 25) samples showed characteristic cytopathic effects of MDV in the form of plaques and syncytia. Additional evidence of presence of MDV in these samples was confirmed by PCR. To analyze diversity in all seven isolates of MDV, a polymorphism study was carried out by cloning and sequencing of full length of Meq gene (1020 bp). Sequence homology of 7 isolates with 23 reference strains showed 98.10–99.40% similarity in nucleotide and 95.90–98.50% similarity in amino acid sequences. Six isolates revealed 5 repeat sequences of 4 prolines (PPPP) whereas, one isolate revealed only 4 repeats. In phylogenetic analysis, these isolates formed a separate cluster showing close relatedness to the Chinese isolates. The study indicates a high mutation rate in field isolates of MDV that may be probable cause of vaccination failure.",amino acid sequence;animal cell;article;controlled study;cytopathogenic effect;embryo;gel electrophoresis;gene mutation;genetic polymorphism;Marek disease;Gallid alphaherpesvirus 2;meq oncogene;nonhuman;oncogene;polymerase chain reaction;priority journal;sequence analysis;sequence homology,"Gupta, M.;Deka, D.;Ramneek",2016,,10.1016/j.mgene.2016.07.009,0
725,Restriction enzyme analysis of bovine herpesvirus-1 DNA from an Indian isolate,"An Indian isolate of BHV-1 was analyzed using several restriction endonucleases. The restriction pattern of BHV-1 DNA with HindIII, BamHI and EcoRI was found to be similar to other reported restriction endonuclease patterns for respiratory isolates of BHV-1. Thus, this isolate could be grouped under BHV-1.1 (respiratory form of BHV-1). Few restriction endonucleases yielded distinct restriction profile of BHV-1 DNA. The total molecular size of BHV-1 DNA for the isolate studied was also estimated to be within 136 kb to 138 kb.",restriction endonuclease;virus DNA;article;Bovine herpesvirus 1;Indian;molecular size;nonhuman;priority journal;restriction mapping;virus classification;virus isolation,"Gupta, P. K.;Rai, A.",1993,,,0
726,Genetic diversity in the VP1 gene of foot-and-mouth disease virus serotype Asia 1,"Complete nucleotide sequence of the 1D (VP1-encoding) gene of 61 foot-and-mouth disease (FMD) serotype Asia I virus isolates recovered from different outbreaks in India between 1985 and 1999 including two vaccine strains currently used were determined. The sequences were compared with each other and those from other Asian countries. On the basis of phylogenetic analysis the viruses could be grouped into four genotypes (genotypes I-IV). All the 61 isolates from India belong to a single genotype (genotype-II) which is further subdivided into three lineages (B1, B2 and B3) under the same genotype. The viruses of the lineage B1 and B3 were found to be more prevalent before 1996 while the viruses of lineage B2 appeared to be new variants responsible for most of the recent outbreaks. Most of the isolates of lineage B1 lack one amino acid in the VP1 protein (position 44) whereas most of the isolates of lineage B2 and B3 contain it which indicates the possibility of these lineages having evolved independently. The rate of evolution of FMDV Asia 1 virus was also estimated and found to be 2.7 x 10(-2) synonymous substitutions per nucleotide per year.","capsid protein;VP1 protein, Foot and mouth disease virus;VP1 protein, Foot-and-mouth disease virus;amino acid sequence;animal;article;bovine;chemistry;classification;DNA sequence;epidemic;epidemiology;foot and mouth disease;Foot and mouth disease virus;genetic variability;genetics;India;molecular evolution;molecular genetics;nucleotide sequence;serotyping;virology;virus capsid","Gurumurthy, C. B.;Sanyal, A.;Venkataramanan, R.;Tosh, C.;George, M.;Hemadri, D.",2002,,,0
727,Turkey coronavirus is more closely related to avian infectious bronchitis virus than to mammalian coronaviruses: a review,"Turkey coronavirus (TCoV) is the cause of an acute highly contagious enteric disease of turkeys. In recent years, TCoV has been increasingly recognized in North America as an important pathogen of young turkeys, resulting in economic loss due to impaired growth and poor feed conversion. While the epidemiology and pathogenesis of TCoV have been extensively studied, TCoV remains one of the least characterized of the known coronaviruses. Avian and mammalian coronaviruses have been subdivided into distinct antigenic/genotypic groups; however, classification of TCoV has been controversial. Previous studies indicated that TCoV was closely related to bovine coronavirus and other group 2 mammalian coronaviruses, but more recent antigenic and genome sequence analyses contradict these findings and, instead, provide evidence that TCoV is closely related to avian infectious bronchitis virus (IBV). Additionally, experimental studies have indicated that the host range of TCoV, once thought to be restricted to turkeys, includes chickens. These studies have raised additional questions regarding the classification of TCoV; particularly, whether IBV and TCoV are taxonomically distinct viruses, or whether TCoV is merely a variant of IBV. Sequence analyses of TCoV have given credence to the idea that TCoV is a variant of IBV, as these studies have shown that TCoV and IBV are very closely related. However, these studies have been limited to only three TCoV strains and relatively small portions of the TCoV genome. TCoV is readily distinguished from IBV based on antigenic and biological differences, and these differences suggest that TCoV should be considered a distinct virus species. Additional studies will be needed to better define the relationship between TCoV and IBV, and to resolve this taxonomic question. Based on our current understanding, it seems prudent to consider TCoV and IBV as distinct virus species that share a close phylogenetic relationship and together comprise group 3 of the coronavirus major antigenic groups.",,"Guy, J. S.",2000,Jun,,0
728,H5 avian and H9 swine influenza virus haemagglutinin structures: Possible origin of influenza subtypes,"There are 15 subtypes of influenza A virus (H1-H15), all of which are found in avian species. Three caused pandemics in the last century: H1 in 1918 (and 1977), H2 in 1957 and H3 in 1968. In 1997, an H5 avian virus and in 1999 an H9 virus caused outbreaks of respiratory disease in Hong Kong. We have determined the three-dimensional structures of the haemagglutinins (HAs) from H5 avian and H9 swine viruses closely related to the viruses isolated from humans in Hong Kong. We have compared them with known structures of the H3 HA from the virus that caused the 1968 H3 pandemic and of the HA-esterase-fusion (HEF) glycoprotein from an influenza C virus. Structure and sequence comparisons suggest that HA subtypes may have originated by diversification of properties that affected the metastability of HAs required for their membrane fusion activities in viral infection.",hemagglutinin;article;evolution;gene sequence;Hong Kong;influenza;Influenza A virus;Influenza C virus;nonhuman;priority journal;respiratory tract disease;swine influenza virus;virus classification;virus isolation,"Ha, Y.;Stevens, D. J.;Skehel, J. J.;Wiley, D. C.",2002,,10.1093/emboj/21.5.865,0
729,The application of genomics to emerging zoonotic viral diseases Review,"Interspecies transmission of pathogens may result in the emergence of new infectious diseases in humans as well as in domestic and wild animals. Genomics tools such as high-throughput sequencing, mRNA expression profiling, and microarray-based analysis of single nucleotide polymorphisms are providing unprecedented ways to analyze the diversity of the genomes of emerging pathogens as well as the molecular basis of the host response to them. By comparing and contrasting the outcomes of an emerging infection with those of closely related pathogens in different but related host species, we can further delineate the various host pathways determining the outcome of zoonotic transmission and adaptation to the newly invaded species. The ultimate challenge is to link pathogen and host genomics data with biological outcomes of zoonotic transmission and to translate the integrated data into novel intervention strategies that eventually will allow the effective control of newly emerging infectious diseases. [References: 29]","Animals;Communicable Diseases, Emerging/tm [Transmission];Communicable Diseases, Emerging/vi [Virology];*Genomics/td [Trends];Humans;*Influenza A virus/ge [Genetics];Influenza, Human/tm [Transmission];Influenza, Human/vi [Virology];Orthomyxoviridae Infections/tm [Transmission];*Orthomyxoviridae Infections/vi [Virology];*SARS Virus/ge [Genetics];Severe Acute Respiratory Syndrome/tm [Transmission];*Severe Acute Respiratory Syndrome/vi [Virology];Zoonoses/tm [Transmission];*Zoonoses","Haagmans, B. L.;Andeweg, A. C.;Osterhaus, A. D.",2009,Oct,,0
730,The application of genomics to emerging zoonotic viral diseases,"Interspecies transmission of pathogens may result in the emergence of new infectious diseases in humans as well as in domestic and wild animals. Genomics tools such as high-throughput sequencing, mRNA expression profiling, and microarray-based analysis of single nucleotide polymorphisms are providing unprecedented ways to analyze the diversity of the genomes of emerging pathogens as well as the molecular basis of the host response to them. By comparing and contrasting the outcomes of an emerging infection with those of closely related pathogens in different but related host species, we can further delineate the various host pathways determining the outcome of zoonotic transmission and adaptation to the newly invaded species. The ultimate challenge is to link pathogen and host genomics data with biological outcomes of zoonotic transmission and to translate the integrated data into novel intervention strategies that eventually will allow the effective control of newly emerging infectious diseases. © 2009 Haagmans et al.",chemokine receptor antagonist;CXCR3 receptor antagonist;messenger RNA;peginterferon alpha;unclassified drug;virus hemagglutinin;animal disease;evolutionary adaptation;gene expression profiling;gene sequence;genetic variability;genome analysis;genomics;high throughput screening;human;Human immunodeficiency virus 1;Human immunodeficiency virus infection;immune response;influenza;Influenza A virus (H1N1);Influenza A virus (H5N1);microarray analysis;molecular mechanics;nonhuman;review;SARS coronavirus;Simian immunodeficiency virus;single nucleotide polymorphism;treatment outcome;virus cell interaction;virus entry;virus genome;virus infection;virus transmission,"Haagmans, B. L.;Andeweg, A. C.;Osterhaus, A. D. M. E.",2009,,10.1371/journal.ppat.1000557,0
731,Possible sources and spreading routes of highly pathogenic avian influenza virus subtype H5N1 infections in poultry and wild birds in Central Europe in 2007 inferred through likelihood analyses,"Recurrent outbreaks of H5N1 HPAIV occurred in several Central European countries in 2007. In-depth phylogenetic analyses which included full-length genomic sequences of the viruses involved were performed to elucidate possible origins of incursions and transmission pathways. Tree reconstructions as well as host-shift and ancestral area inferences were conducted in a maximum likelihood framework. All viruses belonged to a separate subgroup (termed "" EMA-3"") within clade 2.2, and, thus, were distinct from two lineages of HPAIV H5N1 viruses (termed "" EMA-1"" and "" EMA-2"") present in the same geographic area in 2006. Analysis of concatenated coding regions of all eight genome segments significantly improved resolution and robustness of the reconstructed phylogenies as compared to single gene analyses. At the same time, the methodological limits to establish retrospectively transmission networks in a comparatively small geographic region and spanning a short period of time became evident when only few corroborating field-epidemiological data are available. Ambiguities remained concerning the origin of the EMA-3 viruses from a region covering Southeast Germany and the Czech Republic as well as routes of spread to other European countries. AIV monitoring programmes in place for wild birds and poultry in these countries did not reveal presence of these viruses in either population. Host switches between domestic poultry and wild bird populations occurred several times. Analysis of outbreaks in Northeast Germany and nearby Northern Poland in December 2007 demonstrated that geographic and even temporal vicinity of outbreaks does not necessarily indicate a common source of incursion. © 2010 Elsevier B.V.",animal tissue;article;avian influenza;cladistics;controlled study;epidemic;Europe;Germany;influenza A (H5N1);Influenza A virus (H5N1);molecular phylogeny;nonhuman;nucleotide sequence;Poland;poultry;priority journal;virus genome;virus transmission;wild species,"Haase, M.;Starick, E.;Fereidouni, S.;Strebelow, G.;Grund, C.;Seeland, A.;Scheuner, C.;Cieslik, D.;Smietanka, K.;Minta, Z.;Zorman-Rojs, O.;Mojzis, M.;Goletic, T.;Jestin, V.;Schulenburg, B.;Pybus, O.;Mettenleiter, T.;Beer, M.;Harder, T.",2010,,10.1016/j.meegid.2010.07.005,0
732,"In vitro isolation, propagation, and characterization of duck hepatitis virus type III","The in vitro isolation, propagation, and characterization of duck hepatitis virus Type III (DHV-III), is described. This virus, which is serologically distinct from the classical (Type I) DHV, replicated in liver and kidney cell cultures of duck origin. Replication was limited in chicken and quail kidney and duck embryo fibroblast cultures. It did not replicate in a variety of other cell cultures of avian or mammalian origin. The virus was grown successfully in embryonating eggs of ducks, but not of chickens. DHV-III passed through a 50-nm membrane filter, was stable at pH 3.0 and resisted treatment with 5% chloroform. Virus growth was not inhibited by treatment with 5-iodo-2-deoxyuridine. Electron-microscope examination revealed crystalline arrays in the cytoplasm; virus particles had cubic symmetry, and were about 30 nm in diameter. By these properties, this virus can be classified as a member of the picornavirus group.","virus antibody;animal;animal disease;article;bird disease;cell culture;comparative study;duck;Enterovirus;Enterovirus infection;fluorescent antibody technique;growth, development and aging;hepatitis virus;immunology;isolation and purification","Haider, S. A.;Calnek, B. W.",1979,,,0
733,Newly discovered mosquito viruses help control vector-borne viral diseases,"Many well-known mosquito-borne viruses such as dengue, Zika, West Nile, chikungunya and Ross River viruses can be transmitted to vertebratesandare associated withdisease in man or animals. However, the use of deep sequencing and other open-minded approaches to detect viruses in mosquitoes have uncovered many new RNA viruses, most of which do not infect vertebrates. The discovery of these 'insect-specific' viruses (ISVs) has redefined the mosquito virome and prompted the lines of viral taxonomic classification to be redrawn1,2. Despite their benign phenotype, ISVs have become a hot topic of research, with recent studies indicating they have significant application for biotechnology.",double stranded RNA;virus envelope protein;virus RNA;article;biotechnology;Bunyaviridae;chikungunya;convergent evolution;dengue;Flavivirus;human;microbial diversity;mosquito vector;Nodaviridae;nonhuman;phylogeny;priority journal;Reoviridae;RNA virus;Ross River virus;taxonomy;untranslated region;vector control;vertical transmission;virus genome;virus infection;virus transmission;West Nile fever;Zika fever,"Hall, R. A.;Jody, H. P.",2018,,10.1071/ma18020,0
734,Metagenomic Detection of Viruses in Aerosol Samples from Workers in Animal Slaughterhouses,"Published studies have shown that workers in animal slaughterhouses are at a higher risk of lung cancers as compared to the general population. No specific causal agents have been identified, and exposures to several chemicals have been examined and found to be unrelated. Evidence suggests a biological aetiology as the risk is highest for workers who are exposed to live animals or to biological material containing animal faeces, urine or blood. To investigate possible biological exposures in animal slaughterhouses, we used a metagenomic approach to characterise the profile of organisms present within an aerosol sample. An assessment of aerosol exposures for individual workers was achieved by the collection of personal samples that represent the inhalable fraction of dust/bioaerosol in workplace air in both cattle and sheep slaughterhouses. Two sets of nine personal aerosol samples were pooled for the cattle processing and sheep processing areas respectively, with a total of 332,677,346 sequence reads and 250,144,492 sequence reads of 85 bp in length produced for each. Eukaryotic genome sequence was found in both sampling locations, and bovine, ovine and human sequences were common. Sequences from WU polyomavirus and human papillomavirus 120 were detected in the metagenomic dataset from the cattle processing area, and these sequences were confirmed as being present in the original personal aerosol samples. This study presents the first metagenomic description of personal aerosol exposure and this methodology could be applied to a variety of environments. Also, the detection of two candidate viruses warrants further investigation in the setting of occupational exposures in animal slaughterhouses. © 2013 Hall et al.",air analysis;air sampling;article;bovine;controlled study;dust;genome size;high throughput sequencing;human;industrial worker;metagenomics;nonhuman;occupational exposure;Papillomaviridae;Papilloma virus 120;polymerase chain reaction;Polyomavirus;sequence homology;sheep;slaughterhouse;virus detection;workplace;WU Polyoma virus,"Hall, R. J.;Leblanc-Maridor, M.;Wang, J.;Ren, X.;Moore, N. E.;Brooks, C. R.;Peacey, M.;Douwes, J.;McLean, D. J.",2013,,10.1371/journal.pone.0072226,0
735,Detection of arboviruses and other micro-organisms in experimentally infected mosquitoes using massively parallel sequencing,"Human disease incidence attributed to arbovirus infection is increasing throughout the world, with effective control interventions limited by issues of sustainability, insecticide resistance and the lack of effective vaccines. Several promising control strategies are currently under development, such as the release of mosquitoes trans-infected with virus-blocking Wolbachia bacteria. Implementation of any control program is dependent on effective virus surveillance and a thorough understanding of virus-vector interactions. Massively parallel sequencing has enormous potential for providing comprehensive genomic information that can be used to assess many aspects of arbovirus ecology, as well as to evaluate novel control strategies. To demonstrate proof-of-principle, we analyzed Aedes aegypti or Aedes albopictus experimentally infected with dengue, yellow fever or chikungunya viruses. Random amplification was used to prepare sufficient template for sequencing on the Personal Genome Machine. Viral sequences were present in all infected mosquitoes. In addition, in most cases, we were also able to identify the mosquito species and mosquito micro-organisms, including the bacterial endosymbiont Wolbachia. Importantly, naturally occurring Wolbachia strains could be differentiated from strains that had been trans-infected into the mosquito. The method allowed us to assemble near full-length viral genomes and detect other micro-organisms without prior sequence knowledge, in a single reaction. This is a step toward the application of massively parallel sequencing as an arbovirus surveillance tool. It has the potential to provide insight into virus transmission dynamics, and has applicability to the post-release monitoring of Wolbachia in mosquito populations.","*Aedes/mi [Microbiology];*Aedes/vi [Virology];Animals;Arbovirus Infections/ge [Genetics];*Arbovirus Infections/mi [Microbiology];*Arbovirus Infections/vi [Virology];*Arboviruses/ge [Genetics];*Arboviruses/ip [Isolation & Purification];Base Sequence;Genome, Viral/ge [Genetics];*High-Throughput Nucleotide Sequencing/mt [Methods];Humans;RNA, Ribosomal, 16S/ge [Genetics];Sheep;Wolbachia/ge [Genetics];0 (RNA, Ribosomal, 16S)","Hall-Mendelin, S.;Allcock, R.;Kresoje, N.;van den Hurk, A. F.;Warrilow, D.",2013,,,0
736,Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients,"Research on the relationship between changes in the gut microbiota and human disease, including AIDS, is a growing field. However, studies on the eukaryotic component of the intestinal microbiota have just begun and have not yet been conducted in HIV-infected patients. Moreover, eukaryotic community profiling is influenced by the use of different methodologies at each step of culture-independent techniques. Herein, initially, four DNA extraction protocols were compared to test the efficiency of each method in recovering eukaryotic DNA from fecal samples. Our results revealed that recovering eukaryotic components from fecal samples differs significantly among DNA extraction methods. Subsequently, the composition of the intestinal eukaryotic microbiota was evaluated in HIV-infected patients and healthy volunteers through clone sequencing, high-throughput sequencing of nuclear ribosomal internal transcribed spacers 1 (ITS1) and 2 (ITS2) amplicons and real-time PCRs. Our results revealed that not only richness (Chao-1 index) and alpha diversity (Shannon diversity) differ between HIV-infected patients and healthy volunteers, depending on the molecular strategy used, but also the global eukaryotic community composition, with little overlapping taxa found between techniques. Moreover, our results based on cloning libraries and ITS1/ITS2 metabarcoding sequencing showed significant differences in fungal composition between HIV-infected patients and healthy volunteers, but without distinct clusters separating the two groups. Malassezia restricta was significantly more prevalent in fecal samples of HIV-infected patients, according to cloning libraries, whereas operational taxonomic units (OTUs) belonging to Candida albicans and Candida tropicalis were significantly more abundant in fecal samples of HIV-infected patients compared to healthy subjects in both ITS subregions. Finally, real-time PCR showed the presence of Microsporidia, Giardia lamblia, Blastocystis and Hymenolepis diminuta in different proportions in fecal samples from HIV patients as compared to healthy individuals. Our work revealed that the use of different sequencing approaches can impact the perceived eukaryotic diversity results of the human gut. We also provide a more comprehensive view of the eukaryotic community in the gut of HIV-infected patients through the complementarity of the different molecular techniques used. Combining these various methodologies may provide a gold standard for a more complete characterization of the eukaryotic microbiome in future studies.","Case-Control Studies;*DNA Barcoding, Taxonomic;*HIV Infections/mi [Microbiology];Humans;*Intestines/mi [Microbiology];*Microbiota;Real-Time Polymerase Chain Reaction","Hamad, I.;Abou Abdallah, R.;Ravaux, I.;Mokhtari, S.;Tissot-Dupont, H.;Michelle, C.;Stein, A.;Lagier, J. C.;Raoult, D.;Bittar, F.",2018,,,0
737,Using Bayesian network modelling to untangle farm management risk factors for bovine viral diarrhoea virus infection,"Understanding risk factors for bovine viral diarrhoea (BVD) transmission is important for planning national disease control programmes. However, traditional statistical approaches may miss important features of BVD epidemiology due to the highly correlated nature of many farm-level risk factors. In this cross-sectional study, we used data collected from 304 cattle herds in New Zealand during 2015/2016 to compare the results from multivariable logistic regression with Bayesian network (BN) analysis. Blood samples from 15 heifers from each farm were pooled and analysed with an antibody ELISA test to classify BVD virus exposure status. Farmers were surveyed about their general management practices, knowledge about BVD, and risk factors for disease transmission, including onto- and off-farm movements, within- and between-farm contacts, and whether they implemented BVD control measures for their service bulls. Multiple imputation was used to infer missing values in the dataset prior to statistical analysis. The results showed that 57/116 (49.1%) beef farms and 95/188 (50.5%) dairy farms were likely to be actively infected with BVD virus. Almost 60% of farms had movements of heifers/cows onto the premises and 13.8% of farmers reported contact with cattle from other farms. The results of the multivariable logistic regression showed that farms where heifers/cows had been moved onto the premises during all or most of the past five years were at higher risk of being BVD seropositive than farms without those movements (OR 2.21, 95% CI 1.29–4.24). Farms where cattle had occasional or rare contacts with cattle on other farms were also at increased risk compared with farms without any animal contacts between farms (OR 2.63, 95% CI 1.33–5.41) although this association was not frequency-dependent. Only close animal contacts between farms was directly associated with BVD status in the BN model, however, this approach further untangled other complex associations between correlated management factors, and provided additional important insights into BVD epidemiology. Compared to other countries with intensive production systems, over the fence contact appeared to play a more important role in New Zealand pastoral-based production systems and should be considered when developing strategies for a national BVD control programme.",agricultural worker;animal experiment;article;Bayes theorem;Bayesian network analysis;bovine;bovine viral diarrhea;Bovine viral diarrhea virus 1;cattle farming;confidence interval;cow;disease transmission;enzyme linked immunosorbent assay;heifer;herd;human;logistic regression analysis;multivariate logistic regression analysis;New Zealand;nonhuman;odds ratio;priority journal;risk factor;risk management;statistical analysis,"Han, J. H.;Holter, J.;Moffat, J.;Weston, J. F.;Heuer, C.;Gates, M. C.",2018,,10.1016/j.prevetmed.2018.10.014,0
738,Genetic recombination between two genotypes of genogroup III bovine noroviruses (BoNVs) and capsid sequence diversity among BoNVs and Nebraska-like bovine enteric caliciviruses,"To determine the genogroups and genotypes of bovine enteric caliciviruses (BECVs) circulating in calves, we determined the complete capsid gene sequences of 21 BECVs. The nucleotide and predicted amino acid sequences were compared phylogenetically with those of known human and animal enteric caliciviruses. Based on these analyses, 15 BECVs belonged to Norovirus genogroup III and genotype 2 (GIII/2) and were genetically distinct from human Norovirus GI and GII. Six BECVs had capsid gene sequences similar to that of the unclassified Nebraska (NB)-like BECV. The 15 bovine noroviruses (BoNVs) were more closely related to Bo/NLV/ Newbury-2/76/UK (GIII/2) and other known genotype 2 BoNVs than to genotype 1 Bo/NLV/Jena/80/DE. The BoNV Bo/CV521-OH/02/US showed high nucleotide and amino acid identities (84 and 94%, respectively) with the capsid gene of Bo/NLV/Newbury-2/76/UK, whereas the nucleotide and amino acid sequences of the RNA polymerase gene were more closely related to those of Bo/NLV/Jena/80/DE (77 and 87% identities, respectively) than to those of Bo/NLV/Newbury-2/76/UK (69 and 69% identities, respectively), suggesting that Bo/CV521-OH/02/US is a genotype 1-2 recombinant. Gene conversion analysis by the recombinant identification program and SimPlot also predicted that Bo/CV521-OH/02/US was a recombinant. Six NB-like BECVs shared 88 to 92% nucleotide and 94 to 99.5% amino acid identities with the NB BECV in the capsid gene. The results of this study demonstrate genetic diversity in the capsid genes of BECVs circulating in Ohio veal calves, provide new data for coinfections with distinct BECV genotypes or genogroups, and describe the first natural BoNV genotype 1-2 recombinant, analogous to the previously reported human norovirus recombinants.",amino acid sequence;article;Bovine norovirus;Caliciviridae;bovine;gene conversion;gene identification;gene sequence;genetic recombination;genetic variability;genotype;Nebraska like enteric calcivirus;nonhuman;nucleotide sequence;phylogeny;priority journal;viral genetics;virus capsid;virus classification,"Han, M. G.;Smiley, J. R.;Thomas, C.;Saif, L. J.",2004,,10.1128/jcm.42.11.5214-5224.2004,0
739,[Metagenomics-based detection of swine viruses],"Extreme varieties of viruses exist in the environment and animals, some of which are unknown. However, many unknown viruses are barely detected by means of conventional virus isolation and PCR assay. To develop a technology platform for detecting unknown viruses. We established the technology based on viral metagenomics in combination with novel molecular diagnostics. The technology is consisted of removal of host nucleic acid, random PCR amplification, large-scale sequencing, and bioinformatics. The technology was applied to detect classical swine fever virus (CSFV)-infected cells and a tissue sample of a pig infected with porcine circovirus type 2 (PCV2). We amplified 13.7% sequences of CSFV genome and 47.2% those of PCV2 genome, respectively. Moreover, we amplified 16.4% sequences of the simian parainfluenza virus type 5 genome from an unknown virus cell culture using the developed method. In addition, using the developed method combined with the high-throughput sequencing, we detected 1.1% virus sequences, including CSFV, PCV2, torque teno sus virus (TTSuV), porcine bocavirus (PBoV) and human adenovirus type 6 (Ad6) from 7 clinical swine samples of unknown causative agents. The developed metagenomics-based method showed good sensitivity for detection of both DNA and RNA viruses from diverse swine samples, and has potential for universal detection of known and unknown viruses. It might facilitate the diagnosis of emerging viral diseases.",animal;animal disease;article;classification;genetics;isolation and purification;metagenomics;Pestivirus;pig;swine disease;virology;virus;virus infection,"Han, W.;Luo, Y.;Zhao, B.;Sun, Y.;Li, S.;Qiu, H.",2013,,,0
740,Mycoplasma ovipneumoniae--a primary cause of severe pneumonia epizootics in the Norwegian Muskox (Ovibos moschatus) population,"The Norwegian muskox (Ovibos moschatus) population lives on the high mountain plateau of Dovre and originates from animals introduced from Greenland. In the late summers of 2006 and 2012, severe outbreaks of pneumonia with mortality rates of 25-30% occurred. During the 2012 epidemic high quality samples from culled sick animals were obtained for microbiological and pathological examinations. High throughput sequencing (pyrosequencing) of pneumonic lung tissue revealed high concentrations of Mycoplasma ovipneumoniae in all six animals examined by this method and Pasteurella multocida subsp. multocida in four animals, whereas no virus sequences could be identified. Mycoplasma ovipneumoniae and P. multocida multocida were also isolated by culture. Using real time PCR on lung swabs, M. ovipneumoniae was detected in all of the 19 pneumonic lungs examined. Gross pathological examination revealed heavy consolidations primarily in the cranial parts of the lungs and it also identified one case of otitis media. Histologically, lung lesions were characterized as acute to subacute mixed exudative and moderately proliferative bronchoalveolar pneumonia. Immunohistochemical (IHC) examination revealed high load of M. ovipneumoniae antigens within lung lesions, with particularly intensive staining in the neutrophils. Similar IHC finding were observed in archived lung tissue blocks from animals examined during the 2006 epidemic. An M. ovipneumoniae specific ELISA was applied on bio-banked muskox sera from stray muskoxen killed in the period 2004-2013 and sick muskoxen culled, as well as sera from wild reindeer (Rangifer tarandus tarandus) on Dovre and muskoxen from Greenland. Serology and mycoplasma culturing was also carried out on sheep that had been on pasture in the muskox area during the outbreak in 2012. Our findings indicated separate introductions of M. ovipneumoniae infection in 2006 and 2012 from infected co-grazing sheep. Salt licks shared by the two species were a possible route of transmitting infection.","Animals;Base Sequence;Cattle;DNA Primers;Enzyme-Linked Immunosorbent Assay;Mycoplasma ovipneumoniae/ge [Genetics];*Mycoplasma ovipneumoniae/py [Pathogenicity];Norway/ep [Epidemiology];Pneumonia, Bacterial/ep [Epidemiology];Pneumonia, Bacterial/mi [Microbiology];*Pneumonia, Bacterial/ve [Veterinary];Real-Time Polymerase Chain Reaction;0 (DNA Primers)","Handeland, K.;Tengs, T.;Kokotovic, B.;Vikoren, T.;Ayling, R. D.;Bergsjo, B.;Sigurardottir, O. G.;Bretten, T.",2014,,,0
741,Mycoplasma ovipneumoniae - A primary cause of severe pneumonia epizootics in the Norwegian muskox (Ovibos moschatus) population,"The Norwegian muskox (Ovibos moschatus ) population lives on the high mountain plateau of Dovre and originates from animals introduced from Greenland. In the late summers of 2006 and 2012, severe outbreaks of pneumonia with mortality rates of 25-30% occurred. During the 2012 epidemic high quality samples from culled sick animals were obtained for microbiological and pathological examinations. High throughput sequencing (pyrosequencing) of pneumonic lung tissue revealed high concentrations of Mycoplasma ovipneumoniae in all six animals examined by this method and Pasteurella multocida subsp. multocida in four animals, whereas no virus sequences could be identified. Mycoplasma ovipneumoniae and P. multocida multocida were also isolated by culture. Using real time PCR on lung swabs, M. ovipneumoniae was detected in all of the 19 pneumonic lungs examined. Gross pathological examination revealed heavy consolidations primarily in the cranial parts of the lungs and it also identified one case of otitis media. Histologically, lung lesions were characterized as acute to subacute mixed exudative and moderately proliferative bronchoalveolar pneumonia. Immunohistochemical (IHC) examination revealed high load of M. ovipneumoniae antigens within lung lesions, with particularly intensive staining in the neutrophils. Similar IHC finding were observed in archived lung tissue blocks from animals examined during the 2006 epidemic. An M. ovipneumoniae specific ELISA was applied on bio-banked muskox sera from stray muskoxen killed in the period 2004-2013 and sick muskoxen culled, as well as sera from wild reindeer (Rangifer tarandus tarandus) on Dovre and muskoxen from Greenland. Serology and mycoplasma culturing was also carried out on sheep that had been on pasture in the muskox area during the outbreak in 2012. Our findings indicated separate introductions of M. ovipneumoniae infection in 2006 and 2012 from infected co-grazing sheep. Salt licks shared by the two species were a possible route of transmitting infection.",animal cell;animal tissue;article;autopsy;bacterium culture;bacterium detection;bacterium identification;bronchopneumonia;carcass;cellular distribution;contig mapping;controlled study;diarrhea;disease severity;enzyme linked immunosorbent assay;exudative pleurisy;geographic distribution;geographic origin;high throughput sequencing;histopathology;immunohistochemistry;inflammatory infiltrate;lung alveolus macrophage;lung parenchyma;macrophage migration;mesentery lymph node;muskox;Mycoplasma ovipneumoniae;Mycoplasma pneumonia;neutrophil chemotaxis;nonhuman;Norway;nucleotide sequence;otitis media;Pasteurella multocida;pyrosequencing;real time polymerase chain reaction;staining,"Handeland, K.;Tengs, T.;Kokotovic, B.;Vikoren, T.;Ayling, R. D.;Bergsjo, B.;Sigurðardóttir Ó, G.;Bretten, T.",2014,,10.1371/journal.pone.0106116,0
742,Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome,,,"Handley, S. A.;Thackray, L. B.;Zhao, G.;Presti, R.;Miller, A. D.",2012,,,0
743,Porcine epidemic diarrhea in europe: In-detail analyses of disease dynamics and molecular epidemiology,"Porcine epidemic diarrhea (PED) is an acute and highly contagious enteric disease of swine caused by the eponymous virus (PEDV) which belongs to the genus Alphacoronavirus within the Coronaviridae virus family. Following the disastrous outbreaks in Asia and the United States, PEDV has been detected also in Europe. In order to better understand the overall situation, the molecular epidemiology, and factors that might influence the most variable disease impact; 40 samples from swine feces were collected from different PED outbreaks in Germany and other European countries and sequenced by shot-gun next-generation sequencing. A total of 38 new PEDV complete coding sequences were generated. When compared on a global scale, all investigated sequences from Central and South-Eastern Europe formed a rather homogeneous PEDV S INDEL cluster, suggesting a recent re-introduction. However, in-detail analyses revealed two new clusters and putative ancestor strains. Based on the available background data, correlations between clusters and location, farm type or clinical presentation could not be established. Additionally, the impact of secondary infections was explored using the metagenomic data sets. While several coinfections were observed, no correlation was found with disease courses. However, in addition to the PEDV genomes, ten complete viral coding sequences from nine different data sets were reconstructed each representing new virus strains. In detail, three pasivirus A strains, two astroviruses, a porcine sapelovirus, a kobuvirus, a porcine torovirus, a posavirus, and an enterobacteria phage were almost fully sequenced.",complementary DNA;Alphacoronavirus;animal experiment;article;Coronaviridae;DNA library;DNA sequence;DNA synthesis;feces;gene mapping;genotype;Germany;metagenomics;mixed infection;molecular epidemiology;next generation sequencing;nonhuman;phylogenetic tree;pig;porcine epidemic diarrhea;RNA extraction;secondary infection,"Hanke, D.;Pohlmann, A.;Sauter-Louis, C.;Höper, D.;Stadler, J.;Ritzmann, M.;Steinrigl, A.;Schwarz, B. A.;Akimkin, V.;Fux, R.;Blome, S.;Beer, M.",2017,,10.3390/v9070177,1
744,High diversity of picornaviruses in rats from different continents revealed by deep sequencing,"Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler's encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.",viral protein;virus RNA;amino acid sequence;animal;chemistry;classification;Denmark;disease carrier;feces;genetic variation;genetics;high throughput sequencing;Hong Kong;human;intestine flora;isolation and purification;Malaysia;metagenomics;phylogeny;Picornaviridae;picornavirus infection;rat;transmission;virology;virus genome;zoonosis,"Hansen, T. A.;Mollerup, S.;Nguyen, N. P.;White, N. E.;Coghlan, M.;Alquezar-Planas, D. E.;Joshi, T.;Jensen, R. H.;Fridholm, H.;Kjartansdóttir, K. R.;Mourier, T.;Warnow, T.;Belsham, G. J.;Bunce, M.;Willerslev, E.;Nielsen, L. P.;Vinner, L.;Hansen, A. J.",2016,,10.1038/emi.2016.90,0
745,"Human sapoviruses: Genetic diversity, recombination, and classification","The family Caliciviridae contains four genera Sapovirus, Norovirus, Lagovirus and Vesivirus, which include Sapporo virus (SaV), Norwalk virus (NoV), Rabbit hemorrhagic disease virus (RHDV) and Feline calicivirus (FCV), respectively. SaV is a causative agent of gastroenteritis in children and adults. SaV can be divided into five genogroups (GI-GV), among which GI, GII, GIV and GV are known to infect humans, whereas SaV GIII infects porcine species. Detection methods include ELISA, RT-PCR and real-time RT-PCR. Since few SaV studies have been conducted, it is difficult to draw correlations between or conclusions about rates of incidence, detection and overall prevalence. Nevertheless, most studies agree that SaV infection is more frequent in young children than adults and that infection in children almost always occurs by 5 years of age. In addition, children at day-care centres and institutions are at greatest risk of SaV-associated infection and transmission. Recently, a number of important findings concerning human SaV were discovered. SaV strains were detected in water samples, which included untreated wastewater specimens, treated wastewater samples and river samples. SaV strains were also detected in shellfish samples destined for human consumption, and recombinant SaV strains were identified in a number of different countries. The purpose of this review was to highlight the current knowledge of human SaV, which appears to be an increasingly important virus causing gastroenteritis in humans. Copyright © 2007 John Wiley & Sons, Ltd.",blood group A antibody;antigen binding;antigen detection;blood group A;Caliciviridae;correlation analysis;day care;disease course;enzyme linked immunosorbent assay;gastroenteritis;genetic variability;human;incidence;infection;infection risk;Lagovirus;nonhuman;Norovirus;Norwalk virus;Orbivirus;prevalence;reverse transcription polymerase chain reaction;review;risk assessment;Sapovirus;Sapporo virus;pig;Vesivirus;virus classification;virus detection;virus recombinant;virus recombination;virus transmission;waste water,"Hansman, G. S.;Oka, T.;Katayama, K.;Takeda, N.",2007,,10.1002/rmv.533,0
746,Detection and genetic characterization of a novel parvovirus distantly related to human bufavirus in domestic pigs,"In this study, a novel parvovirus (strain swine/Zsana3/2013/HUN, KT965075) was detected in domestic pigs and genetically characterized by viral metagenomics and PCR methods. The novel parvovirus was distantly related to the human bufaviruses and was detected in 19 (90.5 %) of the 21 and five (33.3 %) of the 15 faecal samples collected from animals with and without cases of posterior paraplegia of unknown etiology from five affected farms and one control farm in Hungary, respectively. Swine/Zsana3/2013/HUN is highly prevalent in domestic pigs and potentially represents a novel parvovirus species in the subfamily Parvovirinae.",aging;animal;feces;female;genetics;human;Hungary;isolation and purification;Parvoviridae;parvovirus infection;phylogeny;pig;swine disease;veterinary medicine;virology,"Hargitai, R.;Pankovics, P.;Kertész, A. M.;Bíró, H.;Boros, Á;Phan, T. G.;Delwart, E.;Reuter, G.",2016,,10.1007/s00705-015-2732-4,1
747,"Close phylogenetic relationship between egg drop syndrome virus, bovine adenovirus serotype 7, and ovine adenovirus strain 287","A cloned egg drop syndrome (EDS) virus genomic DNA fragment containing the protease gene has been identified and the complete nucleotide sequence of the protease and partial nucleotide sequence of the hexon genes has been determined. Phylogenetic analysis of the protease gene has revealed EDS virus to be genetically more closely related to bovine adenovirus type 7 (BAV-7) and ovine adenovirus isolate 287 (OAV287) than either of these two viruses are to other members of the genus Mastadenovirus or EDS virus is to an other member of the Aviadenovirus genus. The three viruses share further similarities in that they have a high percentage AT content in their genome and are characterized by having more compact genomes than other adenoviruses. The protease gene from all three viruses contained the active site residues (H55-D72-C122 triad) and C104 (providing a disulfide bond to cofactor pVIc). However, P137, found in all other members of the Mastadenovirus genus, and thought to be involved in trafficking, was missing from the protease of the EDS virus, BAV-7, and OAV287. These results suggest that EDS virus should be classified along with BAV-7 and OAV287 in a separate taxon.",Adenoviridae;amino acid sequence;article;controlled study;DNA sequence;nonhuman;phylogeny;priority journal;virus strain,"Harrach, B.;Meehan, B. M.;Benkö, M.;Adair, B. M.;Todd, D.",1997,,10.1006/viro.1996.8390,0
748,"The Strange, Expanding World of Animal Hepaciviruses","Hepaciviruses and pegiviruses constitute two closely related sister genera of the family Flaviviridae. In the past five years, the known phylogenetic diversity of the hepacivirus genera has absolutely exploded. What was once an isolated infection in humans (and possibly other primates) has now expanded to include horses, rodents, bats, colobus monkeys, cows, and, most recently, catsharks, shedding new light on the genetic diversity and host range of hepaciviruses. Interestingly, despite the identification of these many animal and primate hepaciviruses, the equine hepaciviruses remain the closest genetic relatives of the human hepaciviruses, providing an intriguing clue to the zoonotic source of hepatitis C virus. This review summarizes the significance of these studies and discusses current thinking about the origin and evolution of the animal hepaciviruses as well as their potential usage as surrogate models for the study of hepatitis C virus.",envelope protein;polyprotein;Bat hepacivirus;bovine;Bovine hepacivirus;Canine hepacivirus;Colobus;dog;epidemiological data;Equine hepacivirus;evolutionary rate;experimental model;genetic variability;genome analysis;genotype;genus;Haplorhini;Hepacivirus;hepatitis C;Hepatitis C virus;horse;host range;human;molecular evolution;nonhuman;Pegivirus;persistent virus infection;phylogeny;Primate hepacivirus;priority journal;review;rodent;Rodent hepacivirus;shark;Shark hepacivirus;viral tropism;virus classification,"Hartlage, A. S.;Cullen, J. M.;Kapoor, A.",2016,,10.1146/annurev-virology-100114-055104,0
749,Comparative analysis of selected genes from Diachasmimorpha longicaudata entomopoxvirus and other poxviruses,"The Diachasmimorpha longicaudata entomopoxvirus (DlEPV) is the first symbiotic EPV described from a parasitic wasp. The DlEPV is introduced into the tephritid fruit fly larval host along with the wasp egg at oviposition. We sequenced a shotgun genomic library of the DlEPV DNA and analyzed and compared the predicted protein sequences of eight ORFs with those of selected poxviruses and other organisms. BlastP searches showed that five of these are homologous to poxvirus putative proteins such as metalloprotease, a putative membrane protein, late transcription factor-3, virion surface protein, and poly (A) polymerase (PAP) regulatory small subunit. Three of these are similar to those of other organisms such as the gamma-glutamyltransferase (GGT) of Arabidopsis thaliana, eukaryotic initiation factor 4A (eIF4A) of Caenorhabditis briggsae and lambda phage integrase (λ-Int) of Enterococcus faecium. Transcription motifs for early (TGA,A/T,XXXXA) or late (TAAATG, TAAT, or TAAAT) gene expression conserved in poxviruses were identified with those ORFs. Phylogenetic analysis of multiple alignments of five ORFs and 20 poxvirus homologous sequences and of a concatenate of multiple alignments suggested that DlEPV probably diverged from the ancestral node between the fowlpox virus and the genus B, lepidopteran and orthopteran EPVs, to which Amsacta moorei and Melanoplus sanguinipes EPV, respectively, belong. The DlEPV putative GGT, eIF4A, and λ-Int contained many conserved domains that typified these proteins. These homologues may be involved in either viral pathogenicity or enhancing parasitism via the gamma-glutamyl cycle and compensation of eIF4A levels in the parasitized fly, or via the integration of a portion of the viral genome into the wasp and/or parasitized fly. © 2004 Elsevier Ltd. All rights reserved.",viral protein;amino acid sequence;animal;article;biology;cluster analysis;comparative study;DNA sequence;Entomopoxvirus;gene library;genetics;molecular genetics;nucleotide sequence;open reading frame;phylogeny;protein motif;sequence alignment;virology;wasp,"Hashimoto, Y.;Lawrence, P. O.",2005,,10.1016/j.jinsphys.2004.10.010,0
750,Genetic diversity of chicken anemia virus following cell culture passaging in MSB-1 cells,"It has been shown that a chicken anemia virus (CAV) isolates which had undergone 60 passages in MSB-1 cells (SMSC-1/P60, 3-1/P60) acquired 33-66 nucleotide substitutions at the coding region resulting in 13-16 amino acid changes as compared to the CAV isolates passaged only 5 times in MSB-1 cells (SMSC-1 and 3-1) (Chowdhury et al., Arch. Virol. 148, 2437-2448, 2003). In this study we found that alow CAV (BL-5) and a high CAV passage (BL-5/P90) differed by only 15 nucleotide substitutions resulting in 11 amino acid changes. Phylogenetic analysis based on VP1 also revealed that both isolates were close to each other but not to other CAV isolates from Malaysia, namely SMSC-1 and 3-1.",amino acid sequence;article;cell culture;Circoviridae;controlled study;genetic variability;nonhuman;nucleotide sequence;phylogeny;virus isolation,"Hasmah, M. S.;Omar, A. R.;Wan, K. F.;Hair-Bejo, M.;Aini, I.",2004,,,0
751,Newcastle disease outbreaks in the Sudan from 2003 to 2006 were caused by viruses of genotype 5d,"Newcastle disease (ND) is a serious neurological and respiratory disease of poultry that affects all types of birds but has traditionally not caused symptoms in wild aquatic birds, the natural hosts. In the late 1990s, a new genotype, viz. 5d that is pathogenic to all types of birds, including waterfowl, arose in China and has since spread from East Asia into parts of Europe, the Middle East and Africa. We performed a phylogenetic analysis of the fusion protein gene of isolates obtained from outbreaks of ND in Sudan and found that all contemporary strains isolated between 2003 and 2006 were of genotype 5d, containing the virulent fusion protein cleavage site (F0) motif 112RRQKRF117. Introduction via a Middle Eastern trade partner is likely to be the source of infection since phylogenetic analysis excluded the possibility of introduction from western and southern Africa. © 2009 Springer Science+Business Media, LLC.",article;bird disease;gene isolation;genotype;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;priority journal;protein cleavage;Sudan,"Hassan, W.;Khair, S. A. M.;Mochotlhoane, B.;Abolnik, C.",2010,,10.1007/s11262-009-0424-4,0
752,"Transmission patterns of human enterovirus 71 to, from and among European countries, 2003 to 2013","Enterovirus 71 (EV-71) is involved in epidemics of hand, foot, and mouth disease (HFMD) and has been reported to occur with severe neurological complications in eastern and south-east Asia. In other geographical areas, the transmission of this virus is poorly understood. We used large sequence datasets (of the gene encoding the viral protein 1, VP1) and a Bayesian phylogenetic approach to compare the molecular epidemiology and geographical spread patterns of EV-71 subgenogroups B4, B5, C1, C2, and C4 in Europe relative to other parts of the world. For the study, European countries considered were European Union (EU) Member States and Iceland, Norway and Switzerland. Viruses of the B4, B5, and C4 subgenogroups circulate mainly in eastern and south-east Asia. In Europe sporadic introductions of these subgenogroups are observed, however C1 and C2 viruses predominate. The phylogenies showed evidence of multiple events of spread involving C1 and C2 viruses within Europe since the mid-1990s. Two waves of sporadic C2 infections also occurred in 2010 and 2013. The 2007 Dutch outbreak caused by C2 and the occurrence of B5 and C4 infections in the EU between 2004 and 2013 arose while the circulation of C1 viruses was low. A transmission chain involving a C4 virus was traced from Japan to the EU and then further to Canada between 2001 and 2006. Recent events whereby spread of viruses have occurred from, to, and within Europe appear to be involved in the long term survival of EV-71, highlighting the need for enhanced surveillance of this virus.",capsid protein;article;Bayes theorem;Enterovirus A71;gene cluster;gene sequence;genealogy;genetic variability;nucleotide sequence;phylogeny;phylogeography;polymerase chain reaction;population size;virus transmission,"Hassel, C.;Mirand, A.;Lukashev, A.;Terletskaia Ladwig, E.;Farkas, A.;Schuffenecker, I.;Diedrich, S.;Huemer, H. P.;Archimbaud, C.;Peigue-Lafeuille, H.;Henquell, C.;Bailly, J.",2015,,10.2807/1560-7917.Es.2015.20.34.30005,0
753,Borna disease,"Borna disease virus, a newly classified nonsegmented negative-strand RNA virus with international distribution, infects a broad range of warm-blooded animals from birds to primates. Infection causes movement and behavioral disturbances reminiscent of some neuropsychiatric syndromes. The virus has not been clearly linked to any human disease; however, an association between infection with the virus and selected neuropsychiatric disorders has been suggested. We reviewed recent advances in Borna disease virus research, focusing on evidence of infection in humans.",virus antibody;animal;blood;Borna disease;Borna disease virus;disease transmission;genetics;human;mental disease;review,"Hatalski, C. G.;Lewis, A. J.;Lipkin, W. I.",1997,,,0
754,Detection of Campylobacter jejuni in rectal swab samples from Rousettus amplexicaudatus in the Philippines,"Bats are the second diversity species of mammals and widely distributed in the world. They are thought to be reservoir and vectors of zoonotic pathogens. However, there is scarce report of the evidence of pathogenic bacteria kept in bats. The precise knowledge of the pathogenic bacteria in bat microbiota is important for zoonosis control. Thus, metagenomic analysis targeting the V3-V4 region of the 16S rRNA of the rectal microbiota in Rousettus amplexicaudatus was performed using high throughput sequencing. The results revealed that 103 genera of bacteria including Camplyobacter were detected. Campylobacter was second predominant genus, and Campylobacter coli and Campylobacter jejuni were identified in microbiome of R. amplexicaudatus. Campylobacteriosis is one of the serious bacterial diarrhea in human, and the most often implicated species as the causative agent of campylobacteriosis is C. jejuni. Therefore, we investigated the prevalence of C. jejuni in 91 wild bats with PCR. As a result of PCR assay targeted on 16S-23S intergenic spacer, partial genome of C. jejuni was detected only in five R. amplexicaudatus. This is the first report that C. jejuni was detected in bat rectal swab samples. C. jejuni is the most common cause of campylobacteriosis in humans, transmitted through water and contact with livestock animals. This result indicated that R. amplexicaudatus may be a carrier of C. jejuni.",16S rRNA;bat;Campylobacter;metagenome;microbiota;NIPAH VIRUS;WATER;BATS;SPP.;TRANSMISSION;PATHOGEN;DRINKING,"Hatta, Y.;Omatsu, T.;Tsuchiaka, S.;Katayama, Y.;Taniguchi, S.;Masangkay, J. S.;Puentespina, R.;Eres, E.;Cosico, E.;Une, Y.;Yoshikawa, Y.;Maeda, K.;Kyuwa, S.;Mizutani, T.",2016,Aug,,0
755,Use of reverse transcriptase polymerase chain reaction for detection of vaccine contamination by avian leukosis virus,"A reverse transcriptase polymerase chain reaction (RT-PCR) for avian leukosis virus (ALV) was developed for the detection of contamination of vaccines produced in embryonated eggs and cell cultures derived from chicken. ALV is highly pathogenic and induces a wide spectrum of disease in infected animals. ALV can be divided into five subgroups (A-E). The envelope glycoprotein (env gp85) is the main antigen determinant and responsible for subgroup classification. Viral RNA of all subgroups (A-E) was isolated and amplified using three sets of primers. Subsequently, restriction endonuclease analysis confirmed the product identity and discriminated between subgroups. In specific pathogen free (SPF) eggs experimentally inoculated with ALV, viral RNA was found in allantoic fluids, as well as in vaccines spiked with different subgroups of ALV. No adventitious virus was detected in commercially available preparations. This system provides a rapid and specific in vitro method for the detection of ALV RNA as an extraneous agent and may be applied for quality control of avian vaccines.",vaccine;article;Avian leukosis virus;chicken;drug contamination;drug purity;nonhuman;priority journal;reverse transcription polymerase chain reaction;virus detection;virus isolation,"Häuptli, D.;Bruckner, L.;Ottiger, H. P.",1997,,10.1016/s0166-0934(97)02213-1,0
756,Virus detection using metagenomic sequencing of swine nasal and rectal swabs,"Advances in DNA sequencing have increased our ability to generate large amounts of sequence data at lower costs. These developments have enabled microbial detection and characterization directly from clinical specimens, known as metagenomic sequencing. Viral metagenomic sequencing was performed on five nasal-and five fecal-swab pools collected from each of two primary and two secondary market slaughterhouses and a cull-swine buying station in the southeastern United States. Sequences were assembled de novo and analyzed by BLASTN to identify viruses present in the samples. Twenty seven different viruses were identified. Reads similar to a diverse family of single-stranded circular DNA viruses were identified in nearly every sample (47 of 50). Other viruses identified at all five sampling sites and in over half of the samples were bocavirus, torovirus, posavirus, torque teno virus, IAS virus, picobirnavirus, and teschovirus. Viruses identified in multiple sites in greater than 20% of the samples included enterovirus, parvovirus, influenza A virus, sapelovirus, and Senecavirus A. Other significant swine viruses detected less frequently include porcine circovirus type 2, porcine epidemic diarrhea virus, and porcine deltacoronavirus. Together, these results suggest that metagenomic sequencing is a powerful tool for virus detection and characterization.",swine;DNA sequencing;virus;Senecavirus A;virome;VIRAL METAGENOMICS;IDENTIFICATION;PIGS;PARVOVIRUS;DISEASE;INFECTION;DIARRHEA;SAMPLES;CHINA;FECES,"Hause, B.;Duff, J. W.;Scheidt, A.;Anderson, G.",2016,Nov-Dec,,1
757,Bovine rhinitis viruses are common in U.S. cattle with bovine respiratory disease,"Bovine rhinitis viruses (BRV) are established etiological agents of bovine respiratory disease complex however little research into their epidemiology and ecology has been published for several decades. In the U.S., only bovine rhinitis A virus 1 (BRAV1) has been identified while bovine rhinitis A virus 2 (BRAV2) and bovine rhinitis B virus (BRBV) were previously only identified in England and Japan, respectively. Metagenomic sequencing of a nasal swab from a bovine respiratory disease (BRD) diagnostic submission from Kansas identified contigs with approximately 90% nucleotide similarity to BRAV2 and BRBV. A combination of de novo and templated assemblies using reference genomes yielded near complete BRAV2 and BRBV genomes. The near complete genome of bovine rhinitis A virus 1 (BRAV1) was also determined from a historical isolate to enable further molecular epidemiological studies. A 5'-nuclease reverse transcription PCR assay targeting the 3D polymerase gene was designed and used to screen 204 archived BRD clinical specimens. Thirteen (6.4%) were positive. Metagenomic sequencing of six positive samples identified mixed BRAV1/BRAV2, BRAV1/BRBV and BRAV2/BRBV infections for five samples. One sample showed infection only with BRAV1. Seroprevalence studies using a cell culture adapted BRBV found immunofluorescence assay-reactive antibodies were common in the herds analyzed. Altogether, these results demonstrate that BRV infections are common in cattle with respiratory disease and that BRAV1, BRAV2 and BRBV co-circulate in U.S. cattle and have high similarity to viruses isolated more than 30 years ago from diverse locations.",animal cell;Aphthovirus;article;bovine;bovine rhinitis A virus 1;bovine rhinitis A virus 2;bovine rhinitis B virus;cattle disease;cell culture;contig mapping;controlled study;embryo;herd;immunofluorescence test;Japan;metagenomics;molecular epidemiology;nonhuman;nose smear;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;sequence analysis;seroprevalence;United Kingdom;United States;virus genome;virus identification;virus isolation;virus strain,"Hause, B. M.;Collin, E. A.;Anderson, J.;Hesse, R. A.;Anderson, G.",2015,,10.1371/journal.pone.0121998,1
758,Characterization of a novel influenza virus in cattle and swine: Proposal for a new genus in the Orthomyxoviridae family,"We have recently reported the isolation of a novel virus, provisionally designated C/swine/Oklahoma/1334/2011 (C/ OK), with 50% overall homology to human influenza C viruses (ICV), from a pig in Oklahoma. Deep RNA sequencing of C/OK virus found a matrix 1 (M1) protein expression strategy that differed from that of ICV. The novelty of C/OK virus prompted us to investigate whether C/OK virus could exist in a nonswine species. Significantly, we found that C/OK virus was widespread in U.S. bovine herds, as demonstrated by reverse transcription (RT)-PCR and serological assays. Genome sequencing of three bovine viruses isolated from two herds in different states further confirmed these findings. To determine whether swine/bovine C/OK viruses can undergo reassortment with human ICV, and to clarify the taxonomic status of C/OK, in vitro reassortment and serological typing by agar gel immunodiffusion (AGID) were conducted. In vitro reassortment using two human ICV and two swine and bovine C/OK viruses demonstrated that human ICV and C/OK viruses were unable to reassort and produce viable progeny. Antigenically, no cross-recognition of detergent split virions was observed in AGID between human and nonhuman viruses by using polyclonal antibodies that were reactive to cognate antigens. Taken together, these results demonstrate that C/OK virus is genetically and antigenically distinct from ICV. The classification of the new virus in a separate genus of the Orthomyxoviridae family is proposed. The finding of C/OK virus in swine and bovine indicates that this new virus may spread and establish infection in other mammals, including humans. © 2014 Hause et al.",polyclonal antibody;virus RNA;agar gel immunodiffusion;antigen recognition;article;bovine;controlled study;diffusion;genetic reassortment;human;human cell;in vitro study;Influenza C virus (C/swine/Oklahoma/1334/2011);Influenza C virus;new genus;nonhuman;nucleotide sequence;Orthomyxoviridae;phylogeny;priority journal;strain difference;pig;transcriptomics;virus characterization;virus classification;virus identification;virus strain;virus transmission;virus typing;virus viability,"Hause, B. M.;Collin, E. A.;Liu, R.;Huang, B.;Sheng, Z.;Lu, W.;Wang, D.;Nelson, E. A.;Li, F.",2014,,10.1128/mBio.00031-14,0
759,Discovery of a novel putative atypical porcine pestivirus in pigs in the USA,"Pestiviruses are some of the most significant pathogens affecting ruminants and swine, Here, we assembled a 11 276 bp contig encoding a predicted 3635 aa polyprotein from porcine serum with 68 % pairwise identity to that of a recently partially characterized Rhinolophus affinis pestivirus (RaPV) and approximately 25–28 % pairwise identity to those of other pestiviruses, The virus was provisionally named atypical porcine pestivirus (APPV), Metagenomic sequencing of 182 serum samples identified four additional APPV-positive samples, Positive samples originated from five states and ELISAs using recombinant APPV Erns found cross-reactive antibodies in 94% of a collection of porcine serum samples, suggesting widespread distribution of APPV in the US swine herd, The molecular and serological results suggest that APPV is a novel, highly divergent porcine pestivirus widely distributed in US pigs.",cross reacting antibody;polyprotein;5' untranslated region;affinity chromatography;amino acid sequence;article;atypical porcine Pestivirus;controlled study;enzyme linked immunosorbent assay;genetic variability;herd;metagenomics;nonhuman;Pestivirus;phylogeny;pig;Porcine reproductive and respiratory syndrome virus;priority journal;quantitative analysis;reverse transcription polymerase chain reaction;sequence alignment;serology;virus isolation,"Hause, B. M.;Collin, E. A.;Peddireddi, L.;Yuan, F.;Chen, Z.;Hesse, R. A.;Gauger, P. C.;Clement, T.;Fang, Y.;Anderson, G.",2015,,10.1099/jgv.0.000251,1
760,Identification of a novel Picornavirales virus distantly related to posavirus in swine feces,"De novo assembly of metagenomic sequencing reads from feces from a clinically normal pig identified two approximately 9 kb contigs which each consisted of a single large open reading frame. While one contig encoded a predicted 2990 amino acid protein with 83 % identity to the recently described posavirus 1, the other contig encoded a predicted 2942 amino acid protein with only 25 % identity limited to the genomic region encoding the RNA-dependent RNA polymerase (RdRp) of posavirus 2. Besides RdRp, search of the conserved domain database identified domains associated with picornavirus capsid proteins but failed to identify picornaviral helicase and proteinase domains. In addition, a domain representing a family of Mycoplasma and Ureaplasma immunoglobulin-blocking virulence proteins was identified near the 5′-terminus. Phylogenetic analysis found a distant relationship between this novel virus, provisionally named posavirus 3, to the unclassified posaviruses and fisavirus which are proposed to represent different genera in a novel family of the Picornavirales.",capsid protein;contig;helicase;proteinase;RNA directed RNA polymerase;article;feces;fisavirus;Mycoplasma;nonhuman;nucleotide sequence;open reading frame;phylogeny;Picornavirales;pig;posavirus;posavirus 1;posavirus 2;posavirus 3;priority journal;Ureaplasma;virus genome;virus identification,"Hause, B. M.;Hesse, R. A.;Anderson, G. A.",2015,,10.1007/s11262-015-1215-8,1
761,An inactivated influenza D virus vaccine partially protects cattle from respiratory disease caused by homologous challenge,,,"Hause, B. M.;Huntimer, L.;Falkenberg, S.",2017,,,0
762,"Senecavirus A in pigs, United States, 2015",,animal lameness;Brazil;Canada;clinical feature;controlled study;death;diagnostic test;erosion;foot and mouth disease;gene sequence;health status;letter;metagenomics;nonhuman;North Carolina;nose smear;Picornaviridae;pig;polymerase chain reaction;reverse transcription polymerase chain reaction;Senecavirus A virus;slaughterhouse;swine vesicular disease;United States;vesicular stomatitis;virus infection;virus isolation,"Hause, B. M.;Myers, O.;Duff, J.;Hesse, R. A.",2016,,10.3201/eid2207.151951,1
763,Feral swine virome is dominated by single-stranded DNA viruses and contains a novel Orthopneumovirus which circulates both in feral and domestic swine,"Feral swine are known reservoirs for various pathogens that can adversely affect domestic animals. To assess the viral ecology of feral swine in the USA, metagenomic sequencing was performed on 100 pooled nasal swabs. The virome was dominated by small, ssDNA viruses belonging to the families Circoviridae, Anelloviridae and Parvovirinae. Only four RNA viruses were identified: porcine kobuvirus, porcine sapelovirus, atypical porcine pestivirus and a novel Orthopneumovirus, provisionally named swine orthopneumovirus (SOV). SOV shared ~90% nucleotide identity to murine pneumonia virus (MPV) and canine pneumovirus. A modified, commercially available ELISA for MPV found that approximately 30% of both feral and domestic swine sera were positive for antibodies cross-reactive with MPV. Quantitative reverse transcription-PCR identified two (2 %) and four (5.0 %) positive nasal swab pools from feral and domestic swine, respectively, confirming that SOV circulates in both herds.",cross reacting antibody;single stranded DNA;virus DNA;Anelloviridae;article;Circoviridae;domestic pig;enzyme linked immunosorbent assay;European wild boar;Kobuvirus;Murine pneumonia virus;nonhuman;nose smear;Pneumovirus;Parvovirinae;Pestivirus;priority journal;quantitative analysis;reverse transcription polymerase chain reaction;RNA virus;Sapelovirus,"Hause, B. M.;Padmanabhan, A.;Pedersen, K.;Gidlewski, T.",2016,,10.1099/jgv.0.000554,1
764,Highly diverse posaviruses in swine faeces are aquatic in origin,"Posaviruses are a group of highly divergent viruses identified in swine faeces that are distantly related to other members of the order Picornavirales. Eighteen posavirus genomes were assembled from 10 out of 25 (40 %) faecal-swab pools collected from healthy adult swine. Phylogenetic analysis of the conserved RNA-dependent RNA polymerase (Pol) domain found that posaviruses form a large, highly diverse, monophyletic clade, which includes similar viruses identified in human (husavirus) and fish (fisavirus) faeces or intestinal contents, respectively. Quantitative reverse transcription PCR analysis of water samples collected from commercial swine barns identified four out of 19 (21 %) samples were positive using a 5-nuclease assay targeting the Pol region of posavirus 1. ICPD (immunoprecipitation coupled to PCR detection) assays to explore serological evidence of posavirus infection found only a single positive sample, suggesting posaviruses do not commonly infect swine, and together these results suggests a likely aquatic host.",nuclease;Pol protein;RNA directed RNA polymerase;water;adult;animal experiment;aquatic environment;article;cladistics;controlled study;feces;fisavirus;fish;human;husavirus;immunoprecipitation;immunoprecipitation coupled PCR detection;metagenomics;monophyly;nonhuman;nucleotide sequence;phylogeny;Picornaviridae;pig;polymerase chain reaction;posavirus;priority journal;quantitative analysis;reverse transcription polymerase chain reaction;RNA virus;virus cell interaction;virus genome;virus strain;water sampling,"Hause, B. M.;Palinski, R.;Hesse, R.;Anderson, G.",2016,,10.1099/jgv.0.000461,0
765,Complete genome sequence of a porcine polyomavirus from nasal swabs of pigs with respiratory disease,Metagenomic sequencing of pooled nasal swabs from pigs with unexplained respiratory disease identified a large number of reads mapping to a previously uncharacterized porcine polyomavirus. Sus scrofa polyomavirus 2 was most closely related to betapolyomaviruses frequently detected in mammalian respiratory samples.,contig;protein VP1;protein VP2;article;gene amplification;gene mapping;metagenomics;nonhuman;nose smear;nucleotide sequence;pig;Polyomavirus;polyomavirus infection;porcine respiratory disease;sequence alignment;sequence analysis;sequence homology;Sus scrofa polyomavirus 2;swine disease;virus genome;virus identification;virus strain,"Hause, B. M.;Smith, C.;Bishop, B.;Stewart, C.;Simonson, R.",2018,,10.1128/genomeA.00344-18,1
766,The genome of pseudocowpoxvirus: Comparison of a reindeer isolate and a reference strain,"Parapoxviruses (PPV), of the family Poxviridae, cause a pustular cutaneous disease in sheep and goats (orf virus, ORFV) and cattle (pseudocowpoxvirus, PCPV and bovine papular stomatitis virus, BPSV). Here, we present the first genomic sequence of a reference strain of PCPV (VR634) along with the genomic sequence of a PPV (F00.120R) isolated in Finland from reindeer (Rangifer tarandus tarandus). The F00.120R and VR634 genomes are 135 and 145 kb in length and contain 131 and 134 putative genes, respectively, with their genome organization being similar to that of other PPVs. The predicted proteins of F00.120R and VR634 have an average amino acid sequence identity of over 95 %, whereas they share only 88 and 73% amino acid identity with the ORFV and BPSV proteomes, respectively. The most notable differences were found near the genome termini. F00.120R lacks six and VR634 lacks three genes seen near the right terminus of other PPVs. Four genes at the left end of F00.120R and one in the middle of both genomes appear to be fragmented paralogues of other genes within the genome. VR634 has larger than expected inverted terminal repeats possibly as a result of genomic rearrangements. The high G+C content (64 %) of these two viruses along with amino acid sequence comparisons and whole genome phylogenetic analyses confirm the classification of PCPV as a separate species within the genus Parapoxvirus and verify that the virus responsible for an outbreak of contagious stomatitis in reindeer over the winter of 1999-2000 can be classified as PCPV. © 2010 SGM.",proteome;amino acid sequence;article;controlled study;Finland;gene rearrangement;gene sequence;genome analysis;long terminal repeat;nonhuman;nucleotide sequence;phylogeny;Poxviridae;priority journal;reindeer;species comparison;stomatitis;virus classification;virus genome;virus isolation;virus strain;winter,"Hautaniemi, M.;Ueda, N.;Tuimala, J.;Mercer, A. A.;Lahdenperä, J.;McInnes, C. J.",2010,,10.1099/vir.0.018374-0,0
767,History of Prions and transmission of protein misfolding,"Since J. Cuillé and P. L. Chelle successfully transmitted scrapie between sheep by experi- mental inoculation in 1936 and D. C. Gajdusek kuru and Creutzfeldt-Jakob disease to chimpanzee in 1966 and 1968, respectively, the nature of the agents causing these "" slow virus diseases "" remains a mystery. In 1982, S. Prusiner called them "" PRIONs "" (for "" PROteinaceous INfectious particles "") because they appeared lacking the nucleic acids that would classify them viruses. Although infectious or genetic mechanisms were seldom found, most of the rare human PRION diseases appeared "" sporadic "". They shared many clinical and neuropathological properties with human neurodegenerative diseases (slow development, prominent nervous system involvement, amyloid deposits, paucity of immune response) the mechanism of which was not considered usually infectious. In 1991, H. Braak showed, in Alzheimer's disease brain, the low spreading of neuropathological tau associated lesions along anatomic pathways. They appear long before the clinical signs. The abnor- mally misfolded proteins characteristics of many neurodegenerative diseases are thought to aggregate after an initial seeding. This leads to their cell-cell transmission and dissemina- tion through neuronal and extra-neuronalpathways, which unexpected extent is under study. Whether the seeding is infectious or not remains debated. This new paradigm for unders- tanding their natural history and phenotypic diversity, which has already led to assess the diagnostic value of skin biopsy, should open the door to new therapeutic approach.",degenerative disease;history;human;metabolism;prion disease;proteostasis deficiency,"Hauw, J. J.;Haik, S.;Brandel, J. P.",2015,,,0
768,Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm,"BACKGROUND: The bacterium Salmonella enterica serovar Typhimurium (S. Typhimurium) is one of the most frequent causes of foodborne outbreaks of gastroenteritis. Between 2005-2008 a series of S. Typhimurium outbreaks occurred in Tasmania, Australia, that were all traced to eggs originating from a single chicken farm. We sequenced the genomes of 12 isolates linked to these outbreaks, in order to investigate the microevolution of a pathogenic S. Typhimurium clone in a natural, spatiotemporally restricted population. RESULTS: The isolates, which shared a phage type similar to DT135 known locally as 135@ or 135a, formed a clade within the S. Typhimurium population with close similarity to the reference genome SL1334 (160 single nucleotide polymorphisms, or SNPs). Ten of the isolates belonged to a single clone (<23 SNPs between isolate pairs) which likely represents the population of S. Typhimurium circulating at the chicken farm; the other two were from sporadic cases and were genetically distinct from this clone. Divergence dating indicated that all 12 isolates diverged from a common ancestor in the mid 1990 s, and the clone began to diversify in 2003-2004. This clone spilled out into the human population several times between 2005-2008, during which time it continued to accumulate SNPs at a constant rate of 3-5 SNPs per year or 1x10-6 substitutions site-1 year-1, faster than the longer-term (~50 year) rates estimated previously for S. Typhimurium. Our data suggest that roughly half of non-synonymous substitutions are rapidly removed from the S. Typhimurium population, after which purifying selection is no longer important and the remaining substitutions become fixed in the population. The S. Typhimurium 135@ isolates were nearly identical to SL1344 in terms of gene content and virulence plasmids. Their phage contents were close to SL1344, except that they carried a different variant of Gifsy-1, lacked the P2 remnant found in SL1344 and carried a novel P2 phage, P2-Hawk, in place SL1344's P2 phage SopEphi. DT135 lacks P2 prophage. Two additional plasmids were identified in the S. Typhimurium 135@ isolates, pSTM2 and pSTM7. Both plasmids were IncI1, but phylogenetic analysis of the plasmids and their bacterial hosts shows these plasmids are genetically distinct and result from independent plasmid acquisition events. CONCLUSIONS: This study provides a high-resolution insight into short-term microevolution of the important human pathogen S. Typhimurium. It indicates that purifying selection occurs rapidly in this population (<= 6 years) and then declines, and provides an estimate for the short-term substitution rate. The latter is likely to be more relevant for foodborne outbreak investigation than previous estimates based on longer time scales.","Animals;Australia;Chickens/ge [Genetics];*Chickens/mi [Microbiology];Disease Outbreaks;*Eggs/mi [Microbiology];*Evolution, Molecular;Genome, Bacterial;High-Throughput Nucleotide Sequencing;Humans;Phylogeny;*Prophages/ge [Genetics];Prophages/ip [Isolation & Purification];Salmonella Infections, Animal/ge [Genetics];*Salmonella typhimurium/ge [Genetics];Salmonella typhimurium/py [Pathogenicity]","Hawkey, J.;Edwards, D. J.;Dimovski, K.;Hiley, L.;Billman-Jacobe, H.;Hogg, G.;Holt, K. E.",2013,Nov 19,,0
769,"Diversity in VP3, NSP3, and NSP4 of rotavirus B detected from Japanese cattle","Bovine rotavirus B (RVB) is an etiological agent of diarrhea mostly in adult cattle. Currently, a few sequences of viral protein (VP)1, 2, 4, 6, and 7 and nonstructural protein (NSP)1, 2, and 5 of bovine RVB are available in the DDBJ/EMBL/GenBank databases, and none have been reported for VP3, NSP3, and NSP4. In order to fill this gap in the genetic characterization of bovine RVB strains, we used a metagenomics approach and sequenced and analyzed the complete coding sequences (CDS) of VP3, NSP3, and NSP4 genes, as well as the partial or complete CDS of other genes of RVBs detected from Japanese cattle. VP3, NSP3, and NSP4 of bovine RVBs shared low nucleotide sequence identities (63.3–64.9% for VP3, 65.9–68.2% for NSP3, and 52.6–56.2% for NSP4) with those of murine, human, and porcine RVBs, suggesting that bovine RVBs belong to a novel genotype. Furthermore, significantly low amino acid sequence identities were observed for NSP4 (36.1–39.3%) between bovine RVBs and the RVBs of other species. In contrast, hydrophobic plot analysis of NSP4 revealed profiles similar to those of RVBs of other species and rotavirus A (RVA) strains. Phylogenetic analyses of all gene segments revealed that bovine RVB strains formed a cluster that branched distantly from other RVBs. These results suggest that bovine RVBs have evolved independently from other RVBs but in a similar manner to other rotaviruses. These findings provide insights into the evolution and diversity of RVB strains.",nonstructural protein 3;nonstructural protein 4;protein VP3;virus RNA;amino acid sequence;article;cattle breed;controlled study;feces culture;gene cluster;genetic distance;genetic procedures;genetic variability;genotype;hydrophobic plot analysis;Japanese cattle;metagenomics;molecular evolution;nonhuman;nucleotide sequence;phylogeny;Rotavirus A;Rotavirus B;sequence analysis;sequence homology;virus detection;virus strain,"Hayashi-Miyamoto, M.;Murakami, T.;Minami-Fukuda, F.;Tsuchiaka, S.;Kishimoto, M.;Sano, K.;Naoi, Y.;Asano, K.;Ichimaru, T.;Haga, K.;Omatsu, T.;Katayama, Y.;Oba, M.;Aoki, H.;Shirai, J.;Ishida, M.;Katayama, K.;Mizutani, T.;Nagai, M.",2017,,10.1016/j.meegid.2017.01.003,1
770,Single-stranded genomic RNA from turkey enterovirus-like virus,"Previously, we described a disease syndrome in young turkeys caused by an enterovirus-like virus. The virus was designated an enterovirus-like virus based on size, morphology, and intracytoplasmic crystalline arrays of virus. In the present study, further characterization of the virus was performed to ascertain its classification. The virus has a buoyant density of 1.33 g/ml in CsCl and single-stranded RNA genome of approximately 7.5 kilobases. These combined characteristics indicate that this agent is an enterovirus.",virus RNA;animal;animal disease;article;bird disease;chemistry;electron microscopy;Enterovirus;Enterovirus infection;genetics;microbiology;turkey (bird);ultrastructure;virus genome,"Hayhow, C. S.;Parwani, A. V.;Saif, Y. M.",1993,,,0
771,Analysis of HIV-1 subtype B third variable region peptide motifs for induction of neutralizing antibodies against HIV-1 primary isolates,"The HIV-1 gp120 V3 loop is a potent inducer of neutralizing antibodies for T cell line adapted-HIV-1, but less so for primary isolates. We hypothesized that peptides representative of the diversity of natural HIV-1 V3 loop variants might capture elements of conserved higher order structures and so stimulate broadly reactive neutralizing antibodies. We designed a panel of 29 subtype B V3 sequences postulated to reflect the range of V3 diversity. These peptides were used to immunize guinea pigs. The most effective peptide (62.19) clustered around the subtype B consensus sequence and induced antibodies that reproducibly neutralized 31% of the subtype B HIV-1 primary isolates evaluated, but exhibited limited cross-neutralization of non-subtype B HIV-1 strains. Taken together, these data demonstrated that the limited neutralization profile of antibodies induced by optimal subtype B V3 motifs likely represents the maximum breadth of neutralization of subtype B HIV-1 primary isolates attainable by anti-V3 peptide antibodies. © 2005 Elsevier Inc. All rights reserved.",glycoprotein gp 120;monoclonal antibody;monoclonal antibody v3;neutralizing antibody;unclassified drug;amino acid sequence;article;guinea pig;Human immunodeficiency virus 1;immunization;nonhuman;priority journal;protein motif;sequence alignment;T lymphocyte;virus classification;virus envelope;virus identification;virus isolation;virus strain,"Haynes, B. F.;Ma, B.;Montefiori, D. C.;Wrin, T.;Petropoulos, C. J.;Sutherland, L. L.;Scearce, R. M.;Denton, C.;Xia, S. M.;Korber, B. T.;Liao, H. X.",2006,,10.1016/j.virol.2005.08.042,0
772,"Group A Rotaviruses in Chinese Bats: Genetic Composition, Serology, and Evidence for Bat-to-Human Transmission and Reassortment","Bats are natural reservoirs for many pathogenic viruses, and increasing evidence supports the notion that bats can also harbor group A rotaviruses (RVAs), important causative agents of diarrhea in children and young animals. Currently, 8 RVA strains possessing completely novel genotype constellations or genotypes possibly originating from other mammals have been identified from African and Chinese bats. However, all the data were mainly based on detection of RVA RNA, present only during acute infections, which does not permit assessment of the true exposure of a bat population to RVA. To systematically investigate the genetic diversity of RVAs, 547 bat anal swabs or gut samples along with 448 bat sera were collected from five South Chinese provinces. Specific reverse transcription-PCR (RT-PCR) screening found four RVA strains. Strain GLRL1 possessed a completely novel genotype constellation, whereas the other three possessed a constellation consistent with the MSLH14-like genotype, a newly characterized group of viruses widely prevalent in Chinese insectivorous bats. Among the latter, strain LZHP2 provided strong evidence of cross-species transmission of RVAs from bats to humans, whereas strains YSSK5 and BSTM70 were likely reassortants between typical MSLH14-like RVAs and human RVAs. RVA-specific antibodies were detected in 10.7% (48/448) of bat sera by an indirect immunofluorescence assay (IIFA). Bats in Guangxi and Yunnan had a higher RVA-specific antibody prevalence than those from Fujian and Zhejiang provinces. These observations provide evidence for cross-species transmission of MSLH14-like bat RVAs to humans, highlighting the impact of bats as reservoirs of RVAs on public health. IMPORTANCE Bat viruses, such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), Ebola, Hendra, and Nipah viruses, are important pathogens causing outbreaks of severe emerging infectious diseases. However, little is known about bat viruses capable of causing gastroenteritis in humans, even though 8 group A viruses (RVAs) have been identified from bats so far. In this study, another 4 RVA strains were identified, with one providing strong evidence for zoonotic transmission from bats to humans. Serological investigation has also indicated that RVA infection in bats is far more prevalent than expected based on the detection of viral RNA.",bat;group A rotavirus;cross-species transmission;reassortment;FULL GENOMIC ANALYSIS;GENOTYPE CONSTELLATION;SPECIES TRANSMISSION;METAGENOMIC ANALYSIS;MAMMALIAN VIRUSES;STRAINS;CHILDREN;IDENTIFICATION;DIARRHEA;PORCINE,"He, B.;Huang, X. H.;Zhang, F. Q.;Tan, W. L.;Matthijnssens, J.;Qin, S. M.;Xu, L.;Zhao, Z. H.;Yang, L. E.;Wang, Q. X.;Hu, T. S.;Bao, X. L.;Wu, J. M.;Tu, C. C.",2017,Jun,,0
773,Virome profiling of bats from Myanmar by metagenomic analysis of tissue samples reveals more novel mammalian viruses,,,"He, B.;Li, Z.;Yang, F.;Zheng, J.;Feng, Y.;Guo, H.;Li, Y.",2013,,,0
774,Characterization of a novel G3P[3] rotavirus isolated from a lesser horseshoe bat: A distant relative of feline/canine rotaviruses,"Bats are considered important animal reservoirs for many viruses pathogenic to humans. An approach based on viral metagenomics was used to study gut specimens from 78 insectivorous bats in Yunnan Province, China. Seventy-four reads were found to be related to group A rotavirus (RVA). Further reverse transcription-PCR screening and viral isolation on cell cultures confirmed the presence of a novel RVA strain, named RVA/Bat-tc/MSLH14/2012/G3P[3], in 1 (6%) of 16 lesser horseshoe bats. Full genomic sequencing analyses showed that MSLH14 possessed the genotype constellation G3-P[3]-I8-R3-C3-M3-A9-N3-T3-E3-H6, which is akin to human and animal rotaviruses believed to be of feline/canine origin. Phylogenetic analysis indicated that VP7 was most closely related to bovine RVA strains from India, whereas VP4 was most closely related to an unusual human RVA strain, CMH222, with animal characteristics isolated in Thailand. The remaining gene segments were only distantly related to a range of animal RVA strains, most of which are believed to be related to feline/canine RVAs. Experimental infection showed that bat RVA strain MSLH14 was highly pathogenic to suckling mice, causing 100% mortality when they were inoculated orally with a titer as low as 5×102 50% tissue culture infective doses. As this virus is not closely related to any known RVA strain, it is tempting to speculate that it is a true bat RVA strain rather than a virus transmitted between species. However, further screening of bat populations, preferably juvenile animals, will be crucial in determining whether or not this virus is widely distributed in the bat population.",animal tissue;antibody titer;article;bat;Bayes theorem;Canine rotavirus;China;controlled study;Feline rotavirus;female;gene sequence;genotype;horseshoe bat;human;intestine;metagenomics;mouse;new species;nonhuman;nucleotide sequence;phylogeny;polyacrylamide gel electrophoresis;priority journal;reverse transcription polymerase chain reaction;Rotavirus;skin;Thailand;tissue culture;virus culture;virus isolation;virus strain;virus transmission;virus virulence,"He, B.;Yang, F.;Yang, W.;Zhang, Y.;Feng, Y.;Zhou, J.;Xie, J.;Feng, Y.;Bao, X.;Guo, H.;Li, Y.;Xia, L.;Li, N.;Matthijnssens, J.;Zhang, H.;Tu, C.",2013,,10.1128/jvi.02013-13,0
775,Genome-wide mapping of DNase I hypersensitive sites and association analysis with gene expression in MSB1 cells,"DNase I hypersensitive sites (DHSs) mark diverse classes of cis-regulatory regions, such as promoters and enhancers. MSB-1 derived from chicken Marek's disease (MD) lymphomas is an MDV-transformed CD4+ T-cell line for MD study. Previously, DNase IHS sites were studied mainly in human cell types for mammalian. To capture the regulatory elements specific to MSB1 cells and explore the molecular mechanisms of T-cell transformation caused by MDV in MD, we generated high-quality of DHSs map and gene expression profile for functional analysis in MSB1 cell line. The total of 21,724 significant peaks of DHSs was identified from around 40 million short reads. DHSs distribution varied between chromosomes and they preferred to enrich in the gene-rich chromosomes. More interesting, DHSs enrichments appeared to be scarce on regions abundant in CpG islands. Besides, we integrated DHSs into the gene expression data and found that DHSs tended to enrich on high expressed genes throughout whole gene regions while DHSs did not show significant changes for low and silent expressed genes. Furthermore, the correlation of DHSs with lincRNAs expression was also calculated and it implied that enhancer-associated lincRNAs probably originated from enhancer-like regions of DHSs. Together, our results indicated that DNase I HS sites highly correlate with active genes expression in MSB1 cells, suggesting DHSs can be considered as markers to identify the cis-regulatory elements associated with chicken Marek's disease. © 2014 He, Carrillo, Luo, Ding, Tian and Song.",deoxyribonuclease I;DNA;long untranslated RNA;animal cell;article;cell culture;chromosome;controlled study;CpG island;culture medium;DNA library;DNA methylation;gene activation;gene expression;gene mapping;genetic analysis;genetic association;genetic regulation;genome analysis;high throughput sequencing;Marek disease;nonhuman;pulsed field gel electrophoresis;real time polymerase chain reaction;RNA extraction;sequence alignment;silent gene;validation process,"He, Y.;Carrillo, J. A.;Luo, J.;Ding, Y.;Tian, F.;Song, J.",2014,,10.3389/fgene.2014.00308,0
776,Whole-genome sequencing of genotype VI Newcastle disease viruses from formalin-fixed paraffin-embedded tissues from wild pigeons reveals continuous evolution and previously unrecognized genetic diversity in the U.S,"Background: Newcastle disease viruses (NDV) are highly contagious and cause disease in both wild birds and poultry. A pigeon-adapted variant of genotype VI NDV, often termed pigeon paramyxovirus 1, is commonly isolated from columbids in the United States and worldwide. Complete genomic characterization of these genotype VI viruses circulating in wild columbids in the United States is limited, and due to the genetic variability of the virus, failure of rapid diagnostic detection has been reported. Therefore, in this study, formalin-fixed paraffin-embedded (FFPE) samples were subjected to next-generation sequencing (NGS) to identify and characterize these circulating viruses, providing valuable genetic information. NGS enables multiple samples to be deep-sequenced in parallel. When used on FFPE samples, this methodology allows for retrospective studies of infectious organisms. Methods: FFPE wild pigeon tissue samples (kidney, liver and spleen) from 10 mortality events in the U.S. between 2010 and 2016 were analyzed using NGS to detect and sequence NDV genomes from randomly amplified total RNA. Results were compared to the previously published immunohistochemistry (IHC) results conducted on the same samples. Additionally, phylogenetic analyses were conducted on the complete and partial fusion gene and complete genome coding sequences. Results: Twenty-three out of 29 IHC-positive FFPE pigeon samples were identified as positive for NDV by NGS. Positive samples produced an average genome coverage of 99.6% and an average median depth of 199. A previously described sub-genotype (VIa) and a novel sub-genotype (VIn) of NDV were identified as the causative agent of 10 pigeon mortality events in the U.S. from 2010 to 2016. The distribution of these viruses from the North American lineages match the distribution of the Eurasian collared-doves and rock pigeons in the U.S. Conclusions: This work reports the first successful evolutionary study using deep sequencing of complete NDV genomes from FFPE samples of wild bird origin. There are at least two distinct U.S. lineages of genotype VI NDV maintained in wild pigeons that are continuously evolving independently from each other and have no evident epidemiological connections to viruses circulating abroad. These findings support the hypothesis that columbids are serving as reservoirs of virulent NDV in the U.S.",animal tissue;article;Columbidae;controlled study;fusion gene;gene sequence;genetic code;genetic variability;kidney tissue;liver tissue;molecular phylogeny;mortality;Newcastle disease virus;next generation sequencing;nonhuman;nucleotide sequence;spleen tissue;United States;virus genome;virus virulence;whole genome sequencing,"He, Y.;Taylor, T. L.;Dimitrov, K. M.;Butt, S. L.;Stanton, J. B.;Goraichuk, I. V.;Fenton, H.;Poulson, R.;Zhang, J.;Brown, C. C.;Ip, H. S.;Isidoro-Ayza, M.;Afonso, C. L.",2018,,10.1186/s12985-017-0914-2,0
777,Electrostatic Variation of Haemagglutinin as a Hallmark of the Evolution of Avian Influenza Viruses,"Avian influenza virus is a zoonotic agent that significantly impacts public health and the poultry industry. Monitoring viral evolution and spread is crucial for surveillance and tracing programmes, which are currently based on serological or DNA sequencing-phylogenetics analysis. However, virus-host interactions, antigenic drift and spreading of viral clades strongly depend on variation in the surface features of capsid proteins. We report here that in silico comparative structural analysis of haemagglutinin can reveal relevant evolutionary fingerprints, particularly when integrated with sequence-based analyses. Phylogenetic analyses of H9 viral strains from wild birds and poultry, performed with different methods, reliably led to clustering of viruses into five main groups. Subsequent comparison of structural features showed congruence between such clustering and surface electrostatic fingerprints. These latter fingerprints relate group-specific variations in electrostatic charges and isocontours to well-known haemagglutinin sites involved in the modulation of immune escape and host specificity. This work suggests that the integration of structural and sequence comparisons may enhance investigations of trends and relevant mechanisms in viral evolution.",Influenza virus hemagglutinin;animal;avian influenza;bird;chemical phenomena;chemistry;cluster analysis;evolution;Influenza A virus;metabolism;molecular model;phylogeny;poultry;protein domain;static electricity;virology,"Heidari, A.;Righetto, I.;Filippini, F.",2018,,10.1038/s41598-018-20225-3,0
778,"MChip, a low density microarray, differentiates among seasonal human H1N1, North American swine H1N1, and the 2009 pandemic H1N1","Please cite this paper as: Heil et al. (2010) MChip, a low density microarray, differentiates among seasonal human H1N1, North American swine H1N1, and the 2009 pandemic H1N1. Influenza and Other Respiratory Viruses 4(6), 411-416. Background The MChip uses data from the hybridization of amplified viral RNA to 15 distinct oligonucleotides that target the influenza A matrix (M) gene segment. An artificial neural network (ANN) automates the interpretation of subtle differences in fluorescence intensity patterns from the microarray. The complete process from clinical specimen to identification including amplification of viral RNA can be completed in <8hours for under US$10. Objectives The work presented here represents an effort to expand and test the capabilities of the MChip to differentiate influenza A/H1N1 of various species origin. Methods The MChip ANN was trained to recognize fluorescence image patterns of a variety of known influenza A viruses, including examples of human H1N1, human H3N2, swine H1N1, 2009 pandemic influenza A H1N1, and a wide variety of avian, equine, canine, and swine influenza viruses. Robustness of the MChip ANN was evaluated using 296 blinded isolates. Results Training of the ANN was expanded by the addition of 71 well-characterized influenza A isolates and yielded relatively high accuracy (little misclassification) in distinguishing unique H1N1 strains: nine human A/H1N1 (88·9% correct), 35 human A/H3N2 (97·1% correct), 31 North American swine A/H1N1 (80·6% correct), 14 2009 pandemic A/H1N1 (87·7% correct), and 23 negative samples (91·3% correct). Genetic diversity among the swine H1N1 isolates may have contributed to the lower success rate for these viruses. Conclusions The current study demonstrates the MChip has the capability to differentiate the genetic variations among influenza viruses with appropriate ANN training. Further selective enrichment of the ANN will improve its ability to rapidly and reliably characterize influenza viruses of unknown origin. © 2010 Blackwell Publishing Ltd.",virus RNA;accuracy;article;artificial neural network;avian influenza virus;diagnostic test accuracy study;fluorescence imaging;gene amplification;genetic variability;Influenza A virus (H1N1);Influenza A virus (H3N2);nonhuman;priority journal;RNA extraction;strain difference;swine influenza virus;virus classification;virus isolation,"Heil, G. L.;McCarthy, T.;Yoon, K. J.;Liu, S.;Saad, M. D.;Smith, C. B.;Houck, J. A.;Dawson, E. D.;Rowlen, K. L.;Gray, G. C.",2010,,10.1111/j.1750-2659.2010.00185.x,0
779,Molecular characterization of avian reovirus isolates in Tunisia,"Background: Genotype analyses of avian reoviruses isolated from organ samples collected from chickens with suspicious clinical symptoms, between 1997-2008, was based on sequences for both σC and σB genes and aligned with those published in the Genbank, making it possible to carry out studies of molecular classification and relationships. Methods. The full length of the known variable protein σC and part of the σB encoding genes, were amplified with RT-PCR, using conserved primers. PCR products were sequenced and the sequences were analyzed and aligned with avian reovirus sequences from the Genbank database. Results: The sequences of σC-encoding genes of all the isolated strains indicated their close relationship with the American, Chinese and Indian strains. Taking the American strain S1133 as a reference, the two Tunisian isolates 97.1 and 97.2 showed some nucleotide substitutions. For isolate 97.1, the substitution was silent whereas for strain 97.2 the mutation was at the first position of the corresponding codon and induced the substitution of the amino acid encoded. For the σB-encoding gene, the sequences of the Tunisian strains showed mutations at positions two or three of the corresponding codons, inducing substitutions of amino acids at these positions. The phylogenic trees based on σC and σB encoding genes indicated closer relationship between Tunisian, American and Taiwanese isolates of genotype I. Conclusion: Our study describes the genotype of avian reoviruses that are not yet well characterized genetically. The characterization and classification of these viruses might be significant for understanding the epidemiology of malabsorption syndrome and viral arthritis, and improving our knowledge of the genotype of strains circulating in Tunisian flocks. Furthermore, the study of their variable pathogenicity could be extremely important in the choice of the appropriate vaccine strain to control disease. © 2013 Hellal Kort et al; licensee BioMed Central Ltd.",article;Avian orthoreovirus;chicken;Chinese;codon;controlled study;European American;gene amplification;gene sequence;genotype;Indian;malabsorption;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;sequence alignment;sequence analysis;Tunisia;virus gene;virus isolation;virus strain,"Hellal Kort, Y.;Bourogâa, H.;Gribaa, L.;Scott-Algara, D.;Ghram, A.",2013,,10.1186/1743-422x-10-12,0
780,Serotype C foot-and-mouth disease virus isolates from India belong to a separate so far not described lineage,"Complete 1D gene sequences of 13 Indian foot-and-mouth disease virus (FMDV) type C field isolates and a vaccine strain (C-Bombay/64) were determined. All the field isolates showed a greater genetic homogeneity (95-100%) among themselves and were 19.7-21.2% divergent from the vaccine strain. In the phylogenetic analysis, the Indian field isolates formed a separate lineage (lineage VII) different from the previously identified six lineages (lineage I-VI) in type C FMDV [J. Virol. 66 (1992) 3557]. The vaccine strain was grouped with European lineage (lineage II). Comparison of the deduced amino acid sequences of antigenic sites A and C of field isolates showed no significant variation from the vaccine strain. One-way serological relationship determined in ELISA showed antigenic closeness of the field isolates with C-Bombay/64. © 2002 Elsevier Science B.V. All rights reserved.",foot and mouth disease vaccine;amino acid sequence;antigen specificity;article;enzyme linked immunosorbent assay;foot and mouth disease;Foot and mouth disease virus;gene sequence;genetic line;genetic variability;India;molecular phylogeny;nonhuman;serology;serotype;viral genetics;virus isolation;virus strain,"Hemadri, D.;Sanyal, A.;Tosh, C.;Venkataramanan, R.;Pattnaik, B.",2003,,10.1016/s0378-1135(02)00354-1,0
781,Emergence of a new strain of type O Foot-and-mouth disease virus: Its phylogenetic and evolutionary relationship with the PanAsia pandemic strain,"In India, Foot-and-mouth disease virus (FMDV) serotype O has been associated with more than 75% of the outbreaks. Previous studies with this serotype have indicated that the viruses circulating in India belong to a single genotype. Recent (February 2001) FMD epidemics in Europe have focussed global attention on the source of the virus and have been traced to a strain, PanAsia (serotype O), which is present in India since 1990. In this study, to further characterize the isolates belonging to the PanAsian strain, we sequenced the complete VP1-encoding (1D) gene for 71 FMDV serotype O isolates from India recovered from the field outbreaks during the last 4 decades (1962-2001). All the isolates in the tree were distributed in to three major branches (designated as A, B and C); the branch C is further divided into four groups (I-IV), of which the group IV belongs to the PanAsia strain. Furthermore, we show that the PanAsia strain has been circulating endemically since 1982 (not 1990 as reported earlier) and has been the most dominant outbreak strain in the recent years and distributed at least in 17 states of the country. During the year 2001, another new group (group III) of virus with genetic divergence of 5.4-11.1% at nucleotide level from the PanAsia strain is found to co-circulate endemically, and is slowly replacing it. At amino acid level this strain differed from PanAsia strain at five amino acid positions in the VP1. Although these strains are divergent at nucleotide level, they maintained a good antigenic relationship with one of the vaccine strains (IND R2/75) widely used in the country. Given the ability of the PanAsia virus to persist, spread and to outcompete other strains, the present trend could be of serious concern as the newly emerging virus is replacing it. If this is true, then there is another equally divergent strain as PanAsia that may pose a serious threat to the global dairy and meat industries.",article;dairy industry;disease association;endemic disease;epidemic;evolution;Foot and mouth disease virus;gene sequence;genetic variability;India;meat industry;nonhuman;nucleotide sequence;phylogeny;priority journal;serotype;virus gene;virus isolation;virus strain;virus typing,"Hemadri, D.;Tosh, C.;Sanyal, A.;Venkataramanan, R.",2002,,10.1023/a:1020165923805,0
782,Genetic analysis of foot-and-mouth disease virus type O isolates responsible for field outbreaks in India between 1993 and 1999,"Partial nucleotide sequence at the 3′ end of 1D (VP1-encoding) gene of 90 foot-and-mouth disease virus type O isolates recovered from field outbreaks in India between 1993-9 were determined. The sequences were compared with each other and reference viruses. The published sequences of 15 type O isolates recovered from different parts of Asia and one isolate (O1BFS) from Europe and one from Egypt (O1/Sharquia/Egypt/72) were also included in the analysis for comparison. On the basis of phylogenetic analysis the viruses could be grouped into four distinct genotypes (genotypes I-IV). All 90 isolates from India were genotype-I, as were the reference isolates from Bangladesh, China, Egypt, Iran, Saudi Arabia, Syria and Turkey. Genotype-I isolates were further subdivided into 16 sub-genotypes. The Indian isolates were found to be extremely heterogeneous in nature and clustered into 12 different genetic groups. In genotype-I, the nucleotide sequence difference seen between the isolates was 0-11.6%, while among the Indian isolates it is 0-8.8%. Viruses of similar genetic groups are circulating in India, Bangladesh and countries of the Middle East. Genotype-II and -III are represented by isolates from Lebanon (O1/South Lebanon) and Europe (O1-BFS), respectively. Genotype-IV is formed by isolates from China, Hong Kong and Taiwan. The present study reveals the occurrence of viruses belonging to multiple genetic groups over a short period of time and persistence of single genetic group in the same geographical area over several years. This is consistent with the endemic nature of the disease in the country.",animal disease;animal experiment;animal model;article;Asia;buffalo;bovine;cluster analysis;controlled study;Egypt;endemic disease;epidemic;Europe;foot and mouth disease;Foot and mouth disease virus;gene cluster;genetic analysis;genetic code;genetic heterogeneity;genotype;geographic distribution;India;Middle East;nonhuman;nucleotide sequence;phylogeny;sequence analysis;sequence homology;sheep;strain difference;pig;viral genetics;virus isolation,"Hemadri, D.;Tosh, C.;Venkataramanan, R.;Sanyal, A.;Samuel, A. R.;Knowles, N. J.;Kitching, R. P.",2000,,10.1017/s0950268800004738,0
783,"MERS coronavirus in dromedary camel herd, Saudi Arabia",A prospective study of a dromedary camel herd during the 2013-14 calving season showed Middle East respiratory syndrome coronavirus infection of calves and adults. Virus was isolated from the nose and feces but more frequently from the nose. Preexisting neutralizing antibody did not appear to protect against infection.,Animals;*Camelus/vi [Virology];*Coronavirus/ip [Isolation & Purification];Coronavirus Infections/ve [Veterinary];*Coronavirus Infections/vi [Virology];*Middle East Respiratory Syndrome Coronavirus/ip [Isolation & Purification];Prospective Studies;Respiratory Tract Infections/ve [Veterinary];Respiratory Tract Infections/vi [Virology];Saudi Arabia,"Hemida, M. G.;Chu, D. K.;Poon, L. L.;Perera, R. A.;Alhammadi, M. A.;Ng, H. Y.;Siu, L. Y.;Guan, Y.;Alnaeem, A.;Peiris, M.",2014,Jul,,0
784,Comparison of biological properties of St. Louis encephalitis and Rio Bravo viruses,"St. Louis encephalitis (SLE) virus, an arbovirus, and Rio Bravo (RB) virus, a non-arthropod-borne virus and flaviviruses which cross-react in neutralization tests. Several of their biological properties were compared. Viral growth curves revealed that >99% of infectious SLE (Paton) virus remained cell-associated in Vero cells but was released slowly into the medium of infected BHK-21 cells. In contrast, RB (M-64) virus was released upon maturation into the fluids of Vero and BHK-21 cell cultures. Fortyfold more SLE virus than RB virus adsorbed to monolayer cultures of Aedes dorsalis cells. SLE but not RB virus replicated and reached high titers (108 pfu/ml) in Ae. dorsalis cell cultures maintained in media which were expected to enhance recovery of RB virus. Further, SLE but not RB virus replicated in cultured bat epithelial cells and primary duck embryo cells incubated at 42°C. Clearly, the prototype strains of RN and SLE viruses are distinct viruses. Both the classification of RB virus in the genus flavivirus and the antigenic relationship between RB and SLE viruses require further clarification.",virus antigen;antigenic relationship;Arbovirus;arthropod;cell culture;central nervous system;diagnosis;epidemiology;Flavivirus;geographic distribution;in vitro study;nonhuman;rio bravo flavivirus;St. Louis encephalitis virus;virus infection,"Hendricks, D. A.;Hardy, J. L.;Reeves, W. C.",1983,,,0
785,Human biliary glycoproteins function as receptors for interspecies transfer of mouse hepatitis virus,"A variant Mouse Hepatitis virus (MHV), designated MHV-H2, was isolated by serial passage in mixed cultures of permissive DBT cells and nonpermissive Syrian Hamster Kidney (BHK) cells. MHV-H2 replicated efficiently in hamster, mouse, primate kidney (Vero, Cos 1, Cos 7), and human adenocarcinoma (HRT) cell lines but failed to replicate in porcine testicular (ST), feline kidney (CRFK), and canine kidney (MDCK) cells. To understand the molecular basis for coronavirus cross-species transfer into human cell lines, the replication of MHV-H2 was studied in hepatocellular carcinoma (HepG2) cells which expressed high levels of the human homologue of the normal murine receptor, biliary glycoprotein (Bgp). MHV-H2 replicated efficiently in human HepG2 cells, at low levels in breast carcinoma (MCF7) cells, and poorly, if at all, in human colon adenocarcinoma (LS 174T) cell lines which expressed high levels of carcinoembryonic antigen (CEA). These data suggested that MHV-H2 may utilize the human Bgp homologue as a receptor for entry into HepG2 cells. To further study MHV-H2 receptor utilization in human cell lines, blockade experiments were performed with a panel of different monoclonal or polyclonal antiserum directed against the human CEA genes. Pretreatment of HepG2 cells with a polyclonal antiserum directed against all CEA family members, or with a monoclonal antibody, Kat4c (cd66abde), directed against Bgp1, CGM6, CGM1a, NCA and CEA, significantly reduced virus replication and the capacity of MHV- H2 to infect HepG2 cells. Using another panel of monoclonals with more restricted cross reactivities among the human CEA's, Col-4 and Col-14, but not B6.2, B1.13, Col-1, Col-6 and Col-12 blocked MHV-H2 infection in HepG2 cells. These antibodies did not block sindbis virus (SB) replication in HepG2 cells, or block SB, MHV-A59 or MHV-H2 replication in DBT cells. Monoclonal antibodies Col-4, Col-14, and Kat4c (cd66abde) all reacted strongly with human Bgp and CEA, but displayed variable binding patterns with other CEA genes. Following expression of human Bgp in normally nonpermissive porcine testicular (ST) and feline kidney (CRFK) cells, the cells became susceptible to MHV-H2 infection. These data suggested that phylogenetic homologues of virus receptors represent natural conduits for virus xenotropism and cross- species transfer.",glycoprotein;animal cell;article;Coronavirinae;drug receptor binding;mouse;nonhuman;phylogeny;priority journal;receptor affinity;virus cell interaction;virus expression;virus isolation;virus replication;virus transmission,"Hensley, L. E.;Baric, R. S.",1998,,,0
786,"Metagenomic identification, seasonal dynamics, and potential transmission mechanisms of a Daphnia-associated single-stranded DNA virus in two temperate lakes","We used a metagenomic approach to identify viruses that may be involved in the ecology of Daphnia spp. in Oneida and Cayuga lakes (upstate New York). We identified several highly represented, putative eukaryotic, circular, single-stranded deoxyribonucleic acid (DNA) viral genomes. Among these, we discovered a genotype similar in both sequence and genomic architecture to a virus previously reported from a hyperthermal lake that shares characteristics of both single-stranded ribonucleic acid (RNA) and single-stranded DNA viruses. We used quantitative polymerase chain reactions to study the prevalence and viral load of both positive-sense and negative-sense strands of the Daphnia mendotae-associated (Cladocera) hybrid virus (DMClaHV) over a summer season in Oneida and Cayuga lakes. DMClaHV had high prevalence within Daphnia populations, where viral load and the proportion of virus-positive individuals were higher preceding host population decline. DMClaHV viral load was different between two species of Daphnia (D. mendotae and D. retrocurva), and the dynamics between viruses and their hosts varied between the two lakes. We detected DMClaHV in eggs (ephippia) retrieved from Oneida Lake sediments with an estimated age of 30 yr. Using transmission electron microscopy, we observed small (20 nm diameter) virus-like particles in Daphnia that were well away from gut tissues and not associated with intracellular parasites. Because Daphnia plays a critical role in many lake ecosystems, DMClaHV may have important effects on herbivory and thus carbon flow through the lake ecosystem.",MACROBRACHIUM-ROSENBERGII;PORCINE CIRCOVIRUSES;VIRAL METAGENOMICS;TROPHIC CASCADES;PARASITE SYSTEM;ORGANIC-MATTER;MARINE VIRUSES;WATER;GENOME;ZOOPLANKTON,"Hewson, I.;Ng, G.;Li, W. F.;LaBarre, B. A.;Aguirre, I.;Barbosa, J. G.;Breitbart, M.;Greco, A. W.;Kearns, C. M.;Looi, A.;Schaffner, L. R.;Thompson, P. D.;Hairston, N. G.",2013,Sep,,0
787,Application of high-resolution melt curve analysis for classification of infectious bronchitis viruses in field specimens,"Objective: A real-time polymerase chain reaction (PCR)/high-resolution melt (HRM) curve analysis protocol was developed in our laboratory to differentiate infectious bronchitis (IB) virus reference strains. In the current study, this method was used to detect and classify IB viruses in field submissions. Procedure: Over an 11-month period samples from 40 cases of suspected IB virus were received and 17 submissions were positive for IB virus by polymerase chain reaction. HRM curve analysis classified each strain as subgroup 1, 2 or 3 strain (12 submissions) or a strain that was unable to be classified (5 submissions). The 3' untranslated region (UTR) and partial S1 gene nucleotide sequences for the 17 IB virus strains were determined and their identity with those of the relative reference strains compared to confirm the classifications generated using the HRM curve analysis. Results: Of the 12 IB field viruses classified as subgroup 1, 2, or 3 using HRM curve analysis, the 3'UTR and S1 gene nucleotide sequences had identities ≥99% with the respective subgroup reference strain. Analysis of the 3' UTR and S1 gene nucleotide sequences for the five IB virus strains that could not be classified indicated that four belonged to one of the subgroups, and one was a potential recombinant strain (between strains from subgroups 2 and 3). A novel recombinant strain was also detected. Conclusion: HRM curve analysis can rapidly assign the majority of IB viruses present in field submissions to known subgroups. Importantly, HRM curve analysis also identified variant genotypes that require further investigation. © 2010 The Authors. Australian Veterinary Journal © 2010 Australian Veterinary Association.",virus DNA;virus RNA;3' untranslated region;animal;animal disease;article;Avian infectious bronchitis virus;bird disease;chicken;classification;Coronavirus infection;gene amplification;genetics;genotype;isolation and purification;molecular genetics;nucleotide sequence;phylogeny;virology,"Hewson, K. A.;Browning, G. F.;Devlin, J. M.;Ignjatovic, J.;Noormohammadi, A. H.",2010,,10.1111/j.1751-0813.2010.00622.x,0
788,Crimean-Congo haemorrhagic fever virus: Sequence analysis of the small RNA segments from a collection of viruses world wide,"Crimean-Congo haemorrhagic fever virus (CCHFv) is a member of the genus Nairovirus in the family Bunyaviridae. It possesses a tripartite, single stranded RNA genome of negative polarity consisting of large (L), medium (M) and small (S) segments. CCHF virus is enzootic in life stock and wild animals in many parts of the Middle East, Asia and Africa and is also recognised in Southeast Europe. Severe disease, manifest as haemorrhagic fever and high mortality rates (up to 50%), is only recognised in humans. We have determined the complete sequence of the small genomic RNA segment from several strains of CCHF virus from outbreaks in Pakistan 2000, Baghdad 1976 and Uzbekistan 1967. Phylogenetic analysis of three datasets of sequences from the small genomic RNA segment available from a range of strains indicates that they can be divided into seven subtypes. Superimposed on this pattern are links between distant geographic locations, pointing to the existence of a global reservoir of CCHFv. In some cases these links may originate from trade in livestock, and long-distance carriage of virus or infected ticks during bird migration. © 2004 Elsevier B.V. All rights reserved.",Africa;Asia;bird;Bunyaviridae;conference paper;data base;epidemic;Europe;hemorrhagic fever;livestock;Middle East;mortality;Nairovirus;nonhuman;nucleotide sequence;Pakistan;phylogeny;population migration;priority journal;reservoir;RNA gene;RNA sequence;sequence analysis;tick;unindexed sequence;Uzbekistan;virus strain,"Hewson, R.;Chamberlain, J.;Mioulet, V.;Lloyd, G.;Jamil, B.;Hasan, R.;Gmyl, A.;Gmyl, L.;Smirnova, S. E.;Lukashev, A.;Karganova, G.;Clegg, C.",2004,,10.1016/j.virusres.2003.12.035,0
789,Guinea pig model of infectious disease-viral infections,,,"Hickey, A. J.",2011,,,0
790,Sequences of the coat protein gene of five peanut stripe virus (PStV) strains from Thailand and their evolutionary relationship with other bean common mosaic virus sequences,"The coat protein gene and part of the 3' non-coding region of five strains of peanut stripe virus (PStV) from Thailand have been cloned and sequenced. Phylogenetic comparisons of these strains, known as T1, T3, T5, T6 and T7, and related sequences showed that these strains are indeed strains of PStV. Further, PStV strains appear to be related to each other according to their geographic origin. That is, the Thai strains are more closely related to each other than they are to strains from the USA or Indonesia, despite the variety of symptoms caused by these strains and the overlap of symptom types between the strains from different locations. Like other PStV strains, PStV-Thai can be considered strains of bean common mosaic virus (BCMV) but can be distinguished from bean-infecting strains of BCMV and blackeye cowpea mosaic virus (B1CMV) through sequence and host range. No evidence was found that PStV-Thai strains, unlike PStV-Ib, are recombinants of PStV and B1CMV, although the T3 strain may be a recombinant of different PStV sequences. Phylogenetic analyses of viruses of the BCMV group suggest that acquisition of the ability to infect peanut may have occurred only once.",,"Higgins, C. M.;Cassidy, B. G.;Teycheney, P. Y.;Wongkaew, S.;Dietzgen, R. G.",1998,,10.1007/s007050050407,0
791,High throughput sequencing methods for microbiome profiling: application to food animal systems Review,"Analysis of microbial communities using high throughput sequencing methods began in the mid 2000s permitting the production of 1000s to 10,000s of sequence reads per sample and megabases of data per sequence run. This then unprecedented depth of sequencing allowed, for the first time, the discovery of the 'rare biosphere' in environmental samples. The technology was quickly applied to studies in several human subjects. Perhaps these early studies served as a reminder that though the microbes that inhabit mammals are known to outnumber host cells by an order of magnitude or more, most of these are unknown members of our second genome, or microbiome (as coined by Joshua Lederberg), because of our inability to culture them. High throughput methods for microbial 16S ribosomal RNA gene and whole genome shotgun (WGS) sequencing have now begun to reveal the composition and identity of archaeal, bacterial and viral communities at many sites, in and on the human body. Surveys of the microbiota of food production animals have been published in the past few years and future studies should benefit from protocols and tools developed from large-scale human microbiome studies. Nevertheless, production animal-related resources, such as improved host genome assemblies and increased numbers and diversity of host-specific microbial reference genome sequences, will be needed to permit meaningful and robust analysis of 16S rDNA and WGS sequence data.","Animals;*Animals, Domestic/mi [Microbiology];Archaea/ge [Genetics];Bacteria/cl [Classification];Bacteria/ge [Genetics];DNA, Ribosomal/ch [Chemistry];*DNA, Ribosomal/ge [Genetics];Genes, rRNA;High-Throughput Nucleotide Sequencing/mt [Methods];*High-Throughput Nucleotide Sequencing/ve [Veterinary];Humans;Meat;*Metagenome;*Metagenomics/mt [Methods];*RNA, Ribosomal, 16S/ge [Genetics];Sequence Analysis, RNA/ve [Veterinary];Viruses/ge [Genetics];0 (DNA, Ribosomal);0 (RNA, Ribosomal, 16S)","Highlander, S. K.",2012,Jun,,0
792,Transmission of influenza reflects seasonality of wild birds across the annual cycle,"Influenza A Viruses (IAV) in nature must overcome shifting transmission barriers caused by the mobility of their primary host, migratory wild birds, that change throughout the annual cycle. Using a phylogenetic network of viral sequences from North American wild birds (2008-2011) we demonstrate a shift from intraspecific to interspecific transmission that along with reassortment, allows IAV to achieve viral flow across successive seasons from summer to winter. Our study supports amplification of IAV during summer breeding seeded by overwintering virus persisting locally and virus introduced from a wide range of latitudes. As birds migrate from breeding sites to lower latitudes, they become involved in transmission networks with greater connectivity to other bird species, with interspecies transmission of reassortant viruses peaking during the winter. We propose that switching transmission dynamics may be a critical strategy for pathogens that infect mobile hosts inhabiting regions with strong seasonality.","*Animal Migration;Animals;*Animals, Wild;*Anseriformes/vi [Virology];*Influenza A virus/ph [Physiology];*Influenza in Birds/tm [Transmission];Influenza in Birds/vi [Virology];North America;RNA, Viral;Seasons;Time Factors;0 (RNA, Viral)","Hill, N. J.;Ma, E. J.;Meixell, B. W.;Lindberg, M. S.;Boyce, W. M.;Runstadler, J. A.",2016,08,,0
793,Microbial Ecology along the Gastrointestinal Tract,"The ecosystem of the human gastrointestinal (GI) tract traverses a number of environmental, chemical, and physical conditions because it runs from the oral cavity to the anus. These differences in conditions along with food or other ingested substrates affect the composition and density of the microbiota as well as their functional roles by selecting those that are the most suitable for that environment. Previous studies have mostly focused on Bacteria, with the number of studies conducted on Archaea, Eukarya, and Viruses being limited despite their important roles in this ecosystem. Furthermore, due to the challenges associated with collecting samples directly from the inside of humans, many studies are still exploratory, with a primary focus on the composition of microbiomes. Thus, mechanistic studies to investigate functions are conducted using animal models. However, differences in physiology and microbiomes need to be clarified in order to aid in the translation of animal model findings into the context of humans. This review will highlight Bacteria, Archaea, Fungi, and Viruses, discuss differences along the GI tract of healthy humans, and perform comparisons with three common animal models: rats, mice, and pigs.",animal;animal model;archaeon;bacterium;biodiversity;classification;diet;food;fungus;gastrointestinal tract;human;intestine flora;microbiology;mouse;physiology;pig;rat;virus,"Hillman, E. T.;Lu, H.;Yao, T.;Nakatsu, C. H.",2017,,10.1264/jsme2.ME17017,0
794,"TTV, a new human virus with single stranded circular DNA genome","TT virus (TTV) was found in 1997 from a hepatitis patient without virus markers. However, the real impact of TTV on liver diseases remains uncertain to date. Due to the lack of suitable cell systems to support the growth of TTV, the biology of TTV is still obscure. This review tries to summarise the current status of TTV on aspects other than the taxonomic diversity of TTV. TTV was the first human virus with a single stranded circular DNA genome. TTV was considered to be a member of Circoviridae, but others suggested it conformed to a new family. TTV is distinct from ambisense viruses in the genus Circovirus, since the former genome is negative stranded. The genome structure of TTV is more related to chicken anaemia virus in the genus Gyrovirus, however, the sequence similarity is minimal except for a short stretch at 3816-3851 of TA278. Currently the working group is proposing the full name for TTV as TorqueTenoVirus and the TTV-like mini virus as TorqueTenoMiniVirus (TTMV) in a new genus Anellovirus (ring). TTVs are prevalent in non-human primates and human TTV can cross-infect chimpanzees. Furthermore, TTV sequences have been detected in chickens, pigs, cows and sheep. TTV can be transmitted by mother-to-child infection. However, within a year after birth, the prevalence reaches the same level for children born to both TTV-positive and TTV-negative mothers even without breast-feeding. The noncoding region surrounding a short 113 nt GC-rich stretch and occupying approximately one-third of the genome is considered to contain the putative replication origin. Three mRNAs are expressed by TTV, 3.0 and 1.2 and 1.0 kb species. A protein translated from the 3.0 kb mRNA is considered to be the major capsid protein as well as replicase. The nature of the proteins translated by the other two mRNAs are still putative. Copyright © 2002 John Wiley & Sons, Ltd.",capsid protein;circular DNA;single stranded DNA;biodiversity;Circoviridae;DNA virus;nonhuman;review;sequence homology;taxonomy;Torque teno virus 1;virogenesis;virus classification,"Hino, S.",2002,,10.1002/rmv.351,0
795,Torque teno virus (TTV): Current status,"Torque teno virus (TTV), currently classified into the family Circoviridae, genus Anellovirus, was first found in a patient with non-A-E hepatitis. TTV has a single stranded circular DNA of ∼3.8 kb. TTVs are extraordinarily diverse, spanning five groups including SANBAN and SEN viruses. Torque teno mini virus (TTMV) with ∼2.9 kb genome also has wide variants. Recently, two related 2.2- and 2.6-kb species joined this community. Recombinations between variants are frequent. This extensive TTV diversity remains unexplained; it is unclear how TTVs could be viable, and why they require such genetic variation. An unequivocal culture system is still not available. TTVs are ubiquitous in > 90% of adults worldwide but no human pathogenicity of TTV has been fully established. Epidemiological surveys need to specify the variants being studied and clinical targets, and must calibrate the sensitivity of the assay used. Potentially interesting observations include a higher viral load in patients with severe idiopathic inflammatory myopathies, cancer and lupus. Active replication was also found in infants with acute respiratory diseases. TTV/ TTMV-related viruses were found in chimpanzees, apes, African monkeys and tupaias, and also in chickens, pigs, cows, sheep and dogs. Experimentally, rhesus monkeys were persistently infected by TTV, but only 1/53 chimpanzees. TTV transcribes three species of mRNAs, 3.0-, 1.2- and 1.0-kb in the ratio of 60:5:35. Recently, at least three mRNAs were shown in chicken anaemia virus. The genomic region -154/-76 contains a critical promoter. TTV seems to have at least three proteins; however, the definite functions of these proteins await further research work. Copyright © 2006 John Wiley & Sons, Ltd.",immunoglobulin;virus DNA;viral protein;acute respiratory tract disease;Anelloviridae;ape;calibration;malignant neoplasm;chicken;chimpanzee;cholestasis;Circoviridae;cow;disease severity;dog;gene function;gene structure;genetic variability;hematologic disease;hepatitis non A to E;human;idiopathic disease;liver disease;lung disease;myositis;nonhuman;pathogenicity;promoter region;protein function;review;rhesus monkey;RNA splicing;Scandentia;sensitivity analysis;sheep;standardization;pig;systemic lupus erythematosus;target cell;Torque teno virus 1;transcription regulation;virus culture;virus detection;virus genome;virus infection;virus load;virus recombination;virus replication,"Hino, S.;Miyata, H.",2007,,10.1002/rmv.524,0
796,Relationship of Torque teno virus to chicken anemia virus,"This chapter examines the correlation between Torque teno virus (TTV) and chicken anemia virus (CAV). Each has a circular single-stranded (ss)DNA genome with every one of its known open reading frames (ORF) on its antigenomic strand. This structure is distinct from those of circoviruses. The genomic sizes of TTV and CAV are different, 3.8 kb and 2.3 kb, respectively. While the spectrum of the TTV genome is enormously diverse, that of the CAV genome is quite narrow. Although a 36-nt stretch near the replication origin of TA278 TTV possesses more than 80% similarity to that of CAV, the sequence of the other genomic regions does not exhibit a significant similarity. Nevertheless, the relative allocation of ORFs on each frame in these viruses mimics each other. Three or more messenger RNA (mRNAs) are generated by transcription in both of them. The structural protein with the replicase domain is coded for by frame 1 in each virus, and a nonstructural protein with a phosphatase domain is coded for by frame 2. A protein on frame 3 in each virus induces apoptosis in transformed cells. Recently, we confirmed that apoptin is necessary for the replication of CAV. TTV has been proposed to constitute a new family, Anelloviridae. Considering these similarities and dissimilarities between CAV and TTV, it seems more reasonable to place CAV, the only member of genus Gyrovirus, into Anelloviridae together with TTV, or into a new independent family. © 2009 Springer.",apoptin;messenger RNA;phosphatase;protein VP3;single stranded DNA;structural protein;viral protein;Anelloviridae;apoptosis;Babuvirus;Circoviridae;correlation analysis;gene sequence;genetic transcription;genomics;human;Inoviridae;Maize streak virus;Microviridae;nonhuman;nucleotide sequence;open reading frame;plant virus;point mutation;priority journal;protein domain;protein expression;protein phosphorylation;review;Torque teno virus 1;transcription initiation;transcription regulation;virion;virus classification;virus replication,"Hino, S.;Prasetyo, A. A.",2009,,10.1007/978-3-540-70972-5_8,0
797,Conservation of L and 3C proteinase activities across distantly related aphthoviruses,"The foot-and-mouth disease virus (FMDV) leader (L) proteinase is an important virulence determinant in FMDV infections. It possesses two distinct catalytic activities: (i) C-terminal processing at the L/VP4 junction; and (ii) induction of the cleavage of translation initiation factor eIF4G, an event that inhibits cap-dependent translation in infected cells. The only other member of the Aphthovirus genus, equine rhinitis A virus (ERAV), also encodes an L protein, but this shares only 32% amino acid identity with its FMDV counterpart. Another more distantly related picornavirus, equine rhinitis B virus (ERBV), which is not classified as an aphthovirus, also encodes an L protein. Using in vitro transcription and translation analysis, we have shown that both ERAV and ERBV L proteins have C-terminal processing activity. Furthermore, expression of ERAV L, but not ERBV L, in BHK-21 cells resulted in the efficient inhibition of cap-dependent translation in these cells. We have shown that the EBAV and FMDV L proteinases induce cleavage of eIF4GI at very similar or identical positions. Interestingly, ERAV 3C also induces eIF4GI cleavage and again produces distinct products that co-migrate with those induced by FMDV 3C. The ERBV L proteinase does not induce eIF4GI cleavage, consistent with its inability to shut down cap-dependent translation. We have also shown that another unique feature of FMDV L, the stimulation of enterovirus internal ribosome entry site (IRES) activity, is also shared by the ERAV L proteinase but not by ERBV L. The functional conservation of the divergent ERAV and FMDV proteinases indicates the likelihood of a similar and important role for these enzymes in the pathogenesis of infections caused by these distantly related aphthoviruses.",glycine cleavage system;initiation factor;proteinase;viral protein;amino acid analysis;animal cell;Aphthovirus;carboxy terminal sequence;catalysis;controlled study;enzyme activity;foot and mouth disease;Foot and mouth disease virus;gene expression;genetic conservation;genetic transcription and translation;in vitro study;internal ribosome entry site;nonhuman;Picornaviridae;priority journal;protein degradation;protein function;review;virus classification;virus infection;virus transcription;virus virulence,"Hinton, T. M.;Ross-Smith, N.;Warner, S.;Belsham, G. J.;Crabb, B. S.",2002,,,0
798,"Epidemiology of vampire bat-transmitted rabies virus in Goias, central Brazil: re-evaluation based on G-L intergenic region","BACKGROUND: Vampire bat related rabies harms both livestock industry and public health sector in central Brazil. The geographical distributions of vampire bat-transmitted rabies virus variants are delimited by mountain chains. These findings were elucidated by analyzing a high conserved nucleoprotein gene. This study aims to elucidate the detailed epidemiological characters of vampire bat-transmitted rabies virus by phylogenetic methods based on 619-nt sequence including unconserved G-L intergenic region. FINDINGS: The vampire bat-transmitted rabies virus isolates divided into 8 phylogenetic lineages in the previous nucleoprotein gene analysis were divided into 10 phylogenetic lineages with significant bootstrap values. The distributions of most variants were reconfirmed to be delimited by mountain chains. Furthermore, variants in undulating areas have narrow distributions and are apparently separated by mountain ridges. CONCLUSIONS: This study demonstrates that the 619-nt sequence including G-L intergenic region is more useful for a state-level phylogenetic analysis of rabies virus than the partial nucleoprotein gene, and simultaneously that the distribution of vampire bat-transmitted RABV variants tends to be separated not only by mountain chains but also by mountain ridges, thus suggesting that the diversity of vampire bat-transmitted RABV variants was delimited by geographical undulations.",,"Hirano, S.;Itou, T.;Carvalho, A. A.;Ito, F. H.;Sakai, T.",2010,Nov 08,,0
799,Whole genome analysis of a novel neurotropic bovine astrovirus detected in a Japanese black steer with non-suppurative encephalomyelitis in Japan,"While neurotropic bovine astroviruses (BoAstVs) have been identified in North America and Europe, their presence has never been reported in Asia. In this study, we detected BoAstV in the brain of a steer showing neurological signs. Phylogenetic analysis revealed that the identified virus belongs to the Virginia/Human-Mink-Ovine Glade, which contains most of the neurotropic astroviruses including the neurotropic BoAstVs. Similarity plot analysis showed that the virus was closely related to the American BoAstV NeuroS1 strain with respect to the ORF regions and to the European BoAstV CH13 strain in the 3' untranslated region, suggesting the occurrence of intra-genotypic recombination events.",RESPIRATORY-DISEASE;ENCEPHALITIS;CATTLE;IDENTIFICATION;METAGENOMICS;INFECTION;GENOTYPE;CANADA;MINK,"Hirashima, Y.;Okada, D.;Shibata, S.;Yoshida, S.;Fujisono, S.;Omatsu, T.;Mizutani, T.;Nagai, M.",2018,Oct,,0
800,"Phylogeny and natural history of the primate lentiviruses, SIV and HIV","Studies of primate lentivirus phylogeny over the past decade have established a minimum of five related, but genetically distinct, groups of simian immunodeficiency virus (SIV), each originating from a different African primate species. The hypothesis that HIV-2 (and SIVmac) arose by cross-species transmission from sooty mangabeys (Cercocebus atys) has been strengthened by a more detailed characterization of the SIVsm/SIVmac/HIV-2 group of viruses. SIV from all four subspecies of African green monkeys (SIVagm) have been characterized with an apparent chimeric genome structure of SIVagm from West African green monkeys. Although these naturally infected primates remain healthy, cross-species transmission to other primate species may result in immunodeficiency, as caused by SIVsm infection of macaque monkeys (Macaca sp.) and recently, SIVagm infection of pig-tailed macaques (M. nemestrina). Studies of variation within infected individuals have been facilitated by adaptation of the techniques of heteroduplex analysis and single-stranded conformational polymorphism of PCR generated fragments.",Cercocebus;Cercopithecidae;Human immunodeficiency virus;Human immunodeficiency virus 2;Lentivirus;Macaca;nonhuman;phylogeny;polymerase chain reaction;priority journal;review;Simian immunodeficiency virus;single strand conformation polymorphism;viral genetics;virus classification;virus infection;virus transmission,"Hirsch, V. M.;Dapolito, G.;Goeken, R.;Campbell, B. J.",1995,,10.1016/0959-437x(95)80014-v,0
801,The relationship of the receptors of a new strain of virus to those of the mumps-NDV-influenza group,"The interrelationships of the cellular receptors and the hemagglutinin inhibitors of a new strain of virus (1233) to members of the mumps-Newcastle disease-influenza group have been investigated. It was found that strain. 1233 does not destroy the receptors or inhibitors of the other group, nor does the latter destroy 1233 receptors or inhibitor. The sole exception to this statement was a moderate destruction of 1233 inhibitor in egg white by Newcastle disease virus. The classification of strain 1233 was discussed in the light of this evidence, evidence which tends to place strain 1233 in a different category from that of any other strain of the MNI group.","Animals;Humans;*Influenza, Human;*Mumps;*Newcastle Disease;*Newcastle disease virus;*Parotitis","Hirst, G. K.",1950,Feb,,0
802,Establishment of the concept of prion diseases,"The history of prion diseases is derived from descriptions of scrapie of sheep and goats in the eighteenth century. In 1920, Creutzfeldt-Jakob disease was reported as the first case of human prion diseases, which was recognized as subacute spongiform encephalopathy, one of neurodegenerative diseases. Afterwards, many transmission experiments were performed, which lead to the establishment of the fundamental concept, transmissible spongiform encephalopathy(TSE). The infectious agent was supposed to be a novel virus, so TSE was classified into slow virus infection. In 1982, Prusiner investigated the infectious fraction of scrapie-infected brain homogenate, defined the infectious agent as proteinaceous infectious particles that resist inactivation by procedures that modify nucleic acid and newly designated as prion after virion in viral infection.",animal;bovine;classification;Creutzfeldt Jakob disease;goat;history;human;prion;prion disease;review;scrapie;sheep;slow virus disease,"Hizume, M.;Mizusawa, H.",2007,,,0
803,Book Review: Diseases of Poultry,,,"Hoerr, F. J.",2004,,,0
804,"Novel orthobunyavirus in cattle, Europe, 2011","In 2011, an unidentifi ed disease in cattle was reported in Germany and the Netherlands. Clinical signs included fever, decreased milk production, and diarrhea. Metagenomic analysis identifi ed a novel orthobunyavirus, which subsequently was isolated from blood of affected animals. Surveillance was initiated to test malformed newborn animals in the affected region.",article;controlled study;dairy cattle;diarrhea;disease surveillance;fever;gene sequence;Germany;metagenomics;milk production;new species;newborn;nonhuman;Orthobunyavirus;Orthobunyavirus infection;virus genome;virus identification;virus isolation,"Hoffmann, B.;Scheuch, M.;Höper, D.;Jungblut, R.;Holsteg, M.;Schirrmeier, H.;Eschbaumer, M.;Goller, K. V.;Wernike, K.;Fischer, M.;Breithaupt, A.;Mettenleiter, T. C.;Beer, M.",2012,,10.3201/eid1803.111905,1
805,Differences in virus receptor for type I and type II feline infectious peritonitis virus,"Feline infectious peritonitis viruses (FIPVs) are classified into type I and type II serogroups. Here, we report that feline aminopeptidase N (APN), a cell-surface metalloprotease on the intestinal, lung and kidney epithelial cells, is a receptor for type II FIPV but not for type I FIPV. A monoclonal antibody (MAb) R-G-4, which blocks infection of Felis catus whole fetus (fcwf-4) cells by type II FIPV, was obtained by immunizing mice with fcwf-4 cells which are highly susceptible to FIPV. This MAb also blocked infection of fcwf-4 cells by type II feline enteric coronavirus (FECV), canine coronavirus (CCV), and transmissible gastroenteritis virus (TGEV). On the other hand, it did not block infection by type I FIPVs. MAb R-G-4 recognized a polypeptide of relative molecular mass 120-130 kDa in feline intestinal brush-border membrane (BBM) proteins. The polypeptide possessed aminopeptidase activity, and the first 15 N-terminal amino acid sequence was identical to that of the feline APN. Feline intestinal BBM proteins and the polypeptide reacted with MAb R-G-4 (feline APN) inhibited the infectivity of type II FIPV, type II FECV, CCV and TGEV to fcwf-4 cells, but did not inhibit the infectivity of type I FIPVs.","Amino Acid Sequence;Animals;Antibodies, Monoclonal;CD13 Antigens/ge [Genetics];CD13 Antigens/im [Immunology];CD13 Antigens/ph [Physiology];Cats;Cells, Cultured;Coronavirus/cl [Classification];Coronavirus/py [Pathogenicity];Coronavirus, Canine/py [Pathogenicity];Coronavirus, Feline/cl [Classification];*Coronavirus, Feline/py [Pathogenicity];Dogs;Feline Panleukopenia Virus/py [Pathogenicity];Humans;Intestines/en [Enzymology];Intestines/vi [Virology];Membrane Proteins/ge [Genetics];Membrane Proteins/im [Immunology];Membrane Proteins/ph [Physiology];Mice;Microvilli/en [Enzymology];Microvilli/vi [Virology];Molecular Sequence Data;Receptors, Virus/ge [Genetics];Receptors, Virus/im [Immunology];*Receptors, Virus/ph [Physiology];Swine;Transmissible gastroenteritis virus/py [Pathogenicity];0 (Antibodies, Monoclonal);0 (Membrane Proteins);0 (Receptors, Virus)","Hohdatsu, T.;Izumiya, Y.;Yokoyama, Y.;Kida, K.;Koyama, H.",1998,,,0
806,"Characterization of monoclonal antibodies against feline infectious peritonitis virus type II and antigenic relationship between feline, porcine, and canine coronaviruses","Seven monoclonal antibodies (MAbs) with neutralizing activity against feline infectious peritonitis virus (FIPV) strain 79-1149 (type II) were prepared. When the polypeptide specificity recognized by these monoclonal antibodies (MAbs) was investigated by Western immunoblotting, all of the MAbs reacted with peplomer glycoprotein (S) of the virus. By competitive binding assay these MAbs were found to recognize at least 3 different epitopes. The reactivity of these MAbs with 6 viruses classified as FIPV type I (UCD-1, UCD-2, UCD-3, UCD-4, NW-1, and Black), feline enteric coronavirus (FECV) type II strain 79-1683, canine coronavirus (CCV) strain 1-71, and transmissible gastroenteritis virus (TGEV) strains TO-163 and SH was examined by neutralization tests. All MAbs neutralized FECV strain 79-1683, CCV strain 1-71, and TGEV strains TO-163 and SH, while they did not neutralize the 6 FIPV type I viruses. Moreover, the MAb against TGEV strain TO-163, which has strong neutralizing activity against 7 TGEV viruses, neutralized CCV strain 1-71, FECV strain 79-1683, and FIPv strain 79-1146, but did not neutralize the 6 FIPV type I viruses. These results demonstrated that there are at least 3 epitopes involved in the neutralization of FIPV type II strain 79-1146, and that these epitopes are not present in FIPV type I viruses but are present in FECV strain 79-1683 which does not induce feline infectious peritonitis, TGEV strains TO-163 and SH, and CCV strain 1-71. These results suggest the presence of 2 serotypes of FIPV which can be clearly distinguished by the neutralization test using MAbs.","Animals;*Antibodies, Monoclonal/im [Immunology];Antibodies, Viral/cl [Classification];*Antibodies, Viral/im [Immunology];Antigens, Viral/im [Immunology];Binding, Competitive;Blotting, Western;Cats;*Coronaviridae/im [Immunology];Dogs;Electrophoresis, Polyacrylamide Gel;Epitopes/im [Immunology];Hybridomas;Neutralization Tests;Swine;*Transmissible gastroenteritis virus/im [Immunology];0 (Antibodies, Monoclonal);0 (Antibodies, Viral);0 (Antigens, Viral);0 (Epitopes)","Hohdatsu, T.;Okada, S.;Koyama, H.",1991,,,0
807,Nipah virus classification via fractal dimension & shannon entropy,,,"Holden, T.;Gadura, N.;Cheung, E.",2010,,,0
808,Discovering the phylodynamics of RNA viruses,,hemagglutinin;sialidase;virus DNA;virus RNA;avian influenza;biodiversity;consensus sequence;DNA sequence;epidemiological data;foot and mouth disease;genetic variability;geographic distribution;host;human;Influenza virus;Influenza A virus;Influenza A virus (H3N2);Influenza B virus;metagenomics;mixed infection;molecular dynamics;molecular epidemiology;molecular evolution;molecular phylogeny;nonhuman;polymerase chain reaction;qualitative analysis;quantitative analysis;review;RNA virus;RNA virus infection;virus genome;virus mutation;virus strain;virus transmission,"Holmes, E. C.;Grenfell, B. T.",2009,,10.1371/journal.pcbi.1000505,0
809,Tembusu-like flavivirus (Perak virus) as the cause of neurological disease outbreaks in young Pekin ducks,"A neurological disease of young Pekin ducks characterized by ataxia, lameness, and paralysis was observed at several duck farms in Malaysia in 2012. Gross pathological lesions were absent or inconsistent in most of the cases, but severe and consistent microscopic lesions were found in the brain and spinal cord, characterized by non-purulent panencephalomyelitis. Several virus isolates were obtained in embryonated duck eggs and in cell cultures (Vero and DF-1) inoculated with the brain homogenates of affected ducks. After exclusion of other viruses, the isolates were identified as a flavivirus by flavivirus-specific reverse transcription-polymerase chain reaction (RT-PCR) assays. Inoculation of 2-week-old Pekin ducks with a flavivirus isolate by the subcutaneous or intramuscular route resulted in typical clinical signs and histological lesions in the brain and spinal cord. The inoculated virus was detected by RT-PCR from organ samples of ducks with clinical signs and histological lesions. With a few days delay, the disease was also observed among co-mingled contact control birds. Phylogenetic analysis of NS5 and E gene sequences proved that the isolates were representatives of a novel phylogenetic group within clade XI (Ntaya virus group) of the Flavivirus genus. This Malaysian Duck Tembusu Virus (DTMUV), named Perak virus, has moderate genomic RNA sequence similarity to a related DTMUV identified in China. In our experiment the Malaysian strain of DTMUV could be transmitted in the absence of mosquito vectors. These findings may have implications for the control and prevention of this emerging group of flaviviruses.",animal;Chlorocebus aethiops;DNA sequence;duck;epidemic;Flavivirus;Flavivirus infection;genetics;geography;high throughput sequencing;isolation and purification;Malaysia;molecular genetics;neurologic disease;nucleotide sequence;paralysis;pathology;phylogeny;bird disease;Vero cell line;veterinary medicine;virology;virus genome,"Homonnay, Z. G.;Kovács, E. W.;Bányai, K.;Albert, M.;Fehér, E.;Mató, T.;Tatár-Kis, T.;Palya, V.",2014,,10.1080/03079457.2014.973832,0
810,The high genetic variation of viruses of the genus Nairovirus reflects the diversity of their predominant tick hosts,"The genus Nairovirus (family Bunyaviridae) contains seven serogroups consisting of 34 predominantly tick-borne viruses, including several associated with severe human and livestock diseases [e.g., Crimean Congo hemorrhagic fever (CCHF) and Nairobi sheep disease (NSD), respectively]. Before this report, no comparative genetic studies or molecular detection assays had been developed for this virus genus. To characterize at least one representative from each of the seven serogroups, reverse transcriptase-polymerase chain reaction (RT-PCR) primers targeting the L polymerase-encoding region of the RNA genome of these viruses were successfully designed based on conserved amino acid motifs present in the predicted catalytic core region. Sequence analysis showed the nairoviruses to be a highly diverse group, exhibiting up to 39.4% and 46.0% nucleotide and amino acid identity differences, respectively. Virus genetic relationships correlated well with serologic groupings and with tick host associations. Hosts of these viruses include both the hard (family Ixodidae) and soft (family Argasidae) ticks. Virus phylogenetic analysis reveals two major monophyletic groups: hard tick and soft tick-vectored viruses. In addition, viruses vectored by Ornithodoros, Carios, and Argas genera ticks also form three separate monophyletic lineages. The striking similarities between tick and nairovirus phylogenies are consistent with possible coevolution of the viruses and their tick hosts. Fossil and phylogenetic data placing the hard tick-soft tick divergence between 120 and 92 million years ago suggest an ancient origin for viruses of the genus Nairovirus. © 2003 Elsevier Inc. All rights reserved.",virus vector;amino acid sequence;Argas;article;coevolution;genetic variability;Nairovirus;nonhuman;nucleotide sequence;phylogeny;priority journal;reverse transcription polymerase chain reaction;sequence analysis;tick;virus detection;virus genome,"Honig, J. E.;Osborne, J. C.;Nichol, S. T.",2004,,10.1016/j.virol.2003.09.021,0
811,"Rapid detection, characterization, and enumeration of foodborne pathogens","As food safety management further develops, microbiological testing will continue to play an important role in assessing whether Food Safety Objectives are achieved. However, traditional microbiological culture-based methods are limited, particularly in their ability to provide timely data. The present review discusses the reasons for the increasing interest in rapid methods, current developments in the field, the research needs, and the future trends. The advent of biotechnology has introduced new technologies that led to the emergence of rapid diagnostic methods and altered food testing practices. Rapid methods are comprised of many different detection technologies, including specialized enzyme substrates, antibodies and DNA, ranging from simple differential plating media to the use of sophisticated instruments. The use of non-invasive sampling techniques for live animals especially came into focus with the 1990s outbreak of bovine spongiform encephalopathy that was linked to the human outbreak of Creutzfeldt Jakob's Disease. Serology is still an important tool in preventing foodborne pathogens to enter the human food supply through meat and milk from animals. One of the primary uses of rapid methods is for fast screening of large number of samples, where most of them are expected to be test-negative, leading to faster product release for sale. This has been the main strength of rapid methods such as real-time Polymerase Chain Reaction (PCR). Enrichment PCR, where a primary culture broth is tested in PCR, is the most common approach in rapid testing. Recent reports show that it is possible both to enrich a sample and enumerate by pathogen-specific real-time PCR, if the enrichment time is short. This can be especially useful in situations where food producers ask for the level of pathogen in a contaminated product. Another key issue is automation, where the key drivers are miniaturization and multiple testing, which mean that not only one instrument is flexible enough to test for many pathogens but also many pathogens can be detected with one test. The review is mainly based on the author's scientific work that has contributed with the following new developments to this field: (i) serologic tests for large-scale screening, surveillance, or eradication programs, (ii) same-day detection of Salmonella that otherwise was considered as difficult to achieve, (iii) pathogen enumeration following a short log-phase enrichment, (iv) detection of foodborne pathogens in air samples, and finally (v) biotracing of pathogens based on mathematical modeling, even in the absence of isolate. Rapid methods are discussed in a broad global health perspective, international food supply, and for improvement of quantitative microbial risk assessments. The need for quantitative sample preparation techniques, culture-independent, metagenomic-based detection, online monitoring, a global validation infrastructure has been emphasized. The cost and ease of use of rapid assays remain challenging obstacles to surmount. © 2011 The Author. APMIS © 2011 APMIS.",DNA;enzyme antibody;air sampling;article;automation;bovine spongiform encephalopathy;Campylobacter;catering service;Creutzfeldt Jakob disease;developing country;enzyme linked immunosorbent assay;enzyme substrate;epidemic;food biotechnology;food industry;food safety;health;health program;health survey;human;hygiene;Influenza A virus (H1N1);information processing;investment;mathematical model;meat;metagenomics;microbiological examination;microorganism detection;milk;non invasive procedure;nonhuman;online monitoring;organization;pathogen load;priority journal;quantitative analysis;real time polymerase chain reaction;risk assessment;Salmonella;screening;sensitivity analysis;serology;severe acute respiratory syndrome;validation process;World Health Organization,"Hoorfar, J.",2011,,10.1111/j.1600-0463.2011.02767.x,0
812,Biological and biochemical characterization of sheep scrapie in Japan,"Due to the apparent absence of an agent-specific nucleic acid genome, scrapie strains cannot be classified by genome characterization, which is commonly used for the classification of many viruses. However, scrapie strains can be distinguished to some extent by biological properties such as transmissibility to experimental animals and distribution of neuropathological lesions and by biochemical properties such as the molecular mass and relative protease-resistance of the disease-specific isoform of prion protein (PrPSc). In order to preliminarily characterize the scrapie strains that are prevalent in Japan, we analyzed the transmissibility of sheep scrapie isolates to mice and the relative proteinase K (PK) resistance of the corresponding PrPSc. The results indicate that Japanese scrapie strains can be divided into at least three groups based on biological and biochemical properties. The first group includes isolates which cause disease in mice with an incubation period of ∼400 days and possess PrPSc with relatively high PK resistance. Isolates of the second group contain PrPSc that is highly resistant to PK digestion but transmit poorly to mice. The final group consists of isolates that cause disease in mice with an incubation period of less than 300 days and are associated with PrPSc with reduced PK resistance. Sheep scrapie has occurred sporadically in Japan since 1982, with only ∼60 officially reported cases so far. However, the diversity of scrapie strains in the field suggested by our data raises the concern that a scrapie strain similar to the parental agent of bovine spongiform encephalopathy could exist or emerge in Japan. Thus, continuous surveillance for scrapie will be required to prevent the further spread of scrapie, not only among the sheep population but also to other species, and to eliminate any potential risk of sheep scrapie to public health.",nucleic acid;prion protein;animal experiment;animal model;animal tissue;article;bovine spongiform encephalopathy;brain homogenate;controlled study;genotype;immunoblotting;Japan;mouse;nonhuman;priority journal;scrapie;scrapie agent;sheep;strain difference;strain identification;virus genome;virus isolation;virus transmission,"Horiuchi, M.;Nemoto, T.;Ishiguro, N.;Furuoka, H.;Mohri, S.;Shinagawa, M.",2002,,10.1128/jcm.40.9.3421-3426.2002,0
813,Rabies in Iraq: Trends in Human Cases 2001-2010 and Characterisation of Animal Rabies Strains from Baghdad,"Control of rabies requires a consistent supply of dependable resources, constructive cooperation between veterinary and public health authorities, and systematic surveillance. These are challenging in any circumstances, but particularly during conflict. Here we describe available human rabies surveillance data from Iraq, results of renewed sampling for rabies in animals, and the first genetic characterisation of circulating rabies strains from Iraq. Human rabies is notifiable, with reported cases increasing since 2003, and a marked increase in Baghdad between 2009 and 2010. These changes coincide with increasing numbers of reported dog bites. There is no laboratory confirmation of disease or virus characterisation and no systematic surveillance for rabies in animals. To address these issues, brain samples were collected from domestic animals in the greater Baghdad region and tested for rabies. Three of 40 brain samples were positive using the fluorescent antibody test and hemi-nested RT-PCR for rabies virus (RABV). Bayesian phylogenetic analysis using partial nucleoprotein gene sequences derived from the samples demonstrated the viruses belong to a single virus variant and share a common ancestor with viruses from neighbouring countries, 22 (95% HPD 14-32) years ago. These include countries lying to the west, north and east of Iraq, some of which also have other virus variants circulating concurrently. These results suggest possible multiple introductions of rabies into the Middle East, and regular trans-boundary movement of disease. Although 4000 years have passed since the original description of disease consistent with rabies, animals and humans are still dying of this preventable and neglected zoonosis. © 2013 Horton et al.",virus nucleoprotein;adolescent;animal experiment;animal tissue;article;bovine;child;disease surveillance;dog;dog bite;encephalitis;female;fluorescent antibody technique;gene sequence;genetic trait;health survey;human;incidence;infant;Iraq;laboratory diagnosis;major clinical study;male;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;prophylaxis;rabies;Rabies virus;reverse transcription polymerase chain reaction;unindexed sequence;virus characterization,"Horton, D. L.;Ismail, M. Z.;Siryan, E. S.;Wali, A. R. A.;Ab-dulla, H. E.;Wise, E.;Voller, K.;Harkess, G.;Marston, D. A.;McElhinney, L. M.;Abbas, S. F.;Fooks, A. R.",2013,,10.1371/journal.pntd.0002075,0
814,A new family of vertebrate viruses: Toroviridae,"The proposed family Toroviridae is characterized by enveloped, peplomer-bearing particles containing an elongated tubular nucleocapsid with helical symmetry. The capsid may bend into an open torus, conferring a biconcave disk or kidney-shaped morphology to the virion (largest diameter 120-140 nm) or the capsid may be straight, resulting in a rod-shaped particle (35 x 170 nm). Morphogenesis is by budding of preformed nucleocapsids through membranes mainly of the Golgi system and of the rough endoplasmic reticulum. Berne virus, which is proposed as the family prototype, contains a single strand of infectious positive-sense RNA, M(r) about 6.5 x 106, which is polyadenylated. The RNA is surrounded by the major nucleocapsid phosphoprotein (M(r) about 20,000) which, in turn, is enveloped by a membrane containing one major protein (M(r) 22,000) and a phosphoprotein (M(r) 37,000). The viral peplomers, about 20 nm long, carry determinants for neutralization and hemagglutination; they are formed by a polydisperse N-glycosylated protein (M(r) 75,000-100,000). Four major subgenomic polyadenylated RNAs have been identified in infected cells, with M(r)s of 3.0, 0.71, 0.46 and 0.26 x 106. Torovirus replication is inhibited by actinomycin D, alpha-amanitin and pre-irradiation of the host cell with UV light. All toroviruses identified so far cause enteric infections and are probably transmitted by the fecal-oral route. Serologic relationships between equine, bovine and human toroviruses have been demonstrated.",berne virus;classification;diarrhea;digestive system;etiology;human;nonhuman;priority journal;virus classification,"Horzinek, M. C.;Flewett, T. H.;Saif, L. J.",1987,,,0
815,Prevalence of bovine viral diarrhea virus in dairy cattle herds in eastern China,"Bovine viral diarrhea virus (BVDV) is a worldwide spreading pestivirus affecting cattle and other ruminants; however, there have been few reports on epidemiologic investigation of BVDV in eastern China. In this study, bulk tank milk from 36 herds of dairy cattle in eastern China was submitted to serological investigations, 77.8% of herds was BVDV antibody positive. Individual animal status in two herds was further investigated collecting blood samples, the positive ratio was 49.74% and 24.64%, and the average positive ratio of calves, heifers, and lactating cows was 15.94%, 40.16%, and 41.7%, respectively. Moreover, clinical survey was carried out among 8170 dairy cattle from 36 herds, for diarrhea syndrome, respiratory problems and reproductive failure, and pathogens of all clinical cattle were further investigated. The results showed that BVDV was one of the main pathogen, which infected animals combining with various other viruses. Then, nine BVDV strains were isolated; phylogenetic analysis showed that BVDV subtypes currently circulating in eastern China were BVDV 1a and BVDV 1c. In addition, out of 377 cows tested, the 1.86% detected positive to the BVDV antigen. This study provided the foundation of further study on vaccination and control strategies of BVDV in eastern China.",,"Hou, P.;Zhao, G.;Wang, H.;He, H.",2018,Nov 19,,0
816,Transcriptome Analysis of Rabbit Spleen with Hog Cholera Lapinized Virus Infection Based on High-throughput Sequencing Technology,"In the current study, rabbit spleen was analysed at 12 h,24h,30 h,36h,and 48hpost-infection with hog cholera lapinized virus(C strain)using high-throughput sequencing. The rabbit genome was used as a reference to identify differentially expressed genes(DEGs)at different time points post-infection. The top 10 DEGs were filtered based on significance, and we searched for their biological functions through the Uniprot and NCBI databases. The former three time points have 10co-expressing genes, many of which have a relationship to immunity and inflammation. The latter two time points for the top 10 DEGs are identical, and B2 M,RLA-DR-ALPHA,CD74,and IGJ are involved in the antiviral immune response. GO functional annotation revealed that in biological processes at each time point,except for 24hpost-infection,the immune response has the most terms, followed by metabolism and regulation. According to the KEGG database, the DEGs for 24hpost-infection were enriched for the RIG-I-like receptor signaling pathway and the DEGs for 30hpost-infection were found to have a focal adhesion and ECM-receptor interaction pathway. Moreover, the DEGs for 36 hand 48hpost-infection have seven identical pathways, of which were directly or indirectly related to the antiviral response. These pathways included the proteasome, lysosome, ribosome, chemokine signaling pathways, B cell receptor signaling pathway, antigen processing, and presentation pathway, and the Fc gamma R-mediated phagocytosis pathway.These results provide novel insight into the gene expression in rabbit spleens post-infection with C strain, and provide a theoretical basis for further understanding of the molecular mechanisms by which rabbits adapt to infection with C strain.",viral protein;animal;classical swine fever;Classical swine fever virus;classification;gene expression profiling;genetics;high throughput sequencing;isolation and purification;Leporidae;metabolism;physiology;pig;spleen;virology,"Hou, Y.;Zhao, D.;Liu, G.;He, F.;Liu, B.;Fu, S.;Hao, Y.;Zhang, W.",2016,,,0
817,Molecular and phylogenetic analyses of a new Amphotropic murine leukemia virus (MuLV-1313),"Background: The amphotropic murine leukemia viruses (MuLV-A's) are naturally occurring, exogenously acquired gammaretroviruses that are indigenous to the Southern California wild mice. These viruses replicate in a wide range of cell types including human cells in vitro and they can cause both hematological and neurological disorders in feral as well as in the inbred laboratory mice. Since MuLV-A's also exhibit discrete interference and neutralization properties, the envelope proteins of these viruses have been extremely useful for studying virus-host cell interactions and as vehicles for transfer of foreign genes into a variety of hosts including human cells. However, the genomic structure of any of the several known MuLV-A's has not been established and the evolutionary relationship of amphotropic retroviruses to the numerous exogenous or endogenous MuLV strains remains elusive. Herein we present a complete genetic structure of a novel amphotropic virus designated MuLV-1313 and demonstrate that this retrovirus together with other MuLV-A's belongs to a distinct molecular, biological and phylogenetic class among the MuLV strains isolated from a large number of the laboratory inbred or feral mice. Results: The host range of MuLV-1313 is similar to the previously isolated MuLV-A's except that this virus replicates efficiently in mammalian as well as in chicken cells. Compared to ENV proteins of other MuLV-A's (4070A, 1504A and 10A-1), the gp70 protein of MuLV-1313 exhibits differences in its signal peptides and the proline-rich hinge regions. However, the MuLV-1313 envelope protein is totally unrelated to those present in a broad range of murine retroviruses that have been isolated from various inbred and feral mice globally. Genetic analysis of the entire MuLV-1313 genome by dot plot analyses, which compares each nucleotide of one genome with the corresponding nucleotide of another, revealed that the genome of this virus, with the exception of the env gene, is more closely related to the biologically distinct wild mouse ecotropic retrovirus (Cas-Br-E) isolated from another region of the Southern California, than to any of the 15 MuLV strains whose full-length sequences are present in the GenBank. This finding was corroborated by phylogenetic analyses and hierarchical clustering of the entire genomic sequence of MuLV-1313, which also placed all MULV-A's in a genetically distinct category among the large family of retroviruses isolated from numerous mouse strains globally. Likewise, construction of separate dendrograms for each of the Gag, Pol and Env proteins of MuLV-1313 demonstrated that the amphotropic retroviruses belong to a phylogenetically exclusive group of gammaretroviruses compared to all known MuLV strains. Conclusion: The molecular, biological and phylogenetic properties of amphotropic retroviruses including MuLV-1313 are distinct compared to a large family of exogenously- or endogenously-transmitted ecotropic, polytropic and xenotropic MuLV strains of the laboratory and feral mice. Further, both the naturally occurring amphotropic and a biologically discrete ecotropic retrovirus of the Southern California wild mice are more closely related to each other on the evolutionary tree than any other mammalian gammaretrovirus indicating a common origin of these viruses. This is the first report of a complete genomic analysis of a unique group of phylogenetically distinct amphotropic virus. © 2006 Howard et al; licensee BioMed Central Ltd.",amino acid;virus envelope protein;amino acid sequence;article;biodiversity;controlled study;gene structure;genetic analysis;genome;genome analysis;in vitro study;Murine leukemia virus;nonhuman;nucleotide sequence;phylogeny;Retroviridae;structure analysis;virus cell interaction;virus recombinant;virus strain;virus transmission,"Howard, T. M.;Sheng, Z.;Wang, M.;Wu, Y.;Rasheed, S.",2006,,10.1186/1743-422x-3-101,0
818,"Avian hepatitis E virus in chickens, Taiwan, 2013","A previously unidentified strain of avian hepatitis E virus (aHEV) is now endemic among chickens in Taiwan. Analysis showed that the virus is 81.5%-86.5% similar to other aHEVs. In Taiwan, aHEV infection has been reported in chickens without aHEV exposure, suggesting transmission from asymptomatic cases or repeated introduction through an unknown common source(s).","Animals;*Chickens/vi [Virology];Genes, Viral;Genotype;*Hepatitis, Viral, Animal/ep [Epidemiology];*Hepevirus/cl [Classification];Hepevirus/ge [Genetics];Phylogeny;*RNA Virus Infections/ve [Veterinary];Taiwan/ep [Epidemiology]","Hsu, I. W.;Tsai, H. J.",2014,Jan,,0
819,Detection of diverse novel astroviruses from small mammals in China,"Astroviruses infect humans and many animal species and cause gastroenteritis. To extensively understand the distribution and genetic diversity of astrovirus in small mammals, we tested 968 anal swabs from 39 animal species, most of which were bats and rodents. We detected diverse astroviruses in 10 bat species, including known bat astroviruses and a large number of novel viruses. Meanwhile, novel groups of astroviruses were identified in three wild rodent species and a remarkably high genetic diversity of astrovirus was revealed in Eothenomys cachinus. We detected astroviruses in captive-bred porcupines and a nearly full-length genome sequence was determined for one strain. Phylogenetic analysis of the complete ORF2 sequence suggested that this strain may share a common ancestor with porcine astrovirus type 2. Moreover, to our knowledge, this study reports the first discovery of astroviruses in shrews and pikas. Our results provide new insights for understanding these small mammals as natural reservoirs of astroviruses.",GASTROENTERITIS;IDENTIFICATION;VIRUSES;VIROME;PIGS;BATS;DISEASES;HUMANS,"Hu, B.;Chmura, A. A.;Li, J. L.;Zhu, G. J.;Desmond, J. S.;Zhang, Y. Z.;Zhang, W.;Epstein, J. H.;Daszak, P.;Shi, Z. L.",2014,Nov,,0
820,Avian influenza virus and Newcastle disease virus (NDV) surveillance in commercial breeding farm in China and the characterization of Class I NDV isolates,"In order to determine the actual prevalence of avian influenza virus (AIV) and Newcastle disease virus (NDV) in ducks in Shandong province of China, extensive surveillance studies were carried out in the breeding ducks of an intensive farm from July 2007 to September 2008. Each month cloacal and tracheal swabs were taken from 30 randomly selected birds that appeared healthy. All of the swabs were negative for influenza A virus recovery, whereas 87.5% of tracheal swabs and 100% cloacal swabs collected in September 2007, were positive for Newcastle disease virus isolation. Several NDV isolates were recovered from tracheal and cloacal swabs of apparently healthy ducks. All of the isolates were apathogenic as determined by the MDT and ICPI. The HN gene and the variable region of F gene (nt 47-420) of four isolates selected at random were sequenced. A 374. bp region of F gene and the full length of HN gene were used for phylogenetic analysis. Four isolates were identified as the same isolate based on nucleotide sequences identities of 99.2-100%, displaying a closer phylogenetic relationship to lentogenic Class I viruses. There were 1.9-9.9% nucleotide differences between the isolates and other Class I virus in the variable region of F gene (nt 47-420), whereas there were 38.5-41.2% nucleotide difference between the isolates and Class II viruses. The amino acid sequences of the F protein cleavage sites in these isolates were 112-ERQERL-117. The full length of HN gene of these isolates was 1851. bp, coding 585 amino acids. The homology analysis of the nucleotide sequence of HN gene indicated that there were 2.0-4.2% nucleotide differences between the isolates and other Class I viruses, whereas there were 29.5-40.9% differences between the isolates and Class II viruses. The results shows that these isolates are not phylogenetically related to the vaccine strain (LaSota). This study adds to the understanding of the ecology of influenza viruses and Newcastle disease viruses in ducks and emphasizes the need for constant surveillance in times of an ongoing and expanding epidemic of AIV and NDV. © 2010 Elsevier B.V.",vaccine;virus RNA;amino acid sequence;article;avian influenza virus;bird;breeding;China;cloaca;duck;ecology;epidemic;gene sequence;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;protein cleavage;sequence homology;trachea;virus isolation,"Hu, B.;Huang, Y.;He, Y.;Xu, C.;Lu, X.;Zhang, W.;Meng, B.;Yan, S.;Zhang, X.",2010,,10.1016/j.vetmic.2010.01.003,0
821,Genetic diversity and positive selection analysis of classical swine fever virus envelope protein gene E2 in East China under C-strain vaccination,"Classical swine fever virus (CSFV) causes an economically important and highly contagious disease of pigs worldwide. C-strain vaccination is one of the most effective ways to contain this disease. Since 2014, sporadic CSF outbreaks have been occurring in some C-strain vaccinated provinces of China. To decipher the disease etiology, 25 CSFV E2 genes from 169 clinical samples were cloned and sequenced. Phylogenetic analyses revealed that all 25 isolates belonged to subgenotype 2.1. Twenty-three of the 25 isolates were clustered in a newly defined subgenotype, 2.1d, and shared some consistent molecular characteristics. To determine whether the complete E2 gene was under positive selection pressure, we used a site-by-site analysis to identify specific codons that underwent evolutionary selection, and seven positively selected codons were found. Three positively selected sites (amino acids 17, 34, and 72) were identified in antigenicity-relevant domains B/C of the amino-terminal half of the E2 protein. In addition, another positively selected site (amino acid 200) exhibited a polarity change from hydrophilic to hydrophobic, which may change the antigenicity and virulence of CSFV. The results indicate that the circulating CSFV strains in Shandong province were mostly clustered in subgenotype 2.1d. Moreover, the identification of these positively selected sites could help to reveal molecular determinants of virulence or pathogenesis, and to clarify the driving force of CSFV evolution in East China.",glycoprotein E2;amino acid sequence;animal tissue;article;bleeding;cell proliferation;China;classical swine fever;Classical swine fever virus;controlled study;DNA sequence;gene mutation;genetic identification;genetic similarity;genetic variability;genotype;glia cell;glycoprotein E2 gene;histology;Kikuchi disease;lymphocytic infiltration;maximum likelihood method;nonhuman;nucleic acid base substitution;nucleotide sequence;pig;reverse transcription polymerase chain reaction;sequence alignment;vaccination;virus encephalitis;virus gene;virus pathogenesis,"Hu, D.;Lv, L.;Gu, J.;Chen, T.;Xiao, Y.;Liu, S.",2016,,10.3389/fmicb.2016.00085,0
822,Virome analysis for identification of novel mammalian viruses in bats from Southeast China,,,"Hu, D.;Zhu, C.;Wang, Y.;Ai, L.;Yang, L.;Ye, F.;Ding, C.",2017,,,0
823,Deep sequencing of the mouse lung transcriptome reveals distinct long non-coding RNAs expression associated with the high virulence of H5N1 avian influenza virus in mice,"Long non-coding RNAs (lncRNAs) play multiple key regulatory roles in various biological processes. However, their function in influenza A virus (IAV) pathogenicity remains largely unexplored. Here, using next generation sequencing, we systemically compared the whole-transcriptome response of the mouse lung infected with either the highly pathogenic (A/Chicken/Jiangsu/k0402/2010, CK10) or the nonpathogenic (A/Goose/Jiangsu/k0403/2010, GS10) H5N1 virus. A total of 126 significantly differentially expressed (SDE) lncRNAs from three replicates were identified to be associated with the high virulence of CK10, whereas 94 SDE lncRNAs were related with GS10. Functional category analysis suggested that the SDE lncRNAs-coexpressed mRNAs regulated by CK10 were highly related with aberrant and uncontrolled inflammatory responses. Further canonical pathway analysis also confirmed that these targets were highly enriched for inflammatory-related pathways. Moreover, 9 lncRNAs and 17 lncRNAs-coexpressed mRNAs associated with a large number of targeted genes were successfully verified by qRT-PCR. One targeted lncRNA (NONMMUT011061) that was markedly activated and correlated with a great number of mRNAs was selected for further in-depth analysis, including predication of transcription factors, potential interacting proteins, genomic location, coding ability and construction of the secondary structure. More importantly, NONMMUT011061 was also distinctively stimulated during the highly pathogenic H5N8 virus infection in mice, suggesting a potential universal role of NONMMUT011061 in the pathogenesis of different H5 IAV. Altogether, these results provide a subset of lncRNAs that might play important roles in the pathogenesis of influenza virus and add the lncRNAs to the vast repertoire of host factors utilized by IAV for infection and persistence.","Animals;Chickens;Female;High-Throughput Nucleotide Sequencing;Host-Pathogen Interactions;*Influenza A Virus, H5N1 Subtype/ge [Genetics];Influenza A Virus, H5N1 Subtype/ip [Isolation & Purification];Influenza A Virus, H5N1 Subtype/me [Metabolism];Influenza A Virus, H5N1 Subtype/py [Pathogenicity];*Influenza in Birds/ge [Genetics];Influenza in Birds/me [Metabolism];Influenza in Birds/vi [Virology];*Lung/me [Metabolism];Lung/vi [Virology];Mice;Mice, Inbred BALB C;*Poultry Diseases/ge [Genetics];Poultry Diseases/me [Metabolism];Poultry Diseases/vi [Virology];*RNA, Long Noncoding/ge [Genetics];RNA, Long Noncoding/me [Metabolism];*Transcriptome;Virulence;0 (RNA, Long Noncoding)","Hu, J.;Hu, Z.;Wang, X.;Gu, M.;Gao, Z.;Liang, Y.;Ma, C.;Liu, X.;Hu, S.;Chen, S.;Peng, D.;Jiao, X.;Liu, X.",2018,,,0
824,Cloning and sequence analysis of Duck hepatitis B virus genome from Hubei brown ducks,"Seventy serum samples were collected from adult brown ducks in Hubei were collected in order to clarify the natural Duck hepatitis B virus (DHBV) infection in and to characterize the genome structure of DHBV. The complete genome of the DHBV strain was amplified by polymerase chain reaction (PCR) and cloned into T vector and sequenced. The results showed that the natural infection rate of DHBV in Hubei was 10%. The DHBV genome isolated by PCR (GenBank accession number DQ276978) had 3 024 nucleotides with three overlapping reading frames encoding the surface, core and the polymerase proteins, respectively. Comparison of genome sequences of this strain with those of 17 DHBV strains from the GenBank revealed an identity from 89.3% to 93.5% at the nucleotide level. The amino acid sequences of the S protein, core protein, and functional domain of the Pol protein were highly reserved among all of these DHBV strains. This Hubei strain was found to share more signature amino acids in the polymerase genes with the ""Chinese"" DHBV strains than those of the ""Western"" country strains. This finding was also corroborated by a phylogenetic tree analysis. Therefore, this Hubei DHBV strain should be classified to a subtype of the Chinese strains.",core protein;virus DNA;vitronectin;amino acid sequence;article;bird disease;duck;gene amplification;gene isolation;gene sequence;gene structure;genetic code;genome analysis;Hepatitis B virus;molecular cloning;nonhuman;nucleotide sequence;open reading frame;phylogeny;polymerase chain reaction;protein domain;sequence analysis;viral genetics;virus characterization;virus classification;virus genome;virus identification;virus strain,"Hu, Q.;Lei, Y. C.;Zhang, Z. Z.;Tian, Y. J.;Zhang, Z. M.;Li, L.;Xia, J. B.;Lu, M. J.;Yang, D. L.",2006,,,0
825,Computational study of interdependence between hemagglutinin and neuraminidase of pandemic 2009 H1N1,"Influenza type A viruses are classified into subtypes based on their two surface proteins, hemagglutinin (HA) and neuraminidase (NA). The HA protein facilitates the viral binding and entering a host cell and the NA protein helps the release of viral progeny from the infected cell. The complementary roles of HA and NA entail their collaboration, which has important implications for viral replication and fitness. The HA protein from early strains of pandemic 2009 H1N1 of swine origin preferentially binds to human type receptors with a weak binding to avian type receptors. This virus caused several human deaths in December 2013 in Texas, USA, which motivated us to investigate the changes of genetic features that might contribute to the surged virulence of the virus. Our time series analysis on the strains of this virus collected from 2009 to 2013 implied that the HA binding preference of this virus in USA, Europe, and Asia has been the characteristic of swine H1N1 virus since 2009. However, its characteristic of seasonal human H1N1 and its binding avidity for avian type receptors both were on steady rise and had a clear increase in 2013 with American strains having the sharpest surge. The first change could enhance the viral transmission and replication in humans and the second could increase its ability to cause infection deep in lungs, which might account for the recent human deaths in Texas. In light of HA and NA coadaptation and evolutionary interactions, we also explored the NA activity of this virus to reveal the functional balance between HA and NA during the course of virus evolution. Finally we identified amino acid substitutions in HA and NA of the virus that were critical for the observed evolution.",H1N1 virus hemagglutinin;Influenza virus hemagglutinin;protein binding;sialidase;amino acid sequence;amino acid substitution;binding site;chemistry;genetics;human;Influenza A virus (H1N1);influenza;molecular genetics;mutation;pandemic;statistics and numerical data;United States,"Hu, W.",2015,,10.1109/tnb.2015.2406992,0
826,"A Multiplex PCR for Simultaneous Detection of Three Zoonotic Parasites Ancylostoma ceylanicum, A. caninum, and Giardia lamblia Assemblage A","Ancylostoma ceylanicum, A. caninum, and Giardia lamblia assemblage A are common intestinal parasites of dogs and cats; they can also infect humans, causing parasitic zoonoses. In this study, a multiplex PCR method was developed for simultaneous identification and detection of those three zoonotic parasites. Three pairs of specific primers were designed based on ITS sequence of A. ceylanicum and A. caninum and TPI gene of G. lamblia available in the GenBank. The multiplex PCR reaction system was established by optimizing the reaction condition, and a series of tests on the sensitivity, specificity, and clinical application were also conducted.",*Ancylostoma/ge [Genetics];*Ancylostoma/ip [Isolation & Purification];Animals;*Giardia lamblia/ge [Genetics];*Giardia lamblia/ip [Isolation & Purification];High-Throughput Nucleotide Sequencing/mt [Methods];*Polymerase Chain Reaction/mt [Methods];Reproducibility of Results;Sensitivity and Specificity;*Zoonoses/ps [Parasitology],"Hu, W.;Wu, S.;Yu, X.;Abullahi, A. Y.;Song, M.;Tan, L.;Wang, Z.;Jiang, B.;Li, G.",2015,,,0
827,Rapid genome sequencing and characterization of novel avian-origin influenza A H7N9 virus directly from clinical sample by semiconductor sequencing,"BACKGROUND: Recent outbreaks of severe pneumonia or acute respiratory distress syndrome have attracted much public interest. Rapid and accurate diagnosis of the causative agent is key for an adequate response to suspected outbreaks. OBJECTIVES: We report a case that highlights the potential of semiconductor sequencing to rapidly determine the novel virus genome sequences. STUDY DESIGN: We have developed a method for rapid de novo assembly of the novel influenza A H7N9 virus genome directly from the tracheal aspirate of a patient using semiconductor sequencer without culture and prior sequence information. Further, characteristic amino acids were analyzed and phylogenetic analysis were done for key genes of the influenza A virus. RESULTS: Deep sequencing yielded 435,239 reads assigned to H7N9 viruses, with an average length of 172 bp, accounting for 18.6% of total reads (2,339,680). Complete genome of the virus was obtained by de novo assembly method within 2 days. Genomic average depth of coverage of the Ion Torrent PGM was up to 5679 fold. Selected characteristic amino acids were observed, and phylogenetic analyses showed that the novel H7 virus was genetically close to 2011 duck H7N3 viruses in Zhejiang. The novel N9 sequences were most closely related to gene sequences of N9 derived from ducks H11N9 in 2011 in Jiangxi and H2N9 sequences from Hong Kong in 2010, in China, and therefore they may share a common ancestor. CONCLUSIONS: The sequence-independent semiconductor sequencing is a powerful tool to investigate outbreak of a novel pathogen.","Aged;Genome, Viral;*High-Throughput Nucleotide Sequencing/mt [Methods];Humans;*Influenza A Virus, H7N9 Subtype/ge [Genetics];*Influenza, Human/vi [Virology];Male;Phylogeny;RNA, Viral/an [Analysis];*Sequence Analysis, RNA/mt [Methods];0 (RNA, Viral)","Hu, Y.;Ren, X.;Li, L.;Xiao, Y.;Dong, J.;Sun, L.;Zhu, Y.;Yang, F.;Zhang, X.;Jin, Q.",2015,Dec,,0
828,Different microRNA alterations contribute to diverse outcomes following EV71 and CA16 infections: Insights from high-throughput sequencing in rhesus monkey peripheral blood mononuclear cells,"Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) are the predominant pathogens of hand, foot, and mouth disease (HFMD). Although these viruses exhibit genetic homology, the clinical manifestations caused by the two viruses have some discrepancies. In addition, the underlying mechanisms leading to these differences remain unclear. microRNAs (miRNAs) participate in numerous biological or pathological processes, including host responses to viral infections. Here, we focused on differences in miRNA expression patterns in rhesus monkey peripheral blood mononuclear cells (PBMCs) infected with EV71 and CA16 at various time points using high-throughput sequencing. The results demonstrated that 106 known and 13 novel miRNAs exhibited significant differences, and 32 key miRNAs among them for target prediction presented opposite trends in the EV71- and CA16-infected samples. GO and pathway analysis of the predicted targets showed enrichment in 14 biological processes, 10 molecular functions, 8 cellular components and 104 pathways. Subsequently, regulatory networks of miRNA-transcription factors, miRNA-predicted targets, miRNA-GOs and miRNA-pathways were constructed to reveal the complex regulatory mechanisms of miRNAs during the infection phase. Ultimately, we analysed hierarchical GO categories of the predicted targets involved in immune system processes, which indicated that the innate and adaptive immunity following EV71 and CA16 infections may be remarkably distinct. In conclusion, this report is the first describing miRNA expression profiles in PBMCs with EV71 and CA16 infections using high-throughput sequencing. Our findings could provide a valuable basis for further studies on the regulatory roles of miRNAs related to the different immune responses caused by EV71 and CA16 infections.",microRNA;adaptive immunity;animal experiment;animal model;article;biological phenomena and functions concerning the entire organism;clinical feature;controlled study;Coxsackievirus A16;Enterovirus A71;Enterovirus infection;high throughput sequencing;human;immune response;immunity;magnetic separation;nonhuman;peripheral blood mononuclear cell;quality control;regulatory mechanism;signal transduction,"Hu, Y.;Song, J.;Liu, L.;Li, J.;Tang, B.;Wang, J.;Zhang, X.;Zhang, Y.;Wang, L.;Liao, Y.;He, Z.;Li, Q.",2016,,10.1016/j.biocel.2016.10.011,0
829,Comparison analysis of microRNAs in response to EV71 and CA16 infection in human bronchial epithelial cells by high-throughput sequencing to reveal differential infective mechanisms,"Hand, foot, and mouth disease (HFMD) mainly caused by Enterovirus 71 (EV71) and coxsackievirus A16 (CA16) infections which presented significantly different clinical manifestations. Nevertheless, the factors underlying these differences remain unclear. Recently, the functions of microRNAs (miRNAs) in pathogen-host interactions have been highlighted. Here, we performed comprehensive miRNA profiling in EV71- and CA16-infected human bronchial epithelial (16HBE) cells at multiple time points using high-throughput sequencing. The results showed that 154 known and 47 novel miRNAs exhibited remarkable differences in expression. Of these, 65 miRNAs, including 58 known and 7 novel miRNAs, presented opposite trends in EV71- and CA16-infected samples. Subsequently, we mainly focused on the 56 known differentially expressed miRNAs by further screening for targets prediction. GO and pathway analysis of these targets demonstrated that 18 biological processes, 7 molecular functions, 1 cellular component and 123 pathways were enriched. Among these pathways, Cadherin signalling pathway, Wnt signalling pathway and angiogenesis showed significant alterations. The regulatory networks of these miRNAs with predicted targets, GOs, pathways and transcription factors were determined, which suggested that miRNAs displayed intricate regulatory mechanisms during the infection phase. Consequently, we specifically analysed the hierarchical GO categories of the predicted targets involved in adhesion. The results indicated that the distinct changes induced by EV71 and CA16 infection may be partly linked to airway epithelial barrier function. Taken together, our data provide useful insights that help elucidate the different host-pathogen interactions following EV71 and CA16 infection and might offer novel therapeutic targets for these infections.",cadherin;microRNA;Wnt protein;article;bronchus epithelium;comparative study;controlled study;Coxsackie virus infection;Enterovirus;Enterovirus infection;epithelium cell;high throughput sequencing;host pathogen interaction;human;human cell;nonhuman;priority journal;protein induction;signal transduction,"Hu, Y.;Song, J.;Liu, L.;Li, J.;Tang, B.;Zhang, Y.;Wang, J.;Wang, L.;Fan, S.;Feng, M.;Li, Q.",2017,,10.1016/j.virusres.2016.11.024,0
830,"Characterization of the genes encoding complete US10, SORF3, and US2 proteins from duck enteritis virus","Based on the understanding that the analysis on unique short (US) region of duck enteritis virus (DEV) might contribute to the recognition of the molecular characterization and the evolution of DEV, in the study, a 5,121 bp fragment, which contained three genes encoding complete US10, unique short region open reading frame (SORF) 3, and US2 proteins, was amplified from the DEV (C-KCE) genome. The transcription orientation of the US10 and SORF3 was in a tail-to-tail way, and the SORF3 and US2 was the same. Potential core promoters and polyadenylation (poly(A)) sites were predicted for US10, SORF3, and US2 and further confirmed by polymerase chain reaction. Phylogenetic analysis for the three complete coding sequences showed that DEV was more closely related to avian herpesviruses, especially to Mardivirus, and should be classified to a separate genus of the Alphaherpesvirinae subfamily. © 2009 Springer Science+Business Media, LLC.",protein SORF3;protein US10;protein us2;unclassified drug;viral protein;animal cell;article;duck enteritis virus;evolution;gene amplification;genetic analysis;genetic transcription;Herpesviridae;Mardivirus;nonhuman;nucleotide sequence;open reading frame;phylogeny;polyadenylation;polymerase chain reaction;priority journal;promoter region;SORF3 gene;US10 gene;us2 gene;virus gene,"Hu, Y.;Zhou, H.;Yu, Z.;Chen, H.;Jin, M.",2009,,10.1007/s11262-009-0329-2,0
831,MicroRNA Expression Profiles of Porcine Kidney 15 Cell Line Infected with Porcine Epidemic Diahorrea Virus,"To explore the effect of porcine epidemic diarrhea virus(PEDV)on microRNA expression profiles of porcine kidney 15cell(PK-15),total RNA was isolated from PK-15 cells with or without PEDV infection. Then, we obtained the miRNAs by using solexa sequencing technology and analyzed these differentially expressed miRNAs. Heatmap cluster analysis and GO (ontology, GO) (Gene function, MF, Molecular) analysis was performed on the significant differences in expression of the miRNA, and 10 significant differences in expression of miRNA were selected by RT-qPCR. The result showed 214 kinds of microRNAs (miRNAs) expression levels were significantly different in PEDV-infected cells, compared with normal PK-15 cells. Among of them,175 kinds of miRNAs were significantly up-regulated while 39 kinds of miRNAs were significantly down-regulated. Furthermore, qPCR results of the expression trends of miRNA were similar with that of solexa sequencing. Heatmap cluster analysis showed that the vast majority of the viral groups were differentially expressed in miRNA compared with the control group, Go analysis showed that miRNAs are widely involved in combination, binding protein, protein kinase activity, transfer enzyme activity, phosphorus containing radicals transfer, phosphotransferase enzyme activity and other biological effects. The expression trends of RT-qPCR verified by miRNA were consistent with the high throughput sequencing results. The results showed that the swine epidemic diarrhea virus infection had a significant impact on the level of miRNA expression in PK-15 cells, thus providing a new idea for the further study of the miRNA preparation for the treatment of PEDV.",microRNA;animal;cell line;Coronavirus infection;genetics;high throughput sequencing;isolation and purification;kidney;metabolism;physiology;pig;Porcine epidemic diarrhea virus;swine disease;veterinary medicine;virology,"Huang, J.;Lang, Q.;Li, X.;Xu, Z.;Zhu, L.;Zhou, Y.",2016,,,0
832,Pseudorabies viral replication is inhibited by a novel target of miR-21,"The pseudorabies virus (PRV) is a porcine virus classified as a member of the Alphaherpesvirinae subfamily of Herpesviridae. Recent studies have confirmed that viruses regulate the gene expression in host cells. Commonly affected genes include oxidative-stress response genes, genes involved in the phosphatidylinositol 3-kinase/Protein Kinase B (PI3K/Akt) signaling pathway, and interferon- and interleukin-related genes. However, the post-transcriptional regulation of host genes following PRV infection is hitherto unclear. In this study, we used miRNA microarray approaches to assess miRNA expression in PRV-infected porcine kidney 15 cell line (PK-15), and observed that miR-21 was expressed at high level 12. h after the cells were infected with PRV. Furthermore, we identified chemokine (C-X-C motif) ligand 10 (CXCL10), also named interferon-γ inducible protein-10 (IP-10), as a novel target gene of miR-21. IP-10 was down-regulated at 4. h after PRV infection. PRV replication was significantly inhibited by IP-10 overexpression. © 2014 Elsevier Inc.",gamma interferon inducible protein 10;microRNA 21;animal cell;antiviral activity;article;controlled study;cytokine response;gene expression regulation;gene overexpression;gene targeting;innate immunity;IP 10 gene;microarray analysis;nonhuman;priority journal;pseudorabies;Pseudorabies virus;pig;virus inhibition;virus replication,"Huang, J.;Ma, G.;Fu, L.;Jia, H.;Zhu, M.;Li, X.;Zhao, S.",2014,,10.1016/j.virol.2014.03.032,0
833,"Detection of a novel porcine parvovirus, PPV4, in chinese swine herds","To determine whether the novel porcine parvovirus type 4 (PPV4) recently reported in America is prevalent in China, a set of specific primers was designed and used for molecular survey of PPV4 among the clinical samples collected from various provinces of China between 2006 and 2010. The results showed that PPV4 is present in Chinese swine herds at a rate of 2.09% (12/573) among the clinical samples examined and 0.76% (1/132) among the samples taken from healthy animals. We also noted that PPV4 was not detected in samples taken prior to 2009. Analysis of the coding sequences showed that the Chinese and American PPV4 genome sequences are closely related with greater than 99% nucleotide sequence identity. Similar to a previous study, viral genomes in head-to-tail configuration of various lengths of the non-coding region were detected. Our findings confirmed that PPV4 is a unique recently discovered virus in pigs. Phylogenetically, PPV4 is most closely related to bovine parvovirus 2 (BPV2, which is not a Bocavirus and is not assigned to any Parvovirinae genus) and shares limited ORF1 (33.6%) and ORF2 (24.5%) amino acid identity. With respect to genome structure and organization, PPV4 encodes an ORF3 in the middle of the viral genome that resembles the Bocavirus genus. However, the PPV4 ORF3 encoded protein shares minimal amino acid identity with the ORF3 encoded proteins of the Bocavirus genus. © 2010 Huang et al; licensee BioMed Central Ltd.",single stranded DNA;virus DNA;animal experiment;animal model;article;China;controlled study;mortality;nonhuman;nucleotide sequence;open reading frame;Parvoviridae;phylogeny;polymerase chain reaction;porcine parvovirus type 4;pig;swine disease;virus detection;virus genome;virus infection;virus isolation;virus typing,"Huang, L.;Zhai, S. L.;Cheung, A. K.;Zhang, H. B.;Long, J. X.;Yuan, S. S.",2010,,10.1186/1743-422x-7-333,0
834,Differences in the intestinal microbiota between uninfected piglets and piglets infected with porcine epidemic diarrhea virus,"Porcine epidemic diarrhea, a disastrous gastrointestinal disease, causes great financial losses due to its high infectivity, morbidity and mortality in suckling piglets despite the development and application of various vaccines. In this study, high-throughput sequencing was used to explore differences in the intestinal microbiota between uninfected piglets and piglets infected with porcine epidemic diarrhea virus (PEDV). The results revealed that the small intestinal microbiota of suckling piglets infected with PEDV showed low diversity and was dominated by Proteobacteria (49.1%). Additionally, the composition of the small intestinal microbiota of sucking piglets infected with PEDV showed marked differences from that of the uninfected piglets. Some of the taxa showing differences in abundance between uninfected piglets and piglets infected with PEDV were associated with cellular transport and catabolism, energy metabolism, the biosynthesis of other secondary metabolites, and amino acid metabolism as determined through the prediction of microbial function based on the bacterial 16S rRNA gene. Therefore, adjusting the intestinal microbiota might be a promising method for the prevention or treatment of PEDV.",RNA 16S;Acidobacteria;Actinobacteria;amino acid metabolism;article;bacterial gene;Bacteroidetes;catabolism;cell transport;controlled study;cyanobacterium;energy metabolism;Firmicutes;Fusobacteria;high throughput sequencing;intestine flora;milk;Mollicutes;nonhuman;nutrient content;piglet;porcine epidemic diarrhea;Porcine epidemic diarrhea virus;prediction;Proteobacteria;species diversity;species dominance;spirochete;suckling animal;synthesis;taxonomy;Verrucomicrobium,"Huang, M. Z.;Wang, S. Y.;Wang, H.;Cui, D. A.;Yang, Y. J.;Liu, X. W.;Kong, X. J.;Li, J. Y.",2018,,10.1371/journal.pone.0192992,0
835,A Selective Bottleneck Shapes the Evolutionary Mutant Spectra of Enterovirus A71 during Viral Dissemination in Humans,"RNA viruses accumulate mutations to rapidly adapt to environmental changes. Enterovirus A71 (EV-A71) causes various clinical manifestations with occasional severe neurological complications. However, the mechanism by which EV-A71 evolves within the human body is unclear. Utilizing deep sequencing and haplotype analyses of viruses from various tissues of an autopsy patient, we sought to define the evolutionary pathway by which enterovirus A71 evolves fitness for invading the central nervous system in humans. Broad mutant spectra with divergent mutations were observed at the initial infection sites in the respiratory and digestive systems. After viral invasion, we identified a haplotype switch and dominant haplotype, with glycine at VP1 residue 31 (VP1-31G) in viral particles disseminated into the integumentary and central nervous systems. In vitro viral growth and fitness analyses indicated that VP1-31G conferred growth and a fitness advantage in human neuronal cells, whereas VP1-31D conferred enhanced replication in human colorectal cells. A higher proportion of VP1-31G was also found among fatal cases, suggesting that it may facilitate central nervous system infection in humans. Our data provide the first glimpse of EV-A71 quasispecies from oral tissues to the central nervous system within humans, showing broad implications for the surveillance and pathogenesis of this reemerging viral pathogen.<b>IMPORTANCE</b> EV-A71 continues to be a worldwide burden to public health. Although EV-A71 is the major etiological agent of hand, foot, and mouth disease, it can also cause neurological pulmonary edema, encephalitis, and even death, especially in children. Understanding selection processes enabling dissemination and accurately estimating EV-A71 diversity during invasion in humans are critical for applications in viral pathogenesis and vaccine studies. Here, we define a selection bottleneck appearing in respiratory and digestive tissues. Glycine substitution at VP1 residue 31 helps viruses break through the bottleneck and invade the central nervous system. This substitution is also advantageous for replication in neuronal cells in vitro Considering that fatal cases contain enhanced glycine substitution at VP1-31, we suggest that the increased prevalence of VP1-31G may alter viral tropism and aid central nervous system invasion. Our findings provide new insights into a dynamic mutant spectral switch active during acute viral infection with emerging viral pathogens.","Amino Acid Substitution;Capsid Proteins/ch [Chemistry];Capsid Proteins/ge [Genetics];Central Nervous System/vi [Virology];Child;*Enterovirus A, Human/ge [Genetics];Enterovirus A, Human/gd [Growth & Development];*Enterovirus A, Human/py [Pathogenicity];Enterovirus Infections/pp [Physiopathology];*Enterovirus Infections/vi [Virology];*Evolution, Molecular;Gastrointestinal Tract/vi [Virology];Haplotypes;High-Throughput Nucleotide Sequencing;Humans;*Mutation;Plasma/vi [Virology];*Quasispecies;Respiratory System/vi [Virology];Retrospective Studies;Virus Replication;0 (Capsid Proteins)","Huang, S. W.;Huang, Y. H.;Tsai, H. P.;Kuo, P. H.;Wang, S. M.;Liu, C. C.;Wang, J. R.",2017,12 01,,0
836,Dual ATPase and GTPase activity of the replication-associated protein (Rep) of beak and feather disease virus,"Background: Psittacine beak and feather disease affects parrots resulting in an immunosuppressive disease that is often characterized by an abnormal shape and growth of the animal's beak, feathers, and claws. Beak and feather disease virus (BFDV) is a single-stranded circular DNA virus and is classified as a member of the Circoviridae family. Two major open reading frames (ORFs) are known to encode the replication-associated (Rep) protein and the capsid-associated (Cap) protein. Methods: The Rep and Cap genes of BFDV were fused with tags and then expressed and purified, respectively. Both the ATPase and GTPase activities of the recombinant Rep protein are measured. The substrate and ion preference, the optimal conditions, the effects of ATPase and GTPase inhibitors and the presence of Cap protein on the ATPase and GTPase activity of the Rep protein are examined. Finally, the effects of the Walker A motif, the Walker B motif, and a novel GYDG motif of the Rep protein on the ATPase and GTPase activities are studied by various mutants. Results: The recombinant Rep protein could display ATPase activity and GTPase activity. The Rep protein was able to hydrolyze both deoxyribonucleotides and ribonucleotides. Among nucleoside triphosphates and deoxynucleoside triphosphates, the substrate preference orders were found to be ATP > GTP > CTP >= UTP and dATP > dGTP > dTTP > dCTP, respectively. Both the ATPase and GTPase activity of the BFDV Rep protein required magnesium ions and the presence of calcium ions significantly inhibited the ATPase and GTPase activity of the Rep protein. The optimal temperatures for ATPase activity and GTPase activity were both 56 degrees C, while their optimal pH values were both pH 7.5. Both the ATPase activity and GTPase activity of the BFDV Rep protein were significantly down-regulated by polynucleotides and the dsDNA of 36 bp (located in origin of replication) of BFDV genome. The ATPase activity of the BFDV Rep protein was found to be more sensitive to sodium azide than sodium orthovanadate and N-ethylmaleimide. Linoleic acid more strongly inhibited the GTPase activity of the Rep protein than dynasore. This suggested the Rep protein of BFDV should be classified as an F-type ATPase and polyunsaturated fatty acid-sensitive GTPase. In the presence of 10 ng of the Cap protein, the ATPase activity and GTPase activity of the BFDV Rep protein were significantly increased. Furthermore, the BFDV Rep protein contains the Walker A motif, the Walker B motif and a novel GYDG motif. Both the ATPase activity and the GTPase activity of various deletion and site-directed mutants of the Rep protein affecting these motifs were significantly reduced, suggesting all the three motifs contribute to the ATPase and GTPase activities; specifically. In addition, the ATPase activity and GTPase activity of the deletion mutants of the Rep protein were reversed in the presence of the Cap protein. This is the first example of dual ATPase and GTPase activity being reported in the Rep protein of BFDV. (C) 2015 Elsevier B.V. All rights reserved.",Beak and feather disease virus;Replication-associated protein;ATPase;GTPase;NUCLEOSIDE TRIPHOSPHATE PHOSPHOHYDROLASE;NUCLEOTIDE-SEQUENCE ANALYSIS;PSITTACINE BEAK;ESCHERICHIA-COLI;CAPSID PROTEIN;PORCINE CIRCOVIRUS;AVIAN POLYOMAVIRUS;NTPASE ACTIVITY;NS3 PROTEIN;VIRAL-DNA,"Huang, S. W.;Liu, H. P.;Chen, J. K.;Shien, Y. W.;Wong, M. L.;Wang, C. Y.",2016,Feb,,0
837,Coinfection with multiple strains of bovine papular stomatitis virus,"Bovine papular stomatitis virus (BPSV) infects cattle and, occupationally, humans. Prevalent subclinical infections, frequent reinfections, and virus persistence in healthy animals compound a poorly understood, but likely complex, scenario of BPSV perpetuation and transmission in nature. Here, we report the isolation of multiple BPSV strains coinfecting a single animal. Whole-genome analysis of isolated BPSV strains revealed genomic variability likely affecting virus virulence and infectivity. Further, incongruent phylogenetic relationships between viruses suggested genomic recombination. These results have significant implications for parapoxvirus infection biology and virus evolution in nature.",animal;bovine;cattle disease;genetics;mixed infection;molecular genetics;nucleotide sequence;open reading frame;Parapoxvirus;phylogeny;poxvirus infection;veterinary medicine;virology,"Huang, T.;Tulman, E. R.;Diel, D. G.;Khatiwada, S.;Sims, W.;Edwards, J. F.;Wen, X.;Kutish, G. F.;Rock, D. L.;Delhon, G.",2015,,10.1007/s00705-015-2394-2,0
838,Perpetuation and reassortment of gull influenza A viruses in Atlantic North America,"Gulls are important hosts of avian influenza A viruses (AIVs) and gull AIVs often contain gene segments of mixed geographic and host lineage origins. In this study, the prevalence of AIV in gulls of Newfoundland, Canada from 2008 to 2011 was analyzed. Overall prevalence was low (30/1645, 1.8%) but there was a distinct peak of infection in the fall. AIV seroprevalence was high in Newfoundland gulls, with 50% of sampled gulls showing evidence of previous infection. Sequences of 16 gull AIVs were determined and analyzed to shed light on the transmission, reassortment and persistence dynamics of gull AIVs in Atlantic North America. Intercontinental and waterfowl lineage reassortment was prevalent. Of particular note were a wholly Eurasian AIV and another with an intercontinental reassortant waterfowl lineage virus. These patterns of geographic and inter-host group transmission highlight the importance of characterization of gull AIVs as part of attempts to understand global AIV dynamics.","Animals;*Charadriiformes/vi [Virology];*Genetic Variation;*Influenza A virus/ge [Genetics];Influenza A virus/ip [Isolation & Purification];Influenza in Birds/ep [Epidemiology];*Influenza in Birds/vi [Virology];Molecular Sequence Data;North America/ep [Epidemiology];Prevalence;RNA, Viral/ge [Genetics];*Reassortant Viruses/ge [Genetics];Reassortant Viruses/ip [Isolation & Purification];Sequence Analysis, DNA;0 (RNA, Viral)","Huang, Y.;Wille, M.;Benkaroun, J.;Munro, H.;Bond, A. L.;Fifield, D. A.;Robertson, G. J.;Ojkic, D.;Whitney, H.;Lang, A. S.",2014,May,,0
839,"A 4-year study of avian influenza virus prevalence and subtype diversity in ducks of Newfoundland, Canada","The island of Newfoundland, Canada, is at the eastern edge of North America and has migratory bird connections with the continental mainland as well as across the North Atlantic Ocean. Here, we report a 4-year avian influenza virus (AIV) epidemiological study in ducks in the St. John's region of Newfoundland. The overall prevalence of AIV detection in ducks during this study was 7.2%, with American Black Ducks contributing the vast majority of the collected samples and the AIV positives. The juvenile ducks showed a significantly higher AIV detection rate (10.6%) compared with adults (3.4%). Seasonally, AIV prevalence rates were higher in the autumn (8.4%), but positives were still detected in the winter (4.6%). Preliminary serology tests showed a high incidence of previous AIV infection (20/38, 52.6%). A total of 43 viruses were characterized for their HA-NA or HA subtypes, which revealed a large diversity of AIV subtypes and little recurrence of subtypes from year to year. Investigation of the movement patterns of ducks in this region showed that it is a largely non-migratory duck population, which may contribute to the observed pattern of high AIV subtype turnover. Phylogenetic analysis of 4 H1N1 and one H5N4 AIVs showed these viruses were highly similar to other low pathogenic AIV sequences from waterfowl in North America and assigned all gene segments into American-avian clades. Notably, the H1N1 viruses, which were identified in consecutive years, possessed homologous genomes. Such detection of homologous AIV genomes across years is rare, but indicates the role of the environmental reservoir in viral perpetuation.",article;autumn;avian influenza virus;biodiversity;Canada;duck;female;Influenza A virus (H1N1);male;nonhuman;nucleotide sequence;phylogenetic tree;population movement pattern;priority journal;seasonal variation;sequence analysis;seroprevalence;virus detection;virus transmission,"Huang, Y.;Wille, M.;Dobbin, A.;Robertson, G. J.;Ryan, P.;Ojkic, D.;Whitney, H.;Lang, A. S.",2013,,10.1139/cjm-2013-0507,0
840,"Genetic, pathogenic and antigenic diversity of Newcastle disease viruses in Shandong Province, China","Thirty-one Newcastle disease viruses (NDVs) isolated from domestic and wild birds in Shandong Province, China (2006-2014) were characterized genetically, pathogenically and antigenically. Phylogenetic analysis classified the viruses into a single genotype under Class I, and four genotypes under Class II. The nineteen viruses classified in genotype VII of Class II were velogenic, while the other viruses were either mesogenic or lentogenic to chickens. Some NDV isolates (17/23) showed no neutralizing reactivity with a monoclonal antibody developed against the HN protein of the LaSota strain, reflecting the mutation at the related antigenic epitope. When challenged with two genotype VII NDV isolates, LaSota-vaccinated SPF chickens were prevented from disease development, but virus shedding was detected for at least 5 days post challenge. Circulation of the same NDV isolate for up to 13 years suggested the role of an environmental reservoir in NDV perpetuation, and reinforced the importance of strict biosecurity measures in addition to vaccination for disease control.",epitope;genomic RNA;HN protein;monoclonal antibody;amino acid substitution;antibody titer;antigenicity;article;China;controlled study;cross protection;disease course;genetic variability;germfree chicken;infection control;microbial diversity;Newcastle disease virus;nonhuman;phylogeny;protein cleavage;provocation test;vaccination;virus carrier;virus genome;virus mutation;virus neutralization;virus shedding;virus virulence,"Huang, Y.;Yang, S.;Hu, B.;Xu, C.;Gao, D.;Zhu, M.;Huang, Q.;Zhang, L.;Wu, J.;Zhang, X.;Khan, M. I.",2015,,10.1016/j.vetmic.2015.09.002,0
841,"Molecular characterization of a highly pathogenetic porcine: Reproductive and respiratory syndrome virus variant in Hubei, China","Porcine reproductive and respiratory syndrome virus (PRRSV) has been recognized as one of the most important pathogens of pigs throughout the world. In 2006, more than 10 provinces of China have experienced an epizootic outbreak of pig diseases characterized by high fever, reddened skin and high morbidity and mortality. From June 2006 to April 2007, we have investigated some clinical samples in Hubei province by RT-PCR and cloned several major genes, N, GP5 and NSP2 gene, shown in this study. Phylogenetic analysis of these genes revealed that the highly pathogenic PRRSV variant, ZB, was responsible for 2006 emergent outbreak of pig disease in Hubei province similar with those variants isolated from other provinces in China in 2006, and belongs to the NA-type PRRSV. In the PRRSV variants, the N and GP5 shear about 90% identity with prototypic ATCC VR-2332 and some typical NA-type Chinese isolates, except the 2850bp NSP2 gene (only shares 65% identity with ATCC VR-2332). But they all shear more than and 97% identity with other highly pathogenetic Chinese PRRSV strains. Additionally, there are extensive amino acid (aa) mutations in the GP5 protein and 2 deletions in the Nsp2 protein when compared with the previous isolates. Most of the variants found in 2006 epizootic outbreak of pig diseases in China were the farthest variants from the typical NA-type PRRSV in phylogenetic distance, and these diversities may be responsible for the differences in the pathogenicity observed between these variants and original Chinese PRRSV strains. © Wuhan Institute of Virology, CAS and Springer-Verlag GmbH 2009.",amino acid;guanine nucleotide binding protein;protein GP5;protein NSP2;unclassified drug;viral protein;animal tissue;Arterivirus;article;China;controlled study;epidemic;gene deletion;gene identification;gene mutation;genetic distance;molecular cloning;nonhuman;phylogeny;reverse transcription polymerase chain reaction;swine disease;virus characterization;virus classification;virus gene;virus identification;virus infection;virus isolation;virus strain;virus virulence,"Huang, Y.;Zhang, B.;Fu, Z. F.;Rayner, S.;Zheng, F. L.;Liang, W. W.;Yang, K. L.;Xu, D. P.;Wang, H. Z.",2009,,10.1007/s12250-009-3012-9,0
842,Clinical features and phylogenetic analysis of Coxsackievirus A9 in Northern Taiwan in 2011,"Background: Coxsackievirus A9 (CA9) was one of the most prevalent serotype of enteroviral infections in Taiwan in 2011. After several patient series were reported in the 1960s and 1970s, few studies have focused on the clinical manifestations of CA9 infections. Our study explores and deepens the current understanding of CA9.Methods: We analyzed the clinical presentations of 100 culture-proven CA9-infected patients in 2011 by reviewing their medical records and depicted the CA9 phylogenetic tree.Results: Of the 100 patients with culture-proven CA9 infections, the mean (SD) age was 4.6 (3.4) years and the male to female ratio was 1.9. For clinical manifestations, 96 patients (96%) had fever and the mean (SD) duration of fever was 5.9 (3.4) days. Sixty one patients (61%) developed a skin rash, and the predominant pattern was a generalized non-itchy maculopapular rash without vesicular changes. While most patients showed injected throat, oral ulcers were found in only 19 cases (19%), among whom, 6 were diagnosed as herpangina. Complicated cases included: aseptic meningitis (n=8), bronchopneumonia (n=6), acute cerebellitis (n=1), and polio-like syndrome (n=1). Phylogenetic analysis for current CA9 strains is closest to the CA9 isolate 27-YN-2008 from the border area of mainland China and Myanmar.Conclusions: The most common feature of CA9 during the 2011 epidemic in Taiwan is generalized febrile exanthema rather than herpangina or hand, foot, and mouth disease. Given that prolonged fever and some complications are possible, caution should be advised in assessing patients as well as in predicting the clinical course. © 2013 Huang et al.; licensee BioMed Central Ltd.",adult;age distribution;article;aseptic meningitis;bronchopneumonia;cerebellum disease;child;clinical feature;Enterovirus;coxsackie virus a9;Coxsackie virus infection;disease course;disease duration;epidemic;female;fever;hand foot and mouth disease;herpangina;human;maculopapular rash;major clinical study;male;medical record review;mouth ulcer;newborn;nucleotide sequence;patient assessment;phylogenetic tree;phylogeny;prediction;preschool child;rash;school child;sex ratio;Taiwan;virus culture;virus strain,"Huang, Y. C.;Chu, Y. H.;Yen, T. Y.;Huang, W. C.;Huang, L. M.;Cheng, A. L.;Wang, H. Y.;Chang, L. Y.",2013,,10.1186/1471-2334-13-33,0
843,Multiple infection of porcine Torque teno virus in a single pig and characterization of the full-length genomic sequences of four U.S. prototype PTTV strains: Implication for genotyping of PTTV,"Porcine Torque teno virus (PTTV) was recently shown to partially contribute to the experimental induction of porcine dermatitis and nephropathy syndrome and postweaning multisystemic wasting syndrome in pigs in the United States. We report here the identification of four distinct full-length genomic sequences of PTTV strains from a single pig in Virginia. Detailed analyses of the genomic organization, the degree of variability and the characteristics of conserved nucleotide and amino acid motifs of PTTV were conducted. The results showed that these four prototype U.S. strains of PTTV identified from the same pig represent distinct genotypes or subtypes and a revised classification system for PPTV is subsequently proposed. This is the first study documenting multiple PTTV infections with distinct genotypes or subtypes in a single pig. The identification of novel PTTV strains from pigs in the United States also pave the way for future disease characterization and genotyping of PTTV. © 2009 Elsevier Inc. All rights reserved.",adult animal;article;gene identification;gene sequence;genetic conservation;genetic organization;genetic variability;genome analysis;genotype;male;mixed infection;nonhuman;nucleotide sequence;priority journal;protein motif;sequence analysis;pig;Torque teno virus 1;United States;virus characterization;virus classification;virus genome;virus infection;virus strain,"Huang, Y. W.;Ni, Y. Y.;Dryman, B. A.;Meng, X. J.",2010,,10.1016/j.virol.2009.10.031,0
844,The Hemagglutinin-Neuraminidase Protein of Newcastle Disease Virus Determines Tropism and Virulence,"The hemagglutinin-neuraminidase (HN) protein of Newcastle disease virus (NDV) plays a crucial role in the process of infection. However, the exact contribution of the HN gene to NDV pathogenesis is not known. In this study, the role of the HN gene in NDV virulence was examined. By use of reverse genetics procedures, the HN genes of a virulent recombinant NDV strain, rBeaudette C (rBC), and an avirulent recombinant NDV strain, rLaSota, were exchanged. The hemadsorption and neuraminidase activities of the chimeric viruses showed significant differences from those of their parental strains, but heterotypic F and HN pairs were equally effective in fusion promotion. The tissue tropism of the viruses was shown to be dependent on the origin of the HN protein. The chimeric virus with the HN protein derived from the virulent virus exhibited a tissue predilection similar to that of the virulent virus, and vice versa. The chimeric viruses with reciprocal HN proteins either gained or lost virulence, as determined by a standard intracerebral pathogenicity index test of chickens and by the mean death time in chicken embryos (a measure devised to classify these viruses), indicating that virulence is a function of the amino acid differences in the HN protein. These results are consistent with the hypothesis that the virulence of NDV is multigenic and that the cleavability of F protein alone does not determine the virulence of a strain.",hemagglutinin;sialidase;animal cell;article;chicken;chimera;enzyme activity;hemadsorption;immunohistochemistry;molecular recognition;Newcastle disease virus;nonhuman;pathogenicity;plant growth;priority journal;protein analysis;reverse transcription polymerase chain reaction;strain difference;virogenesis;virus cell interaction;virus isolation;virus virulence,"Huang, Z.;Panda, A.;Elankumaran, S.;Govindarajan, D.;Rockemann, D. D.;Samal, S. K.",2004,,10.1128/jvi.78.8.4176-4184.2004,0
845,Comparison of Microbiomes between Red Poultry Mite Populations (Dermanyssus gallinae): Predominance of Bartonella-like Bacteria,"Blood feeding red poultry mites (RPM) serve as vectors of pathogenic bacteria and viruses among vertebrate hosts including wild birds, poultry hens, mammals, and humans. The microbiome of RPM has not yet been studied by high-throughput sequencing. RPM eggs, larvae, and engorged adult/nymph samples obtained in four poultry houses in Czechia were used for microbiome analyses by Illumina amplicon sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. A laboratory RPM population was used as positive control for transcriptome analysis by pyrosequencing with identification of sequences originating from bacteria. The samples of engorged adult/nymph stages had 100-fold more copies of 16S rRNA gene copies than the samples of eggs and larvae. The microbiome composition showed differences among the four poultry houses and among observed developmental stadia. In the adults' microbiome 10 OTUs comprised 90 to 99% of all sequences. Bartonella-like bacteria covered between 30 and 70% of sequences in RPM microbiome and 25% bacterial sequences in transcriptome. The phylogenetic analyses of 16S rRNA gene sequences revealed two distinct groups of Bartonella-like bacteria forming sister groups: (i) symbionts of ants; (ii) Bartonella genus. Cardinium, Wolbachia, and Rickettsiella sp. were found in the microbiomes of all tested stadia, while Spiroplasma eriocheiris and Wolbachia were identified in the laboratory RPM transcriptome. The microbiomes from eggs, larvae, and engorged adults/nymphs differed. Bartonella-like symbionts were found in all stadia and sampling sites. Bartonella-like bacteria was the most diversified group within the RPM microbiome. The presence of identified putative pathogenic bacteria is relevant with respect to human and animal health issues while the identification of symbiontic bacteria can lead to new control methods targeting them to destabilize the arthropod host.",Bartonella;Ricketsiella;Tsukamurella;Wolbachia;Mite;Blood sucking;Poultry;Transmission;COMMUNITY COMPOSITION;MAXIMUM-LIKELIHOOD;POTENTIAL VECTOR;ACARI;ASTIGMATA;LAYING HENS;ENDOSYMBIONTS;DIVERSITY;GENERATION;SEQUENCES;CARDINIUM,"Hubert, J.;Erban, T.;Kopecky, J.;Sopko, B.;Nesvorna, M.;Lichovnikova, M.;Schicht, S.;Strube, C.;Sparagano, O.",2017,Nov,,0
846,ISOLATION AND CLASSIFICATION OF VIRUSES FROM CATTLE DURING OUTBREAKS OF,,article;cattle disease;classification;EXPERIMENTAL LAB STUDY;mucosa;research;respiratory tract infection;serodiagnosis;serology;veterinary abortion;virus infection,"Huck, R. A.;Cartwright, S. F.",1964,,,0
847,Documentation and classification of oncogenic viruses,,antibody;virus vaccine;Adenoviridae;animal;article;bovine;cell nucleus;child;classification;cytoplasm;dog;experimental neoplasm;hamster;Haplorhini;horse;human;immunology;infant;microbiology;mouse;Papillomaviridae;Polyomavirus;Poxviridae;preschool child;Leporidae;rat;Simian virus 40;standard;tumor virus;virus;virus culture;virus inclusion;virus interference,"Huebner, R. J.",1968,,,0
848,Cowpox virus isolate virulent in humans shows attenuated phenotype in mice,"We have cultured Cowpox virus (CPXV) from skin lesion material of a human patient from Austria. Phylogenetic comparison of the HA-gene revealed a rather homogeneous cluster with other local isolates from recent years, the A36R-gene was mostly related to elephant derived strains from Germany. Despite causing disease in human, the isolate AT/Carinthia/788/07 surprisingly even at high titers showed a highly reduced virulence in BALB/c mice upon intranasal inoculation as compared to vaccinia virus. This contrasts earlier reports on other CPXV isolates. Using shotgun DNA sequencing several insertions and deletions were found in genes presumably involved in host range, immune regulation as well as established virulence factors. These preliminary data could be an indication that CPXV strains with proven pathogenicity for humans may have reduced virulence in mice and vice versa. Additionally strains with a reduced virulence may have an advantage in persisting in less dense rodent populations. © 2011 Elsevier Ltd.",A36R gene;adolescent;animal cell;animal experiment;article;controlled study;Cowpox virus;DNA determination;DNA sequence;female;gene deletion;gene insertion;Germany;HA gene;human;kidney cell;mouse;nonhuman;nucleotide sequence;phenotype;phylogeny;Leporidae;Vaccinia virus;virus culture;virus gene;virus strain;virus virulence,"Huemer, H. P.;Lassnig, C.;Nowotny, N.",2012,,10.1016/j.rvsc.2011.03.011,0
849,Oral fluids as a live-animal sample source for evaluating cross-reactivity and cross-protection following intranasal influenza a virus vaccination in pigs,"In North American swine, there are numerous antigenically distinct H1 influenza A virus (IAV) variants currently circulating, making vaccine development difficult due to the inability to formulate a vaccine that provides broad cross-protection. Experimentally, live-attenuated influenza virus (LAIV) vaccines demonstrate increased cross-protection compared to inactivated vaccines. However, there is no standardized assay to predict cross-protection following LAIV vaccination. Hemagglutination-inhibiting (HI) antibody in serum is the gold standard correlate of protection following IAV vaccination. LAIV vaccination does not induce a robust serum HI antibody titer; however, a local mucosal antibody response is elicited. Thus, a live-animal sample source that could be used to evaluate LAIV immunogenicity and cross-protection is needed. Here, we evaluated the use of oral fluids (OF) and nasal wash (NW) collected after IAV inoculation as a live-animal sample source in an enzyme-linked immunosorbent assay (ELISA) to predict cross-protection in comparison to traditional serology. Both live-virus exposure and LAIV vaccination provided heterologous protection, though protection was greatest against more closely phylogenetically related viruses. IAV-specific IgA was detected inNWand OF samples and was cross-reactive to representative IAV from each H1 cluster. Endpoint titers of cross-reactive IgA in OF from pigs exposed to live virus was associated with heterologous protection. While LAIV vaccination provided significant protection, LAIV immunogenicity was reduced compared to live-virus exposure. These data suggest that OF from pigs inoculated with wild-type IAV, with surface genes that match the LAIV seed strain, could be used in an ELISA to assess cross-protection and the antigenic relatedness of circulating and emerging IAV in swine.",immunoglobulin A;swine influenza vaccine;animal experiment;animal tissue;antibody titer;article;body fluid;controlled study;cross protection;cross reaction;enzyme linked immunosorbent assay;immunogenicity;infection prevention;infection resistance;influenza A;influenza vaccination;intermethod comparison;nonhuman;nose smear;oral fluid;pig;priority journal;serology;swine influenza;virus load,"Hughes, H. R.;Vincent, A. L.;Brockmeier, S. L.;Gauger, P. C.;Pena, L.;Santos, J.;Braucher, D. R.;Perez, D. R.;Loving, C. L.",2015,,10.1128/cvi.00358-15,0
850,"Capsid protein properties of cowpea aphid-borne mosaic virus and blackeye cowpea mosaic virus confirm the existence of two major subgroups of aphid-transmitted, legume-infecting potyviruses","A study of the capsid proteins of different legume-infecting potyviruses using specific monoclonal antibodies on immunoblots of crude extracts from infected plants revealed that cowpea aphid-borne mosaic virus (CAMV) and blackeye cowpea mosaic virus (BlCMV) have coat protein M(r) values of 32K and 35K, respectively. Immunoblot comparisons of BlCMV, peanut stripe mosaic virus (PStV), bean common mosaic virus (BCMV) and azuki bean mosaic virus (AzMV) revealed equal reactivity of their 35K coat proteins. Similar comparisons between CAMV and the necrotic strain of BCMV (isolate NL3) showed a serological relationship between their 32K coat proteins, results providing the first evidence of a possible similarity between CAMV and BCMV NL3. Peptides from trypsin digests of the coat proteins of several of these legume-infecting potyviruses were analysed by HPLC. Comparison of the peptide profiles confirmed the serological results in distinguishing the two subgroups. Peptide profiles of coat protein from BICMV, PStV, AzMV and BCMV were almost identical, results suggesting that they could be considered as strains of one virus. In contrast, peptide profiles of various CAMV serotypes and BCMV NL3 were distinct from the first group and exhibited limited similarities to each other.",capsid protein;monoclonal antibody;peptide;trypsin;viral protein;aphid;article;comparative study;controlled study;high performance liquid chromatography;immunoblotting;legume;plant virus;nonhuman;priority journal;protein degradation;serotype;virus characterization;virus classification;virus transmission,"Huguenot, C.;Furneaux, M. T.;Hamilton, R. I.",1994,,,0
851,Evidence that cowpea aphid-borne mosaic and blackeye cowpea mosaic viruses are two different potyviruses,"The immunoreactivity of a panel of polyclonal antibodies and monoclonal antibodies (MAbs) raised against African isolates of potyviruses from cowpea and African yam bean was examined in ELISAs. A serological study including reference isolates followed by further characterization in differential hosts resulted in separation of the potyviruses into two distinct serogroups, one containing blackeye cowpea mosaic virus (B1CMV) and the other containing cowpea aphid-borne mosaic virus (CAMV). Using biotin-labelled MAbs, the B1CMV isolates were further subdivided into two serotypes and the CAMV isolates into five serotypes. Because both B1CMV and CAMV induce a very similar mosaic disease in cowpea, different ELISA procedures using mixed MAbs were evaluated and a single protocol was developed which allowed reliable diagnosis of both viruses.",virus antibody;article;diagnostic test;enzyme linked immunosorbent assay;plant virus;nonhuman;priority journal;serotyping;virus characterization;virus classification;virus typing,"Huguenot, C.;Furneaux, M. T.;Thottappilly, G.;Rossel, H. W.;Hamilton, R. I.",1993,,,0
852,The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology,,,"Hurwitz, B. L.;Sullivan, M. B.",2013,,,0
853,"Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present, and future","The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in ""omic"" data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent ""omics"" approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.",biological marker;adult animal;agriculture;archaeon;bacteriophage;biofilm;diet;fungus;lower gastrointestinal tract;mathematical model;membrane vesicle;metabolomics;metagenome;metagenomics;metaproteomics;metatranscriptomics;microbial genome;microbiome;nonhuman;nutrient availability;phenotype;proteomics;protozoon;review;rumen;rumen microorganism;ruminant;taxonomy;transcriptomics,"Huws, S. A.;Creevey, C. J.;Oyama, L. B.;Mizrahi, I.;Denman, S. E.;Popova, M.;Muñoz-Tamayo, R.;Forano, E.;Waters, S. M.;Hess, M.;Tapio, I.;Smidt, H.;Krizsan, S. J.;Yáñez-Ruiz, D. R.;Belanche, A.;Guan, L.;Gruninger, R. J.;McAllister, T. A.;Newbold, C. J.;Roehe, R.;Dewhurst, R. J.;Snelling, T. J.;Watson, M.;Suen, G.;Hart, E. H.;Kingston-Smith, A. H.;Scollan, N. D.;Do Prado, R. M.;Pilau, E. J.;Mantovani, H. C.;Attwood, G. T.;Edwards, J. E.;McEwan, N. R.;Morrisson, S.;Mayorga, O. L.;Elliott, C.;Morgavi, D. P.",2018,,10.3389/fmicb.2018.02161,0
854,Sample size calculations for Bayesian prediction of bovine viral-diarrhoea-virus infection in beef herds,"We used a Bayesian classification approach to predict the bovine viral-diarrhoea-virus infection status of a herd when the prevalence of persistently infected animals in such herds is very small (e.g. <1%). An example of the approach is presented using data on beef herds in Wyoming, USA. The approach uses past covariate information (serum-neutralization titres collected on animals in 16 herds) within a predictive model for classification of a future observable herd. Simulations to estimate misclassification probabilities for different misclassification costs and prevalences of infected herds can be used as a guide to the sample size needed for classification of a future herd. © 2004 Elsevier B.V. All rights reserved.",animal;article;Bayes theorem;Bovine viral diarrhea virus 1;bovine;cattle disease;prevalence;United States,"Huzurbazar, S.;Van Campen, H.;McLean, M. B.",2004,,10.1016/j.prevetmed.2004.01.003,0
855,High diversity and potential translocation of DNA viruses in ballast water,"Ballast water is a common vector for the transport of invasive species to new marine and aquatic environments. We used a metagenomics approach to examine the composition and diversity of viral communities in ballast water from ships originating in Mexico, Saudi Arabia, New York, and Panama, and in water from the port of their destination in Busan, Korea. Myoviridae was the most abundant virus family in ballast water, followed Podoviridae and Siphoviridae. We also identified viruses that infect invertebrates, amoebas, and algae in ballast water and in the Busan port water. Interestingly, there were several viruses that infect humans or other animals (Swinepox virus, Raccoonpox virus, Suid herpesvirus, and Human endogenous retrovirus) in the samples from New York and Panama. In addition, there were giant viruses in all the ballast water samples, especially, identified Megavirus chilensis in New York and Panama, and Pandoravirus salinus in Mexico and Saudi Arabia. These results provide detailed descriptions of the characteristics of the viruses present in ballast water, document significant viral diversity, and indicate the potential translocation of viruses via ballast water.",genetic analyzer;ballast water;unclassified drug;water;alga;amoeba (life cycle stage);article;controlled study;DNA virus;endogenous retrovirus;environmental impact;Korea;Megavirus chilensis;metagenome;metagenomics;Mexico;Myoviridae;New York;nonhuman;Panama;Pandoravirus salinus;Podoviridae;population abundance;Pseudorabies virus;Raccoonpox virus;Saudi Arabia;Siphoviridae;species composition;species diversity;species translocation;Swinepox virus;virus characterization;virus identification,"Hwang, J.;Park, S. Y.;Lee, S.;Lee, T. K.",2018,,10.1016/j.marpolbul.2018.10.053,0
856,Molecular identification of three novel herpesviruses found in Australian farmed saltwater crocodiles (Crocodylus porosus) and Australian captive freshwater crocodiles (Crocodylus johnstoni),"As part of a larger investigation into three emerging disease syndromes highlighted by conjunctivitis and pharyngitis, systemic lymphoid proliferation and encephalitis, and lymphonodular skin infiltrates in farmed saltwater crocodiles (Crocodylus porosus) and one emerging syndrome of systemic lymphoid proliferation in captive freshwater crocodiles (Crocodylus johnstoni), cytopathic effects (CPE), including syncytial cell formation, were observed in primary crocodile cell lines exposed to clarified tissue homogenates from affected crocodiles. Ten cell cultures with CPE were then screened for herpesviruses using two broadly-reactive herpesvirus PCRs. Amplicons were obtained from 9 of 10 cell cultures and were sequenced. Three novel herpesviruses were discovered and the phylogenetic analysis of these viruses showed there was a 63% Bayesian posterior probability value supporting these viruses clustering with the subfamily Alphaherpesvirinae, and 100% posterior probability of clustering with a clade containing the Alphaherpesvirinae and other unassigned reptile herpesviruses. It is proposed that they are named Crocodyline herpesvirus (CrHV) 1, 2 and 3. CrHV1 and 2 were only isolated from saltwater crocodiles and CrHV3 was only isolated from freshwater crocodiles. A duplex PCR was designed that was able to detect these herpesviruses in formalin-fixed paraffin-embedded tissues, a sample type that neither of the broadly-reactive PCRs was able to detect these herpesviruses in. This work describes the isolation, molecular detection and phylogeny of these novel herpesviruses but the association that they have with the emerging disease syndromes requires further investigation.","*Alligators and Crocodiles/vi [Virology];Animals;Animals, Domestic;Australia;Bayes Theorem;Cells, Cultured;*DNA, Viral/an [Analysis];*Herpesviridae/cl [Classification];Herpesviridae/ge [Genetics];Herpesviridae/ip [Isolation & Purification];*Herpesviridae Infections/ve [Veterinary];Herpesviridae Infections/vi [Virology];*Phylogeny;Polymerase Chain Reaction/ve [Veterinary];Sequence Alignment;Sequence Analysis, Protein/ve [Veterinary];Water Microbiology;0 (DNA, Viral)","Hyndman, T. H.;Shilton, C. M.;Wellehan, J. F., Jr.;Davis, S.;Isberg, S. R.;Phalen, D.;Melville, L.",2015,Dec 31,,0
857,Indigenous Hepatitis E in England and Wales From 2003 to 2012: Evidence of an Emerging Novel Phylotype of Viruses,"Background. Enhanced surveillance and molecular characterisation studies of hepatitis E virus (HEV) in England and Wales have been undertaken since 2003. The dynamics of hepatitis E have changed recently with an increase in the number of indigenous cases and an observed viral shift. Methods. HEV antibody and RNA data were analysed to ascertain the annual number of acute infections, the HEV genotype disposition and viral phylogeny. These data were investigated in the context of collected travel history and demographic data. Results. In total, 2713 acute hepatitis E cases were diagnosed, of which 1376 were indigenous infections. Travel associated cases remained steady and mainly associated with Genotype 1 infections. In contrast, major fluctuations were noted in indigenously-acquired cases with a dramatic year on year increase during 2010-2012. Molecular characterisation demonstrated indigenous infections to cluster into two distinct phylogenetic groups with the emergence of a novel group of Genotype 3 viruses coinciding with the recent increase in cases. Conclusions. HEV infection rates are dynamic in England and Wales, influenced by changing trends in indigenously-acquired cases. The recent increase in indigenous cases and the emergence of indigenous viruses not commonly circulating prior to 2010 suggest that the risk of acquiring HEV has changed.",hepatitis E;surveillance;molecular characterisation;phylogeny;indigenous;England and Wales;patient demography;UNITED-KINGDOM;BLOOD-DONORS;WILD BOAR;TRANSMISSION;INFECTION;DEER;PREVALENCE;SEQUENCES;GENOTYPE;RISK,"Ijaz, S.;Said, B.;Boxall, E.;Smit, E.;Morgan, D.;Tedder, R. S.",2014,Apr,,0
858,Identification of bovine enteric Caliciviruses (BEC) from cattle in Baden-Württemberg,"Caliciviruses are known to cause different diseases in many animal species. The bovine enteric caliciviruses (BEC) are associated with diarrhoea in cattle. These viruses have been classified in the genus Norovirus and are closely related to human noroviruses, the leading cause of gastroenteritis in humans. This has raised questions about zoonotic transmission and an animal reservoir for the human viruses. Two samples from 41 stool samples collected for diagnostic purposes from diarrheic cattle in Aulendorf, Germany tested positive for BEC. The samples were amplified with new degenerate BEC specific primers, which amplify a 263 bp portion of the RNA polymerase region. Analysis of the nucleotide sequences showed that these viruses are most closely related to the Norovirus genogroup III/2 (Bo/NLV/Newbury-2/76/UK) viruses.",animal;animal disease;article;Caliciviridae;bovine;cattle disease;diarrhea;disease carrier;disease transmission;Germany;human;isolation and purification;methodology;molecular genetics;nucleotide sequence;reverse transcription polymerase chain reaction;virology;virus infection;zoonosis,"Ike, A. C.;Roth, B. N.;Böhm, R.;Pfitzner, A. J.;Marschang, R. E.",2007,,,0
859,Herd immunity and fatal cases of influenza among the population exposed to poultry and wild birds in Russian Asia in 2013-2014,"In total 1,525 blood serum samples were collected in October, 2013 in Russian Asia from people who reside in territories that are at high risk for emergence of influenza viruses with pandemic potential. Presence of antibodies to influenza viruses in the sera was tested in hemagglutination inhibition test. None of the samples produced positive results with the antigens A/H5 and A/H7. Twelve strains of influenza A(H1N1pdm09) virus were isolated from people who died presumably from influenza during 2013-2014 epidemic season. All strains were similar to vaccine strain A/California/07/09 according to their antigenic properties and sensitivity to anti-neuraminidase drugs (oseltamivir and zanamivir). Genetic analysis revealed that all strains belong to group 6, subgroup 6B of influenza A(H1N1)pdm09 virus. Substitutions in HA1: S164F add E235K as well as E47G, A86V, K331R, N386K, N397K in NA, and K131E, N29S in NS1, and N29S, R34Q in NEP separate investigated strains into two groups: 1st group-A/Chita/1114/2014, A/Chita/1115/2014, A/Chita/853/2014, A/Barnaul/269/2014 and 2nd group-A/Chita/655/2014, A/Chita/656/2014, A/Chita/709/2014, A/Chita/873/2014. Mutation D222G in HA1, which is often associated with high morbidity of the illness, was present in strain A/Novosibirsk/114/2014. Substitution N386K in NA removes a potential N-glycosylation site in neuraminidases of A/Chita/1114/2014, A/Chita/1115/2014, A/Chita/853/2014, A/Barnaul/269/2014, A/Novosibirsk/114/2014, and A/Blagoveshensk/252/2014.",alanine;arginine;asparagine;aspartic acid;glutamic acid;glycine;influenza vaccine;lysine;oseltamivir;phenylalanine;serine;valine;virus antibody;virus antigen;zanamivir;adult;aged;amino acid substitution;animal cell;antigenicity;antiviral susceptibility;article;Asia;bird;blood sampling;child;controlled study;epidemic;fatality;female;flu like syndrome;genetic analysis;hemagglutination inhibition test;herd immunity;human;infection risk;Influenza A virus (H1N1);Influenza A virus (H3N2);Influenza A virus (H5N1);Influenza A virus (H7N9);Influenza A virus;Influenza virus;major clinical study;male;middle aged;morbidity;nonhuman;pandemic influenza;population research;poultry farming;preschool child;protein glycosylation;Russian Asia;virus isolation;virus strain;wild animal;young adult,"Ilyicheva, T.;Abdurashitov, M.;Durymanov, A.;Susloparov, I.;Goncharova, N.;Kolosova, N.;Mikheev, V.;Ryzhikov, A.",2016,,10.1002/jmv.24301,0
860,Molecular identification of enteroviruses from cattle and goat feces and environment in Thailand,,,"Income, N.;Kosoltanapiwat, N.;Taksinoros, S.",2018,,,0
861,Variations in the major envelope glycoprotein GP5 of Czech strains of porcine reproductive and respiratory syndrome virus,"The major envelope glycoprotein genes (ORF5) of seven Czech isolates of porcine reproductive and respiratory syndrome virus (PRRSV) were amplified and their nucleotide sequences were determined. ORF5 displayed nucleotide and amino acid identities of 87·5-100% and 87·6-100%, respectively, among the isolates. In a phylogenetic tree, all European isolates were grouped in a genotype distinct from that of reference American strains (VR-2332, IAF-Klop). Among the European isolates, two different clades were identified. Two Czech isolates (V-501 and V-503) and Italian strain PRRSV 2156 fell into one clade. The remaining European strains comprised the second clade. Surprisingly, two separately clustered strains (V-501 and V-516) were isolated from the same herd. Additionally, the possible effect of in vitro cultivation on the nucleotide sequence was analysed. Nine point mutations in the ORF5 region resulted from 152 in vitro passages of the V-502 isolate in MARC-145 cells.",amino acid;nucleotide;virus envelope protein;virus glycoprotein;amino acid sequence;Arterivirus;article;controlled study;Czech Republic;gene amplification;genotype;in vitro study;nonhuman;nucleotide sequence;phylogeny;point mutation;priority journal;virus classification;virus culture;virus gene;virus isolation;virus strain,"Indik, S.;Valicek, L.;Klein, D.;Klanova, J.",2000,,,0
862,Bats Are an Untapped System for Understanding Microbiome Evolution in Mammals,"Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies focus on domestic animals, laboratory models, or charismatic megafauna (e.g., pandas and chimpanzees). The result is a plethora of studies covering few taxa across the mammal tree of life, leaving broad patterns of microbiome function and evolution unclear. Wildlife microbiome research urgently needs a model system in which to test hypotheses about metagenomic involvement in host ecology and evolution. We propose that bats (Order: Chiroptera) represent a model system ideal for comparative microbiome research, affording opportunities to examine host phylogeny, diet, and other natural history characteristics in relation to the evolution of the gut microbiome.",Chiroptera;bats;macroevolution;microbial ecology;microbiota;MONKEY ALOUATTA-PIGRA;PANDA GUT MICROBIOME;LIFE-HISTORY;HOST;ECOLOGY;RESERVOIRS;PHYLOGENY;VIRUS;CHIROPTERA;PHYSIOLOGY,"Ingala, M. R.;Simmons, N. B.;Perkins, S. L.",2018,Sep-Oct,,0
863,"Genetic heterogeneity among parapoxviruses isolated from sheep, cattle and Japanese serows (Capricornis crispus)","Standard strains of four parapoxviruses and seven unclassified Japanese strains isolated from sheep, cattle and wild Japanese serows (Capricornis crispus) were compared molecularly. Restriction fragment length polymorphism (RFLP) analysis of viral DNA, indirect immunofluorescence assays using monoclonal antibodies, partial nucleotide sequencing of the envelope gene, phylogenetic analysis and PCR-RFLP were carried out. These analyses revealed that the parapoxviruses were divided into four groups and the region sequenced in this study was highly conserved within each group. Each of the Japanese isolates was classified into one of these groups. These findings also indicated that parapoxvirus infections among wild Japanese serows seem to be caused by at least two different parapoxviruses, bovine papular stomatitis virus and orf virus. The methods presented here are useful for genetic characterization and classification of parapoxviruses.",monoclonal antibody;virus DNA;animal;animal cell;article;bovine papular stomatitis;Capricornis crispus;bovine;controlled study;envelope gene;fetus;immunofluorescence test;Japan;molecular biology;nonhuman;nucleotide sequence;Parapoxvirus;phylogeny;polymerase chain reaction;Poxviridae;priority journal;restriction fragment length polymorphism;sheep;strain difference;virus characterization;virus classification;virus infection;virus isolation,"Inoshima, Y.;Murakami, K.;Yokoyama, T.;Sentsui, H.",2001,,,0
864,Identification and characterization of Highlands J virus from a Mississippi sandhill crane using unbiased next-generation sequencing,"Advances in massively parallel DNA sequencing platforms, commonly termed next-generation sequencing (NGS) technologies, have greatly reduced time, labor, and cost associated with DNA sequencing. Thus, NGS has become a routine tool for new viral pathogen discovery and will likely become the standard for routine laboratory diagnostics of infectious diseases in the near future. This study demonstrated the application of NGS for the rapid identification and characterization of a virus isolated from the brain of an endangered Mississippi sandhill crane. This bird was part of a population restoration effort and was found in an emaciated state several days after Hurricane Isaac passed over the refuge in Mississippi in 2012. Post-mortem examination had identified trichostrongyliasis as the possible cause of death, but because a virus with morphology consistent with a togavirus was isolated from the brain of the bird, an arboviral etiology was strongly suspected. Because individual molecular assays for several known arboviruses were negative, unbiased NGS by Illumina MiSeq was used to definitively identify and characterize the causative viral agent. Whole genome sequencing and phylogenetic analysis revealed the viral isolate to be the Highlands J virus, a known avian pathogen. This study demonstrates the use of unbiased NGS for the rapid detection and characterization of an unidentified viral pathogen and the application of this technology to wildlife disease diagnostics and conservation medicine.","*Alphavirus/ip [Isolation & Purification];*Alphavirus Infections/ve [Veterinary];Alphavirus Infections/vi [Virology];Animals;*Bird Diseases/vi [Virology];Birds;*Brain/vi [Virology];Cluster Analysis;Female;Genome, Viral;*High-Throughput Nucleotide Sequencing/mt [Methods];Molecular Sequence Data;Phylogeny;Sequence Analysis, DNA","Ip, H. S.;Wiley, M. R.;Long, R.;Palacios, G.;Shearn-Bochsler, V.;Whitehouse, C. A.",2014,Sep,,0
865,Virus pathotype and deep sequencing of the HA gene of a low pathogenicity H7N1 avian influenza virus causing mortality in Turkeys,"Low pathogenicity avian influenza (LPAI) viruses of the H7 subtype generally cause mild disease in poultry. However the evolution of a LPAI virus into highly pathogenic avian influenza (HPAI) virus results in the generation of a virus that can cause severe disease and death. The classification of these two pathotypes is based, in part, on disease signs and death in chickens, as assessed in an intravenous pathogenicity test, but the effect of LPAI viruses in turkeys is less well understood. During an investigation of LPAI virus infection of turkeys, groups of three-week-old birds inoculated with A/chicken/Italy/1279/99 (H7N1) showed severe disease signs and died or were euthanised within seven days of infection. Virus was detected in many internal tissues and organs from culled birds. To examine the possible evolution of the infecting virus to a highly pathogenic form in these turkeys, sequence analysis of the haemagglutinin (HA) gene cleavage site was carried out by analysing multiple cDNA amplicons made from swabs and tissue sample extracts employing Sanger and Next Generation Sequencing. In addition, a RT-PCR assay to detect HPAI virus was developed. There was no evidence of the presence of HPAI virus in either the virus used as inoculum or from swabs taken from infected birds. However, a small proportion (<0.5%) of virus carried in individual tracheal or liver samples did contain a molecular signature typical of a HPAI virus at the HA cleavage site. All the signature sequences were identical and were similar to HPAI viruses collected during the Italian epizootic in 1999/2000. We assume that the detection of HPAI virus in tissue samples following infection with A/chicken/Italy/1279/99 reflected amplification of a virus present at very low levels within the mixed inoculum but, strikingly, we observed no new HPAI virus signatures in the amplified DNA analysed by deep-sequencing.","Animals;*Genes, Viral;*Hemagglutinins/ge [Genetics];*High-Throughput Nucleotide Sequencing;*Influenza A Virus, H7N1 Subtype/ge [Genetics];*Influenza in Birds/vi [Virology];RNA, Viral/ge [Genetics];Real-Time Polymerase Chain Reaction;Sequence Analysis, DNA;Survival Analysis;*Turkeys/vi [Virology];0 (Hemagglutinins);0 (RNA, Viral)","Iqbal, M.;Reddy, K. B.;Brookes, S. M.;Essen, S. C.;Brown, I. H.;McCauley, J. W.",2014,,,0
866,The intestinal microbiome of the pig,,,"Isaacson, R.;Kim, H. B.",2012,,,0
867,Genetic analysis of ORF5 in porcine reproductive and respiratory syndrome virus in Japan,"In recent years, no reports regarding genetic information on porcine reproductive and respiratory syndrome virus (PRRSV) with a focus on Japan have been published. To clarify the effect of time on PRRSV genomic evolution, we sequenced the open reading frame 5 (600 or 603 bases) obtained from Japanese PRRSV isolates for three periods (1992-1993, 2000-2001, and 2007-2008) and compared their phylogenetic relationships. Assessment of mean pairwise homology of nucleotide sequences of PRRSV isolates indicated a trend towards increasing heterogeneity over time. In addition, we newly detected a virus classified in cluster IV, indicative of the increasing genetic variation of PRRSV in Japan. © 2011 The Societies and Blackwell Publishing Asia Pty Ltd.",Arterivirus;article;controlled study;gene cluster;genetic analysis;genetic heterogeneity;genetic variability;Japan;nonhuman;nucleotide sequence;open reading frame;phylogenetic tree;reverse transcription polymerase chain reaction;pig;virus detection;virus gene;virus isolation,"Iseki, H.;Takagi, M.;Miyazaki, A.;Katsuda, K.;Mikami, O.;Tsunemitsu, H.",2011,,10.1111/j.1348-0421.2010.00303.x,0
868,The genome segment B encoding the RNA-dependent RNA polymerase protein VP1 of very virulent infectious bursal disease virus (IBDV) is phylogenetically distinct from that of all other IBDV strains,"A full-length cDNA clone of the segment B of the very virulent infectious bursal disease virus (IBDV) strain BD 3/99 was constructed and the full-length nucleotide sequence was established. The nucleotide sequence encoding VP1, an RNA-dependent RNA polymerase, of BD 3/99 was aligned with that of 17 other IBDV strains including six very virulent, three classical virulent, five classical attenuated, one antigenic variant and two serotype 2 strains. The VP1 genes of all very virulent strains were 97.5% to 99.8% identical. With the exception of an atypical Australian strain, 002-73, all of the classical virulent or attenuated and antigenic variant strains were also 97.5% to 100% identical. Serotype 2 strains showed only 4-6% divergence from serotype 1 classical virulent or attenuated strains; in contrast, however, the very virulent strains were 10.5% to 12.5% divergent from the classical virulent or attenuated strains as well as serotype 2 strains. Analysis of the deduced amino acid sequence of VP1 revealed 17 common, including 8 unique amino acid substitutions in the very virulent strains. In the phylogenetic tree the very virulent strains formed a distinct cluster and all other strains including classical virulent, attenuated and antigenic variant strains and even serotype 2 strains were grouped together. It is suggested that the VP1 of very virulent IBDV is phylogenetically distinct from that of all other IBDV strains and probably originated from a hitherto unidentified source.","Amino Acid Sequence;Animals;Birnaviridae Infections/vi [Virology];Chickens;Cloning, Molecular;DNA, Complementary;*Genome, Viral;Infectious bursal disease virus/cl [Classification];Infectious bursal disease virus/ge [Genetics];*Infectious bursal disease virus/py [Pathogenicity];Molecular Sequence Data;Phylogeny;*Poultry Diseases/vi [Virology];*RNA Replicase/ge [Genetics];Sequence Alignment;Sequence Analysis, DNA;Viral Structural Proteins/ch [Chemistry];*Viral Structural Proteins/ge [Genetics];Virulence;0 (DNA, Complementary);0 (VP1 protein, infectious bursal disease virus);0 (Viral Structural Proteins)","Islam, M. R.;Zierenberg, K.;Muller, H.",2001,Dec,,0
869,Whole genome analysis of porcine astroviruses detected in Japanese pigs reveals genetic diversity and possible intra-genotypic recombination,"Porcine astroviruses (PoAstVs) are ubiquitous enteric virus of pigs that are distributed in several countries throughout the world. Since PoAstVs are detected in apparent healthy pigs, the clinical significance of infection is unknown. However, AstVs have recently been associated with a severe neurological disorder in animals, including humans, and zoonotic potential has been suggested. To date, little is known about the epidemiology of PoAstVs among the pig population in Japan. In this report, we present an analysis of nearly complete genomes of 36 PoAstVs detected by a metagenomics approach in the feces of Japanese pigs. Based on a phylogenetic analysis and pairwise sequence comparison, 10, 5, 15, and 6 sequences were classified as PoAstV2, PoAstV3, PoAstV4, and PoAstV5, respectively. Co-infection with two or three strains was found in individual fecal samples from eight pigs. The phylogenetic trees of ORF1a, ORF1b, and ORF2 of PoAstV2 and PoAstV4 showed differences in their topologies. The PoAstV3 and PoAstV5 strains shared high sequence identities within each genotype in all ORFs; however, one PoAstV3 strain and one PoAstV5 strain showed considerable sequence divergence from the other PoAstV3 and PoAstV5 strains, respectively, in ORF2. Recombination analysis using whole genomes revealed evidence of multiple possible intra-genotype recombination events in PoAstV2 and PoAstV4, suggesting that recombination might have contributed to the genetic diversity and played an important role in the evolution of Japanese PoAstVs.",article;Astroviridae;feces analysis;genetic variability;genome analysis;genotype;Japan;metagenomics;mixed infection;nonhuman;nucleotide sequence;open reading frame;phylogeny;pig;Porcine astrovirus;sequence analysis;virus detection;virus genome;virus recombination;virus strain,"Ito, M.;Kuroda, M.;Masuda, T.;Akagami, M.;Haga, K.;Tsuchiaka, S.;Kishimoto, M.;Naoi, Y.;Sano, K.;Omatsu, T.;Katayama, Y.;Oba, M.;Aoki, H.;Ichimaru, T.;Mukono, I.;Ouchi, Y.;Yamasato, H.;Shirai, J.;Katayama, K.;Mizutani, T.;Nagai, M.",2017,,10.1016/j.meegid.2017.02.008,1
870,Whole genome analysis of Japanese bovine toroviruses reveals natural recombination between porcine and bovine toroviruses,"Bovine toroviruses (BToVs), belong to the subfamily Toroviridae within the family Coronaviridae, and are pathogens, causing enteric disease in cattle. In Japan, BToVs are distributed throughout the country and cause gastrointestinal infection of calves and cows. In the present study, complete genome sequences of two Japanese BToVs and partial genome sequences of two Japanese BToVs and one porcine torovirus (PToV) from distant regions in Japan were determined and genetic analyses were performed. Pairwise nucleotide comparison and phylogenetic analyses revealed that Japanese BToVs shared high identity with each other and showed high similarities with BToV Breda1 strain in S, M, and HE coding regions. Japanese BToVs showed high similarities with porcine toroviruses in ORF1a, ORF1b, and N coding regions and the 5' and 3' untranslated regions, suggestive of a natural recombination event. Recombination analyses mapped the putative recombinant breakpoints to the 3' ends of the ORF1b and HE regions. These findings suggest that the interspecies recombinant nature of Japanese BToVs resulted in a closer relationship between BToV Breda1 and PToVs.","Animals;Base Sequence;Cattle;*Cattle Diseases/vi [Virology];*Genome, Viral;High-Throughput Nucleotide Sequencing;Japan;Molecular Sequence Data;Open Reading Frames;Phylogeny;*Recombination, Genetic;Sequence Alignment;Sequence Analysis, DNA;*Swine/vi [Virology];Swine Diseases;Torovirus/cl [Classification];*Torovirus/ge [Genetics]","Ito, M.;Tsuchiaka, S.;Naoi, Y.;Otomaru, K.;Sato, M.;Masuda, T.;Haga, K.;Oka, T.;Yamasato, H.;Omatsu, T.;Sugimura, S.;Aoki, H.;Furuya, T.;Katayama, Y.;Oba, M.;Shirai, J.;Katayama, K.;Mizutani, T.;Nagai, M.",2016,Mar,,0
871,"The potyvirus associated with the dappled fruit of Passiflora edulis in Kagoshima prefecture, Japan is the third strain of the proposed new species East Asian Passiflora virus (EAPV) phylogenetically distinguished from strains of Passion fruit woodiness virus","A potyvirus (isolate IB) causing dappled or faded fruits and foliar mosaic symptoms of purple passionfruit, was found in the botanical garden of Kagoshima University, Japan. This isolate - differed in host range from isolates of Passion fruit woodiness virus (PWV)-AO, previously reported to cause ""woodiness"" in Japan. Isolates IB and AO had 83% amino acid identity in their coat proteins (CPs). In phylogenetic analysis, East Asian isolates IB, AO, and PWV-Taiwan clustered together, and were distinguishable from Australian PWV and Brazilian Cowpea aphid-borne mosaic virus isolates, which also cause ""woodiness"" in passionfruit. We propose the name ""East Asian Passiflora virus (EAPV)"" for the new potyvirus species. © Springer-Verlag 2005.",capsid protein;article;classification;genetics;Japan;molecular genetics;nucleotide sequence;passion fruit;plant disease;Potyvirus;sequence homology;species difference;virology;virus gene,"Iwai, H.;Yamashita, Y.;Nishi, N.;Nakamura, M.",2006,,10.1007/s00705-005-0659-x,0
872,Novel bioinformatics strategies for prediction of directional sequence changes in influenza virus genomes and for surveillance of potentially hazardous strains,"Background: With the remarkable increase of microbial and viral sequence data obtained from high-throughput DNA sequencers, novel tools are needed for comprehensive analysis of the big sequence data. We have developed "" Batch-Learning Self-Organizing Map (BLSOM)"" which can characterize very many, even millions of, genomic sequences on one plane. Influenza virus is one of zoonotic viruses and shows clear host tropism. Important issues for bioinformatics studies of influenza viruses are prediction of genomic sequence changes in the near future and surveillance of potentially hazardous strains.Methods: To characterize sequence changes in influenza virus genomes after invasion into humans from other animal hosts, we applied BLSOMs to analyses of mono-, di-, tri-, and tetranucleotide compositions in all genome sequences of influenza A and B viruses and found clear host-dependent clustering (self-organization) of the sequences.Results: Viruses isolated from humans and birds differed in mononucleotide composition from each other. In addition, host-dependent oligonucleotide compositions that could not be explained with the host-dependent mononucleotide composition were revealed by oligonucleotide BLSOMs. Retrospective time-dependent directional changes of mono- and oligonucleotide compositions, which were visualized for human strains on BLSOMs, could provide predictive information about sequence changes in newly invaded viruses from other animal hosts (e.g. the swine-derived pandemic H1N1/09).Conclusions: Basing on the host-dependent oligonucleotide composition, we proposed a strategy for prediction of directional changes of virus sequences and for surveillance of potentially hazardous strains when introduced into human populations from non-human sources. Millions of genomic sequences from infectious microbes and viruses have become available because of their medical and social importance, and BLSOM can characterize the big data and support efficient knowledge discovery. © 2013 Iwasaki et al.; licensee BioMed Central Ltd.",oligonucleotide;article;batch learning self organizing map;bioinformatics;controlled study;genetic procedures;genome analysis;Influenza A virus;Influenza B virus;nonhuman;nucleic acid analysis;prediction;process development;sequence analysis;species comparison;strain difference;virus cell interaction;virus genome;virus identification;virus isolation;virus strain,"Iwasaki, Y.;Abe, T.;Wada, Y.;Wada, K.;Ikemura, T.",2013,,10.1186/1471-2334-13-386,0
873,Arboviruses: Incorporation in a general system of virus classification,,,"J, Casals",1971,,,0
874,Molecular characteristics of infectious bursal disease viruses from asymptomatic broiler flocks in Europe,"Infectious bursal disease virus (IBDV) exists in several different antigenic and pathogenic forms. The immune suppression caused by this virus in young chickens is not always associated with clinical signs of disease. The antigenic variant viruses originally described in the United States typically do not cause clinical signs of disease but can cause a marked immune suppression via the destruction of B lymphocytes. Using a reverse transcription-polymerase chain reaction (RT-PCR) assay we conducted a survey of asymptomatic broiler chicken flocks in Europe for IBDV. Restriction fragment length polymorphisms in the viral protein 2 (VP2) gene of four isolates from Spain and four isolates from France indicated they may be different from the classic and very virulent (vv) IBDV strains found throughout Europe. Nucleotide sequence and phylogenetic analysis of the hypervariable region of the VP2 gene indicated that all eight viruses were more similar to U.S. variant viruses than classic viruses. In two viruses, one from France and one from Spain, threonine was observed at amino acid position 222 and serine was found at position 254. These two substitution mutations are characteristic of Delaware variant viruses. In addition, all eight viruses had mutated amino acid position 318 from glycine to aspartic acid, another substitution mutation commonly found in U.S. variant viruses. Although importation restrictions prevented us from directly testing the antigenicity of these viruses, their nucleotide and predicted amino acid sequences suggest they could be antigenically distinctive compared to classic and vvIBDV commonly found in Europe. Confirmation of the presence of antigenic variant IBDV strains in Europe requires additional immunologic studies to elucidate the exact nature of the viral epitopes. Our data support the need for these immunologic studies.",viral protein;amino acid sequence;animal;animal disease;article;bird disease;chemistry;chicken;Europe;genetics;infectious bursal disease virus;isolation and purification;molecular genetics;nucleotide sequence;phylogeny;virology;virus infection,"Jackwood, D. J.;Cookson, K. C.;Sommer-Wagner, S. E.;Le Galludec, H.;De Wit, J. J.",2006,,10.1637/7528-032006r1.1,0
875,Diversity of genome segment B from infectious bursal disease viruses in the United States,"Several phylogenetic lineages of the infectious bursal disease virus (IBDV) genome segment B have been identified. Although this genome segment has been shown to contribute to virulence, little is known about the genetic lineages that exist in the United States. The nucleotide genome segment B sequences of 67 IBDV strains collected from 2002 to 2011 in the United States were examined. Although they were from nine different states, a majority (47) of these viruses were from California. A 722-base pair region near the 5' end of genome segment B, starting at nucleotide 168 and ending at 889, was examined and compared to sequences available in GenBank. The nucleotide sequence alignment revealed that mutations were frequently observed and that they were uniformly spaced throughout the region. When the predicted amino acids were aligned, amino acids at positions 145, 146, and 147 were found to change frequently. Six different amino acid triplets were observed and the very virulent (vv) IBDV strains (based on presence of vvIBDV genome segment A sequence) all had the triplet T145, D146, and N147. None of the non-vvIBDV strains had this TDN triplet. Phylogenetic analysis of the 67 nucleotide sequences revealed four significant genome segment B lineages among the U.S. viruses. One of these included the genome segment B typically found in vvIBDV and three contained non-vvIBDV genome segment B sequences. When the available sequences in GenBank were added to the analysis, two additional lineages were observed that did not contain U.S. viruses; one included viruses from China and the other contained viruses from the Ivory Coast. Although the samples tested do not represent all poultry producing regions in the United States, serotype 1 viruses from states outside California all belonged to one genome segment B lineage. The other three lineages observed in the United States were populated with viruses exclusively found in California, except the serotype 2 lineage, where the type strain was a serotype 2 virus from Ohio. The data provide further evidence for the importance of genome segment B identification during routine molecular diagnosis of all IBDV strains. © 2012 American Association of Avian Pathologists.",virus RNA;amino acid sequence;animal;animal disease;article;bird disease;birnavirus infection;chemistry;chicken;classification;female;genetic reassortment;genetics;infectious bursal disease virus;isolation and purification;molecular genetics;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;sequence alignment;sequence analysis;serotyping;United States;untranslated region;virology,"Jackwood, D. J.;Crossley, B. M.;Stoute, S. T.;Sommer-Wagner, S.;Woolcock, P. R.;Charlton, B. R.",2012,,10.1637/9900-081811-Reg.1,0
876,Different evolutionary trajectories of vaccinecontrolled and non-controlled avian infectious bronchitis viruses in commercial poultry,"To determine the genetic and epidemiological relationship of infectious bronchitis virus (IBV) isolates from commercial poultry to attenuated live IBV vaccines we conducted a phylogenetic network analysis on the full-length S1 sequence for Arkansas (Ark), Massachusetts (Mass) and Delmarva/1639 (DMV/1639) type viruses isolated in 2015 from clinical cases by 3 different diagnostic laboratories. Phylogenetic network analysis of Ark isolates showed two predominant groups linked by 2 mutations, consistent with subpopulations found in commercial vaccines for this IBV type. In addition, a number of satellite groups surrounding the two predominant populations were observed for the Ark type virus, which is likely due to mutations associated with the nature of this vaccine to persist in flocks. The phylogenetic network analysis of Mass-type viruses shows two groupings corresponding to different manufacturers vaccine sequences. No satellite groups were observed for Masstype viruses, which is consistent with no persistence of this vaccine type in the field. At the time of collection, no vaccine was being used for the DMV/1639 type viruses and phylogenetic network analysis showed a dispersed network suggesting no clear change in genetic distribution. Selection pressure analysis showed that the DMV/1639 and Mass-type strains were evolving under negative selection, whereas the Ark type viruses had evolved under positive selection. This data supports the hypothesis that live attenuated vaccine usage does play a role in the genetic profile of similar IB viruses in the field and phylogenetic network analysis can be used to identify vaccine and vaccine origin isolates, which is important for our understanding of the role live vaccines play in the evolutionary trajectory of those viruses.",live vaccine;virus vaccine;article;Avian infectious bronchitis virus;Avian infectious bronchitis virus Arkansas strain;Avian infectious bronchitis virus Delmarva/1639 strain;Avian infectious bronchitis virus Massachusetts strain;chicken;controlled study;embryo;gene expression profiling;gene mutation;gene sequence;genetic association;genetic selection;Massachusetts;molecular epidemiology;molecular evolution;nonhuman;phylogeny;poultry;S1 gene;viral genetics;virus gene;virus isolation;virus typing,"Jackwood, M. W.;Lee, D. H.",2017,,10.1371/journal.pone.0176709,0
877,"The delta hepatitis agent: 'Viral hepatitis, type D'","The δ-agent has been adequately characterized to merit its designation as a virus and standardization of its nomenclature. Therefore, as suggested by Rizzetto and coworkers, the following conventions are being adopted: the δ-agent will be called hepatitis D virus (HDV), its antigen, hepatitis D antigen (HDAg), and the illness associated with infection, viral hepatitis, type D.",circulating antibody;delta antibody;delta antigen;unclassified drug;article;classification;clinical article;cytology;diagnosis;Hepatitis B virus;hepatitis virus;human;immunofluorescence;liver;short survey;therapy;virus classification;virus replication,"Jacobson, I. M.;Dienstag, J. L.",1984,,,0
878,"Genetic analysis of avian influenza A viruses isolated from domestic waterfowl in live-bird markets of Hanoi, Vietnam, preceding fatal H5N1 human infections in 2004","The first known cases of human infection with highly pathogenic avian influenza (HPAI) H5N1 viruses in Vietnam occurred in late 2003. However, HPAI H5N1 and low-pathogenic avian influenza (LPAI) H5N2 and H9N3 viruses were isolated from domestic waterfowl during live-bird market (LBM) surveillance in Vietnam in 2001 and 2003. To understand the possible role of these early viruses in the genesis of H5N1 strains infecting people, we performed sequencing and molecular characterization. Phylogenetic analysis revealed that the hemagglutinin (HA) genes of two geese HPAI H5N1 strains belonged to clade 3, and their surface glycoprotein and replication complex genes were most closely related (98.5-99.7% homologous) to A/duck/Guangxi/22/01 (H5N1) virus, detected contemporarily in southern China, whilst the M and NS genes were derived from an A/duck/Hong Kong/2986.1/00 (H5N1)-like virus. The H5 HA gene of the duck HPAI H5N1 strain belonged to clade 5 and acquired a gene constellation from A/quail/Shantou/3846/02 (H5N1), A/teal/China/2978.1/02 (H5N1) and A/partridge/Shantou/2286/03 (H5N1)-like viruses. The phylogenetic analysis further indicated that all eight gene segments of goose and duck HPAI H5N1 and LPAI H5N2 viruses were distinct from those of H5N1 clade-1 viruses known to have caused fatal human infections in Vietnam since late 2003. The duck H9N3 isolates derived genes from aquatic-bird influenza viruses, and their H9 HA belonged to the Korean lineage. The PB2 gene of A/duck/Vietnam/340/01 (H9N3) virus had lysine at position 627. Based on the molecular characterization of specific amino acid residues in the surface and relevant internal protein-coding genes, the Vietnamese H5N1 and H9N3 virus isolates indicated specificity to avian cell surface receptor and susceptibility for currently licensed anti-influenza A virus chemotherapeutics. Our findings suggest that the H5N1 and H5N2 viruses that circulated among geese and ducks in LBMs in Hanoi, Vietnam, during 2001 and 2003 were not the immediate ancestors of the clade-1 viruses associated with fatal human infections in Vietnam. The clade-1 HPAI H5N1 viruses were independently introduced into Vietnam.","hemagglutinin, avian influenza A virus;Influenza virus hemagglutinin;amino acid sequence;animal;article;avian influenza;bird;bird disease;China;classification;duck;epidemiology;genetics;goose;human;influenza;Influenza A virus;Influenza A virus (H5N1);Influenza A virus (H5N2);isolation and purification;molecular genetics;phylogeny;poultry;sequence alignment;Viet Nam;virology;virus genome","Jadhao, S. J.;Nguyen, D. C.;Uyeki, T. M.;Shaw, M.;Maines, T.;Rowe, T.;Smith, C.;Huynh, L. P.;Nghiem, H. K.;Nguyen, D. H.;Nguyen, H. K.;Nguyen, H. H.;Hoang, L. T.;Nguyen, T.;Phuong, L. S.;Klimov, A.;Tumpey, T. M.;Cox, N. J.;Donis, R. O.;Matsuoka, Y.;Katz, J. M.",2009,,10.1007/s00705-009-0429-2,0
879,Genetic analysis of avian influenza viruses: Cocirculation of avian influenza viruses with allele A and B nonstructural gene in Northern Pintail (Anas acuta) ducks wintering in Japan,"The pandemic influenza virus strains of 1918 (H1N1), 1957 (H2N2), 1968 (H3N2), and 2009 (H1N1) have genes related to avian influenza viruses (AIVs). The nonstructural (NS) gene of AIVs plays a significant role in host-viral interaction. However, little is known about the degree of diversity of this gene in Northern pintail (Anas acuta) ducks wintering in Japan. This study describes characteristics of pintail-originated H1N1, H1N2, H1N3, H5N2, H5N3, H5N9, and H7N7 viruses. Most of the viruses were revealed to be avian strains and not related to pandemic and seasonal flu strains. Nevertheless, the NP genes of 62.5% (5/8) viruses were found closely related to a A/swine/Korea/C12/08, indicating exchange of genetic material and ongoing mammalian-linked evolution of AIVs. Besides, all the viruses, except Aomori/422/07 H1N1, contain PSIQSRGLF motif usually found in avian, porcine, and human H1 strains. The Aomori/422/07 H1N1 has a PSVQSRGLF motif identical to a North American strain. This findings linked to an important intercontinental, Asian-American biogeographical interface. Phylogenetically all the viruses were clustered in Eurasian lineage. Cocirculation of allele A and B (NS gene) viruses was evident in the study implying the existence of a wide reservoir of influenza A viruses in pintail wintering in Japan. © 2012 Alam Jahangir et al.",viral protein;allele;Anas acuta;article;avian influenza virus;biogeography;controlled study;duck;genetic analysis;genetic variability;Influenza A virus (H1N1);Influenza A virus (H1N2);Influenza virus A H1N3;Japan;Korea;molecular evolution;nonhuman;pandemic;priority journal;protein motif;seasonal influenza;viral genetics;virus cell interaction;virus gene;winter,"Jahangir, A.;Ruenphet, S.;Sultana, N.;Shoham, D.;Takehara, K.",2012,,10.1155/2012/847505,0
880,Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak,"The present study reports isolation and characterization of H9N2 virus responsible for disease characterized by symptoms including difficulty in respiration, head swelling, nasal discharge, reduced feed intake, cyanotic comb, reduced egg production and mortality. Virus isolation from allantoic fluid inoculated with tracheal aspirates and whole genome sequencing of two isolates were performed on an Ion-Torrent sequencer. Phylogenetic analysis revealed that the two H9N2 isolates are reassortant viruses showing a G1-like lineage for HA, NA and NP, a Hok/49/98-like lineage for PB1 and PA, PK/UDL-01/05-like lineage for PB2, IL/90658/00-like lineage for NS and an unknown lineage for M gene. Analyses of the HA cleavage site showed a sequence of (333PARSSRGL340) indicating that these isolates are of low pathogenicity. Isolate 2 has leucine at amino acid position 226, a substitution which is associated with mammalian adaptation of avian influenza virus. Isolate 1 has the S31N substitution in the M2 gene that has been associated with drug resistance as well as R57Q and C241Y mutations in the NP gene which are associated with human adaptation. The result reported here gives deep insight in to H9N2 viruses circulating in domestic poultry of India and supports the policy of active efforts to control and manage H9N2 infections in Indian poultry.",,"Jakhesara, S. J.;Bhatt, V. D.;Patel, N. V.;Prajapati, K. S.;Joshi, C. G.",2014,,,0
881,Emergence of a genotype I variant of avian infectious bronchitis virus from Northern part of India,"Infectious bronchitis virus (IBV) is one of the foremost causes of a persistent economic burden to poultry industries worldwide. IBV belongs to the genus Gammacoronavirus within the family Coronaviridae. The IBV infection leads to respiratory and nephrogenic symptoms in broiler chickens. In addition, its infection leads to reduced fertility and hatchability in layer birds. We determined the first complete genome sequence of a variant IBV from an outbreak in Haryana state of the Northern part of India using next generation sequencing. On phylogenetic analysis of the IBV isolate, it clustered with genotype I lineage 1 (GI-1). The deduced amino acid sequence of S gene of IBV isolates showed a high level of identity with strains isolated from Tamil Nadu and the reference vaccine strains. Our result suggests that the IBV virus isolated from unvaccinated chicken flocks in North India might be a revertant strain originally evolved from the live attenuated vaccine strains used in the region. Determination of the complete genome sequence of additional IBV isolates from India is necessary to understand the epidemiology of IBV in India.",Amino Acid Sequence;Animals;Chickens/ge [Genetics];*Chickens/vi [Virology];Coronavirus Infections/pc [Prevention & Control];*Coronavirus Infections/ve [Veterinary];Coronavirus Infections/vi [Virology];Genotype;High-Throughput Nucleotide Sequencing;India;*Infectious bronchitis virus/ge [Genetics];*Infectious bronchitis virus/ip [Isolation & Purification];Phylogeny;Poultry Diseases/pc [Prevention & Control];*Poultry Diseases/vi [Virology];Viral Vaccines;0 (Viral Vaccines),"Jakhesara, S. J.;Nath, B.;Pal, J. K.;Joshi, C. G.;Kumar, S.",2018,Jul,,0
882,"Pathotypic and Sequence Characterization of Newcastle Disease Viruses from Vaccinated Chickens Reveals Circulation of Genotype II, IV and XIII and in India","Newcastle disease virus (NDV) causes a highly contagious disease which continuously haunts the global poultry industry. The nature and molecular epidemiology of NDVs prevalent in recent outbreaks in India is poorly understood. This study aimed to characterize NDVs prevalent in vaccinated flocks in India using whole-genome sequencing and biological pathotyping. Twelve field isolates were collected from outbreaks which occurred in different parts of India and characterized as velogenic based on their intracerebral pathogenicity index (ICPI) and amino acid sequence at the F protein cleavage site. All 12 of the field isolates and five commonly used vaccine strains were selected for whole-genome sequencing using Ion Torrent PGM technology, yielding complete genome sequences for ten field isolates and all vaccine strains. The genome of all isolates was found to be 15 192 nt long with a high level of conservation across multiple genomic features with APMV-I viruses. Phylogenetic analysis and evolutionary distance calculations placed the isolates in genotypes II, IV and XIII. Revisiting other recently reported strains provided preliminary evidence of genotypes VI, VII and XVIII circulating in India. Comparison between the field and vaccine virus sequences revealed unique genomic and amino acid differences in important antigenic regions of the F and hemagglutinin-neuraminidase (HN) genes which can be targeted for site directed mutagenesis to evaluate the impact of these substitutions on virus pathogenicity. This study highlights the requirement to evaluate current vaccines through systematic protection assays to determine protection efficacy against field isolates.",virus vaccine;animal;chicken;DNA sequence;genetic variation;genetics;genotype;India;Newcastle disease;Newcastle disease virus;phylogeny;virology,"Jakhesara, S. J.;Prasad, V. V.;Pal, J. K.;Jhala, M. K.;Prajapati, K. S.;Joshi, C. G.",2016,,10.1111/tbed.12294,0
883,"Porcine Deltacoronavirus, Thailand, 2015",,"Animals;Coronavirus/cl [Classification];*Coronavirus/ge [Genetics];Coronavirus/ip [Isolation & Purification];Coronavirus/py [Pathogenicity];Coronavirus Infections/ep [Epidemiology];Coronavirus Infections/pa [Pathology];*Coronavirus Infections/ve [Veterinary];Coronavirus Infections/vi [Virology];*Disease Outbreaks;Farms;Female;*Genome, Viral;High-Throughput Nucleotide Sequencing;Male;Phylogeny;Survival Analysis;Swine;*Swine Diseases/ep [Epidemiology];Swine Diseases/pa [Pathology];Swine Diseases/vi [Virology];Thailand/ep [Epidemiology];*Viral Proteins/ge [Genetics];0 (Viral Proteins)","Janetanakit, T.;Lumyai, M.;Bunpapong, N.;Boonyapisitsopa, S.;Chaiyawong, S.;Nonthabenjawan, N.;Kesdaengsakonwut, S.;Amonsin, A.",2016,Apr,,0
884,Sequence analysis of the S1 glycoprotein gene of infectious bronchitis viruses: Identification of a novel phylogenetic group in Korea,"Twelve Korean infectious bronchitis viruses (IBVs) were isolated in the field from chickens suspected of being carriers of infectious bronchitis between 2001 and 2003. The S1 glycoprotein genes of these IBV isolates were amplified by reverse transcriptase-polymerase chain reaction (RT-PCR) and analyzed by restriction fragment length polymorphism (RFLP) analysis. These Korean IBV isolates were classified into three groups according to their RFLP patterns obtained using the restriction enzyme HaeIII. Half of the twelve isolates were similar to the KM91 RFLP pattern, which is a common pattern in Korea. Three more isolates were related to the Arkansas strain pattern, but with some unique variations. The other three viruses showed variant RFLP patterns. For a comparison with the published sequences for non-Korean IBV strains, amplified PCR products from the twelve isolates were cloned and sequenced. The Korean IBV field isolates had 71.2-99.7% nucleotide sequence homology with each other and 45.9-80.7% nucleotide sequence homology with non-Korean IBV strains. With respect to the deduced amino acid sequence, the Korean IBV isolates had 71.5-99.3% similarity with each other and 44.9-80.3% similarity with non-Korean IBV strains. Phylogenetic tree analysis revealed that some of the IBV isolates appear to belong to a new group, different from the non-Korean IBV strains or from previously isolated Korean IBV strains. Specifically, the new Korean IBV isolates K10217-03, K3-3 and K1255-03 represented a separate group. These findings suggest that the Korean IBVs appear to be continuously evolving.",glycoprotein;viral protein;amino acid sequence;animal;animal disease;article;Avian infectious bronchitis virus;bird disease;chemistry;classification;genetics;isolation and purification;molecular genetics;phylogeny;poultry;restriction fragment length polymorphism;reverse transcription polymerase chain reaction;sequence alignment;sequence analysis;sequence homology;virology;virus infection,"Jang, J. H.;Sung, H. W.;Song, C. S.;Kwon, H. M.",2007,,,0
885,Antigenic and genetic analyses of foot-and-mouth disease virus type A isolates for selection of candidate vaccine strain reveals emergence of a variant virus that is responsible for most recent outbreaks in India,"Recent reports indicated presence of two antigenic and genetic groups (genotypes VI and VII) of foot-and-mouth disease virus (FMDV) type A in India and are divergent from the vaccine strains. In order to choose suitable field isolate as candidate vaccine strain, anti-sera against representative isolates from both the genotypes and two in-use vaccine strains are tested in neutralization assay. Two candidate vaccine strains from both the genotypes are selected with close antigenic match to the field isolates. From the result it is evident that IND 81/00 (genotypes VII), gave a better antigenic coverage (antigenic relationship (r)-value >0.40 with 79% of isolates of 2002-2003) than IND 258/99 (genotype VI; r-value > 0.40 with 42% of 2002-2003 isolates). Phylogenetic analysis based on P1 genomic region placed all the recent isolates (2001-2003) into genotype VII, with emergence of a new variant virus (VIIb-VP359del) having amino acid deletion at an antigenically critical residue (VP359), indicating a major evolutionary jump probably due to immune selection. Though very limited in its extent, this data indicates an apparent dominance of genotype VII over genotype VI and underscores the need to continue further molecular epidemiological investigations to substantiate this finding. © 2005 Elsevier B.V. All rights reserved.",virus vaccine;antigenicity;article;Foot and mouth disease virus;genetic analysis;genome;genotype;India;nonhuman;nucleotide sequence;phylogeny;priority journal;virus immunity;virus isolation;virus neutralization,"Jangra, R. K.;Tosh, C.;Sanyal, A.;Hemadri, D.;Bandyopadhyay, S. K.",2005,,10.1016/j.virusres.2005.03.021,0
886,"Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals","Next-generation sequencing has expanded our understanding of the viral populations that constitute the mammalian virome. We describe a novel taxon of viruses named Statoviruses, for Stool associated Tombus-like viruses, present in multiple metagenomic datasets. These viruses define a novel clade that is phylogenetically related to the RNA virus families Tombusviridae and Flaviviridae. Five distinct statovirus types were identified in human, macaque, mouse, and cow gastrointestinal tract samples. The prototype genome, statovirus A, was frequently identified in macaque stool samples from multiple geographically distinct cohorts. Another genome, statovirus C1, was discovered in a stool sample from a human child with fever, cough, and rash. Further experimental data will clarify whether these viruses are infectious to mammals or if they originate from another source present in the mammalian gastrointestinal tract.",article;child;cladistics;cohort analysis;coughing;feces analysis;female;fever;Flaviviridae;gastrointestinal tract;genetic database;human;mammal;metagenomics;nonhuman;phylogeny;preschool child;rash;RNA virus;Statovirus;taxon;Tombusviridae;virus genome;virus identification,"Janowski, A. B.;Krishnamurthy, S. R.;Lim, E. S.;Zhao, G.;Brenchley, J. M.;Barouch, D. H.;Thakwalakwa, C.;Manary, M. J.;Holtz, L. R.;Wang, D.",2017,,10.1016/j.virol.2017.01.010,0
887,Epidemiologic investigation of an outbreak of goose parvovirus infection in Sweden,"An outbreak of goose parvovirus (GPV) infection on a Swedish goose farm in the spring of 2004 increased the mortality rates from 2% in the early unaffected hatches to 90% and 99% respectively in the two hatches following virus introduction and 40% in goslings hatched later in the same breeding season. In this paper we describe the clinical observations, diagnostic procedures, and epidemiologic investigation carried out to elucidate the source of the infection. The diagnosis was confirmed by serology, virus isolation, and sequence analysis of a 493-bp-long fragment of the VP1 gene. Phylogenetically the causative virus was closely related to pathogenic GPV strains isolated in 2003 and 2004 from Poland and the United Kingdom, respectively. The Swedish isolate exhibited less homology with pathogenic strains from Hungary and Asia and with attenuated vaccine strains. The epidemiologic investigation showed that the virus was first introduced to a contract farm (farm A) and then was transferred with newly hatched goslings to the farm that had submitted the birds for necropsy (index farm). The exact time and source of the virus introduction to farm A could not be determined with absolute certainty. Possible sources of the infection included backyard goose eggs that had been delivered to farm A for subcontract incubation and hatching, wild geese that frequented the flock of breeding geese on pasture on farm A, and a clutch of Canada goose eggs (Branta canadensis) that had been produced by wild geese and was hatched in the same machine as the eggs produced by farm A.",animal;animal disease;article;bird disease;goose;isolation and purification;Parvoviridae;pathology;phylogeny;Sweden;virology;virus infection,"Jansson, D. S.;Feinstein, R.;Kardi, V.;Mató, T.;Palya, V.",2007,,10.1637/0005-2086(2007)51[609:Eioaoo]2.0.Co;2,0
888,A novel bovine papillomavirus (BPV-6) causing true epithelial papillomas of the mammary gland skin: A member of a proposed new BPV subgroup,"A papillomavirus has been isolated from frond epithelial papillomas of the bovine udder. It is clearly distinguishable from all other bovine papillomaviruses (BPVs) based on DNA sequence homology and antigenic properties and is thus characterised as a new entity, designated BPV-6. BPV-6 does not possess the interspecific papillomavirus antigen, its genomic DNA (7.2 kb) is smaller than, and does not show any sequence homology to BPV-1, BPV-2, or BPV-5, whereas it is approximately the same length as BPV-3 or BPV-4, with which it shares some sequence homology. The bovine papillomaviruses have been classified into two subgroups: subgroup A, composed of BPV-1, BPV-2, and BPV-5, all of which induce fibropapillomas, and subgroup B, composed of BPV-3, BPV-4 and BPV-6, all of which cause true epithelial papillomas.",radioisotope;virus antigen;breast;bovine;classification;diagnosis;electron microscopy;etiology;gene sequence;heredity;nonhuman;nucleic acid hybridization;papilloma;Papillomaviridae;virus classification;virus isolation,"Jarrett, W. F. H.;Campo, M. S.;O'Neil, B. W.",1984,,,0
889,ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing,"MOTIVATION: The combined effect of a high replication rate and the low fidelity of the viral polymerase in most RNA viruses and some DNA viruses results in the formation of a viral quasispecies. Uncovering information about quasispecies populations significantly benefits the study of disease progression, antiviral drug design, vaccine design and viral pathogenesis. We present a new analysis pipeline called ViQuaS for viral quasispecies spectrum reconstruction using short next-generation sequencing reads. ViQuaS is based on a novel reference-assisted de novo assembly algorithm for constructing local haplotypes. A significantly extended version of an existing global strain reconstruction algorithm is also used. RESULTS: Benchmarking results showed that ViQuaS outperformed three other previously published methods named ShoRAH, QuRe and PredictHaplo, with improvements of at least 3.1-53.9% in recall, 0-12.1% in precision and 0-38.2% in F-score in terms of strain sequence assembly and improvements of at least 0.006-0.143 in KL-divergence and 0.001-0.035 in root mean-squared error in terms of strain frequency estimation, over the next-best algorithm under various simulation settings. We also applied ViQuaS on a real read set derived from an in vitro human immunodeficiency virus (HIV)-1 population, two independent datasets of foot-and-mouth-disease virus derived from the same biological sample and a real HIV-1 dataset and demonstrated better results than other methods available.",algorithm;classification;Foot and mouth disease virus;genetics;haplotype;high throughput sequencing;human;Human immunodeficiency virus 1;procedures,"Jayasundara, D.;Saeed, I.;Maheswararajah, S.;Chang, B. C.;Tang, S. L.;Halgamuge, S. K.",2015,,10.1093/bioinformatics/btu754,0
890,Mixed triple: allied viruses in unique recent isolates of highly virulent type 2 bovine viral diarrhea virus detected by deep sequencing,"UNLABELLED: In February 2013, very severe acute clinical symptoms were observed in calves, heifers, and dairy cattle in several farms in North Rhine Westphalia and Lower Saxony, Germany. Deep sequencing revealed the coexistence of three distinct genome variants within recent highly virulent bovine viral diarrhea virus type 2 (BVDV-2) isolates. While the major portion (ca. 95%) of the population harbored a duplication of a 222-nucleotide (nt) segment within the p7-NS2-encoding region, the minority reflected the standard structure of a BVDV-2 genome. Additionally, unusual mutations were found in both variants, within the highly conserved p7 protein and close to the p7-NS2 cleavage site. Using a reverse genetic system with a BVDV-2a strain harboring a similar duplication, it could be demonstrated that during replication, genomes without duplication are generated de novo from genomes with duplication. The major variant with duplication is compulsorily escorted by the minor variant without duplication. RNA secondary structure prediction allowed the analysis of the unique but stable mixture of three BVDV variants and also provided the explanation for their generation. Finally, our results suggest that the variant with duplication plays the major role in the highly virulent phenotype. IMPORTANCE: This study emphasizes the importance of full-genome deep sequencing in combination with manual in-depth data analysis for the investigation of viruses in basic research and diagnostics. Here we investigated recent highly virulent bovine viral diarrhea virus isolates from a 2013 series of outbreaks. We discovered a unique special feature of the viral genome, an unstable duplication of 222 nucleotides which is eventually deleted by viral polymerase activity, leading to an unexpectedly mixed population of viral genomes for all investigated isolates. Our study is of high importance to the field because we demonstrate that these insertion/deletion events allow another level of genome plasticity of plus-strand RNA viruses, in addition to the well-known polymerase-induced single nucleotide variations which are generally considered the main basis for viral adaptation and evolution.","Animals;*Bovine Virus Diarrhea-Mucosal Disease/vi [Virology];Cattle;Diarrhea Virus 2, Bovine Viral/cl [Classification];*Diarrhea Virus 2, Bovine Viral/ge [Genetics];*Diarrhea Virus 2, Bovine Viral/ip [Isolation & Purification];Diarrhea Virus 2, Bovine Viral/py [Pathogenicity];Genome, Viral;High-Throughput Nucleotide Sequencing;Molecular Sequence Data;Nucleic Acid Conformation;Phylogeny;RNA, Viral/ch [Chemistry];RNA, Viral/ge [Genetics];Repetitive Sequences, Nucleic Acid;Virulence;0 (RNA, Viral)","Jenckel, M.;Hoper, D.;Schirrmeier, H.;Reimann, I.;Goller, K. V.;Hoffmann, B.;Beer, M.",2014,Jun,,0
891,"Identification of Two novel reassortant avian influenza a (H5N6) viruses in whooper swans in Korea, 2016","Background: On November 20, 2016 two novel strains of H5N6 highly pathogenic avian influenza virus (HPAIVs) were isolated from three whooper swans (Cygnus cygnus) at Gangjin Bay in South Jeolla province, South Korea. Identification of HPAIVs in wild birds is significant as there is a potential risk of transmission of these viruses to poultry and humans. Results: Phylogenetic analysis revealed that Gangjin H5N6 viruses classified into Asian H5 clade 2.3.4.4 lineage and were distinguishable from H5N8 and H5N1 HPAIVs previously isolated in Korea. With the exception of the polymerase acidic (PA) gene, the viruses were most closely related to A/duck/Guangdong/01.01SZSGXJK005-Y/2016 (H5N6) (98.90 ~ 99.74%). The PA genes of the two novel Gangjin H5N6 viruses were most closely related to AIV isolates previously characterized from Korea, A/hooded crane/Korea/1176/2016 (H1N1) (99.16%) and A/environment/Korea/W133/2006 (H7N7) (98.65%). The lack of more recent viruses to A/environment/Korea/W133/2006 (H7N7) indicates the need for analysis of recent wild bird AIVs isolated in Korea because they might provide further clues as to the origin of these novel reassortant H5N6 viruses. Conclusions: Although research on the origins and epidemiology of these infections is ongoing, the most likely route of infection for the whooper swans was through direct or indirect contact with reassortant viruses shed by migratory wild birds in Korea. As H5N6 HPAIVs can potentially be transmitted to poultry and humans, continuous monitoring of AIVs among wild birds will help to mitigate this risk.",cladistics;clinical article;duck;genetic reassortment;highly pathogenic avian influenza virus;human;Influenza A virus (H1N1);Influenza A virus (H5N1);Influenza A virus (H5N8);Influenza A virus (H7N7);Korea;monitoring;nonhuman;phylogeny;poultry;swan,"Jeong, J.;Woo, C.;Ip, H. S.;An, I.;Kim, Y.;Lee, K.;Jo, S. D.;Son, K.;Lee, S.;Oem, J. K.;Wang, S. J.;Kim, Y.;Shin, J.;Sleeman, J.;Jheong, W.",2017,,10.1186/s12985-017-0731-7,0
892,Genetic characterization of H1 avian influenza viruses isolated from migratory birds and domestic ducks in Korea,"H1 avian influenza viruses (AIVs) isolated from migratory birds and domestic ducks from 2003 to 2007 were analyzed to determine their genetic relationship. Phylogenic analysis with nucleotide sequences of all eight gene segments showed that 13 H1 AIVs from migratory birds and domestic ducks belonged to Eurasian avian lineages and were closely related to each other. Compared with H1 influenza viruses of swine or human origin in Korea, there was no evidence of reassortment among the human, swine, and avian hosts. Our results show that H1 AIVs isolated in Korea from 2003 to 2007 were genetically stable. However, continued surveillance is needed considering the role of migratory birds and domestic duck as a source of AIVs. © Springer Science+Business Media, LLC 2010.",article;avian influenza virus;bird;controlled study;domestic animal;duck;genetic reassortment;genetic stability;host pathogen interaction;human versus animal comparison;Korea;migratory species;molecular phylogeny;nonhuman;nucleotide sequence;priority journal;species comparison;pig;viral genetics;virus isolation;virus transmission,"Jeong, O. M.;Kim, Y. J.;Choi, J. G.;Kang, H. M.;Kim, M. C.;Kwon, J. H.;Lee, Y. J.",2011,,10.1007/s11262-010-0539-7,0
893,Detection of the Newcastle disease virus and its effect on development of post-vaccination immunity in a commercial flock of laying hens,"The aim of this study was to monitor the concentration of antibodies against Newcastle disease after vaccination of laying hens at the beginning and in the end of the laying period. The study was carried out in one commercial flock of laying hens in Opatovice in the Czech Republic in the years 2008-2010. A total of 280 samples of blood sera were taken from laying hens coming from four poultry houses. The sera were tested by the haemagglutination inhibition test according to the OIE Manual. Virological testing was conducted as a consequence of atypical results of serological testing. Newcastle disease virus RNA was proved by the RT-nested PCR method in the pooled tissue samples of 5 hens, in the samples of intestines with ileocaecal tonsila, in trachea and also in one swab sample from the environment of one house. Based on sequencing analysis and subsequent phylogenetic analysis, the virus was identified as a low pathogenic strain of paramyxovirus (PMV-1). This low pathogenic strain did not have any impact on the health of laying hens.",Poultry;antibodies;RT-nested PCR;sequencing;PROTEIN CLEAVAGE SITE;FUSION PROTEIN;EPIDEMIOLOGY;VIRULENT;STRAINS;REGION,"Jerabkova, J.;Juranova, R.;Rosenbergova, K.;Kulikova, L.;Hera, A.;Lany, P.;Kubicek, O.;Kolacek, J.",2012,,,0
894,"A new prototype IIS/IIC/IIG endonuclease-methyltransferase TsoI from the thermophile Thermus scotoductus, recognising 5'-TARCCA(N11/9)-3' sequences","The Thermus sp. family of IIS/IIG/IIC enzymes includes the thermostable, bifunctional, fused restriction endonuclease (REase)-methyltransferases (MTase): TaqII, Tth111II/TthHB27I, TspGWI, TspDTI and TsoI. The enzymes are large proteins (approximately 120. kDa), their enzymatic activities are affected by S-adenosylmethionine (SAM), they recognise similar asymmetric cognate sites and cleave at a distance of 11/9 nucleotides (nt). The enzymes exhibit similarities of their amino acid (aa) sequences and DNA catalytic motifs. Thermus sp. enzymes are an example of functional aa sequence homologies among REases recognising different, yet related DNA sequences. The family consists of TspGWI- and TspDTI-subfamilies. TsoI appears to be a non-identical 'triplet', related to TspDTI and Tth111II/TthHB27I. The discovery of TsoI, purified from Thermus scotoductus, is described. This prototype, displaying a novel specificity, which was determined by: (i) cleavage of a reference plasmid and bacteriophage DNA, (ii) cleavage of custom PCR DNA substrates, (iii) run-off sequencing of cleavage products and (iv) shotgun cloning and sequencing of bacteriophage lambda (λ) DNA digested with TsoI. The enzyme recognises a degenerated 5'-TARCCA-3' sequence, whereas DNA strands are cut 11/9 nt downstream. The discovery of the TsoI prototype is of practical importance in biotechnology, as it extends the palette of cleavage specificities for gene cloning.",bacterial enzyme;bacteriophage DNA;deoxyribozyme;DNA fragment;IIS IIC IIG endonuclease methyltransferase TsoI;plasmid DNA;restriction endonuclease;s adenosylmethionine;unclassified drug;3' untranslated region;5' untranslated region;amino acid sequence;article;bacterial strain;controlled study;DNA fragmentation;DNA protein complex;DNA purification;DNA sequence;DNA strand;DNA template;Enterobacteria phage lambda;enzyme active site;enzyme activity;enzyme assay;enzyme degradation;enzyme isolation;enzyme purification;enzyme specificity;horizontal gene transfer;molecular cloning;nonhuman;sequence homology;Thermus;Thermus scotoductus,"Jezewska-Frackowiak, J.;Lubys, A.;Vitkute, J.;Zakareviciene, L.;Zebrowska, J.;Krefft, D.;Skowron, M. A.;Zylicz-Stachula, A.;Skowron, P. M.",2015,,10.1016/j.jbiotec.2014.11.023,0
895,Characterization of the hemagglutinin gene of subtype H9 avian influenza viruses isolated in 2007-2009 in China,"Subtype H9 avian influenza viruses (AIVs) circulating in China have aroused concerns for their impact on poultry and risk to public health. In this report, three surveys of the viruses were reported, and the hemagglutinin gene of 55 strains of the viruses isolated in China in 2007-2009 was sequenced and analyzed. The results indicated that the prevalence of the viruses was rising in China, and most of the H9 AIVs circulating in the past decade in China belonged to sublineage h9.4.2. The viruses isolated in China in 2007-2009 were a little different from previous strains (genetic distances >7.1%). Meanwhile, a presumably predominant clade of the viruses circulating in China in 2007-2009 was identified. Mutation analysis suggested that the viruses have become of greater risk to public health in recent years. © 2009 Elsevier B.V. All rights reserved.",hemagglutinin;article;China;cladistics;controlled study;gene amplification;genetic distance;H9 avian influenza virus;hemagglutination;Influenza virus;mutational analysis;nonhuman;nucleotide sequence;phylogeny;priority journal;sequence alignment;sequence analysis;virus isolation;virus strain,"Ji, K.;Jiang, W. M.;Liu, S.;Chen, J. M.;Chen, J.;Hou, G. Y.;Li, J. P.;Huang, B. X.",2010,,10.1016/j.jviromet.2009.09.013,0
896,Transcriptome analysis of sheep oral mucosa response to Orf virus infection,"Contagious ecthyma is a highly contagious disease with worldwide distribution, which is caused by the Orf virus (ORFV) belonging to the Parapoxvirus. To study the alteration of host gene expression in response to ORFV infection at the transcriptional level, several young small-tailed Han sheep were inoculated with ORFV, and their oral mucosa tissue samples (T0, T3, T7 and T15) were collected on day 0, 3, 7 and 15 after ORFV infection respectively. RNA-seq transcriptome comparisons were performed, showing that 1928, 3219 and 2646 differentially expressed genes (DEGs) were identified among T3 vs. T0, T7 vs. T0, and T15 vs. T0 respectively. Gene Ontology (GO) analyses of the DEGs from these comparisons, revealed that ORFV might provoke vigorous immune response of the host cells during the early stage of infection. Moreover, GO and network analysis showed that positive and negative regulative mechanisms of apoptosis were integrated in the host cells through up or down-regulating the expression level of DEGs involved in apoptotic pathways, in order to reach a homeostasis of oral mucosa tissues during the exposure to ORFV infection. In conclusion, our study for the first time describes the direct effects of ORFV on the global host gene expression of its host using high-throughput RNA sequencing, which provides a resource for future characterizing the interaction mechanism between the mammalian host and ORFV.",transcriptome;animal experiment;animal model;apoptosis;article;controlled study;DNA virus infection;down regulation;gene expression regulation;genetic transcription;high throughput sequencing;homeostasis;host cell;immune response;male;mouth mucosa;nonhuman;ontology;Orf virus infection;RNA sequence;sheep;virus cell interaction,"Jia, H.;Zhan, L.;Wang, X.;He, X.;Chen, G.;Zhang, Y.;Feng, Y.;Wei, Y.;Zhang, Y.;Jing, Z.",2017,,10.1371/journal.pone.0186681,0
897,Phylogenetic analysis using E2 gene of classical swine fever virus reveals a new subgenotype in China,"Outbreaks of classical swine fever (CSF) have caused serious economic consequences in China. Phylogenetic analysis based on full-length E2 gene sequences showed that five classical swine fever virus (CSFV) isolates collected from Hunan province in 2011 and 2012, together with seven other isolates from neighboring provinces, Guangdong (5) and Guangxi (2), could be classified as a new subgenotype 2.1c, which may have been endemic in the south of China for at least fourteen years. Subgenotype 2.1c isolates share 90.2-94.9% and 89.9-93.8% nucleotide sequence similarity separately with those of subgenotype 2.1a and 2.1b in E2 gene, which are lower than the nucleotide identities between subgenotype 2.1a and 2.1b (91.1-95.7%). Further analysis based on a partial E2 gene sequence (216. nt) indicated that subgenotype 2.1c isolates are also circulating in Thailand. Alignment of E2 amino acid sequences showed that subgenotype 2.1c isolates exhibit a SPA. →. TPV substitution at positions 777 and 779 compared with subgenotypes 2.1a and 2.1b. © 2013 Elsevier B.V.",viral protein;amino acid sequence;amino acid substitution;animal tissue;article;China;controlled study;E2 gene;endemic disease;gene sequence;genotype;nonhuman;nucleotide sequence;Pestivirus;phylogeny;priority journal;sequence alignment;sequence analysis;sequence homology;Thailand;unindexed sequence;virus isolation,"Jiang, D. L.;Gong, W. J.;Li, R. C.;Liu, G. H.;Hu, Y. F.;Ge, M.;Wang, S. Q.;Yu, X. L.;Tu, C.",2013,,10.1016/j.meegid.2013.04.004,0
898,[The genotyping and molecular evolution of varicella-zoster virus],"Varicella-zoster virus (VZV, Human herpesvirus 3) is a member of the family Herpesviridae, and is classified as alpha-subfamily along with HSV-1 and HSV-2. VZV is the causative agent of chicken pox (varicella) mostly in children, after which it establishes latency in the sensory ganglia with the potential to reactivate at a later time to cause shingles (zoster). Increasing molecular epidemiological studies in recent years have been performed to monitor the mutations in VZV genome, discriminate vaccine virus from wild type virus, study the phylogeny of VZV strains throughout the world, and understand the evolution of the different clades of VZV. The progress has great impact on the fields of epidemiology, virology and bioinformatics. In this review, the currently available data concerning the geographic distribution and molecular evolution of VZV clades are discussed.",animal;classification;genetics;genotype;herpes zoster;human;isolation and purification;molecular evolution;molecular genetics;nucleotide sequence;phylogeny;review;Varicella zoster virus;virology,"Jiang, L. F.;Gan, L.;Chen, J. X.;Wang, M. L.",2012,,,0
899,Integrative analysis of differentially expressed microRNAs of pulmonary alveolar macrophages from piglets during H1N1 swine influenza A virus infection,"H1N1 swine influenza A virus (H1N1 SwIV) is one key subtype of influenza viruses with pandemic potential. MicroRNAs (miRNAs) are endogenous small RNA molecules that regulate gene expression. MiRNAs relevant with H1N1 SwIV have rarely been reported. To understand the biological functions of miRNAs during H1N1 SwIV infection, this study profiled differentially expressed (DE) miRNAs in pulmonary alveolar macrophages from piglets during the H1N1 SwIV infection using a deep sequencing approach, which was validated by quantitative real-time PCR. Compared to control group, 70 and 16 DE miRNAs were respectively identified on post-infection day (PID) 4 and PID 7. 56 DE miRNAs were identified between PID 4 and PID 7. Our results suggest that most host miRNAs are down-regulated to defend the H1N1 SwIV infection during the acute phase of swine influenza whereas their expression levels gradually return to normal during the recovery phase to avoid the occurrence of too severe porcine lung damage. In addition, targets of DE miRNAs were also obtained, for which bioinformatics analyses were performed. Our results would be useful for investigating the functions and regulatory mechanisms of miRNAs in human influenza because pig serves as an excellent animal model to study the pathogenesis of human influenza.",microRNA;animal;biology;cluster analysis;DNA sequence;down regulation;high throughput sequencing;immunology;Influenza A virus (H1N1);lung;lung alveolus macrophage;metabolism;orthomyxovirus infection;pathology;physiology;pig;protein protein interaction;real time polymerase chain reaction;swine disease;veterinary medicine;virology,"Jiang, P.;Zhou, N.;Chen, X.;Zhao, X.;Li, D.;Wang, F.;Bi, L.;Zhang, D.",2015,,10.1038/srep08167,0
900,Transcriptome analysis reveals dynamic changes in coxsackievirus A16 infected HEK 293T cells,"BACKGROUND: Coxsackievirus A16 (CVA16) and enterovirus 71 (EV71) are two of the major causes of hand, foot and mouth disease (HFMD) world-wide. Although many studies have focused on infection and pathogenic mechanisms, the transcriptome profile of the host cell upon CVA16 infection is still largely unknown. RESULTS: In this study, we compared the mRNA and miRNA expression profiles of human embryonic kidney 293T cells infected and non-infected with CVA16. We highlighted that the transcription of SCARB2, a cellular receptor for both CVA16 and EV71, was up-regulated by nearly 10-fold in infected cells compared to non-infected cells. The up-regulation of SCARB2 transcription induced by CVA16 may increase the possibility of subsequent infection of CVA16/EV71, resulting in the co-infection with two viruses in a single cell. This explanation would partly account for the co-circulation and genetic recombination of a great number of EV71 and CVA16 viruses. Based on correlation analysis of miRNAs and genes, we speculated that the high expression of SCARB2 is modulated by down-regulation of miRNA has-miR-3605-5p. At the same time, we found that differentially expressed miRNA target genes were mainly reflected in the extracellular membrane (ECM)-receptor interaction and circadian rhythm pathways, which may be related to clinical symptoms of patients infected with CVA16, such as aphthous ulcers, cough, myocarditis, somnolence and potentially meningoencephalitis. The miRNAs hsa-miR-149-3p and hsa-miR-5001-5p may result in up-regulation of genes in these morbigenous pathways related to CVA16 and further cause clinical symptoms. CONCLUSIONS: The present study elucidated the changes in 293T cells upon CVA16 infection at transcriptome level, containing highly up-regulated SCARB2 and genes in ECM-receptor interaction and circadian rhythm pathways, and key miRNAs in gene expression regulation. These results provided novel insight into the pathogenesis of HFMD induced by CVA16 infection.","Cells, Cultured;Cluster Analysis;*Enterovirus/ph [Physiology];*Gene Expression Profiling;*Gene Expression Regulation;Gene Regulatory Networks;HEK293 Cells;High-Throughput Nucleotide Sequencing;Humans;Lysosome-Associated Membrane Glycoproteins/ge [Genetics];MicroRNAs/ge [Genetics];RNA, Messenger/ge [Genetics];Receptors, Scavenger/ge [Genetics];*Transcriptome;0 (Lysosome-Associated Membrane Glycoproteins);0 (MicroRNAs);0 (RNA, Messenger);0 (Receptors, Scavenger);0 (SCARB2 protein, human)","Jin, J.;Li, R.;Jiang, C.;Zhang, R.;Ge, X.;Liang, F.;Sheng, X.;Dai, W.;Chen, M.;Wu, J.;Xiao, J.;Su, W.",2017,01 25,,0
901,Genetic characterization of a new astrovirus in goslings suffering from gout,"Since early 2016, the Chinese goose industry has experienced severe outbreaks of gout; however, the etiological factor of the disease is still unclear. Here, we investigated the possible involvement of viral infection in the disease. Using sequence-independent PCR amplification, astrovirus sequences were generated from a gout case. Full-length genomic sequencing and sequence analysis of three goose astrovirus (GoAstV) strains revealed that they belong to a new avastrovirus most closely related to viruses classified within species Avastrovirus 3. The GoAstV was detected in 16/16 gout cases collected from two provinces, supporting a pathogenic role for the new avastrovirus.",animal;astrovirus infection;Avastrovirus;bird disease;classification;duck;genetics;goose;gout;isolation and purification;open reading frame;phylogeny;turkey (bird);veterinary medicine;virology;virus genome,"Jin, M.;Wang, X.;Ning, K.;Liu, N.;Zhang, D.",2018,,10.1007/s00705-018-3932-5,0
902,Genome sequencing and characterization analysis of a Beiffing isolate of chicken coronavirus infectious bronchitis virus,"Avian infectious bronchitis virus (AIBV) is classified as a member of the genus coronavirus in the family coronaviridae. The enveloped virus has a positive-sense, single-stranded RNA genome of approximately 28 kilo-bases, which has a 5' cap structure and 3' polyadenylation tract. The complete genome sequence of infectious bronchitis virus (IBV), Beijing isolate, was determined by cloning sequencing and primer walking. The whole genome is 27733 nucleotides in length, has ten open reading frames: 5'-orf1a-orf1ab-s-3a-3b-e-m- 6a-6b-n-3'. Alignments of the genome sequence of IBV Beijing isolate with those of two AIBV strains and one SARS coronavirus were performed respectively. The genome sequence of IBV Beijing isolate compared with that of the IBV strain LX4 (uncompleted, 19440 bp in size) was 91.2% similarity. However, the full-length genome sequence of IBV Beijing isolate was 85.2% identity to that of IBV Strain Beaudette, and was only 50.8% homology to that of SARS coronavirus. The results showed that the genome of IBV has remarkable variation. And IBV Beijing isolate is not closely related to SARS coronavirus. Phylogenetic analyses based on the whole genome sequence, S protein, M protein and N protein, also showed that AIBV Beijing isolate is lone virus in group III and is distant from SARS coronavirus. In conclusion, this study will contribute to the studies of diagnosis and diseases control on IBV in China.",avian infectious bronchitis virus (AIBV);severe acute;respiratory;syndrome coronavirus (SARS-CoV);primer walking;sequence analysis;SEROTYPES;IBV,"Jin, W. W.;Chen, C.;Zhang, Y.;Zhao, Y. Q.;Feng, J. D.;Chen, F. Y.;Wu, Q. M.;Yang, H. C.;Wang, M.;Yu, J. L.;Li, N.;Gong, Y. S.;Sun, Q. X.;Chen, Z. L.",2004,Mar,,0
903,Detection and molecular characterization of enteric viruses in breeder turkeys,"The present study was undertaken to detect and characterize enteric viruses (rotavirus, astrovirus, reovirus, and coronavirus) in breeder poults. Five turkey breeder flocks were selected. Faecal samples were collected from all flocks at 1 week of age and then every other week until the poults reached 9 weeks of age. The faecal samples were pooled in groups of five. Of the 193 pools (""samples"") tested by reverse transcriptionpolymerase chain reaction, 47.2%, 30.6%, and 10.4% samples were positive for astrovirus, rotavirus, and reovirus, respectively. No coronavirus was detected in any of the samples. Overall, 118 (61.1%) samples were positive for one or more enteric viruses. Of the 118 samples, 70 (59.3%) were positive for a single virus and 48 (40.7%) for a combination of viruses. Phylogenetic analysis based on the polymerase gene showed that astroviruses clustered into two groups with sequence homology ranging from 85.6 to 100% at the nucleotide level. Based on NSP4 gene sequences, rotaviruses clustered in a group and had 96.3 to 99.9% sequence homology at the nucleotide level. The reoviruses, based on their S4 gene sequences, clustered in a single group with sequence homology of 96.9 to 100%. Differing amino acid sequences of all three viruses may affect the antigenicity and/or pathogenicity of these viruses and may merit further study. The presence of two or three different viruses in combination may affect the dynamics of turkey health and disease. © 2010 Houghton Trust Ltd.","glycoprotein;NS28 protein, rotavirus;sigma NS protein, Reovirus;toxin;viral protein;age;amino acid sequence;animal;animal disease;animal husbandry;article;Astroviridae;astrovirus infection;Avian orthoreovirus;Coronavirinae;feces;genetics;isolation and purification;phylogeny;Rotavirus;Rotavirus infection;transmissible enteritis of turkeys;turkey (bird);virology","Jindal, N.;Patnayak, D. P.;Chander, Y.;Ziegler, A. F.;Goyal, S. M.",2010,,10.1080/03079450903490289,0
904,Molecular characterization of foot-and-mouth disease virus in Hong Kong during 2001-2002,"Most of the molecular epidemiological studies of foot-and-mouth disease virus (FMDV) are based on comparison of VP1 gene sequence. In this report, The nucleotide sequences of the VP1 coding region of FMDV type O strains O/HKN/3/01, O/HKN/5/01, O/HKN/12/01, O/HKN/7/02 and O/HKN/10/02, isolated from the disease outbreak that occurred in Hong Kong Special Administrative Region (Hong Kong SAR) of China during 2001-2002, were determined and compared with the sequences of other FMDVs. The results revealed that the VP1 gene of the five isolates had the same nucleotide (nt) sequences (639 nt), coding for 213 amino acids, and no changes were found either at the critical amino acid sites 144 (Val), 148 (Leu), 154 (Lys) and 208 (Pro) within the VP1 protein epitope (amino acids 140-160, 200-213), or in the amino acids 145-147 comprising the arginine-glycine-aspartic acid (RGD) sequence that is involved in the adsorption of virus to host cell. Analysis of the VP1 gene nucleotide sequence revealed that the five isolates examined were most closely related to FMDVs found in Hong Kong from 1991 to 1999 and Taiwan in 1997. Furthermore, although the critical amino acids on the antigen epitope of the prevalent Hong Kong isolates and the serotype O vaccine strain, O1/Manisa/Turkey/69, showed relative conservativeness, they were distantly related genetically, which showed that there existed variation between the prevalent Hong Kong FMDV strains and the vaccine strain. © Springer Science+Business Media, Inc. 2006.",arginine derivative;aspartic acid derivative;epitope;leucine;lysine;proline;protein VP1;valine;amino acid sequence;article;China;comparative study;epidemic;Foot and mouth disease virus;genetic analysis;Hong Kong;molecular genetics;nonhuman;nucleotide sequence;priority journal;sequence analysis;virus gene;virus isolation;virus strain,"Jinding, C.;Mingqiu, Z.;Hui, K. H.;Leung, F. C.",2006,,10.1007/s11262-005-6869-1,0
905,One-Way Traffic of a Viral Motor Channel for Double-Stranded DNA Translocation,"Linear double-stranded DNA (dsDNA) viruses package their genome into a procapsid using an ATP-driven nanomotor. Here we report that bacteriophage phi29 DNA packaging motor exercises a one-way traffic property for dsDNA translocation from N-terminal entrance to C-terminal exit with a valve mechanism in DNA packaging, as demonstrated by voltage ramping, electrode polarity switching, and sedimentation force assessment. Without the use of gating control as Found in other biological channels, the observed single direction dsDNA transportation provides a novel system with a natural valve to control dsDNA loading and gene delivery in bioreactors, liposomes, or high throughput DNA sequencing apparatus.",Viral assembly;nanotechnology;nanostructure;nanobiotechnology;nanomedicine;bacteriophage phi29;liposomes;ion channel;rectification;DNA packaging;nanomotors;membrane channel;PACKAGING PROTEIN GP16;BACTERIAL-VIRUS PHI29;BACTERIOPHAGE-LAMBDA;PHAGE PHI-29;IN-VITRO;3-DIMENSIONAL STRUCTURE;NANOFLUIDIC DIODE;CRYSTAL-STRUCTURE;ATPASE ACTIVITIES;FORCE GENERATION,"Jing, P.;Haque, F.;Shu, D.;Montemagno, C.;Guo, P. X.",2010,Sep,,0
906,"Molecular analysis of hepatitis E virus from farm rabbits in Inner Mongolia, China and its successful propagation in A549 and PLC/PRF/5 cells","Rabbit hepatitis E virus (HEV) strains have recently been isolated in several areas of China and in the US and France. However, the host range, distribution and zoonotic potential of these HEV strains remain unknown and their propagation in cultured cells has not yet been reported. A total of 211 4-month-old rabbits raised on a farm in Inner Mongolia were tested for the presence of anti-HEV antibodies and HEV RNA. Overall, 121 rabbits (57.3%) tested positive for anti-HEV antibodies, and 151 (71.6%) had detectable HEV RNA. The 174 HEV strains recovered from these viremic rabbits, including two distinct strains each from 23 rabbits, differed from each other by up to 13.6% in a 412-nucleotide (nt) sequence within ORF2, and were 89.3-95.9% identical to the reported rabbit HEV strains in other provinces of China. Three representative Inner Mongolian strains, one each from three phylogenetic clusters, whose entire genomic sequences were determined, shared 79.6-96.7% identities with reported rabbit HEV strains within the entire or 242- to 1349-nt partial genomic sequence. Rabbit HEV strains recovered from liver tissues of rabbits with a high HEV load propagated efficiently in human cell lines (A549 and PLC/PRF/5 cells), suggesting the potential zoonotic risk of rabbit HEV. © 2012 Elsevier B.V.",animal experiment;animal tissue;article;China;farm animal;gene cluster;gene sequence;Hepatitis E virus;molecular biology;Mongolia;nonhuman;phylogeny;priority journal;Leporidae,"Jirintai, S.;Jinshan;Tanggis;Manglai, D.;Mulyanto;Takahashi, M.;Nagashima, S.;Kobayashi, T.;Nishizawa, T.;Okamoto, H.",2012,,10.1016/j.virusres.2012.09.015,0
907,Characterization of fitzroy river virus and serologic evidence of human and animal infection,"In northern Western Australia in 2011 and 2012, surveillance detected a novel arbovirus in mosquitoes. Genetic and phenotypic analyses confirmed that the new flavivirus, named Fitzroy River virus, is related to Sepik virus and Wes-selsbron virus, in the yellow fever virus group. Most (81%) isolates came from Aedes normanensis mosquitoes, providing circumstantial evidence of the probable vector. In cell culture, Fitzroy River virus replicated in mosquito (C6/36), mammalian (Vero, PSEK, and BSR), and avian (DF-1) cells. It also infected intraperitoneally inoculated weanling mice and caused mild clinical disease in 3 intracranially inoculated mice. Specific neutralizing antibodies were detected in sentinel horses (12.6%), cattle (6.6%), and chickens (0.5%) in the Northern Territory of Australia and in a subset of humans (0.8%) from northern Western Australia.",Aedes;animal experiment;Anopheles;antibody titer;Arbovirus;article;enzyme linked immunosorbent assay;female;fitzroy river virus;genetic recombination;hemagglutination inhibition;high throughput sequencing;human;limb weakness;male;mouse;nonhuman;nucleotide sequence;phenotype;photophobia;phylogeny;reverse transcription polymerase chain reaction;serology;virogenesis;virus identification;virus isolation;virus replication;virus virulence;whole genome sequencing,"Johansen, C. A.;Williams, S. H.;Melville, L. F.;Nicholson, J.;Hall, R. A.;Bielefeldt-Ohmann, H.;Prow, N. A.;Chidlow, G. R.;Wong, S.;Sinha, R.;Williams, D. T.;Lipkin, W. I.;Smith, D. W.",2017,,10.3201/eid2308.161440,0
908,Rat hepatitis E virus: Geographical clustering within Germany and serological detection in wild Norway rats (Rattus norvegicus),"Zoonotic hepatitis E virus (HEV) infection in industrialised countries is thought to be caused by transmission from wild boar, domestic pig and deer as reservoir hosts. The detection of HEV-specific antibodies in rats and other rodents has suggested that these animals may represent an additional source for HEV transmission to human. Recently, a novel HEV (ratHEV) was detected in Norway rats from Hamburg, Germany, showing the typical genome organisation but a high nucleotide and amino acid sequence divergence to other mammalian and to avian HEV strains. Here we describe the multiple detection of ratHEV RNA and HEV-specific antibodies in Norway rats from additional cities in north-east and south-west Germany. The complete genome analysis of two novel strains from Berlin and Stuttgart confirmed the association of ratHEV to Norway rats. The present data indicated a continuing existence of this virus in the rat populations from Berlin and Hamburg. The phylogenetic analysis of a short segment of the open reading frame 1 confirmed a geographical clustering of the corresponding sequences. Serological investigations using recombinant ratHEV and genotype 3 capsid protein derivatives demonstrated antigenic differences which might be caused by the high amino acid sequence divergence in the immunodominant region. The high amount of animals showing exclusively ratHEV RNA or anti-ratHEV antibodies suggested a non-persistent infection in the Norway rat. Future studies have to prove the transmission routes of the virus in rat populations and its zoonotic potential. The recombinant ratHEV antigen generated here will allow future seroepidemiological studies to differentiate ratHEV and genotype 3 infections in humans and animals. © 2012 Elsevier B.V.",capsid protein;virus antibody;amino acid sequence;animal experiment;animal model;antibody response;antibody titer;antigenicity;article;controlled study;genotype;geographic distribution;geographic origin;Germany;Hepatitis E virus;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;rat;rat strain;sequence analysis;serology;virus detection;virus strain;virus transmission;wild Norway rat,"Johne, R.;Dremsek, P.;Kindler, E.;Schielke, A.;Plenge-Bönig, A.;Gregersen, H.;Wessels, U.;Schmidt, K.;Rietschel, W.;Groschup, M. H.;Guenther, S.;Heckel, G.;Ulrich, R. G.",2012,,10.1016/j.meegid.2012.02.021,0
909,Hepeviridae: An expanding family of vertebrate viruses,"The hepatitis E virus (HEV) was first identified in 1990, although hepatitis E-like diseases in humans have been recorded for a long time dating back to the 18th century. The HEV genotypes 1-4 have been subsequently detected in human hepatitis E cases with different geographical distribution and different modes of transmission. Genotypes 3 and 4 have been identified in parallel in pigs, wild boars and other animal species and their zoonotic potential has been confirmed. Until 2010, these genotypes along with avian HEV strains infecting chicken were the only known representatives of the family Hepeviridae. Thereafter, additional HEV-related viruses have been detected in wild boars, distinct HEV-like viruses were identified in rats, rabbit, ferret, mink, fox, bats and moose, and a distantly related agent was described from closely related salmonid fish. This review summarizes the characteristics of the so far known HEV-like viruses, their phylogenetic relationship, host association and proposed involvement in diseases. Based on the reviewed knowledge, a suggestion for a new taxonomic grouping scheme of the viruses within the family Hepeviridae is presented.",3' untranslated region;5' untranslated region;bat;bird;Mustela putorius furo;fish;fox;gene identification;genome analysis;geographic distribution;Hepatitis E virus;Hepeviridae;Hepevirus;Neovison vison;moose;nonhuman;nucleotide sequence;open reading frame;phylogenetic tree;Leporidae;review;virus detection;virus genome;virus morphology;virus strain;virus transmission;European wild boar,"Johne, R.;Dremsek, P.;Reetz, J.;Heckel, G.;Hess, M.;Ulrich, R. G.",2014,,10.1016/j.meegid.2014.06.024,0
910,Sequence analysis of the VP6-encoding genome segment of avian group F and G rotaviruses,"Rotavirus groups A to E are mainly defined by antibody reactivity to the capsid protein VP6. Additionally, two putative rotavirus groups (F and G) have been identified in birds. Here, the first nucleotide sequences of the VP6-encoding genome segment of group F (strain 03V0568) and group G (strain 03V0567) rotaviruses, both derived from chickens, are presented. The group F rotavirus is most closely related to avian group A and D rotaviruses, with 49.9-52.3% nucleotide and 36.5-39.0% amino acid sequence identity. The group G rotavirus is most closely related to mammalian group B rotaviruses, with 55.3-57.5% nucleotide and 48.2-49-9% amino acid sequence identity. The terminal sequences of the genome segment were similar in groups A, D and F, and in groups B and G. The findings indicate a long-term evolution of rotavirus groups in two separated clades and support the development of a sequence-based classification system for rotavirus groups. © 2011 Elsevier Inc.",arginine;glutamic acid;nucleotide;protein VP6;amino acid sequence;article;chicken;controlled study;nonhuman;nucleotide sequence;phylogeny;priority journal;Rotavirus;Rotavirus A;Rotavirus B;Rotavirus D;Rotavirus F;Rotavirus G;sequence alignment;sequence analysis;virus genome,"Johne, R.;Otto, P.;Roth, B.;Löhren, U.;Belnap, D.;Reetz, J.;Trojnar, E.",2011,,10.1016/j.virol.2011.01.031,0
911,Epidemiology of rabies in Southeast Europe,"Rabies remains endemic within a number of countries in Southeast Europe including Romania, Bulgaria and Turkey. With the probable expansion of the European Union eastwards, it is likely that rabies elimination programs will be increased to reduce the burden of disease in new accession countries. A clear understanding of the epidemiology of the virus in this area of Europe is vital before such programs are introduced. With the exception of Turkey, the red fox (Vulpes vulpes) is the principal disease reservoir in Southeastern Europe. However, cases of rabies in the dog (Canis familiaris) are regularly reported. In contrast to Northern Europe, the raccoon dog (Nyctereutes procyonoides) does not appear to be a vector in the south. This study summarises the current rabies situation in Southeast Europe and demonstrates the phylogenetic relationships between the viruses in a number of the countries within the region. Rabies virus RNA was extracted from original samples and a fragment of the nucleoprotein gene amplified by reverse-transcriptase PCR. Automated sequencing was used to derive nucleoprotein gene sequences and these were used to prepare a molecular phylogeny of rabies viruses in Southeast Europe. In Bulgaria, the dog is the main vector bringing rabies into contact with humans and livestock. However, other species may also act as reservoirs for the disease, complicating the development of elimination strategies. The fox is the principal reservoir species for rabies in Romania although cases in dogs are regularly reported. Despite a gradual decline in dog rabies, urban pockets of the disease remain in many regions of Turkey. Furthermore, there is some evidence that the fox has been a significant vector for rabies and may be responsible for increases in rabies in cattle in the Aegean region of the country. Throughout the region there is evidence for cross-border movement of rabies by both wildlife and canine vectors.",rabies vaccine;virus RNA;animal;animal disease;bovine;cattle disease;chemistry;classification;conference paper;disease carrier;dog;dog disease;Eastern Europe;Europe;female;fox;genetics;human;immunology;isolation and purification;male;phylogeny;rabies;Rabies virus;species difference;virology,"Johnson, N.;Freuling, C.;Vos, A.;Un, H.;Valtchovski, R.;Turcitu, M.;Dumistrescu, F.;Vuta, V.;Velic, R.;Sandrac, V.;Aylan, O.;Müller, T.;Fooks, A. R.",2008,,,0
912,The in-feed antibiotic carbadox induces phage gene transcription in the swine gut microbiome,"Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases. When the beta diversities of microbial FIGfam annotations were compared, the control and carbadox communities were distinct 2 days after carbadox introduction. This effect was driven by carbadox-associated lower expression of FIGfams (n = 66) related to microbial respiration, carbohydrate utilization, and RNA metabolism (q < 0.1), suggesting bacteriostatic or bactericidal effects within certain populations. Interestingly, carbadox treatment caused greater expression of FIGfams related to all stages of the phage lytic cycle 2 days following the introduction of carbadox (q ≤0.07), suggesting the carbadox-mediated induction of prophages and phage DNA recombination. These effects were diminished by 7 days of continuous carbadox in the feed, suggesting an acute impact. Additionally, the viromes included a few genes that encoded resistance to tetracycline, aminoglycoside, and betalactam antibiotics but these did not change in frequency over time or with treatment. The results show decreased bacterial growth and metabolism, prophage induction, and potential transduction of bacterial fitness genes in swine gut bacterial communities as a result of carbadox administration. IMPORTANCE FDA regulations on agricultural antibiotic use have focused on antibiotics that are important for human medicine. Carbadox is an antibiotic not used in humans but frequently used on U.S. pig farms. It is important to study possible side effects of carbadox use because it has been shown to promote bacterial evolution, which could indirectly impact antibiotic resistance in bacteria of clinical importance. Interestingly, the present study shows greater prophage gene expression in feces from carbadox-fed animals than in feces from nonmedicated animals 2 days after the initiation of in-feed carbadox treatment. Importantly, the phage genetic material isolated in this study contained genes that could provide resistance to antibiotics that are important in human medicine, indicating that human-relevant antibiotic resistance genes are mobile between bacteria via phages. This study highlights the collateral effects of antibiotics and demonstrates the need to consider diverse antibiotic effects whenever antibiotics are being used or new regulations are considered.",aminoglycoside antibiotic agent;beta lactam antibiotic;carbadox;double stranded DNA;metatranscriptome;RNA 16S;tetracycline;transcriptome;unclassified drug;animal food;antibiotic resistance;article;bacterial growth;bacterial metabolism;bacterial phenomena and functions;bacterial respiration;bactericidal activity;bacteriostasis;carbohydrate metabolism;controlled study;DNA recombination;drug effect;feces analysis;gene expression regulation;gene function;gene mapping;genetic database;genetic transcription;genetic variability;gut microbiome;heredity;horizontal gene transfer;in vivo study;longitudinal study;metagenome;metagenomics;metatranscriptomics;microbial community;microbial respiration;microbiome;nonhuman;open reading frame;phylogenetic tree;pig;population dynamics;priority journal;prophage;RNA gene;RNA metabolism;sequence analysis;sequence homology;taxonomic inference;taxonomy;transcriptomics;virome,"Johnson, T. A.;Looft, T.;Severin, A. J.;Bayles, D. O.;Nasko, D. J.;Wommack, K. E.;Howe, A.;Allen, H. K.",2017,,10.1128/mBio.00709-17,0
913,Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue,"Background: Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic bacteria in lung tissue following stress and/or viral infection. Next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis) is a powerful culture-independent open reference method that has recently been used to increase understanding of BRD-associated bacteria in the upper respiratory tract of BRD cattle. However, it has not yet been used to examine the microbiome of the bovine lower respiratory tract. The objective of this study was to use NGS 16S amplicon analysis to identify bacteria in post-mortem lung and lymph node tissue samples harvested from fatal BRD cases and clinically healthy animals. Cranial lobe and corresponding mediastinal lymph node post-mortem tissue samples were collected from calves diagnosed as BRD cases by veterinary laboratory pathologists and from clinically healthy calves. NGS 16S amplicon libraries, targeting the V3-V4 region of the bacterial 16S rRNA gene were prepared and sequenced on an Illumina MiSeq. Quantitative insights into microbial ecology (QIIME) was used to determine operational taxonomic units (OTUs) which corresponded to the 16S rRNA gene sequences. Results: Leptotrichiaceae, Mycoplasma, Pasteurellaceae, and Fusobacterium were the most abundant OTUs identified in the lungs and lymph nodes of the calves which died from BRD. Leptotrichiaceae, Fusobacterium, Mycoplasma, Trueperella and Bacteroides had greater relative abundances in post-mortem lung samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Leptotrichiaceae, Mycoplasma and Pasteurellaceae showed higher relative abundances in post-mortem lymph node samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Two Leptotrichiaceae sequence contigs were subsequently assembled from bacterial DNA-enriched shotgun sequences. Conclusions: The microbiomes of the cranial lung lobe and mediastinal lymph node from calves which died from BRD and from clinically healthy H-F calves have been characterised. Contigs corresponding to the abundant Leptotrichiaceae OTU were sequenced and found not to be identical to any known bacterial genus. This suggests that we have identified a novel bacterial species associated with BRD.",RNA 16S;animal tissue;article;bacterial growth;bacterium;bacterium identification;Bacteroides;biochemical equipment;bioinformatics;cattle disease;Clostridium;controlled study;disease association;female;Fusobacterium;gene library;Helcococcus;histopathology;Leptotrichiaceae;lung;male;mediastinum lymph node;metagenomics;Mycoplasma;nonhuman;Pasteurellaceae;population abundance;Prevotella;real time polymerase chain reaction;sequence analysis;spectrophotometry;taxonomic identification;Trueperella;Ureaplasma;Illumina MiSeq,"Johnston, D.;Earley, B.;Cormican, P.;Murray, G.;Kenny, D. A.;Waters, S. M.;McGee, M.;Kelly, A. K.;McCabe, M. S.",2017,,10.1186/s12917-017-1035-2,0
914,Identification of avian influenza virus subtype H9N2 in chicken farms in Indonesia,"Avian influenza virus subtype H9N2 (AIV-H9N2) has become established in domestic poultry in Asia and Africa. AIV-H9N2 has not been reported previously in Indonesia. Here we describe the presence of AIV-H9N2 in chicken farms in Indonesia. Ninety-nine cases were observed in various provinces in Indonesia. Clinical signs, pathologic lesions and egg production were recorded. Confirmation was made using virus isolation, reverse transcriptase PCR (RT-PCR), and sequencing. To construct hemaglutinin (HA) phylogeny, the secondary data of Eurasian lineages were downloaded from GenBank. For neuraminidase, five sequences with the highest similarities with every sequence found in this study were downloaded. Phylogeny was inferred using Neighbor-Joining method in MEGA6 package. Forty-nine AIV-H9N2-positive cases were observed, of which 35 were tested positive for AIV-H9N2 only. The age of the infected chickens was 43.17 ± 16.56 weeks, and their egg production was 35.85 ± 17.80% lower than before outbreak. BLAST search revealed that the nucleotide sequence of the HA-encoding gene identified in this study shared 98% sequence identity with that of A/Muscovy duck/Vietnam/LBM719/2014(H9N2), while its neuraminidase-encoding gene sequences shared 94%, 98%, and 100% identities with three different influenza viruses. The phylogeny shows that the HA of AIV-H9N2 found in this study forms distinct cluster with some Vietnam and China's sequence data. The NA sequence data form three distinct clusters. We conclude that AIV-H9N2 is widespread in many provinces in Indonesia. To lessen economic losses to the poultry industry, flock biosecurity and vaccination against this virus subtype should be implemented rapidly. Thorough and rigid AIV surveillance is paramount to prevent further veterinary and public health consequences of the circulation of this virus in Indonesia.",hemagglutinin;sialidase;agricultural land;article;avian influenza virus;chicken;egg production;GenBank;gene identification;gene sequence;genetic code;Indonesia;Influenza A virus (H9N2);neighbor joining method;nonhuman;nucleotide sequence;phylogeny;priority journal;reverse transcription polymerase chain reaction;virus identification;virus isolation,"Jonas, M.;Sahesti, A.;Murwijati, T.;Lestariningsih, C. L.;Irine, I.;Ayesda, C. S.;Prihartini, W.;Mahardika, G. N.",2018,,10.1016/j.prevetmed.2018.09.003,0
915,"Molecular identification and characterization of novel coronaviruses infecting graylag geese (Anser anser), feral pigeons (Columbia livia) and mallards (Anas platyrhynchos)","In light of the finding of a previously unknown coronavirus as the aetiology of the severe acute respiratory syndrome (SARS), it is probable that other coronaviruses, than those recognized to date, are circulating in animal populations. Here, the results of a screening for coronavirus are presented, using a universal coronavirus RT-PCR, of the bird species graylag goose (Anser anser), feral pigeon (Columbia livia) and mallard (Anas platyrhynchos). Coronaviruses were found in cloacal swab samples from all the three bird species. In the graylag goose, 40 of 163 sampled birds were coronavirus positive, whereas two of 100 sampled pigeons and one of five sampled mallards tested positive. The infected graylag geese showed lower body weights compared with virus-negative birds, suggesting clinical significance of the infection. Phylogenetic analyses performed on the replicase gene and nucleocapsid protein sequences, indicated that the novel coronaviruses described in the present study all branch off from group III coronaviruses. All the novel avian coronaviruses harboured the conserved s2m RNA structure in their 3′ untranslated region, like other previously described group III coronaviruses, and like the SARS coronavirus. Sequencing of the complete nucleocapsid gene and downstream regions of goose and pigeon coronaviruses, evidenced the presence of two additional open reading frames for the goose coronavirus with no sequence similarity to known proteins, but with predicted transmembrane domains for one of the encoded proteins, and one -additional open reading frame for the pigeon coronavirus, with a predicted transmembrane domain, downstream of the nucleocapsid gene. © 2005 SGM.",nucleocapsid protein;RNA polymerase;3' untranslated region;amino acid sequence;Anas platyrhynchos;animal disease;animal experiment;animal tissue;Anser anser;article;bird;body weight disorder;cloaca;Columbia livia;controlled study;Coronavirinae;downstream processing;female;genetic conservation;goose;male;nonhuman;nucleotide sequence;open reading frame;phylogeny;Columbidae;priority journal;promoter region;protein domain;reverse transcription polymerase chain reaction;RNA structure;sampling;SARS coronavirus;sequence analysis;sequence homology;species difference;virus classification;virus identification;virus infection,"Jonassen, C. M.;Kofstad, T.;Larsen, I. L.;Løvland, A.;Handeland, K.;Follestad, A.;Lillehaug, A.",2005,,10.1099/vir.0.80927-0,0
916,Phylogenetic analysis of bovine pestiviruses: testing the evolution of clinical symptoms,"This study presents a phylogenetic analysis of 115 bovine pestiviruses. A sequence data set front the 5' untranslated genomic region was analyzed with maximum parsimony, bootstrapping and parsimony jackknifing. We tested for the proposed classifications of the group and analyzed the evolution of the symptoms associated with Pestivirus infections in bovines. Based on the historical framework provided by our phylogenetic trees, we also characterized the extent and importance of contamination caused in biologicals by the virus. Our phylogenetic analyses showed that the previously defined genotypes are monophyletic. except for genotype 1a. Based on our cladograms, we propose the existence of more than 12 monophyletic groups within the species BVDV 1. The mapping of clinical symptoms suggests that the emergence of some genotypes could have been driven by a change in the pathogenic process. Enteric Problems appear to be ancestral, while Reproductive and Respiratory Problems arise with the emergence of genotypes 1b, 1d and the herein-proposed genotype Arg 1. The distribution of contaminant strains on the cladograms shows that pestiviral contamination is a common process, and also suggests that a contaminated product might be a vehicle for virus dispersion. Implications for virus evolution, virus taxonomy, veterinary medicine and biotechnology are discussed. (C) The Willi Hennig Society 2004.",VIRAL DIARRHEA VIRUS;GENETIC-HETEROGENEITY;RESPIRATORY-DISEASE;BVDV;INFECTIONS;MUCOSAL DISEASE;BORDER DISEASE;DAIRY HERDS;CATTLE;SEQUENCE;VACCINE,"Jones, L. R.;Cigliano, M. M.;Zandomeni, R. O.;Weber, E. L.",2004,Oct,,0
917,Homologous recombination in bovine pestiviruses - Phylogenetic and statistic evidence,"Bovine pestiviruses (Bovine Viral Diarrea Virus 1 (BVDV 1) and Bovine Viral Diarrea Virus 2 (BVDV 2)) belong to the genus Pestivirus (Flaviviridae), which is composed of positive stranded RNA viruses causing significant economic losses world-wide. We used phylogenetic and bootstrap analyses to systematically scan alignments of previously sequenced genomes in order to explore further the evolutionary mechanisms responsible for variation in the virus. Previously published data suggested that homologous crossover might be one of the mechanisms responsible for the genomic rearrangements observed in cytopathic (cp) strains of bovine pestiviruses. Nevertheless, homologous recombination involves not just homologous crossovers, but also replacement of a homologous region of the acceptor RNA. Furthermore, cytopathic strains represent dead paths in evolution, since they are isolated exclusively from the fatal cases of mucosal disease. Herein, we report evidence of homologous inter-genotype recombination in the genome of a non-cytopathic (ncp) strain of Bovine Viral Diarrea Virus 1, the type species of the genus Pestivirus. We also show that intra-genotype homologous recombination might be a common phenomenon in both species of Pestivirus. This evidence demonstrates that homologous recombination contribute to the diversification of bovine pestiviruses in nature. Implications for virus evolution, taxonomy and phylogenetics are discussed. © 2004 Elsevier B.V. All rights reserved.",article;Bovine viral diarrhea virus 1;cattle disease;controlled study;cytopathogenic effect;evolution;genetic variability;genotype;homologous recombination;nonhuman;nucleotide sequence;Pestivirus;phylogeny;priority journal;species difference;statistical analysis;taxonomy;virus strain,"Jones, L. R.;Weber, E. L.",2004,,10.1016/j.meegid.2004.04.004,0
918,Emergence of the virulence-associated PB2 E627K substitution in a fatal human case of highly pathogenic avian influenza virus A(H7N7) infection as determined by Illumina ultra-deep sequencing,"Avian influenza viruses are capable of crossing the species barrier and infecting humans. Although evidence of human-to-human transmission of avian influenza viruses to date is limited, evolution of variants toward more-efficient human-to-human transmission could result in a new influenza virus pandemic. In both the avian influenza A(H5N1) and the recently emerging avian influenza A(H7N9) viruses, the polymerase basic 2 protein (PB2) E627K mutation appears to be of key importance for human adaptation. During a large influenza A(H7N7) virus outbreak in the Netherlands in 2003, the A(H7N7) virus isolated from a fatal human case contained the PB2 E627K mutation as well as a hemagglutinin (HA) K416R mutation. In this study, we aimed to investigate whether these mutations occurred in the avian or the human host by Illumina Ultra-Deep sequencing of three previously uninvestigated clinical samples obtained from the fatal case. In addition, we investigated three chicken samples, two of which were obtained from the source farm.","*Amino Acid Substitution;Animals;Chickens;Fatal Outcome;High-Throughput Nucleotide Sequencing;Humans;*Influenza A Virus, H7N7 Subtype/en [Enzymology];Influenza A Virus, H7N7 Subtype/ge [Genetics];Influenza A Virus, H7N7 Subtype/ip [Isolation & Purification];*Influenza A Virus, H7N7 Subtype/py [Pathogenicity];*Influenza in Birds/vi [Virology];*Influenza, Human/vi [Virology];Male;Mutation Rate;Mutation, Missense;*Poultry Diseases/vi [Virology];*RNA Replicase/ge [Genetics];RNA Replicase/me [Metabolism];*Viral Proteins/ge [Genetics];Viral Proteins/me [Metabolism];Virulence;0 (PB2 protein, Influenzavirus A);0 (Viral Proteins)","Jonges, M.;Welkers, M. R.;Jeeninga, R. E.;Meijer, A.;Schneeberger, P.;Fouchier, R. A.;de Jong, M. D.;Koopmans, M.",2014,Feb,,0
919,Bat related virus infection: A summary on reports from Thailand,"Bat is an interesting mammal that can fly. The disease of human beings relating to bat is very interesting but limited mentioned. There are many virus infections that can be transmitted to human beings by bat. Those virus infections are usually serious and difficult to manage. In this mini-review, the authors hereby summarize and discuss on the bat related virus infection mentioned in the previous publications in Thailand, a tropical country in Southeast Asia.",bat related virus infection;Coronavirus infection;disease surveillance;help seeking behavior;human;Kaeng Khoi virus infection;metagenomics;Nipah virus infection;nonhuman;priority journal;public health;rabies;severe acute respiratory syndrome;short survey;Thailand;virus detection;virus infection;virus shedding;virus strain;virus transmission;zoonosis,"Joob, B.;Wiwanitkit, V.",2017,,10.12980/apjtd.7.2017D7-27,0
920,Detection of Fowlpox virus carrying distinct genome segments of Reticuloendotheliosis virus,"Fowlpox virus (FWPV), the type species of the genus Avipoxvirus family Poxviridae, is a large double-stranded DNA virus that causes fowlpox in chickens and turkeys. Notably, sequences of the avian retrovirus reticuloendotheliosis virus (REV) are frequently found integrated into the genome of FWPV. While some FWPV strains carry remnants of the REV long terminal repeats (LTRs), other strains have been shown to contain insertions of nearly the full-length REV provirus in their genome. In the present study we detected heterogeneous FWPV populations carrying the REV LTR or the near full-length REV provirus genome in a Merriam's wild turkey (Meleagris gallopavo merriami). The bird presented papules distributed throughout the non-feathered areas of the head. Avipoxvirus-like virions were observed in the lesions by transmission electron microscopy and the presence of FWPV was confirmed by DNA sequencing. Metagenomic sequencing performed on nucleic acid extracted from the skin lesions revealed two FWPV genome populations carrying either a 197-nt remnant of the REV LTR or a 7939-nt long fragment corresponding to the full-length REV provirus. Notably, PCR amplification using primers targeting FWPV sequences flanking the REV insertion site, confirmed the natural occurrence of the heterogeneous FWPV genome populations in one additional clinical sample from another turkey affected by fowlpox. Additionally, sequencing of a historical FWPV isolate obtained from chickens in the US in 2000 also revealed the presence of the two FWPV-REV genome populations. Results here demonstrate distinct FWPV populations containing variable segments of REV genome integrated into their genome. These distinct genome populations are likely a result of homologous recombination events that take place during FWPV replication.",animal cell;animal cell culture;article;DNA sequence;fibroblast;fowlpox;Fowlpox virus;histopathology;homologous recombination;long terminal repeat;male;Meleagris gallopavo;metagenomics;next generation sequencing;nonhuman;papule;polymerase chain reaction;priority journal;Reticuloendotheliosis virus;skin defect;transmission electron microscopy;virion;virus detection;virus genome;virus replication,"Joshi, L. R.;Bauermann, F. V.;Hain, K. S.;Kutish, G. F.;Armién, A. G.;Lehman, C. P.;Neiger, R.;Afonso, C. L.;Tripathy, D. N.;Diel, D. G.",2019,,10.1016/j.virusres.2018.10.017,0
921,"West Nile virus lineage 2 infection in a blood donor from Vienna, Austria, August 2014","Eastern Austria is neighbouring regions with ongoing West Nile virus (WNV) transmissions. Three human WNV infections had been diagnosed during the past decade in Austria. The Austrian Red Cross Blood Service (ARC-BS) started a first voluntary screening for WNV in blood donors from Eastern Austria by Nucleic Acid Testing (NAT) in June 2014. This is also the most extensive WNV surveillance programme in humans in Austria so far. In August 2014, one autochthonous WNV infection was detected in a blood donor from Vienna. By now, one in 67,800 whole blood donations was found to be positive for WNV RNA.",virus RNA;adult;article;Austria;blood donor;case report;female;human;maculopapular rash;malaise;myalgia;nonhuman;priority journal;screening;West Nile fever;West Nile virus,"Jungbauer, C.;Hourfar, M. K.;Stiasny, K.;Aberle, S. W.;Cadar, D.;Schmidt-Chanasit, J.;Mayr, W. R.",2015,,10.1016/j.jcv.2015.01.003,0
922,Generation of henipavirus nucleocapsid proteins in yeast Saccharomyces cerevisiae,"Hendra and Nipah viruses are newly emerged, zoonotic viruses and their genomes have nucleotide and predicted amino acid homologies placing them in the family Paramyxoviridae. Currently these viruses are classified in the new genus Henipavirus, within the subfamily Paramyxovirinae, family Paramyxoviridae. The genes encoding HeV and NiV nucleocapsid proteins were cloned into the yeast Saccharomyces cerevisiae expression vector pFGG3 under control of GAL7 promoter. A high level of expression of these proteins (18-20 mg l-1 of yeast culture) was obtained. Mass spectrometric analysis confirmed the primary structure of both proteins with 92% sequence coverage obtained using MS/MS analysis. Electron microscopy demonstrated the assembly of typical herring-bone structures of purified recombinant nucleocapsid proteins, characteristic for other paramyxoviruses. The nucleocapsid proteins revealed stability in yeast and can be easily purified by cesium chloride gradient ultracentrifugation. HeV nucleocapsid protein was detected by sera derived from fruit bats, humans, horses infected with HeV, and NiV nucleocapsid protein was immunodetected with sera from, fruit bats, humans and pigs. The development of an efficient and cost-effective system for generation of henipavirus nucleocapsid proteins might help to improve reagents for diagnosis of viruses. © 2006 Elsevier B.V. All rights reserved.",cesium chloride;nucleocapsid protein;article;electron microscopy;fungus culture;Henipavirus;nonhuman;nucleotide sequence;priority journal;protein expression;protein purification;protein stability;protein structure;protein synthesis;Saccharomyces cerevisiae,"Juozapaitis, M.;Serva, A.;Zvirbliene, A.;Slibinskas, R.;Staniulis, J.;Sasnauskas, K.;Shiell, B. J.;Wang, L. F.;Michalski, W. P.",2007,,10.1016/j.virusres.2006.10.008,0
923,The MET gene is a common integration target in avian leukosis virus subgroup j-induced chicken hemangiomas,"Avian leukosis virus subgroup J (ALV-J) is a simple retrovirus that can cause hemangiomas and myeloid tumors in chickens and is currently a major economic problem in Asia. Here we characterize ALV-J strain PDRC-59831, a newly studied U.S. isolate of ALV-J. Five-day-old chicken embryos were infected with this virus, and the chickens developed myeloid leukosis and hemangiomas within 2 months after hatching. To investigate the mechanism of pathogenesis, we employed high-throughput sequencing to analyze proviral integration sites in these tumors. We found expanded clones with integrations in the MET gene in two of the five hemangiomas studied. This integration locus was not seen in previous work characterizing ALV-J-induced myeloid leukosis. MET is a known proto-oncogene that acts through a diverse set of signaling pathways and is involved in many neoplasms. We show that tumors harboring MET integrations exhibit strong overexpression of MET mRNA.",messenger RNA;scatter factor;scatter factor receptor;virus envelope protein;3' untranslated region;5' untranslated region;animal experiment;animal model;animal tissue;article;avian leukosis;Avian leukosis virus;Avian leukosis virus subgroup J;bird disease;bone marrow tumor;chicken;controlled study;embryo;envelope gene;gene deletion;gene expression regulation;gene function;gene identification;gene locus;gene overexpression;genetic similarity;hemangioma;high throughput sequencing;intracellular signaling;intron;MET gene;nonhuman;nucleotide sequence;phylogeny;priority journal;proto oncogene;strain identification;virus carcinogenesis;virus pathogenesis;virus strain,"Justice, J.;Malhotra, S.;Ruano, M.;Li, Y.;Zavala, G.;Lee, N.;Morgan, R.;Beemon, K.",2015,,10.1128/jvi.03225-14,0
924,Common viral integration sites identified in avian leukosis virus- induced B-cell lymphomas,"Avian leukosis virus (ALV) induces B-cell lymphoma and other neoplasms in chickens by integrating within or near cancer genes and perturbing their expression. Four genes—MYC, MYB, Mir-155, and TERT—have previously been identified as common integration sites in these virus-induced lymphomas and are thought to play a causal role in tumorigenesis. In this study, we employ high-throughput sequencing to identify additional genes driving tumorigenesis in ALV-induced B-cell lymphomas. In addition to the four genes implicated previously, we identify other genes as common integration sites, including TNFRSF1A, MEF2C, CTDSPL, TAB2, RUNX1, MLL5, CXorf57, and BACH2. We also analyze the genome-wide ALV integration landscape in vivo and find increased frequency of ALV integration near transcriptional start sites and within transcripts. Previous work has shown ALV prefers a weak consensus sequence for integration in cultured human cells. We confirm this consensus sequence for ALV integration in vivo in the chicken genome. IMPORTANCE Avian leukosis virus induces B-cell lymphomas in chickens. Earlier studies showed that ALV can induce tumors through insertional mutagenesis, and several genes have been implicated in the development of these tumors. In this study, we use high-throughput sequencing to reveal the genome-wide ALV integration landscape in ALV-induced B-cell lymphomas. We find elevated levels of ALV integration near transcription start sites and use common integration site analysis to greatly expand the number of genes implicated in the development of these tumors. Interestingly, we identify several genes targeted by viral insertions that have not been previously shown to be involved in cancer.",microRNA 155;telomerase reverse transcriptase;transcription factor RUNX1;animal experiment;animal tissue;article;Avian leukosis virus;B cell lymphoma;BACH2 gene;carcinogenesis;chicken;consensus sequence;controlled study;CTDSPL gene;CXorf57 gene;embryo;gene;gene expression;gene identification;gene insertion;genome;high throughput sequencing;MEF2C gene;MLL5 gene;nonhuman;oncogene myb;oncogene myc;priority journal;TNFRSF1A gene;transcription initiation site;tumor gene;virus DNA cell DNA interaction,"Justice, J. F.;Morgan, R. W.;Beemon, K. L.",2015,,10.1128/mBio.01863-15,0
925,Detection of hepatitis E virus in archived German wild boar serum samples,"Hepatitis E is a rare human disease in Central Europe commonly imported from endemic regions. For autochthonous infections a zoonotic transmission from pigs, deer and wild boar is assumed. Using three different RT-PCR protocols, hepatitis E virus (HEV) RNA was detected in 10 out of 189 (5.3%) serum samples collected in 1995/1996 from wild boars in Germany. Sequence analysis indicates a close relationship with genotype 3 isolates of pigs and humans from the Netherlands and Japan. The results indicate that HEV is present in Germany since more than 10 years and that wild boar may function as a reservoir for HEV. © 2007 Elsevier B.V. All rights reserved.",virus RNA;animal experiment;article;female;genotype;Hepatitis E virus;male;nonhuman;real time polymerase chain reaction;sequence analysis;serum;virus detection,"Kaci, S.;Nöckler, K.;Johne, R.",2008,,10.1016/j.vetmic.2007.10.030,0
926,Genetic heterogeneity of bovine viral diarrhoea virus (BVDV) isolates from Turkey: Identification of a new subgroup in BVDV-1,"Genetic heterogeneity of Turkish ruminant pestiviruses was investigated by phylogenetic analysis of complete Npro encoding nucleotide sequences. A total of 30 virus isolates obtained from 15 provinces around the country between 1997 and 2005 were included in the phylogenetic analysis. Virus isolates mostly originated from cattle with one isolate from sheep. The bovine isolates all belonged to BVDV-1, the sheep isolate to BVDV-2. Fifteen isolates formed a new subgroup within BVDV-1, tentatively named BVDV-1l. The remaining bovine isolates were typed as BVDV-1a (n = 4), BVDV-1b (n = 4), BVDV-1d (n = 3), BVDV-1f (n = 2) and BVDV-1h (n = 1). The isolates allocated to BVDV-1l originated from various geographical regions in different years. There was no correlation between genetic grouping and locations where isolates were obtained. Viruses originating from one farm in most cases belonged to the same subgroup (n = 5). This study indicates that the newly detected subgroup BVDV-1l is predominant and widespread in Turkey. Moreover, an ovine virus isolate was identified as the first member of BVDV-2 reported in Turkey. A serological survey using samples from western Turkey indicated that BVDV-2 is also present in cattle. © 2008 Elsevier B.V. All rights reserved.",article;Bovine viral diarrhea virus 1;bovine;controlled study;gene sequence;genetic analysis;nonhuman;phylogeny;reverse transcription polymerase chain reaction;serology;turkey (bird);virus identification;virus isolation,"Kadir, Y.;Christine, F.;Barbara, B. W.;Zeki, Y.;Feray, A.;Aykut, O.;Ibrahim, B.;Sibilina Cedillo, R.;Heinz-Jürgen, T.;Matthias, K.",2008,,10.1016/j.vetmic.2008.01.016,0
927,Virus propagation in a swine monocyte cell line,"The propagation of seventeen virus strains, classified into five virus families, in a swine monocyte cell line (SW/K99) was studied in the point of infective progeny production. The viruses examined were adapted to grow in a swine epithelial cell line (KSEK6) and were proved to show clear CPE in advance. These viruses were successively passaged in the monocyte cultures regardless of CPE occurrence. The cultures at 3rd passage level were titrated for their infectivity using KSEK6 cells. Out of the viruses examined, only Aujeszky's disease virus (ADV) was able to propagate in the monocytes. Four ADV strains, two virulent and two attenuated strains, were compared for their growth in two cell lines. The final amount of infective progeny measured at 72 hours incubation at 36.5 degrees C was almost in a similar order between 2 cell lines. However, the amount of infective progeny produced at 24 hours incubation was higher in SW/K99 cells than that in KSEK6 cells. The occurrence of CPE was also more evident in SW/K99 cells in an early incubation. The data indicate that viral susceptibility of the monocytes to ADV is higher than that of epithelium. Other viruses were abortive in the monocytes.",Adenoviridae;animal;article;cell line;monocyte;physiology;pig;virology;virus culture,"Kadoi, K.",2002,,,0
928,Full-length infectious clone of an Iranian isolate of chicken anemia virus,"An Iranian field strain of chicken anemia virus (CAV), designated IR CAV, was isolated in the Marek’s disease virus-transformed lymphoblastoid cell line MDCC-MSB1 (MSB1) culture for the first time. The full-length CAV DNA of this strain was cloned in the bacterial plasmid pTZ57R/T to create the molecular clone pTZ-CAV. The nucleotide and deduced amino acid sequences of viral proteins of IR CAV were compared with those of representative CAV sequences including reference and commercial vaccine strains. IR CAV was not related to vaccine strains and also found to have glutamine at positions 139 and 144 confirming previous studies in which such mutations were associated with a slow rate of virus spread in cell culture. pTZ-CAV was digested with PstI to release IR CAV DNA and then transfected into MSB1 cell by electroporation. The transfected cells showed cytopathic effect similar to virion-initiated infection. One-day old specific pathogen-free chicks were inoculated with the regenerated virus, which had been obtained from transfected MSB1 cells, and compared with the chicks inoculated with IR CAV. Gross lesions in the birds inoculated with the regenerated virus illustrated the infectious nature of the regenerated virus from the cloned IR CAV DNA.",glutamine;viral protein;virus DNA;amino acid sequence;animal cell;animal experiment;animal model;animal tissue;article;cell culture;chicken anemia virus;controlled study;cytopathogenic effect;germfree chicken;Iran;lymphoblastoid cell line;Marek disease;molecular cloning;nonhuman;nucleotide sequence;plasmid;virion;virus cell interaction;virus infection;virus isolation,"Kaffashi, A.;Eshratabadi, F.;Shoushtari, A.",2017,,10.1007/s11262-016-1417-8,0
929,Partial sequence of the DNA-dependent DNA polymerase gene of fowl adenoviruses: A reference panel for a general diagnostic PCR in poultry,"Adenoviruses are frequent infectious agents in different poultry species. The traditional, serological typing of new isolates by virus neutralisation tests is now in transition to be replaced by PCR and sequencing. The first PCRs, recommended for the detection of adenoviruses, had been designed to target the gene of the major capsid protein, the hexon. In birds, members of three different genera of the family Adenoviridae may occur. Accordingly, three specific hexon PCRs had to be elaborated for the detection of adenoviruses in poultry. A significantly more sensitive PCR, targeting the viral DNA-dependent DNA polymerase gene, has been described recently. This method proved to be an efficient alternative for the general detection of adenoviruses irrespective of their genus affiliation. Fowl adenoviruses (FAdVs), isolated from chicken to date, comprise twelve serotypes classified into five virus species (FAdV-A to E). The polymerase gene sequence has been determined yet only from three FAdV types representing three species. In the present work, the panel of polymerase gene sequences was completed with those of the rest of FAdVs. The newly determined sequences will facilitate the identification of new FAdV isolates as an existing species or as a putative new FAdV. Once the polymerase sequence is known, more specific PCRs for the amplification of the hexon and other genes can be designed and performed according to the preliminary species classification.",DNA directed DNA polymerase;virus DNA;adenovirus infection;animal;animal disease;article;Aviadenovirus;bird disease;enzymology;gene expression regulation;genetics;metabolism;nucleotide sequence;phylogeny;physiology;polymerase chain reaction;poultry;virology,"Kaján, G.;Sameti, S.;Benko, M.",2011,,10.1556/AVet.2011.006,0
930,Japanese encephalitis in a 114-month-old cow: pathological investigation of the affected cow and genetic characterization of Japanese encephalitis virus isolate,"Japanese encephalitis virus (JEV) is classified into the genus Flavivirus in the family Flaviviridae. JEV can cause febrile illness and encephalitis mainly in humans and horses, and occasionally in cattle. In late September 2010, a 114-month-old cow showed neurological symptoms similar to the symptoms observed in previous bovine cases of Japanese encephalitis (JE); therefore, we conducted virological and pathological tests on the cow. As a result, JEV was isolated from the cerebrum of the affected cow. We determined the complete genome sequence of the JEV isolate, which we named JEV/Bo/Aichi/1/2010, including the envelope (E) gene region and 3' untranslated region (3'UTR). Our phylogenetic analyses of the E region and complete genome showed that the isolate belongs to JEV genotype 1 (G1). The isolate, JEV/Bo/Aichi/1/2010, was most closely related to several JEV G1 isolates in Toyama Prefecture, Japan in 2007-2009 by the phylogenetic analysis of the E region. In addition, the nucleotide alignment revealed that the deletion in the 3'UTR was the same between JEV/Bo/Aichi/1/2010 and several other JEV G1 isolates identified in Toyama Prefecture in 2008-2009. A hemagglutination inhibition (HI) test was conducted for the detection of anti-JEV antibodies in the affected cow, and the test detected 2-mercaptoethanol (2-ME)-sensitive HI antibodies against JEV in the serum of the affected cow. The histopathological investigation revealed nonsuppurative encephalomyelitis in the affected cow, and the immunohistochemical assay detected JEV antigen in the cerebrum. We diagnosed the case as JE of a cow based on the findings of nonsuppurative encephalomyelitis observed in the central nervous system, JEV antigen detected in the cerebrum, JEV isolated from the cerebrum, and 2-ME-sensitive HI antibodies against JEV detected in the serum. This is the first reported case of JE in a cow over 24 months old.",virus antibody;animal;animal disease;article;blood;case report;bovine;cattle disease;epidemiology;female;genetics;Japanese encephalitis;Japanese encephalitis virus;phylogeny;virology,"Kako, N.;Suzuki, S.;Sugie, N.;Kato, T.;Yanase, T.;Yamakawa, M.;Shirafuji, H.",2014,,10.1186/1746-6148-10-63,0
931,Genetic reclassification of porcine enteroviruses,"The genetic diversity of porcine teschoviruses (PTVs; previously named porcine enterovirus 1) and most serotypes of porcine enteroviruses (PEVs) was studied. Following the determination of the major portion of the genomic sequence of PTV reference strain Talfan, the nucleotide and derived amino acid sequences of the RNA-dependent RNA polymerase (RdRp) region, the capsid VP2 region and the 3′ non-translated region (3′-NTR) were compared among PTVs and PEVs and with other picornaviruses. The sequences were obtained by RT-PCR and 3′-RACE with primers based on the sequences of Talfan and available PEV strains. Phylogenetic analysis of RdRp/VP2 and analysis of the predicted RNA secondary structure of the 3′-NTR indicated that PEVs should be reclassified genetically into at least three groups, one that should be assigned to PTVs and two PEV subspecies represented by strain PEV-8 V 13 and strain PEV-9 UKG4 10/73.",amino acid;capsid protein;primer DNA;RNA directed RNA polymerase;3' untranslated region;amino acid sequence;animal cell;article;biodiversity;comparative study;controlled study;Enterovirus;gene sequence;nonhuman;nucleotide sequence;phylogeny;Picornaviridae;prediction;priority journal;protein domain;reverse transcription polymerase chain reaction;RNA structure;serotype;species difference;pig;Teschovirus;viral genetics;virus capsid;virus classification;virus genome;virus strain;virus transcription,"Kaku, Y.;Sarai, A.;Murakami, Y.",2001,,,0
932,Influenza Vaccine Review,"Influenza viruses belong to Orthomyxoviridae RNA virus family and classify into three distinct types based on their major antigenic differences; influenza A, influenza B and influenza C. Influenza viruses cause the annual human epidemics, seasonal and pandemic. Seasonal influenza epidemics caused by influenza A and B viruses result in 3-5 million severe cases and thousands of deaths globally each year. Influenza pandemics caused by influenza A virus emerge at unpredictable intervals. The influenza A virus will cause epidemics and pandemics because of its spread from migrating birds, pigs, horses, and humans. Transmission can be human to human from fomites, coughing and sneezing. Pandemics are responsible for increased morbidity and mortality, compared with seasonal influenza. Four such pandemics have occurred in the past century, during 1918, 1957, 1968, and 2009. Influenza B causes only human to human spread with a particular emphasis on the fact that no other hosts are involved, therefore, not involved in pandemics. Influenza C is a mild disease.[1] It causes seasonal episodes of influenza such as Northern infections when they happen from September to March while Southern infections happen from May to September. Due to the variation in viruses responsible for infections in these two seasons; it needs two different sets of vaccines. Influenza generally has an incubation period of 2 days, ranging from 1 to 4 days.",,"Kalarikkal, S. M.;Jaishankar, G. B.",2018,01,,0
933,Co-circulation of three clusters of 793/B-like avian infectious bronchitis virus genotypes in Iranian chicken flocks,"Avian infectious bronchitis (IB) is an acute and highly contagious viral disease causing severe economic losses in the poultry industry. The 793/B IB virus is an important infectious bronchitis virus (IBV) genotype currently circulating in several countries, including Iran. One hundred confirmed IBV samples (between 2014 and 2015; from 15 provinces in Iran) were selected for genotyping based on S1 sequencing. After phylogenetic analysis, it was found that 30% of the IBV isolates belonged to the 793/B genotype. Results showed that the Iranian 793/B-like IBV isolates could be divided in to three clusters: 4/91-like (50%), 1/96-like (40%), and IB88-like (10%). The sequence similarity between Iranian 793/B-like IBV isolates is 87.69%-100%. The highest identity is between the 4/91 and IB88 clusters (96.38%), and the lowest similarity is between the 1/96 and IB88 clusters (87.62%). This study provides a comprehensive analysis of 793/B-type IBV in Iran and characterization of IBV molecular epidemiology in the country.",animal;Avian infectious bronchitis virus;bird disease;chicken;Coronavirus infection;genetics;genotype;Iran;phylogeny;veterinary medicine;virology,"Kalokhoran, A. Y.;Ghalyanchilangeroudi, A.;Hosseini, H.;Madadgar, O.;Karimi, V.;Hashemzadeh, M.;Hesari, P.;Zabihi Petroudi, M. T.;Najafi, H.",2017,,10.1007/s00705-017-3473-3,0
934,(Highly pathogenic) avian influenza as a zoonotic agent,"Zoonotic agents challenging the world every year afresh are influenza A viruses. In the past, human pandemics caused by influenza A viruses had been occurring periodically. Wild aquatic birds are carriers of the full variety of influenza virus A subtypes, and thus, most probably constitute the natural reservoir of all influenza A viruses. Whereas avian influenza viruses in their natural avian reservoir are generally of low pathogenicity (LPAIV), some have gained virulence by mutation after transmission and adaptation to susceptible gallinaceous poultry. Those so-called highly pathogenic avian influenza viruses (HPAIV) then cause mass die-offs in susceptible birds and lead to tremendous economical losses when poultry is affected. Besides a number of avian influenza virus subtypes that have sporadically infected mammals, the HPAIV H5N1 Asia shows strong zoonotic characteristics and it was transmitted from birds to different mammalian species including humans. Theoretically, pandemic viruses might derive directly from avian influenza viruses or arise after genetic reassortment between viruses of avian and mammalian origin. So far, HPAIV H5N1 already meets two conditions for a pandemic virus: as a new subtype it has been hitherto unseen in the human population and it has infected at least 438 people, and caused severe illness and high lethality in 262 humans to date (August 2009). The acquisition of efficient human-to-human transmission would complete the emergence of a new pandemic virus. Therefore, fighting H5N1 at its source is the prerequisite to reduce pandemic risks posed by this virus. Other influenza viruses regarded as pandemic candidates derive from subtypes H2, H7, and H9 all of which have infected humans in the past. Here, we will give a comprehensive overview on avian influenza viruses in concern to their zoonotic potential. © 2009 Elsevier B.V. All rights reserved.",avian influenza;bird disease;chemotaxonomy;flu like syndrome;genetic reassortment;genetic susceptibility;human;influenza;Influenza A virus;Influenza A virus (H5N1);nonhuman;pandemic;pathogenesis;poultry;review;seroconversion;virus cell interaction;virus characterization;virus classification;virus mutation;virus strain;virus transmission;virus virulence;zoonosis,"Kalthoff, D.;Globig, A.;Beer, M.",2010,,10.1016/j.vetmic.2009.08.022,0
935,Serologic classification of feline caliciviruses by plaque reduction neutralization and immunodiffusion,"Serologic classification of 14 isolates of feline caliciviruses was carried out, using plaque reduction neutralization tests. Sixty to 200 plaque forming units of virus were employed against 20 antibody units of hyperimmune goat antiserums prepared to individual isolates. The results established that these viruses were related in various degrees, but no 2 were identical. Arrangements in order of the greatest intergroup reactions yielded essentially 1 serotype with the exception of 1 virus showing 1 way neutralization reactions with heterologous isolates. The geographic origin, the site of viral isolation, or the plaque size had no relationship with the neutralization pattern. The F 9 isolate that showed the greatest intergroup reactions was proposed as the possible reference virus. The viruses were indistinguishable by using gel diffusion analysis against cat antiserums.",virus antibody;Caliciviridae;cat;cell culture;classification;methodology;microorganism;Picornaviridae;theoretical study;virus classification;virus inhibition;virus isolation,"Kalunda, M.;Lee, K. M.;Holmes, D. F.;Gillespie, J. H.",1975,,,0
936,Evidence of the co-circulation of enteric viruses in sewage and in the population of Greater Cairo,"Aims: To characterize major enteric viruses (enterovirus, rotavirus, norovirus, astrovirus and adenovirus) in the sewage of Greater Cairo and to compare the results with clinical data collected during the same period. Methods and Results: Seventy-two sewage samples from two waste water treatment plants were collected from April 2006 through February 2007. Enteroviruses, noroviruses (NoVs) and rotaviruses (RVs) were detected by RT-PCR in 22%, 18% and 8·3% of the samples, respectively. No adenovirus and astrovirus was detected. G2P[8], G9P[8], G1P[8], G2P[4] and rare G12 RV isolates were detected in the environment as well as a bovine RV. The environmental NoV strains mostly belonged to genogroup I (84%). Rotaviruses and some of the NoVs were similar to those found in the clinical samples at the same time. Conclusions: The comparison of environmental and clinical data suggests that similar RV and NoV isolates were circulating in the environment and in the population during the same period. Significance and Impact of the Study: Few studies have investigated the prevalence and the epidemiology of RVs and NoVs in Cairo. This work is the first to establish a correlation between viral gastroenteritis and the concomitant presence of enteric viruses in the environment for Greater Cairo where combined environmental and clinical surveys should help to prevent infections caused by these major pathogens. © 2009 The Society for Applied Microbiology.",Adenoviridae;article;Astroviridae;controlled study;Egypt;enteric virus;Enterovirus;nonhuman;Norovirus;reverse transcription polymerase chain reaction;Rotavirus;sewage;strain difference;virus classification;virus detection;virus isolation;virus strain;waste water treatment plant,"Kamel, A. H.;Ali, M. A.;El-Nady, H. G.;Aho, S.;Pothier, P.;Belliot, G.",2010,,10.1111/j.1365-2672.2009.04562.x,0
937,A simple method for the parallel deep sequencing of full influenza A genomes,"Given the major threat of influenza A to human and animal health, and its ability to evolve rapidly through mutation and reassortment, tools that enable its timely characterization are necessary to help monitor its evolution and spread. For this purpose, deep sequencing can be a very valuable tool. This study reports a comprehensive method that enables deep sequencing of the complete genomes of influenza A subtypes using the Illumina Genome Analyzer IIx (GAIIx). By using this method, the complete genomes of nine viruses were sequenced in parallel, representing the 2009 pandemic H1N1 virus, H5N1 virus from human and H1N1 virus from swine, on a single lane of a GAIIx flow cell to an average depth of 122-fold. This technique can be applied to cultivated and uncultivated virus. © 2011 Elsevier B.V.",virus RNA;animal cell;article;controlled study;deep sequencing;gene amplification;gene mapping;gene sequence;genetic variability;human;human cell;Influenza A virus;Influenza A virus (H1N1);Influenza A virus (H5N1);molecular library;nonhuman;parallel design;priority journal;RNA extraction;sequence analysis;species difference;virus genome;virus strain,"Kampmann, M. L.;Fordyce, S. L.;Ávila-Arcos, M. C.;Rasmussen, M.;Willerslev, E.;Nielsen, L. P.;Gilbert, M. T. P.",2011,,10.1016/j.jviromet.2011.09.001,0
938,"Nucleotide sequence of avian carcinoma virus MH2: Two potential onc genes, one related to avian virus MC29 and the other related to murine sarcoma virus 3611","The 5.2-kilobase (kb) RNA genome of avian carcinoma virus MH2 has the genetic structure 5'-Δgag (0.2 kg)-mhg (1.2 kg)-myc (1.4kb)-c (0.4 kg)-poly)A) (0.2 kb)-3'. Δgag is a partial retroviral core protein gene, mht and myc are cell-derived MH2-specific sequences, and c is the 3'-terminal retroviral vector sequence. Here we have determined the nucleotide sequence of 3.5 kb from the 3' end of δgag to the 3' end of molecularly cloned proviral MH2 DNA, in order to elucidate the genetic structure of the virus and to compare it with other mht- and myc-containing oncogenic virus as well as with the chicken proto-myc gene. The following results were obtained: (i) δgag-mht forms a hybrid gene with a contiguous reading frame of 2682 nucleotides that terminates with a stop codon near the 3' end of mht. The 3' 969 nucleotides of mht up to the stop codon are 80% sequence related to the onc-specific raf sequence of murine sarcoma virus 3611 (94% homologous at the deduced amino acid level). (ii) The myc sequence is preceded by an RNA splice acceptor site shared with the cellular proto-myc gene, beyond which it is colinear up to a 3'-termination codon and 40 noncoding nucleotides with the myc sequences of avian retrovirus MC29 and chicken proto-myc. Thus, myc forms, together with a 5' retroviral exon, a second MH2-specific gene. (iii) myc is followed by the 3'-terminal c region of about 400 nucleotides, which is colinear with that of Rous sarcoma virus except for a substitution near the 5' end of the long terminal repeat. It is concluded that MH2 contains two genes with oncogenic potential, the Δgag-mht gene, which is closely related to the Δgag-raf transforming gene of MSV 3611, and the myc gene, which is related to the transforming gene of MC29. Furthermore, it may be concluded that the cellular proto-onc genes, which on sequence transuduction become viral onc genes, are a small group because among the 19 known onc sequences, 5 are shared by different taxonomic groups of viruses of which the mht/raf homology is the closest determined so far.",radioisotope;endocrine system;female genital system;human;human cell;molecular cloning;Moloney murine sarcoma virus;nucleotide sequence;oncogene;ovary carcinoma,"Kan, N. C.;Flordellis, C. S.;Mark, G. E.",1984,,,0
939,"Impact of Coxsackievirus A6 emergence on hand, foot, and mouth disease epidemic in Osaka City, Japan","Hand, foot, and mouth disease (HFMD) is an acute febrile illness characterized by fever; sore throat; and vesicular eruptions on the hands, feet, and oral mucosa. Until 2010, HFMD was predominantly associated with enterovirus (EV) A71 and coxsackievirus (CV) A16 in Japan. In 2011, CV-A6 emerged as a primary causative agent, causing the largest HFMD epidemic in Japan since 1981. Since then, CV-A6 has caused large HFMD epidemics every 2 years. The phylogenetic analysis of complete Viral Protein 1 (VP1) sequences revealed that most CV-A6 strains detected from 2011 to 2015 in Osaka City were classified into a different clade compared with CV-A6 strains detected from 1999 until 2009. The majority of CV-A6 strains detected in 2011 and most CV-A6 strains detected from 2013 to 2015 were mainly divided into two distinct genetic groups. Each epidemic strain carried unique amino acid substitutions in the presumed DE, EF, and GH loops of the VP1 protein that is exposed on the surface of the virion. There is a possibility that the appearance of substitutions on the surface of the virion and an accumulation of a susceptible population are significant factors in recent HFMD epidemics.",viral protein;adolescent;adult;age distribution;aged;amino acid sequence;amino acid substitution;article;child;cladistics;controlled study;Coxsackievirus A6;Enterovirus;epidemic;female;hand foot and mouth disease;human;infant;Japan;major clinical study;male;phylogeny;virion;virus strain,"Kanbayashi, D.;Kaida, A.;Yamamoto, S. P.;Hirai, Y.;Kubo, H.;Fujimori, R.;Hakui, N.;Hirokawa, H.;Iritani, N.",2017,,10.1002/jmv.24905,0
940,Genetic characterization of highly pathogenic avian influenza A H5N8 viruses isolated from wild birds in Egypt,"A newly emerged H5N8 influenza virus was isolated from green-winged teal in Egypt during December 2016. In this study, we provide a detailed characterization of full genomes of Egyptian H5N8 viruses and some virological features. Genetic analysis demonstrated that the Egyptian H5N8 viruses are highly pathogenic avian influenza viruses. Phylogenetic analysis revealed that the genome of the Egyptian H5N8 viruses was related to recently characterized reassortant H5N8 viruses of clade 2.3.4.4 isolated from different Eurasian countries. Multiple peculiar mutations were characterized in the Egyptian H5N8 viruses, which probably permits transmission and virulence of these viruses in mammals. The Egyptian H5N8 viruses preferentially bound to avian-like receptors rather than human-like receptors. Also, the Egyptian H5N8 viruses were fully sensitive to amantadine and neuraminidase inhibitors. Chicken sera raised against commercial inactivated avian influenza- H5 vaccines showed no or very low reactivity with the currently characterized H5N8 viruses in agreement with the genetic dissimilarity. Surveillance of avian influenza in waterfowl provides early warning of specific threats to poultry and human health and hence should be continued.",amantadine;avian influenza vaccine;sialidase inhibitor;viral protein;amino acid sequence;amino acid substitution;animal cell;animal experiment;antiviral susceptibility;article;cladistics;controlled study;cross reaction;drug antigenicity;drug efficacy;Egypt;gene amplification;genetic analysis;genetic reassortment;hemagglutination inhibition;highly pathogenic avian influenza;highly pathogenic avian influenza virus;Influenza A virus (H5N1);Influenza A virus (H5N2);Influenza A virus (H5N8);MDCK cell line;molecular phylogeny;nonhuman;nucleotide sequence;phylogenetic tree;priority journal;receptor binding;sequence analysis;viral genetics;virus genome;virus isolation;virus mutation;virus transmission;virus virulence,"Kandeil, A.;Kayed, A.;Moatasim, Y.;Webby, R. J.;McKenzie, P. P.;Kayali, G.;Ali, M. A.",2017,,10.1099/jgv.0.000847,0
941,Reassortant swine influenza viruses isolated in Japan contain genes from pandemic A(H1N1) 2009,"In 2013, three reassortant swine influenza viruses (SIVs)-two H1N2 and one H3N2-were isolated from symptomatic pigs in Japan; each contained genes from the pandemic A(H1N1) 2009 virus and endemic SIVs. Phylogenetic analysis revealed that the two H1N2 viruses, A/swine/Gunma/1/2013 and A/swine/Ibaraki/1/2013, were reassortants that contain genes from the following three distinct lineages: (i) H1 and nucleoprotein (NP) genes derived from a classical swine H1 HA lineage uniquely circulating among Japanese SIVs; (ii) neuraminidase (NA) genes from human-like H1N2 swine viruses; and (iii) other genes from pandemic A(H1N1) 2009 viruses. The H3N2 virus, A/swine/Miyazaki/2/2013, comprised genes from two sources: (i) hemagglutinin (HA) and NA genes derived from human and human-like H3N2 swine viruses and (ii) other genes from pandemic A(H1N1) 2009 viruses. Phylogenetic analysis also indicated that each of the reassortants may have arisen independently in Japanese pigs. A/swine/Miyazaki/2/2013 were found to have strong antigenic reactivities with antisera generated for some seasonal human-lineage viruses isolated during or before 2003, whereas A/swine/Miyazaki/2/2013 reactivities with antisera against viruses isolated after 2004 were clearly weaker. In addition, antisera against some strains of seasonal human-lineage H1 viruses did not react with either A/swine/Gunma/1/2013 or A/swine/Ibaraki/1/2013. These findings indicate that emergence and spread of these reassortant SIVs is a potential public health risk. © 2014 The Societies and Wiley Publishing Asia Pty Ltd.",virus hemagglutinin;virus nucleoprotein;virus sialidase;amino acid sequence;animal cell;article;gene sequence;genetic line;genetic reassortment;genome analysis;glycosylation;hemagglutinin gene;Influenza A virus (H1N1);Japan;molecular phylogeny;neuraminidase gene;nonhuman;nucleoprotein gene;phylogenetic tree;virus gene;virus isolation;virus strain,"Kanehira, K.;Takemae, N.;Uchida, Y.;Hikono, H.;Saito, T.",2014,,10.1111/1348-0421.12152,0
942,"Genetic analyses of avian influenza viruses in Mongolia, 2007 to 2009, and their relationships with Korean isolates from domestic poultry and wild birds","The present study was conducted to monitor wild birds based on the concern that they could disseminate avian influenza virus (AIV) between Mongolia and Korea, which shares the same migratory flyway. Of 1,528 fecal samples analyzed, 21 low-pathogenic AIV were isolated from 2007 to 2009. Nineteen AIV-positive fecal samples were identified as Anseriformes by DNA bar coding. The most frequently isolated subtype was H3 (61.9%), and the most prevalent hemagglutinin/ neuraminidase combination was H3N8 (52.4%). Phylogenetic analysis was performed to assess their genetic relationships with those of domestic poultry and wild birds in Korea. The H3 and H7 surface genes belonged to the Eurasian lineage and clustered together in a group with Korean wild birds and poultry. Most N8 genes clustered phylogenetically with viruses isolated in Eurasia, whereas 1 of the Mongolian viruses and some Korean viruses belonged to the North American lineage. The polymerase acidic protein of the internal gene was not distinguishable from the H5N1 highly pathogenic AIV of the goose/guangdong/1/1996 (gs/ gd)-like virus. Our study suggests that Mongolian AIV isolates have evolved with genetically multiple genotypes and are closely related to those of AIV in poultry as well as in wild birds in Korea. © 2011 Poultry Science Association Inc.",animal;article;bird;classification;comparative study;disease transmission;feces;genetics;Influenza A virus;isolation and purification;Mongolia;orthomyxovirus infection;phylogeny;population migration;poultry;South Korea;virology,"Kang, H.;Kim, M.;Choi, J.;Batchuluun, D.;Erdene-Ochir, T.;Paek, M.;Sodnomdarjaa, R.;Kwon, J.;Lee, Y.",2011,,10.3382/ps.2011-01524,0
943,Isolation of a reassortant H13N2 virus from a mallard fecal sample in South Korea,"Background: Virus subtype H13N2, A/mallard/Kr/SH38-45/2010 (H13N2), was first isolated from a mallard fecal sample in South Korea. Results: Phylogenetic analysis of all eight viral genes revealed that this virus emerged by genetic mixing between Eurasian and North American gene pools, and possibly between wild ducks and gulls. The H13 and N2 surface genes clustered together in a group with Eurasian isolates from gulls and wild birds, respectively. The PB2, PA, NP, M and NS segments belonged to the Eurasian lineage, whereas the PB1 gene clustered in the North American lineage. Furthermore, they showed a bird-dependent pattern in phylogenetic analysis: the M gene was similar to subtype H13 viruses within gulls, whereas other segments were similar to avian influenza viruses of other subtypes from wild ducks. Conclusions: The data suggests that the novel reassortant H13N2 virus isolated in South Korea might have emerged by genetic reassortment between intercontinental and interspecies transmission in wild birds. © 2012 Kang et al.; licensee BioMed Central Ltd.",article;avian influenza virus;bird;Charadriiformes;controlled study;duck;feces microflora;gene cluster;gene pool;genetic reassortment;Influenza virus A H13N1;nonhuman;nonstructural protein gene;nucleoprotein gene;nucleotide sequence;phylogenetic tree;phylogeny;polymerase acidic gene;polymerase subunit PB2 gene;sea gull;sequence homology;South Korea;virus gene;virus isolation;wild animal,"Kang, H. M.;Choi, J. G.;Kim, M. C.;Kim, H. R.;Oem, J. K.;Bae, Y. C.;Paek, M. R.;Kwon, J. H.;Lee, Y. J.",2012,,10.1186/1743-422x-9-133,0
944,Isolation of avian influenza virus (H9N2) from emu in China,"This is the first reported isolation of avian influenza virus (AIV) from emu in China. An outbreak of AIV infection occurred at an emu farm that housed 40 four-month-old birds. Various degrees of haemorrhage were discovered in the tissues of affected emus. Cell degeneration and necrosis were observed microscopically Electron microscopy revealed round or oval virions with a diameter of 80nm to 120nm, surrounded by an envelope with spikes. The virus was classified as low pathogenic AIV (LPAIV), according to OIE standards. It was named A/Emu/HeNen/14/2004(H9N2)(Emu/HN/2004). The HA gene (168315p) was amplified by RT-PCR and it was compared with other animal H9N2 AIV sequences in GenBank, the US National Institutes of Health genetic sequence database. The results suggested that Emu/HN/2004 may have come from an avian influenza virus (H9N2) from Southern China.",emu;avian influenza virus;H9N2;OSTRICHES STRUTHIO-CAMELUS;A VIRUSES;PATHOGENICITY;HEMAGGLUTININ;H5;CHICKENS;SEQUENCE;H7N1,"Kang, W. H.;Pang, W. Y.;Hao, J. F.;Zhao, D. M.",2006,Mar,,0
945,Phylogenetic relationships and pathogenicity variation of two Newcastle disease viruses isolated from domestic ducks in Southern China,"Background: Newcastle disease (ND) is an OIE listed disease caused by virulent avian paramyxovirus type 1 (APMV-1) strains, which is enzootic and causes large economic losses in the poultry sector. Genotype VII and genotype IX NDV viruses were the predominant circulating genotype in China, which may possibly be responsible for disease outbreaks in chicken flocks in recent years. While ducks and geese usually have exhibited inapparent infections. Methods. In the present study, we investigate the complete genome sequence, the clinicopathological characterization and transmission of two virulent Newcastle disease viruses, SS-10 and NH-10, isolated from domestic ducks in Southern China in 2010. Results: F, and the complete gene sequences based on phylogenetic analysis demonstrated that SS-10 (genotype VII) and NH-10 (genotype IX) belongs to class II. The deduced amino acid sequence was <sup>(112)</sup>R-R-Q-K/R-R-F<sup>(117)</sup>at the fusion protein cleavage site. Animal experiment results showed that the SS-10 virus isolated from ducks was highly pathogenic for chickens and geese, but low pathogenic for ducks. It could be detected from spleen, lung, kidney, trachea, small intestine, bursa of fabricius, thymus, pancreas and cecal tonsils, oropharyngeal and cloacal swabs, and could transmit to the naive contact birds. Moreover, it could transmit to chickens, ducks and geese by naive contact. However, the NH-10 virus isolated from ducks could infect some chickens, ducks and geese, but only caused chickens to die. Additionally, it could transmit to the naive contact chickens, ducks, and geese. Conclusion: The two NDV isolates exhibited different biological properties with respect to pathogenicity and transmission in chickens, ducks and geese. Therefore, no species-preference exists for chicken, duck or goose viruses and more attention should be paid to the trans-species transmission of VII NDVs between ducks, geese and chickens for the control and eradication of ND.",amino acid sequence;Anas platyrhynchos;animal experiment;article;bursa Fabricii;China;controlled study;gene sequence;genotype;kidney;Newcastle disease;Newcastle disease virus;nonhuman;nucleotide sequence;pancreas;pathogenicity;phylogeny;protein cleavage;small intestine;spleen;thymus;tonsil;trachea;virus strain;virus transmission;waterfowl,"Kang, Y.;Li, Y.;Yuan, R.;Li, X.;Sun, M.;Wang, Z.;Feng, M.;Jiao, P.;Ren, T.",2014,,10.1186/1743-422x-11-147,0
946,Phylogenetic and pathotypic characterization of newcastle disease viruses circulating in South China and transmission in different birds,"Although Newcastle disease virus (NDV) with high pathogenicity has frequently been isolated in poultry in China since 1948, the mode of its transmission among avian species remains largely unknown. Given that various wild bird species have been implicated as sources of transmission, in this study we genotypically and pathotypically characterized 23 NDV isolates collected from chickens, ducks, and pigeons in live bird markets (LBMs) in South China as part of an H7N9 surveillance program during December 2013-February 2014. To simulate the natural transmission of different kinds of animals in LBMs, we selected three representative NDVs-namely, GM, YF18, and GZ289-isolated from different birds to evaluate the pathogenicity and transmission of the indicated viruses in chickens, ducks, and pigeons. Furthermore, to investigate the replication and shedding of NDV in poultry, we inoculated the chickens, ducks, and pigeons with 106 EID50 of each virus via intraocular and intranasal routes. Eight hour after infection, the naïve contact groups were housed with those inoculated with each of the viruses as a means to monitor contact transmission. Our results indicated that genetically diverse viruses circulate in LBMs in South China's Guangdong Province and that NDV from different birds have different tissue tropisms and host ranges when transmitted in different birds. We therefore propose the continuous epidemiological surveillance of LBMs to support the prevention of the spread of these viruses in different birds, especially chickens, and highlight the need for studies of the virus-host relationship.",article;chicken;duck;feces analysis;genetic analysis;hemagglutination test;Newcastle disease;Newcastle disease virus;nonhuman;phylogeny;Columbidae;reverse transcription polymerase chain reaction;sequence analysis;virus characterization;virus isolation;virus replication;virus transmission;virus virulence,"Kang, Y.;Xiang, B.;Yuan, R.;Zhao, X.;Feng, M.;Gao, P.;Li, Y.;Li, Y.;Ning, Z.;Ren, T.",2016,,10.3389/fmicb.2016.00119,0
947,Isolation and characterization of a parapoxvirus from sheep with papular stomatitis,"An outbreak of papular stomatitis occurred in a sheep herd in Hokkaido, Japan. Histological examination, immunohistochemistry, electron microscopic observation, and polymerase chain reaction (PCR) were carried out. Lesions were characterized by epithelial hyperplasia, acanthosis, ballooning degeneration of the spiny layer and stratum granulosum. A parapoxvirus was isolated from the skin lesion of affected sheep and characterized genetically and antigenically. Restriction endonuclease analysis of the PCR product showed an orf virus (ORFV)-specific pattern and the isolate reacted with monoclonal antibodies against ORFV. The partially deduced amino acid sequence of the viral envelope gene was identical to those of the major Japanese ORFVs. These results indicated that the outbreak was due to infection by parapoxvirus. The isolated virus could be classified into ORFV, and was closely related to the major Japanese ORFVs, but not foreign ORFVs or other parapoxviruses.",orf virus;outbreak;SEROWS CAPRICORNIS-CRISPUS;ENDOTHELIAL GROWTH-FACTOR;ORF VIRUS;CATTLE;INFECTION;JAPAN,"Kanou, Y.;Inoshima, Y.;Shibahara, T.;Ishikawa, Y.;Kadota, K.;Ohashi, S.;Morioka, K.;Yoshida, K.;Yamada, S.",2005,Jul,,0
948,Classification of Dutch and German avian reoviruses by sequencing the σC protein,"We have amplified, cloned and sequenced (part of) the open reading frame of the S1 segment encoding the σ C protein of avian reoviruses isolated from chickens with different disease conditions in Germany and The Netherlands during 1980 up to 2000. These avian reoviruses were analysed phylogenetically and compared with sequences of avian reoviruses in the Genbank database. The avian reoviruses could be grouped in 5 different genotyping clusters and this classification was identical when the sequences were compared of the 5′ end, the 3′ end or the whole open reading frame of the σ C protein. Therefore sequencing of either part of the gene encoding the σ C protein seems to be reliable for classification. We were unable to identify a correlation between σ C sequences of the avian reoviruses and the disease condition they were isolated from. The sequences found in The Netherlands and in Germany are, like those in Taiwan, more dispersed than the known avian reovirus σ C sequences in the USA and Australia. We did not establish temporal or geographic differences in the avian reoviruses studied.",capsid protein;sigma C protein;unclassified drug;3' untranslated region;5' untranslated region;amino acid sequence;article;Australia;chicken;controlled study;correlation analysis;fowl;GenBank;gene amplification;genetic code;genotype;geographic distribution;Germany;molecular cloning;molecular phylogeny;Netherlands;nonhuman;nucleotide sequence;open reading frame;reliability;Reoviridae;sequence analysis;Taiwan;United States;virus classification;virus isolation,"Kant, A.;Balk, F.;Born, L.;Van Roozelaar, D.;Heijmans, J.;Gielkens, A.;Ter Huurne, A.",2003,,,0
949,Hepatitis E virus in young pigs in finland and characterization of the isolated partial genomic sequences of genotype 3 HEV,"Hepatitis E virus (HEV) infections occur in swine worldwide. The porcine infection is usually subclinical, but HEV genotypes 3 and 4 are zoonotic agents that cause sporadic, indigenous human cases of hepatitis E. The aims of this study were to investigate the occurrence and dynamics of HEV infections in young pigs by analyzing a total of 273 fecal samples collected from six farrowing farms, to genetically characterize the HEV isolates obtained, and to examine the phylogenetic relationships of HEV isolates occurring at different swine farms in Finland. Fecal shedding of HEV of individual piglets was followed at two farms that were selected from five farms identified as HEV RNA positive. Excretion of HEV was detected in 87.5% of the piglets during the survey. Piglets contracted primary HEV infection 3-8 weeks after weaning, and at the time they were transferred to fattening farms, practically all (96.6%) of the pigs with a sample available at this occasion still excreted the virus. According to phylogenetic analysis, all HEV isolates obtained belonged to HEV genotype 3, subtype e, and a separate, farm-specific isolate originated from 10 of 11 farms examined. The results of our study show that HEV infections are highly common in young pigs, and HEV RNA-positive pigs enable HEV transmission from farrowing to fattening farms, creating a possible risk of infection for pig handlers, and that genetic variations in HEVs originating from different farms occur.",virus RNA;article;feces analysis;Finland;gene sequence;genotype;hepatitis E;Hepatitis E virus;Hepatitis E virus genotype 3;molecular phylogeny;nonhuman;pig farming;piglet;priority journal;pig;viral genetics;virus characterization;virus detection;virus excretion;virus isolation;virus shedding;weaning,"Kantala, T.;Heinonen, M.;Oristo, S.;Von Bonsdorff, C. H.;Maunula, L.",2015,,10.1089/fpd.2014.1841,0
950,Supersize me: How whole-genome sequencing and big data are transforming epidemiology,"In epidemiology, the identification of 'who infected whom' allows us to quantify key characteristics such as incubation periods, heterogeneity in transmission rates, duration of infectiousness, and the existence of high-risk groups. Although invaluable, the existence of many plausible infection pathways makes this difficult, and epidemiological contact tracing either uncertain, logistically prohibitive, or both. The recent advent of next-generation sequencing technology allows the identification of traceable differences in the pathogen genome that are transforming our ability to understand high-resolution disease transmission, sometimes even down to the host-to-host scale. We review recent examples of the use of pathogen whole-genome sequencing for the purpose of forensic tracing of transmission pathways, focusing on the particular problems where evolutionary dynamics must be supplemented by epidemiological information on the most likely timing of events as well as possible transmission pathways. We also discuss potential pitfalls in the over-interpretation of these data, and highlight the manner in which a confluence of this technology with sophisticated mathematical and statistical approaches has the potential to produce a paradigm shift in our understanding of infectious disease transmission and control. © 2014 Elsevier Ltd.",bovine tuberculosis;disease transmission;epidemic;epidemiology;evolutionary homology;foot and mouth disease;forensic science;gene amplification;gene mutation;gene sequence;gene transfer;genetic distance;high risk population;high throughput sequencing;incubation time;infection;infection control;multilocus sequence typing;Mycobacterium tuberculosis;nonhuman;priority journal;review;RNA virus,"Kao, R. R.;Haydon, D. T.;Lycett, S. J.;Murcia, P. R.",2014,,10.1016/j.tim.2014.02.011,0
951,Next-generation sequencing technologies: Tool to study avian virus diversity,"Increased globalisation, climatic changes and wildlife-livestock interface led to emergence of novel viral pathogens or zoonoses that have become serious concern to avian, animal and human health. High biodiversity and bird migration facilitate spread of the pathogen and provide reservoirs for emerging infectious diseases. Current classical diagnostic methods designed to be virus-specific or aim to be limited to group of viral agents, hinder identifying of novel viruses or viral variants. Recently developed approaches of next-generation sequencing (NGS) provide culture-independent methods that are useful for understanding viral diversity and discovery of novel virus, thereby enabling a better diagnosis and disease control. This review discusses the different possible steps of aNGS study utilizing sequence-independent amplification, high-throughput sequencing and bioinformatics approaches to identify novel avian viruses and their diversity. NGS lead to the identification of awide range of new viruses such as picobirnavirus, picornavirus, orthoreovirus and avian gamma coronavirus associated with fulminating disease in guinea fowl and is also used in describing viral diversity among avian species. The review also briefly discusses areas of viral-host interaction and disease associated causalities with newly identified avian viruses.",avian virus;bioinformatics;bird;genetic variability;high throughput sequencing;metagenomics;microbial diversity;next generation sequencing;nonhuman;review;transcriptomics;viral genetics;virus;virus cell interaction;virus diversity;virus genome,"Kapgate, S. S.;Barbuddhe, S. B.;Kumanan, K.",2015,,10.4149/av_2015_01_3,0
952,"Avian parvovirus: classification, phylogeny, pathogenesis and diagnosis","Poultry parvoviruses identified during the early 1980s are found worldwide in intestines from young birds with enteric disease syndromes as well as healthy birds. The chicken parvovirus (ChPV) and turkey parvovirus (TuPV) belong to the Aveparvovirus genus within the subfamily Parvovirinae. Poultry parvoviruses are small, non-enveloped, single-stranded DNA viruses consisting of three open reading frames, the first two encoding the non-structural protein (NS) and nuclear phosphoprotein (NP) and the third encoding the viral capsid proteins 1 (VP1 and VP2). In contrast to other parvoviruses, the VP1-unique region does not contain the phospholipase A2 sequence motif. Recent experimental studies suggested the parvoviruses to be the candidate pathogens in cases of enteric disease syndrome. Current diagnostic methods for poultry parvovirus detection include PCR, real-time PCR, enzyme linked immunosorbent assay using recombinant VP2 or VP1 capsid proteins. Moreover, sequence-independent amplification techniques combined with next-generation sequencing platforms have allowed rapid and simultaneous detection of the parvovirus from affected and healthy birds. There is no commercial vaccine; hence, the development of an effective vaccine to control the spread of infection should be of primary importance. This review presents the current knowledge on poultry parvoviruses with emphasis on taxonomy, phylogenetic relationship, genomic analysis, epidemiology, pathogenesis and diagnostic methods.",phospholipase A2;protein VP1;protein VP2;virus phosphoprotein;bird disease;clinical feature;genome analysis;genomics;infection control;nonhuman;Parvoviridae;parvovirus infection;pathology;phylogeny;poultry;protein expression;review;virus classification;virus pathogenesis;virus transmission,"Kapgate, S. S.;Kumanan, K.;Vijayarani, K.;Barbuddhe, S. B.",2018,,10.1080/03079457.2018.1517938,0
953,Multiple novel astrovirus species in human stool,"Diarrhoea remains a significant cause of morbidity and mortality in developing countries where numerous cases remain without identified aetiology. Astroviruses are a recently identified cause of animal gastroenteritis which currently includes two species suspected of causing human diarrhoea. Using pan-astrovirus RT-PCR, we analysed human stool samples from different continents for astrovirus-related RNA sequences. We identified variants of the two known human astrovirus species plus, based on genetic distance criteria, three novel astrovirus species all distantly related to mink and ovine astroviruses, which we provisionally named HMOAstV species A-C. The complete genome of species A displayed all the conserved characteristics of mammalian astroviruses. Each of the now three groups of astroviruses found in human stool (HAstV, AstV-MLB and HMOAstV) were more closely related to animal astroviruses than to each other, indicating that human astroviruses may periodically emerge from zoonotic transmissions. Based on the pathogenic impact of their closest phylogenetic relatives in animals, further investigations of the role of HMOAstV, so far detected in Nigeria, Nepal and Pakistan, in human gastroenteritis are warranted. © 2009 SGM.",RNA directed RNA polymerase;article;Astroviridae;feces analysis;genetic distance;human mink and ovine like astrovirus;new species;nonhuman;nucleotide sequence;phylogeny;priority journal;reverse transcription polymerase chain reaction;RNA sequence;sequence alignment;virus classification;virus genome;virus strain,"Kapoor, A.;Li, L.;Victoria, J.;Oderinde, B.;Mason, C.;Pandey, P.;Zaidi, S. Z.;Delwart, E.",2009,,10.1099/vir.0.014449-0,0
954,A Newly Identified Bocavirus Species in Human Stool,"Viral metagenomic analysis was used to identify a previously uncharacterized parvovirus species, ""HBoV2,"" whose closest phylogenetic relative is the human bocavirus (HBoV). HBoV2 has a genomic organization identical to that of HBoV but has only 78%, 67%, and 80% identity, respectively, with the latter's NS1, NP1, and VP1/VP2 proteins. The study used polymerase chain reaction to detect HBoV2 sequences in 5 of 98 stool samples from Pakistani children and in 3 of 699 stool samples from Edinburgh. Nearly-full-length genome sequencing revealed the presence of 3 HBoV2 genotypes and evidence of recombination between genotypes. Further studies are necessary to identify anatomical sites of HBoV2 replication and potential associations with clinical symptoms or disease.",POLYMERASE-CHAIN-REACTION;HUMAN PARVOVIRUS PARV4;ACUTE;GASTROENTERITIS;MOLECULAR EPIDEMIOLOGY;BOVINE PARVOVIRUS;VIRUS;EVOLUTION;BLOOD-DONORS;HUMAN PLASMA;CHILDREN;INFECTION,"Kapoor, A.;Slikas, E.;Simmonds, P.;Chieochansin, T.;Naeem, A.;Shaukat, S.;Alam, M. M.;Sharif, S.;Angez, M.;Zaidi, S.;Delwart, E.",2009,Jan,,0
955,"Detection of non-polio enteroviruses in Hungary 2000-2008 and molecular epidemiology of enterovirus 71, coxsackievirus A16, and echovirus 30","Human enteroviruses are associated with various clinical syndromes from minor febrile illness to severe, potentially fatal conditions like aseptic meningitis, paralysis, myocarditis, and neonatal enteroviral sepsis. Between June 2000 and August 2008 echovirus (E) type 2, 4, 6, 7, 9, 11, 13, 25, 30, coxsackievirus (CV) -A16, -A19, -B5, and enterovirus 71 (EV71) were reported in Hungary. In this study, 29 previously enterovirus positive samples from 28 patients diagnosed with hand, foot and mouth disease, meningitis and encephalitis, were molecularly typed. The genetic relationships of identified serotypes CV-A16, EV71, and E30 were assessed by direct sequencing of genomic region encoding the capsid protein VP1. The sequences were compared to each other and sequences from other geographical regions possessed in Genbank. The phylogenetic analysis of CV-A16 revealed that the viruses were mostly of Far-Eastern or Asia-Pacific origin. Typing of EV71 showed that one virus from 2000 belonged to genotype C1 and five viruses observed in 2004 and 2005 were identified as genotype C4. The 11 echovirus 30 strains showed homology with those of neighbor European countries. The molecular examination of E30 revealed that three separate lineages circulated in 2000, 2001, and 2004- 2006 in Hungary. © Springer Science+Business Media, LLC 2009.",protein VP1;adolescent;adult;article;Asia;child;clinical article;Enterovirus;Coxsackievirus A16;Enterovirus B;echo virus 30;encephalitis;Enterovirus 17;female;gene sequence;genetic association;genotype;geographic distribution;hand foot and mouth disease;human;Hungary;male;meningitis;molecular epidemiology;nonhuman;nucleotide sequence;phylogeny;priority journal;sequence homology;serotype;unindexed sequence;viral genetics;virus classification;virus detection,"Kapusinszky, B.;Szomor, K. N.;Farkas, A.;Takács, M.;Berencsi, G.",2010,,10.1007/s11262-009-0440-4,0
956,Supplement to international catalogue of arboviruses including certain other viruses of vertebrates,"The first edition was issued in 1967 and represented the working Catalogue at one point in time, February 1967, when it contained information on 204 registered viruses. Thirty-seven additional viruses registered through June 1970 were published in a supplement in November 1970. A second updating supplement, with 14 newly registered viruses, was published in November 1971. A second edition of the Catalogue was published in 1975 and contained information on 359 viruses registered in the working Catalogue as of December 1974. This present report comprises the first supplement to the second published Catalogue edition and includes 30 additional virus registrations. With retraction of Samford virus, which was determined to be a strain of Aino virus, the number of registered viruses now stands at 388. The 30 new registrations in this supplement contain information on 17 viruses isolated from arthropods, 2 isolated from human beings, and 11 isolated from other vertebrates. The two viruses from man (ROC, EBO) were associated with severe human disease. One of the arthropod isolates (ORU) and a virus isolated from a mule (VSA) have also been implicated in human disease, and SSH virus from a hare has been noted to cause subclinical infections in man. Three viruses (BEF, IBA, VSA), isolated from cattle and a mule, cause extensive disease in domestic animals. The ACAV's Subcommittee on Evaluation of Arthropod-Borne Status (SEAS) has rated only one (SSH) of these newly registered viruses as a proven arbovirus, based on experimental demonstration of transmission by mosquitoes. Another (ORU) was rated a probable arbovirus; a third (EBO) probably not arbovirus; and the remainder as possible arboviruses, pending further definitive information on arthropod infection and transmission.",Arbovirus;arthropod;classification;virus classification,"Karabatsos, N.",1978,,,0
957,A novel method for the multiplexed target enrichment of MinION next generation sequencing libraries using PCR-generated baits,"The enrichment of targeted regions within complex next generation sequencing libraries commonly uses biotinylated baits to capture the desired sequences. This method results in high read coverage over the targets and their flanking regions. Oxford Nanopore Technologies recently released an USB3.0-interfaced sequencer, the MinION. To date no particular method for enriching MinION libraries has been standardized. Here, using biotinylated PCR-generated baits in a novel approach, we describe a simple and efficient way for multiplexed enrichment of MinION libraries, overcoming technical limitations related with the chemistry of the sequencing-adapters and the length of the DNA fragments. Using Phage Lambda and Escherichia coli as models we selectively enrich for specific targets, significantly increasing the corresponding read-coverage, eliminating unwanted regions. We show that by capturing genomic fragments, which contain the target sequences, we recover reads extending targeted regions and thus can be used for the determination of potentially unknown flanking sequences. By pooling enriched libraries derived from two distinct E. coli strains and analyzing them in parallel, we demonstrate the efficiency of this method in multiplexed format. Crucially we evaluated the optimal bait size for large fragment libraries and we describe for the first time a standardized method for target enrichment in MinION platform.","Bacteriophage lambda/ge [Genetics];Escherichia coli/ge [Genetics];*Gene Library;Genes, rRNA;Genome, Viral;*High-Throughput Nucleotide Sequencing/mt [Methods];Operon;*Polymerase Chain Reaction;*Sequence Analysis, DNA/mt [Methods]","Karamitros, T.;Magiorkinis, G.",2015,Dec 15,,0
958,"Genetic characterization of H3N2 influenza viruses isolated from pigs in North America, 1977-1999: Evidence for wholly human and reassortant virus genotypes","Since 1998, H3N2 viruses have caused epizootics of respiratory disease in pigs throughout the major swine production regions of the U.S. These outbreaks are remarkable because swine influenza in North America had previously been caused almost exclusively by H1N1 viruses. We sequenced the full-length protein coding regions of all eight RNA segments from four H3N2 viruses that we isolated from pigs in the Midwestern U.S. between March 1998 and March 1999, as well as from H3N2 viruses recovered from a piglet in Canada in January 1997 and from a pig in Colorado in 1977. Phylogenetic analyses demonstrated that the 1977 Colorado and 1997 Ontario isolates are wholly human influenza viruses. However, the viruses isolated since 1998 from pigs in the Midwestern U.S. are reassortant viruses containing hemagglutinin, neuraminidase and PB1 polymerase genes from human influenza viruses, matrix, non-structural and nucleoprotein genes from classical swine viruses, and PA and PB2 polymerase genes from avian viruses. The HA proteins of the Midwestern reassortant swine viruses can be differentiated from those of the 1995 lineage of human H3 viruses by 12 amino acid mutations in HA1. In contrast, the Sw/ONT/97 virus, which did not spread from pig-to-pig, lacks 11 of these changes. (C) 2000 Elsevier Science B.V.",matrix protein;sialidase;virus enzyme;virus hemagglutinin;virus nucleoprotein;animal cell;article;Canada;controlled study;genotype;Influenza A virus;nonhuman;nucleotide sequence;phylogeny;priority journal;sequence analysis;sequence homology;species difference;structural gene;swine disease;swine influenza virus;symptom;United States;virus isolation,"Karasin, A. I.;Schutten, M. M.;Cooper, L. A.;Smith, C. B.;Subbarao, K.;Anderson, G. A.;Carman, S.;Olsen, C. W.",2000,,10.1016/s0168-1702(00)00154-4,0
959,Characterization of avian H3N3 and H1N1 influenza A viruses isolated from pigs in Canada,H3N3 and H1N1 influenza A viruses were isolated from Canadian pigs in 2001 and 2002. These viruses are phylogenetically related to waterfowl viruses and antigenically distinct from reference swine influenza viruses. The isolation of these viruses reemphasizes the potential for interspecies transmission of influenza viruses from waterfowl to pigs in North America.,antigenicity;article;avian influenza virus;Canada;waterfowl;Influenza virus;Influenza A virus;nonhuman;nucleotide sequence;phylogeny;priority journal;pig;unindexed sequence;virology;virus characterization;virus isolation;virus strain;virus transmission,"Karasin, A. I.;West, K.;Carman, S.;Olsen, C. W.",2004,,10.1128/jcm.42.9.4349-4354.2004,0
960,The intestinal eukaryotic virome in healthy and diarrhoeic neonatal piglets,"Neonatal porcine diarrhoea of uncertain aetiology has been reported from a number of European countries. The aim of the present study was to use viral metagenomics to examine a potential viral involvement in this diarrhoea and to describe the intestinal virome with focus on eukaryotic viruses. Samples from the distal jejunum of 50 diarrhoeic and 19 healthy piglets from 10 affected herds were analysed. The viral fraction of the samples was isolated and nucleic acids (RNA and DNA fractions) were subjected to sequence independent amplification. Samples from diarrhoeic piglets from the same herds were pooled whereas samples from healthy piglets were analysed individually. In total, 29 clinical samples, plus two negative controls and one positive control consisting of a mock metagenome were sequenced using the Ion Torrent platform. The resulting sequence data was subjected to taxonomic classification using Kraken, Diamond and HMMER. In the healthy specimens, eight different mammalian virus families were detected (Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picornaviridae, and Reoviridae) compared to four in the pooled diarrhoeic samples (Anelloviridae, Circoviridae, Picornaviridae, and Reoviridae). It was not possible to associate a particular virus family with the investigated diarrhoea. In conclusion, this study does not support the hypothesis that the investigated diarrhoea was caused by known mammalian viruses. The results do, however, indicate that known mammalian viruses were present in the intestine as early as 24-48 hours after birth, indicating immediate infection post-partum or possibly transplacental infection.",DNA;nucleic acid;RNA;Adenoviridae;Anelloviridae;animal tissue;article;Astroviridae;Caliciviridae;Circoviridae;controlled study;diarrhea;female;gene sequence;jejunum;male;metagenomics;newborn;nonhuman;Parvoviridae;Picornaviridae;piglet;Reoviridae;sequence analysis;swine disease;virus genome;virus identification,"Karlsson, O. E.;Larsson, J.;Hayer, J.;Berg, M.;Jacobson, M.",2016,,10.1371/journal.pone.0151481,1
961,"A severe pediatric infection with a novel enterovirus A71 strain, Thuringia, Germany","Infection by Enterovirus A71 (EV-A71) is an important cause of hand, foot, and mouth disease (HFMD). Outbreaks including severe cases with neurological and cardiopulmonary complications have been reported particularly from Southeast Asia. In Europe, the epidemiology of EV-A71 is not well understood. In summer 2015, a two-year-old girl from Thuringia, Germany, presented with rhombencephalitis/brainstem encephalitis associated with severe neurological and cardiopulmonary complications. EV-A71 was detected in stool and almost the entire viral genome was amplified and sequenced. While the capsid protein VP1-encoding region belongs to the EV-A71 subgenogroup C1, the 3D polymerase encoding region represents a unique lineage. Thus, the data suggest that the Thuringian EV-A71 sequence likely represents a recombinant. The case underlines the importance of intensified EV-A71 surveillance in Germany and Europe including analysis of full-genome data.","Capsid Proteins/ge [Genetics];Child, Preschool;Disease Outbreaks;Encephalitis, Viral/di [Diagnosis];Encephalitis, Viral/ep [Epidemiology];*Encephalitis, Viral/vi [Virology];Enterovirus A, Human/cl [Classification];Enterovirus A, Human/ge [Genetics];*Enterovirus A, Human/ip [Isolation & Purification];Enterovirus A, Human/py [Pathogenicity];Enterovirus Infections/di [Diagnosis];Enterovirus Infections/ep [Epidemiology];*Enterovirus Infections/vi [Virology];Feces/vi [Virology];Female;Genome, Viral;Germany/ep [Epidemiology];High-Throughput Nucleotide Sequencing;Humans;Recombination, Genetic;Seasons;0 (Capsid Proteins)","Karrasch, M.;Fischer, E.;Scholten, M.;Sauerbrei, A.;Henke, A.;Renz, D. M.;Mentzel, H. J.;Boer, K.;Bottcher, S.;Diedrich, S.;Krumbholz, A.;Zell, R.",2016,11,,0
962,Understanding the evolutionary relationship of hemagglutinin protein from influenza viruses using phylogenetic and molecular modeling studies,"The existing H1N1 (2009) swine flu is pandemic in nature and is responsible for global economic losses and fatalities. Among the eight gene segments of H1N1, hemagglutinin (HA) plays a major role in the attachment of the virus to the host cell surface and entry of viral RNA into the host cell leads to infection. In this study, sequence and phylogenetic analysis of the H1N1 (2009) HA, from Mexico City along with 1952 sequences, from different subtypes of pandemic influenza A virus were studied and results showed that the closest relationship of H1N1 (2009) Mexico strain was with the H1N1 (2007) Mallard Norway strain. Analysis of secondary structures predicted from the protein sequence revealed that diminishing of alpha helixes was observed in many areas of the sequences between the years 2005 to 2010. Conversely, analysis at the structural level is necessary to critically assess the functional significance. Structural level investigation was therefore done for the above said proteins by constructing the 3D structure of these proteins through homology modeling. The models were validated and structural level similarities were evaluated through superimposition. Subsequently, docking studies were done to find the binding mode of the sialic acid (SA) with influenza HA. Molecular dynamics simulations were executed to study the interactions of SA molecule with the HA. Energetic analysis reveals that van der Waal interaction is more favorable for binding of HA with SA of the whole influenza virus. Binding pocket analysis shows that intensities of H-bond donor and acceptor are more in H1N1 (2009). © 2013 © 2013 Taylor & Francis.",Influenza virus hemagglutinin;sialic acid;alpha helix;article;binding affinity;binding site;controlled study;hydrogen bond;Influenza virus;Influenza A virus (H1N1);Mexico;molecular docking;molecular dynamics;molecular evolution;molecular model;molecular phylogeny;nonhuman;prediction;priority journal;protein binding;protein protein interaction;quality control;receptor binding;sequence analysis;structure analysis;three dimensional imaging;validation process;virus identification;virus strain,"Karthikeyan, M.;Kirubakaran, P.;Singh, K. D.;Sampath, B.;Krishnasamy, G.",2014,,10.1080/07391102.2013.793211,0
963,Possible risks posed by single-stranded DNA viruses of pigs associated with xenotransplantation,"Routine large-scale xenotransplantation from pigs to humans is getting closer to clinical reality owing to several state-of-the-art technologies, especially the ability to rapidly engineer genetically defined pigs. However, using pig organs in humans poses risks including unwanted cross-species transfer of viruses and adaption of these pig viruses to the human organ recipient. Recent developments in the field of virology, including the advent of metagenomic techniques to characterize entire viromes, have led to the identification of a plethora of viruses in many niches. Single-stranded DNA (ssDNA) viruses are the largest group prevalent in virome studies in mammals. Specifically, the ssDNA viral genomes are characterized by a high rate of nucleotide substitution, which confers a proclivity to adapt to new hosts and cross-species barriers. Pig-associated ssDNA viruses include torque teno sus viruses (TTSuV) in the Anelloviridae family, porcine parvoviruses (PPV), and porcine bocaviruses (PBoV) both in the family of Parvoviridae, and porcine circoviruses (PCV) in the Circoviridae family, some of which have been confirmed to be pathogenic to pigs. The risks of these viruses for the human recipient during xenotransplantation procedures are relatively unknown. Based on the scant knowledge available on the prevalence, predilection, and pathogenicity of pig-associated ssDNA viruses, careful screening and monitoring are required. In the case of positive identification, risk assessments and strategies to eliminate these viruses in xenotransplantation pig stock may be needed.",Anelloviridae;Circovirus;DNA virus;epidemic;human;infection rate;infection risk;nonhuman;Parvoviridae;pig;Porcine endogenous retrovirus;prevalence;priority journal;review;single-stranded DNA virus;Torque teno virus 1;viral tropism;virus genome;virus infection;xenotransplantation;zoonosis,"Karuppannan, A. K.;Opriessnig, T.",2018,,10.1111/xen.12453,0
964,"Phylogenetic relationships of the G gene sequence of bovine ephemeral fever virus isolated in Japan, Taiwan and Australia","The G gene encoding the neutralization antigen of bovine ephemeral fever virus (BEFV) was characterized in order to define the virus's molecular epidemiology in Japan and the genetic relationships among the Japanese, Taiwanese and Australian isolates. The nucleotide and amino acid sequences of the gene were highly conserved among the Japanese strains, regardless of the year of isolation, and were closely related to the Taiwanese strains. By phylogenetic analysis, the Japanese and Taiwanese strains were classified clearly into three chronological clusters: 1966, 1984-1989 and 1996-2004, indicating that the epidemics of bovine ephemeral fever may occur almost simultaneously in both countries by the same genotype. On the other hand, the Australian strains were distantly related to these East Asian strains and placed in the independent fourth cluster of the phylogenetic tree. It is suggested that three amino acid substitutions at residues 224, 271 and 499 in the neutralizing epitopes, of which two generate new glycosylation sequences, are responsible for antigenic variations of bovine ephemeral fever virus. The cross-neutralization test using the bovine ephemeral fever virus isolated in Japan demonstrated that the vaccine developed based on the oldest Japanese strain, YHL, appears to still be effective for controlling bovine ephemeral fever in Japan. © 2009 Elsevier B.V. All rights reserved.",virus vaccine;amino acid sequence;amino acid substitution;antigenic variation;article;Australia;cattle disease;G gene;gene;gene sequence;genetic conservation;glycosylation;Japan;molecular epidemiology;nonhuman;nucleotide sequence;phylogeny;Taiwan;virus classification;virus neutralization;virus strain,"Kato, T.;Aizawa, M.;Takayoshi, K.;Kokuba, T.;Yanase, T.;Shirafuji, H.;Tsuda, T.;Yamakawa, M.",2009,,10.1016/j.vetmic.2009.01.021,0
965,Infection of carp (Cyprinus carpio) with Cyprinid Herpesvirus 3 (CyHV-3) - an update,"Infection of carp (Cyprinus carpio) with Cyprinid Herpesvirus 3 (CyHV-3) - an update Common carp and koi (Cyprinus carpio) are bred intensively worldwide, both as farm animals and as pet fish with an ever growing circle of enthusiasts. Since the late 90s of the last century, the species has been threatened by a novel virus, recently classified as a herpesvirus. The virus, now known as Cyprinid Herpesvirus 3 (CyHV-3) or Koi Herpesvirus (KHV), causes massive losses in both industrial branches each year. This review aims to provide a general overview of current knowledge concerning the disease and the pathogen, as well as describing why, 14 years since its discovery, CyHV-3 still poses a serious problem in both carp and koi aquacultures.",Koi;carp;Herpesvirus;infection;KHVD;CyHV-3;GILL NECROSIS VIRUS;MEDIATED ISOTHERMAL AMPLIFICATION;POLYMERASE-CHAIN-REACTION;KHV DISEASE KHVD;KOI HERPESVIRUS;COMMON;CARP;INTERSTITIAL NEPHRITIS;VIRAL DISEASE;PHYLOGENETIC-RELATIONSHIPS;THYMIDINE KINASE,"Kattlun, J.;Gotesman, M.;Bergmann, S. M.;El-Matbouli, M.",2013,,,0
966,Analysis of codon usage pattern evolution in avian rotaviruses and their preferred host,"Rotavirus infection is a worldwide problem, with occurrence of highly divergent viruses classified in 8 species (A-H). We report here the evolution assessment of codon usage patterns in virus-host system in avian rotavirus (AvRV) of species RVA, RVD, RVF and RVG (preferentially affecting birds). The nucleotide contents, codon usage bias (CUB), relative synonymous codon usage (RSCU), and effective number of codons (ENCs) values were investigated targeting overexpressing major inner capsid viral protein (VP6) of these AvRV species. The results confirm that the evolutionary characteristics influences the rotavirus (RV) genetic diversity and impact of host's natural selection on the AvRVs codons. Synonymous codon usage patterns were evaluated following multivariate statistical procedures on all available AvRV coding gene sequences. RSCU trees accommodated all AvRV species and preferred host sequences in one topology confirming greater imminence of AvRVs with the host chicken cell genes. Similarly, the codon adaptation index (CAI) results also displayed a higher adaptation of AvRVs to its chicken host. The codon preference analysis of RVs revealed that VP6 gene express more proficiently in the yeast system, whereas, codon optimization might be required for the effectual expression in Escherichia coli and Homo sapiens. The findings provide basic evidence on the dynamics of AvRV evolution and its host adaptation, which could be exploited for additional research on avian species in future.",protein VP6;article;codon;codon usage;correlation analysis;Escherichia coli;gene overexpression;gene rearrangement;genetic variability;hydrophobicity;molecular evolution;nonhuman;open reading frame;priority journal;Rotavirus;single nucleotide polymorphism;virus replication,"Kattoor, J. J.;Malik, Y. S.;Sasidharan, A.;Rajan, V. M.;Dhama, K.;Ghosh, S.;Bányai, K.;Kobayashi, N.;Singh, R. K.",2015,,10.1016/j.meegid.2015.06.018,0
967,CRISPRs of Enterococcus faecalis and E. hirae isolates from pig feces have species-specific repeats but share some common spacer sequences,"Clustered regularly interspaced short palindromic repeats (CRISPR) are currently a topic of interest in microbiology due to their role as a prokaryotic immune system. Investigations of CRISPR distribution and characterization to date have focused on pathogenic bacteria, while less is known about CRISPR in commensal bacteria, where they may have a significant role in the ecology of the microbiota of humans and other animals, and act as a recorder of interactions between bacteria and viruses. A combination of PCR and sequencing was used to determine prevalence and distribution of CRISPR arrays in Enterococcus faecalis and Enterococcus hirae isolates from the feces of healthy pigs. Both type II CRISPR-Cas and Orphan CRISPR (without Cas genes) were detected in the 195 isolates examined. CRISPR-Cas was detected in 52 (46/88) and 42 % (45/107) E. faecalis and E. hirae isolates, respectively. The prevalence of Orphan CRISPR arrays was higher in E. faecalis isolates (95 %, 84/88) compared with E. hirae isolates (49 %, 53/107). Species-specific repeat sequences were identified in Orphan CRISPR arrays, and 42 unique spacer sequences were identified. Only two spacers matched previously characterized pig virome sequences, and many were apparently derived from chromosomal sequences of enterococci. Surprisingly, 17 (40 %) of the spacers were detected in both species. Shared spacer sequences are evidence of a lack of species specificity in the agents and mechanisms responsible for integration of spacers, and the abundance of spacer sequences corresponding to bacterial chromosomal sequences reflects interspecific interactions within the intestinal microbiota.",bacterial DNA;spacer DNA;animal;clustered regularly interspaced short palindromic repeat;Enterococcus;Enterococcus faecalis;feces;genetics;isolation and purification;microbiology;species difference;pig,"Katyal, I.;Chaban, B.;Ng, B.;Hill, J. E.",2013,,10.1007/s00248-013-0217-0,0
968,Insights into the bovine rumen plasmidome,"Plasmids are self-replicating genetic elements capable of mobilization between different hosts. Plasmids often serve as mediators of lateral gene transfer, a process considered to be a strong and sculpting evolutionary force in microbial environments. Our aim was to characterize the overall plasmid population in the environment of the bovine rumen, which houses a complex and dense microbiota that holds enormous significance for humans. We developed a procedure for the isolation of total rumen plasmid DNA, termed rumen plasmidome, and subjected it to deep sequencing using the Illumina paired-end protocol and analysis using public and custom-made bioinformatics tools. A large number of plasmidome contigs aligned with plasmids of rumen bacteria isolated from different locations and at various time points, suggesting that not only the bacterial taxa, but also their plasmids, are defined by the ecological niche. The bacterial phylum distribution of the plasmidome was different from that of the rumen bacterial taxa. Nevertheless, both shared a dominance of the phyla Firmicutes, Bacteroidetes, and Proteobacteria. Evidently, the rumen plasmidome is of a highly mosaic nature that can cross phyla. Interestingly, when we compared the functional profile of the rumen plasmidome to two plasmid databases and two recently published rumen metagenomes, it became apparent that the rumen plasmidome codes for functions, which are enriched in the rumen ecological niche and could confer advantages to their hosts, suggesting that the functional profiles of mobile genetic elements are associated with their environment, as has been previously implied for viruses.",metagenomics;microbial ecology;rumen microbiology;HORIZONTAL GENE-TRANSFER;BACTERIUM SELENOMONAS-RUMINANTIUM;COMPLETE;NUCLEOTIDE-SEQUENCE;CRYPTIC PLASMID;TETRACYCLINE RESISTANCE;PREVOTELLA-RUMINICOLA;STREPTOCOCCUS-BOVIS;GENOMIC ISLANDS;H+-ATPASE;ELEMENTS,"Kav, A. B.;Sasson, G.;Jami, E.;Doron-Faigenboim, A.;Benhar, I.;Mizrahi, I.",2012,Apr,,0
969,"Circulation of reassortant influenza A(H7N9) viruses in poultry and humans, Guangdong Province, China, 2013","Influenza A(H7N9) virus emerged in eastern China in February 2013 and continues to circulate in this region, but its ecology is poorly understood. In April 2013, the Guangdong Provincial Center for Disease Control and Prevention (CDC) implemented environmental and human syndromic surveillance for the virus. Environmental samples from poultry markets in 21 city CDCs (n=8,942) and respiratory samples from persons with influenza-like illness or pneumonia (n=32,342) were tested; viruses isolated from 6 environmental samples and 16 patients were sequenced. Sequence analysis showed co-circulation of 4 influenza A(H7N9) virus strains that evolved by reassortment with avian influenza A(H9N2) viruses circulating in this region. In addition, an increase in human cases starting in late 2013 coincided with an increase in influenza A H7 virus isolates detected by environmental surveillance. Co-circulation of multiple avian influenza viruses that can infect humans highlights the need for increased surveillance of poultry and potential environmental sources.","Adolescent;Adult;Aged;Animals;China/ep [Epidemiology];Environmental Monitoring;Female;Genome, Viral;Geography, Medical;Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];High-Throughput Nucleotide Sequencing;Humans;Influenza A Virus, H7N9 Subtype/cl [Classification];*Influenza A Virus, H7N9 Subtype/ge [Genetics];Influenza in Birds/ep [Epidemiology];*Influenza in Birds/vi [Virology];Influenza, Human/ep [Epidemiology];*Influenza, Human/vi [Virology];Male;Middle Aged;Neuraminidase/ge [Genetics];Phylogeny;Phylogeography;*Poultry/vi [Virology];Public Health Surveillance;Reassortant Viruses/ge [Genetics];*Reassortant Viruses;Viral Proteins/ge [Genetics];Young Adult;0 (Hemagglutinin Glycoproteins, Influenza Virus);0 (Viral Proteins)","Ke, C.;Lu, J.;Wu, J.;Guan, D.;Zou, L.;Song, T.;Yi, L.;Zeng, X.;Liang, L.;Ni, H.;Kang, M.;Zhang, X.;Zhong, H.;He, J.;Lin, J.;Smith, D.;Burke, D.;Fouchier, R. A.;Koopmans, M.;Zhang, Y.",2014,Dec,,0
970,Characterization of newly emerging Newcastle disease viruses isolated during 2002-2008 in Taiwan,"To elucidate the epidemiological relationships between ND outbreaks and genetic lineages, a portion of the F gene (535 bp) and the full-length HN gene (1922 bp) of recent Taiwanese NDVs isolated in 2002-2008 was amplified by reverse transcription (RT)-polymerase chain reaction (PCR) and sequenced. Only a portion of above amplified PCR products of the F and HN genes (374 and 1713 bp) and their deduced amino acid residues were compared with the other 60 NDVs retrieved from GenBank. Most (29/30) of the recent Taiwanese isolates were clustered in subgenotype VIIe while only one isolate was classified as subgenotype VIIc. All the 29 isolates of subgenotype VIIe were further subclassified and termed provisionally as sub-subgenotypes VIIe2 (13 isolates), VIIe3 (5 isolates), and VIIe4 (11 isolates). The sub-subgenotype VIIe2 isolates possessing the motif 112R-R-Q-K-R-F117 and amino acid residue substitutions at positions 23 (L to F) and 90 (T to A) were collected during 2002-2005. The sub-subgenotype VIIe3 isolates possessing the motif 112R-R-K-K-R-F117 and amino acid residue substitutions at positions 74 (E to G) and 75 (A to G) within epitopes and 114 (Q to K) within cleavage site of F protein were collected during 2003-2006. The sub-subgenotype VIIe4 isolates possessing the motif 112R-R-Q-K-R-F117 and amino acid residue substitutions at positions 23 (L to F), 26 (I to T), and 90 (T to A) were collected during 2007-2008. All the NDV isolates in this study exhibited a high intra-cerebral pathogenicity index (ICPI), they were all classified as velogenic type of NDVs. The sub-subgenotype VIIe2 and VIIe4 viruses are now dominant and have been implicatd in most of the recent ND outbreaks in Taiwan. Phylogenetic analysis of these isolates revealed that they may have evolved from previously reported local strains (VIIe1). This finding is essential for improving the disease control strategies and development of vaccines for ND. © 2009 Elsevier B.V. All rights reserved.",alanine;amino acid;arginine;glutamine;inactivated virus vaccine;isoleucine;leucine;lysine;phenylalanine;threonine;virus RNA;amino acid sequence;amino acid substitution;animal experiment;article;bird disease;controlled study;embryo;genetic analysis;genetic linkage;infection control;infection prevention;Newcastle disease virus;nonhuman;nucleotide sequence;phylogenetic tree;priority journal;protein cleavage;protein motif;reverse transcription polymerase chain reaction;RNA extraction;Taiwan;unindexed sequence;virus characterization;virus classification;virus gene;virus isolation;virus virulence,"Ke, G. M.;Yu, S. W.;Ho, C. H.;Chu, P. Y.;Ke, L. Y.;Lin, K. H.;Tsai, Y. C.;Liu, H. J.;Lin, M. Y.",2010,,10.1016/j.virusres.2009.11.008,0
971,Baculovirus infection of the armyworm (Lepidoptera: Noctuidae) feeding on spiny- or smooth-edged grass (Festuca spp.) leaf blades,"Susceptibility of the armyworm, Mythimna unipuncta (Haworth), to infection by a baculovirus (NPV) isolated from a Kentucky armyworm population was compared on two suspected progenitors of tall fescue, Festuca mairei and Festuca arundinacea subsp. fenas, with spiny leaf margins intact or removed to test whether leaf spines abrade or puncture the peritrophic matrix (PM) and facilitate passage of virions to infection sites in midgut tissue. PCR amplification and sequencing of selected genes from the virus and phylogenetic inference from aligned sequences were carried out to identify and classify the virus. Edge spines had no effect on percentage infection or days to death of newly molted 5th instars fed spiny- or smooth-edged F. mairei leaf blades for 24 h before and after droplet feeding doses of 10(8) or 10(9) OBs ml (1). Fifth instars fed spiny- or smooth-edged grass blades had similarly undamaged PMs when viewed by scanning electron microscope. Fourth instars fed virus-treated F. arundinacea subsp. fenas leaf blades with spiny edges intact or removed did not differ in proportion infected or days to death. The food bolus moves in a liquid medium within the PM, and frass dissections showed that edge spines were often located inside a food bolus separated from the PM by non-spiny plant material rather than contiguous with the PM; therefore, friction of edge spines with the PM may have been low. These results suggest that armyworms will not be less susceptible to baculovirus infection when feeding on tall fescue cultivars with smooth leaf edges planted for improved livestock performance compared with those feeding on standard spiny-edged cultivars. We believe this to be the first study to investigate the effects of a natural physical structure on disruption of the PM and infection by a baculovirus. (C) 2012 Elsevier Inc. All rights reserved.",Baculovirus;Peritrophic matrix;Tritrophic interaction;Trichomes;Leaf;spines;NUCLEAR-POLYHEDROSIS-VIRUS;SPODOPTERA-FRUGIPERDA LEPIDOPTERA;MULTIPLE-REGRESSION ANALYSIS;PSEUDALETIA-UNIPUNCTA;PERITROPHIC;MEMBRANE;FALL ARMYWORM;MIDGUT EPITHELIUM;GRANULOSIS VIRUS;TRICHOPLUSIA NI;LARVAE,"Keathley, C. P.;Harrison, R. L.;Potter, D. A.",2012,May,,0
972,Genetic variability of porcine circovirus 2 in vaccinating and non-vaccinating commercial farms,"Vaccines against porcine circovirus 2 (PCV2) are now widely used to control the diseases caused by the virus. Although the vaccines protect pigs against the disease, they do not lead to sterilizing immunity and therefore infections with PCV2 continue in farms. It is expected that, due to its high evolutionary rate, PCV2 can adapt quickly to environmental pressures such as vaccination. The goal of this study was to elucidate the molecular variation of PCV2 in relation to vaccination. PCV2 variability was investigated from samples of infected pigs from five farms where vaccination had never been applied and two farms where pigs had been vaccinated for at least 2 years. For the genetic analysis, full PCV2 genomes were amplified and subsequently pooled by vaccination status from serum of eight vaccinated, infected pigs and 16 non-vaccinated, infected pigs. Variability of viral populations was quantified using next-generation sequencing and subsequent bioinformatics analysis. The number of segregating sites was similar in the non-vaccinated (n=109) and vaccinated pools (n=96), but the distribution of these sites in the genome differed. Most notably, in the capsid gene, the number of segregating sites was observed only in the non-vaccinated population. Based on the structural analysis, it is expected that some low-frequency amino acids result in biologically low-fit viruses. On the contrary, D294 in replicase represents a novel amino acid which was dominant and unique in the vaccinated pool. This work showed that variable PCV2 populations were circulating in commercial farms, and that this variability was different in samples obtained from vaccinating and non-vaccinating farms.","Animals;Circoviridae Infections/pc [Prevention & Control];*Circoviridae Infections/ve [Veterinary];Circoviridae Infections/vi [Virology];*Circovirus/cl [Classification];*Circovirus/ge [Genetics];Circovirus/ip [Isolation & Purification];Computational Biology;DNA, Viral/ch [Chemistry];DNA, Viral/ge [Genetics];*Genetic Variation;High-Throughput Nucleotide Sequencing;Molecular Sequence Data;Swine;Swine Diseases/pc [Prevention & Control];*Swine Diseases/vi [Virology];*Viral Vaccines/ad [Administration & Dosage];Viral Vaccines/im [Immunology];0 (DNA, Viral);0 (Viral Vaccines)","Kekarainen, T.;Gonzalez, A.;Llorens, A.;Segales, J.",2014,Aug,,0
973,Sequencing and molecular modeling identifies candidate members of Caliciviridae family in bats,"Emerging viral diseases represent an ongoing challenge for globalized world and bats constitute an immense, partially explored, reservoir of potentially zoonotic viruses. Caliciviruses are important human and animal pathogens and, as observed for human noroviruses, they may impact on human health on a global scale. By screening fecal samples of bats in Hungary, calicivirus RNA was identified in the samples of Myotis daubentonii and Eptesicus serotinus bats. In order to characterize more in detail the bat caliciviruses, large portions of the genome sequence of the viruses were determined. Phylogenetic analyses and molecular modeling identified firmly the two viruses as candidate members within the Caliciviridae family, with one calicivirus strain resembling members of the Sapovirus genus and the other bat calicivirus being more related to porcine caliciviruses of the proposed genus Valovirus. This data serves the effort for detecting reservoir hosts for potential emerging viruses and recognize important evolutionary relationships.",article;bat;Caliciviridae;Eptesicus serotinus;feces analysis;gene sequence;molecular model;molecular phylogeny;Myotis;Myotis daubentonii;nonhuman;priority journal;Sapovirus;sequence analysis;sequence homology;virus identification;virus strain,"Kemenesi, G.;Gellért, Á;Dallos, B.;Görföl, T.;Boldogh, S.;Estók, P.;Marton, S.;Oldal, M.;Martella, V.;Bányai, K.;Jakab, F.",2016,,10.1016/j.meegid.2016.04.004,0
974,The microbiome of the soft palate of swine,,,"Kernaghan, S.;Bujold, A. R.;MacInnes, J. I.",2012,,,0
975,Genetic characterization of Indian peste des petits ruminants virus (PPRV) by sequencing and phylogenetic analysis of fusion protein and nucleoprotein gene segments,"Peste des petits ruminants (PPR) is an important viral disease of sheep and goats, endemic in India. The study was undertaken to characterize the local PPRV by sequencing fusion (F) protein and nucleoprotein (N) gene segments and phylogenetic analysis, so as to focus on genetic variation in the field viruses. Selected regions of PPRV genome were amplified from clinical samples collected from 32 sheep and goats by RT-PCR and the resulting amplicons were sequenced for phylogenetic analysis. The phylogenetic tree based on the 322 bp F gene sequences of PPRV from five different locations clustered them into lineage 4 along with other Asian isolates. While the 425 bp N gene sequences revealed a different pattern of branching, yielding three distinct clusters for Nigerian, Turkey and Indian isolates. Thus, classification of PPRV into lineages based on the N gene sequences appeared to yield better picture of molecular epidemiology for PPRV. © 2007 Elsevier Ltd. All rights reserved.",fusion protein;nucleoprotein;amplicon;article;Asia;gene cluster;gene sequence;genetic variability;goat;India;Measles virus;Nigeria;nonhuman;nucleotide sequence;peste des petits ruminant virus;phylogenetic tree;phylogeny;reverse transcription polymerase chain reaction;sheep;Turkey (republic);viral genetics;virus genome,"Kerur, N.;Jhala, M. K.;Joshi, C. G.",2008,,10.1016/j.rvsc.2007.07.007,0
976,Comparison of Schmallenberg virus sequences isolated from mammal host and arthropod vector,"Schmallenberg virus (SBV) is the member of Peribunyaviridae family, which comprises pathogens of importance for human and veterinary medicine. The virus is transmitted only between animals and mainly by biting midges of the genus Culicoides. This study was performed in order to determine SBV genetic diversity and elucidate the host-vector adaptation. All three viral segments were analysed for sequence variability and phylogenetic relations. The Polish SBV strains obtained from acute infections of cattle, congenital cases in sheep, and from Culicoides midges were sequenced using Sanger and next-generation sequencing (NGS) methods. The obtained sequences were genetically similar (99.2-100% identity) to the first-detected strain BH80/11-4 from German cattle. The sampling year and origin of Polish sequences had no effect on molecular diversity of SBV. Considering all analysed Polish as well as European sequences, ovine-derived sequences were the most variable, while the midge ones were more conserved and encompassed unique substitutions located mainly in nonstructural protein S. SBV sequences isolated from Culicoides are the first submitted to GenBank and reported.","Animals;*Arthropod Vectors/vi [Virology];Genetic Variation;Genome, Viral;High-Throughput Nucleotide Sequencing;*Mammals/vi [Virology];Orthobunyavirus/cl [Classification];*Orthobunyavirus/ge [Genetics];Orthobunyavirus/ip [Isolation & Purification];Phylogeny;Phylogeography","Kesik-Maliszewska, J.;Antos, A.;Rola, J.;Larska, M.",2018,Dec,,0
977,"Cygnet river virus, a novel orthomyxovirus from Ducks, Australia","A novel virus, designated Cygnet River virus (CyRV), was isolated in embryonated eggs from Muscovy ducks in South Australia. CyRV morphologically resembles arenaviruses; however, sequencing identifi ed CyRV as an orthomyxovirus. The high mortality rate among ducks co-infected with salmonellae suggests that CyRV may be pathogenic, either alone or in concert with other infections.",amnion fluid;animal cell;animal tissue;article;Australia;Cygnet River Virus;duck;embryo;enteritis;hemolysis;hepatitis;high throughput sequencing;immunohistochemistry;nonhuman;nucleotide sequence;Orthomyxoviridae;polymerase chain reaction;Salmonella enterica;sequence homology;spleen disease;tissue necrosis;transmission electron microscopy;virus hemagglutination;virus identification,"Kessell, A.;Hyatt, A.;Lehmann, D.;Shan, S.;Crameri, S.;Holmes, C.;Marsh, G.;Williams, C.;Tachedjian, M.;Yu, M.;Bingham, J.;Payne, J.;Lowther, S.;Wang, J.;Wang, L. F.;Smith, I.",2012,,10.3201/eid1812.120500,0
978,Epidemiology of human and animal kobuviruses,"Kobuviruses are member of the family Picornaviridae. Initially, members in Kobuvirus genus were named according to the basis of their host species. The viruses found in humans called “Aichi virus”, the viruses from cattle called “bovine kobuvirus”, and the viruses isolated from pigs called “porcine kobuvirus”. Currently, taxonomy of kobuviruses has been proposed and the virus species have been renamed. The “Aichi virus” has been renamed as “Aichivirus A”, “bovine kobuvirus” has been renamed as “Aichivirus B”, and “porcine kobuvirus” has been changed to “Aichivirus C”. Among Aichivirus A, three distinct members, including Aichi virus 1 (Aichivirus in human), canine kobuvirus 1, and murine kobuvirus 1, have been described. Aichi virus 1 in human is globally distributed and has been identified at low incidence (0–3 %) in sporadic acute gastroenteritis cases. Aichi virus 1 has been reported to be associated with variety types of clinical illnesses including diarrhea, vomiting, fever, purulent conjunctivitis, and respiratory symptoms. The studies from Japan, Spain, Germany, and Tunisia demonstrated that high antibody prevalence against Aichi virus 1 were found in the populations. Aichivirus B or previously known as bovine kobuvirus was first reported in 2003. Since then, Aichivirus B has also been reported from several countries worldwide. An overall prevalence of Aichivirus B varies from 1 to 34.5 %, and the highest prevalence was found in cattle with diarrhea in Korea. Aichivirus C or porcine kobuvirus is widely distributed in pigs. Aichivirus C has been found in both diarrhea and healthy pigs and the positive rate of this virus varies from 3.9 up to 100 %. It was reported that Aichivirus C was found with high prevalence in wild boars in Hungary. The accumulated data of the biological, pathological, as well as epidemiological studies of kobuviruses are still limited. Comprehensive global investigations of the prevalence and diversity are required and will be helpful for providing further insight into pathogenicity, genetic heterogeneity, interspecies transmission, and global distribution of kobuviruses.",Aichi virus;Aichi virus A;aichi virus A infection;Aichi virus B;aichi virus B infection;Aichi virus C;aichi virus C infection;article;enzyme immunoassay;enzyme linked immunosorbent assay;genetic heterogeneity;genetic variability;history of medicine;human;Kobuvirus;kobuvirus infection;nonhuman;nucleotide sequence;picornavirus infection;real time polymerase chain reaction;reverse transcription polymerase chain reaction;taxonomy;virus classification;virus detection;virus strain;virus transmission,"Khamrin, P.;Maneekarn, N.;Okitsu, S.;Ushijima, H.",2014,,10.1007/s13337-014-0200-5,0
979,Novel nonstructural protein 4 genetic group in rotavirus of porcine origin,,protein VP4;protein VP7;Rotavirus nonstructural protein 4;amino acid analysis;animal experiment;animal model;comparative study;diarrhea;feces analysis;GenBank;gene amplification;genetic variability;genotype;health survey;letter;molecular genetics;nonhuman;nucleotide sequence;piglet;polymerase chain reaction;Rotavirus;sequence analysis;virus classification;virus transmission,"Khamrin, P.;Okitsu, S.;Ushijima, H.;Maneekarn, N.",2008,,,0
980,A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection,"The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses makes it a powerful tool for broad microbial investigations, such as evaluation of novel cell substrates that may be used for the development of new biological products. However, like any new assay, regulatory applications of HTS need method standardization. Therefore, our three laboratories initiated a study to evaluate performance of HTS for potential detection of viral adventitious agents by spiking model viruses in different cellular matrices to mimic putative materials for manufacturing of biologics. Four model viruses were selected based upon different physical and biochemical properties and commercial availability: human respiratory syncytial virus (RSV), Epstein-Barr virus (EBV), feline leukemia virus (FeLV), and human reovirus (REO). Additionally, porcine circovirus (PCV) was tested by one laboratory. Independent samples were prepared for HTS by spiking intact viruses or extracted viral nucleic acids, singly or mixed, into different HeLa cell matrices (resuspended whole cells, cell lysate, or total cellular RNA). Data were obtained using different sequencing platforms (Roche 454, Illumina HiSeq1500 or HiSeq2500). Bioinformatic analyses were performed independently by each laboratory using available tools, pipelines, and databases. The results showed that comparable virus detection was obtained in the three laboratories regardless of sample processing, library preparation, sequencing platform, and bioinformatic analysis: between 0.1 and 3 viral genome copies per cell were detected for all of the model viruses used. This study highlights the potential for using HTS for sensitive detection of adventitious viruses in complex biological samples containing cellular background. <b>IMPORTANCE</b> Recent high-throughput sequencing (HTS) investigations have resulted in unexpected discoveries of known and novel viruses in a variety of sample types, including research materials, clinical materials, and biological products. Therefore, HTS can be a powerful tool for supplementing current methods for demonstrating the absence of adventitious or unwanted viruses in biological products, particularly when using a new cell line. However, HTS is a complex technology with different platforms, which needs standardization for evaluation of biologics. This collaborative study was undertaken to investigate detection of different virus types using two different HTS platforms. The results of the independently performed studies demonstrated a similar sensitivity of virus detection, regardless of the different sample preparation and processing procedures and bioinformatic analyses done in the three laboratories. Comparable HTS detection of different virus types supports future development of reference virus materials for standardization and validation of different HTS platforms.",,"Khan, A. S.;Ng, S. H. S.;Vandeputte, O.;Aljanahi, A.;Deyati, A.;Cassart, J. P.;Charlebois, R. L.;Taliaferro, L. P.",2017,Sep-Oct,,0
981,Sequence data to settle the taxonomic position of bean common mosaic virus and blackeye cowpea mosaic virus isolates,"The nucleotide sequences of the coat protein genes and 3' non-translated regions (3'-NTRs) of three isolates of bean common mosaic virus (NL1, NL3 and NY15) and one isolate of blackeye cowpea mosaic virus (W) were determined. Comparison of these sequences revealed that the coat proteins of NL1, NY15 and W were identical in size (287 amino acids) and exhibited an overall sequence similarity (94 to 97%), and 84 to 98% in their N-terminal regions. Furthermore, their 3'-NTRs were very similar in length [253 to 256 nucleotides (nt)] and sequence (93 to 96% similarity). In contrast, the coat protein of NL3 had only 261 amino acids and showed 87 to 89% similarity with NL1, NY15 and W whereas its N-terminal region revealed only 46 to 61% similarity. The 3'-NTR of NL3 also displayed appreciable differences, both in length (240 nt) and sequence (56 to 63% similarity). These results, in combination with earlier serological findings, justify the conclusion that NL1, NY15 and W should be considered strains of the same virus, i.e. bean common mosaic virus, and that NL3 is a strain of a different potyvirus for which the name 'bean black root virus' is proposed.",coat protein;amino acid sequence;amino terminal sequence;article;plant virus;nonhuman;nucleotide sequence;priority journal;sequence homology;virus classification;virus isolation,"Khan, J. A.;Lohuis, D.;Goldbach, R.;Dijkstra, J.",1993,,,0
982,Distinction of Strains of Bean Common Mosaic-Virus and Blackeye Cowpea Mosaic-Virus Using Antibodies to N-Terminal and C-Terminal or N-Terminal Peptide Domains of Coat Proteins,"Earlier attempts to discriminate serologically strains NL1, NL3 and NY15 of bean common mosaic virus (BCMV) and strain W of blackeye cowpea mosaic virus (B1CMV) had been unsuccessful. Antibodies directed towards N- and C-, or N-terminal peptide regions of the coat proteins of the above strains enabled the distinction between B1CMV-W, BCMV-NY15 and BCMV-NL3 in electroblot immunoassay and in ELISA. The distinction was better with antibodies directed towards N-termini than with those to N- and C-termini. Strain NL1 of BCMV cross-reacted with both B1CMV-W and BCMV-NY15, but not with BCMV-NL3. Taxonomic implications of these findings are discussed.",PLANT VIRUS TAXONOMY;POTYVIRUSES;BEAN COMMON MOSAIC VIRUS;PEPTIDE;DOMAINS;IMMUNOASSAY;POTYVIRUS GROUP;TAXONOMY;EPITOPES;SEROLOGY,"Khan, J. A.;Lohuis, H.;Goldbach, R. W.;Dijkstra, J.",1990,Dec,,0
983,Molecular characterization of classical swine fever virus isolates from India during 2012–14,"Classical swine fever is a highly contagious and economically important viral disease of pigs. Outbreaks of classical swine fever virus (CSFV) were recorded in different places in the Kamrup district of Assam in India between the years 2012 and 2014. The nucleotide sequences of the 10 CSFV isolates were analyzed based on the partial nucleotide sequences of the E2, 5'NTR and NS5B genes. Phylogenetic analysis indicated the dominance of subgroup 2.2 along with 2.1 strains in the northeast part of India. Variation in the nucleotide sequences of E2, 5'NTR and 3'NS5B genes of CSFV allows tracking changes in the virus population over time. The study will provide epidemiological information useful for assessing CSFV circulating genogroups in India.",5 NTR gene;article;Classical swine fever virus;controlled study;E2 gene;genetic variation;India;nonhuman;NS5B gene;nucleotide sequence;phylogeny;viral genetics;virus gene;virus genome;virus isolation;virus strain,"Khatoon, E.;Barman, N. N.;Deka, M.;Rajbongshi, G.;Baruah, K.;Deka, N.;Bora, D. P.;Kumar, S.",2017,,10.1016/j.actatropica.2017.03.004,0
984,Viral diversity and clonal evolution from unphased genomic data,"Background: Clonal expansion is a process in which a single organism reproduces asexually, giving rise to a diversifying population. It is pervasive in nature, from within-host pathogen evolution to emergent infectious disease outbreaks. Standard phylogenetic tools rely on full-length genomes of individual pathogens or population consensus sequences (phased genotypes). Although high-throughput sequencing technologies are able to sample population diversity, the short sequence reads inherent to them preclude assessing whether two reads originate from the same clone (unphased genotypes). This obstacle severely limits the application of phylogenetic methods and investigation of within-host dynamics of acute infections using this rich data source. Methods: We introduce two measures of diversity to study the evolution of clonal populations using unphased genomic data, which eliminate the need to construct full-length genomes. Our method follows a maximum likelihood approach to estimate evolutionary rates and times to the most recent common ancestor, based on a relaxed molecular clock model; independent of a growth model. Deviations from neutral evolution indicate the presence of selection and bottleneck events. Results: We evaluated our methods in silico and then compared it against existing approaches with the well-characterized 2009 H1N1 influenza pandemic. We then applied our method to high-throughput genomic data from marburgvirus-infected non-human primates and inferred the time of infection and the intra-host evolutionary rate, and identified purifying selection in viral populations. Conclusions: Our method has the power to make use of minor variants present in less than 1% of the population and capture genomic diversification within days of infection, making it an ideal tool for the study of acute RNA viral infection dynamics.",MOLECULAR EVOLUTION;DIVERGENCE TIMES;VIRUS;SEQUENCES;ORIGINS;SWINE;RATES,"Khiabanian, H.;Carpenter, Z.;Kugelman, J.;Chan, J.;Trifonov, V.;Nagle, E.;Warren, T.;Iversen, P.;Bavari, S.;Palacios, G.;Rabadan, R.",2014,Oct,,0
985,Genetic characterization and pathogenicity assessment of Newcastle disease virus isolated from wild peacock,"The continued spread and occurrence of Newcastle disease virus (NDV) has posed potential threat to domestic poultry industry around the globe. Mainly, wild avian species has always been implicated for the natural reservoir for virus and spread of the disease. In the present study, we report the isolation of Newcastle disease virus (NDV/Peacock/India/2012) in necropsy brain tissue sample of wild peacock from North India. Complete genome of the virus was found to be 15,186 nucleotides (nts) with six genes in order of 3′-N–P-M-F-HN-L-5′, which was limited by 55-nts leader region at the 3′ end and a 114-nts trailer sequence at 5′ end. Sequence analysis of fusion protein revealed the dibasic amino acid cleavage site <sup>112</sup>R-R-Q-K-R-F<sup>117</sup>, a characteristic motif of virulent virus. Phylogenetic analysis placed the isolate in genotype II of Newcastle disease virus showing the lowest mean percent divergence (6 %) with other genotype II counterparts. The isolate was characterized as mesogenic (intermediate pathotype) based on the mean death time (63 h) in embryonated chicken eggs and the intra-cerebral pathogenicity index (1.40) in day-old chicks. The report emphasizes the dynamic ecology of NDV strains circulating in a wild avian host during the outbreak of 2012 in North India. Further the genotypic and pathotypical characterizations of the isolate could help in development of homologous vaccine against NDV strain circulating in avian population.",virus fusion protein;amino acid sequence;animal experiment;animal model;animal tissue;article;cock (bird);genotype;India;Newcastle disease virus;nonhuman;nucleotide sequence;peafowl;phylogeny;protein motif;viral genetics;virus gene;virus genome;virus isolation;virus virulence;wild animal,"Khulape, S. A.;Gaikwad, S. S.;Chellappa, M. M.;Mishra, B. P.;Dey, S.",2014,,10.1007/s11262-014-1116-2,0
986,Sequence and phylogenetic analysis of the fusion protein cleavage site of Newcastle disease virus field isolates from Iran,"Nine Newcastle disease virus (NDV) isolates from Newcastle disease (ND) outbreaks in different regions of Iran were characterized at molecular level. Sequence analysis revealed that the isolates shared two pairs of arginine and a phenylalanine at the N-terminus of the fusion (F) protein cleavage site similarly to other velogenic isolates of NDV characterized earlier. Eight of the nine isolates had the same amino acid sequence as VOL95, a Russian NDV isolate from 1995. However, one isolate, MK13 showed 5 amino acid substitutions, of which 3 have been reported for other velogenic NDV isolates. These results suggest that the origin of the outbreaks of ND in different parts of Iran in 1995-1998 is VOL95.",arginine;fusion protein;phenylalanine;virus RNA;amino acid sequence;amino acid substitution;article;bird disease;controlled study;epidemic;Iran;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;protein degradation;reverse transcription polymerase chain reaction;virus isolation,"Kianizadeh, M.;Aini, I.;Omar, A. R.;Yusoff, K.;Sahrabadi, M.;Kargar, R.",2002,,,0
987,Classification of avian paramyxoviruses by immunodiffusion on the basis of antigenic specificity of their M protein antigens,"Seventeen avian paramyxoviruses consisting of ten reference strains and seven recent isolates were classified by immunodiffusion into six species on the basis of the antigenic specificity of their M protein (MP) antigens. The species were represented by the following viruses. (1) Newcastle disease virus, (2) Chicken/California/Yucaipa/56, (3) Turkey/Wisconsin/68, (4) Duck/Mississippi/75, (5) Pigeon/Otaru/76 and (6) Budgerigar/Kunitachi/1/74. The differences in the HN antigens between viruses which were classified into the same species on the basis of the antigenic specificity of their MP antigens, may provide a basis for classifying them into types.",antigen;membrane protein;protein;article;Avulavirus;bird;classification;in vitro study;methodology,"Kida, H.;Yanagawa, R.",1981,,,0
988,"Complete Genome Sequence of Mannheimia haemolytica Strain Mh10517, Isolated from Sheep in South Africa","Respiratory disease caused by Mannheimia haemolytica is a major concern in the cattle and small stock industry worldwide. This problem arises due to the interaction of numerous contributing factors, including physical stresses associated with weaning, shipment, inclement weather, and overcrowding coupled with viral and bacterial infections. The whole genome of M. haemolytica strain Mh10517 was analyzed using an Illumina MiSeq high-throughput sequencing platform. The genome size is 2.67 Mb with 2,879 predicted gene sequences. The availability of this genome sequence will advance studies on various aspects of the biology of M. haemolytica in Africa and the world at large.",,"Kidanemariam Gelaw, A.;Bihon, W.;Faranani, R.;Mafofo, J.;Rees, J.;Madoroba, E.",2015,Apr 09,,0
989,Genetic variability in hepatitis B viruses,"In 1988, it was reported that the full nucleotide sequences of 18 hepatitis B virus (HBV) strains clustered into four genetic groups (A to D) with more than 8% divergence between the groups. This classification of strains in terms of genome sequence has since proven to be an important tool in the understanding of HBV epidemiology and evolution and has been expanded to include three more genotypes. In parallel with the HBV genotypes described in humans, HBV strains isolated from different primates and hepadnaviruses found in woodchucks, ground squirrels, ducks and herons have been studied. Sequence differences between HBV genotypes can lead to structural differences at the level of the pregenome and can also lead to dramatic differences at the translational level when specific and commonly occurring mutations occur. There is increasing evidence that the clinical picture, the response to treatment and the long-term prognosis may differ depending on which genotype has infected the patient. The consideration of traditional serological patterns in a patient must therefore take the genotype of the infecting strain into account. Nucleotide variability between HBV strains has been used in several studies to trace routes of transmission and, since it is becoming increasingly clear that the differences between HBV genotypes are important, the need for reliable and easy methods of differentiating HBV genotypes has arisen. This review summarizes the knowledge of HBV genotypes with regard to their genetic, structural and clinically significant differences and their origin and evolution in the context of the hepadnaviruses in general.",interferon;lamivudine;nucleoside analog;clinical feature;controlled study;drug response;duck;fowl;gene cluster;gene mutation;genetic epidemiology;genetic variability;genotype;Hepadnaviridae;hepatitis B;Hepatitis B virus;molecular evolution;nonhuman;nucleotide sequence;primate;priority journal;prognosis;reliability;review;RNA translation;sequence analysis;serology;Sciuridae;virus classification;virus isolation;virus strain;virus transmission;woodchuck,"Kidd-Ljunggren, K.;Miyakawa, Y.;Kidd, A. H.",2002,,,0
990,Identification of plant protein kinases in response to abiotic and biotic stresses using superSAGE,"Plants are sessile organisms subjected to many environmental adversities. For their survival they must sense and respond to biotic and abiotic stresses efficiently. During this process, protein kinases are essential in the perception of environmental stimuli, triggering signaling cascades. Kinases are among the largest and most important gene families for biotechnological purposes, bringing many challenges to the bioinformaticians due to the combination of conserved domains besides diversified regions. Cowpea [Vigna unguiculata (L.) Walp.] is an important legume that is adapted to different agroclimatic conditions, including drought, humidity and a range of temperatures. For this crop, the association of the SuperSAGE method with high-throughput sequencing technology would generate reliable transcriptome profiles with millions of tags counted and statistically analyzed. An approach evaluating biotic and abiotic stresses was carried out generating over 13 million cowpea SuperSAGE tags available from leaves/roots of plants under abiotic (mechanical injury and salinity) or biotic (CABMV, Cowpea aphid born mosaic virus) stresses. The annotation and identification of tags linked by BlastN to previously well described ESTs, allowed the posterior identification of kinases. The annotation efficiency depended on the database used, with the KEGG figuring as a good source for annotated ESTs especially when complemented by an independent Gene Ontology categorization, as well as the Gene Index using selected species. The use of different approaches allowed the identification of 1,350 kinase candidates considering biotic libraries and 2,268 regarding abiotic libraries, based on a combination of both, adequate descriptions and GO terms. Additional searches in kinase specific databases allowed the identification of a relatively low number of additional kinases, uncovering the lack of kinase databases for non-model organisms, especially plants. Concerning the kinase families, a total of 713 potential kinases were classified into 13 families of the CMGC and STE groups. Concerning the differentially expressed kinases, 169 of the 713 potential kinases were identified (p < 0.05), 100 upand 69 down-regulated when comparing distinct libraries, allowing the generation of a comprehensive panel of the differentially expressed kinases under biotic and abiotic stresses in a non-model plant as cowpea. © 2011 Bentham Science Publishers.",adenosine kinase;adenylate kinase;choline kinase;cyclin dependent kinase;diacylglycerol kinase;dual specificity tyrosine(y)phosphorylation regulated kinase;frutokinase;glucan water dikinase;glycogen synthase kinase 3;hexokinase;leucine zipper protein;mitogen activated protein kinase;mitogen activated protein kinase kinase;mitogen activated protein kinase kinase kinase;phosphatidilinositol 4 kinase;phosphofrutokinase;phosphoglycerate kinase;phosphoribulokinase;protein kinase;protein serine threonine kinase;protein tyrosine kinase;pyruvate kinase;receptor like kinase 4;receptor like protein kinase;s receptor kinase like protein 1;shaggo like protein kinase;sterile alpha motif and leucine zipper containing kinase;unclassified drug;plant protein;wall associated protein kinase;abiotic stress;article;biotechnology;biotic stress;cowpea;down regulation;high throughput sequencing;multigene family;nonhuman;protein analysis;protein expression;protein motif;sequence analysis;upregulation,"Kido, E. A.;de Araújo Barbosa, P. K.;Neto, J. R. C. F.;Pandolfi, V.;Houllou-Kido, L. M.;Crovella, S.;Molina, C.;Kahl, G.;Benko-Iseppon, A. M.",2011,,,0
991,Predicting the global spread of H5N1 avian influenza,"The spread of highly pathogenic H5N1 avian influenza into Asia, Europe, and Africa has resulted in enormous impacts on the poultry industry and presents an important threat to human health. The pathways by which the virus has and will spread between countries have been debated extensively, but have yet to be analyzed comprehensively and quantitatively. We integrated data on phylogenetic relationships of virus isolates, migratory bird movements, and trade in poultry and wild birds to determine the pathway for 52 individual introduction events into countries and predict future spread. We show that 9 of 21 of H5N1 introductions to countries in Asia were most likely through poultry, and 3 of 21 were most likely through migrating birds. In contrast, spread to most (20/23) countries in Europe was most likely through migratory birds. Spread in Africa was likely partly by poultry (2/8 introductions) and partly by migrating birds (3/8). Our analyses predict that H5N1 is more likely to be introduced into the Western Hemisphere through infected poultry and into the mainland United States by subsequent movement of migrating birds from neighboring countries, rather than from eastern Siberia. These results highlight the potential synergism between trade and wild animal movement in the emergence and pandemic spread of pathogens and demonstrate the value of predictive models for disease control. © 2006 by The National Academy of Sciences of the USA.",Africa;article;Asia;avian influenza;disease control;Europe;geographic distribution;introduced species;nonhuman;pandemic;phylogeny;population migration;poultry farming;prediction;priority journal;quantitative analysis;Russian Federation;virus strain;virus transmission;virus virulence;Western Hemisphere;wild type,"Kilpatrick, A. M.;Chmura, A. A.;Gibbons, D. W.;Fleischer, R. C.;Marra, P. P.;Daszak, P.",2006,,10.1073/pnas.0609227103,0
992,Characterization of a complete genome of a circular single-stranded DNA virus from porcine stools in Korea,"Porcine circular single-stranded DNA viruses have been just identified from swine feces in Korea. This virus was mentioned as bovine stool-associated circular DNA virus (BoSCV)-like virus discovered from porcine stools. However, the thorough characteristics of the virus were not identified. Therefore, this research focuses on finding a full genome sequence and analyzing the genetic features of the virus. The virus, now called porcine stool-associated circular DNA virus in Korea (PoSCV Kor), consists of 2,589 bases forming circular structure. It has two major ORFs inversely encoding replicase and capsid protein, with each stem-loop structure between 5' ends and 3' ends of the two putative ORFs. This characteristics is the same as PoSCV in New Zealand, but different from chimpanzee stool-associated circular virus (ChiSCVs) and BoSCV, which have one stem-loop structure. Therefore, it would be sure that PoSCV Kor is very similar to PoSCV in respect to the genetic aspect; the same number of nucleotide bases and the amino acid identity of replicase and capsid protein (96 and 93 %, respectively). This fact could be certified through the finding that PoSCV Kor and PoSCV are in the same cluster by phylogenetic analysis based on the comparison with full-sequences of other circular ssDNA viruses.",PoSCV;Korea;Genetic analysis;Circular DNA virus;Complete genome;WASTING SYNDROME PMWS;VIRAL METAGENOMICS;CONSERVED SEQUENCE;HUMAN;FECES;IDENTIFICATION;CIRCOVIRUS;LIKELIHOOD;DIVERSITY;COMMUNITY;PROTEIN,"Kim, A. R.;Chung, H. C.;Kim, H. K.;Kim, E. O.;Nguyen, V. G.;Choi, M. G.;Yang, H. J.;Kim, J. A.;Park, B. K.",2014,Feb,,0
993,"Detection of Severe Acute Respiratory Syndrome-Like, Middle East Respiratory Syndrome-Like Bat Coronaviruses and Group H Rotavirus in Faeces of Korean Bats","Bat species around the world have recently been recognized as major reservoirs of several zoonotic viruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), Nipah virus and Hendra virus. In this study, consensus primer-based reverse transcriptase polymerase chain reactions (RT-PCRs) and high-throughput sequencing were performed to investigate viruses in bat faecal samples collected at 11 natural bat habitat sites from July to December 2015 in Korea. Diverse coronaviruses were first detected in Korean bat faeces, including alphacoronaviruses, SARS-CoV-like and MERS-CoV-like betacoronaviruses. In addition, we identified a novel bat rotavirus belonging to group H rotavirus which has only been described in human and pigs until now. Therefore, our results suggest the need for continuing surveillance and additional virological studies in domestic bat.",animal;bat;Coronaviridae;feces;isolation and purification;Rotavirus;SARS coronavirus;South Korea;virology,"Kim, H. K.;Yoon, S. W.;Kim, D. J.;Koo, B. S.;Noh, J. Y.;Kim, J. H.;Choi, Y. G.;Na, W.;Chang, K. T.;Song, D.;Jeong, D. G.",2016,,10.1111/tbed.12515,0
994,H5N1 subtype highly pathogenic avian influenza virus isolated from healthy mallard captured in South Korea,"On December 7, 2010, H5N1 highly pathogenic avian influenza virus was isolated from a healthy mallard captured at the Mankyung River in South Korea. Phylogenetic analysis showed that this virus was classified into clade 2.3.2 and closely related to H5N1 viruses isolated from wild birds in Mongolia, Russia and China in 2009 and 2010. © 2011 Elsevier B.V.",Anas platyrhynchos;animal experiment;article;avian influenza virus;bird;China;disease surveillance;Influenza A virus (H5N1);Mongolia;nonhuman;nucleotide sequence;phylogeny;Russian Federation;sequence analysis;South Korea;virus isolation;virus virulence,"Kim, H. R.;Kim, B. S.;Bae, Y. C.;Moon, O. K.;Oem, J. K.;Kang, H. M.;Choi, J. G.;Lee, O. S.;Lee, Y. J.",2011,,10.1016/j.vetmic.2011.03.004,0
995,Molecular characterization of chicken infectious anemia viruses detected from breeder and broiler chickens in south korea,"In South Korea, 32 sequences of chicken infectious anemia virus (CIAV) from various flocks of breeder and commercial chickens were genetically characterized for the first time. Phylogenetic analysis of the viral protein 1 gene, including a hypervariable region of the CIAV genome, indicated that Korean CIAV strains were separated into groups II, IIIa, and IIIb. Strains were commonly identified in great-grandparent and grandparent breeder farms as well as commercial chicken farms. In the field, CIAV strains from breeder farms had no clinical effects, but commercial farm strains were associated with depression, growth retardation, and anemia regardless of the group from which the strain originated. In addition, we identified 7 CIAV genomes that were similar to vaccine strains from vaccinated and unvaccinated breeder flocks. These data suggest that further studies on pathogenicity and vaccine efficacy against the different CIAV group are needed, along with continuous CIAV surveillance and genetic analysis at breeder farms. © 2010 Poultry Science Association Inc.",virus DNA;animal;animal disease;article;bird disease;chicken;Circoviridae infection;classification;genetics;Gyrovirus;isolation and purification;phylogeny;polymerase chain reaction;South Korea;virology,"Kim, H. R.;Kwon, Y. K.;Bae, Y. C.;Oem, J. K.;Lee, O. S.",2010,,10.3382/ps.2010-00911,0
996,Characterization of Avian Encephalomyelitis Outbreaks Occurred in South Korea from 2006 to 2013,"This study was conducted to characterize avian encephalomyelitis (AE) viruses obtained from various flocks of breeder and commercial chickens in South Korea. Young chicken less than 4 weeks old showed neurological sign were diagnosed as typical AE infection between 2006 and 2011. In 2013, idiopathic AE occurred on the unvaccinated 79 day-old chickens that had clinical signs of ataxia and paralysis. Phylogenetic analysis of viral protein 2 genes of AE viruses showed that all AE field viruses tested were genetically similar to vaccine strain [Calnek 1143]. In the embryo-inoculation test via the yolk sac, only one field strain and one commercial vaccine were embryo-adapted. The results indicated that the AE outbreaks in South Korea were caused by strains genetically similar to vaccine strain indicating possibility of vaccine breakdown or persistence in the chicken population.",avian encephalomyelitis;live vaccine;RT-PCR;viral encephalitis;VIRUS,"Kim, H. R.;Kwon, Y. K.;Lee, H. S.",2015,Apr,,0
997,Ostrich ( Struthio camelus ) Infected with H5N8 Highly Pathogenic Avian Influenza Virus in South Korea in 2014,"Highly pathogenic avian influenza (HPAI) virus of the H5N8 subtype was isolated from a young ostrich in South Korea in March 2014. Clinical signs characterized by anorexia, depression, and signs of nervousness were observed. The isolated A/ostrich/Korea/H829/2014 (H5N8) virus had a cleavage site motif containing multiple basic amino acids, typical of HPAI virus. The phylogenetic tree of the hemagglutinin gene of the H5 HPAI virus showed that this ostrich H5N8 virus belongs to clade 2.3.4.4 viruses together with H5N8 strains isolated from ducks and wild birds in South Korea in 2014. Pathologically, redness of pancreas, enlargement and hemorrhage of spleen, friability of brain, and hydropericardium were prominently found. Histologic legions were observed in pancreas, spleen, liver, lung, heart, and brain, and influenza A nucleoproteins were detected in the same organs by immunohistochemistry. Other ostriches farmed together in open camps were not infected with HPAI virus based on the serologic and virologic tests. The findings indicate that ostriches are susceptible to H5N8 HPAI virus, but this virus does not spread efficiently among ratites.",avian protein;hemagglutinin;animal;case report;classification;DNA sequence;genetics;Influenza A virus (H5N8);avian influenza;isolation and purification;phylogeny;South Korea;Struthioniformes;transmission;veterinary medicine;virology,"Kim, H. R.;Kwon, Y. K.;Lee, Y. J.;Kang, H. M.;Lee, E. K.;Song, B. M.;Jung, S. C.;Lee, K. H.;Lee, H. K.;Baek, K. H.;Bae, Y. C.",2016,,10.1637/11357-122315-CaseR,0
998,Identification of a picornavirus from chickens with transmissible viral proventriculitis using metagenomic analysis,"Transmissible viral proventriculitis (TVP), an infectious disease in chickens, is responsible for economic losses in the commercial poultry industry. The major etiologic agent, however, is unknown. Using metagenomics, we compared the diversity of viruses present in proventriculus samples from flocks diagnosed with TVP to those of healthy flocks in South Korea between 2003 and 2012. Each sample had a mean of 21,538,726 sequence reads generated by high-throughput sequencing, with a mean length of 160 nt. Enrichment in viral sequences suggested that at least three viruses were present in each TVP sample. Although we could not determine a pathogen of TVP that matched the known morphology, picornavirus sequences were present in all five disease samples, suggesting an association with TVP. The five samples yielded 1,045-1,720 bp contigs with 81-84 % nt sequence identity to turkey hepatitis virus (accession number: HM751199). Whole-genome analysis indicated that the QIA01 strain of the novel picornavirus was similar to turkey hepatitis virus in the P2 and P3 regions (82.7 % nt and 95.5 % aa sequence identity), but different in the structural region and partial 2A peptides (56.2 % nt and 23.9 % aa sequence identity). In addition, the QIA01 virus was similar (87.0 % nt and 95.6 % aa sequence identity) to chicken megrivirus, recently detected in chickens with malabsorption syndrome in Hungary. Our results are useful for understanding the genetic diversity of avian picornaviruses and for classifying chicken megrivirus as a pathogen affecting the digestive tract of chickens.",virus RNA;animal;bird disease;chicken;cluster analysis;DNA sequence;gene order;genetics;isolation and purification;metagenomics;molecular genetics;phylogeny;Picornaviridae;picornavirus infection;sequence homology;South Korea;veterinary medicine;virology;virus genome,"Kim, H. R.;Yoon, S. J.;Lee, H. S.;Kwon, Y. K.",2015,,10.1007/s00705-014-2325-7,1
999,Characterization and phylogenetic analysis of Varicella-zoster virus strains isolated from Korean patients,"Varicella-zoster virus (VZV) is a causative agent of chickenpox in primary infection and shingles after its reactivation from latency. Complete or almost-complete genomic DNA sequences for various VZV strains have been reported. Recently, clinical VZV strains were isolated from Korean patients whose genome was sequenced using high-throughput sequencing technology. In this study, we analyzed single nucleotide polymorphism (SNP) of VZV strains to genetically characterize Korean clinical isolates. Phylogenetic analyses revealed that three Korean strains, YC01, YC02, and YC03, were linked to clade 2. Comprehensive SNP analysis identified 86 sites specific for the 5 VZV clades. VZV strains isolated from Korea did not form a phylogenetic cluster. Rather, YC02 and YC03 clustered strongly with Chinese strain 84-7 within clade 2, more specifically cluster 2a. Signature sequences for the cluster 2a were identified and found to play an important role in the separation of cluster 2a strains from other clade 2 strains, as shown in substitution studies. Further genetic analysis with additional strains isolated from Japan, China, and other Asian countries would provide a novel insight into the significance of two distinct subclades within clade 2.",classification;DNA sequence;genetic variation;genetics;high throughput sequencing;human;isolation and purification;Korea;phylogeny;single nucleotide polymorphism;Varicella zoster virus;virus genome,"Kim, M. H.;Jeon, J. S.;Kim, I. K.;Park, J. S.;Park, H.;Shin, O. S.;Lee, C. H.",2017,,10.1007/s12275-017-7171-3,0
1000,Efficient selection of antibodies reactive to homologous epitopes on human and mouse hepatocyte growth factors by next-generation sequencing-based analysis of the B cell repertoire,"YYB-101 is a humanized rabbit anti-human hepatocyte growth factor (HGF)-neutralizing antibody currently in clinical trial. To test the effect of HGF neutralization with antibody on anti-cancer T cell immunity, we generated surrogate antibodies that are reactive to the mouse homologue of the epitope targeted by YYB-101. First, we immunized a chicken with human HGF and monitored changes in the B cell repertoire by next-generation sequencing (NGS). We then extracted the VH gene repertoire from the NGS data, clustered it into components by sequence homology, and classified the components by the change in the number of unique VH sequences and the frequencies of the VH sequences within each component following immunization. Those changes should accompany the preferential proliferation and somatic hypermutation or gene conversion of B cells encoding HGF-reactive antibodies. One component showed significant increases in the number and frequencies of unique VH sequences and harbored genes encoding antibodies that were reactive to human HGF and competitive with YYB-101 for HGF binding. Some of the antibodies also reacted to mouse HGF. The selected VH sequences shared 98.3% identity and 98.9% amino acid similarity. It is therefore likely that the antibodies encoded by them all react to the epitope targeted by YYB-101.",genetic analyzer;100 39 h;B lymphocyte receptor;epitope;neutralizing antibody;panel reactive antibody;recombinant scatter factor;single chain fragment variable antibody;animal cell;animal experiment;antigen antibody reaction;article;B lymphocyte;bacteriophage;binding affinity;biopanning;cell fractionation;cell proliferation;cellular immunity;complementarity determining region;enzyme linked immunosorbent assay;Escherichia coli;gene amplification;gene conversion;high throughput sequencing;immunization;Leghorn chicken;next generation sequencing;nonhuman;phage display;polymerase chain reaction;sequence analysis;sequence homology;somatic hypermutation;whole genome sequencing;MiSeq,"Kim, S.;Lee, H.;Noh, J.;Lee, Y.;Han, H.;Yoo, D. K.;Kim, H.;Kwon, S.;Chung, J.",2019,,10.3390/ijms20020417,0
1001,The prevalence and genetic characteristics of porcine circovirus type 2 and 3 in Korea,"BACKGROUND: Porcine circovirus-associated diseases (PCVAD), caused by porcine circovirus type 2 (PCV2), threaten the pig industry worldwide. Five genotypes of PCV2 were recently identified: PCV2a, PCV2b, PCV2c, PCV2d and PCV2e. In addition, a novel porcine circovirus from a case of a sow with dermatitis, nephropathy syndrome and reproductive failure has been identified based on metagenomic analysis and classified as porcine circovirus type 3 (PCV3). Therefore, the current study was conducted to determine the prevalence and genetic characteristics of PCV2 and PCV3 in clinical samples. RESULTS: A total of 471 samples (161 tissue samples of lungs and lymph nodes from 34 farms and 310 serum samples from 47 farms) were tested for PCV2. Among them, 171 samples from 59 farms that had been positive for PCV2 were genotyped. Another 690 samples (296 tissue samples of lungs and lymph nodes from 91 farms, 108 samples of aborted foetuses from 26 farms, and 286 serum samples from 47 farms) were tested for PCV3. Based on PCV2 genotyping results, PCV2d was the most prevalent genotype (107 of 171 samples), and co-infections with combinations of PCV2a, 2b and 2d were identified in 48 samples from 17 farms. A total of 14 samples from 11 farms were also positive for both PCV2 and PCV3. For PCV3, 57 samples (9.8%) from 32 farms (23.2%) were positive. Among the 108 aborted foetuses from 26 farms, only 2 samples were positive for PCV3. Based on sequence comparisons, PCV2d shares 89.6-91.0% and 93.2-94.3% homology with PCV2a and PCV2b, respectively; 98.6-100% homology is shared among PCV2d strains. The PCV3 strains identified in this study share 98.0-99.5% homology. CONCLUSIONS: Our study concludes that PCV2d has become the most predominant genotype in Korea. PCV3 was also identified in clinical samples, though no significant association with clinical symptoms was observed in PCV3-positive cases.",animal;Circoviridae infection;Circovirus;classification;female;genetics;genotype;male;phylogeny;pig;prevalence;South Korea;swine disease;veterinary medicine;virology,"Kim, S. C.;Nazki, S.;Kwon, S.;Juhng, J. H.;Mun, K. H.;Jeon, D. Y.;Jeong, C. G.;Khatun, A.;Kang, S. J.;Kim, W. I.",2018,,10.1186/s12917-018-1614-x,0
1002,Complete genome sequence of a novel newcastle disease virus: Strain isolated from a chicken in West Africa,"The complete genome sequence of an African Newcastle disease virus (NDV) strain isolated from a chicken in Togo in 2009 was determined. The genome is 15,198 nucleotides (nt) in length and is classified in genotype VII in the class II cluster. Compared to common vaccine strains, the African strain contains a previously described 6-nt insert in the downstream untranslated region of the N gene and a novel 6-nt insert in the HN-L intergenic region. Genome length differences are a marker of the natural history of NDV. This is the first description of a class II NDV strain with a genome of 15,198 nt and a 6-nt insert in the HN-L intergenic region. Sequence divergence relative to vaccine strains was substantial, likely contributes to outbreaks, and illustrates the continued evolution of new NDV strains in West Africa. © 2012, American Society for Microbiology.",asparagine;histidine;leucine;nucleotide;Africa;article;chicken;evolution;gene cluster;gene insertion;gene sequence;genetic variability;genotype;Newcastle disease virus;nonhuman;nucleotide sequence;priority journal;Togo;virus classification;virus genome;virus isolation;virus strain,"Kim, S. H.;Nayak, S.;Paldurai, A.;Nayak, B.;Samuel, A.;Aplogan, G. L.;Awoume, K. A.;Webby, R. J.;Ducatez, M. F.;Collins, P. L.;Samal, S. K.",2012,,10.1128/jvi.01922-12,0
1003,Genetic diversity and pathogenic potential of low pathogenic H7 avian influenza viruses isolated from wild migratory birds in Korea,"To detect the circulation of H7 avian influenza viruses, we characterized H7 viruses found in migratory birds and live poultry markets of South Korea from 2005 to 2014. Phylogenic analysis revealed that while all viruses clustered into the Eurasian-lineage of H7 avian viruses, at least 12 distinct genotypes were represented. Most H7 viruses contained at least one gene segment from the highly-pathogenic A/Sck/Hong Kong/YU100/02(H5N1)-like avian virus, and they could be separated into at least two antigenic groups. Although we did not detect genetically identical strains, HI assay demonstrated close cross-reactivity of some isolates with the H7N9 viruses from China. Animal studies revealed that most of the genotypes could replicate in the lungs of mice and chickens without prior adaptation and some, particularly H7N4 and H7N7 subtypes, induced mortality in mice. These results reinforce growing pandemic concerns regarding recent H7 viruses and emphasize the importance of continued surveillance of avian influenza viruses in the wild.",animal experiment;animal model;animal tissue;article;avian influenza virus;chicken;controlled study;cross reaction;experimental influenza;female;genetic variability;Influenza A virus (H7N9);Influenza A virus H7N4;Influenza A virus H7N7;migrant bird;molecular phylogeny;mouse;nonhuman;nucleotide sequence;prevalence;priority journal;South Korea;virus replication;virus virulence;wild animal,"Kim, Y. I.;Kim, S. W.;Si, Y. J.;Kwon, H. I.;Park, S. J.;Kim, E. H.;Kim, S. M.;Lee, I. W.;Song, M. S.;Choi, Y. K.",2016,,10.1016/j.meegid.2016.09.005,0
1004,Genetic and phylogenetic characterizations of a novel genotype of highly pathogenic avian influenza (HPAI) H5N8 viruses in 2016/2017 in South Korea,"During the outbreaks of highly pathogenic avian influenza (HPAI) H5N6 viruses in 2016 in South Korea, novel H5N8 viruses were also isolated from migratory birds. Phylogenetic analysis revealed that the HA gene of these H5N8 viruses belonged to clade 2.3.4.4, similarly to recent H5Nx viruses, and originated from A/Brk/Korea/Gochang1/14(H5N8), a minor lineage of H5N8 that appeared in 2014 and then disappeared. At least four reassortment events occurred with different subtypes (H5N8, H7N7, H3N8 and H10N7) and a chicken challenge study revealed that they were classified as HPAI viruses according to OIE criteria.",article;cladistics;genetic analysis;genome analysis;genotype;geographical variation (species);Influenza A virus (H10N7);Influenza A virus (H3N8);Influenza A virus (H5N8);Influenza A virus (H7N7);nonhuman;phylogeny;priority journal;sequence analysis;sequence homology;South Korea;virus genome;virus isolation;virus virulence,"Kim, Y. I.;Park, S. J.;Kwon, H. I.;Kim, E. H.;Si, Y. J.;Jeong, J. H.;Lee, I. W.;Nguyen, H. D.;Kwon, J. J.;Choi, W. S.;Song, M. S.;Kim, C. J.;Choi, Y. K.",2017,,10.1016/j.meegid.2017.05.001,0
1005,Foot and mouth disease virus: A review,"Foot-and-mouth disease has been for a long time a major plague for animal health but is now close to be a disease of the past, at least in Europe. The efficient but expensive and not totally without danger vaccination was stopped in 1991 in all European Union states. However, the research on this virus, one of the most studied virus, both in the field of fondamental virology and animal health keeps on bringing new data on still badly known aspects of its biology like cell penetration, RNA translation, replication and capsid assembly. These different aspects are reviewed. The development of biotechnology permitted the rise of new vaccines, if not more efficient, at least completely secured. The intrinsic mutation properties of this virus are still a major challenge for its total eradication.",foot and mouth disease vaccine;virus RNA;biotechnology;foot and mouth disease;Foot and mouth disease virus;nonhuman;review;vaccination;vaccine production;virus assembly;virus cell interaction;virus classification;virus genome;virus mutation;virus particle;virus replication;virus transcription;zoonosis,"Kim, Y. J.;Remond, M.",2000,,,0
1006,Analysis of rotavirus species diversity and evolution including the newly determined full-length genome sequences of rotavirus F and G,"Rotaviruses are a leading cause of viral acute gastroenteritis in humans and animals. Eight different rotavirus species (A-H) have been defined based on antigenicity and nucleotide sequence identities of the VP6 gene. Here, the first complete genome sequences of rotavirus F (strain 03V0568) and G (strain 03V0567) with lengths of 18,341 and 18,186 bp, respectively, are described. Both viruses have open reading frames for rotavirus proteins VP1 to VP7 and NSP1 to NSP5 located at the 11 genome segments. Nucleotide sequence identities to other rotaviruses ranged between 29.8% (NSP1 gene) and 61.7% (VPI gene) for rotavirus F and between 29.3% (NSP1-2 gene) and 65.9% (NSP2 gene) for rotavirus G, thus confirming their classification as separate virus species. Encoded proteins revealed remarkable sequence differences among the rotavirus species. In contrast, the non-coding 5'-terminal sequences of the genome segments are highly conserved among all rotavirus species. Different 3'-terminal consensus sequences are found between rotavirus A/D/F, rotavirus C and rotavirus B/G/H. Phylogenetic analyses indicated a separation of rotaviruses in two major clades consisting of rotavirus A/C/D/F and rotavirus B/G/H. Within these clades, rotavirus F mainly clustered with rotavirus D and rotavirus G with rotavirus B. In addition, differentiation among mammalian and avian rotavirus A strains, host-specific evolution of rotavirus B and C as well as an ancient reassortment event between avian rotavirus A and D are indicated by the phylogenetic data. These results underline the high diversity of rotaviruses as a result of a complex evolutionary history. (C) 2012 Elsevier B.V. All rights reserved.",Rotavirus;Genome;Phylogeny;Evolution;GROUP-A;MAXIMUM-LIKELIHOOD;BINDING DOMAIN;GROUP-B;RECOGNITION;REPLICATION;CHICKENS;GUANYLYLTRANSFERASE;MECHANISM;PROTEINS,"Kindler, E.;Trojnar, E.;Heckel, G.;Otto, P. H.;Johne, R.",2013,Mar,,0
1007,Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus,"Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT–PCR method was developed to amplify a 7.6 kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0.24% frequency. These data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks. In 7 samples, from 6 different animals, a total of 5 consensus level variants were identified, in addition to 104 sub-consensus variants of which 22 were shared between 2 or more animals. Further analysis revealed differences in swarm structures from samples derived from the same animal suggesting the presence of distinct viral populations evolving independently at different lesion sites within the same infected animal.",nucleotide;polyprotein;article;bovine;epidemic;Foot and mouth disease virus;gene sequence;gene structure;genetic code;genetic variability;herd;host;nonhuman;organism social group;population dynamics;population structure;priority journal;reverse transcription polymerase chain reaction;United Kingdom;virus genome;virus swarm;virus transmission,"King, D. J.;Freimanis, G. L.;Orton, R. J.;Waters, R. A.;Haydon, D. T.;King, D. P.",2016,,10.1016/j.meegid.2016.07.010,0
1008,Rapid serotyping of infectious bronchitis virus isolates with the hemagglutination-inhibition test,"The hemagglutination-inhibition (HI) test was evaluated as a method of typing recent suspect infectious bronchitis virus (IBV) isolates. Hemagglutination (HA) antigen was prepared from each isolate by phospholipase C treatment of virus concentrated from allanto-amniotic fluids of infected chicken embryos. An HI test was run with the HA antigen of each isolate against a battery of 17 antisera that had been prepared against different IBV strains classified by virus neutralization (VN). The HI test identified Ark 99 and Holland isolates that were similar to strains previously classified by VN. Two isolates included in this study were not inhibited by any of the reference antisera and therefore appeared to be antigenically different. The isolates were also evaluated by VN, and the results of the VN and HI methods agreed. Therefore the results suggest that the HI test can be useful for making a rapid, presumptive identification of new IBV isolates.",epitope;animal;article;Avian infectious bronchitis virus;chick embryo;chicken;classification;Coronavirinae;hemagglutination inhibition test;methodology;microbiology;serotyping,"King, D. J.;Hopkins, S. R.",1984,,,0
1009,Enhanced bioinformatic profiling of VIDISCA libraries for virus detection and discovery,"VIDISCA is a next-generation sequencing (NGS) library preparation method designed to enrich viral nucleic acids from samples before highly-multiplexed low depth sequencing. Reliable detection of known viruses and discovery of novel divergent viruses from NGS data require dedicated analysis tools that are both sensitive and accurate. Existing software was utilised to design a new bioinformatic workflow for high-throughput detection and discovery of viruses from VIDISCA data. The workflow leverages the VIDISCA library preparation molecular biology, specifically the use of Mse1 restriction enzyme which produces biological replicate library inserts from identical genomes. The workflow performs total metagenomic analysis for classification of non-viral sequence including parasites and host, and separately carries out virus specific analyses. Ribosomal RNA sequence is removed to increase downstream analysis speed and remaining reads are clustered at 100% identity. Known and novel viruses are sensitively detected via alignment to a virus-only protein database, and false positives are removed. A new cluster-profiling analysis takes advantage of the viral biological replicates produced by Mse1 digestion, using read clustering to flag the presence of short genomes at very high copy number. Importantly, this analysis ensures that highly repeated sequences are identified even if no homology is detected, as is shown here with the detection of a novel gokushovirus genome from human faecal matter. The workflow was validated using read data derived from serum and faeces samples taken from HIV-1 positive adults, and serum samples from pigs that were infected with atypical porcine pestivirus.",restriction endonuclease;ribosome RNA;article;bioinformatics;gene expression profiling;high throughput screening;human;metagenomics;molecular library;next generation sequencing;nonhuman;priority journal;protein database;RNA sequence;virus detection,"Kinsella, C. M.;Deijs, M.;van der Hoek, L.",2019,,10.1016/j.virusres.2018.12.010,0
1010,The genome structure of a new chicken virus identifies it as a parvovirus,The nucleic acid of chicken parvovirus-like particles showed sensitivity to DNase and S1 nuclease treatment and resistance to digestion with RNase. Viral DNA readily served as a template for self-primed conversion in vitro into a double-stranded form of about 5200 base pairs. There was no evidence for encapsidation of strands of opposite polarities. These findings confirm the taxonomic classification of chicken parvovirus-like particles as fowl parvovirus type 1 within the Parvovirus genus of the Parvoviridae.,radioisotope;virus DNA;agar gel electrophoresis;chicken;classification;electron microscopy;nonhuman;Parvoviridae;priority journal;virus characterization;virus classification,"Kisary, J.;Avalosse, B.;Miller-Faures, A.;Rommelaere, J.",1985,,,0
1011,Recent knowledge on the bovine virus diarrhoea virus review article,"The Pestivirus genus in one of the most intensively studied groups of animal viruses. Detailed studies on pestiviruses make necessary also the re-classification of the genus. The recent study has summarized the recent knowledge on the bovine diarrhoea virus (BVDV). Actual taxonomic questions have also been dealt with, namely the two genotypes of BVDV, as well as the new, non host-specific classification of pestiviruses. The morphological and physical characterization of the virus has not been dealt with. Genome structure (Fig.1) genome organization, proteins responsible for the cytopathogenic effect have been discussed according to our present knowledge. The differences between the two biotypes of BVDV - cytopathogenic (cp, Fig.2) and non-cytopathogenic (ncp) viruses - have also been discussed, classifying according to recombinative events suffered by the virus genome. For the time being it seems on the basis of the results of recent research that the recombinative events of the aminoterminal of non-structural p80 enzyme protein of BVDV (Fig.3) are principally responsible for the transformation of ncp BVDV - mainly present in the nature - to cp BVDV and thus to the development of mucosal disease, MD.",,"Kiss, I.;Kecskemeti, S.",1998,Jul,,0
1012,Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent,"BACKGROUND: Proventricular dilatation disease (PDD) is a fatal disorder threatening domesticated and wild psittacine birds worldwide. It is characterized by lymphoplasmacytic infiltration of the ganglia of the central and peripheral nervous system, leading to central nervous system disorders as well as disordered enteric motility and associated wasting. For almost 40 years, a viral etiology for PDD has been suspected, but to date no candidate etiologic agent has been reproducibly linked to the disease. RESULTS: Analysis of 2 PDD case-control series collected independently on different continents using a pan-viral microarray revealed a bornavirus hybridization signature in 62.5% of the PDD cases (5/8) and none of the controls (0/8). Ultra high throughput sequencing was utilized to recover the complete viral genome sequence from one of the virus-positive PDD cases. This revealed a bornavirus-like genome organization for this agent with a high degree of sequence divergence from all prior bornavirus isolates. We propose the name avian bornavirus (ABV) for this agent. Further specific ABV PCR analysis of an additional set of independently collected PDD cases and controls yielded a significant difference in ABV detection rate among PDD cases (71%, n = 7) compared to controls (0%, n = 14) (P = 0.01; Fisher's Exact Test). Partial sequence analysis of a total of 16 ABV isolates we have now recovered from these and an additional set of cases reveals at least 5 distinct ABV genetic subgroups. CONCLUSION: These studies clearly demonstrate the existence of an avian reservoir of remarkably diverse bornaviruses and provide a compelling candidate in the search for an etiologic agent of PDD.","Animals;Base Sequence;*Bird Diseases/vi [Virology];*Birds/vi [Virology];Bornaviridae/ge [Genetics];*Bornaviridae/ip [Isolation & Purification];Bornaviridae/py [Pathogenicity];*Cranial Nerve Diseases/ve [Veterinary];Cranial Nerve Diseases/vi [Virology];Dilatation, Pathologic/ve [Veterinary];Molecular Sequence Data;Oligonucleotide Array Sequence Analysis;Phylogeny;*Proventriculus;Sequence Alignment;*Stomach Diseases/ve [Veterinary];Stomach Diseases/vi [Virology]","Kistler, A. L.;Gancz, A.;Clubb, S.;Skewes-Cox, P.;Fischer, K.;Sorber, K.;Chiu, C. Y.;Lublin, A.;Mechani, S.;Farnoushi, Y.;Greninger, A.;Wen, C. C.;Karlene, S. B.;Ganem, D.;DeRisi, J. L.",2008,Jul 31,,0
1013,"Persistent circulation of African swine fever virus in Tanzania, 2010–2012",,,"Kitambi, A.;Council, K. D.",,,,0
1014,Current Knowledge on Porcine circovirus 3 (PCV-3): A Novel Virus With a Yet Unknown Impact on the Swine Industry Review,"Porcine circovirus 3 (PCV-3) is a recently described virus belonging to the family Circoviridae. It represents the third member of genus Circovirus able to infect swine, together with PCV-1, considered non-pathogenic, and PCV-2, one of the most economically relevant viruses for the swine worldwide industry. PCV-3 was originally found by metagenomics analyses in 2015 in tissues of pigs suffering from porcine dermatitis and nephropathy syndrome, reproductive failure, myocarditis and multisystemic inflammation. The lack of other common pathogens as potential infectious agents of these conditions prompted the suspicion that PCV-3 might etiologically be involved in disease occurrence. Subsequently, viral genome was detected in apparently healthy pigs, and retrospective studies indicated that PCV-3 was already present in pigs by early 1990s. In fact, current evidence suggests that PCV-3 is a rather widespread virus worldwide. Recently, the virus DNA has also been found in wild boar, expanding the scope of infection susceptibility among the Suidae family; also, the potential reservoir role of this species for the domestic pig has been proposed. Phylogenetic studies with available PCV-3 partial and complete sequences from around the world have revealed high nucleotide identity (>96%), although two main groups and several subclusters have been described as well. Moreover, it has been proposed the existence of a most common ancestor dated around 50 years ago. Taking into account the economic importance and the well-known effects of PCV-2 on the swine industry, a new member of the same family like PCV-3 should not be neglected. Studies on epidemiology, pathogenesis, immunity and diagnosis are guaranteed in the next few years. Therefore, the present review will update the current knowledge and future trends of research on PCV-3.",,"Klaumann, F.;Correa-Fiz, F.;Franzo, G.;Sibila, M.;Nunez, J. I.;Segales, J.",2018,,,0
1015,Occurrence and phylogenetic analysis of bovine respiratory syncytial virus in outbreaks of respiratory disease in Norway,"Bovine respiratory syncytial virus (BRSV) is one of the major pathogens involved in the bovine respiratory disease (BRD) complex. The seroprevalence to BRSV in Norwegian cattle herds is high, but its role in epidemics of respiratory disease is unclear. The aims of the study were to investigate the etiological role of BRSV and other respiratory viruses in epidemics of BRD and to perform phylogenetic analysis of Norwegian BRSV strains. BRSV infection was detected either serologically and/or virologically in 18 (86%) of 21 outbreaks and in most cases as a single viral agent. When serology indicated that bovine coronavirus and/or bovine parainfluenza virus 3 were present, the number of BRSV positive animals in the herd was always higher, supporting the view of BRSV as the main pathogen. Sequencing of the G gene of BRSV positive samples showed that the current circulating Norwegian BRSVs belong to genetic subgroup II, along with other North European isolates. One isolate from an outbreak in Norway in 1976 was also investigated. This strain formed a separate branch in subgroup II, clearly different from the current Scandinavian sequences. The currently circulating BRSV could be divided into two different strains that were present in the same geographical area at the same time. The sequence variations between the two strains were in an antigenic important part of the G protein. The results demonstrated that BRSV is the most important etiological agent of epidemics of BRD in Norway and that it often acts as the only viral agent. The phylogenetic analysis of the Norwegian strains of BRSV and several previously published isolates supported the theory of geographical and temporal clustering of BRSV.",virus antibody;animal;animal disease;article;blood;bovine;cattle disease;enzyme linked immunosorbent assay;genetics;isolation and purification;Norway;phylogeny;real time polymerase chain reaction;Human respiratory syncytial virus;respiratory syncytial virus infection;serology;virology,"Klem, T. B.;Rimstad, E.;Stokstad, M.",2014,,10.1186/1746-6148-10-15,0
1016,Reliable classification and recombination analysis of porcine endogenous retroviruses,"Prevention of cross-species infection with porcine endogenous retroviruses (PERV) is crucial for xenotransplantation. Previous studies described the potential risk of infection for the PERV γ1 subfamilies A, B and C. Replication competent PERV γ1 proviruses designated to a particular subfamily and hybrid viruses originating from retroviral recombination events between the subfamilies were observed. Future pig genome sequencing projects will reveal multiple novel PERV proviruses from additional breeds and animals. Evaluation of these viral genomes has to be carried out to assess the potential risk of retroviral cross-species infection. In this study, we tested common sequence comparison methods for the classification of PERV sequences and the detection of hybrid clones. The examination of the polymorphic nucleotide positions was found to be the most suitable procedure. We describe a fast and simple method using bioinformatic software tools which can also be applied to analogous analyses of other viral genomes. © 2005 Springer Science+Business Media, Inc.",article;clone;software;controlled study;gene sequence;genetic recombination;hybrid;nonhuman;nucleotide sequence;Porcine endogenous retrovirus;priority journal;reliability;Retroviridae;sequence analysis;virus classification;virus gene;virus genome,"Klymiuk, N.;Aigner, B.",2005,,10.1007/s11262-004-6779-7,0
1017,Public health impact of the Enteroviruses and Parechoviruses,"Enteroviruses (EV) comprise viruses originally classified on cell culture replication patterns and clinical manifestations into a number of groups: poliovirus, coxsackievirus A, coxsackievirus B and ECHOvirus. The closely related genus Parechovirus has more recently been associated with human disease. EVs are common commensals of the human gut, often found without any ill effects on the person, but are also associated with a wide range of diseases and syndromes including non-specific rash illnesses, hand, foot and mouth disease (HFMD), conjunctivitis, meningitis and encephalitis, myocarditis and polio. This results in a significant burden of disease worldwide, often due to a particular genotype of EV. An estimated 1 billion people are infected with EV every year.",71 VACCINE;CHILDREN;AUSTRALIA;TAIWAN,"Knippenberg, B.;Ferson, M. J.",2017,Nov,,0
1018,A serological classification of bovine enteroviruses,"Cross virus neutralization (VN), complement fixation (CF) and immunoprecipitation (IP) tests were employed to compare the seven currently recognized bovine enterovirus (BEV) serotypes with seven serologically distinct strains previously isolated in Great Britain and two other BEV from the United Kingdom. Based on criteria used to differentiate other human and animal picornavirus serotypes, it was discovered that BEV types 1, 4, 5 and 6 were related to each other and could be included in a single serotype. Types 3 and 7 were found to be identical, and related to serotype 2. All of the other nine BEV were included in either serotype 1 or 2. Not all of the strains in each serotype were identical and antigenic variants were designated as subtypes. Antigenic relationships not revealed by VN were demonstrated in CF and IP tests. Bovine enterovirus strains whose antisera had the broadest intratypic reactivity were suggested as prototypes. The two proposed BEV serotypes could also be distinguished by their ability to agglutinate erythrocytes. Guinea pig erythrocytes were agglutinates by both serotypes while sheep red cells only reacted with serotype 1.",virus antigen;bovine;classification;Enterovirus;epidemiology;nonhuman;priority journal;virus classification,"Knowles, N. J.;Barnett, I. T. R.",1985,,10.1007/bf01309912,0
1019,Classification of porcine enteroviruses by antigenic analysis and cytopathic effects in tissue culture: Description of 3 new serotypes,"Porcine enteroviruses isolated in the United Kingdom between 1972 and 1976 were compared with the 8 serotypes previously described and with human coxsackie B virus type 1 to 6 for ability to grow in different cell lines. This allowed the classification of all strains into 3 broad groups according to type of cytopathic effect in IBRS-2 cells and further subdivision on the basis of production of cytopathic effect in BHK 21, HeLa and VERO cells. None of the porcine enterovirus strains was neutralized by antisera to human enteroviruses (Lim Benyesh-Melnick Pools) with the exception of swine vesicular disease virus, which was neutralised by coxsackie B5 antiserum. Antisera prepared either in gnotobiotic pigs or in guinea pigs against the 8 porcine enterovirus serotypes failed to neutralize 9 isolates which could be classified into 3 new serotypes, for which Nos. 9, 10 and 11 are proposed. Guinea pig sera could be used as an alternative to gnotobiotic pig sera for type differentiation.",virus antigen;animal experiment;cell culture;cytopathogenic effect;Enterovirus;in vitro study;pig;virus classification,"Knowles, N. J.;Buckley, L. S.;Pereira, H. G.",1979,,10.1007/bf01317552,0
1020,A study of antigenic variants of foot-and-mouth disease virus by polyacrylamide gel electrophoresis of their structural polypeptides,"Twenty-nine foot-and-mouth disease (FMD) type A virus strains, previously classified serologically as distinct subtypes were analysed by polyacrylamide gel electrophoresis (PAGE) to determine the extent of variation in the pattern of the structural polypeptides and to evaluate the technique as an aid to existing subtyping techniques. The majority of the subtypes examined had distinct polypeptide patterns, however, some variation also occurred between strains within a subtype. The position of VP2(1B) and VP3(1C) was often unchanged in different strains within a subtype and between geographically related subtypes over long periods of time. Changes in the position of VP1(1D) were also observed within a subtype. The technique was considered to be a value for the screening of isolates prior to conventional serological procedures and in the tracing of the possible origin of FMD outbreaks.",virus antigen;viral protein;diagnosis;epidemiology;Foot and mouth disease virus;nonhuman;polyacrylamide gel electrophoresis;priority journal,"Knowles, N. J.;Hedger, R. S.",1985,,10.1016/0378-1135(85)90005-7,0
1021,VP1 sequencing protocol for foot and mouth disease virus molecular epidemiology,"Nucleotide sequences of field strains of foot and mouth disease virus (FMDV) contribute to our understanding of the distribution and evolution of viral lineages that circulate in different regions of the world. This paper outlines a practical reversetranscription polymerase chain reaction (RT-PCR) and sequencing strategy that can be used to generate RNA sequences encoding the VP1 (1D) region of FMDV. The protocol contains a panel of PCR and sequencing primers that can be selected to characterise genetically diverse isolates representing all seven FMDV serotypes. A list of sequences is also described, comprising prototype sequences for all proposed FMDV topotypes, in order to provide a framework for phylogenetic analysis. The technical details and prototype sequences provided in this paper can be employed by FMD Reference Laboratories and others in an approach to harmonise the molecular epidemiology of FMDV.","capsid protein;primer DNA;virus RNA;VP1 protein, Foot-and-mouth disease virus;animal;chemistry;classification;Foot and mouth disease virus;genetics;isolation and purification;livestock;phylogeny;reverse transcription polymerase chain reaction;veterinary medicine","Knowles, N. J.;Wadsworth, J.;Bachanek-Bankowska, K.;King, D. P.",2016,,10.20506/rst.35.3.2565,0
1022,A porcine enterovirus G associated with enteric disease contains a novel papain-like cysteine protease,"Identification of unknown pathogens in pigs displaying enteric illness is difficult due to the large diversity of bacterial and viral species found within faecal samples. Current methods often require bacterial or viral isolation, or testing only a limited number of known species using quantitative PCR analysis. Herein, faeces from two 25-day-old piglets with diarrhoea from Texas, USA, were analysed by metagenomic next-generation sequencing to rapidly identify possible pathogens. Our analysis included a bioinformatics pipeline of rapid short-read classification and de novo genome assembly which resulted in the identification of a porcine enterovirus G (EV-G), a complete genome with substantial nucleotide differences (>30 %) among current sequences, and a novel non-structural protein similar in sequence to the Torovirus papain-like cysteine protease (PLpro). This discovery led to the identification and circulation of an EV-G with a novel PLpro in the USA that has not been previously reported.",cysteine proteinase;papain like cysteine protease;protein VP1;unclassified drug;article;diarrhea;feces analysis;gene insertion sequence;genotype;metagenomics;nonhuman;nucleotide sequence;phylogenetic tree;piglet;porcine enterovirus G;priority journal;protein degradation;Teschovirus;Texas;virus genome;virus identification,"Knutson, T. P.;Velayudhan, B. T.;Marthaler, D. G.",2017,,10.1099/jgv.0.000799,1
1023,Gentian mosaic virus: A New Species in the Genus Fabavirus,"ABSTRACT A viral isolate, designated N-1 and obtained from a gentian (Gentiana scabra) plant that exhibited mosaic symptoms, was transmitted mechanically to nine plant species in six families. These plants are known as hosts of fabaviruses. The N-1 isolate was composed of isometric particles 30 nm in diameter and included two RNA molecules of approximately 6.0 and 3.6 kb in length, as estimated by agarose gel electrophoresis. The RNAs were encapsidated separately in two of the three types of particle. Each particle contained two distinct proteins with Mr values of 39.3 x 10(3) and 26.6 x 10(3), as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Analysis of complete nucleotide sequences of the RNAs suggested that each encoded a single large polyprotein, in which putative functional proteins were arranged in a manner similar to those in Broad bean wilt virus 1 (BBWV-1) and Broad bean wilt virus 2 (BBWV-2), which are members of the genus Fabavirus (family Comoviridae). Analysis of the deduced amino acid sequences of the proteins indicated that those of isolate N-1 shared 38 to 66% identity with those of BBWV-1 and BBWV-2 but only 16 to 42% identity with those of a comovirus, Cowpea mosaic virus. Phylogenetic analysis, based on the amino acid sequences of RNA polymerase, placed isolate N-1 in a separate lineage from BBWV-1 and BBWV-2. In indirect-enzyme-linked immunosorbent assay, isolate N-1 exhibited distant serological relationship to BBWV-1, BBWV-2, and Lamium mild mosaic virus, another fabavirus. Our results suggest that N-1 represents a new species of Fabavirus. We propose the name Gentian mosaic virus for this new species.",,"Kobayashi, Y. O.;Kobayashi, A.;Hagiwara, K.;Uga, H.;Mikoshiba, Y.;Naito, T.;Honda, Y.;Omura, T.",2005,Feb,,0
1024,Bovine diarrhea virus: an update,"Bovine Viral Diarrhea Virus (BVDV) is a pathogen of cattle, member of the family Flaviviridae, genus pestivirus, which also includes Classical Swine Fever Virus (CSFV, or hog cholera virus), and Border Disease Virus of sheep (BDV). It causes important economical losses associated mainly with reproductive failure. Pestiviruses are small enveloped viruses, with a diameter of about 40 nm. The nucleocapsid is probably icosahedral . The genome consists of a single stranded positive RNA, encoding approximately 430 kD of proteic product. Genetic expression consists of the synthesis of a polyprotein which is co- and post-translationally processed. According to its behavior ""in vitro"" two biotypes can be distinguished: non cytopathic (ncp) and cytopathic (cp), most probably derived from the ncp through mutations and/or recombination. BVDV is able to cross the placenta and infect the fetus, causing a variety of problems, from fetal death to the birth of a persistently infected (P) calf, according to the fetal age at the time of infection. PI animals are immunotolerant to the virus and shed it in all secretions. Only the ncp biotype has been isolated from PI animals. The superinfection of a PI animal with a cp strain causes mucosal disease, always fatal. Outbreaks of a severe, sometimes hemorrhagic disease, caused by ncp BVDV, have occurred in Canada and USA since 1993. Genomic and serological differences between the ""traditional"" strains and the viruses isolated from these outbreaks led to the division of BVDV in subtypes I and II, both including cp and ncp strains. Analyses of the non coding 5'-UTR zone of the genome of pestiviruses from different species (bovine, ovine, porcine) suggest that there are at least 3 genotypes within the genus. A new classification of these viruses, based on genomic sequence instead of species of origin, has been proposed. Genomic heterogeneity exists in the BVDV genome, which presents 3 hypervariable zones, 2 of them in the major neutralizing protein. In Argentina prevalence of BVDV antibodies in cattle population is 70%, and the prevalence of persistent infections is around 1%.",virus antibody;virus antigen;animal;animal disease;antigenic variation;Argentina;blood;Bovine viral diarrhea virus 1;bovine;cattle disease;classification;cytopathogenic effect;female;fetus disease;genetics;immunology;physiology;pregnancy;pregnancy complication;prevalence;review;ultrastructure;veterinary abortion;virology;virus genome,"Kobrak, A.;Weber, E. L.",1997,,,0
1025,Influenza A viruses isolated from migrating ducks in Oklahoma,"Nine type A influenza viruses were isolated from migrating and wintering ducks in Oklahoma in 1976-77. Antigenic classification of the viruses isolated revealed three different subtypes: Hav1 Nav2, Hws N1, and Hav6 N2. Transmission of influenza viruses from the wild ducks to sentinel birds (McGraw mallards) on the same lakes was not detected.",virus antigen;animal;article;comparative study;duck;immunology;Influenza A virus;isolation and purification;microbiology;United States,"Kocan, A. A.;Hinshaw, V. S.;Daubney, G. A.",1980,,,0
1026,"Genomic comparison of bovine papillomavirus 1 isolates from bovine, equine and asinine lesional tissue samples","Several attempts have been made to categorize equid- and bovid-specific bovine papillomavirus 1 (BPV1) isolates based on sequence tags. This study includes newly determined sequence information from 33 BPV1 isolates of equine, asinine and bovine origin and investigates sequence bias due to host species. Twenty of the viral genomes were sequenced over their entire length and a further thirteen were sequenced, including flanking sequences, at two specific sites, the LCR and the E5 ORF. Alignment and analyses of the sequences did not reveal statistically significant site differences between the sequences of bovine and equid origin. None of the proposed sites of divergence noted by other authors demonstrated significant species-specific characteristics. Our results suggest that BPV1 is shared between equine, asinine and bovine host species, and that viral transfer between bovines and equids is a repeated and ongoing phenomenon.","Animals;Base Sequence;Bayes Theorem;Bovine papillomavirus 1/cl [Classification];*Bovine papillomavirus 1/ge [Genetics];Bovine papillomavirus 1/ip [Isolation & Purification];Cattle;*Cattle Diseases/vi [Virology];Computational Biology;DNA, Viral/ch [Chemistry];*DNA, Viral/ip [Isolation & Purification];Equidae/vi [Virology];*Genome, Viral;High-Throughput Nucleotide Sequencing;*Horse Diseases/vi [Virology];Horses/vi [Virology];Host Specificity;Open Reading Frames;*Papillomavirus Infections/ve [Veterinary];Papillomavirus Infections/vi [Virology];Phylogeny;Sequence Alignment;Sequence Homology, Nucleic Acid;0 (DNA, Viral)","Koch, C.;Ramsauer, A. S.;Drogemuller, M.;Ackermann, M.;Gerber, V.;Tobler, K.",2018,01 15,,0
1027,Metagenomics-driven virome: current procedures and new additions,,,"Kohl, C.;Nitsche, A.;Kurth, A.",2016,,,0
1028,Use of RNALater® preservation for Virome sequencing in outbreak settings,,,"Kohl, C.;Wegener, M.;Nitsche, A.;Kurth, A.",2017,,,0
1029,Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus,"BACKGROUND: The varicelloviruses comprise a genus within the alphaherpesvirus subfamily, and infect both humans and other mammals. Recently, next-generation sequencing has been used to generate genomic sequences of several members of the Varicellovirus genus. Here, currently available varicellovirus genomic sequences were used for phylogenetic, recombination, and genetic distance analysis. RESULTS: A phylogenetic network including genomic sequences of individual species, was generated and suggested a potential restriction between the ungulate and non-ungulate viruses. Intraspecies genetic distances were higher in the ungulate viruses (pseudorabies virus (SuHV-1) 1.65%, bovine herpes virus type 1 (BHV-1) 0.81%, equine herpes virus type 1 (EHV-1) 0.79%, equine herpes virus type 4 (EHV-4) 0.16%) than non-ungulate viruses (feline herpes virus type 1 (FHV-1) 0.0089%, canine herpes virus type 1 (CHV-1) 0.005%, varicella-zoster virus (VZV) 0.136%). The G + C content of the ungulate viruses was also higher (SuHV-1 73.6%, BHV-1 72.6%, EHV-1 56.6%, EHV-4 50.5%) compared to the non-ungulate viruses (FHV-1 45.8%, CHV-1 31.6%, VZV 45.8%), which suggests a possible link between G + C content and intraspecies genetic diversity. Varicellovirus clade nomenclature is variable across different species, and we propose a standardization based on genomic genetic distance. A recent study reported no recombination between sequenced FHV-1 strains, however in the present study, both splitstree, bootscan, and PHI analysis indicated recombination. We also found that the recently sequenced Brazilian CHV-1 strain BTU-1 may contain a genetic signal in the UL50 gene from an unknown varicellovirus. CONCLUSION: Together, the data contribute to a greater understanding of varicellovirus genomics, and we also suggest a new clade nomenclature scheme based on genetic distances.","Base Composition;Codon;Herpesvirus 1, Bovine/cl [Classification];Herpesvirus 1, Bovine/ge [Genetics];Herpesvirus 1, Equid/cl [Classification];Herpesvirus 1, Equid/ge [Genetics];Herpesvirus 4, Equid/cl [Classification];Herpesvirus 4, Equid/ge [Genetics];Mutation;Phylogeny;Recombination, Genetic;*Varicellovirus/cl [Classification];*Varicellovirus/ge [Genetics];0 (Codon)","Kolb, A. W.;Lewin, A. C.;Moeller Trane, R.;McLellan, G. J.;Brandt, C. R.",2017,Nov 21,,0
1030,"African swine fever virus, Siberia, Russia, 2017","African swine fever (ASF) is arguably the most dangerous and emerging swine disease worldwide. ASF is a serious problem for the swine industry. The first case of ASF in Russia was reported in 2007. We report an outbreak of ASF in Siberia, Russia, in 2017.",capsid protein;spacer DNA;African swine fever;comparative study;Czech Republic;death;disease surveillance;DNA extraction;epidemic;gene nomenclature;genotype phenotype correlation;geographic distribution;high throughput sequencing;infection;letter;molecular biology;nonhuman;pork;real time polymerase chain reaction;sanitation;sequence analysis;tandem repeat;USSR;vaccination;veterinary pathology,"Kolbasov, D.;Titov, I.;Tsybanov, S.;Gogin, A.;Malogolovkin, A.",2018,,10.3201/eid2404.171238,0
1031,Genetic typing of bovine viral diarrhoea virus from Austrian field samples,"Twenty-five bovine viral diarrhoea virus (BVDV) positive field samples were typed in the 5'-UTR by sequencing of PCR products amplified using universal 324/326 pestivirus primers. All viruses were classified as BVDV-1, no BVDV-2 isolates were identified. Fourteen viruses were typed as BVDV-1f, six viruses as BVDV-1b, four viruses as BVDV-1 h and one virus fell into BVDV-1g group. The comparison of data presented in this work with data for other BVDV isolates originating from Austria suggests that the BVDV-1f subgenotype is predominant in Austrian cattle populations.",pestivirus;cattle;BVDV;sequencing;genetic types;IDENTIFICATION;CATTLE;GENOTYPE-1;DIVERSITY;SHEEP,"Kolesarova, M.;Franz, S.;Jackova, A.;Vilcek, S.;Mostl, K.;Benetka, V.;Schopf, K.;Schoder, G.;Hofer, J.;Baumgartner, W.",2004,,,0
1032,"Genetic clustering of Borna disease virus natural animal isolates, laboratory and vaccine strains strongly reflects their regional geographical origin","The aim of this study was to gain more detailed insights into the genetic evolution and variability of Borna disease virus (BDV). Phylogenetic analyses were performed on field viruses originating from naturally infected animals, the BDV vaccine strain 'Dessau', four widely used laboratory strains and the novel BDV subtype No/98. Four regions of the BDV genome were analysed: the complete p40, p10 and p24 genes and the 5'-untranslated region of the X/P transcript. BDV isolates from the same geographical area exhibited a clearly higher degree of identity to each other than to BDV isolates from other regions, independent of host species and year of isolation. Five different clusters could be established within endemic areas, corresponding to the geographical regions from which the viruses originated: (i) a Swiss, Austrian and Liechtenstein Rhine valley group, related closely to the geographically bordering Baden-Wurttemberg and Bavaria II group (ii) in the western part of Germany; (iii) a third group, called Bavaria I group, limited in occurrence to Bavaria; (iv) a southern Saxony-Anhalt and bordering northern Saxony group, bound to the territories of these federal states in the eastern part of Germany; and (v) a mixed group, consisting of samples from different areas of Germany; however, these were mainly from the federal states of Thuringia and Lower Saxony. The laboratory strains and the vaccine strain clustered within these groups according to their geographical origins. All field and laboratory strains, as well as the vaccine strain, clearly segregated from the recently described and highly divergent BDV strain No/98, which originated from an area in Austria where Borna disease is not endemic.","5' Untranslated Regions/ge [Genetics];Animals;Austria;*Borna disease virus/ge [Genetics];Borna disease virus/ip [Isolation & Purification];*Equidae/vi [Virology];*Evolution, Molecular;*Genome, Viral;Germany;*Horses/vi [Virology];Liechtenstein;Molecular Epidemiology;Molecular Sequence Data;Multigene Family;Phylogeny;*RNA, Viral/ge [Genetics];*Sheep/vi [Virology];Switzerland;Viral Proteins/ge [Genetics];0 (5' Untranslated Regions);0 (RNA, Viral);0 (Viral Proteins);0 (p10 protein, Borna disease virus);146209-77-0 (p24 protein, Borna disease virus);148998-61-2 (p40 protein, Borna disease virus)","Kolodziejek, J.;Durrwald, R.;Herzog, S.;Ehrensperger, F.;Lussy, H.;Nowotny, N.",2005,Feb,,0
1033,"West Nile virus positive blood donation and subsequent entomological investigation, Austria, 2014","The detection of West Nile virus (WNV) nucleic acid in a blood donation from Vienna, Austria, as well as in Culex pipiens pupae and egg rafts, sampled close to the donor's residence, is reported. Complete genomic sequences of the human- and mosquito-derived viruses were established, genetically compared and phylogenetically analyzed. The viruses were not identical, but closely related to each other and to recent Czech and Italian isolates, indicating co-circulation of related WNV strains within a confined geographic area. The detection of WNV in a blood donation originating from an area with low WNV prevalence in humans (only three serologically diagnosed cases between 2008 and 2014) is surprising and emphasizes the importance of WNV nucleic acid testing of blood donations even in such areas, along with active mosquito surveillance programs.",polyprotein;viral protein;adult;animal;Austria;blood donor;case report;classification;Culex;epidemiological monitoring;female;genetics;high throughput sequencing;human;insect vector;Institute for Cancer Research mouse;isolation and purification;molecular typing;mouse;phylogeny;polymerase chain reaction;transmission;virology;West Nile fever;West Nile virus,"Kolodziejek, J.;Seidel, B.;Jungbauer, C.;Dimmel, K.;Kolodziejek, M.;Rudolf, I.;Hubálek, Z.;Allerberger, F.;Nowotny, N.",2015,,10.1371/journal.pone.0126381,0
1034,Whole genomic analysis of human and bovine G8P 1 rotavirus strains isolated in Nigeria provides evidence for direct bovine-to-human interspecies transmission,"Bovine group A rotavirus (RVA) G8P[1] strains have been rarely detected in humans. Two Nigerian G8P[1] strains, HMG035 (RVA/Human-tc/NGA/HMG035/1999/G8P[1]) and NGRBg8 (RVA/Cow-tc/NGA/NGRBg8/1998/G8P[1]), were previously suggested to have the VP7, VP4, and NSP1 genes of bovine origin. In order to obtain precise information on the origin and evolution of these G8P[1] strains, the complete nucleotide sequences of the whole genomes of strains HMG035 and NGRBg8 were determined and analyzed in the present study. On whole genomic analysis, strains HMG035 and NGRBg8 were found to be very closely related to each other in all the 11 segments, and were found to have a bovine RVA-like genotype constellation (G8-P[1]-I2-R2-C2-M2-A11-N2-T6-E2-H3). Furthermore, on phylogenetic analysis, each of the 11 genes of strains HMG035 and NGRBg8 appeared to be of bovine origin. Thus, strains HMG035 and NGRBg8 were suggested to be derived from a common origin, and strain NGRBg8 was assumed to represent an example of bovine RVA strains that were transmitted to humans. Our findings provide clear evidence for direct bovine-to-human interspecies transmission of RVA strains.","Animals;Base Sequence;Biological Evolution;Cattle;Child;*Diarrhea/ep [Epidemiology];Diarrhea/vi [Virology];Female;*Genome, Viral;Genotype;High-Throughput Nucleotide Sequencing;Humans;Male;Nigeria/ep [Epidemiology];*Phylogeny;Rotavirus/cl [Classification];*Rotavirus/ge [Genetics];Rotavirus/ip [Isolation & Purification];*Rotavirus Infections/ep [Epidemiology];*Rotavirus Infections/tm [Transmission];Rotavirus Infections/vi [Virology]","Komoto, S.;Adah, M. I.;Ide, T.;Yoshikawa, T.;Taniguchi, K.",2016,09,,0
1035,Reassortment of Human and Animal Rotavirus Gene Segments in Emerging DS-1-Like G1P 8 Rotavirus Strains,"The emergence and rapid spread of novel DS-1-like G1P[8] human rotaviruses in Japan were recently reported. More recently, such intergenogroup reassortant strains were identified in Thailand, implying the ongoing spread of unusual rotavirus strains in Asia. During rotavirus surveillance in Thailand, three DS-1-like intergenogroup reassortant strains having G3P[8] (RVA/Human-wt/THA/SKT-281/2013/G3P[8] and RVA/Human-wt/THA/SKT-289/2013/G3P[8]) and G2P[8] (RVA/Human-wt/THA/LS-04/2013/G2P[8]) genotypes were identified in fecal samples from hospitalized children with acute gastroenteritis. In this study, we sequenced and characterized the complete genomes of strains SKT-281, SKT-289, and LS-04. On whole genomic analysis, all three strains exhibited unique genotype constellations including both genogroup 1 and 2 genes: G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2 for strains SKT-281 and SKT-289, and G2-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2 for strain LS-04. Except for the G genotype, the unique genotype constellation of the three strains (P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2) is commonly shared with DS-1-like G1P[8] strains. On phylogenetic analysis, nine of the 11 genes of strains SKT-281 and SKT-289 (VP4, VP6, VP1-3, NSP1-3, and NSP5) appeared to have originated from DS-1-like G1P[8] strains, while the remaining VP7 and NSP4 genes appeared to be of equine and bovine origin, respectively. Thus, strains SKT-281 and SKT-289 appeared to be reassortant strains as to DS-1-like G1P[8], animal-derived human, and/or animal rotaviruses. On the other hand, seven of the 11 genes of strain LS-04 (VP7, VP6, VP1, VP3, and NSP3-5) appeared to have originated from locally circulating DS-1-like G2P[4] human rotaviruses, while three genes (VP4, VP2, and NSP1) were assumed to be derived from DS-1-like G1P[8] strains. Notably, the remaining NSP2 gene of strain LS-04 appeared to be of bovine origin. Thus, strain LS-04 was assumed to be a multiple reassortment strain as to DS-1-like G1P[8], locally circulating DS-1-like G2P[4], bovine-like human, and/or bovine rotaviruses. Overall, the great genomic diversity among the DS-1-like G1P[8] strains seemed to have been generated through reassortment involving human and animal strains. To our knowledge, this is the first report on whole genome-based characterization of DS-1-like intergenogroup reassortant strains having G3P[8] and G2P[8] genotypes that have emerged in Thailand. Our observations will provide important insights into the evolutionary dynamics of emerging DS-1-like G1P[8] strains and related reassortant ones.","Animals;Child, Preschool;Genes, Viral;Genome, Viral;Genomics/mt [Methods];Genotype;High-Throughput Nucleotide Sequencing;Humans;Infant;Japan;Phylogeny;RNA, Viral;*Reassortant Viruses;Rotavirus/cl [Classification];*Rotavirus/ge [Genetics];Rotavirus/ip [Isolation & Purification];*Rotavirus Infections/vi [Virology];Sequence Analysis, DNA;0 (RNA, Viral)","Komoto, S.;Tacharoenmuang, R.;Guntapong, R.;Ide, T.;Tsuji, T.;Yoshikawa, T.;Tharmaphornpilas, P.;Sangkitporn, S.;Taniguchi, K.",2016,,,0
1036,Isolation and Phylogenetic Analysis of H9N2 Swine Influenza Virus from Sick Pigs in Southern China in 2010,"In January, 201 0 before swine were infected with foot and mouth disease in Guangdong, some pigs have shown flu-like symptoms; cough, sneeze, runny nose and fever. Researchers collected the nasopharyngeal swab of all sick pigs as much as possible. One H9N2 influenza viruses were isolated from the pig population. The complete genome of one isolate, designated A/Swine/Guangdong/L1/2010(H9N2) was sequenced and compared with sequences available in GenBank. The results of analyses indicated that the sequence of A/Swine/Guangdong/L1/2010(H9N2) was similar to those of several avian influenza viruses. According to phylogenetic analysis of the complete gene sequences, A/Swine/Guangdong/L1/2010(H9N2) possibly originated from the reassortment of avian influenza viruses.",Influenza A virus;phylogenetic analysis;H9N2;swine;fever;China;AVIAN INFLUENZA;A VIRUSES;HONG-KONG;EVOLUTION;POULTRY;GENES,"Kong, W. L.;Huang, L. Z.;Cao, N.;Qi, H. T.;Zhao, M. M.;Guan, S. S.;Wang, W. H.;Zao, F. R.;Qi, W. B.;Jiao, P. R.;Zhang, G. H.",2011,,,0
1037,The varicella-zoster virus induces apoptosis in vitro in subpopulations of primary human peripheral blood mononuclear cells,"Varicella-zoster virus (VZV), a member of Herpesviridae, subfamily α-Herpesvirinae, is pathogenic exclusively in the human. Chickenpox is the result of primary infection of VZV. During the viremic stage, VZV infects peripheral blood mononuclear cells (PBMC) and spreads to the periphery. In skin cells it causes typical lesions. Apoptosis has been demonstrated in different cell types by other α-herpesviruses. VZV-infected T lymphocytes, B lymphocytes, and monocytes, respectively, were examined in this in vitro study by flow cytometry, immunofluorescence and electron microscopy. All infected cell types showed signs of apoptosis: a lower DNA content, DNA fragmentation, loss of membrane integrity, and an altered nuclear morphology. The results observed led to the suggestion that VZV can induce apoptosis during infection in vivo in the PBMC subpopulations. © 2003 Éditions scientifiques et médicales Elsevier SAS. All rights reserved.",DNA;DNA fragment;apoptosis;article;B lymphocyte;cell structure;cell subpopulation;cells by body anatomy;chickenpox;controlled study;DNA content;electron microscopy;flow cytometry;Herpesviridae;herpes zoster;human;human cell;immunofluorescence;in vitro study;monocyte;mononuclear cell;nonhuman;priority journal;skin cell;T lymphocyte;Varicella zoster virus;viremia;virus classification,"König, A.;Hömme, C.;Hauröder, B.;Dietrich, A.;Wolff, M. H.",2003,,10.1016/s1286-4579(03)00177-1,0
1038,Phylogenetic analysis of foot-and-mouth disease viruses isolated in Argentina,"We have analysed complete or partial VPI sequences of 31 foot-and-mouth disease (FMD) viruses belonging to serotypes A, O and C to determine the genetic relatedness of field strains of FMD virus (FMDV) that have circulated in Argentina between 1961 and 1994. Phylogenetic analysis, which also included 15 previously published Argentinean sequences and six reference strains, revealed that (i) FMD type A strains showed the highest genetic heterogeneity and could be divided into five lineages with a sequence divergence of 0.9-18.5% between strains (ii) most of the FMD type O viruses grouped in two clusters (within cluster sequence divergence ranging from 0.2% to 6.0%) circulating in Argentina since the early 1960s, and (iii) FMD type C viruses were grouped in two clusters with a 13.4% nucleotide sequence divergence between each cluster. The availability of sequence data for many more field isolates from the region will enable us to understand the genetic relationships between FMDV strains and to rapidly trace the source of an FMD outbreak for epidemiological surveillance.",capsid protein;nucleotide;protein VP1;unclassified drug;Argentina;article;Foot and mouth disease virus;genetic analysis;genetic heterogeneity;molecular evolution;nonhuman;nucleotide sequence;phylogeny;priority journal;serotype;viral genetics;virus strain,"König, G.;Blanco, C.;Knowles, N. J.;Palma, E. L.;Maradei, E.;Piccone, M. E.",2001,,10.1023/a:1011844204945,0
1039,Molecular epidemiology of foot-and-mouth disease virus types A and O isolated in Argentina during the 2000-2002 epizootic,"During 2000-2002 a foot-and-mouth disease (FMD) epizootic affected Argentina and spread across the country resulting in more than 2500 outbreaks. In order to study the evolution of the FMD viruses (FMDV) and help with disease control measures, a genetic characterization and phylogenetic analysis was performed of 43 field isolates representative of the epizootic. The nucleotide sequence of the VP1-coding region was determined for the viruses and used in this study. Two serotype A lineages, A/Arg/00 and A/Arg/01 (1000/1000 bootstrap value) and two different serotype O/Arg/00 lineages (848/1000 bootstrap value) were identified. Phylogenetic analysis showed that viruses A/Arg/01 and O/Arg/00 could be related with former South American isolates, while the origin of A Argentina 2000 viruses remains unclear. Comparison of the amino acid sequences with vaccine reference strains revealed differences at critical antigenic sites for emergent strains A/Arg/00 and A/Arg/01, leading to a change in the current vaccine formulation. © 2007 Elsevier B.V. All rights reserved.",amino acid sequence;Argentina;article;epidemic;epizootiology;foot and mouth disease;Foot and mouth disease virus;molecular epidemiology;nonhuman;nucleotide sequence;phylogeny;serotype;strain difference;viral genetics;virus isolation;virus strain;virus typing;zoonosis,"König, G. A.;Palma, E. L.;Maradei, E.;Piccone, M. E.",2007,,10.1016/j.vetmic.2007.03.015,0
1040,Heterogeneity of ruminant pestiviruses: Academic interest or important basis for the development of vaccines and diagnostics?,"Pestiviruses cause economically important diseases of farm animals. Members of the Pestiviruses are bovine viral diarrhea virus 1 (BVDV-1), BVDV-2, classical swine fever virus (CSFV) and border disease virus (BDV). Phylogenetic analyses based on the entire nucleic acid sequence encoding the Npro allow a statistically significant segregation of established species and of subgroups within the species. BVDV-1 strains isolated in Germany can be associated with at least five different subgroups. In contrast all BVDV-2 isolates detected in Germany so far are closely related, belonging to one subgroup. A group of virus isolates from sheep and zoo animals is clearly different from established pestivirus species and can be designated as BDV-2. Antigenetic relatedness of pestiviruses was studied using defined virus isolates and antisera in cross-neutralization assays. Six antigenic groups were distinguished corresponding to the genetic clusters BVDV-1, BVDV-2, CSFV, BDV-1, BDV-2 and Giraffe-1. A significant antigenic difference was also observed between members of subgroups 1a and 1b of BVDV-1. Studies on the genetic and antigenic heterogeneity of pestiviruses are important for the development of new vaccines, diagnostic tests and for eradication programs.",virus vaccine;animal;animal disease;article;bovid;classification;pathogenicity;Pestivirus;phylogeny;virus infection,"König, M.;Cedillo Rosales, S.;Becher, P.;Thiel, H. J.",2003,,,0
1041,"Characterization and identification of Oya virus, a Simbu serogroup virus of the genus Bunyavirus, isolated from a pig suspected of Nipah virus infection","A virus, named Oya virus, was isolated in Vero cell cultures from the lungs of a pig suspected of Nipah virus infection. The virus was revealed as a spherical enveloped RNA virus with a diameter of 79 nm. For identification of Oya virus, RT-PCR was performed. A common primer set for S-RNA of the Simbu serogroup of the genus Bunyavirus was able to amplify a cDNA from Oya virus RNA. The sequence data of the product revealed that the partial gene of Oya virus S-RNA segment had 65-70% homology with published cDNA sequences of Simbu serogroup viruses. The phylogenetic analysis of the data showed that the Oya virus is grouped in Simbu serogroup, but is genetically distinct from the serogroup viruses that have been analyzed molecularly. Serological surveys revealed that the virus distributed widely and densely in Malaysia.",virus antibody;animal;animal disease;article;blood;Bunyaviridae;Cercopithecus;classification;cytopathogenic effect;isolation and purification;molecular genetics;nucleotide sequence;Paramyxoviridae;reverse transcription polymerase chain reaction;pig;Vero cell line;virology;virus infection,"Kono, Y.;Yusnita, Y.;Mohd Ali, A. R.;Maizan, M.;Sharifah, S. H.;Fauzia, O.;Kubo, M.;Aziz, A. J.",2002,,,0
1042,Virological and pathological characterization of an avian H1N1 influenza A virus,"Gene segments from avian H1N1 influenza A viruses have reassorted with other influenza viruses to generate pandemic strains over the past century. Nevertheless, little effort has been invested in understanding the characteristics of avian H1N1 influenza viruses. Here, we present the genome sequence and a molecular and virological characterization of an avian influenza A virus, A/wild bird/Korea/SK14/2014 (A/SK14, H1N1), isolated from migratory birds in South Korea during the winter season of 2014-2015. Full-genome sequencing and phylogenetic analysis revealed that the virus belongs to the Eurasian avian lineage. Although it retained avian-receptor binding preference, A/SK14 virus also exhibited detectable human-like receptor binding and was able to replicate in differentiated primary normal human bronchial epithelial cells. In animal models, A/SK14 virus was moderately pathogenic in mice, and virus was detected in nasal washes from inoculated guinea pigs, but not in direct-contact guinea pigs. Although A/SK14 showed moderate pathogenicity and no evidence of transmission in a mammalian model, our results suggest that the dual receptor specificity of A/SK14-like virus might allow for a more rapid adaptation to mammals, emphasizing the importance of further continuous surveillance and risk-assessment activities.",virus receptor;animal;avian influenza;bird;bronchus;cell culture;classification;cytology;genetic reassortment;genetics;high throughput sequencing;human;Influenza A virus (H1N1);metabolism;orthomyxovirus infection;pathogenicity;phylogeny;physiology;South Korea;veterinary medicine;virology;virus attachment;virus genome;virus replication;wild animal,"Koo, B. S.;Kim, H. K.;Song, D.;Na, W.;Song, M. S.;Kwon, J. J.;Wong, S. S.;Noh, J. Y.;Ahn, M. J.;Kim, D. J.;Webby, R. J.;Yoon, S. W.;Jeong, D. G.",2018,,10.1007/s00705-018-3730-0,0
1043,Evolution of thymidine and thymidylate kinases: the possibility of independent capture of TK genes by different groups of viruses,"Phylogenetic analysis of viral and cellular thymidine and thymidylate kinases was performed using computer-assisted methods. Multiple alignments and tentative phylogenetic trees were generated for the two families of these enzymes, which include a) thymidine kinases (TK) of mammals, poxviruses, African swine fever virus, E. coli, and bacteriophage T4; and b) thymidylate kinases (ThyK) of yeast and poxviruses and distantly related herpesvirus proteins with both enzymatic activities. Analysis of the alignment of the TKs of the first family highlighted three strongly conserved segments. Two of these corresponded to the A and B motifs of the purine NTP-binding pattern. The third, C-terminal segment, showing the highest conservation, encompassed a modified Zn finger motif. It is speculated that this motif might be involved in TK oligomerization. Phylogenetic trees constructed by three different methods suggested that cellular TK genes could be captured independently by T4 bacteriophage, African swine fever virus, fowlpox virus, and the other poxviruses. The observed tree topologies appear to contradict the popular virus-host coevolution schemes and to imply that different subdivisions of poxviruses diverged at earlier stages of evolution than their hosts did. It was shown that deoxynucleoside monophosphate kinase of bacteriophage T4 is related to the ThyK family. Phylogenetic analysis suggested that ThyK genes probably have been acquired independently by phage T4, poxviruses, and herpes-viruses.",Amino Acid Sequence;Animals;*Biological Evolution;Humans;Molecular Sequence Data;*Nucleoside-Phosphate Kinase/ge [Genetics];Phylogeny;Sequence Alignment;*Thymidine Kinase/ge [Genetics];Viruses/cl [Classification];*Viruses/en [Enzymology];Viruses/ge [Genetics],"Koonin, E. V.;Senkevich, T. G.",1992,Apr,,0
1044,Characterization of RKZ isolate of Ovine herpesvirus 1,Cytopathic effect (CPE) characterized mainly by foci of rounded cells was observed in cultures of primary plexus choroideus cells from healthy lamb following cryopreservation. It was possible to transmit the infectious agent to other primary cells of ovine origin by co-cultivation with infected cells. By indirect immunofluorescence microscopy it was found that high percentage of sheep (65-80% in 3 different herds from Slovakia) are infected with this infectious agent. Electron microscopy of cells with CPE revealed the presence of herpesvirus particles. Viral DNA was isolated from infected cells using pulse-field gel electrophoresis and further used as probe in Southern blot analysis. The probe reacted specifically only with DNA from cells infected with Ovine herpesvirus 1 (OvHV-1) but not with DNA of other ruminant herpesviruses. Some of the HindIII restriction fragments of DNA of the obtained OvHV-1 isolate denominated RKZ were cloned. Part of the H9 clone was sequenced identifying a gene that encoded a polypeptide homologous to conserved herpesvirus VP23 structural protein. From comparison of the sequence of this clone with VP23 sequences of other herpesviruses it was deduced that OvHV-1 might be classified within the Rhadinovirus genus of the Gammaherpesvirinae subfamily. The sequencing of the H9 clone of DNA of RKZ isolate enabled establishment of sensitive and highly specific polymerase chain reaction (PCR) assay for detection of OvHV-1.,virus DNA;animal cell;article;controlled study;cytopathogenic effect;DNA sequence;genetic analysis;Human alphaherpesvirus 1;molecular cloning;nonhuman;nucleotide sequence;Rhadinovirus;sequence analysis;sheep;virus characterization;virus classification;virus isolation,"Kopáček, J.;Rejholcová, O.;Koptidesová, D.;Čiampor, F.;Rijsewijk, F. M.;Reid, H. W.;Pastorek, J.;Zelník, V.",2000,,,0
1045,"Molecular genetic characteristics of the Newcastle disease virus velogenic strains isolated in Russia, Ukraine, Kazakhstan, and Kirghizia","The F gene fragment of 79 Newcastle disease virus (NDV) strains Isolated from domestic and synanthropic birds in Kazakhstan, Kirghizia, Ukraine, and Russia in 1993 to 2007 was comparatively analyzed. Phylogenetic analysis of test isolates and reference NDV strains obtained from the GenBank was carried out by polymerase chain reaction with subsequent sequencing and comparative analysis of 154-bp nucleotide sequences in the main functional region of the F gene. All newly characterized isolates belong to three NDV genotype VII subgroups: Vila, VIIb, VIId. The results show it necessary to monitor of NDV strains isolated In the CIS countries since the spread of NDV among migratory and synanthropic birds (pigeons, crows, and jackdaws) poses a serious threat to commercial poultry Industry.",virus fusion protein;animal;article;bird;classification;genetics;isolation and purification;Kazakhstan;Kyrgyzstan;molecular epidemiology;Newcastle disease;Newcastle disease virus;phylogeny;Russian Federation;Ukraine;virology;virus gene,"Korotetsky, I. S.;Bogoyavlensky, A. P.;Prilipov, A. G.;Usachev, E. V.;Usacheva, O. V.;Turmagambetova, A. S.;Zaitseva, I. A.;Kydyrmanov, A.;Shakhvorostova, L. I.;Kh Sayatov, M.;Borisov, V. V.;Pchelkina, I. P.;Gerilovich, A. P.;Berezin, V. E.",2010,,,0
1046,Differentiation of classical swine fever virus (CSFV) strains using monoclonal antibodies against structural glycoproteins,"Two panels of monoclonal antibodies (mAbs) against the classical swine fever virus (CSFV) envelope glycoproteins E2 (12 mAbs) and EO (11 mAbs) were established and tested by immunoperoxidase binding assay against 135 pestivirus strains and isolates. Variability of the binding pattern was demonstrated for CSFV and also for bovine viral diarrhea virus (BVDV) strains and isolates. The panels of mAbs against E2 and EO led to very different reactivity patterns. Particular mAbs against E2 reacted with (i) all CSFV isolates, (ii) only 4 out of 126 CSFV isolates, or (in) about 90% of the tested CSFV isolates and 78% of ruminant pestivirus isolates. Anti CSFV EO mAbs allowed the detection of a greater variability among the CSFV strains and isolates than the anti E2 mAbs. None of the 11 anti EO mAbs recognized an epitope conserved for CSFV or showed cross-reactivity with ruminant pestiviruses. The use of both panels of mAbs against two CSFV structural glycoproteins led to the discrimination of 21 antigenic types of CSFV strains and isolates. The described panels can be used to trace the origin of CSFV after outbreaks of the disease.",monoclonal antibody;virus glycoprotein;animal experiment;antigenic variation;article;controlled study;nonhuman;Pestivirus;veterinary medicine;virus envelope;virus isolation;virus strain,"Kosmidou, A.;Ahl, R.;Thiel, H. J.;Weiland, E.",1995,,10.1016/0378-1135(95)00054-e,0
1047,Phylogenetic correlation of Greek and Italian orf virus isolates based on VIR gene,"Thirteen orf virus isolates obtained during the time period between 1995 and 2004 from crusted scab lesions of nine sheep and four goats from different geographical areas of Greece and Italy with suspected contagious ecthyma infection were analyzed. DNA of all isolates was successfully amplified by PCR with the primers 045F-045R and identified them as parapox virus. Partial DNA sequence of orf virus interferon resistant (VIR) gene, phylogenetic analysis of the available isolates and amino acid comparison of the interferon resistance protein encoded by this genomic region was carried out. According to the results of the present report a precise characterisation of the genomic region studied might provide evidence for the genetic variation and movement of the circulating orf virus strains. © 2006 Elsevier B.V. All rights reserved.",amino acid;virus DNA;animal cell;article;controlled study;correlation analysis;DNA sequence;ecthyma;gene amplification;genetic analysis;genetic variability;geography;goat;Greece;Italy;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;Poxviridae;promoter region;sheep;time series analysis;virus gene;virus genome;virus identification;virus interferon resistant gene;virus isolation;virus strain,"Kottaridi, C.;Nomikou, K.;Teodori, L.;Savini, G.;Lelli, R.;Markoulatos, P.;Mangana, O.",2006,,10.1016/j.vetmic.2006.04.020,0
1048,Phylogenetic evolution of swine-origin human influenza virus: A pandemic H1N1 2009,"The knowledge of the genome constellation in pandemic influenza A virus H1N1 2009 from different countries and different hosts is valuable for monitoring and understanding of the evolution and migration of these strains. The complete genome sequences of selected worldwide distributed influenza A viruses are publicly available and there have been few longitudinal genome studies of human, avian and swine influenza A viruses. All possible to download SIV sequences of influenza A viruses available at GISAID Platform (Global Initiative on Sharing Avian Influenza Data) were analyzed firstly through the web servers of the Influenza Virus Resource in NCBI. Phylogenetic study of circulating human pandemic H1N1 virus indicated that the new variant possesses a distinctive evolutionary trait. There is no one way the pandemic H1N1 have acquired new genes from other distinguishable viruses circulating recently in local human, pig or domestic poultry populations from various geographic regions. The extensive genetic diversity among whole segments present in pandemic H1N1 genome suggests that multiple introduction of virus have taken place during the period 1999-2009. The initial interspecies transmission could have occurred in the long-range past and after it the reassortants steps lead to three lineages: classical SIV prevalent in the North America, avian-like SIV in Europe and avian-like related SIV in Asia. This analysis contributes to the evidence that pigs are not the only hosts playing the role of ""mixing vessel"", as it was suggested for many years.",hemagglutinin;sialidase;viral protein;animal;animal disease;article;gene expression regulation;genetics;human;influenza;Influenza A virus (H1N1);metabolism;orthomyxovirus infection;pandemic;phylogeny;physiology;pig;virology;zoonosis,"Kowalczyk, A.;Markowska-Daniel, I.",2010,,,0
1049,Biological and molecular characterization of chicken anemia virus isolates from Slovenia,"The presence of chicken anemia virus (CAV) in Slovenia was confirmed by inoculation of 1-day-old chickens without antibodies against CAV and isolation of the virus on the Marek's disease chicken cell-MSB1 line and by polymerase chain reaction (PCR). Experimental inoculation of 1-day-old chickens resulted in lower hematocrit values, atrophy of the thymus, and atrophy of bone marrow. CAV was confirmed by PCR in the thymus, bone marrow, bursa of Fabricius, liver, spleen, ileocecal tonsils, duodenum, and proventriculus. The nucleotide sequence of the whole viral protein (VP)1 gene was determined by direct sequencing. Alignment of VP1 nucleotide sequences of Slovenian CAV isolates (CAV-69/00, CAV-469/01, and CAV-130/03) showed 99.4% to 99.9% homology. The VP1 nucleotide sequence alignment of Slovenian isolates with 19 other CAV strains demonstrated 94.4% to 99.4% homology. Slovenian isolates shared highest homology with the BD-3 isolate from Bangladesh. Alignment of the deduced VP1 amino acids showed that the Slovenian isolates shared 100% homology and had an amino acid sequence most similar to the BD-3 strain from Bangladesh (99.6%) and were 99-1% similar to the G6 strain from Japan and the L-028 strain from the United States. The Slovenian isolates were least similar (96.6%) to the 82-2 strain from Japan. A phylogenetic analysis on the basis of the alignment of the VP1 amino acids showed that CAV isolates used in the study formed three groups that indicated the possible existence of genetic groups among CAV strains. The CAV isolates were grouped together independent of their geographic origin and pathogenicity.",virus DNA;viral protein;amino acid sequence;animal;animal disease;article;bird disease;chemistry;chicken;Circoviridae;genetics;isolation and purification;molecular genetics;nucleotide sequence;phylogeny;Slovenia;virology;virus infection,"Krapež, U.;Barlič-Maganja, D.;Toplak, I.;Hostnik, P.;Rojs, O. Z.",2006,,10.1637/7413.1,0
1050,Circulation of infectious bronchitis virus strains from Italy 02 and QX genotypes in Slovenia between 2007 and 2009,"Fourteen infectious bronchitis viruses (IBVs) detected in broiler, broiler breeder, and layer flocks in Slovenia between 2007 and 2009 were molecularly analyzed by reverse transcription-PCR and direct sequencing of the S1 gene. Phylogenetic analyses based on partial S1 gene sequences revealed that seven strains were classified as the Italy 02 genotype, a genetic group of IBV that has not previously been detected in Slovenia. Another seven strains were classified as the QX genotype. The results of phylogenetic analyses and epidemiologic investigations revealed that the genetic classification correlates with the geographic origins of the IBV strains. Greater genetic variability (maximum nucleotide and amino acid divergences were 4.8% and 9.9%, respectively) was observed within the Slovenian strains from the Italy 02 genotype detected between 2007 and 2009 than within strains from the QX genotype isolated in 2008 and 2009 (1.2% and 1.3%, respectively). The Slovenian strains classified as the Italy 02 genotype form a separate genetic cluster. These strains shared five specific amino acid substitutions that became fixed during the period of surveillance. Strains from the QX genotype that shared one specific amino acid substitution also form a separate genetic cluster. © 2011 American Association of Avian Pathologists.",virus RNA;animal;animal disease;article;Avian infectious bronchitis virus;chicken;Coronavirus infection;genetic variability;genetics;genotype;Italy;phylogeny;Slovenia;virology,"Krapež, U.;Slavec, B.;Rojs, O. Z.",2011,,10.1637/9533-091710-Case.1,0
1051,Importance of structure for the classification of poultry viruses,,animal;article;classification;DNA virus;electron microscopy;poultry;RNA virus;virus,"Krauss, H.",1968,,,0
1052,Metagenomics - a new approach to study our microbial neighbours,"Background: In our age, the information society, the computer based technologies, including the data analytical procedures are parts of each site of the life. Bioinformatics provides approaches for the knowledge gathering and update which were not imaginable two decades ago. Metagenomics is the area of bioinformatics which helps improve our knowledge about the composition of microbial species in the production or companion animals, human being or environment. Objectives: The present work describes the main steps of a metagenomics analysis. As an example, the metagenomics investigation of swine dysentery as an important animal disease is shown. Materials and methods: From three clinically diseased fattening pigs intestinal contents were sampled from three different sections of the gut (i.e. caecum, colon and rectum). All DNA was extracted from the samples, thereafter sequenced by next generation sequencing technology. The produced 1,782,466 reads were pooled and analysed. The reads were aligned to archea, bacteria and virus genome databases by the Kraken bioinformatics tool. The results of the alignments were visualized by the tool Krona. Results and Discussion: The presented case study helps the reader understand how metagenomics studies work and provide new professional knowledge on the microbiome of selected organs in different creatures. The proportions of the different taxa allow to have an insight to the microbial communities of the gut in the diseased animals. Beside this, a short review is presented to demonstrate the application possibilities of metagenomics in the field of animal health. Bioinformatics is an emerging area and it is very important to have knowledge -clinicians and researchers as well -about the methods, their possible results and the limitations. This work provides a simple introduction to metagenomics in the language of veterinarians.",GUT,"Kriko, E.;Farkas, R.;Adorjan, A.;Makrai, L.;Solymosi, N.",2018,Jul,,0
1053,Deep sequencing analysis reveals temporal microbiota changes associated with development of bovine digital dermatitis,"Bovine digital dermatitis (DD) is a leading cause of lameness in dairy cattle throughout the world. Despite 35 years of research, the definitive etiologic agent associated with the disease process is still unknown. Previous studies have demonstrated that multiple bacterial species are associated with lesions, with spirochetes being the most reliably identified organism. This study details the deep sequencing-based metagenomic evaluation of 48 staged DD biopsy specimens collected during a 3-year longitudinal study of disease progression. Over 175 million sequences were evaluated by utilizing both shotgun and 16S metagenomic techniques. Based on the shotgun sequencing results, there was no evidence of a fungal or DNA viral etiology. The bacterial microbiota of biopsy specimens progresses through a systematic series of changes that correlate with the novel morphological lesion scoring system developed as part of this project. This scoring system was validated, as the microbiota of each stage was statistically significantly different from those of other stages (P<0.001). The microbiota of control biopsy specimens were the most diverse and became less diverse as lesions developed. Although Treponema spp. predominated in the advanced lesions, they were in relatively low abundance in the newly described early lesions that are associated with the initiation of the disease process. The consortium of Treponema spp. identified at the onset of disease changes considerably as the lesions progress through the morphological stages identified. The results of this study support the hypothesis that DD is a polybacterial disease process and provide unique insights into the temporal changes in bacterial populations throughout lesion development. © 2014, American Society for Microbiology.",animal tissue;article;bacterial flora;Bacteroidaceae;Campylobacteraceae;controlled study;Corynebacteriaceae;dairy cattle;digital dermatitis;disease association;disease course;DNA sequence;downstream processing;longitudinal study;metagenomics;microbial community;microbial consortium;Moraxellaceae;Mycoplasmataceae;nonhuman;Pasteurellaceae;population dynamics;Porphyromonadaceae;priority journal;scoring system;sequence analysis;skin biopsy;spirochete;Staphylococcaceae;Streptococcaceae;Treponema,"Krull, A. C.;Shearer, J. K.;Gorden, P. J.;Cooper, V. L.;Phillips, G. J.;Plummera, P. J.",2014,,10.1128/iai.02077-14,0
1054,Molecular classification of enteroviruses not identified by neutralization tests,"We isolated six viruses from patients diagnosed with aseptic meningitis or hand, foot, and mouth disease. The cytopathic effect of these viruses on cultured cells was like that of enteroviruses. However, viral neutralization tests against standard antisera were negative. Phylogenetic analysis with the complete VP4 nucleotide sequences of these 6 viruses and 29 serotypes of enteroviruses classified 3 of the viruses as serotype echovirus type 18 (EV18) and 3 as serotype human enterovirus 71 (HEV71). These results were confirmed by remicroneutralization tests with HEV-monospecific antisera or an additional phylogenetic analysis with the complete VP4 nucleotide sequences. Phylogenetic analysis with complete VP4 genes is more useful than neutralization tests with enterovirus serotype-specific antisera in identifying enterovirus serotypes.",gene product;protein VP4;unclassified drug;article;aseptic meningitis;cell culture;clinical article;controlled study;cytopathogenic effect;Enterovirus;hand foot and mouth disease;human;human cell;nonhuman;nucleotide sequence;phylogeny;sequence analysis;serotype;virus classification;virus gene;virus identification;virus neutralization,"Kubo, H.;Iritani, N.;Seto, Y.",2002,,,0
1055,Novel flu viruses in bats and cattle:“Pushing the Envelope” of Influenza Infection,,,"Kuchipudi, S.;Nissly, R.",2018,,,0
1056,Whole genome characterization of a chelonian orthoreovirus strain identifies significant genetic diversity and may classify reptile orthoreoviruses into distinct species,"In this study we report the sequence and phylogenetic characterization of an orthoreovirus strain, CH1197/96, isolated from a spur-thighed tortoise (Testudo graeca) on chicken embryo fibroblast cells. The 23,957 bp long genome sequence was obtained by combined use of semiconductor and capillary sequencing. Although the genomic characterization showed that the virus was most similar to the bush viper reovirus strain, 47/02, and in phylogenies performed with all segments the two strains formed a monophyletic group, the nucleotide (48.4-70.3%) and amino acid (39.2-80.7%) sequence identity values were moderate between the two reptile origin reoviruses. Based on our results and existing classification criteria for the genus Orthoreovirus, the tortoise reovirus strain CH1197/96 might be the first representative of a novel reptilian origin Orthoreovirus species.",animal cell;animal experiment;article;chicken;controlled study;embryo;fibroblast;gene sequence;genetic variability;genome analysis;high throughput sequencing;monophyly;nonhuman;Orthoreovirus;phylogeny;priority journal;reptile;semiconductor;Testudo;Testudo graeca;tortoise;virus genome,"Kugler, R.;Marschang, R. E.;Ihász, K.;Lengyel, G.;Jakab, F.;Bányai, K.;Farkas, S. L.",2016,,10.1016/j.virusres.2016.02.005,0
1057,Next generation sequencing (NGS): testing of feces samples from pigs with diarrhea,"Next-generation sequencing (NGS) technologies are a major breakthrough in the field of infectious disease diagnostics as they allow novel pathogen detection without prior sequence knowledge and enable simultaneous detection of multiple pathogens, whole genome studies and metagenome studies. The aim of this study was to determine the value of NGS in the detection of pathogens in clinical samples, namely diarrheic pig fecal samples. Fecal samples from four pigs with severe diarrhea were analyzed. NGS libraries were prepared from sample suspensions and used for Ion Torrent sequencing. Altogether, 396.486 reads were assembled into 1.537 contigs. Taxonomy units were assigned to 786 contigs, while 751 contigs remained unassigned. All four samples were positive for porcine epidemic diarrhea virus (PED). In two samples, viruses from the genus Picobirnavirus and porcine astrovirus were also detected, while one sample was positive for the virus from genus Torovirus. In addition to viral sequences, sequences from bacteria, archaea, nematodes, Protista and amoebae were also detected in investigated samples. Based on these results, we can conclude that the NGS technology is a powerful tool for infectious disease diagnostics which enables us simultaneous detection of multiple pathogens in complex samples.",next generation sequencing;NGS;clinical samples;diagnostics,"Kuhar, U.;Kusar, D.;Papic, B.;Toplak, I.",2016,,,0
1058,Virus nomenclature below the species level: A standardized nomenclature for laboratory animal-adapted strains and variants of viruses assigned to the family Filoviridae,"The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of viruses into taxa, but is not responsible for the nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and nomenclature for filoviruses. Subsequently, and together with numerous other filovirus experts, a consistent nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoviruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filovirus genetic variant naming (<virus name> <isolation host-suffix>/<country of sampling>/<year of sampling>/<genetic variant designation>-<isolate designation>) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology ""Vector"" to cause disease in guinea pigs after seven passages would be akin to ""Ebola virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7"". As was proposed for the names of natural filovirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as ""EBOV VECTOR/C.por/COD/76/May-GPA-P7"") and abbreviations (such as ""EBOV/May-GPA-P7"") could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. ""EBOV"" would suffice if only one EBOV strain/variant/isolate is addressed. © 2013 Springer-Verlag Wien (outside the USA).",animal;article;classification;experimental animal;Filoviridae;nomenclature;virology,"Kuhn, J. H.;Bao, Y.;Bavari, S.;Becker, S.;Bradfute, S.;Brister, J. R.;Bukreyev, A. A.;Caì, Y.;Chandran, K.;Davey, R. A.;Dolnik, O.;Dye, J. M.;Enterlein, S.;Gonzalez, J. P.;Formenty, P.;Freiberg, A. N.;Hensley, L. E.;Honko, A. N.;Ignatyev, G. M.;Jahrling, P. B.;Johnson, K. M.;Klenk, H. D.;Kobinger, G.;Lackemeyer, M. G.;Leroy, E. M.;Lever, M. S.;Lofts, L. L.;Mühlberger, E.;Netesov, S. V.;Olinger, G. G.;Palacios, G.;Patterson, J. L.;Paweska, J. T.;Pitt, L.;Radoshitzky, S. R.;Ryabchikova, E. I.;Saphire, E. O.;Shestopalov, A. M.;Smither, S. J.;Sullivan, N. J.;Swanepoel, R.;Takada, A.;Towner, J. S.;van der Groen, G.;Volchkov, V. E.;Wahl-Jensen, V.;Warren, T. K.;Warfield, K. L.;Weidmann, M.;Nichol, S. T.",2013,,10.1007/s00705-012-1594-2,0
1059,Nyamiviridae: Proposal for a new family in the order Mononegavirales,"Nyamanini virus (NYMV) and Midway virus (MIDWV) are unclassified tick-borne agents that infect land birds and seabirds, respectively. The recent molecular characterization of both viruses confirmed their already known close serological relationship and revealed them to be nonsegmented, single- and negative-stranded RNA viruses that are clearly related to, but quite distinct from, members of the order Mononegavirales (bornaviruses, filoviruses, paramyxoviruses, and rhabdoviruses). A third agent, soybean cyst nematode virus 1 (SbCNV-1, previously named soybean cyst nematode nyavirus), was recently found to be an additional member of this new virus group. Here, we review the current knowledge about all three viruses and propose classifying them as members of a new mononegaviral family, Nyamiviridae. © 2013 Springer-Verlag Wien (outside the USA).",animal;article;bird;bird disease;classification;genetics;nematode;phylogeny;RNA virus;tissue culture technique;virology;virus culture;virus replication,"Kuhn, J. H.;Bekal, S.;Caì, Y.;Clawson, A. N.;Domier, L. L.;Herrel, M.;Jahrling, P. B.;Kondo, H.;Lambert, K. N.;Mihindukulasuriya, K. A.;Nowotny, N.;Radoshitzky, S. R.;Schneider, U.;Staeheli, P.;Suzuki, N.;Tesh, R. B.;Wang, D.;Wang, L. F.;Dietzgen, R. G.",2013,,10.1007/s00705-013-1674-y,0
1060,Taxonomic reorganization of the family Bornaviridae,"Knowledge of bornaviruses has expanded considerably during the last decade. A possible reservoir of mammalian Borna disease virus has been identified, divergent bornaviruses have been detected in birds and reptiles, and endogenous bornavirus-like elements have been discovered in the genomes of vertebrates of several species. Previous sequence comparisons and alignments have indicated that the members of the current family Bornaviridae are phylogenetically diverse and are not adequately classified in the existing bornavirus taxonomy supported by the International Committee on Taxonomy of Viruses (ICTV). We provide an update of these analyses and describe their implications for taxonomy. We propose retaining the family name Bornaviridae and the genus Bornavirus but reorganizing species classification. PAirwise Sequence Comparison (PASC) of bornavirus genomes and Basic Local Alignment Search Tool (BLAST) comparison of genomic and protein sequences, in combination with other already published phylogenetic analyses and known biological characteristics of bornaviruses, indicate that this genus should include at least five species: Mammalian 1 bornavirus (classical Borna disease virus and divergent Borna disease virus isolate No/98), Psittaciform 1 bornavirus (avian/psittacine bornaviruses 1, 2, 3, 4, 7), Passeriform 1 bornavirus (avian/canary bornaviruses C1, C2, C3, LS), Passeriform 2 bornavirus (estrildid finch bornavirus EF), and Waterbird 1 bornavirus (avian bornavirus 062CG). This classification is also in line with biological characteristics of these viruses and their vertebrate hosts. A snake bornavirus, proposed to be named Loveridge's garter snake virus 1, should be classified as a member of an additional species (Elapid 1 bornavirus), unassigned to a genus, in the family Bornaviridae. Avian bornaviruses 5, 6, MALL, and another ""reptile bornavirus"" (""Gaboon viper virus"") should stay unclassified until further information becomes available. Finally, we propose new virus names and abbreviations when necessary to achieve clear differentiation and unique identification.",amino acid sequence;animal;Borna disease;Bornaviridae;classification;disease carrier;genetics;phylogeny;sequence alignment;virology;virus genome,"Kuhn, J. H.;Dürrwald, R.;Bào, Y.;Briese, T.;Carbone, K.;Clawson, A. N.;deRisi, J. L.;Garten, W.;Jahrling, P. B.;Kolodziejek, J.;Rubbenstroth, D.;Schwemmle, M.;Stenglein, M.;Tomonaga, K.;Weissenböck, H.;Nowotny, N.",2015,,10.1007/s00705-014-2276-z,0
1061,Reorganization and expansion of the nidoviral family Arteriviridae,"The family Arteriviridae presently includes a single genus Arterivirus. This genus includes four species as the taxonomic homes for equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), porcine respiratory and reproductive syndrome virus (PRRSV), and simian hemorrhagic fever virus (SHFV), respectively. A revision of this classification is urgently needed to accommodate the recent description of eleven highly divergent simian arteriviruses in diverse African nonhuman primates, one novel arterivirus in an African forest giant pouched rat, and a novel arterivirus in common brushtails in New Zealand. In addition, the current arterivirus nomenclature is not in accordance with the most recent version of the International Code of Virus Classification and Nomenclature. Here we outline an updated, amended, and improved arterivirus taxonomy based on current data. Taxon-specific sequence cut-offs are established relying on a newly established open reading frame 1b phylogeny and pairwise sequence comparison (PASC) of coding-complete arterivirus genomes. As a result, the current genus Arterivirus is replaced by five genera: Equartevirus (for EAV), Rodartevirus (LDV + PRRSV), Simartevirus (SHFV + simian arteriviruses), Nesartevirus (for the arterivirus from forest giant pouched rats), and Dipartevirus (common brushtail arterivirus). The current species Porcine reproductive and respiratory syndrome virus is divided into two species to accommodate the clear divergence of the European and American ""types"" of PRRSV, both of which now receive virus status. The current species Simian hemorrhagic fever virus is divided into nine species to accommodate the twelve known simian arteriviruses. Non-Latinized binomial species names are introduced to replace all current species names to clearly differentiate them from virus names, which remain largely unchanged.",virus RNA;Arteriviridae;classification;cluster analysis;genetics;isolation and purification;nomenclature;open reading frame;phylogeny;RNA virus infection;sequence homology;veterinary medicine;virus genome,"Kuhn, J. H.;Lauck, M.;Bailey, A. L.;Shchetinin, A. M.;Vishnevskaya, T. V.;Bào, Y.;Ng, T. F.;LeBreton, M.;Schneider, B. S.;Gillis, A.;Tamoufe, U.;Diffo Jl.e, D.;Takuo, J. M.;Kondov, N. O.;Coffey, L. L.;Wolfe, N. D.;Delwart, E.;Clawson, A. N.;Postnikova, E.;Bollinger, L.;Lackemeyer, M. G.;Radoshitzky, S. R.;Palacios, G.;Wada, J.;Shevtsova, Z. V.;Jahrling, P. B.;Lapin, B. A.;Deriabin, P. G.;Dunowska, M.;Alkhovsky, S. V.;Rogers, J.;Friedrich, T. C.;O'Connor, D. H.;Goldberg, T. L.",2016,,10.1007/s00705-015-2672-z,0
1062,Genomic characterization of the genus nairovirus (Family Bunyaviridae),"Nairovirus, one of five bunyaviral genera, includes seven species. Genomic sequence information is limited for members of the Dera Ghazi Khan, Hughes, Qalyub, Sakhalin, and Thiafora nairovirus species. We used next-generation sequencing and historical virus-culture samples to determine 14 complete and nine coding-complete nairoviral genome sequences to further characterize these species. Previously unsequenced viruses include Abu Mina, Clo Mor, Great Saltee, Hughes, Raza, Sakhalin, Soldado, and Tillamook viruses. In addition, we present genomic sequence information on additional isolates of previously sequenced Avalon, Dugbe, Sapphire II, and Zirqa viruses. Finally, we identify Tunis virus, previously thought to be a phlebovirus, as an isolate of Abu Hammad virus. Phylogenetic analyses indicate the need for reassignment of Sapphire II virus to Dera Ghazi Khan nairovirus and reassignment of Hazara, Tofla, and Nairobi sheep disease viruses to novel species. We also propose new species for the Kasokero group (Kasokero, Leopards Hill, Yogue viruses), the Ketarah group (Gossas, Issyk-kul, Keterah/soft tick viruses) and the Burana group (Wēnzhōu tick virus, Huángpí tick virus 1, Tǎchéng tick virus 1). Our analyses emphasize the sister relationship of nairoviruses and arenaviruses, and indicate that several nairo-like viruses (Shāyáng spider virus 1, Xīnzhōu spider virus, Sānxiá water strider virus 1, South Bay virus, Wǔhàn millipede virus 2) require establishment of novel genera in a larger nairovirus-arenavirus supergroup.",glycoprotein;interferon;interferon regulatory factor 3;nucleocapsid protein;ribonucleoprotein;article;Bunyaviridae;DNA recombination;Dugbe virus;gastroenteritis;gene identification;gene sequence;hemorrhagic fever;Nairobi sheep disease virus;Nairovirus;next generation sequencing;nonhuman;open reading frame;phylogeny;sequence analysis;virus mutation;virus transmission,"Kuhn, J. H.;Wiley, M. R.;Rodriguez, S. E.;Bào, Y.;Prieto, K.;Travassos da Rosa, A. P. A.;Guzman, H.;Savji, N.;Ladner, J. T.;Tesh, R. B.;Wada, J.;Jahrling, P. B.;Bente, D. A.;Palacios, G.",2016,,10.3390/v8060164,0
1063,Incidence of endogenous viral genes in two strains of white leghorn chickens selected for egg production and susceptibility or resistance to Marek's disease,"Endogenous viral (ev) genes related to the avian leukosis virus were classified in two differentially selected strains of Leghorns in order to investigate whether such genes affect production traits. Strain K had been selected for resistance to Marek's disease (MD) and for high egg production and egg weight, whereas strain S had been selected only for MD susceptibility. Except that founders of strain K included a few commercial birds, both strains were derived from a common genetic base. DNA restriction fragment length analyses of 110 strain K and 94 strain S birds revealed the presence of 8 different ev-genes, 6 of which were identical to previously identified loci. This result was confirmed by assays for group specific antigen (gs-antigen), the product of the gag region of the ev-genes. The levels of gs-antigen in the birds closely followed what had been predicted from data obtained from previously described ev-genes. Both strains had a similar average number of ev-genes per bird (3.5 and 3.2 for strains S and K, respectively). However, strain K carried only five different ev-genes while strain S carried seven. Four of these loci were present in both strains. Among the ev-genes absent or occurring less frequently in strain K were those that code either for infectious endogenous virus (ev-10 and possibly ev-19) or for the internal viral gag-proteins (ev-3). Only those ev-genes which are transcriptionally silent or which code for the viral envelope gene were present in increased frequencies in strain K. The results indicate that selection for egg traits and/or Marek's disease resistance reduces the frequency of ev-genes which produce endogenous virus or the viral gag-proteins.",,"Kuhnlein, U.;Gavora, J. S.;Spencer, J. L.;Bernon, D. E.;Sabour, M.",1989,Jan,,0
1064,Natural peste des petits ruminants virus infection: Novel pathologic findings resembling other morbillivirus infections,"The present study describes pathologic and virologic findings in 15 sheep and 6 goats that died of natural peste des petits ruminants virus infection in Turkey. Pathologic findings included erosive-ulcerative stomatitis, fibrino-necrotic tracheitis, bronchointerstitial pneumonia, multifocal coagulation necroses in the liver, and severe lymphocytolysis in lymphoid tissues. Syncytial cells were conspicuous, especially in the oral mucosa, pulmonary alveoli, liver, and lymphoid tissues. In addition to the typical tissue distribution, eosinophilic intracytoplasmic and/or intranuclear inclusions were observed in epithelial cells lining the renal pelvis and abomasal mucosa. Immunolabeling of the viral antigen was observed in the kidney, brain, rumen, abomasum, heart, and myocytes of the tongue besides its more typical locations. In this study, we report and describe in detail the first peste des petits ruminants endemic in Kirikkale Province, Central Anatolia of Turkey. In conclusion, these previously unreported pathologic findings in natural peste des petits ruminants virus infection establish a basis for resemblance to other morbillivirus infections, such as canine distemper and distemper of sea mammals. Reverse transcriptase-polymerase chain reaction analyses indicated that the 448-bp genome fragment was amplified in 18 cases (18/21, 85.7 %). Phylogenetic analysis showed that viruses belong to lineage 4 in the peste des petits ruminants virus common phylogenetic tree.",animal;animal disease;article;genetics;goat;goat disease;cardiac muscle;ileum;kidney;liver;Measles virus;mouth mucosa;pathology;phylogeny;sheep;sheep disease;tongue;trachea,"Kul, O.;Kabakci, N.;Atmaca, H. T.;Özkul, A.",2007,,10.1354/vp.44-4-479,0
1065,Emergence of novel reassortant H6N2 avian influenza viruses in ducks in India,"The recent reports of human infection due to H6 subtype avian influenza viruses (AIV), which are prevalent in terrestrial poultry, indicate evolution of the virus to a possible pandemic strain. Here, we report antigenic and genetic characterization of two H6N2 viruses isolated from apparently healthy domestic ducks in Kerala and Assam, India during 2014 and 2015, respectively. Hemagglutination inhibition assay revealed antigenic divergence between the two isolates, which was corroborated by amino acid differences at 55 positions (15.98%) between their hemagglutinin (HA) 1.The sequence analyses indicated that both the viruses are avian origin with avian receptor specificity, low pathogenic to poultry and sensitive to oseltamivir. However, Kerala14 had V27I mutation marker for amantadine resistance in M2. The Assam15 virus had an additional N-linked glycosylation on HA2 (position 557) compared to Kerala14 virus. Phylogenetic analysis of the HA gene revealed that both the viruses belonged to distinct lineages (Eurasian and Asia II). Phylogeny of neuraminidase and internal gene segments revealed that both the viruses are novel reassortants and are genetically distinct with different gene constellations. The results suggest independent introductions of the two H6N2 viruses into India and migratory wild birds in the Central Asian flyway might be the source of H6N2 viruses in ducks in India. Therefore, continued AIV surveillance in poultry and wild birds is essential for early detection of emergence of novel strains with pandemic potential and control of their spread.",amino acid;oseltamivir;sialidase;amino acid analysis;amino acid sequence;Anas platyrhynchos;antigenicity;article;avian influenza virus;avian influenza virus H6N2;controlled study;genetic reassortment;hemagglutination inhibition;host pathogen interaction;India;neuraminidase gene;nonhuman;phylogeny;priority journal;viral genetics;virus isolation,"Kumar, M.;Nagarajan, S.;Murugkar, H. V.;Saikia, B.;Singh, B.;Mishra, A.;Tripathi, S. K.;Agarwal, S.;Shukla, S.;Kulkarni, D. D.;Singh, V. P.;Tosh, C.",2018,,10.1016/j.meegid.2018.03.005,0
1066,"Isolation and phylogenetic analysis of an orf virus from sheep in Makhdoom, India","Orf (contagious ecthyma) is an exanthematic disease caused by a parapoxvirus and occurs primarily in sheep and goats with zoonotic implications. In the present investigation, an orf outbreak in the Muzzaffarnagari sheep flock at the Central Institute for Research on Goats (CIRG), Makhdoom, Mathura, Uttar Pradesh, India, was investigated. Primary goat testes cell culture was used for isolation of the orf virus (ORFV) for the first time. The identity of the virus was confirmed by amplification and sequence analysis of the major envelope glycoprotein (B2L) gene and named ORFV/sheep/India/2012/CIRG. On phylogenetic analysis of B2L protein gene, it clustered with the ORFV strains from China suggesting distinct ORFV strains are circulating in India. On comparison of nucleotide and deduced amino acid sequence analysis (n = 63), a unique 126S residue was observed in ORFV/sheep/India/2012/CIRG. On further sequence analysis (B2L) of different ORFV strains (n = 63), some conserved amino acid residues were identified as host-specific (sheep, human, camel, takin, and musk ox) and have been summarized. © 2013 Springer Science+Business Media New York.",animal cell;animal tissue;article;B2L gene;contagious ecthyma;epidemic;female;gene amplification;goat;herd;India;kid (goat);male;molecular phylogeny;nonhuman;nucleotide sequence;Poxviridae;primary cell culture;priority journal;sequence analysis;sequence homology;testis cell;unindexed sequence;virus gene;virus identification;virus isolation;virus strain,"Kumar, N.;Wadhwa, A.;Chaubey, K. K.;Singh, S. V.;Gupta, S.;Sharma, S.;Sharma, D. K.;Singh, M. K.;Mishra, A. K.",2014,,10.1007/s11262-013-1025-9,0
1067,Hepatitis E virus: The current scenario,"Hepatitis E infection, caused by the hepatitis E virus (HEV), is a common cause of acute hepatitis in developing countries with poor sanitation and hygiene. The virus is classified into four genotypes (1-4) with one serotype. Genotypes 1 and 2 exclusively infect humans, whereas genotypes 3 and 4 also infect other animals, particularly pigs. In endemic areas, large outbreaks of acute hepatitis caused by viruses of genotype 1 or 2 frequently occur due to fecal-oral transmission, usually through contamination of drinking water. With a high attack rate in young adults (aged 15-45 years), the disease is particularly severe among pregnant women (20-30% mortality). HEV appears to be a zoonotic disease, with transmission from pigs, wild boars, and deer, or foodborne. Chronic infections are rare, except in immunosuppressed persons, such as organ transplant recipients. A subunit vaccine has been shown to be effective in preventing the clinical disease, but is not yet commercially available. Our understanding of HEV has undergone major changes in recent years and in this article we review the currently available information with regard to the molecular biology, pathobiology, and epidemiology of HEV infection. We also review the current therapeutic interventions and strategies being used to control HEV infection, with emphasis on possible approaches that could be used to develop an effective vaccine against HEV. © 2012 International Society for Infectious Diseases.",alanine aminotransferase;alkaline phosphatase;aspartate aminotransferase;bilirubin;DNA vaccine;gamma glutamyltransferase;hepatitis E vaccine;hev 239 vaccine;immunoglobulin;liver enzyme;protein ORF2;recombinant protein;unclassified drug;alanine aminotransferase blood level;alkaline phosphatase blood level;aspartate aminotransferase blood level;asymptomatic infection;bilirubin blood level;blood transfusion;cerebrospinal fluid;chronic hepatitis;disease course;disease severity;disease transmission;drug efficacy;drug safety;endemic disease;enzyme blood level;epidemic;genotype;hepatitis E;Hepatitis E virus;human;immunocompromised patient;incubation time;infection control;liver function test;liver injury;molecular biology;molecular pathology;open reading frame;reverse transcription polymerase chain reaction;review;virus isolation;water contamination,"Kumar, S.;Subhadra, S.;Singh, B.;Panda, B. K.",2013,,10.1016/j.ijid.2012.11.026,0
1068,"Full-length sequencing and genomic characterization of Bagaza, Kedougou, and Zika viruses","Many members of the genus Flavivirus are the agents of important diseases of humans, livestock, and wildlife. Currently, no complete genome sequence is available for the three African viruses, Bagaza, Zika, and Kedougou viruses, each representing a distinct virus subgroup according to the latest virus classification. In this study, we obtained a complete genome sequence of each of those three viruses and characterized the open reading frames (ORFs) with respect to gene sizes, cleavage sites, potential glycosylation sites, distribution of cysteine residues, and unique motifs. The sequences of the three viruses were then scanned across the entire length of the ORF against available sequences of other African flaviviruses and selected reference viruses for genetic relatedness. The data collectively indicated that Kedougou virus was close to dengue viruses but nonetheless distinct, while Bagaza virus shared genetic relatedness with West Nile virus in several genomic regions. In the non-coding regions, it was found that a particular organizational pattern of conserved sequences in the 37prime; terminal region generally correlated with the current virus grouping. © 2007 Springer-Verlag.",complementary DNA;viral protein;virus RNA;3' untranslated region;article;chemical structure;classification;conformation;Dengue virus;DNA sequence;Flavivirus;genetics;human;molecular genetics;nucleotide sequence;open reading frame;sequence homology;virus genome;West Nile virus,"Kuno, G.;Chang, G. J. J.",2007,,10.1007/s00705-006-0903-z,0
1069,Muscovy duck reovirus σC protein is atypically encoded by the smallest genome segment,"Although muscovy duck reovirus (DRV) shares properties with the reovirus isolated from chicken, commonly named avian reovirus (ARV), the two virus species are antigenically different. Similar to the DRV σB-encoded gene (1201 bp long) previously identified, the three other double-stranded RNA small genome segments of DRV have been cloned and sequenced. They were 1325, 1191 and 1124 bp long, respectively, and contained conserved terminal sequences common to ARVs. They coded for single expression products, except the smallest (S4), which contained two overlapping open reading frames (ORF1 and ORF2). BLAST analyses revealed that the proteins encoded by the 1325 and 1191 bp genes shared high identity levels with ARV σA and σNS, respectively, and to a lesser extent with other orthoreovirus counterparts. No homology was found for the S4 ORF1-encoded p10 protein. The 29.4 kDa product encoded by S4 ORF2 appeared to be 25% identical to ARV S1 ORF3-encoded σC, a cell-attachment oligomer inducing type-specific neutralizing antibodies. Introduction of large gaps in the N-terminal part of the DRV protein was necessary to improve DRV and ARV σC amino acid sequence alignments. However, a leucine zipper motif was conserved and secondary structure analyses predicted a three-stranded α-helical coiled-coil feature at this amino portion. Thus, despite extensive sequence divergence, DRV σC was suggested to be structurally and probably functionally related to ARV σC. This work provides evidence for the diversity of the polycistronic S class genes of reoviruses isolated from birds and raises the question of the relative classification of DRV in the Orthoreovirus genus.",double stranded RNA;leucine zipper protein;neutralizing antibody;oligomer;protein C;viral protein;alpha helix;amino acid sequence;amino terminal sequence;article;cell adhesion;controlled study;duck;gene sequence;genetic code;genetic conservation;genetic variability;genus;molecular cloning;nonhuman;nucleotide sequence;open reading frame;Orthoreovirus;priority journal;protein secondary structure;Reoviridae;sequence alignment;sequence homology;structure analysis;virus classification,"Kuntz-Simon, G.;Le Gall-Reculé, G.;de Boisséson, C.;Jestin, V.",2002,,,0
1070,"Comparative Metagenomic Profiling of Symbiotic Bacterial Communities Associated with Ixodes persulcatus, Ixodes pavlovskyi and Dermacentor reticulatus Ticks","Ixodes persulcatus, Ixodes pavlovskyi, and Dermacentor reticulatus ticks inhabitingWestern Siberia are responsible for the transmission of a number of etiological agents that cause human and animal tick-borne diseases. Because these ticks are abundant in the suburbs of large cities, agricultural areas, and popular tourist sites and frequently attack people and livestock, data regarding the microbiomes of these organisms are required. Using metagenomic 16S profiling, we evaluate bacterial communities associated with I. persulcatus, I. pavlovskyi, and D. reticulatus ticks collected from the Novosibirsk region of Russia. A total of 1214 ticks were used for this study. DNA extracted fromthe ticks was pooled according to tick species and sex. Sequencing of the V3-V5 domains of 16S rRNA genes was performed using the Illumina Miseq platform. The following bacterial genera were prevalent in the examined communities: Acinetobacter (all three tick species), Rickettsia (I. persulcatus and D. reticulatus) and Francisella (D. reticulatus). B. burgdorferi sensu lato and B. miyamotoi sequences were detected in I. persulcatus and I. pavlovskyi but not in D. reticulatus ticks. The pooled samples of all tick species studied contained bacteria from the Anaplasmataceae family, although their occurrence was low. DNA from A. phagocytophilumand Candidatus Neoehrlichia mikurensis was first observed in I. pavlovskyi ticks. Significant inter-species differences in the number of bacterial taxa as well as intra-species diversity related to tick sex were observed. The bacterial communities associated with the I. pavlovskyi ticks displayed a higher biodiversity compared with those of the I. persulcatus and D. reticulatus ticks. Bacterial community structure was also diverse across the studied tick species, as shown by permutational analysis of variance using the Bray-Curtis dissimilarity metric (p = 0.002). Between-sex variation was confirmed by PERMANOVA testing in I. persulcatus (p = 0.042) and I. pavlovskyi (p = 0.042) ticks. Our study indicated that 16S metagenomic profiling could be used for rapid assessment of the occurrence ofmedically important bacteria in tick populations inhabiting different natural biotopes and therefore the epidemic danger of studied foci.",BORNE ENCEPHALITIS-VIRUS;BURGDORFERI SENSU-LATO;WESTERN SIBERIA;TOMSK;CITY;NOVOSIBIRSK REGION;RUSSIA;RICKETTSIA;DISEASES;BIOLOGY;SURVEILLANCE,"Kurilshikov, A.;Livanova, N. N.;Fomenko, N. V.;Tupikin, A. E.;Rar, V. A.;Kabilov, M. R.;Livanov, S. G.;Tikunova, N. V.",2015,Jul,,0
1071,Genetic diversity and intergenogroup recombination events of sapoviruses detected from feces of pigs in Japan,"Sapoviruses (SaV) are enteric viruses infecting humans and animals. SaVs are highly diverse and are divided into multiple genogroups based on structural protein (VP1) sequences. SaVs detected from pigs belong to eight genogroups (GIII, GV, GVI, GVII, GVIII, GIX, GX, and GXI), but little is known about the SaV genogroup distribution in the Japanese pig population. In the present study, 26 nearly complete genome (> 6000 nucleotide: nt) and three partial sequences (2429 nt, 4364 nt, and 4419 nt in length, including the entire VP1 coding region) of SaV were obtained from one diarrheic and 15 non-diarrheic porcine feces in Japan via a metagenomics approach. Phylogenetic analysis of the complete VP1 amino acid sequence (aa) revealed that 29 porcine SaVs were classified into seven genogroups; GIII (11 strains), GV (1 strain), GVI (3 strains), GVII (6 strains), GVIII (1 strain), GX (3 strains), and GXI (4 strains). This manuscript presents the first nearly complete genome sequences of GX and GXI, and demonstrates novel intergenogroup recombination events.",amino acid sequence;article;controlled study;diarrhea;feces culture;genetic recombination;genetic variability;genome analysis;genome size;Japan;metagenomics;nonhuman;nucleotide sequence;phylogeny;pig;priority journal;Sapovirus;virus classification;virus detection;virus genome,"Kuroda, M.;Masuda, T.;Ito, M.;Naoi, Y.;Doan, Y. H.;Haga, K.;Tsuchiaka, S.;Kishimoto, M.;Sano, K.;Omatsu, T.;Katayama, Y.;Oba, M.;Aoki, H.;Ichimaru, T.;Sunaga, F.;Mukono, I.;Yamasato, H.;Shirai, J.;Katayama, K.;Mizutani, T.;Oka, T.;Nagai, M.",2017,,10.1016/j.meegid.2017.09.013,1
1072,A fast and robust method for full genome sequencing of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Type 1 and Type 2,"PRRSV is a positive-sense RNA virus with a high degree of genetic variability among isolates. For diagnostic sensitivity and vaccine design it is essential to monitor PRRSV genetic diversity. However, to date only a few full genome sequences of PRRSV isolates have been made publicly available. In the present study, fast and robust methods for long range RT-PCR amplification and subsequent next generation sequencing (NGS) were developed and validated on nine Type 1 and nine Type 2 PRRSV viruses. The methods generated robust and reliable sequences both on primary material and cell culture adapted viruses and the protocols performed well on all three NGS platforms tested (Roche 454 FLX, Illumina HiSeq2000, and Ion Torrent PGMTM Sequencer). These methods will greatly facilitate the generation of more full genome PRRSV sequences globally.","Animals;*Genome, Viral;*High-Throughput Nucleotide Sequencing/mt [Methods];Porcine Reproductive and Respiratory Syndrome/vi [Virology];*Porcine respiratory and reproductive syndrome virus/ge [Genetics];Porcine respiratory and reproductive syndrome virus/ip [Isolation & Purification];*RNA, Viral/ge [Genetics];*Reverse Transcriptase Polymerase Chain Reaction/mt [Methods];Swine;*Virology/mt [Methods];0 (RNA, Viral)","Kvisgaard, L. K.;Hjulsager, C. K.;Fahnoe, U.;Breum, S. O.;Ait-Ali, T.;Larsen, L. E.",2013,Nov,,0
1073,Molecular epidemiology of Newcastle disease in Republic of Korea,"Twenty-three strains of Newcastle disease virus (NDV) isolated between 1988 and 1999 in Republic of Korea were studied by partial nucleotide sequencing of fusion (F) gene and phylogenetic analysis. Most of Korean strains formed a distinctive cluster in genotype VI and they were genetically distant (4.0-8.7%) from other subtypes (a, b, c, d, and e), and termed provisionally VIf. Some Korean strains isolated in 1995 were grouped into genotype VIIa and they were closer to Taiwan strains than western Europe. The results suggest that the genotype VIf strains have been maintained by enzootic infections during the past decade, while genotype VIIa appears to be introduced more recently in Republic of Korea. © 2003 Elsevier Science B.V. All rights reserved.",animal disease;article;bird disease;fusion gene;gene cluster;genetic analysis;genotype;Korea;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;virus isolation;virus strain,"Kwon, H. J.;Cho, S. H.;Ahn, Y. J.;Seo, S. H.;Choi, K. S.;Kim, S. J.",2003,,10.1016/s0378-1135(03)00130-5,0
1074,Molecular epizootiology of recurrent low pathogenic avian influenza by H9N2 subtype virus in Korea,"The first outbreak of low pathogenic avian influenza (LPAI), H9N2 virus subtype, in 1996 prompted an eradication response, but LPAI returned to Korea in 1999. The relationship between the first and the recurrent viruses is unclear. To determine the molecular epizootiology of recurrent LPAI, we performed phylogenetic analysis with partial nucleotide sequences of four gene segments ( HA , NA , NP and PB2 ) from eight chicken-origin H9N2 viruses. The recurrent H9N2 viruses showed higher nucleotide similarity in haemagglutinin and neuraminidase genes to the 1996 Korean isolates than other Eurasian viruses, and formed a distinct cluster with the early Korean isolates and some isolates from migratory and domestic ducks in Japan and China. Phylogenetic analysis with internal genes showed that some Korean isolates formed a cluster with other subtypes, such as H5N1, H6N1, and H6N2 in China and Taiwan. These results suggest that the recurrent viruses are progeny of the early Korean H9N2 isolates, but further studies are required to explain their phylogenetic relatedness to viruses in China. © 2006 Houghton Trust Ltd.",animal;article;avian influenza;chicken;epidemiology;genetics;Influenza A virus (H9N2);isolation and purification;Korea;phylogeny;virology,"Kwon, H. J.;Cho, S. H.;Kim, M. C.;Ahn, Y. J.;Kim, S. J.",2006,,10.1080/03079450600821166,0
1075,"Highly pathogenic avian influenza a(H5N8) viruses reintroduced into south korea by migratory waterfowl, 2014-2015","Highly pathogenic avian influenza A(H5N8) viruses were isolated from migratory waterfowl in South Korea during fall 2014-winter 2015, a recurrence after initial introduction in winter 2014. These reappeared viruses were phylogenetically distinct from isolates circulating in poultry farms in South Korea.",hemagglutinin;M protein;nucleoprotein;polymerase basic protein 1;polymerase basic protein 2;sialidase;unclassified drug;viral protein;article;feces analysis;gene;gene sequence;hemagglutinin gene;Influenza A virus (H5N8);Influenza A virus;migration;next generation sequencing;nonhuman;phylogeny;real time polymerase chain reaction;reverse transcription polymerase chain reaction;sequence analysis;sequence homology;South Korea;virus genome;virus isolation;waterfowl,"Kwon, J. H.;Lee, D. H.;Swayne, D. E.;Noh, J. Y.;Yuk, S. S.;Erdene-Ochir, T. O.;Hong, W. T.;Jeong, J. H.;Jeong, S.;Gwon, G. B.;Song, C. S.",2016,,10.3201/eid2103.151006,0
1076,Prevalence of novel porcine circovirus 3 in Korean pig populations,"Porcine circovirus 3 (PCV3) is a novel porcine circovirus that was identified in pigs with porcine dermatitis and nephropathy syndrome, reproductive failure, and multi-systemic inflammation. However, the distribution and genetic characteristics of emerging PCV3 in Korea remains unclear. In this study, we determined the nationwide prevalence and genetic characteristics of PCV3 using pen-based oral fluid samples. The total prevalence of PCV3 in individual samples and at the farm level was 44.2% (159/360) and 72.6% (53/73), respectively. Korean PCV3 shared 99.2 ± 0.2% (98.9–99.8%) and 98.6 ± 0.5% (97.9–99.8%) nucleotide identity in the complete genome and ORF2, respectively, when compared to those of US strains. These data suggested that PCV3 is widely distributed throughout Korean pig populations.",virus DNA;animal cell;article;Circoviridae infection;Circovirus;gene identification;genetic trait;genetic variability;health status;herd;in vitro study;metagenomics;nonhuman;pig farming;porcine circovirus 3;prevalence;swine disease;virus genome;virus isolation;virus strain,"Kwon, T.;Yoo, S. J.;Park, C. K.;Lyoo, Y. S.",2017,,10.1016/j.vetmic.2017.06.013,0
1077,Different routes of inoculation impact infectivity and pathogenesis of H5N1 high pathogenicity avian influenza virus infection in chickens and domestic ducks,"The H5N1 type A influenza viruses classified as Qinghai-like virus (clade 2.2) are a unique lineage of type A influenza viruses with the capacity to produce significant disease and mortality in gallinaceous and anseriform birds, including domestic and wild ducks. The objective of this study was to determine the susceptibility and pathogenesis of chickens and domestic ducks to A/Whooper Swan/Mongolia/224/05 (H5N1) high pathogenicity avian influenza (HPAI) virus when administered through respiratory or alimentary routes of exposure. The chickens and ducks were more susceptible to the H5N1 HPAI virus, as evidenced by low infectious and lethal viral doses, when exposed by intranasal as compared to alimentary routes of inoculation (intragastric or oral-fed infected chicken meat). In the alimentary exposure pathogenesis study, pathologic changes included hemorrhage, necrosis, and inflammation in association with virus detection. These changes were generally observed in most of the visceral organs of chickens, between 2 and 4 days postinoculation (DPI), and are similar to lesions and virus localization seen in birds in natural cases or in experimental studies using the intranasal route. Alimentary exposure to the virus caused systemic infection in the ducks, characterized by moderate lymphocytic encephalitis, necrotized hepatitis, and pancreatitis with a corresponding demonstration of virus within the lesions. In both chickens and ducks with alimentary exposure, lesions, virus, or both were first demonstrated in the upper alimentary tract on 1 DPI, suggesting that the alimentary tract was the initial site affected upon consumption of infected meat or on gavage of virus in liquid medium. However, as demonstrated in the infectivity study in chickens, alimentary infection required higher exposure doses to produce infection as compared to intranasal exposure in chickens. These data suggest that upper respiratory exposure to H5N1 HPAI virus in birds is more likely to result in virus infection and transmission than will consumption of infected meat, unless the latter contains high doses of virus, as found in cannibalized infected carcasses. © American Association of Avian Pathologists 2010.",animal;article;avian influenza;chicken;duck;gastrointestinal tract;germfree animal;Influenza A virus (H5N1);pathogenicity;pathology;respiratory system;species difference;virology,"Kwon, Y. K.;Swayne, D. E.",2010,,10.1637/9397-051810-Reg.1,0
1078,Virological Surveillance and Preliminary Antigenic Characterization of Influenza Viruses in Pigs in Five European Countries from 2006 to 2008,"This study presents the results of the virological surveillance for swine influenza viruses (SIVs) in Belgium, UK, Italy, France and Spain from 2006 to 2008. Our major aims were to clarify the occurrence of the three SIV subtypes - H1N1, H3N2 and H1N2 - at regional levels, to identify novel reassortant viruses and to antigenically compare SIVs with human H1N1 and H3N2 influenza viruses. Lung tissue and/or nasal swabs from outbreaks of acute respiratory disease in pigs were investigated by virus isolation. The hemagglutinin (HA) and neuraminidase (NA) subtypes were determined using standard methods. Of the total 169 viruses, 81 were classified as 'avian-like' H1N1, 36 as human-like H3N2 and 47 as human-like H1N2. Only five novel reassortant viruses were identified: two H1N1 viruses had a human-like HA and three H1N2 viruses an avian-like HA. All three SIV subtypes were detected in Belgium, Italy and Spain, while only H1N1 and H1N2 viruses were found in UK and Northwestern France. Cross-hemagglutination inhibition (HI) tests with hyperimmune sera against selected older and recent human influenza viruses showed a strong antigenic relationship between human H1N1 and H3N2 viruses from the 1980s and H1N2 and H3N2 human-like SIVs, confirming their common origin. However, antisera against human viruses isolated during the last decade did not react with currently circulating H1 or H3 SIVs, suggesting that especially young people may be, to some degree, susceptible to SIV infections. © 2009 Blackwell Verlag GmbH.",antiserum;hemagglutinin;sialidase;acute respiratory tract disease;animal cell;animal tissue;article;avian influenza virus;bacteriophage;Belgium;controlled study;disease surveillance;France;genetic reassortment;hemagglutination inhibition;influenza;Influenza A virus (H1N1);Influenza A virus (H1N2);Influenza A virus (H3N2);Italy;lung parenchyma;nonhuman;nose smear;priority journal;Simian immunodeficiency virus;Spain;swine influenza virus;United Kingdom;virus isolation,"Kyriakis, C. S.;Brown, I. H.;Foni, E.;Kuntz-Simon, G.;Maldonado, J.;Madec, F.;Essen, S. C.;Chiapponi, C.;Van Reeth, K.",2011,,10.1111/j.1863-2378.2009.01301.x,0
1079,Deep Sequencing for Evaluation of Genetic Stability of Influenza A/California/07/2009 (H1N1) Vaccine Viruses,"Virus growth during influenza vaccine manufacture can lead to mutations that alter antigenic properties of the virus, and thus may affect protective potency of the vaccine. Different reassortants of pandemic ""swine"" H1N1 influenza A vaccine (121XP, X-179A and X-181) viruses as well as wild type A/California/07/2009(H1N1) and A/PR/8/34 strains were propagated in embryonated eggs and used for DNA/RNA Illumina HiSeq and MiSeq sequencing. The RNA sequences of these viruses published in NCBI were used as references for alignment of the sequencing reads generated in this study. Consensus sequences of these viruses differed from the NCBI-deposited sequences at several nucleotides. 121XP stock derived by reverse genetics was more heterogeneous than X-179A and X-181 stocks prepared by conventional reassortant technology. Passaged 121XP virus contained four non-synonymous mutations in the HA gene. One of these mutations (Lys226Glu) was located in the Ca antigenic site of HA (present in 18% of the population). Two non-synonymous mutations were present in HA of viruses derived from X-179A: Pro314Gln (18%) and Asn146Asp (78%). The latter mutation located in the Sa antigenic site was also detected at a low level (11%) in the wild-type A/California/07/2009(H1N1) virus, and was present as a complete substitution in X-181 viruses derived from X-179A virus. In the passaged X-181 viruses, two mutations emerged in HA: a silent mutation A1398G (31%) in one batch and G756T (Glu252Asp, 47%) in another batch. The latter mutation was located in the conservative region of the antigenic site Ca. The protocol for RNA sequencing was found to be robust, reproducible, and suitable for monitoring genetic consistency of influenza vaccine seed stocks.","Animals;*Genome, Viral;*Genomic Instability;High-Throughput Nucleotide Sequencing;Humans;*Influenza A Virus, H1N1 Subtype/ge [Genetics];Influenza A Virus, H1N1 Subtype/im [Immunology];*Influenza Vaccines/ge [Genetics];Influenza Vaccines/im [Immunology];Mutation;Mutation Rate;Nucleic Acid Amplification Techniques;Virus Replication;0 (Influenza Vaccines)","Laassri, M.;Zagorodnyaya, T.;Plant, E. P.;Petrovskaya, S.;Bidzhieva, B.;Ye, Z.;Simonyan, V.;Chumakov, K.",2015,,,0
1080,"Genomic and phylogenetic characterization of viruses included in the Manzanilla and Oropouche species complexes of the genus Orthobunyavirus, family Bunyaviridae","A thorough characterization of the genetic diversity of viruses present in vector and vertebrate host populations is essential for the early detection of and response to emerging pathogenic viruses, yet genetic characterization of many important viral groups remains incomplete. The Simbu serogroup of the genus Orthobunyavirus, family Bunyaviridae, is an example. The Simbu serogroup currently consists of a highly diverse group of related arboviruses that infect both humans and economically important livestock species. Here, we report complete genome sequences for 11 viruses within this group, with a focus on the large and poorly characterized Manzanilla and Oropouche species complexes. Phylogenetic and pairwise divergence analyses indicated the presence of high levels of genetic diversity within these two species complexes, on a par with that seen among the five other species complexes in the Simbu serogroup. Based on previously reported divergence thresholds between species, the data suggested that these two complexes should actually be divided into at least five species. Together these five species formed a distinct phylogenetic clade apart from the rest of the Simbu serogroup. Pairwise sequence divergences among viruses of this clade and viruses in other Simbu serogroup species complexes were similar to levels of divergence among the other orthobunyavirus serogroups. The genetic data also suggested relatively high levels of natural reassortment, with three potential reassortment events present, including two well-supported events involving viruses known to infect humans.",article;Bunyaviridae;gene sequence;genetic database;genetic reassortment;genetic variability;genomics;manzanilla bunyavirus;nonhuman;nucleotide sequence;Oropouche virus;Orthobunyavirus;phylogeny;priority journal;unindexed sequence;virus genome,"Ladner, J. T.;Savji, N.;Lofts, L.;da Rosa, A. T.;Wiley, M. R.;Gestole, M. C.;Rosen, G. E.;Guzman, H.;Vasconcelos, P. F. C.;Nunes, M. R. T.;Kochel, T. J.;Ian Lipkin, W.;Tesh, R. B.;Palacios, G.",2014,,10.1099/vir.0.061309-0,0
1081,Diversity of viruses detected by deep sequencing in pigs from a common background,"Although advances in nucleic acid sequencing have enabled the discovery of many infectious agents, challenges remain for scientists and veterinary diagnosticians trying to design animal studies with a minimum of variables and to interpret laboratory results. To evaluate pyrosequencing technology as a potential screening method to estimate the virome in pigs, fecal samples were collected from 4 pigs out of a group of 175 that had been raised together since birth. A number of viruses were detected, demonstrating the application of this technology to determine the background ""noise"" in the pigs. However, pyrosequencing also demonstrated the diversity of viruses within a group of animals and how that can confound experimental design and obscure a definitive diagnosis. © 2012 The Author(s).",animal;animal disease;article;genetic variability;genetics;pig;swine disease;virology;virus;virus infection,"Lager, K. M.;Ng, T. F.;Bayles, D. O.;Alt, D. P.;Delwart, E. L.;Cheung, A. K.",2012,,10.1177/1040638712463212,1
1082,Characterization of Highly Pathogenic Avian Influenza H5N1 Viruses Isolated from Domestic Poultry in China,"The highly pathogenic avian influenza (HPAI) H5N1 virus has caused several outbreaks in domestic poultry. Despite great efforts to control the spread of this virus, it continues to evolve and poses a substantial threat to public health because of a high mortality rate. In this study, we sequenced whole genomes of eight H5N1 avian influenza viruses isolated from domestic poultry in eastern China and compared them with those of typical influenza virus strains. Phylogenetic analyses showed that all eight genomes belonged to clade 2.3.2.1 and clade 7.2, the two main circulating clades in China. Viruses that clustered in clade 2.3.2.1 shared a high degree of homology with H5N1 isolates located in eastern Asian. Isolates that clustered in clade 7.2 were found to circulate throughout China, with an east-to-west density gradient. Pathogenicity studies in mice showed that these isolates replicate in the lungs, and clade 2.3.2.1 viruses exhibit a notably higher degree of virulence compared to clade 7.2 viruses. Our results contribute to the elucidation of the biological characterization and pathogenicity of HPAI H5N1 viruses.",animal;avian influenza;Bagg albino mouse;China;genetics;Influenza A virus (H5N1);isolation and purification;pathogenicity;phylogeny;poultry;virology,"Lai, C. C.;Wang, K. Y.;Chen, R.;Zhang, A. J.;Gu, H. J.;Yin, Y. B.;Wang, D. D.;Liu, L. L.;Xing, L.;Tong, Y. G.;Ma, Z. J.;Yang, P. H.;Wang, X. L.",2017,,10.3967/bes2017.009,0
1083,Serological characterization of buffalopox virus,"The buffalopox virus has been classified as a member of variola vaccinia subgroup of poxviruses on the basis of a number of biological properties and serological tests. A recent study indicated differences in the electrophoretic behavior between buffalopox and vaccinia virus antigens. The present study was undertaken to extend previous findings on the close relationship of buffalopox, vaccinia and cowpox viruses using gel diffusion, immunoelectrophoresis and complement fixation tests. All these observations indicate that buffalopox virus is a separate entity closely related to vaccinia and cowpox viruses and support the inclusion of buffalopox virus in subgroup I of poxviruses.",classification;microorganism;theoretical study;virus classification,"Lal, S. M.;Singh, I. P.",1973,,,0
1084,"Real time PCR method for simultaneous detection, quantitation and differentiation of capripoxviruses","The genus Capripoxvirus (CaPV) comprises three members namely, sheep poxvirus (SPPV.), goat poxvirus (GTPV) and lumpy skin disease virus (LSDV) affecting sheep, goats and cattle, respectively. CaPV infections produce similar symptoms in sheep and goats, and the three viruses cannot be distinguished serologically. Since there are conflicting opinions regarding the host specificity of CaPVs, particularly for goatpox and sheeppox viruses, the development of rapid genotyping tools will facilitate more accurate disease diagnosis and surveillance for better management of capripox outbreaks. This paper describes a species-specific, real time polymerase chain reaction (PCR), based on unique molecular markers that were found in the G-protein-coupled chemokine receptor (GPCR) gene sequences of CaPVs, that uses dual hybridization probes for their simultaneous detection, quantitation and genotyping. The assay can differentiate between CaPV strains based on differences in the melting point temperature (Tm) obtained after fluorescence melting curve analysis (FMCA). It is highly sensitive and presents low intra- and inter-run variation. This real time PCR assay will make a significant contribution to CaPV diagnosis and to the better understanding of the epidemiology of CaPVs by enabling rapid genotyping and gene-based classification of viral strains and unequivocal identification of isolates. © 2010 Elsevier B.V.",animal cell;article;Capripoxvirus;controlled study;embryo;genotype;melting point;nonhuman;priority journal;quantitative analysis;real time polymerase chain reaction;sensitivity and specificity;sheep;strain difference;virus detection;virus gene;virus identification;virus strain,"Lamien, C. E.;Lelenta, M.;Goger, W.;Silber, R.;Tuppurainen, E.;Matijevic, M.;Luckins, A. G.;Diallo, A.",2011,,10.1016/j.jviromet.2010.10.014,0
1085,Circulation of multiple subtypes of bovine viral diarrhoea virus type 1 with no evidence for HoBi-like pestivirus in cattle herds of southern Italy,"Pestiviruses of cattle include bovine viral diarrhoea 1 (BVDV-1) and 2 (BVDV-2) plus an emerging group, named HoBi-like pestivirus. In the present paper, the results of an epidemiological survey for pestiviruses circulating in cattle in southern Italy are presented. Molecular assays carried out on a total of 924 bovine samples detected 74 BVDV strains, including 73 BVDV-1 and 1 BVDV-2 viruses. Phylogenetic analysis carried out on partial 5′UTR and Npro sequences revealed the presence of 6 different subtypes of BVDV-1 and a single BVDV-2c strain. BVDV-1 displayed a high level of genetic heterogeneity, which can have both prophylactic and diagnostic implications. In addition, the detection of BVDV-2c highlights the need for a continuous surveillance for the emergence of new pestivirus strains in cattle farms in southern Italy.",5' untranslated region;animal tissue;article;bovine;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;cattle farming;controlled study;genetic heterogeneity;herd;HoBi like pestivirus;Italy;nonhuman;nucleotide sequence;Pestivirus;phylogeny;virus detection;virus strain,"Lanave, G.;Decaro, N.;Lucente, M. S.;Guercio, A.;Cavaliere, N.;Purpari, G.;Padalino, I.;Larocca, V.;Antoci, F.;Marino, P. A.;Buonavoglia, C.;Elia, G.",2017,,10.1016/j.meegid.2017.02.009,0
1086,"Novel Orthopoxvirus and Lethal Disease in Cat, Italy","We report detection and full-genome characterization of a novel orthopoxvirus (OPXV) responsible for a fatal infection in a cat. The virus induced skin lesions histologically characterized by leukocyte infiltration and eosinophilic cytoplasmic inclusions. Different PCR approaches were unable to assign the virus to a defined OPXV species. Large amounts of typical brick-shaped virions, morphologically related to OPXV, were observed by electron microscopy. This OPXV strain (Italy_09/17) was isolated on cell cultures and embryonated eggs. Phylogenetic analysis of 9 concatenated genes showed that this virus was distantly related to cowpox virus, more closely related to to ectromelia virus, and belonged to the same cluster of an OPXV recently isolated from captive macaques in Italy. Extensive epidemiologic surveillance in cats and rodents will assess whether cats are incidental hosts and rodents are the main reservoir of the virus. The zoonotic potential of this novel virus also deserves further investigation.",,"Lanave, G.;Dowgier, G.;Decaro, N.;Albanese, F.;Brogi, E.;Parisi, A.;Losurdo, M.;Lavazza, A.;Martella, V.;Buonavoglia, C.;Elia, G.",2018,09,,0
1087,Novel bocaparvoviruses in rabbits,"Bocaparvovirus is a newly established genus within the family Parvoviridae and has been identified as a possible cause of enteric, respiratory, reproductive/neonatal and neurological disease in humans and several animal species. In this study, metagenomic analysis was used to identify and characterise a novel bocaparvovirus in the faeces of rabbits with enteric disease. To assess the prevalence of the novel virus, rectal swabs and faecal samples obtained from rabbits with and without diarrhoea were screened with a specific PCR assay.The complete genome sequence of the novel parvovirus was reconstructed. The virus was distantly related to other bocaparvoviruses; the three ORFs shared 53%, 53% and 50% nucleotide identity, respectively, to homologous genes of porcine bocaparvoviruses. The virus was detected in 8/29 (28%) and 16/95 (17%) samples of rabbits with and without diarrhoea, respectively. Sequencing of the capsid protein fragment targeted by the diagnostic PCR identified two distinct bocaparvovirus populations/sub-types, with 91.7-94.5% nucleotide identity to each other. Including these novel parvoviruses in diagnostic algorithms of rabbit diseases might help inform their potential pathogenic role and impact on rabbit production and the virological profiles of laboratory rabbits.",capsid protein;nucleotide;article;Bocaparvovirus;controlled study;diarrhea;experimental rabbit;feces analysis;gene sequence;genetic algorithm;homologous recombination;metagenomics;nonhuman;nucleotide sequence;open reading frame;polymerase chain reaction;prevalence;Leporidae;screening test,"Lanave, G.;Martella, V.;Farkas, S. L.;Marton, S.;Fehér, E.;Bodnar, L.;Lavazza, A.;Decaro, N.;Buonavoglia, C.;Bányai, K.",2015,,10.1016/j.tvjl.2015.08.005,0
1088,Avian influenza - Eradication from commercial poultry is still not in sight,"Avian influenza viruses are highly infectious micro-organisms that primarily affect birds. Nevertheless, they have also been isolated from a number of mammals, including humans. Avian influenza virus can cause large economic losses to the poultry industry because of its high mortality. Although there are pathogenic variants with a low virulence and which generally cause only mild, if any, clinical symptoms, the subtypes H5 and H7 can mutate from a low to a highly virulent (pathogenic) virus and should be taken into consideration in eradication strategies. The primary source of infection for commercial poultry is direct and indirect contact with wild birds, with waterfowl forming a natural reservoir of the virus. Live-poultry markets, exotic birds, and ostriches also play a significant role in the epidemiology of avian influenza. The secondary transmission (i.e., between poultry farms) of avian influenza virus is attributed primarily to fomites and people. Airborne transmission is also important, and the virus can be spread by aerosol in humans. Diagnostic tests detect viral proteins and genes. Virus-specific antibodies can be traced by serological tests, with virus isolation and identification being complementary procedures. The number of outbreaks of avian influenza seems to be increasing - over the last 5 years outbreaks have been reported in Italy, Hong Kong, Chile, the Netherlands, South Korea, Vietnam, Japan, Thailand, Cambodia, Indonesia, Laos, China, Pakistan, United States of America, Canada, South Africa, and Malaysia. Moreover, a growing number of human cases of avian influenza, in some cases fatal, have paralleled the outbreaks in commercial poultry. There is great concern about the possibility that a new virus subtype with pandemic potential could emerge from these outbreaks. From the perspective of human health, it is essential to eradicate the virus from poultry; however, the large number of smallholdings with poultry, the lack of control experience and resources, and the international scale of transmission and infection make rapid control and long-term prevention of recurrence extremely difficult. In the Western world, the renewed interest in free-range housing carries a threat for future outbreaks. The growing ethical objections to the largescale culling of birds require a different approach to the eradication of avian influenza.",aerosol;airborne infection;avian influenza;bird;Cambodia;Canada;Chile;China;diagnostic procedure;disease transmission;duck;epidemic;epidemiological data;fatality;goose;health care;Hong Kong;housing;human;Indonesia;infection prevention;Influenza virus;Italy;Japan;Laos;long term care;Malaysia;market;medical ethics;Netherlands;nonhuman;ostrich;Pakistan;pathogenesis;poultry;poultry farming;recurrent disease;review;scale up;South Africa;South Korea;Thailand;United States;Viet Nam;virus classification;virus identification;virus isolation;wild type,"Landman, W. J. M.;Schrier, C. C.",2004,,,0
1089,Three novel canine papillomaviruses support taxonomic clade formation,"More than 100 human papillomaviruses (HPVs) have been identified and had their whole genomes sequenced. Most of these HPVs can be classified into three distinct genera, the alpha-, beta- and gamma-papillomaviruses (PVs). Of note, only one or a small number of PVs have been identified for each individual animal species. However, four canine PVs (CPVs) (COPV, CPV2, CPV3 and CPV4) have been described and their entire genomic sequences have been published. Based on their sequence similarities, they belong to three distinct clades. In the present study, circular viral DNA was amplified from three dogs showing signs of pigmented plaques, endophytic papilloma or in situ squamous cell carcinoma. Analysis of the DNA sequences suggested that these are three novel viruses (CPV5, CPV6 and CPV7) whose genomes comprise all the conserved sequence elements of known PVs. The genomes of these seven CPVs were compared in order properly classify them. Interestingly, phylogenetic analyses, as well as pairwise sequence alignments of the putative amino acid sequences, revealed that CPV5 grouped well with CPV3 and CPV4, whereas CPV7 grouped with CPV2 but neither group fitted with other classified PVs. However, CPV6 grouped with COPV, a lambda-PV. Based on this evidence, allocation of CPVs into three distinct clades could therefore be supported. Thus, similar to HPVs, it might be that the known and currently unknown CPVs are related and form just a few clades or genera. © 2009 SGM.",virus DNA;amino acid sequence;animal tissue;article;Canine oral papillomavirus;Canine papillomavirus type 2;Canine papillomavirus type 3;Canine papillomavirus type 4;Canine papillomavirus type 5;Canine papillomavirus type 6;Canine papillomavirus type 7;carcinoma in situ;controlled study;DNA sequence;dog;gene amplification;genetic conservation;genetic similarity;Lambdapapillomavirus;male;nonhuman;nucleotide sequence;papilloma;Papillomaviridae;phylogeny;priority journal;sequence alignment;squamous cell carcinoma;taxonomy;virus classification;virus plaque,"Lange, C. E.;Tobler, K.;Ackermann, M.;Panakova, L.;Thoday, K. L.;Favrot, C.",2009,,10.1099/vir.0.014498-0,0
1090,Tick-borne viruses: A review from the perspective of therapeutic approaches,"Several important human diseases worldwide are caused by tick-borne viruses. These diseases have become important public health concerns in recent years. The tick-borne viruses that cause diseases in humans mainly belong to 3 families: Bunyaviridae, Flaviviridae, and Reoviridae. In this review, we focus on therapeutic approaches for several of the more important tick-borne viruses from these 3 families. These viruses are Crimean-Congo hemorrhagic fever virus (CCHF) and the newly discovered tick-borne phleboviruses, known as thrombocytopenia syndromevirus (SFTSV), Heartland virus and Bhanja virus from the family Bunyaviridae, tick-borne encephalitis virus (TBEV), Powassan virus (POWV), Louping-ill virus (LIV), Omsk hemorrhagic fever virus (OHFV), Kyasanur Forest disease virus (KFDV), and Alkhurma hemorrhagic fever virus (AHFV) from the Flaviviridae family. To date, there is no effective antiviral drug available against most of these tick-borne viruses. Although there is common usage of antiviral drugs such as ribavirin for CCHF treatment in some countries, there are concerns that ribavirin may not be as effective as once thought against CCHF. Herein, we discuss also the availability of vaccines for the control of these viral infections. The lack of treatment and prevention approaches for these viruses is highlighted, and we hope that this review may increase public health awareness with regard to the threat posed by this group of viruses. © 2014 Elsevier GmbH.","3 deazauridine;3' deoxy 3' fluoroadenosine;9 (2,3 dihydroxypropyl)adenine;antioxidant;corticosteroid;cycloferon;cytoflavin;deoxyadenosine derivative;dezaguanine;DNA vaccine;emoxypine;fresh frozen plasma;immunoglobulin;interferon inducing agent;live vaccine;methylprednisolone;Myxovirus resistance protein A;panavir;replivax;ribavirin;suramin;unclassified drug;virus vaccine;antiviral activity;antiviral therapy;Bunyaviridae;bunyavirus infection;Colorado tick fever;Colorado tick fever virus;Crimean Congo hemorrhagic fever;Crimean-Congo hemorrhagic fever virus;evidence based medicine;Flavivirus infection;Heartland virus;human;infection control;Kyasanur Forest disease;louping ill;nonhuman;Omsk hemorrhagic fever;Phlebovirus;Phlebovirus infection;prevalence;preventive medicine;priority journal;public health;randomized controlled trial (topic);Reoviridae;reovirus infection;review;severe fever with thrombocytopenia syndromevirus infection;thrombocytopenia syndromevirus;Tick borne bunyavirus;tick borne disease;tick borne encephalitis;Tick borne encephalitis virus;Tick borne flavivirus;Tick borne reovirus;vaccination;virus classification;virus replication;virus transmission","Lani, R.;Moghaddam, E.;Haghani, A.;Chang, L. Y.;AbuBakar, S.;Zandi, K.",2014,,10.1016/j.ttbdis.2014.04.001,0
1091,Life-Style and Genome Structure of Marine Pseudoalteromonas Siphovirus B8b Isolated from the Northwestern Mediterranean Sea,"Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. Here we isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. Host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but not abundant in any sample (average per sample abundance was 0.65% of the reads). Together these data improve our understanding of siphoviruses in nature, and provide foundational information for a new 'rare virosphere' phage-host model system.",CONTAINING BACTERIAL-VIRUS;PLASMID-LIKE PROPHAGE;ESCHERICHIA-COLI;HOST-RANGE;EVOLUTIONARY RELATIONSHIPS;BACTERIOPHAGE-LAMBDA;COASTAL;ENVIRONMENT;VIRAL ASSEMBLAGES;OCEAN VIRUSES;GENE-TRANSFER,"Lara, E.;Holmfeldt, K.;Solonenko, N.;Sa, E. L.;Ignacio-Espinoza, J. C.;Cornejo-Castillo, F. M.;Verberkmoes, N. C.;Vaque, D.;Sullivan, M. B.;Acinas, S. G.",2015,Jan,,0
1092,Blood transcriptomes reveal novel parasitic zoonoses circulating in Madagascar's lemurs,"Zoonotic diseases are a looming threat to global populations, and nearly 75% of emerging infectious diseases can spread among wildlife, domestic animals and humans. A 'One World, One Health' perspective offers us an ideal framework for understanding and potentially mitigating the spread of zoonoses, and the island of Madagascar serves as a natural laboratory for conducting these studies. Rapid habitat degradation and climate change on the island are contributing to more frequent contact among humans, livestock and wildlife, increasing the potential for pathogen spillover events. Given Madagascar's long geographical isolation, coupled with recent and repeated introduction of agricultural and invasive species, it is likely that a number of circulating pathogens remain uncharacterized in lemur populations. Thus, it is imperative that new approaches be implemented for de novo pathogen discovery. To this end, we used non-targeted deep sequencing of blood transcriptomes from two species of critically endangered wild lemurs (Indri indri and Propithecus diadema) to characterize blood-borne pathogens. Our results show several undescribed vector-borne parasites circulating within lemurs, some of which may cause disease in wildlife, livestock and humans. We anticipate that advanced methods for de novo identification of unknown pathogens will have broad utility for characterizing other complex disease transmission systems.","Animals;Endangered Species;Gram-Negative Bacterial Infections/bl [Blood];Gram-Negative Bacterial Infections/ve [Veterinary];Lemur/bl [Blood];*Lemur/mi [Microbiology];*Lemur/ps [Parasitology];Madagascar;Protozoan Infections, Animal/bl [Blood];*Transcriptome;Zoonoses","Larsen, P. A.;Hayes, C. E.;Williams, C. V.;Junge, R. E.;Razafindramanana, J.;Mass, V.;Rakotondrainibe, H.;Yoder, A. D.",2016,Jan,,0
1093,Characterization of a new potyvirus naturally infecting chickpea,"During the 1999 to 2001 growing seasons, symptoms consisting of mosaic, stunting, yellowing, wilting, shortening of internodes, and phloem discoloration were observed in chickpea (Cicer arietinum) grown in the Department of Chuquisaca in southern Bolivia. In some fields, approximately 10% of the plants exhibited viruslike symptoms and suffered greatly reduced seed yields. Lentil (Lens culinaris) was also observed to be infected but not pea (Pisum sativum) or faba bean (Vicia faba) growing in nearby fields. Infected chickpea tissue reacted positively to the potyvirus group-specific monoclonal antibody (MAb), but there was no serological reaction with antisera to the potyviruses Bean yellow mosaic virus, Clover yellow vein virus, Cowpea aphid-borne mosaic virus, Pea seedborne mosaic virus, Bean common mosaic virus, or Bean common mosaic necrosis virus. Western blots of total protein extracts probed with the potyvirus MAb revealed a single band ca. 32 kDa. Comparative sequence analysis of cDNA clones generated from the putative coat protein gene consisted of 282 amino acids (31.9 kDa) and showed moderate identities of 67, 66,163, 63, and 61% with the coat proteins of potyviruses Pepper severe mosaic virus, Pepper yellow mosaic virus, Potato virus Y, Plum pox virus, and Pepper mottle virus, respectively. Phylogenetic analysis of the coat protein amino acid sequence revealed that this virus is a unique member of the family Potyviridae and is phylogenetically most closely related to a group of Solanaceae-infecting potyviruses rather than to other legume-infecting potyviruses. The proposed name for the new causal agent is Chickpea yellow mosaic virus.",AMINO-ACID-COMPOSITION;MOSAIC-VIRUS;SEED TRANSMISSION;CAPSID PROTEIN;DISEASE;POLYACRYLAMIDE;CARLAVIRUS;SEROLOGY;GELS,"Larsen, R. C.;Kaiser, W. J.;Wyatt, S. D.;Buxton-Druffel, K. L.;Berger, P. H.",2003,Nov,,0
1094,Recent developments in research involving BHV-4,"Bovine herpesvirus type 4 is widespread in cattle populations all over the world. Even though the virus is not a direct pathogen, it is an important agent because of research purposes and its role in secondary infections. The paper summarises the results of foreign and domestic laboratories from the last five years. Most important results of foreign research groups were the identification of a protein which play a role in virus-cell interaction, some data about the replication cycle, and a detailed study of viral DNA, which provided new evidence for classification of this virus into the Gammaherpesvirinae subfamily. Since the first BHV-4 strain was isolated in Hungary (BARTHA, 1963), this virus has always been one of the prime targets of their research activities. In animal experiments they studied the spread, distribution, viraemia, latency of the virus by several methods, such as polymerase chain reaction, immuno-histochemistry and virus isolation. The virus possesses some features of Beta- and Gammaherpesviruses. During infection the virus is bound mostly to the respiratory and immune system, persists very long in leukocytes, it appears periodically in blood serum and establishes persistent infection in neural and. immune tissues. By decreasing in vitro mitotic activity of leukocytes the virus might play a role in inhibiting some immune functions.",BOVINE HERPESVIRUS TYPE-4;IN-VITRO;GLYCOPROTEIN;REPLICATION;INFECTION,"Laszlo, E.",1999,Apr,,0
1095,Bats host diverse parvoviruses as possible origin of mammalian dependoparvoviruses and source for bat–swine interspecies transmission,,,"Lau, S. K. P.;Ahmed, S. S.;Tsoi, H. W.",2017,,,0
1096,Discovery and Sequence Analysis of Four Deltacoronaviruses from Birds in the Middle East Reveal Interspecies Jumping with Recombination as a Potential Mechanism for Avian-to-Avian and Avian-to-Mammalian Transmission,"The emergence of Middle East respiratory syndrome showed once again that coronaviruses (CoVs) in animals are potential source for epidemics in humans. To explore the diversity of deltacoronaviruses in animals in the Middle East, we tested fecal samples from 1,356 mammals and birds in Dubai, The United Arab Emirates. Four novel deltacoronaviruses were detected from eight birds of four species by reverse transcription-PCR (RT-PCR): FalCoV UAE-HKU27 from a falcon, HouCoV UAE-HKU28 from a houbara bustard, PiCoV UAE-HKU29 from a pigeon, and QuaCoV UAE-HKU30 from five quails. Complete genome sequencing showed that FalCoV UAE-HKU27, HouCoV UAE-HKU28, and PiCoV UAE-HKU29 belong to the same CoV species, suggesting recent interspecies transmission between falcons and their prey, houbara bustards and pigeons, possibly along the food chain. Western blotting detected specific anti-FalCoV UAE-HKU27 antibodies in 33 (75%) of 44 falcon serum samples, supporting genuine infection in falcons after virus acquisition. QuaCoV UAE-HKU30 belongs to the same CoV species as porcine coronavirus HKU15 (PorCoV HKU15) and sparrow coronavirus HKU17 (SpCoV HKU17), discovered previously from swine and tree sparrows, respectively, supporting avian-to-swine transmission. Recombination involving the spike protein is common among deltacoronaviruses, which may facilitate cross-species transmission. FalCoV UAE-HKU27, HouCoV UAE-HKU28, and PiCoV UAE-HKU29 originated from recombination between white-eye coronavirus HKU16 (WECoV HKU16) and magpie robin coronavirus HKU18 (MRCoV HKU18), QuaCoV UAE-HKU30 from recombination between PorCoV HKU15/SpCoV HKU17 and munia coronavirus HKU13 (MunCoV HKU13), and PorCoV HKU15 from recombination between SpCoV HKU17 and bulbul coronavirus HKU11 (BuCoV HKU11). Birds in the Middle East are hosts for diverse deltacoronaviruses with potential for interspecies transmission.<b>IMPORTANCE</b> During an attempt to explore the diversity of deltacoronaviruses among mammals and birds in Dubai, four novel deltacoronaviruses were detected in fecal samples from eight birds of four different species: FalCoV UAE-HKU27 from a falcon, HouCoV UAE-HKU28 from a houbara bustard, PiCoV UAE-HKU29 from a pigeon, and QuaCoV UAE-HKU30 from five quails. Genome analysis revealed evidence of recent interspecies transmission between falcons and their prey, houbara bustards and pigeons, possibly along the food chain, as well as avian-to-swine transmission. Recombination, which is known to occur frequently in some coronaviruses, was also common among these deltacoronaviruses and occurred predominantly at the spike region. Such recombination, involving the receptor binding protein, may contribute to the emergence of new viruses capable of infecting new hosts. Birds in the Middle East are hosts for diverse deltacoronaviruses with potential for interspecies transmission.",Animals;Bird Diseases/ge [Genetics];Bird Diseases/tm [Transmission];*Bird Diseases;*Birds/vi [Virology];Coronaviridae Infections/ge [Genetics];Coronaviridae Infections/tm [Transmission];Coronaviridae Infections/ve [Veterinary];*Coronaviridae Infections;Coronavirus/cl [Classification];Coronavirus/ge [Genetics];Coronavirus/ip [Isolation & Purification];Coronavirus/py [Pathogenicity];*Coronavirus;*High-Throughput Nucleotide Sequencing;Saudi Arabia;*Swine/vi [Virology],"Lau, S. K. P.;Wong, E. Y. M.;Tsang, C. C.;Ahmed, S. S.;Au-Yeung, R. K. H.;Yuen, K. Y.;Wernery, U.;Woo, P. C. Y.",2018,08 01,,0
1097,Chickens host diverse picornaviruses originated from potential interspecies transmission with recombination,"While chickens are an important reservoir for emerging pathogens such as avian influenza viruses, little is known about the diversity of picornaviruses in poultry. We discovered a previously unknown diversity of picornaviruses in chickens in Hong Kong. Picornaviruses were detected in 87 cloacal and 7 tracheal samples from 93 of 900 chickens by reverse transcription-PCR, with their partial 3Dpol gene sequences forming five distinct clades (I to V) among known picornaviruses. Analysis of eight genomes from different clades revealed seven different picornaviruses, including six novel picornavirus species (ChPV1 from clade I, ChPV2 and ChPV3 from clade II, ChPV4 and ChPV5 from clade III, ChGV1 from clade IV) and one existing species (Avian encephalomyelitis virus from clade V). The six novel chicken picornavirus genomes exhibited distinct phylogenetic positions and genome features different from related picornaviruses, supporting their classification as separate species. Moreover, ChPV1 may potentially belong to a novel genus, with low sequence homologies to related picornaviruses, especially in the P1 and P2 regions, including the predicted L and 2A proteins. Nevertheless, these novel picornaviruses were most closely related to picornaviruses of other avian species (ChPV1 related to Passerivirus A, ChPV2 and ChPV3 to Avisivirus A and Duck hepatitis A virus, ChPV4 and ChPV5 to Melegrivirus A, ChGV1 to Gallivirus A). Furthermore, ChPV5 represented a potential recombinant picornavirus, with its P2 and P3 regions possibly originating from Melegrivirus A. Chickens are an important reservoir for diverse picornaviruses that may cross avian species barriers through mutation or recombination. © 2014 The Authors.",virus RNA;article;Avian encephalomyelitis enterovirus;chicken;cladistics;controlled study;gene sequence;genome analysis;Hong Kong;host;molecular phylogeny;nonhuman;nucleotide sequence;Picornaviridae;priority journal;reverse transcription polymerase chain reaction;species diversity;virus classification;virus detection;virus genome;virus recombination;virus transmission,"Lau, S. K. P.;Woo, P. C. Y.;Yip, C. C. Y.;Li, K. S. M.;Fan, R. Y. Y.;Bai, R.;Huang, Y.;Chan, K. H.;Yuen, K. Y.",2014,,10.1099/vir.0.066597-0,0
1098,Detection and genetic characterization of a novel pig astrovirus: Relationship to other astroviruses,"Emerging viruses represent a continuous threat to human health and to farmed animals, as evidenced on multiple occasions by outbreaks of influenza, henipavirus and SARS. Knowledge about the diversity of viromes present in reservoir species can lead to a better understanding of the origin of emerging pathogens. In this study, we extend the knowledge of astrovirus diversity in pigs by reporting the genetic characterization of an unknown astrovirus lineage. Phylogenetic analyses provided evidence that this porcine astrovirus lineage is unique and does not appear to share a recent common ancestor with any known mamastrovirus. The data reported in this study extend the number of porcine astrovirus lineages to a total of five, all of which most likely represent distinct species of different origins. © 2011 Her Majesty the Queen in the Right of Canada as represented by the Minister of the Environment.",animal;animal disease;article;Astroviridae;astrovirus infection;classification;genetic variability;genetics;human;isolation and purification;molecular genetics;phylogeny;pig;swine disease;virology,"Laurin, M. A.;Dastor, M.;L'Homme, Y.",2011,,10.1007/s00705-011-1088-7,0
1099,Molecular variation in the nucleoprotein gene (ORF7) of the porcine reproductive and respiratory syndrome virus (PRRSV),"The nucleoprotein gene (ORF7) of 15 European isolates of porcine reproductive and respiratory syndrome virus (PRRSV) was sequenced and compared with corresponding sequences of other PRRSV isolates (2 European and 13 American) and one isolate each of other arteriviruses (the lactate dehydrogenase elevating virus (LDV), the simian haemorrhagic fever virus (SHFV) and the equine arteritis virus (EAV)). Their phylogenetic relationships were established using neighbour-joining and parsimony methods. Four lineages (PRRSV, LDV, SHFV and EAV) were discriminated. Two genotypes of PRRSV, European and American, could be further identified. The European genotype of PRRSV was highly conserved. Analysis of the nucleotide and amino acid substitutions in PRRSV ORF7 revealed four stable regions, probably conserved because of their requirement for nucleocapsid function and/or structure. No constant mutations accumulation in the ORF7 could be determined precisely when either synonymous or non-synonymous mutations were studied. Passage of the European PRRSV in vivo had little influence on the ORF7 sequence: only a small number of synonymous substitutions in ORF7 was detectable, confirming its low variability. Copyright (C) 1998 Elsevier Science B.V.",nucleoprotein;amino acid sequence;Arterivirus;article;Equine arteritis virus;gene sequence;genetic variability;Lactate dehydrogenase-elevating virus;nonhuman;phylogeny;priority journal;RNA virus;virus gene;virus infection,"Le Gall, A.;Legeay, O.;Bourhy, H.;Arnauld, C.;Albina, E.;Jestin, A.",1998,,10.1016/s0168-1702(97)00146-9,0
1100,Biochemical and genomic characterization of muscovy duck parvovirus,"A duck parvovirus (DPV) isolated from muscovy ducks during the epizootic in France in 1989 was purified from inoculated allanto-amniotic fluids by CsCl density gradient centrifugation and characterized. Full and empty non-enveloped icosahedral viral particles were observed banding at densities of 1.39 to 1.42 and 1.38 respectively, with a diameter of 22 to 23 nm. Viral proteins were analyzed by SDS-PAGE and the estimated molecular weights of the 3 major proteins were 91, 78 and 58 kDa. The nucleic acid was shown to be a single-stranded DNA of about 5,300 bases with terminal palindromic hairpins. These results confirm the previous classification of the virus in the family Parvoviridae established by Jestin et al. [14] on morphological and serological bases. The DPV DNA was reannealed indicating that complementary DNA strands were encapsidated. A partial restriction endonuclease map was also established. This work constitutes the first biochemical and genomic description of a muscovy duck parvovirus.","Animals;*Bird Diseases;*DNA, Viral/an [Analysis];DNA, Viral/ip [Isolation & Purification];*Ducks/vi [Virology];France;Heart/vi [Virology];Liver/vi [Virology];*Parvoviridae Infections/ve [Veterinary];Parvoviridae Infections/vi [Virology];Parvovirus/ge [Genetics];Parvovirus/ip [Isolation & Purification];*Parvovirus/me [Metabolism];Restriction Mapping;Spleen/vi [Virology];Viral Proteins/an [Analysis];0 (DNA, Viral);0 (Viral Proteins)","Le Gall-Recule, G.;Jestin, V.",1994,,,0
1101,Molecular characterization of serotype A foot-and-mouth disease viruses circulating in Vietnam in 2009,"Foot-and-mouth disease (FMD) is a major cause of endemic outbreaks in Vietnam in recent years. In this work, six serotype A foot-and-mouth disease viruses (FMDV), collected from endemic outbreaks during January and February of 2009 in four different provinces in Vietnam, were genetically characterized for their complete genome sequences. Genetic analysis based on the complete viral genome sequence indicated that they were closely related to each other and shared 99.0-99.8% amino acid (aa) identity. Genetic and deduced aa analysis of the capsid coding gene VP1 showed that the six Vietnamese strains were all classified into the genotype IX from a total of 10 major genotypes worldwide, sharing 98.1-100% aa identity each other. They were most closely related to the type A strains recently isolated in Laos (A/LAO/36/2003, A/LAO/1/2006, A/LAO/6/2006, A/LAO/7/2006, and A/LAO/8/2006), Thailand (A/TAI/2/1997 and A/TAI/118/1987), and Malaysia (A/MAY/2/2002), sharing 88.3-95.5% nucleotide (nt) identities. In contrast, Vietnamese type A strains showed low nt identities with the two old type A FMDVs, isolated in 1960 in Thailand (a15thailand iso43) and in 1975 in the Philippines (aphilippines iso50), ranging from 77.3 to 80.9% nt identity. A multiple alignment based on the deduced amino acid sequences of the capsid VP1 coding gene of type A FMDV revealed three amino acid substitutions between Vietnamese strains and the strains of other Southeast Asian countries (Laos, Thailand, Malaysia, and the Philippines). Alanine was replaced by valine at residue 24, asparagine by arginine at residue 85, and serine by threonine at residue 196. Furthermore, type A FMDV strains recently isolated in Vietnam, Laos, Thailand, and Malaysia all have one amino acid deletion at residue 140 of the capsid VP1 protein compared with the two old type A FMDV strains from Thailand and the Philippines as well as most other type A representatives worldwide. This article is the first to report on the comprehensive genetic characterization of type A FMDV circulating in Vietnam. © 2010 Elsevier B.V.",alanine;amino acid;arginine;asparagine;nucleotide;protein VP1;serine;threonine;valine;amino acid sequence;amino acid substitution;article;endemic disease;epidemic;Foot and mouth disease virus;gene sequence;genetic analysis;genetic identification;genotype;geographic distribution;Laos;Malaysia;nonhuman;nucleotide sequence;Philippines;phylogenetic tree;serotype;Thailand;Viet Nam;virus genome;virus isolation;virus strain,"Le, V. P.;Nguyen, T.;Lee, K. N.;Ko, Y. J.;Lee, H. S.;Nguyen, V. C.;Mai, T. D.;Do, T. H.;Kim, S. M.;Cho, I. S.;Park, J. H.",2010,,10.1016/j.vetmic.2009.12.033,0
1102,Heterogeneity and genetic variations of serotypes O and Asia 1 foot-and-mouth disease viruses isolated in Vietnam,"Six field foot-and-mouth disease viruses (FMDVs), including four serotype O and two serotype Asia 1 strains, were collected from endemic outbreaks in 2005, 2006, and 2007 from four different provinces in Vietnam. The viruses were isolated and genetically characterized for their complete genomic sequences. The genetic analysis based on the complete genomic coding sequences revealed that the four serotype O FMDVs were related to each other, sharing 95.2% nucleotide (nt) identity and 97.5-97.6% amino acid (aa) identity. Genetic analysis and a phylogenetic tree, based on the VP1 gene of FMDV, showed that the four present Vietnamese serotype O strains have a high level of identity with other serotype O representatives of the Mya-98 lineage of the Southeast Asian (SEA) topotype. The four viruses were all clustered into the Mya-98 lineage of the SEA topotype, sharing 92.3-95.6% nt and 93.4-96.7% aa identity. This finding of the Mya-98 lineage was different from previous reports that the Vietnamese serotype O strains belonged to the Cam-94 lineage of the SEA topotype and two other topotypes, Middle East-South Asia (ME-SA) and Cathay. For the two serotype Asia 1 FMDVs, the genetic analysis based on the complete genomic coding sequences as well as on the VP1 gene revealed that they belonged to two genogroups, IV and V. Of note, the As1/VN/QT03/2007 strain of genogroup V, isolated in 2007, was very closely related to the pandemic Asia 1 strain which caused FMD outbreaks in China (Asia1/WHN/CHA/06, FJ906802) and Mongolia (Asia1/MOG/05, EF614458) in 2005, sharing 99.0-99.3% nt and 99.5-100% aa identity. In contrast, the second strain As1/VN/LC04/2005 of genogroup IV, isolated in 2005, was closely related to all referenced Vietnamese serotype Asia 1 strains found in the GenBank databases, sharing 86.4-100% nt and 90.9-100% aa identity with each. This study is the first description of the full-length genomic sequence of Vietnamese FMDV serotypes O and Asia 1 and may provide the evidence of the concurrent circulation of different serotypes and subtypes of FMDV in recent years in Vietnam. © 2010 Elsevier B.V.",amino acid sequence;article;cluster analysis;endemic disease;Foot and mouth disease virus;gene sequence;genetic analysis;genetic heterogeneity;nonhuman;phylogenetic tree;serotype;Viet Nam;viral genetics;virus isolation;virus strain,"Le, V. P.;Nguyen, T.;Park, J. H.;Kim, S. M.;Ko, Y. J.;Lee, H. S.;Nguyen, V. C.;Mai, T. D.;Do, T. H.;Cho, I. S.;Lee, K. N.",2010,,10.1016/j.vetmic.2010.04.005,0
1103,The human virome: new tools and concepts,,,"Lecuit, M.;Eloit, M.",2013,,,0
1104,Sequence analysis of the hemagglutinin gene of H9N2 Korean avian influenza viruses and assessment of the pathogenic potential of isolate MS96,"Sequence analysis of the hemagglutinin (HA) gene of five Korean H9N2 avian influenza virus (AIV) isolates showed that these viruses were closely related and possibly came from the same source. Phylogenetic analysis of the HA1 subunit of H9 subtype isolates revealed that Korean AIV isolates were different from isolates from the poultry markets in Hong Kong in 1997. None of the Korean AIVs had multiple basic amino acids at the HA cleavage site that confer high pathogenicity to some H5 and H7 AIVs. Phylogenetic analysis of the nucleoprotein and matrix gene demonstrated that Korean isolates cluster with Eurasian origin AIVs. The pathogenic potential of one of the isolates (MS96) was assessed after several passages in 14-day-old embryonated chicken eggs (ECE). Fourteen-day-old ECE derivatives of MS96 showed increased HA titer and embryo mortality in eggs; this was apparent after the third passage in 14-day-old ECE. Sequence analysis of the cleavage site of MS96 after the third and tenth passages in 14-day-old ECE revealed no changes in the amino acid sequence. The pathogenicity of MS96 after the tenth passage in 14-day-old eggs (MS96p10(ECE14)) was tested with 4-wk-old specific-pathogen-free chickens. The 14-day-old derivative, MS96p10(ECE14), showed wider tissue tropism and induced more severe clinical signs than the parent virus. Furthermore, after intranasal inoculation of 86-wk-old broiler breeders and 30-wk-old layers, the MS96p10(ECE14) derivative induced more severe signs of depression than the parent virus as well as a transient drop in egg production.",,"Lee, C. W.;Song, C. S.;Lee, Y. J.;Mo, I. P.;Garcia, M.;Suarez, D. L.;Kim, S. J.",2000,,,0
1105,"Highly Pathogenic Avian Influenza Viruses and Generation of Novel Reassortants, United States, 2014-2015","Asian highly pathogenic avian influenza A(H5N8) viruses spread into North America in 2014 during autumn bird migration. Complete genome sequencing and phylogenetic analysis of 32 H5 viruses identified novel H5N1, H5N2, and H5N8 viruses that emerged in late 2014 through reassortment with North American low-pathogenicity avian influenza viruses.","Animals;Animals, Wild;Birds;*Influenza A virus/ge [Genetics];*Influenza A virus/py [Pathogenicity];Influenza in Birds/ep [Epidemiology];*Influenza in Birds/vi [Virology];Reassortant Viruses/ge [Genetics];*Reassortant Viruses/py [Pathogenicity];Viral Tropism","Lee, D. H.;Bahl, J.;Torchetti, M. K.;Killian, M. L.;Ip, H. S.;DeLiberto, T. J.;Swayne, D. E.",2016,07,,0
1106,Characterization of low-pathogenicity H5 and H7 Korean avian influenza viruses in chickens,"To date, all isolated highly pathogenic avian influenza (HPAI) viruses that cause systemic infection with a high mortality rate in poultry species have been known to belong to either the H5 or H7 subtypes. The HPAI viruses may originate because of the insertion of multiple basic amino acids at the cleavage site of the hemagglutinin protein after the low-pathogenic H5 and H7 viruses have been introduced into poultry. In the present study, we investigated the phylogenetic characteristics of the H5 (n = 4) and H7 (n = 3) low-pathogenic avian influenza (LPAI) viruses isolated from wild birds in Korea by using nucleotide sequences of all 8 gene segments of the viral genome. Further, we evaluated the infectivity, transmissibility, and pathogenic potential of these viruses in chickens. Phylogenetic analysis showed that all viruses used in the study clustered in the Eurasian lineage and were similar to the viruses isolated in Asian countries that share the East Asian-Australasian migratory bird fly-way. Our H5N2 isolates could not be replicated and transmitted in chickens, but the H7N8 isolates could efficiently be replicated and transmitted to contact-exposure chickens. In addition, because our H7N8 isolates caused watery diarrhea in chickens, these viruses cannot only serve as progenitors of novel HPAI strains but also potentially cause clinical disease in poultry. Although there have been no reports of LPAI mutation to HPAI in these regions, the wild bird surveillance effort should focus on monitoring the introduction and transmission of the HPAI H5N1 and LPAI H5 and H7 viruses. © 2012 Poultry Science Association Inc.","hemagglutinin, avian influenza A virus;Influenza virus hemagglutinin;animal;animal disease;article;avian influenza;chicken;epidemic;genetics;Influenza A virus (H5N2);pathogenicity;phylogeny;South Korea;virology","Lee, D. H.;Kwon, J. H.;Park, J. K.;Lee, Y. N.;Yuk, S. S.;Lee, J. B.;Park, S. Y.;Choi, I. S.;Song, C. S.",2012,,10.3382/ps.2012-02543,0
1107,"Novel Reassortant Clade 2.3.4.4 Avian Influenza A(H5N8) Virus in Wild Aquatic Birds, Russia, 2016","The emergence of novel avian influenza viruses in migratory birds is of concern because of the potential for virus dissemination during fall migration. We report the identification of novel highly pathogenic avian influenza viruses of subtype H5N8, clade 2.3.4.4, and their reassortment with other avian influenza viruses in waterfowl and shorebirds of Siberia.","Animals;*Animals, Wild;*Birds/vi [Virology];Disease Outbreaks;Genes, Viral;History, 21st Century;*Influenza A Virus, H5N8 Subtype/cl [Classification];*Influenza A Virus, H5N8 Subtype/ge [Genetics];*Influenza in Birds/ep [Epidemiology];Influenza in Birds/hi [History];*Influenza in Birds/vi [Virology];Phylogeny;Public Health Surveillance;*Reassortant Viruses;Russia/ep [Epidemiology]","Lee, D. H.;Sharshov, K.;Swayne, D. E.;Kurskaya, O.;Sobolev, I.;Kabilov, M.;Alekseev, A.;Irza, V.;Shestopalov, A.",2017,02,,0
1108,"Highly Pathogenic Avian Influenza A(H7N9) Virus, Tennessee, USA, March 2017","In March 2017, highly pathogenic avian influenza A(H7N9) was detected at 2 poultry farms in Tennessee, USA. Surveillance data and genetic analyses indicated multiple introductions of low pathogenicity avian influenza virus before mutation to high pathogenicity and interfarm transmission. Poultry surveillance should continue because low pathogenicity viruses circulate and spill over into commercial poultry.","Animals;*Chickens;Genome, Viral;Influenza A Virus, H7N9 Subtype/ge [Genetics];*Influenza A Virus, H7N9 Subtype/py [Pathogenicity];Influenza in Birds/th [Therapy];*Influenza in Birds/vi [Virology];*Poultry Diseases/vi [Virology];Tennessee;Whole Genome Sequencing","Lee, D. H.;Torchetti, M. K.;Killian, M. L.;Berhane, Y.;Swayne, D. E.",2017,11,,0
1109,"Reoccurrence of Avian Influenza A(H5N2) Virus Clade 2.3.4.4 in Wild Birds, Alaska, USA, 2016","We report reoccurrence of highly pathogenic avian influenza A(H5N2) virus clade 2.3.4.4 in a wild mallard in Alaska, USA, in August 2016. Identification of this virus in a migratory species confirms low-frequency persistence in North America and the potential for re-dissemination of the virus during the 2016 fall migration.","Alaska/ep [Epidemiology];Animals;*Animals, Wild;*Birds/vi [Virology];Genotype;History, 21st Century;*Influenza A Virus, H5N2 Subtype/cl [Classification];*Influenza A Virus, H5N2 Subtype/ge [Genetics];*Influenza in Birds/ep [Epidemiology];Influenza in Birds/hi [History];*Influenza in Birds/vi [Virology];Phylogeny;Public Health Surveillance","Lee, D. H.;Torchetti, M. K.;Killian, M. L.;DeLiberto, T. J.;Swayne, D. E.",2017,02,,0
1110,Deep sequencing of H7N8 avian influenza viruses from surveillance zone supports H7N8 high pathogenicity avian influenza was limited to a single outbreak farm in Indiana during 2016,"In mid-January 2016, an outbreak of H7N8 high-pathogenicity avian influenza virus (HPAIV) in commercial turkeys occurred in Indiana. Surveillance within the 10km control zone identified H7N8 low-pathogenicity avian influenza virus (LPAIV) in nine surrounding turkey flocks but no other HPAIV-affected premises. We sequenced four of the H7N8 HPAIV isolated from the single farm and nine LPAIV identified during control zone surveillance. Evaluation included phylogenetic network analysis indicating close relatedness across the HPAIV and LPAIV, and that the progenitor H7N8 LPAIV spread among the affected turkey farms in Indiana, followed by spontaneous mutation to HPAIV on a single premise through acquisition of three basic amino acids at the hemagglutinin cleavage site. Deep sequencing of the available viruses failed to identify subpopulations in either the HPAIV or LPAIV suggesting mutation to HPAIV likely occurred on a single farm and the HPAIV did not spread to epidemiologically linked LPAIV-affected farms.",Animals;Chickens/vi [Virology];Disease Outbreaks;High-Throughput Nucleotide Sequencing;Indiana/ep [Epidemiology];Influenza A virus/cl [Classification];Influenza A virus/ge [Genetics];*Influenza A virus/ip [Isolation & Purification];*Influenza A virus/py [Pathogenicity];Influenza in Birds/ep [Epidemiology];*Influenza in Birds/vi [Virology];Phylogeny;Poultry Diseases/ep [Epidemiology];*Poultry Diseases/vi [Virology];Turkeys/vi [Virology];Virulence,"Lee, D. H.;Torchetti, M. K.;Killian, M. L.;Swayne, D. E.",2017,07,,0
1111,Molecular epidemiological investigation of Newcastle disease virus from domestic ducks in Korea,"To expand the epidemiological understanding of Newcastle disease virus (NDV) found in domestic ducks in Korea, 14 NDV isolates from apparently healthy domestic ducks were biologically and genetically characterized. Thirteen and 1 isolates of NDV were categorized into lentogenic and velogenic viruses, respectively, based on in vivo pathogenicity tests. Twelve lentogenic viruses showed HA activity to horse RBCs, while 1 lentogenic virus and the velogenic virus were negative. Lentogenic viruses (n = 13) had sequence motifs of 112ERQERL117 (n = 1) or 112GRQGRL117 (n = 12) at the F0 cleavage site, while the velogenic virus (n = 1) had a sequence motif of 112RRQKRF117 at the same site. Phylogenetic analysis revealed that at least three distinct genotypes may exist in domestic ducks in Korea; one class I genotype (genotype 2), and two class II (genotypes I and VII) genotypes. The class I virus was most closely related to strains of genotype 2 which were isolated in birds from the USA, Germany and Denmark. Twelve lentogenic class II viruses were grouped together in genotype I, and were then divided into at least three clusters, namely Aomori-like, Ulster2C-like, and V4-like. The velogenic class II virus was assigned to genotype VII which represents viruses responsible for recent epidemics in many Asian countries including Korea. The epidemiological importance of domestic duck isolates of NDV in Korea is discussed. © 2008 Elsevier B.V. All rights reserved.",protein derivative;animal cell;article;Asian;biology;bird;controlled study;Denmark;domestic animal;duck;embryo;epidemic;erythrocyte;genetics;genotype;Germany;hemagglutination;horse;in vivo study;Korea;molecular epidemiology;Newcastle disease virus;nonhuman;nucleotide sequence;pathogenicity;phylogeny;protein motif;unindexed sequence;United States;virus characterization;virus isolation;virus strain,"Lee, E. K.;Jeon, W. J.;Kwon, J. H.;Yang, C. B.;Choi, K. S.",2009,,10.1016/j.vetmic.2008.08.020,0
1112,Genetic diversity of avian infectious bronchitis virus isolates in Korea between 2003 and 2006,"Thirty-three field isolates of avian infectious bronchitis virus (IBV) were recovered from commercial chicken flocks in Korea between 2003 and 2006 and were characterized phylogenetically by nucleotide sequence analysis of the IBV S1 gene hyper-variable region. Our phylogenetic analysis revealed that recent field isolates of IBV formed at least three distinct phylogenetic types, including K-I, K-II, and K-III. K-I type IBV consisted of indigenous, 13 IBV isolates which evolved from the Kr-EJ/95 strain and then separated into the lineages of type K-Ia and type K-Ib. K-II type IBV isolates (n = 19) were closely related to nephropathogenic IBV variants from China and Japan. The K-III type isolate (Kr/D064/05), first identified by this study, was closely related to enteric IBV variants from the Chinese strains that cause proventriculitis. Sequence comparisons showed amino acid differences of >27.5% between IBV types. The molecular epidemiologic characteristics of IBV field isolates are briefly discussed.",primer DNA;virus RNA;amino acid sequence;animal;animal disease;article;Avian infectious bronchitis virus;bird disease;chicken;classification;genetic variability;genetics;isolation and purification;Korea;molecular genetics;nucleotide sequence;phylogeny;sequence homology;virology;virus gene;virus infection,"Lee, E. K.;Jeon, W. J.;Lee, Y. J.;Jeong, O. M.;Choi, J. G.;Kwon, J. H.;Choi, K. S.",2008,,10.1637/8117-092707-ResNote.1,0
1113,"The genome sequence of Yaba-like disease virus, a yatapoxvirus","The genome sequence of Yaba-like disease virus (YLDV), an unclassified member of the yatapoxvirus genus, has been determined. Excluding the terminal hairpin loops, the YLDV genome is 144,575 bp in length and contains inverted terminal repeats (ITRs) of 1883 bp. Within 20 nucleotides of the termini, there is a sequence that is conserved in other poxviruses and is required for the resolution of concatemeric replicative DNA intermediates. The nucleotide composition of the genome is 73% A+T, but the ITRs are only 63% A+T. The genome contains 151 tightly packed open reading frames (ORFs) that either are ≥180 nucleotides in length or are conserved in other poxviruses. ORFs within 23 kb of each end are transcribed toward the termini, whereas ORFs within the central region of the genome are encoded on either DNA strand. In the central region ORFs have a conserved position, orientation, and sequence compared with vaccinia virus ORFs and encode many enzymes, transcription factors, or structural proteins. In contrast, ORFs near the termini are more divergent and in seven cases are without counterparts in other poxviruses. The YLDV genome encodes several predicted immunomodulators; examples include two proteins with similarity to CC chemokine receptors and predicted secreted proteins with similarity to MHC class I antigen, OX-2, interleukin-10/mda-7, poxvirus growth factor, serpins, and a type I interferon-binding protein. Phylogenic analyses indicated that YLDV is very closely related to yaba monkey tumor virus, but outside the yatapoxvirus genus YLDV is more closely related to swinepox virus and leporipoxviruses than to other chordopoxvirus genera. © 2001 Academic Press.",chemokine receptor;growth factor;immunomodulating agent;interleukin 10;major histocompatibility antigen class 1;transcription factor;article;Chordopoxvirinae;DNA repair;DNA replication;gene sequence;Leporipoxvirus;nonhuman;nucleotide sequence;open reading frame;phylogeny;Poxviridae;priority journal;sequence analysis;signal transduction;transcription regulation;Vaccinia virus;yaba like disease virus,"Lee, H. J.;Essani, K.;Smith, G. L.",2001,,10.1006/viro.2000.0761,0
1114,Generation of reassortant influenza viruses within the non-industrial poultry system,"We compared the genetic and biologic characteristics of 35 influenza viruses of different epidemiological backgrounds in Korea, including H3N2 canine influenza virus (CIV). Phylogenetic analysis revealed that chicken adapted H9N2 viruses (A/chicken/Korea/96006/96 [CK/Kor/96006-like]) have acquired aquatic avian gene segments through reassortment, and these reassorted H9N2 viruses were more frequently detected from minor poultry species than from industrial poultry. Conversely, gene segments from CK/Kor/96006-like viruses were also detected in most of the viruses from domestic ducks. Interestingly, domestic ducks, rather than wild aquatic birds, harbored close relatives of all eight gene segments of H3N2 CIV, which preferred binding to avian receptors. Therefore, bidirectional virus transmission events are assumed to have occurred between land-based poultry and aquatic poultry, in particular within the non-industrial poultry system. These events have contributed to the generation of a novel reassortant, H3N2 CIV. To prevent generating other reassortants capable of interspecies transmission, gene movements in the non-industrial poultry systems should be clarified and managed. © 2012 Elsevier B.V.",amino acid sequence;article;binding affinity;bird;canine influenze virus;controlled study;duck;gene;genetic reassortment;genotype;H3HA gene;HA gene;Influenza virus;Influenza virus A H11N9;Influenza A virus (H3N2);Influenza virus A H3N6;Influenza A virus (H3N8);Influenza virus A H6N2;Influenza A virus (H9N2);Korea;M gene;nonhuman;NP gene;nucleotide sequence;PB1 gene;PB2 gene;phylogeny;poultry;priority journal;receptor binding;virus detection;virus isolation;virus transmission,"Lee, H. J.;Lee, D. H.;Lee, Y. N.;Kwon, J. S.;Lee, Y. J.;Lee, J. B.;Park, S. Y.;Choi, I. S.;Song, C. S.",2012,,10.1016/j.meegid.2012.02.001,0
1115,Survival of prototype strains of somatic coliphage families in environmental waters and when exposed to UV low-pressure monochromatic radiation or heat,"The potential use of specific somatic coliphage taxonomic groups as viral indicators based on their persistence and prevalence in water was investigated. Representative type strains of the 4 major somatic coliphage taxonomic groups were seeded into reagent water and an ambient surface water source of drinking water and the survival of the added phages was measured over 90 days at temperatures of 23-25 and 4 °C. Microviridae (type strain PhiX174), Siphoviridae (type strain Lambda), and Myoviridae (type strain T4) viruses were the most persistent in water at the temperatures tested. The Microviridae (type strain PhiX174) and the Siphoviridae (type strain Lambda) were the most resistant viruses to UV radiation and the Myoviridae (type strain T4) and the Microviridae (type strain PhiX174) were the most resistant viruses to heat. Based on their greater persistence in water over time and their relative resistance to heat and/or UV radiation, the Myoviridae (type strain T4), the Microviridae (type strain PhiX174), and the Siphoviridae (type strain Lambda) were the preferred candidate somatic coliphages as fecal indicator viruses in water, with the Microviridae (type strain PhiX174) the most resistant to these conditions overall. © 2011 Elsevier Ltd.",drinking water;surface water;article;coliphage;controlled study;environmental exposure;heat tolerance;high temperature;Microviridae;nonhuman;priority journal;survival rate;ultraviolet radiation;virus resistance;virus strain;water supply;water temperature;water treatment,"Lee, H. S.;Sobsey, M. D.",2011,,10.1016/j.watres.2011.04.024,0
1116,Genome-wide analysis of influenza viral RNA and nucleoprotein association,"Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments that are coated by viral nucleoprotein (NP) molecules. Classically, the interaction between NP and viral RNA (vRNA) is depicted as a uniform pattern of 'beads on a string'. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP), we identified the vRNA binding profiles of NP for two H1N1 IAV strains in virions. Contrary to the prevailing model for vRNA packaging, NP does not bind vRNA uniformly in the A/WSN/1933 and A/California/07/2009 strains, but instead each vRNA segment exhibits a unique binding profile, containing sites that are enriched or poor in NP association. Intriguingly, both H1N1 strains have similar yet distinct NP binding profiles despite extensive sequence conservation. Peaks identified by HITS-CLIP were verified as true NP binding sites based on insensitivity to DNA antisense oligonucleotide-mediated RNase H digestion. Moreover, nucleotide content analysis of NP peaks revealed that these sites are relatively G-rich and U-poor compared to the genome-wide nucleotide content, indicating an as-yet unidentified sequence bias for NP association in vivo. Taken together, our genome-wide study of NP-vRNA interaction has implications for the understanding of influenza vRNA architecture and genome packaging.",A VIRUS NUCLEOPROTEIN;SWINE-ORIGIN H1N1;RIBONUCLEOPROTEIN COMPLEXES;NUCLEOTIDE-RESOLUTION;MUTATION-RATES;AVIAN H5N1;HITS-CLIP;SEGMENTS;POLYMERASE;REASSORTMENT,"Lee, N.;Le Sage, V.;Nanni, A. V.;Snyder, D. J.;Cooper, V. S.;Lakdawala, S. S.",2017,Sep,,0
1117,First detection of novel enterovirus G recombining a torovirus papain‐like protease gene associated with diarrhoea in swine in South Korea,,,"Lee, S.;Lee, C.",2018,,,0
1118,Attenuated vaccines can recombine to form virulent field viruses,"Recombination between herpesviruses has been seen in vitro and in vivo under experimental conditions. This has raised safety concerns about using attenuated herpesvirus vaccines in human and veterinary medicine and adds to other known concerns associated with their use, including reversion to virulence and disease arising from recurrent reactivation of lifelong chronic infection. We used high-throughput sequencing to investigate relationships between emergent field strains and vaccine strains of infectious laryngotracheitis virus (ILTV, gallid herpesvirus 1). We show that independent recombination events between distinct attenuated vaccine strains resulted in virulent recombinant viruses that became the dominant strains responsible for widespread disease in Australian commercial poultry flocks. These findings highlight the risks of using multiple different attenuated herpesvirus vaccines, or vectors, in the same populations.","Animals;*Chickens;DNA, Viral/ge [Genetics];Genome, Viral;*Herpesviridae Infections/ve [Veterinary];Herpesviridae Infections/vi [Virology];*Herpesvirus 1, Gallid/ge [Genetics];Herpesvirus 1, Gallid/im [Immunology];*Herpesvirus 1, Gallid/py [Pathogenicity];Herpesvirus 1, Gallid/ph [Physiology];*Herpesvirus Vaccines;High-Throughput Nucleotide Sequencing;Molecular Sequence Data;Polymorphism, Single Nucleotide;*Poultry Diseases/vi [Virology];*Recombination, Genetic;Sequence Analysis, DNA;Specific Pathogen-Free Organisms;Vaccines, Attenuated;Virulence;Virus Replication;0 (DNA, Viral);0 (Herpesvirus Vaccines);0 (Vaccines, Attenuated)","Lee, S. W.;Markham, P. F.;Coppo, M. J.;Legione, A. R.;Markham, J. F.;Noormohammadi, A. H.;Browning, G. F.;Ficorilli, N.;Hartley, C. A.;Devlin, J. M.",2012,Jul 13,,0
1119,First complete genome sequence of infectious laryngotracheitis virus,"Background: Infectious laryngotracheitis virus (ILTV) is an alphaherpesvirus that causes acute respiratory disease in chickens worldwide. To date, only one complete genomic sequence of ILTV has been reported. This sequence was generated by concatenating partial sequences from six different ILTV strains. Thus, the full genomic sequence of a single (individual) strain of ILTV has not been determined previously. This study aimed to use high throughput sequencing technology to determine the complete genomic sequence of a live attenuated vaccine strain of ILTV.Results: The complete genomic sequence of the Serva vaccine strain of ILTV was determined, annotated and compared to the concatenated ILTV reference sequence. The genome size of the Serva strain was 152,628 bp, with a G + C content of 48%. A total of 80 predicted open reading frames were identified. The Serva strain had 96.5% DNA sequence identity with the concatenated ILTV sequence. Notably, the concatenated ILTV sequence was found to lack four large regions of sequence, including 528 bp and 594 bp of sequence in the UL29 and UL36 genes, respectively, and two copies of a 1,563 bp sequence in the repeat regions. Considerable differences in the size of the predicted translation products of 4 other genes (UL54, UL30, UL37 and UL38) were also identified. More than 530 single-nucleotide polymorphisms (SNPs) were identified. Most SNPs were located within three genomic regions, corresponding to sequence from the SA-2 ILTV vaccine strain in the concatenated ILTV sequence.Conclusions: This is the first complete genomic sequence of an individual ILTV strain. This sequence will facilitate future comparative genomic studies of ILTV by providing an appropriate reference sequence for the sequence analysis of other ILTV strains. © 2011 Lee et al; licensee BioMed Central Ltd.",genomic DNA;protein UL29;protein UL30;protein UL36;protein UL37;protein UL38;protein UL54;unclassified drug;viral protein;article;controlled study;DNA base composition;DNA sequence;gene dosage;gene identification;gene location;genome analysis;genome size;high throughput sequencing;Iltovirus;nonhuman;nucleotide sequence;open reading frame;RNA translation;sequence alignment;sequence homology;single nucleotide polymorphism;UL29 gene;UL30 gene;UL36 gene;UL37 gene;UL38 gene;UL54 gene;virus gene;virus genome;virus strain,"Lee, S. W.;Markham, P. F.;Markham, J. F.;Petermann, I.;Noormohammadi, A. H.;Browning, G. F.;Ficorilli, N. P.;Hartley, C. A.;Devlin, J. M.",2011,,10.1186/1471-2164-12-197,0
1120,Dicer-2- and Piwi-mediated RNA interference in Rift Valley fever virus-infected mosquito cells,"Rift Valley fever virus (RVFV) is a Phlebovirus (Bunyaviridae family) transmitted by mosquitoes. It infects humans and ruminants, causing dramatic epidemics and epizootics in Africa, Yemen, and Saudi Arabia. While recent studies demonstrated the importance of the nonstructural protein NSs as a major component of virulence in vertebrates, little is known about infection of mosquito vectors. Here we studied RVFV infection in three different mosquito cell lines, Aag2 cells from Aedes aegypti and U4.4 and C6/36 cells from Aedes albopictus. In contrast with mammalian cells, where NSs forms nuclear filaments, U4.4 and Aag2 cells downregulated NSs expression such that NSs filaments were never formed in nuclei of U4.4 cells and disappeared at an early time postinfection in the case of Aag2 cells. On the contrary, in C6/36 cells, NSs nuclear filaments were visible during the entire time course of infection. Analysis of virus-derived small interfering RNAs (viRNAs) by deep sequencing indicated that production of viRNAs was very low in C6/36 cells, which are known to be Dicer-2 deficient but expressed some viRNAs presenting a Piwi signature. In contrast, Aag2 and U4.4 cells produced large amounts of viRNAs predominantly matching the S segment and displaying Dicer-2 and Piwi signatures. Whereas 21-nucleotide (nt) Dicer-2 viRNAs were prominent during early infection, the population of 24- to 27-nt Piwi RNAs (piRNAs) increased progressively and became predominant later during the acute infection and during persistence. In Aag2 and U4.4 cells, the combined actions of the Dicer-2 and Piwi pathways triggered an efficient antiviral response permitting, among other actions, suppression of NSs filament formation and allowing establishment of persistence. In C6/36 cells, Piwi-mediated RNA interference (RNAi) appeared to be sufficient to mount an antiviral response against a secondary infection with a superinfecting virus. This study provides new insights into the role of Dicer and Piwi in mosquito antiviral defense and the development of the antiviral response in mosquitoes.","Aedes/im [Immunology];*Aedes/vi [Virology];Animals;*Argonaute Proteins/me [Metabolism];Cell Line;Down-Regulation;Gene Expression Profiling;High-Throughput Nucleotide Sequencing;*Insect Proteins/me [Metabolism];*RNA Helicases/me [Metabolism];*RNA Interference;RNA, Viral/bi [Biosynthesis];RNA, Viral/ge [Genetics];Rift Valley fever virus/ge [Genetics];*Rift Valley fever virus/im [Immunology];Viral Nonstructural Proteins/bi [Biosynthesis];0 (Argonaute Proteins);0 (Insect Proteins);0 (RNA, Viral);0 (Viral Nonstructural Proteins)","Leger, P.;Lara, E.;Jagla, B.;Sismeiro, O.;Mansuroglu, Z.;Coppee, J. Y.;Bonnefoy, E.;Bouloy, M.",2013,Feb,,0
1121,Exploring the contribution of bacteriophages to antibiotic resistance,"Bacteriophages (phages) are the most abundant and diverse biological entities in our planet. They infect susceptible bacterial hosts into which they either multiply or persist. In the latter case, phages can confer new functions to their hosts as a result of gene transfer, thus contributing to their adaptation (short-term) and evolution (long-term). In this regard, the role of phages on the dissemination of antibiotic resistance genes (ARGs) among bacterial hosts in natural environments has not yet been clearly resolved. Here, we carry out a comprehensive analysis of thirty-three viromes from different habitats to investigate whether phages harbor ARGs. Our results demonstrate that while human-associated viromes do not or rarely carry ARGs, viromes from non-human sources (e.g. pig feces, raw sewage, and freshwater and marine environments) contain a large reservoir of ARGs, thus pointing out that phages could play a part on the spread of antibiotic resistance. Given this, the role of phages should not be underestimated and it should be considered when designing strategies to tackle the global crisis of antibiotic resistance.",aminoglycoside antibiotic agent;beta lactam antibiotic;chloramphenicol derivative;fresh water;glycopeptide;macrolide;polypeptide;quinoline derived antiinfective agent;sulfanilamide;tetracycline derivative;antibiotic resistance;antibiotic resistance gene;article;bacterial gene;bacteriophage;bacterium contamination;controlled study;DNA determination;Enterobacteriaceae;environmental exposure;feces;gene sequence;genetic association;manure;marine environment;nonhuman;population abundance;sewage;species diversity;species habitat;Streptococcus;virus genome,"Lekunberri, I.;Subirats, J.;Borrego, C. M.;Balcázar, J. L.",2017,,10.1016/j.envpol.2016.11.059,0
1122,First identification of mammalian orthoreovirus type 3 in diarrheic pigs in Europe,Mammalian Orthoreoviruses 3 (MRV3) have been described in diarrheic pigs from USA and Asia. We firstly detected MRV3 in Europe (Italy) in piglets showing severe diarrhea associated with Porcine Epidemic Diarrhea. The virus was phylogenetically related to European reoviruses of human and bat origin and to US and Chinese pig MRV3.,article;cytopathogenic effect;epidemic;Europe;gene sequence;Mammalian orthoreovirus 3;nonhuman;phylogenetic tree;phylogeny;porcine epidemic diarrhea;reverse transcription polymerase chain reaction;sequence homology;transmission electron microscopy;virus detection;virus genome;virus identification;virus morphology,"Lelli, D.;Beato, M. S.;Cavicchio, L.;Lavazza, A.;Chiapponi, C.;Leopardi, S.;Baioni, L.;De Benedictis, P.;Moreno, A.",2016,,10.1186/s12985-016-0593-4,0
1123,Nucleotide sequence analysis and expression from recombinant vectors demonstrate that the attachment protein G of bovine respiratory syncytial virus is distinct from that of human respiratory syncytial virus,"Bovine respiratory syncytial (BRS) virus causes a severe lower respiratory tract disease in calves similar to the disease in children caused by human respiratory syncytial (HRS) virus. While there is antigenic cross-reactivity among the other major viral structural proteins, the major glycoprotein, G, of BRS virus and that of HRS virus are antigenically distinct. The G glycoprotein has been implicated as the attachment protein for HRS virus. We have carried out a molecular comparison of the glycoprotein G of BRS virus with the HRS virus counterparts. cDNA clones corresponding to the BRS virus G glycoprotein mRNA were isolated and analyzed by dideoxynucleotide sequencing. The BRS virus G mRNA contained 838 nucleotides exclusive of poly(A) and had a major open reading frame coding for a polypeptide of 257 amino acid residues. The deduced amino acid sequence of the BRS virus G polypeptide showed only 29 to 30% amino acid with the G protein of either the subgroup A or B HRS virus. However, despite this low level of identity, there were strong similarities in the predicted hydropathy profiles of the BRS virus and HRS virus G proteins. A cDNA molecule containing the complete BRS virus G major open reading frame was inserted into the thymidine kinase gene of vaccinia virus by homologous recombination, and a recombinant virus containing the BRS virus G protein gene was isolated. This recombinant virus expressed the BRS virus G protein, as demonstrated by Western immunoblot analysis and immunofluorescence of infected cells. The BRS virus G protein expressed from the recombinant vector was transported to and expressed on the surface of infected cells. Antisera to the BRS virus G protein made by using the recombinant vector to immunize animals recognized the BRS virus attachment protein but not the HRS virus G protein and vice versa, confirming the lack of antigenic cross-reactivity between the BRS and HRS virus attachment proteins. On the basis of the data presented here, we conclude that BRS virus should be classified within the genus Pneumovirus in a group separate from HRS virus and that it is no more closely related to HRS virus subgroup A than it is to HRS virus subgroup B.",virus glycoprotein;virus vector;article;cell culture;gene expression;human respiratory syncytial pneumovirus;molecular cloning;nonhuman;nucleotide sequence;priority journal;Human respiratory syncytial virus;virus attachment;virus recombinant,"Lerch, R. A.;Anderson, K.;Wertz, G. W.",1990,,,0
1124,Real-time PCR for simultaneous detection and genotyping of bovine viral diarrhea virus,"Since two genotypes of bovine viral diarrhea viruses (BVDV) occur in Belgian herds, their differentiation is important for disease surveillance. A quantitative real-time PCR assay was developed to detect and classify bovine viral diarrhea viruses in genotype I and II. A pair of primers specific for highly conserved regions of the 5′UTR and two TaqMan probes were designed. The FAM and VIC-labeled probe sequences differed by three nucleotides, allowing the differentiation between genotype I and II. The assay detectability of genotype I and II real-time PCR assay was 1000 and 100 copies, respectively. Highly reproducible data were obtained as the coefficients of variation of threshold cycle values in inter-runs were less than 2.2%. The correct classification of genotype I and II viruses was assessed by using reference strains and characterized field isolates of both genotypes. The application to clinical diagnosis was evaluated on pooled blood samples by post run measurement of the FAM- and VIC- associated fluorescence. The 100% agreement with the conventional RT-PCR method confirmed that this new technique could be used for routine detection of persistently infected immunotolerant animals. © 2003 Elsevier B.V. All rights reserved.",5' untranslated region;accuracy;article;blood sampling;Bovine viral diarrhea virus 1;control;diagnostic value;DNA probe;fluorescence;genotype;nonhuman;nucleotide sequence;priority journal;reproducibility;reverse transcription polymerase chain reaction;species differentiation;virus detection;virus isolation;virus strain;TaqMan,"Letellier, C.;Kerkhofs, P.",2003,,10.1016/j.jviromet.2003.08.004,0
1125,Detection and genotyping of bovine diarrhea virus by reverse transcription-polymerase chain amplification of the 5' untranslated region,"A reverse-transcription polymerase chain reaction (RT-PCR) was developed to differentiate the bovine diarrhea virus (BVDV) from other pestiviruses, and to determine the genotype of the BVDV isolates. For this purpose, primer pairs were selected in the 5' untranslated region (5'UTR). The primers B(E) and B2 were located in highly conserved regions and were pestivirus-specific. Two primer pairs named B3B4 and B5B6 were specific of BVDV genotypes I and II, respectively. With this technique, an amplification product of the expected size was obtained with either the B3B4 or the B5B6 primer pairs for the 107 BVDV isolates tested but not for BDV or CSFV. For some isolates that were grouped in the genotype II, sequence analysis of the PCR fragments confirmed their classification into this genotype.",complementary DNA;DNA fragment;primer RNA;animal cell;Bovine viral diarrhea virus 1;cattle disease;conference paper;differential diagnosis;gene amplification;genotype;nonhuman;Pestivirus;reverse transcription polymerase chain reaction;sequence analysis;virus classification,"Letellier, C.;Kerkhofs, P.;Wellemans, G.;Vanopdenbosch, E.",1999,,10.1016/s0378-1135(98)00267-3,0
1126,Avian Influenza Virus Surveillance in Wild Birds in Georgia: 2009-2011,"The Caucasus, at the border of Europe and Asia, is important for migration and over-wintering of wild waterbirds. Three flyways, the Central Asian, East Africa-West Asia, and Mediterranean/Black Sea flyways, converge in the Caucasus region. Thus, the Caucasus region might act as a migratory bridge for influenza virus transmission when birds aggregate in high concentrations in the post-breeding, migrating and overwintering periods. Since August 2009, we have established a surveillance network for influenza viruses in wild birds, using five sample areas geographically spread throughout suitable habitats in both eastern and western Georgia. We took paired tracheal and cloacal swabs and fresh feces samples. We collected 8343 swabs from 76 species belonging to 17 families in 11 orders of birds, of which 84 were real-time RT-PCR positive for avian influenza virus (AIV). No highly pathogenic AIV (HPAIV) H5 or H7 viruses were detected. The overall AIV prevalence was 1.6%. We observed peak prevalence in large gulls during the autumn migration (5.3-9.8%), but peak prevalence in Black-headed Gulls in spring (4.2-13%). In ducks, we observed increased AIV prevalence during the autumn post-moult aggregations and migration stop-over period (6.3%) but at lower levels to those observed in other more northerly post-moult areas in Eurasia. We observed another prevalence peak in the overwintering period (0.14-5.9%). Serological and virological monitoring of a breeding colony of Armenian Gulls showed that adult birds were seropositive on arrival at the breeding colony, but juveniles remained serologically and virologically negative for AIV throughout their time on the breeding grounds, in contrast to gull AIV data from other geographic regions. We show that close phylogenetic relatives of viruses isolated in Georgia are sourced from a wide geographic area throughout Western and Central Eurasia, and from areas that are represented by multiple different flyways, likely linking different host sub-populations. © 2013 Lewis et al.",article;avian influenza virus;bird;breeding;disease surveillance;DNA sequence;feces analysis;influenza;nonhuman;nucleotide sequence;phylogenetic tree;real time polymerase chain reaction;reverse transcription polymerase chain reaction;seasonal variation;serology;species habitat;virus concentration;virus detection;virus isolation;virus transmission;virus virulence;wild species,"Lewis, N. S.;Javakhishvili, Z.;Russell, C. A.;Machablishvili, A.;Lexmond, P.;Verhagen, J. H.;Vuong, O.;Onashvili, T.;Donduashvili, M.;Smith, D. J.;Fouchier, R. A. M.",2013,,10.1371/journal.pone.0058534,0
1127,The evolution of foot-and-mouth disease virus: Impacts of recombination and selection,"Foot-and-mouth disease virus is an economically important animal virus that exhibits extensive genetic and antigenic heterogeneity. To examine the evolutionary forces that have influenced the population dynamics of foot-and-mouth disease virus, individual genes and the coding genomes for the Eurasian (Asia1, A, C, and O) serotypes were examined for phylogenetic relationships, recombination, genetic diversity and selection. Our analyses demonstrate that paraphyletic relationships among serotypes are not as prevalent as previously proposed and suggest that convergent evolution might be obscuring phylogenetic relationships. We provide evidence that identification of recombinant sequences and recombination breakpoint patterns among and within serotypes are heavily dependent on the level of genetic diversity and convergent characters present in a particular data set as well as the methods used to detect recombination. Here, we also investigate the impact of adaptive positive selection on the capsid proteins and the non-structural genes 2B, 2C, 3A, and 3Cpro to identify genome regions involved in genetic diversity and antigenic variation. Two different categories of positive selection at the amino acid level were examined; conservative (stabilizing) selection that maintains particular phenotypic properties of an amino acid residue and radical (destabilizing), and selection that dramatically alters the phenotype and potentially the functional and/or structural features of the protein. Approximately, 29% of residues in the capsid proteins were under positive selection. Of those, 64% were under the influence of destabilizing selection, 80% were under the influence of stabilizing selection, and 44% had phenotypic properties influenced by both selection types. The majority of residues under selection (74%) were located outside of known antigenic sites; suggestive of additional uncharacterized epitopes and genomic regions involved in antigenic drift. © 2008 Elsevier B.V. All rights reserved.",amino acid;capsid protein;nonstructural protein 2B;nonstructural protein 2C;nonstructural protein 3A;nonstructural protein 3c;unclassified drug;viral protein;antigenic variation;article;controlled study;Foot and mouth disease virus;genetic selection;genetic variability;molecular evolution;molecular phylogeny;nonhuman;nucleotide sequence;paraphyly;phenotype;population dynamics;priority journal;protein function;protein structure;sequence alignment;sequence analysis;serotype;virus genome;virus recombination,"Lewis-Rogers, N.;McClellan, D. A.;Crandall, K. A.",2008,,10.1016/j.meegid.2008.07.009,0
1128,Close relationship between the 2009 H1N1 virus and South Dakota AIV strains,"Although previous publications suggest the 2009 pandemic influenza A (H1N1) virus was reassorted from swine viruses of North America and Eurasia, the immediate ancestry still remains elusive due to the big evolutionary distance between the 2009 H1N1 virus and the previously isolated strains. Since the unveiling of the 2009 H1N1 influenza, great deal of interest has been drawn to influenza, consequently a large number of influenza virus sequences have been deposited into the public sequence databases. Blast analysis demonstrated that the recently submitted 2007 South Dakota avian influenza virus strains and other North American avian strains contained genetic segments very closely related to the 2009 H1N1 virus, which suggests these avian influenza viruses are very close relatives of the 2009 H1N1 virus. Phylogenetic analyses also indicate that the 2009 H1N1 viruses are associated with both avian and swine influenza viruses circulating in North America. Since the migrating wild birds are preferable to pigs as the carrier to spread the influenza viruses across vast distances, it is very likely that birds played an important role in the inter-continental evolution of the 2009 H1N1 virus. It is essential to understand the evolutionary route of the emerging influenza virus in order to find a way to prevent further emerging cases. This study suggests the close relationship between 2009 pandemic virus and the North America avian viruses and underscores enhanced surveillance of influenza in birds for understanding the evolution of the 2009 pandemic influenza. © 2011 Wuhan Institute of Virology, CAS and Springer-Verlag Berlin Heidelberg.",article;avian influenza virus;bird;Influenza A virus (H1N1);nonhuman;North America;nucleotide sequence;phylogeny;swine influenza virus;unindexed sequence;viral genetics;virus genome;virus strain,"Li, C.;An, X. P.;Mi, Z. Q.;Liu, D. B.;Jiang, H. H.;Pan, B.;Wang, S.;Chen, B.;Tong, Y. G.",2011,,10.1007/s12250-011-3149-6,0
1129,Rumen microbiome associated with feed efficiency and host genetics in beef cattle,,,"Li, F.",2017,,,0
1130,"Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3","Porcine circovirus 3 (PCV3) is a novel virus associated with acute PDNS (porcine dermatitis and nephropathy syndrome)-like clinical signs identified by metagenomic sequencing from swine. Its high occurrence may pose a potential threat to the swine industry worldwide. The processes resulting in the emergence and spread of PCV3 remain poorly understood. Herein, the possible origin, genotypes, and evolutionary dynamics of PCV3 based on available genomic sequences are determined. The closest ancestor of PCV3 is found to be within the clade 1 bat CVs. Using different phylogenetic methods, two major genotypes are identified, PCV3a and PCV3b. It is found that the effective population size of PCV3 increased rapidly during late 2013 to early 2014 and this is associated with the diversification of PCV3a and PCV3b. A relatively high effective reproductive number (Re) value and higher evolutionary rate were found compared to other single-stranded DNA viruses, and positive selection on codons 122 and 320 (24 of ORF2) is identified. It is hypothesized that this, together with the prediction of a potential change of an antigenic epitope at position 320, might have allowed PCV3 to escape from the host immune response. Overall, this study has important implications for understanding the ongoing PCV3 cases worldwide and will guide future efforts to develop effective preventive and control measures.",,"Li, G.;He, W.;Zhu, H.;Bi, Y.;Wang, R.;Xing, G.;Zhang, C.;Zhou, J.;Yuen, K. Y.;Gao, G. F.;Su, S.",2018,Sep,,0
1131,Comparative analysis of the genes UL1 through UL7 of the duck enteritis virus and other herpesviruses of the subfamily Alphaherpesvirinae,"The nucleotide sequences of eight open reading frames (ORFs) located at the 5′ end of the unique long region of the duck enteritis virus (DEV) Clone-03 strain were determined. The genes identified were designated UL1, UL2, UL3, UL4, UL5, UL6 and UL7 homologues of the herpes simplex virus 1 (HSV-1). The DEV UL3.5 located between UL3 and UL4 had no homologue in the HSV-1. The arrangement and transcription orientation of the eight genes were collinear with their homologues in the HSV-1. Phylogenetic trees were constructed based on the alignments of the deduced amino acids of eight proteins with their homologues in 12 alpha-herpesviruses. In the UL1, UL3, UL3.5, UL5 and UL7 proteins trees, the branches were more closely related to the genus Mardivirus. However, the UL2, UL4, and UL6 proteins phylogenetic trees indicated a large distance from Mardivirus, indicating that the DEV evolved differently from other viruses in the subfamily Alphaherpesvirinae and formed a single branch within this subfamily. Copyright © 2009, Sociedade Brasileira de Genética.",protein UL;protein UL1;protein UL2;protein UL3;protein UL4;protein UL5;protein UL6;protein UL7;unclassified drug;viral protein;article;comparative study;duck enteritis virus;genetic analysis;genetic transcription;Herpesviridae;molecular evolution;nonhuman;nucleotide sequence;open reading frame;phylogenetic tree;species difference;virus gene;virus genome;virus strain,"Li, H.;Liu, S.;Han, Z.;Shao, Y.;Chen, S.;Kong, X.",2009,,,0
1132,"Characterization of the genes encoding UL24, TK and gH proteins from duck enteritis virus (DEV): A proof for the classification of DEV","Duck enteritis virus (DEV) is classified to the family Herpesviridae, but has not been grouped into any genus so far. Four overlapped fragments were amplified from the DEV genome with polymerase chain reaction (PCR). The assembled length of the four fragments was 6202 bp, which contained the genes encoding unique long (UL) 24, thymidine kinase (TK) and glycoprotein H (gH) proteins. The UL24 overlapped with TK by 64 nucleotides (nt), in a head-to-head transcription orientation, and the TK and gH had the same transcription orientation. The comparison of amino acid sequences of these 3 deduced DEV proteins with other 12 alphaherpesviruses displayed 5 highly conserved sites in the UL24, as well as another 5 consensus regions in the TK and 4 consensus regions in the gH. The RNA polymerase II transcriptional control elements were identified in all the UL24, TK and gH of DEV. These elements included core promoters, TATA motifs and polyadenylation sites. Phylogenetic analysis for the genetic classification of DEV in the Alphaherpesvirinae subfamily with other 12 alphaherpesviruses was computed. The result showed that DEV was more closely related to avian herpesviruses, except infectious laryngotracheitis virus (ILTV), than to other alphaherpesviruses. Conclusively, according to the phylogenesis-based analysis and the homology comparison of functional domains of UL24, TK and gH, DEV should be classified to a separate genus of the Alphaherpesvirinae subfamily in the family Herpesviridae. © 2006 Springer Science+Business Media, LLC.",gh protein;RNA polymerase II;tk protein;ul24 protein;unclassified drug;viral protein;amino acid sequence;article;comparative study;consensus sequence;controlled study;duck enteritis virus;genetic analysis;genetic transcription;Herpesviridae;nonhuman;nucleotide sequence;phylogeny;polyadenylation;priority journal;promoter region;protein domain;sequence homology;transcription regulation;virus classification;virus gene;virus strain,"Li, H.;Liu, S.;Kong, X.",2006,,10.1007/s11262-005-0060-6,0
1133,"Avian Influenza Virus Subtype H9N2 Affects Intestinal Microbiota, Barrier Structure Injury, and Inflammatory Intestinal Disease in the Chicken Ileum","Avian influenza virus subtype H9N2 (H9N2 AIV) has caused significant losses to the poultry industry due to the high mortality associated with secondary infections attributable to E. coli. This study tries to address the underlying secondary mechanisms after H9N2 AIV infection. Initially, nine day-old specific pathogen-free chickens were assigned to control (uninfected) and H9N2-infected groups, respectively. Using Illumina sequencing, histological examination, and quantitative real-time PCR, it was found that H9N2 AIV caused intestinal microbiota disorder, injury, and inflammatory damage to the intestinal mucosa. Notably, the genera Escherichia, especially E. coli, significantly increased (p < 0.01) at five days post-infection (dpi), while Lactobacillus, Enterococcus, and other probiotic organisms were significantly reduced (p < 0.01). Simultaneously, the mRNA expression of tight junction proteins (ZO-1, claudin 3, and occludin), TFF2, and Muc2 were significantly reduced (p < 0.01), indicating the destruction of the intestinal epithelial cell tight junctions and the damage of mucin layer construction. Moreover, the mRNA expression of proinflammatory cytokines IFN-gamma, IL-22, IFN-alpha, and IL-17A in intestinal epithelial cells were significantly upregulated, resulting in the inflammatory response and intestinal injury. Our findings may provide a theoretical basis for observed gastroenteritis-like symptoms such as diarrhea and secondary E. coli infection following H9N2 AIV infection.","Animals;*Chickens/vi [Virology];Cytokines/ge [Genetics];Cytokines/me [Metabolism];DNA, Bacterial/ge [Genetics];Enteritis/me [Metabolism];Escherichia coli/me [Metabolism];*Gastrointestinal Microbiome;*Influenza A Virus, H9N2 Subtype/ph [Physiology];Influenza in Birds/im [Immunology];Influenza in Birds/me [Metabolism];*Influenza in Birds/mi [Microbiology];*Intestinal Mucosa/in [Injuries];Metagenomics;RNA, Messenger/me [Metabolism];RNA, Ribosomal, 16S/ge [Genetics];Specific Pathogen-Free Organisms;0 (Cytokines);0 (DNA, Bacterial);0 (RNA, Messenger);0 (RNA, Ribosomal, 16S)","Li, H.;Liu, X.;Chen, F.;Zuo, K.;Wu, C.;Yan, Y.;Chen, W.;Lin, W.;Xie, Q.",2018,05 18,,0
1134,Fowl adenovirus species C serotype 4 is attributed to the emergence of hepatitis-hydropericardium syndrome in chickens in China,"Since July in 2015, an emerging infectious disease of Hepatitis-Hydropericardium syndrome (HHS) was prevalent in chicken flocks in China. To confirm the causative agent and investigate the epidemiology of the disease, a total of 38 chicken flocks including 187 samples from Jilin, Liaoning, Heilongjiang, Henan, Anhui, Hubei, Jiangxi, Xinjiang, Shandong and Hunan provinces in China were collected and determined by PCR detection, sequencing, phylogenetic analysis and virus isolation. 81 samples (positive rate of samples, 81/187, 43.3%) distributed in 33 chicken flocks (positive rate of chicken flocks, 33/38, 86.8%) were detected to be positive for fowl adenovirus (FAdV) by PCR method, of which 30 were determined as FAdV species C, 41 were species D, 9 were species E and 1 was uncertain for the viral species by phylogenetic analysis, implicating that at least three species (C, D and E) of FAdVs were prevalent in China and the species C and D were predominantly the prevalent viral strains. Interestingly, our results indicated that two types of FAdVs (C and D) co-existed in one flock, resulting in complex condition for the prevalence of the disease. In addition, 13 viral strains of FAdV-C were isolated from different geographic areas and one of the isolates from Henan province, designated HN/151025 strain, was inoculated into 40-day-old specific pathogen free chickens via intramuscular or oral route to evaluate the pathogenicity. It was found that 90% (9/10) chickens died in the intramuscular injection group and 30% (3/10) birds died in the oral route infection group after challenge. Histopathology examination displayed that the pathology confined to liver, kidney, spleen, and heart. These results indicated that the virus was a highly virulent strain.",adenovirus infection;animal experiment;animal model;animal tissue;antibody response;article;Aviadenovirus;bird disease;chicken;China;controlled study;embryo;Fowl adenovirus species C serotype 4;Fowl adenovirus species D;Fowl adenovirus species E;gene sequence;geographic distribution;hepatitis hydropericardium syndrome;histopathology;mixed infection;nonhuman;phylogeny;polymerase chain reaction;prevalence;priority journal;seroconversion;viremia;virus isolation;virus shedding;virus virulence,"Li, H.;Wang, J.;Qiu, L.;Han, Z.;Liu, S.",2016,,10.1016/j.meegid.2016.09.006,0
1135,"Diagnosis of Peste des Petits Ruminants in Wild and Domestic Animals in Xinjiang, China, 2013–2016","Peste des petits ruminants viruses (PPRVs) re-emerged in China at the end of 2013 and then spread rapidly into 22 provinces through movement of live goats and sheep. In this study, 96 samples of domestic animals and 13 samples of wildlife were analysed for the presence of PPRV infection by ELISA or RT-PCR. Of 96 samples from sheep and goats, 91 were PPRV positive, whereas all of the 13 samples from three wild species, Capra ibex (Capra ibex sibirica), argali (Ovis ammon) and Goitered gazelle (Gazella subgutturosa), were found to be positive. Five wildlife-origin isolates from the above samples were identified as the lineage IV by a multiple alignment of the partial sequences in N gene.",animal experiment;animal tissue;article;Capra ibex;China;domestic animal;domestic sheep;enzyme linked immunosorbent assay;gazelle;gene sequence;geographic distribution;goat;immune response;nonhuman;nucleotide sequence;Peste-des-petits-ruminants virus;phylogeny;real time polymerase chain reaction;RNA virus infection;viral clearance;virus diagnosis;virus isolation;virus virulence;wild animal,"Li, J.;Li, L.;Wu, X.;Liu, F.;Zou, Y.;Wang, Q.;Liu, C.;Bao, J.;Wang, W.;Ma, W.;Lin, H.;Huang, J.;Zheng, X.;Wang, Z.",2017,,10.1111/tbed.12600,0
1136,Analysis of microRNAs expression profiles in madin-darby bovine kidney cells infected with caprine parainfluenza virus type 3,"Caprine parainfluenza virus type 3 (CPIV3) is a newly emerging pathogenic respiratory agent infecting both young and adult goats, and it was identified in eastern China in 2013. Cellular microRNAs (miRNAs) have been reported to be important modulators of the intricate virus-host interactions. In order to elucidate the role of miRNAs in madin-darby bovine kidney (MDBK) cells during CPIV3 infection. In this study, we performed high-throughput sequencing technology to analyze small RNA libraries in CPIV3-infected and mock-infected MDBK cells. The results showed that a total of 249 known and 152 novel candidate miRNAs were differentially expressed in MDBK cells after CPIV3 infection, and 22,981 and 22,572 target genes were predicted, respectively. In addition, RT-qPCR assay was used to further confirm the expression patterns of 13 of these differentially expressed miRNAs and their mRNA targets. Functional annotation analysis showed these up- and downregulated target genes were mainly involved in MAPK signaling pathway, Jak-STAT signaling pathway, Toll-like receptor signaling pathway, p53 signaling pathway, focal adhesion, NF-kappa B signaling pathway, and apoptosis, et al. To our knowledge, this is the first report of the comparative expression of miRNAs in MDBK cells after CPIV3 infection. Our finding provides information concerning miRNAs expression profile in response to CPIV3 infection, and offers clues for identifying potential candidates for antiviral therapies against CPIV3.",immunoglobulin enhancer binding protein;Janus kinase;messenger RNA;microRNA;mitogen activated protein kinase;protein p53;STAT protein;toll like receptor;transfer RNA;animal cell;apoptosis;article;caprine parainfluenza virus 3;controlled study;down regulation;focal adhesion;gene expression profiling;gene targeting;high throughput sequencing;Human parainfluenza virus 3;JAK-STAT signaling;MAPK signaling;MDBK cell line;nonhuman;Parainfluenza virus infection;Paramyxovirinae;reverse transcription polymerase chain reaction;TLR signaling;upregulation,"Li, J.;Mao, L.;Li, W.;Hao, F.;Zhong, C.;Zhu, X.;Ji, X.;Yang, L.;Zhang, W.;Liu, M.;Jiang, J.",2018,,10.3389/fcimb.2018.00093,0
1137,"Metagenomic identification, genetic characterization and genotyping of porcine sapoviruses","Sapoviruses (SaVs), belonging to the genus Sapovirus of the family Caliciviridae, were known as the enteric pathogen causing acute gastroenteritis. SaVs have been detected in humans and several animals including pigs and some porcine SaVs showed close sequence relationship with human strains suggesting the possibility of interspecies transmission. Here, we sequenced the genomes of two porcine SaVs (with strain names of p38 and SH1703) using the metagenomic analyses and traditional RT-PCR methods. Phylogenetic trees were constructed based on the complete genome, the full-length VP 1 nucleotide and amino acid sequences to group those two strains. The two porcine SaV strains, p38 and SH1703, detected in this study, were classified as genogroup III and genogroup VII, respectively. These two strains showed similar genomic organization with that of other SaVs. We firstly divided SaVs into 51 genotypes within 19 genogroups. Our data are helpful for genetic characterization and classification of newly detected SaVs worldwide.",amino acid sequence;article;China;gene sequence;genetic analysis;genetic identification;genotype;metagenomics;nonhuman;nucleotide sequence;phylogenetic tree;priority journal;real time polymerase chain reaction;Sapovirus;virus characterization;virus detection;virus strain,"Li, J.;Zhang, W.;Cui, L.;Shen, Q.;Hua, X.",2018,,10.1016/j.meegid.2018.04.034,1
1138,Faecal shedding of rotavirus vaccine in Chinese children after vaccination with Lanzhou lamb rotavirus vaccine,"Lanzhou lamb rotavirus vaccine (LLR) is an oral live attenuated vaccine first licensed in China in 2000. To date, > 60 million doses of LLR have been distributed to children. However, very little is known about faecal shedding of LLR in children. Therefore, faecal samples (n = 1,184) were collected from 114 children for 15 days post-vaccination in September-November 2011/2012. Faecal shedding and viral loads were determined by an enzyme immunoassay kit (EIA) and real-time RT-PCR. The complete genome was sequenced and the vaccine strain was isolated by culture in MA104 cells. Approximately 14.0% (16/114) of children had rotavirus-positive samples by EIA for at least 1 day post-vaccination. Viral loads in EIA-positive samples ranged from < 1.0 × 103 to 1.9 × 108 copies/g. Faecal shedding occurred as early as post-vaccination day 2 and as late as post-vaccination day 13 and peaked on post-vaccination day 5-10. One LLR strain was isolated by culture in MA104 cells. Sequence analysis showed 99% identity with LLR prototype strain. Faecal shedding of LLR in stool is common within 15 days of LLR vaccination, indicating vaccine strains can replicate in human enteric tissues.",Rotavirus vaccine;animal;cell line;China;Chlorocebus aethiops;epithelium cell;feces;female;genetics;high throughput sequencing;human;immunology;infant;male;mass immunization;preschool child;Rotavirus;Rotavirus infection;sheep;statistics and numerical data;virology;virus genome;virus load;virus replication,"Li, J. S.;Cao, B.;Gao, H. C.;Li, D.;Lin, L.;Li, L. L.;Liu, N.;Duan, Z. J.",2018,,10.1038/s41598-018-19469-w,0
1139,Partial nucleotide sequencing of hepatitis E viruses detected in sera of patients with hepatitis E from 14 cities in China,"Objective. To investigate the genotypes of hepatitis E viruses (HEV) detected in sera of patients from different regions of China. Methods. The partial genome (nt6461-6860, nt5994-6294) of open reading frame 2 (ORF2) of 45 HEV strains detected from 14 cities of China was amplified and sequenced using polymerase chain reaction (PCR) and direct sequencing. Results. Forty-one of 45 strains (91%) share the same genotype with HEV Burma strain (B), with nucleotide identities higher than 98% with the representative HEV Chinese strain. Only 4 HEV strains are significantly divergent from the 3 prototype strains of HEV, with nucleotide identities of 77% - 80% with HEV Burmese/Chinese strain, 74% - 76% with Mexican strain and 74% - 77% with the newly discovered HEV US/swine strain, respectively. Phylogenetic analysis suggests that these 4 strains may represent 2 different subtypes that belong to a novel genotype of HEV, which is significantly divergent from the prototype Mexico, Burmese and US/swine strains. Conclusion. Among patients with hepatitis E in China, most are infected by the Chinese prototype HEV, and only a small part by the new genotype HEV.",immunoglobulin G;immunoglobulin M;nucleotide;article;blood analysis;China;clinical article;controlled study;gene amplification;gene sequence;genotype;hepatitis E;Hepatitis E virus;human;Mexico;Myanmar;nonhuman;nucleotide sequence;open reading frame;phylogeny;polymerase chain reaction;United States;virus detection;virus genome;virus strain,"Li, K.;Zhuang, H.;Zhu, W.",2002,,,0
1140,Identification and genomic analysis of two duck-origin Tembusu virus strains in southern China,"Egg-laying duck flocks in Guangdong province, southern China, have been suffering a widely spreading infectious disease with abrupt egg drops and death since the winter of 2010. However, the causative pathogen was not known. We obtained two independent virus isolates named FS and JM from the diseased layer duck flocks and identified them as duck-origin Tembusu virus by PCR detection, sequencing the entire length of the open reading frames (ORFs). The two isolates FS and JM shared high sequence similarity to the isolates of duckorigin Tembusu virus that was first emerged in eastern China in April 2010. Blast analysis shows that the whole ORF sequences of FS and JM have the highest similarity ([99 %) to BYD-1(the first reported duck-origin Tembusu virus) and JS804 (the first reported goose-origin Tembusu virus), indicating that the full-length genomes were highly conserved in waterfowl-origin Tembusu viruses. The present study suggests that duck-origin Tembusu viruses have spread fast from eastern China to southern China, causing widely spreading infections. The high conservation of duck-origin Tembusu virus strains provides the genomic basis for choosing the strains for vaccine preparation for better protection against this new virus infection. © Springer Science+Business Media, LLC 2012.",virus envelope protein;animal tissue;article;China;duck;duck origin Tembusu virus;embryo;envelope gene;female;Flavivirus;Flavivirus infection;genetic conservation;genome analysis;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;reverse transcription polymerase chain reaction;sequence homology;virus detection;virus genome;virus identification;virus isolation;virus strain,"Li, L.;An, H.;Sun, M.;Dong, J.;Yuan, J.;Hu, Q.",2012,,10.1007/s11262-012-0753-6,0
1141,Virome analysis of antiretroviral-treated HIV patients shows no correlation between T-cell activation and anelloviruses levels,,,"Li, L.;Deng, X.;Costa, A. C. Da;Bruhn, R.;Deeks, S. G.",2015,,,0
1142,Divergent astrovirus associated with neurologic disease in cattle,"Using viral metagenomics of brain tissue from a young adult crossbreed steer with acute onset of neurologic disease, we sequenced the complete genome of a novel astrovirus (BoAstV-NeuroS1) that was phylogenetically related to an ovine astrovirus. In a retrospective analysis of 32 cases of bovine encephalitides of unknown etiology, 3 other infected animals were detected by using PCR and in situ hybridization for viral RNA. Viral RNA was restricted to the nervous system and detected in the cytoplasm of affected neurons within the spinal cord, brainstem, and cerebellum. Microscopically, the lesions were of widespread neuronal necrosis, microgliosis, and perivascular cuffing preferentially distributed in gray matter and most severe in the cerebellum and brainstem, with increasing intensity caudally down the spinal cord. These results suggest that infection with BoAstV-NeuroS1 is a potential cause of neurologic disease in cattle.",animal tissue;article;Astroviridae;astrovirus infection;bioinformatics;BoAstV NeuroS1;bovine;controlled study;disease association;electron microscopy;encephalomyelitis;gene sequence;genome;histology;immunohistochemistry;in situ hybridization;metagenomics;necrosis;neurologic disease;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;retrospective study;reverse transcription polymerase chain reaction;transmission electron microscopy;ultrastructure,"Li, L.;Diab, S.;McGraw, S.;Barr, B.;Traslavina, R.;Higgins, R.;Talbot, T.;Blanchard, P.;Rimoldi, G.;Fahsbender, E.;Page, B.;Phan, T. G.;Wang, C.;Deng, X.;Pesavento, P.;Delwart, E.",2013,,10.3201/eid1909.130682,1
1143,Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces,"Circoviruses are known to infect birds and pigs and can cause a wide range of severe symptoms with significant economic impact. Using viral metagenomics, we identified circovirus-like DNA sequences and characterized 15 circular viral DNA genomes in stool samples from humans in Pakistan, Nigeria, Tunisia, and the United States and from wild chimpanzees. Distinct genomic features and phylogenetic analysis indicate that some viral genomes were part of a previously unrecognized genus in the Circoviridae family we tentatively named ""Cyclovirus"" whose genetic diversity is comparable to that of all the known species in the Circovirus genus. Circoviridae detection in the stools of U.S. adults was limited to porcine circoviruses which were also found in most U.S. pork products. To determine whether the divergent cycloviruses found in non-U.S. human stools were of dietary origin, we genetically compared them to the cycloviruses in muscle tissue samples of commonly eaten farm animals in Pakistan and Nigeria. Limited genetic overlap between cycloviruses in human stool samples and local cow, goat, sheep, camel, and chicken meat samples indicated that the majority of the 25 Cyclovirus species identified might be human viruses. We show that the genetic diversity of small circular DNA viral genomes in various mammals, including humans, is significantly larger than previously recognized, and frequent exposure through meat consumption and contact with animal or human feces provides ample opportunities for cyclovirus transmission. Determining the role of cycloviruses, found in 7 to 17% of non-U.S. human stools and 3 to 55% of non-U.S. meat samples tested, in both human and animal diseases is now facilitated by knowledge of their genomes. Copyright © 2010, American Society for Microbiology. All Rights Reserved.",circular DNA;article;camel;chicken;chimpanzee;Circoviridae;controlled study;cow;DNA sequence;economic aspect;farm animal;feces analysis;female;genetic variability;geographic distribution;goat;human;meat;Nigeria;nonhuman;nucleotide sequence;open reading frame;Pakistan;priority journal;sheep;viral genetics;virus infection,"Li, L.;Kapoor, A.;Slikas, B.;Bamidele, O. S.;Wang, C.;Shaukat, S.;Masroor, M. A.;Wilson, M. L.;Ndjango, J. B. N.;Peeters, M.;Gross-Camp, N. D.;Muller, M. N.;Hahn, B. H.;Wolfe, N. D.;Triki, H.;Bartkus, J.;Zaidi, S. Z.;Delwart, E.",2010,,10.1128/jvi.02109-09,0
1144,A gyrovirus infecting a sea bird,"We characterized the genome of a highly divergent gyrovirus (GyV8) in the spleen and uropygial gland tissues of a diseased northern fulmar (Fulmarus glacialis), a pelagic bird beached in San Francisco, California. No other exogenous viral sequences could be identified using viral metagenomics. The small circular DNA genome shared no significant nucleotide sequence identity, and only 38-42 % amino acid sequence identity in VP1, with any of the previously identified gyroviruses. GyV8 is the first member of the third major phylogenetic clade of this viral genus and the first gyrovirus detected in an avian species other than chicken.",animal;bird;bird disease;Circoviridae infection;classification;genetics;Gyrovirus;isolation and purification;molecular genetics;phylogeny;veterinary medicine;virology;virus genome,"Li, L.;Pesavento, P. A.;Gaynor, A. M.;Duerr, R. S.;Phan, T. G.;Zhang, W.;Deng, X.;Delwart, E.",2015,,10.1007/s00705-015-2468-1,0
1145,Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses,,,"Li, L.;Victoria, J. G.;Wang, C.;Jones, M.;Fellers, G. M.",2010,,,0
1146,Isolation and genetic analysis revealed no predominant new strains of avian infectious bronchitis virus circulating in South China during 2004-2008,"Twenty-seven strains of avian infectious bronchitis virus (IBV) were isolated from dead or diseased chickens at different chicken farms in South China during 2004-2008, of which the S1 gene was sequenced. Phylogenetic analysis of the S1 gene sequences of the isolated 27 strains together with 29 strains published in Genbank revealed that all IBV strains except for one isolated and one published were clustered into six distinct genotypes I-VI. 26 isolated strains belong to genotypes I, II, and III, forming a big phylogenetic branch without new predominant strains, whereas all five vaccine strains belong to genotype V that is evolutionarily distant from genotypes I, II, and III. The study of the protease cleavage motif within the S1 protein found 12 different cleavage motifs, of which 3 motifs are shared by both isolated and published strains, 2 motifs unique to isolated strains, and 7 motifs unique to published strains, further bolstering the notion of no new predominant strains. Alignment analysis of the S1 amino acid sequences indicated that the amino acid substitutions, insertions, and deletions are polymorphic and diverse, showing no sign of predominant genetic changes among the isolated strains. Taken together, there was no predominant new strain circulating in South China during 2004-2008. Nonetheless, circulating IBV strains have been continuously evolving with genetic compositions distant from vaccine strains; this explains why there have been constant but infrequent outbreaks in commercial flocks in South China during 2004-2008. Furthermore, in order to safe guard against the sudden emergence of new predominant strains, continuing surveillance of IBV strains circulating in the field is of extreme importance. © 2009 Elsevier B.V.",proteinase;amino acid sequence;amino acid substitution;article;Avian infectious bronchitis virus;chicken;China;embryo;gene deletion;gene insertion;gene sequence;genetic analysis;genotype;nonhuman;nucleotide sequence;phylogeny;protein cleavage;protein motif;sequence alignment;sequence analysis;virus isolation,"Li, L.;Xue, C.;Chen, F.;Qin, J.;Xie, Q.;Bi, Y.;Cao, Y.",2010,,10.1016/j.vetmic.2009.11.022,0
1147,Exploring the virome of diseased horses,"Metagenomics was used to characterize viral genomes in clinical specimens of horses with various organ-specific diseases of unknown aetiology. A novel parvovirus as well as a previously described hepacivirus closely related to human hepatitis C virus and equid herpesvirus 2 were identified in the cerebrospinal fluid of horses with neurological signs. Four co-infecting picobirnaviruses, including an unusual genome with fused RNA segments, and a divergent anellovirus were found in the plasma of two febrile horses. A novel cyclovirus genome was characterized from the nasal secretion of another febrile animal. Lastly, a small circular DNA genome with a Rep gene, from a virus we called kirkovirus, was identified in the liver and spleen of a horse with fatal idiopathic hepatopathy. This study expands the number of viruses found in horses, and characterizes their genomes to assist future epidemiological studies of their transmission and potential association with various equine diseases.",PARVOVIRUS B19 INFECTION;VIRAL METAGENOMICS;RESPIRATORY-TRACT;GENOGROUP I;PORCINE PARVOVIRUS;GENETIC DIVERSITY;FECAL VIROME;TT;VIRUSES;IDENTIFICATION;PICOBIRNAVIRUSES,"Li, L. L.;Giannitti, F.;Low, J.;Keyes, C.;Ullmann, L. S.;Deng, X. T.;Aleman, M.;Pesavento, P. A.;Pusterla, N.;Delwart, E.",2015,Sep,,0
1148,A novel bocavirus in canine liver,"Background: Bocaviruses are classified as a genus within the Parvoviridae family of single-stranded DNA viruses and are pathogenic in some mammalian species. Two species have been previously reported in dogs, minute virus of canines (MVC), associated with neonatal diseases and fertility disorders; and Canine bocavirus (CBoV), associated with respiratory disease. Findings: In this study using deep sequencing of enriched viral particles from the liver of a dog with severe hemorrhagic gastroenteritis, necrotizing vasculitis, granulomatous lymphadenitis and anuric renal failure, we identified and characterized a novel bocavirus we named Canine bocavirus 3 (CnBoV3). The three major ORFs of CnBoV3 (NS1, NP1 and VP1) shared less than 60% aa identity with those of other bocaviruses qualifying it as a novel species based on ICTV criteria. Inverse PCR showed the presence of concatemerized or circular forms of the genome in liver. Conclusions: We genetically characterized a bocavirus in a dog liver that is highly distinct from prior canine bocaviruses found in respiratory and fecal samples. Its role in this animal's complex disease remains to be determined.",Canine bocavirus 3;Episome;Coinfection;BOVINE PARVOVIRUS;MINUTE VIRUS;VIRAL FLORA;IDENTIFICATION;VIROME,"Li, L. L.;Pesavento, P. A.;Leutenegger, C. M.;Estrada, M.;Coffey, L. L.;Naccache, S. N.;Samayoa, E.;Chiu, C.;Qiu, J. M.;Wang, C. L.;Deng, X. T.;Delwart, E.",2013,Feb,,0
1149,Viruses in diarrhoeic dogs include novel kobuviruses and sapoviruses,"The close interactions of dogs with humans and surrounding wildlife provide frequent opportunities for cross-species virus transmissions. In order to initiate an unbiased characterization of the eukaryotic viruses in the gut of dogs, this study used deep sequencing of partially purified viral capsid-protected nucleic acids from the faeces of 18 diarrhoeic dogs. Known canine parvoviruses, coronaviruses and rotaviruses were identified, and the genomes of the first reported canine kobuvirus and sapovirus were characterized. Canine kobuvirus, the first sequenced canine picornavirus and the closest genetic relative of the diarrhoea-causing human Aichi virus, was detected at high frequency in the faeces of both healthy and diarrhoeic dogs. Canine sapovirus constituted a novel genogroup within the genus Sapovirus, a group of viruses also associated with human and animal diarrhoea. These results highlight the high frequency of new virus detection possible even in extensively studied animal species using metagenomics approaches, and provide viral genomes for further disease-association studies.",HIGH GENETIC DIVERSITY;CANINE PARVOVIRUS;PORCINE SAPOVIRUS;MOLECULAR;CHARACTERIZATION;ACUTE GASTROENTERITIS;COMPLETE GENOME;EVOLUTION;CALICIVIRUS;IDENTIFICATION;PICORNAVIRIDAE,"Li, L. L.;Pesavento, P. A.;Shan, T. L.;Leutenegger, C. M.;Wang, C. L.;Delwart, E.",2011,Nov,,0
1150,"Highly Pathogenic Avian Influenza A(H5N8) Virus in Wild Migratory Birds, Qinghai Lake, China","In May 2016, a highly pathogenic avian influenza A(H5N8) virus strain caused deaths among 3 species of wild migratory birds in Qinghai Lake, China. Genetic analysis showed that the novel reassortant virus belongs to group B H5N8 viruses and that the reassortment events likely occurred in early 2016.","*Animal Migration;Animals;*Animals, Wild;*Anseriformes;*Charadriiformes;China/ep [Epidemiology];Disease Outbreaks/ve [Veterinary];Influenza A Virus, H5N8 Subtype/ge [Genetics];*Influenza A Virus, H5N8 Subtype;Influenza in Birds/ep [Epidemiology];*Influenza in Birds/vi [Virology];Phylogeny;Reassortant Viruses","Li, M.;Liu, H.;Bi, Y.;Sun, J.;Wong, G.;Liu, D.;Li, L.;Liu, J.;Chen, Q.;Wang, H.;He, Y.;Shi, W.;Gao, G. F.;Chen, J.",2017,04,,0
1151,"Genetic characterization of continually evolving highly pathogenic H5N6 influenza viruses in China, 2012-2016","H5N6 is a highly pathogenic avian influenza (HPAI) and a zoonotic disease that causes recurring endemics in East Asia. At least 155 H5N6 outbreaks, including 15 human infections, have been reported in China. These repeated outbreaks have increased concern that the H5N6 virus may cross over to humans and cause a pandemic. In February, 2016, peafowls in a breeding farm exhibited a highly contagious disease. Post-mortem examinations, including RT-PCR, and virus isolation, confirmed that the highly pathogenic H5N6 influenza virus was the causative agent, and the strain was named A/Pavo Cristatus/Jiangxi/JA1/2016. In animal experiments, it exhibited high pathogenicity in chickens and an estimated median lethal dose in mice of ~104.3 TCID50. A phylogenetic analysis showed that JA1/2016 was clustered in H5 clade 2.3.4.4. FG594-like H5N6 virus from Guangdong Province was the probable predecessor of JA1/2016, and the estimated divergence time was June 2014. Furthermore, we found that H5N6 influenza viruses can be classified into the two following groups: Group 1 and Group 2. Group 2 influenza viruses have not been detected since the end of 2014, whereas Group 1 influenza viruses have continually evolved and reassorted with the ""gene pool"" circulating in south China, resulting in the rise of novel subtypes of this influenza virus. An increase in the number of its identified hosts, the expanding range of its distribution, and the continual evolution of H5N6 AIVs enhance the risk that an H5N6 virus may spread to other continents and cause a pandemic.",animal experiment;animal model;animal tissue;article;autopsy;avian influenza (H5N6);chicken;China;communicable disease;controlled study;diarrhea;encephalitis;evolutionary rate;gastrointestinal hemorrhage;gene pool;gene sequence;genetic analysis;highly pathogenic avian influenza;histopathology;Influenza virus;LD50;mouse;neurologic disease;nonhuman;pandemic influenza;Pavo cristatus;peafowl;pneumonia;recurrent disease;reverse transcription polymerase chain reaction;virus isolation,"Li, M.;Zhao, N.;Luo, J.;Li, Y.;Chen, L.;Ma, J.;Zhao, L.;Yuan, G.;Wang, C.;Wang, Y.;Liu, Y.;He, H.",2017,,10.3389/fmicb.2017.00260,0
1152,Isolation and characterization of novel goose parvovirus-related virus reveal the evolution of waterfowl parvovirus,"Short beak and dwarfism syndrome (SBDS) has been constantly breaking out in China since 2015. It is caused by a novel goose parvovirus-related virus (NGPV) and can severely restrict the growth of ducks. In this study, seven NGPV stains were isolated from different regions in China between 2015 and 2016. To better understand the correlation between NGPV and goose parvovirus (GPV), we conducted complete genome sequencing and a comprehensive analysis of the NGPV genome. The phylogenetic and alignment analysis showed that NGPV is a branch of GPV, sharing 92.2%–97.1% nucleotide identity with GPV. Compared with classical GPV, five consensus nucleotide mutations in all the seven NGPV isolates and two 14-nucleotide-pair deletions in six NGPV isolates were found in the inverted terminal repeats, twelve and eight synchronous amino acid changes were found in the replication protein and capsid protein of NGPV, respectively, which might be important for viral gene regulation, humoral immune responses, and host transfer. Notably, SDLY1602 was demonstrated a recombinant strain, with the potential major parent GPV vaccine strain 82-0321v and the minor parent GPV wild strain GDaGPV. This is the first report showing that the recombination between two classical GPV strains generated a NGPV strain circulating in nature. This study will advance our understanding of NGPV molecular biology and facilitate to elucidate the evolutionary characteristics of GPV.",capsid protein;epitope;amino acid sequence;animal experiment;animal tissue;article;embryo;gene control;gene expression;genetic recombination;Goose parvovirus;inverted terminal repeat;nonhuman;Parvoviridae;phylogeny;sequence alignment;sequence analysis;sequence homology;structure analysis;virus characterization;virus isolation;waterfowl;whole genome sequencing,"Li, P.;Lin, S.;Zhang, R.;Chen, J.;Sun, D.;Lan, J.;Song, S.;Xie, Z.;Jiang, S.",2018,,10.1111/tbed.12751,0
1153,A set of UV-inducible autolytic vectors for high throughput screening,"A high throughput screening scheme is often a prerequisite for directed evolution of enzymes or metagenomic analysis of DNA samples. For assaying intracellular enzymes of interest (e.g. when Escherichia coli is used), it requires cell lysis in many cases, chemical or enzymatic, which can be tedious and cost-consuming. In this study, a set of UV-inducible autolytic vectors was constructed to offer a simpler means of cell lysis that is free of additional liquid handling. The SRRz lysis gene cassette from bacteriophage Lambda was cloned downstream of a UV-inducible promoter, the recA promoter or the umuDC promoter, and further inserted into the backbone of pUC18, and transformed into E. coli BL21 cells. The SRRz expression and cell lysis was induced by UV irradiation. For both the recA and umuDC promoters, at 30 °C the lysis efficiency was found to be consistent and above 60% as measured using β-galactosidase as the reporter. However, at 37 °C the lysis profiles were found to be erratic. UV lysis in 96-well plates also produced consistent lysis results that were comparable to those obtained by lysozyme treatment, demonstrating the utility of these autolytic vectors in high throughput screening. This set of artificial SRRz autolysis units should be transferable to other vectors. Surprisingly, it was found that the E. coli BL21(DE3) was also partially disrupted under UV irradiation, with a lysis efficiency of 44.5% at 30 °C, and 22.5% at 37 °C. © 2006 Elsevier B.V. All rights reserved.",article;autolysis;Enterobacteria phage lambda;cytolysis;DNA determination;gene cassette;high throughput screening;priority journal;promoter region;ultraviolet irradiation,"Li, S.;Xu, L.;Hua, H.;Ren, C.;Lin, Z.",2007,,10.1016/j.jbiotec.2006.07.030,0
1154,Scrutinizing Virus Genome Termini by High-Throughput Sequencing,"Analysis of genomic terminal sequences has been a major step in studies on viral DNA replication and packaging mechanisms. However, traditional methods to study genome termini are challenging due to the time-consuming protocols and their inefficiency where critical details are lost easily. Recent advances in next generation sequencing (NGS) have enabled it to be a powerful tool to study genome termini. In this study, using NGS we sequenced one iridovirus genome and twenty phage genomes and confirmed for the first time that the high frequency sequences (HFSs) found in the NGS reads are indeed the terminal sequences of viral genomes. Further, we established a criterion to distinguish the type of termini and the viral packaging mode. We also obtained additional terminal details such as terminal repeats, multi-termini, asymmetric termini. With this approach, we were able to simultaneously detect details of the genome termini as well as obtain the complete sequence of bacteriophage genomes. Theoretically, this application can be further extended to analyze larger and more complicated genomes of plant and animal viruses. This study proposed a novel and efficient method for research on viral replication, packaging, terminase activity, transcription regulation, and metabolism of the host cell.",SUBTILIS BACTERIOPHAGE SPO1;BACILLUS-SUBTILIS;DNA-REPLICATION;HOST-TAKEOVER;PHAGE;COMPONENT;STRATEGY;PROTEIN;LAMBDA;REVEAL,"Li, S. S.;Fan, H.;An, X. P.;Fan, H. H.;Jiang, H. H.;Chen, Y. B.;Tong, Y. G.",2014,Jan,,0
1155,Genome comparison of a novel classical swine fever virus isolated in China in 2004 with other CSFV strains,"The genome of a novel classical swine fever virus (CSFV), SWH/CA/2004, isolated from a hog pen in Henan Province, central China, is 12296 nucleotides (nt) in length. It is composed of a 373-nt 5′ terminal non-translated region (NTR), a 11697-nt open reading frame (ORF) encoding a polyprotein of 3898 amino acids (aa), and a 226-nt 3′-NTR. Genome comparison of the SWH/CA/2004 isolate (GenBank Accession: DQ127910) with other known CSFV isolates was performed and analyzed. Corresponding segments from SWH/CA/2004 and other reported strains shared 80.4-99.8% identity at the nucleotide level and 89.5-99.8% identity at the amino acid level. From an evolutionary point of view, isolate SWH/CA/2004 is closely related to the highly virulent isolate cF114/CA/2001, with a pairwise distance of 0.013; and distantly related to the moderately virulent isolate GXWZ02/CA/2003, with pairwise distance 0.170. The phylogenetic trees of the full-length genome and the following region E rns, E1, E2, and NS5B-based neighbor-joining (NJ) method were constructed and approximately divided into different genetic groups according to avirulence, moderate virulence and high virulence, while other region-based NJ trees demonstrated sequence conservation between these groups. The four genomic regions may constitute important criteria for genetic typing of diverse CSFV isolates. Based on these analyses, isolate SWH/CA/2004 was deduced to belong to the highly virulent isolate group. However, SWH/CA/2004 also contains a 14-U deletion in the 3′-NTR that is characteristic of avirulent isolates. These analyses constitute a comprehensive study of the phylogenetics of CSF based on distinct regions of the genome and may provide the basis for future molecular epidemiology research to identify virulent strain outbreaks and trigger implementation of appropriate control measures. © 2006 Springer Science+Business Media, LLC.",5' untranslated region;amino acid sequence;animal cell;article;China;controlled study;gene deletion;genetic code;genome analysis;nonhuman;nucleotide sequence;open reading frame;Pestivirus;phylogenetic tree;priority journal;viral genetics;virus genome;virus isolation;virus strain;virus virulence,"Li, X.;Xu, Z.;He, Y.;Yao, Q.;Zhang, K.;Jin, M.;Chen, H.;Qian, P.",2006,,10.1007/s11262-005-0048-2,0
1156,Differential expression of micrornas in porcine parvovirus infected porcine cell line,"Background: Porcine parvovirus (PPV), a member of the Parvoviridae family, causes great economic loss in the swine industry worldwide. MicroRNAs (miRNAs) are a class of non-protein-coding genes that play many diverse and complex roles in viral infections. Finding: Aiming to determine the impact of PPV infections on the cellular miRNAome, we used high-throughput sequencing to sequence two miRNA libraries prepared from porcine kidney 15 (PK-15) cells under normal conditions and during PPV infection. There was differential miRNA expression between the uninfected and infected cells: 65 miRNAs were upregulated and 128 miRNAs were downregulated. We detected the expression of miR-10b, miR-20a, miR-19b, miR-181a, miR-146b, miR-18a, and other previously identified immune-related miRNAs. Gene Ontology analysis and KEGG function annotations of the host target genes suggested that the miRNAs are involved in complex cellular pathways, including cellular metabolic processes, immune system processes, and gene expression. Conclusions: These data suggest that a large group of miRNAs is expressed in PK-15 cells and that some miRNAs were altered in PPV-infected PK-15 cells. A number of microRNAs play an important role in regulating immune-related gene expression. Our findings should help with the development of new control strategies to prevent or treat PPV infections in swine.",microRNA;microRNA 10b;microRNA 135;microRNA 142 3p;microRNA 146b;microRNA 152;microRNA 155 5p;microRNA 16;microRNA 17 5p;microRNA 181a;microRNA 185;microRNA 18a;microRNA 191;microRNA 192;microRNA 194a;microRNA 19b;microRNA 20a;microRNA 22 3p;microRNA 221 3p;microRNA 296 3p;microRNA 301;microRNA 30a 5p;microRNA 31;microRNA 34a;microRNA 361 5p;microRNA 424 5p;microRNA 499 5p;microRNA 542 5p;microRNA 92b 3p;unclassified drug;animal cell;article;controlled study;down regulation;gene expression;gene ontology;high throughput sequencing;immune system;nonhuman;parvovirus infection;Porcine parvovirus;RNA sequence;signal transduction;upregulation,"Li, X.;Zhu, L.;Liu, X.;Sun, X.;Zhou, Y.;Lang, Q.;Li, P.;Cai, Y.;Qiao, X.;Xu, Z.",2015,,10.1186/s12985-015-0359-4,0
1157,Genetic analysis of two porcine reproductive and respiratory syndrome viruses with different virulence isolated in China,"The S1 and SY0608 strains of porcine reproductive and respiratory syndrome virus (PRRSV) were individually isolated and had different pathogenicity in pigs in 1997 and 2006. In order to understand their genomic characteristics, the full-length genome of S1 and SY0608 isolates were sequenced and analyzed. The results indicated that their genome composition differed significantly and shared only 88.5% nucleotide identity with each other. The genetic variation and amino acid substitutions were not randomly distributed in the genome, and mainly focused on ORF1a, ORF3 and ORF5. The SY0608 strain, with high pathogenicity, had a 30-amino-acid deletion at amino acid positions 480 and 532-560 in comparison with the S1 strain. The alignment of amino acid sequence of Nsp1-Nsp8, GP2-GP5, M and N of S1 and SY0608 with other PRRSV isolates demonstrated that variation was mainly found in the Nsp2, GP3 and GP5 proteins. In comparison with the S1 strain, the SY0608 strain showed some potential glycosylation site mutations in GP5 at amino acid positions between 26 and 39, which might be associated with viral antigenicity. Phylogenetic analysis showed that the two strains belonged to two different branches that do not indicate differences in pathogenicity. Interestingly, the deletion strains isolated recently in China formed a new minor branch, revealing the same evolutionary trend. © 2008 Springer-Verlag.",viral protein;virus RNA;amino acid substitution;animal;Arterivirus;article;China;cluster analysis;comparative study;DNA sequence;gene deletion;genetics;isolation and purification;open reading frame;pathogenicity;phylogeny;sequence alignment;sequence homology;pig;virulence;virus genome,"Li, Y.;Wang, X.;Jiang, P.;Chen, W.;Wang, X.",2008,,10.1007/s00705-008-0207-6,0
1158,From discovery to spread: The evolution and phylogeny of Getah virus,"Getah virus (GETV) was first isolated in Malaysia in 1955. Since then, epidemics in horses and pigs caused by GETV have resulted in huge economic losses. At present, GETV has spread across Eurasia and Southeast Asia, including mainland China, Korea, Japan, Mongolia, and Russia. Data show that the Most Recent Common Ancestor (MRCA) of GETV existed about 145 years ago (95% HPD: 75–244) and gradually evolved into four distinct evolutionary populations: Groups I–IV. The MRCA of GETVs in Group III, which includes all GETVs isolated from mosquitoes, pigs, horses, and other animals since the 1960s (from latitude 19°N to 60°N), existed about 51 years ago (95% HPD: 51–72). Group III is responsible for most viral epidemics among domestic animals. An analysis of the GETV E2 protein sequence and structure revealed seven common amino acid mutation sites. These sites are responsible for the structural and electrostatic differences detected between widespread Group III isolates and the prototype strain MM2021. These differences may account for the recent geographical radiation of the virus. Considering the economic significance of GETV infection in pigs and horses, we recommend the implementation of strict viral screening and monitoring programs.",amino acid;viral protein;Alphavirus;amino acid sequence;animal;article;controlled study;evolution;Getah virus;horse;molecular phylogeny;mosquito;mutation;nonhuman;nucleotide sequence;pig;priority journal;protein structure;virus genome;virus isolation;virus strain;virus transmission,"Li, Y. Y.;Liu, H.;Fu, S. H.;Li, X. L.;Guo, X. F.;Li, M. H.;Feng, Y.;Chen, W. X.;Wang, L. H.;Lei, W. W.;Gao, X. Y.;Lv, Z.;He, Y.;Wang, H. Y.;Zhou, H. N.;Wang, G. Q.;Liang, G. D.",2017,,10.1016/j.meegid.2017.08.016,0
1159,MicroRNA-23b Promotes Avian Leukosis Virus Subgroup J (ALV-J) Replication by Targeting IRF1,"Avian leukosis virus subgroup J (ALV-J) can cause several different leukemia-like proliferative diseases in the hemopoietic system of chickens. Here, we investigated the transcriptome profiles and miRNA expression profiles of ALV-J-infected and uninfected chicken spleens to identify the genes and miRNAs related to ALV-J invasion. In total, 252 genes and 167 miRNAs were differentially expressed in ALV-J-infected spleens compared to control uninfected spleens. miR-23b expression was up-regulated in ALV-J-infected spleens compared with the control spleens, and transcriptome analysis revealed that the expression of interferon regulatory factor 1 (IRF1) was down-regulated in ALV-J-infected spleens compared to uninfected spleens. A dual-luciferase reporter assay showed that IRF1 was a direct target of miR-23b. miR-23b overexpression significantly (P = 0.0022) decreased IRF1 mRNA levels and repressed IRF1-3'-UTR reporter activity. In vitro experiments revealed that miR-23b overexpression strengthened ALV-J replication, whereas miR-23b loss of function inhibited ALV-J replication. IRF1 overexpression inhibited ALV-J replication, and IRF1 knockdown enhanced ALV-J replication. Moreover, IRF1 overexpression significantly (P = 0.0014) increased IFN-β expression. In conclusion, these results suggested that miR-23b may play an important role in ALV-J replication by targeting IRF1.",3' untranslated region;interferon regulatory factor 1;messenger RNA;microRNA;transcriptome;animal;avian leukosis;Avian leukosis virus;chicken;classification;gene expression profiling;gene expression regulation;gene regulatory network;genetics;high throughput sequencing;isolation and purification;physiology;reproducibility;RNA interference;virology;virus replication,"Li, Z.;Chen, B.;Feng, M.;Ouyang, H.;Zheng, M.;Ye, Q.;Nie, Q.;Zhang, X.",2015,,10.1038/srep10294,0
1160,The evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets,"An acute outbreak of porcine hemagglutinating encephalomyelitis virus (PHEV) infection in piglets, characterized with neurological symptoms, vomiting, diarrhea, and wasting, occurred in China. Coronavirus-like particles were observed in the homogenized tissue suspensions of the brain of dead piglets by electron microscopy, and a wild PHEV strain was isolated, characterized, and designated as PHEV-CC14. Histopathologic examinations of the dead piglets showed characteristics of non-suppurative encephalitis, and some neurons in the cerebral cortex were degenerated and necrotic, and neuronophagia. Similarly, mice inoculated with PHEV-CC14 were found to have central nervous system (CNS) dysfunction, with symptoms of depression, arched waists, standing and vellicating front claws. Furthmore, PHEV-positive labeling of neurons in cortices of dead piglets and infected mice supported the viral infections of the nervous system. Then, the major structural genes of PHEV-CC14 were sequenced and phylogenetically analyzed, and the strain shared 95%-99.2% nt identity with the other PHEV strains available in GenBank. Phylogenetic analysis clearly proved that the wild strain clustered into a subclass with a HEV-JT06 strain. These findings suggested that the virus had a strong tropism for CNS, in this way, inducing nonsuppurative encephalitis as the cause of death in piglets. Simultaneously, the predicted risk of widespread transmission showed a certain variation among the PHEV strains currently circulating around the world. Above all, the information presented in this study can not only provide good reference for the experimental diagnosis of PHEV infection for pig breeding, but also promote its new effective vaccine development.",,"Li, Z.;He, W.;Lan, Y.;Zhao, K.;Lv, X.;Lu, H.;Ding, N.;Zhang, J.;Shi, J.;Shan, C.;Gao, F.",2016,,,0
1161,MicroRNAs in the immune organs of chickens and ducks indicate divergence of immunity against H5N1 avian influenza,"Chickens are susceptible to the highly pathogenic H5N1 strain of avian influenza virus (HPAIV), whereas ducks are not. Here, we used high-throughput sequencing to analyse the microRNA expression in the spleen, thymus and bursa of Fabricius of H5N1-HPAIV-infected and non-infected chickens and ducks. We annotated the genomic positions of duck microRNAs and we compared the microRNA repertoires of chickens and ducks. Our results showed that the microRNA expression patterns in the homologous immune organs of specific-pathogen-free (SPF) chickens and ducks diverge substantially. Moreover, there was larger divergence between the microRNA expression patterns in immune organs of HPAIV-infected chickens than HPAIV-infected ducks. Together, our results might help to elucidate the roles of microRNAs in the divergent immunity of chickens and ducks against H5N1 HPAIV.",microRNA;microRNA 122;microRNA 122 5p;microRNA 146b 5p;microRNA 200b 5p;microRNA 2188 5p;microRNA 34c 5p;unclassified drug;Anas platyrhynchos;animal experiment;animal model;animal tissue;article;bursa Fabricii;comparative study;controlled study;down regulation;gene expression;high throughput sequencing;immunity;infection sensitivity;influenza A (H5N1);Leghorn chicken;nonhuman;real time polymerase chain reaction;sequence analysis;spleen;thymus;upregulation,"Li, Z.;Zhang, J.;Su, J.;Liu, Y.;Guo, J.;Zhang, Y.;Lu, C.;Xing, S.;Guan, Y.;Li, Y.;Sun, B.;Zhao, Z.",2015,,10.1016/j.febslet.2014.12.019,0
1162,"Novel avian coronavirus and fulminating disease in Guinea Fowl, France","For decades, French guinea fowl have been affected by fulminating enteritis of unclear origin. By using metagenomics, we identified a novel avian gammacoronavirus associated with this disease that is distantly related to turkey coronaviruses. Fatal respiratory diseases in humans have recently been caused by coronaviruses of animal origin.",animal tissue;article;autopsy;Avian infectious bronchitis virus;controlled study;Coronavirinae;Coronavirus infection;fowl;France;gene sequence;guineafowl;high throughput sequencing;histopathology;nonhuman;nucleotide sequence;ornithosis;phylogenetic tree;phylogeny;sequence homology;viral tropism,"Liais, E.;Croville, G.;Mariette, J.;Delverdier, M.;Lucas, M. N.;Klopp, C.;Lluch, J.;Donnadieu, C.;Guy, J. S.;Corrand, L.;Ducatez, M. F.;Guérin, J. L.",2014,,10.3201/eid2001.130774,0
1163,A systematic analysis of miRNA transcriptome in Marek's disease virus-induced lymphoma reveals novel and differentially expressed miRNAs,"Marek's disease is a lymphoproliferative neoplastic disease of the chicken, which poses a serious threat to poultry health. Marek's disease virus (MDV)-induced T-cell lymphoma is also an excellent biomedical model for neoplasia research. Recently, miRNAs have been demonstrated to play crucial roles in mediating neoplastic transformation. To investigate host miRNA expression profiles in the tumor transformation phase of MDV infection, we performed deep sequencing in two MDV-infected samples (tumorous spleen and MD lymphoma from liver), and two non-infected controls (non-infected spleen and lymphocytes). In total, 187 and 16 known miRNAs were identified in chicken and MDV, respectively, and 17 novel chicken miRNAs were further confirmed by qPCR. We identified 28 down-regulated miRNAs and 11 up-regulated miRNAs in MDV-infected samples by bioinformatic analysis. Of nine further tested by qPCR, seven were verified. The gga-miR-181a, gga-miR-26a, gga-miR-221, gga-miR-222, gga-miR-199*, and gga-miR-140* were down-regulated, and gga-miR-146c was up-regulated in MDV-infected tumorous spleens and MD lymphomas. In addition, 189 putative target genes for seven differentially expressed miRNAs were predicted. The luciferase reporter gene assay showed interactions of gga-miR-181a with MYBL1, gga-miR-181a with IGF2BP3, and gga-miR-26a with EIF3A. Differential expression of miRNAs and the predicted targets strongly suggest that they contribute to MDV-induced lymphomagenesis.","3' Untranslated Regions/ge [Genetics];Animals;Base Pairing/ge [Genetics];Base Sequence;Binding Sites/ge [Genetics];*Chickens/ge [Genetics];Chickens/vi [Virology];*Gene Expression Profiling;Gene Regulatory Networks/ge [Genetics];Genes, Reporter;*Herpesvirus 2, Gallid/ph [Physiology];High-Throughput Nucleotide Sequencing;Luciferases/me [Metabolism];Lymphoma/ge [Genetics];*Lymphoma/ve [Veterinary];Lymphoma/vi [Virology];*Marek Disease/ge [Genetics];*MicroRNAs/ge [Genetics];MicroRNAs/me [Metabolism];Molecular Sequence Data;Poultry Diseases/ge [Genetics];Poultry Diseases/vi [Virology];Reproducibility of Results;*Transcriptome/ge [Genetics];0 (3' Untranslated Regions);0 (MicroRNAs)","Lian, L.;Qu, L.;Chen, Y.;Lamont, S. J.;Yang, N.",2012,,,0
1164,"Cloning, sequencing, and polymorphism analysis of novel classical MHC class I alleles in northern pig-tailed macaques (Macaca leonina)","The northern pig-tailed macaque (Macaca leonina) has been confirmed to be an independent species from the pig-tailed macaque group of Old World monkey. We have previously reported that the northern pig-tailed macaques were also susceptible to HIV-1. Here, to make this animal a potential HIV/AIDS model and to discover the mechanism of virus control, we attempted to assess the role of major histocompatibility complex (MHC) class I-restricted immune responses to HIV-1 infection, which was associated with viral replication and disease progression. As an initial step, we first cloned and characterized the classical MHC class I gene of northern pig-tailed macaques. In this study, we identified 39 MHC class I alleles including 17 MHC-A and 22 MHC-B alleles. Out of these identified alleles, 30 were novel and 9 were identical to alleles previously reported from other macaque species. The MHC-A and MHC-B loci were both duplicates as rhesus macaques and southern pig-tailed macaques. In addition, we also detected the patterns of positive selection in northern pig-tailed macaques and revealed the existence of balance selection with 20 positive selection sites in the peptide binding region. The analysis of B and F peptide binding pockets in northern and southern pig-tailed macaques and rhesus macaques suggested that they were likely to share a few common peptides to present. Thus, this study provides important MHC immunogenetics information and adds values to northern pig-tailed macaques as a promising HIV/AIDS model.","Animals;Cloning, Molecular;Disease Models, Animal;*HIV Infections/ge [Genetics];HIV Infections/im [Immunology];HIV Infections/vi [Virology];HIV-1/im [Immunology];High-Throughput Nucleotide Sequencing;*Histocompatibility Antigens Class I/ge [Genetics];Histocompatibility Antigens Class I/im [Immunology];Humans;*Macaca/ge [Genetics];Macaca/im [Immunology];Macaca/vi [Virology];*Phylogeny;Polymorphism, Genetic;Species Specificity;0 (Histocompatibility Antigens Class I)","Lian, X. D.;Zhang, X. H.;Dai, Z. X.;Zheng, Y. T.",2016,Apr,,0
1165,Arboviruses and their related infections in China: A comprehensive field and laboratory investigation over the last 3 decades,"Since the 1980s, a comprehensive field and laboratory investigation has been conducted throughout China, and a total of 29 virus species belonging to 7 families and 13 genera were identified through virological, morphological, and immunological methods, as well as whole-genome sequencing and molecular genetic analyses. Most of the virus isolates belong to 9 genera in the families Flaviviridae, Bunyaviridae, Togaviridae, and Reoviridae. Among them, 4 genera (Orthobunyavirus, Bunyavirus, Phlebovirus, and Nairovirus) belong to the family Bunyaviridae and 3 genera (Seadonavirus, Orbivirus, and Cypovirus) belong to the family Reoviridae. Analyses of the relationships between viruses and human/animal diseases indicated that Japanese encephalitis virus, dengue virus, severe fever with thrombocytopenia syndrome virus, tick-borne encephalitis virus, Crimean-Congo hemorrhagic fever virus, West Nile virus, and Tahyna virus can cause human and animal infections and disease epidemics in China. This review systematically introduces the current status of the diversity and geographical distribution of arboviruses and vectors in China. In addition, our results provide strong technical support for the prevention and control of arboviral diseases, the treatment of epidemics, and the early warning and prediction of diseases, and so they are significant for the control and prevention of arboviral diseases in Asia and around the world.",virus vector;Akabane virus;Arbovirus;arbovirus infection;Armigeres subalbatus;Banna virus;banna virus infection;Batai virus;bird disease;Bunyaviridae;Cat Que virus;Chaoyang virus;Chikungunya virus;China;Crimean-Congo hemorrhagic fever virus;Culex;Culex pipiens pallens;Cypovirus;dengue;Dengue virus 1;Dengue virus 2;Dengue virus 3;Dengue virus 4;Densovirinae;egg drop syndrome;field study;Flavivirus;genetic analysis;genetic trait;geographic distribution;Getah virus;human;Japanese encephalitis;Japanese encephalitis virus;Kadipiro virus;Kyasanur Forest disease;laboratory test;Manzanilla virus;Mayaro virus;molecular genetics;mosquito;nonhuman;Orbivirus;prevalence;Reoviridae;review;RNA virus infection;Ross River virus;Seadornavirus;severe fever with thrombocytopenia syndrome;severe fever with thrombocytopenia syndrome virus;Sindbis virus;Tahyna virus;Tembusu virus;Tibet orbivirus;tick borne encephalitis;Tick borne encephalitis virus;Totivirus;viral genetics;virus classification;virus diagnosis;virus encephalitis;virus isolation;virus meningitis;virus strain;west nile encephalitis;West Nile fever;West Nile virus;Yunnan orbivirus,"Liang, G.;Li, X.;Gao, X.;Fu, S.;Wang, H.;Li, M.;Lu, Z.;Zhu, W.;Lu, X.;Wang, L.;Cao, Y.;He, Y.;Lei, W.",2018,,10.1002/rmv.1959,0
1166,Newcastle disease outbreaks in western China were caused by the genotypes VIIa and VIII,"Twelve Newcastle disease virus (NDV) strains were isolated from chickens involved in outbreaks of Newcastle disease (ND) in western China (Shaanxi, Gansu, Xinjiang, Qinghai and Guangxi provinces) between 1979 and 1999. All strains were determined to be velogenic by plaque formation, the mean death time (MDT) of embryonated eggs, and the intracerebral pathogenicity index (ICPI). For preparation of virus RNA, the acid guanidinium-thiocyanate method was used. A 908bp fragment of nucleotide was amplified by RT-PCR starting from the N terminal of the F gene and the PCR segments were cloned into the PGEM-T vector and sequenced. The similarities of the nucleotide sequences (1-519bp) and predicted amino acid sequences of the F gene (1-125) were analyzed by comparing the 12 NDV isolates with the NDV vaccine strains Lasota, B1, H1 and V4, with classical NDV strains and recent epizootic strains. Phylogenetic analysis demonstrated that all strains were of two novel genotypes; the NDV strains that caused the outbreak of ND in western China during 1998-1999 was of the genotype VIIa, whereas the strains from the Qinghai province (1979-1985) were of genotype VIII, which has been found predominately in southern Africa. © 2002 Elsevier Science B.V. All rights reserved.",thiocyanic acid derivative;virus RNA;Africa;amino terminal sequence;animal experiment;animal model;article;bird disease;chicken;China;controlled study;F gene;gene;genotype;Newcastle disease virus;nonhuman;nucleotide sequence;pathogenicity;phylogeny;plaque forming cell;reverse transcription polymerase chain reaction;time of death;virus isolation;zygote,"Liang, R.;Cao, D. J.;Li, J. Q.;Chen, J.;Guo, X.;Zhuang, F. F.;Duan, M. X.",2002,,10.1016/s0378-1135(02)00050-0,0
1167,Provirus variants of bovine leukemia virus in naturally infected cattle from Argentina and Japan,"A serologic subgroup of bovine leukemia virus (BLV) has not been identified, whereas genetic diversity among BLVs has been reported by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP). To investigate the distribution of BLV provirus variants, 42 isolates from Argentina and Japan were examined by nested PCR for a segment of the env gene, followed by DNA sequencing. The nucleotide sequences were compared with other previously characterized BLV variants from different geographical areas (Belgium, France, Italy, North America, Australia, Japan and Argentina). The majority of analyzed segments had a tendency for nucleotide substitution without changing the amino acid. The constructed phylogenetic tree showed the relations and differences between proviruses and within each one. Most of the samples in Argentina formed one cluster. The samples in Japan, except one, also formed one cluster and some of them showed high homology with the isolates from Australia and the USA. Considering the sequence analysis of env PCR products of all Japanese and Argentine samples and comparing them with the other previously isolated sequences, the variation was up to 3.5% and was characterized geographically in each area. © 2003 Elsevier B.V. All rights reserved.",Argentina;article;bovine;controlled study;DNA sequence;envelope gene;genetic variability;geography;Japan;leukemia virus;nonhuman;nucleotide sequence;phylogenetic tree;polymerase chain reaction;provirus;restriction fragment length polymorphism;sequence analysis;serology,"Licursi, M.;Inoshima, Y.;Wu, D.;Yokoyama, T.;González, E. T.;Sentsui, H.",2003,,10.1016/s0378-1135(03)00202-5,0
1168,"Taxonomy of viruses in etiologic relationship to gastroenteritis of man, cattle and swine",,animal;animal disease;article;bovine;cattle disease;classification;gastroenteritis;human;pig;swine disease;virus;virus infection,"Liebermann, H.",1983,,,0
1169,Phylogenetic characterization of Newcastle disease viruses isolated in Taiwan during 2003-2006,"Isolates of Newcastle disease virus (NDV) from chicken cases were obtained from various locations in Taiwan during 2003-2006 and were genotypically analyzed by using reverse transcription polymerase chain reaction (RT-PCR) with primers specific to the viral fusion (F) protein gene (534 bp). Part of the amplified F protein DNA product (nucleotide sequence 47-418) and the deduced amino acid sequences were compared phylogenetically with those from strains previously reported in Taiwan and other geographic regions. Our results showed that all Taiwanese isolates (n = 20) collected during 2003-2006, according to the phylogenetic tree, belong to the genotype VIId. In addition, all the six Taiwanese isolates obtained in 2003, carry the motif 112R-R-Q-K-R116 and have the amino acid L23 replaced by F23 (assigned as Group 1). On the other hand, 12 out of the 14 Taiwanese isolates obtained during 2004-2006 possess the motif 112R-R-K-K-R116 and have the amino acid G74, instead of E74 (assigned as Group 2). To our best knowledge, this is the first reported VIId isolates that possess the sequences of G74/112R-R-K-K-R116 within the F0 protein. Since a high mortality, severe clinical signs, typical postmortem lesions, and a high intra-cerebral pathogenicity index (ICPI) were observed in the NDV-infected chickens, these isolates acquired between 2003 and 2006 are considered as the velogenic type. The Group 2 viruses have become dominant and responsible for the majority of Taiwanese outbreaks during recent years. Based on our phylogenetic analysis, it can be postulated that these isolates were evolved from previously reported local strains, and the Group 2 family emerged the latest in the genotype VIId. The information is fundamental to improving the efficiency of controlling strategies and vaccine development for NDV. © 2007 Elsevier B.V. All rights reserved.",virus fusion protein;amino acid sequence;article;chicken;controlled study;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;Taiwan;virus isolation,"Lien, Y. Y.;Lee, J. W.;Su, H. Y.;Tsai, H. J.;Tsai, M. C.;Hsieh, C. Y.;Tsai, S. S.",2007,,10.1016/j.vetmic.2007.03.006,0
1170,Live attenuated nephropathogenic infectious bronchitis virus vaccine provides broad cross protection against new variant strains,"Infectious bronchitis virus (IBV) infections cause great economic losses to the poultry industry worldwide, and the emergence of new variant strains complicates disease control. The present study investigated the genetic and protectotypic features of newly emerged Korean IBV strains. A phylogenetic analysis showed that several recent isolates formed 2 different clusters (new cluster 1 and 2), which were distinct from other preexisting clusters. New cluster 1 IBV strains represented recombinants between Korean nephropathogenic strain KM91 and the QXIBV strain. New cluster 2 IBV strains showed low amino acid homology (<58.7%) compared with previous isolates. We evaluated the protective efficacy of commercial IBV vaccines (H120 and K2 strain) against these new isolates. In cross-protection studies, the H120 strain did not provide sufficient protection against these variants. However, highly attenuated nephropathogenic IBV vaccine, K2 strain, provided significantly higher levels of protection against variants compared with chickens vaccinated with H120 (P < 0.05 or better). These results indicate that the K2 vaccine could be helpful for the reduction of economic losses caused by newly evolving IBV recombinants (new cluster 1) and variants (new cluster 2). © 2012 Poultry Science Association Inc.",live vaccine;membrane protein;coronavirus spike glycoprotein;virus envelope protein;virus RNA;virus vaccine;animal;animal disease;article;Avian infectious bronchitis virus;bird disease;chick embryo;chicken;classification;Coronavirus infection;cross protection;DNA sequence;genetics;germfree animal;immunology;kidney;molecular genetics;pathology;phylogeny;reverse transcription polymerase chain reaction;South Korea;trachea;virology,"Lim, T. H.;Kim, M. S.;Jang, J. H.;Lee, D. H.;Park, J. K.;Youn, H. N.;Lee, J. B.;Park, S. Y.;Choi, I. S.;Song, C. S.",2012,,10.3382/ps.2011-01739,0
1171,"Faecal virome of healthy chickens reveals a large diversity of the eukaryote viral community, including novel circular ssDNA viruses","This study is focused on the identification of the faecal virome of healthy chickens raised in high-density, export-driven poultry farms in Brazil. Following high-throughput sequencing, a total of 7743 de novo-assembled contigs were constructed and compared with known nucleotide/amino acid sequences from the GenBank database. Analyses with BLASTx revealed that 279 contigs (4%) were related to sequences of eukaryotic viruses. Viral genome sequences (total or partial) indicative of members of recognized viral families, including Adenoviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, were identified, some of those representing novel genotypes. In addition, a range of circular replication-associated protein encoding DNA viruses were also identified. The characterization of the faecal virome of healthy chickens described here not only provides a description of the viruses encountered in such niche but should also represent a baseline for future studies comparing viral populations in healthy and diseased chicken flocks. Moreover, it may also be relevant for human health, since chickens represent a significant proportion of the animal protein consumed worldwide.",circular DNA;contig;genomic DNA;Adenoviridae;article;Brazil;Caliciviridae;chicken;Circoviridae;eukaryote;fecal virome;genome analysis;genotype;high throughput sequencing;metagenomics;nonhuman;Parvoviridae;phylogeny;Picobirnaviridae;Picornaviridae;poultry farming;priority journal;Reoviridae;single-stranded DNA virus;virus genome;virus replication,"Lima, D. A.;Cibulski, S. P.;Finkler, F.;Teixeira, T. F.;Varela, A. P. M.;Cerva, C.;Loiko, M. R.;Scheffer, C. M.;Dos Santos, H. F.;Mayer, F. Q.;Roehe, P. M.",2017,,10.1099/jgv.0.000711,1
1172,The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics,"Malabsorption syndrome (MAS) is an economically important disease of young, commercially reared broilers, characterized by growth retardation, defective feather development and diarrheic faeces. Several viruses have been tentatively associated to such syndrome. Here, in order to examine potential associations between enteric viruses and MAS, the faecal viromes of 70 stool samples collected from diseased (n = 35) and healthy (n = 35) chickens from seven flocks were characterized and compared. Following high-throughput sequencing, a total of 8,347,319 paired end reads, with an average of 231 nt, were generated. Through analysis of de novo assembled contigs, 144 contigs > 1000 nt were identified with hits to eukaryotic viral sequences, as determined by GenBank database. A number of known and unknown representatives of Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, as well as novel uncharacterized CRESS-DNA viruses, were identified. However, the distribution of sequence reads of viral genomes identified in diseased or healthy birds revealed no statistically significant differences. These findings indicate no association between the occurrence of MAS and enteric viruses. The viral genomes reported in the present study, including a variety of novel viruses, seem part of the normal intestinal microbiota of chickens.",capsid protein;DNA helicase;nonstructural protein 1;protein VP1;RNA directed RNA polymerase;spacer DNA;Adenoviridae;Anelloviridae;animal experiment;animal model;article;Astroviridae;broiler;Caliciviridae;case control study;Circoviridae;controlled study;enteric virus;feces analysis;high throughput sequencing;intestine flora;malabsorption;metagenomics;nonhuman;nucleotide sequence;Parvoviridae;phylogeny;Picobirnaviridae;Picornaviridae;priority journal;Reoviridae;virus genome,"Lima, D. A.;Cibulski, S. P.;Tochetto, C.;Varela, A. P. M.;Finkler, F.;Teixeira, T. F.;Loiko, M. R.;Cerva, C.;Junqueira, D. M.;Mayer, F. Q.;Roehe, P. M.",2019,,10.1016/j.virusres.2018.12.005,1
1173,"Ocular Vaccinia Infection in Dairy Worker, Brazil",We studied a clinical case of vaccinia virus that caused an ocular manifestation in a dairy worker in Brazil. Biologic and molecular analyses identified a co-infection with 2 isolates from different Brazilian vaccinia virus phylogenetic groups.,"Animals;Brazil/ep [Epidemiology];Cattle;*Dairying;*Eye Diseases/vi [Virology];Genome, Viral;Humans;Male;Middle Aged;Occupational Exposure;Phylogeny;*Vaccinia/ep [Epidemiology];*Vaccinia/vi [Virology];Vaccinia virus/ge [Genetics];*Vaccinia virus/ip [Isolation & Purification]","Lima, M. T.;Oliveira, G. P.;Assis, F. L.;Bretas de Oliveira, D.;Vaz, S. M.;Trindade, G. S.;Abrahao, J. S.;Kroon, E. G.",2018,01,,0
1174,"Nucleotide-Sequence of the Genes Encoding the Canine Herpesvirus Gb, Gc and Gd Homologs","The nucleotide sequence of the genes encoding the canine herpesvirus (CHV) gB, gC and gD homologues was determined. These genes are predicted to encode polypeptides of 879, 459 and 345 amino acids, respectively. Comparison of the predicted amino acid sequences of CHV gB, gC and go with the homologous sequences from other herpesviruses indicates that CHV is an alphaherpesvirus, a conclusion that is consistent with the previous classification of this virus according to biological properties. Alignment of the homologous gB, gC and gD amino acid sequences indicates that most of the cysteine residues are conserved, suggesting that these glycoproteins possess similar tertiary structures. The nucleotide sequence of the open reading frame downstream from the CHV gC gene was also determined. The predicted amino acid sequence of this putative polypeptide appears to be homologous to a family of proteins encoded downstream from the gC gene in most, although not all, alphaherpesviruses.",SIMPLEX VIRUS TYPE-1;VARICELLA-ZOSTER VIRUS;COMPLETE DNA-SEQUENCE;GLYCOPROTEIN-D;PSEUDORABIES VIRUS;BOVINE HERPESVIRUS-1;EQUINE;HERPESVIRUS-1;PROTEIN;GENOME;IDENTIFICATION,"Limbach, K. J.;Limbach, M. P.;Conte, D.;Paoletti, E.",1994,Aug,,0
1175,High prevalence of hepatitis e virus in Swedish moose--a phylogenetic characterization and comparison of the virus from different regions,"BACKGROUND: Hepatitis E virus (HEV) infects a range of species, including humans, pigs, wild boars and deer. Zoonotic transmission may contribute to the high HEV seroprevalence in the human population of many countries. A novel divergent HEV from moose (Alces alces) in Sweden was recently identified by partial genome sequencing. Since only one strain was found, its classification within the HEV family, prevalence in moose and zoonotic potential was unclear. We therefore investigated samples from 231 moose in seven Swedish counties for HEV, and sequenced a near complete moose HEV genome. Phylogenetic analysis to classify this virus within the family Hepeviridae and to explore potential host specific determinants was performed. METHODS AND FINDINGS: The HEV prevalence of moose was determined by PCR (marker for active infection) and serological assays (marker of past infection) of sera and 51 fecal samples from 231 Swedish moose. Markers of active and past infection were found in 67 (29%) animals, while 34 (15%) were positive for HEV RNA, 43 (19%) were seropositive for anti-HEV antibodies, and 10 (4%) had both markers. The number of young individuals positive for HEV RNA was larger than for older individuals, and the number of anti-HEV antibody positive individuals increased with age. The high throughput sequenced moose HEV genome was 35-60% identical to existing HEVs. Partial ORF1 sequences from 13 moose strains showed high similarity among them, forming a distinct monophyletic clade with a common ancestor to HEV genotype 1-6 group, which includes members known for zoonotic transmission. CONCLUSIONS: This study demonstrates a high frequency of HEV in moose in Sweden, with markers of current and past infection demonstrated in 30% of the animals. Moose is thus an important animal reservoir of HEV. The phylogenetic relationship demonstrated that the moose HEV belonged to the genotype 1-6 group, which includes strains that also infect humans, and therefore may signify a potential for zoonotic transmission of this HEV.","Animals;*Deer/vi [Virology];Feces/vi [Virology];Female;Genome, Viral/ge [Genetics];Hepatitis Antibodies/bl [Blood];Hepatitis E/bl [Blood];*Hepatitis E/ep [Epidemiology];Hepatitis E/vi [Virology];*Hepatitis E virus/ge [Genetics];Male;Phylogeny;Prevalence;RNA, Viral/ge [Genetics];Serologic Tests/mt [Methods];Sweden/ep [Epidemiology];Zoonoses/bl [Blood];Zoonoses/ep [Epidemiology];Zoonoses/vi [Virology];0 (Hepatitis Antibodies);0 (RNA, Viral)","Lin, J.;Karlsson, M.;Olofson, A. S.;Belak, S.;Malmsten, J.;Dalin, A. M.;Widen, F.;Norder, H.",2015,,,0
1176,High prevalence of hepatitis E virus in Swedish moose - A phylogenetic characterization and comparison of the virus from different regions,"Background: Hepatitis E virus (HEV) infects a range of species, including humans, pigs, wild boars and deer. Zoonotic transmission may contribute to the high HEV seroprevalence in the human population of many countries. A novel divergent HEV from moose (Alces alces) in Sweden was recently identified by partial genome sequencing. Since only one strain was found, its classification within the HEV family, prevalence in moose and zoonotic potential was unclear. We therefore investigated samples from 231 moose in seven Swedish counties for HEV, and sequenced a near complete moose HEV genome. Phylogenetic analysis to classify this virus within the family Hepeviridae and to explore potential host specific determinants was performed. Methods and Findings: The HEV prevalence of moose was determined by PCR (marker for active infection) and serological assays (marker of past infection) of sera and 51 fecal samples from 231 Swedish moose. Markers of active and past infection were found in 67 (29%) animals, while 34 (15%) were positive for HEV RNA, 43 (19%) were seropositive for anti-HEV antibodies, and 10 (4%) had both markers. The number of young individuals positive for HEV RNA was larger than for older individuals, and the number of anti-HEV antibody positive individuals increased with age. The high throughput sequenced moose HEV genome was 35-60% identical to existing HEVs. Partial ORF1 sequences from 13 moose strains showed high similarity among them, forming a distinct monophyletic clade with a common ancestor to HEV genotype 1-6 group, which includes members known for zoonotic transmission. Conclusions: This study demonstrates a high frequency of HEV in moose in Sweden, with markers of current and past infection demonstrated in 30% of the animals. Moose is thus an important animal reservoir of HEV. The phylogenetic relationship demonstrated that the moose HEV belonged to the genotype 1-6 group, which includes strains that also infect humans, and therefore may signify a potential for zoonotic transmission of this HEV.",hepatitis E antibody;virus RNA;age;amino acid sequence;amino acid substitution;animal tissue;antibody detection;article;blood analysis;controlled study;feces analysis;female;genotype;geographic distribution;hepatitis E;Hepatitis E virus;high throughput sequencing;male;moose;nonhuman;nucleotide sequence;open reading frame;phylogeny;polymerase chain reaction;prevalence;sequence homology;species comparison;Sweden;virus genome;virus reactivation;virus transmission,"Lin, J.;Karlsson, M.;Olofson, A. S.;Belák, S.;Malmsten, J.;Dalin, A. M.;Widén, F.;Norder, H.",2015,,10.1371/journal.pone.0122102,0
1177,Evidence from nature: interspecies spread of heron hepatitis B viruses,"Heron hepatitis B viruses (HHBVs) in three subspecies of free-living great blue herons (Ardea herodias) from Florida, USA, were identified and characterized. Eight of 13 samples were positive in all assays used, whereas sera from egrets, which are also members of the family Ardeidae, were negative in the same assays. Comparative phylogenetic analysis of viral DNA sequences from the preS/S region of previously reported and novel HHBV strains isolated from captive grey herons (Germany) and free-ranging great blue herons (USA), respectively, revealed a strong conservation (95 % sequence similarity) with two separate clusters, implying a common ancestor of all strains. Our data demonstrate for the first time that different subspecies of herons are infected by HHBV and that these infections exist in non-captive birds. Phylogenetic analysis and the fact that the different heron species are geographically isolated populations suggest that lateral transmission, virus adaptation and environmental factors all play a role in HHBV spreading and evolution.","Animals;Avihepadnavirus/ge [Genetics];*Avihepadnavirus/ip [Isolation & Purification];Base Sequence;*Bird Diseases/tm [Transmission];Bird Diseases/vi [Virology];*Birds/vi [Virology];DNA, Viral/ch [Chemistry];DNA, Viral/ip [Isolation & Purification];Disease Transmission, Infectious;Hepadnaviridae Infections/tm [Transmission];*Hepadnaviridae Infections/ve [Veterinary];Hepadnaviridae Infections/vi [Virology];Molecular Sequence Data;Phylogeny;Sequence Alignment;Sequence Analysis, DNA;Sequence Homology;Viral Envelope Proteins/ge [Genetics];0 (DNA, Viral);0 (S envelope protein, hepatitis B virus);0 (Viral Envelope Proteins)","Lin, L.;Prassolov, A.;Funk, A.;Quinn, L.;Hohenberg, H.;Frolich, K.;Newbold, J.;Ludwig, A.;Will, H.;Sirma, H.;Steinbach, F.",2005,May,,0
1178,"Influenza A(H9N2) Virus, Myanmar, 2014-2015","Routine surveillance of influenza A virus was conducted in Myanmar during 2014-2015. Influenza A(H9N2) virus was isolated in Shan State, upper Myanmar. Whole-genome sequencing showed that H9N2 virus from Myanmar was closely related to H9N2 virus of clade 4.2.5 from China.","Animals;Chickens;Ducks;*Genome, Viral;High-Throughput Nucleotide Sequencing;Influenza A Virus, H9N2 Subtype/cl [Classification];*Influenza A Virus, H9N2 Subtype/ge [Genetics];Influenza A Virus, H9N2 Subtype/ip [Isolation & Purification];*Influenza in Birds/ep [Epidemiology];Influenza in Birds/tm [Transmission];Influenza in Birds/vi [Virology];Myanmar/ep [Epidemiology];Phylogeny;*Poultry Diseases/ep [Epidemiology];Poultry Diseases/tm [Transmission];Poultry Diseases/vi [Virology];*RNA, Viral/ge [Genetics];0 (RNA, Viral)","Lin, T. N.;Nonthabenjawan, N.;Chaiyawong, S.;Bunpapong, N.;Boonyapisitsopa, S.;Janetanakit, T.;Mon, P. P.;Mon, H. H.;Oo, K. N.;Oo, S. M.;Mar Win, M.;Amonsin, A.",2017,06,,0
1179,Molecular epidemiology of J-subgroup avian leukosis virus isolated from meat-type chickens in southern China between 2013 and 2014,"Members of avian leukosis virus subgroup J (ALV-J) cause various diseases associated with tumor formation and decreased fertility, resulting in major economic losses in the poultry industry worldwide. To assess the status of ALV-J infection in meat-type chickens in southern China, the molecular epidemiology of ALV-J strains was investigated. A total of 265 clinical samples collected from southern China from 2013 to 2014 were investigated in this study for the presence of ALV-J, which resulted in 12 virus isolates. Phylogenetic analysis showed that 91.7 % (11/12) of the ALV-J isolates have possessed high homology to Chinese layer isolates and belong to one subgroup. One of the ALV isolates (designated GD1411-1) was relatively closely related to the ALV-J broiler isolates, indicating that the GD1411-1 isolate might be a transition strain. Several unique nucleotide substitutions in gp85 and the U3 region were detected in all 12 ALV-J isolates. This study provides some interesting information on the molecular characterization of ALV-J isolates. These findings will be beneficial for understanding of the pathogenic mechanism of ALV-J infection.",animal;avian leukosis;Avian leukosis virus;chicken;China;classification;DNA sequence;genetics;genotype;isolation and purification;molecular epidemiology;phylogeny;point mutation;bird disease;virology,"Lin, W.;Li, X.;Dai, Z.;Zhang, X.;Chang, S.;Zhao, P.;Zhang, H.;Chen, F.;Xie, Q.",2016,,10.1007/s00705-016-3003-8,0
1180,Genetic and pathobiologic characterization of H3N2 canine influenza viruses isolated in the Jiangsu Province of China in 2009-2010,"The newly emerging canine influenza virus (CIV) causes considerable concerns for both veterinary and public health. During 2009-2010, six strains of H3N2 influenza virus were isolated from dogs in Jiangsu Province, China. Sequence and phylogenetic analysis of eight gene segments revealed that the six viruses were most similar to a recent canine-derived subtype H3N2 influenza virus isolated in cats from South Korea, which originated from avian strain. By comparing the deduced amino acid sequences of the hemagglutinin 1 (HA1) and neuraminidase (NA) genes of the six Jiangsu isolates against the most similar avian strains, we found that all isolates had several common mutations at the receptor-binding sites, potential glycosylation sites and cleavage site in HA1, and antigenic sites in both the HA1 and NA segments. Significantly, a unique two amino acid insertion in the NA stalk was found. Experimental infection of BALB/c mice revealed that viral RNA could be detected in the major rodent organs, such as brain, heart, spleen, kidney, liver and intestine, as well as the lung. All the sampled organs from infected mice showed significant lesions and viral antigen staining. This study highlights the potential of domesticated animals to become a reservoir for influenza virus and the need for surveillance programs to detect cross-species transmission. © 2012 Elsevier B.V.",amino acid;hemagglutinin;sialidase;virus antigen;virus RNA;amino acid sequence;animal cell;animal experiment;animal model;animal tissue;article;binding site;brain;cat;China;controlled study;dog;domestic animal;experimental infection;gene;genetics;glycosylation;H3N2 canine influenza virus;heart;Influenza virus;Influenza A virus (H3N2);intestine;kidney;liver;lung;mouse;mutation;nonhuman;pathology;phylogeny;sequence analysis;South Korea;spleen;staining;virus isolation;virus strain;virus transmission,"Lin, Y.;Zhao, Y.;Zeng, X.;Lu, C.;Liu, Y.",2012,,10.1016/j.vetmic.2012.02.016,0
1181,"Detection and characterization of viruses causing hand, foot and mouth disease from children in Seri Kembangan, Malaysia","Hand, foot and mouth disease (HFMD) is a common viral infection among infants and children. The major causative agents of HFMD are enterovirus 71 (EV71) and coxsackievirus A16 (CVA16). Recently, coxsackievirus A6 (CVA6) infections were reported in neighboring countries. Infected infants and children may present with fever, mouth/throat ulcers, rashes and vesicles on hands and feet. Moreover, EV71 infections might cause fatal neurological complications. Since 1997, EV71 caused fatalities in Sarawak and Peninsula Malaysia. The purpose of this study was to identify and classify the viruses which detected from the patients who presenting clinical signs and symptoms of HFMD in Seri Kembangan, Malaysia. From December 2012 until July 2013, a total of 28 specimens were collected from patients with clinical case definitions of HFMD. The HFMD viruses were detected by using semi-nested reverse transcription polymerase chain reaction (snRT-PCR). The positive snRT-PCR products were sequenced and phylogenetic analyses of the viruses were performed. 12 of 28 specimens (42.9%) were positive in snRT-PCR, seven are CVA6 (58.3%), two CVA16 (16.7%) and three EV71 (25%). Based on phylogenetic analysis studies, EV71 strains were identified as sub-genotype B5; CVA16 strains classified into sub-genotype B2b and B2c; CVA6 strains closely related to strains in Taiwan and Japan. In this study, HFMD in Seri Kembangan were caused by different types of Enterovirus, which were EV71, CVA6 and CVA16.",animal;child;classification;cluster analysis;DNA sequence;Enterovirus;female;genetic variability;genetics;hand foot and mouth disease;human;infant;isolation and purification;Malaysia;male;molecular genetics;newborn;pathology;phylogeny;polymerase chain reaction;preschool child;reverse transcription polymerase chain reaction;sequence homology;virology,"Ling, B. P.;Jalilian, F. A.;Harmal, N. S.;Yubbu, P.;Sekawi, Z.",2014,,,0
1182,"Hypothesis on the source, transmission and characteristics of infection of avian influenza A (H7N9) virus - based on analysis of field epidemiological investigation and gene sequence analysis","Summary: On 31 March 2013, the National Health and Family Planning Commission announced that human infections with influenza A (H7N9) virus had occurred in Shanghai and Anhui provinces, China. H7N9 cases were later detected in Jiangsu and Zhejiang provinces. It was estimated that the virus first spread northward along the route taken by migratory birds and then spread to neighbouring provinces with the sale of poultry. Epidemiological studies were carried out on samples from the external environment of infected cases, transmission routes, farmers markets and live poultry markets. Phylogenetic study of viral sequences from human and avian infections in Zhejiang showed that those from Shanghai and Jiangsu provinces along Taihu Lake were highly homologous with those from the external environment. This suggests that avian viruses carried by waterfowl combined with the virus carried by migratory birds, giving rise to avian influenza virus H7N9, which is highly pathogenic to humans. It is possible that the virus was transmitted by local wildfowl to domestic poultry and then to humans, or spread further by means of trading in wholesale poultry markets. As the weather has turned warm, and with measures adopted to terminate poultry trade and facilitate health communication, the epidemic in the first half of the year has been kept under control. However, the infection source in the triangular area around Taihu Lake still remains. The H7N9 epidemic will probably hit the area later in the year and next spring when the migratory birds return and may even spread to other areas. Great importance should therefore be attached to the wildfowl in Taihu Lake as the repository and disseminator of the virus: investigation and study of this population is essential.",fresh water;article;avian influenza;avian influenza virus;human;hypothesis;influenza A (H7N9);influenza A;Influenza A virus (H7N9);lake;major clinical study;migrant bird;nonhuman;nucleotide sequence;phylogeny;priority journal;real time polymerase chain reaction;reverse transcription polymerase chain reaction;sequence analysis;virus transmission,"Ling, F.;Chen, E.;Liu, Q.;Miao, Z.;Gong, Z.",2015,,10.1111/zph.12110,0
1183,Turkey rhinotracheitis virus: in vivo and in vitro polypeptide synthesis,"Turkey rhinotracheitis (TRT) virus is a paramyxovirus associated with recent outbreaks of acute respiratory disease in turkeys. On morphological criteria it resembles the pneumoviruses more than the other members of the paramyxovirus family. In this communication we report the identification of five virus-induced polypeptides in TRT virus-infected BS-C-1 cells. The Mr of these polypeptides were estimated as 38K, 35K, 30K, 19K and 15K from their electrophoretic mobility in SDS-polyacrylamide 6 to 15% gradient gels. The virus specificity of four (the 38K, 35K, 30K and 19K Mr polypeptides) of these five was confirmed by their predominance as products of in vitro translation of mRNA from TRT virus-infected BS-C-1 cells. An additional virus-specific polypeptide with an estimated Mr of 22K was revealed by in vitro translation and may be either a non-structural polypeptide or a minor structural protein. All six polypeptides were immunoprecipitated by a murine antiserum. Three other polypeptides (129K, 57K and 45K) were also immunoprecipitated. The 57K, 45K and 15K Mr polypeptides were glycosylated, and the 57K glycopolypeptide may be a disulphide-bonded dimer of the 45K and 15K glycopolypeptides. Another major glycopolypeptide of 83K Mr was observed but its virus-specificity could not be confirmed. Taken together our results tentatively identify eight or nine TRT virus-specified polypeptides and are consistent with the classification of TRT virus as a new member of the genus Pneumovirus.",glycoprotein;messenger RNA;peptide;virus antibody;viral protein;virus RNA;animal;article;biosynthesis;cell line;Cercopithecus;classification;immunology;kidney;metabolism;microbiology;molecular weight;Paramyxoviridae;peptide synthesis;turkey (bird),"Ling, R.;Pringle, C. R.",1988,,,0
1184,Viral metagenomics reveals significant viruses in the genital tract of apparently healthy dairy cows,"The virome in genital tract secretion samples collected from 80 dairy cattle in Shanghai, China, was characterized. Viruses detected included members of the families Papillomaviridae, Polyomaviridae, Hepeviridae, Parvoviridae, Astroviridae, Picornaviridae, and Picobirnaviridae. A member of a new species within the genus Dyoxipapillomavirus and six circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viral genomes were fully sequenced and phylogenetically analyzed. The prevalence of bovine polyomaviruses 1 and 2 was measured by PCR to be 10% (8/80) and 6.25% (5/80), respectively. PCR screening also indicated that the novel papillomavirus ujs-21015 and bovine herpesvirus 6 were present in three and two out of the 80 samples, respectively.",,"Ling, Y.;Zhang, X.;Qi, G.;Yang, S.;Jingjiao, L.;Shen, Q.;Wang, X.;Cui, L.;Hua, X.;Deng, X.;Delwart, E.;Zhang, W.",2019,Feb 19,,1
1185,"The fecal virome of children with hand, foot, and mouth disease that tested PCR negative for pathogenic enteroviruses","Hand, foot, and mouth disease (HFMD) affects infant and young children. A viral metagenomic approach was used to identify the eukaryotic viruses in fecal samples from 29 Thai children with clinical diagnosis of HFMD collected during the 2012 outbreak. These children had previously tested negative by PCR for enterovirus 71 and coxsackievirus A16 and A6. Deep sequencing revealed nine virus families: Picornaviridae, Astroviridae, Parvoviridae, Caliciviridae, Paramyxoviridae, Adenoviridae, Reoviridae, Picobirnaviridae, and Polyomaviridae. The highest number of viral sequences belonged to human rhinovirus C, astrovirus- MLB2, and coxsackievirus A21. Our study provides an overview of virus community and highlights a broad diversity of viruses found in feces from children with HFMD. Copyright:",Adenoviridae;article;Astroviridae;Caliciviridae;child;controlled study;Coxsackievirus A16;Coxsackievirus A6;Enterovirus;Enterovirus A71;feces analysis;female;hand foot and mouth disease;human;infant;male;nonhuman;Paramyxoviridae;Parvoviridae;Picobirnaviridae;Picornaviridae;polymerase chain reaction;Polyomaviridae;preschool child;Reoviridae;sequence analysis;species diversity;virus identification,"Linsuwanon, P.;Poovorawan, Y.;Li, L.;Deng, X.;Vongpunsawad, S.;Delwart, E.",2015,,10.1371/journal.pone.0135573,0
1186,"Influenza (H5N1) viruses in poultry, Russian Federation, 2005-2006","We studied 7 influenza (H5N1) viruses isolated from poultry in western Siberia and the European part of the Russian Federation during July 2005-February 2006. Full genome sequences showed high homology to Qinghai-like influenza (H5N1) viruses. Phylogenetic analysis not only showed a close genetic relationship between the H5N1 strains isolated from poultry and wild migratory waterfowls but also suggested genetic reassortment among the analyzed isolates. Analysis of deduced amino acid sequences of the M2 and neuraminidase proteins showed that all isolates are potentially sensitive to currently available antiviral drugs. Pathogenicity testing showed that all studied viruses were highly pathogenic in chickens; for 3 isolates tested in mice and 2 tested in ferrets, pathogenicity was heterogeneous. Pathogenicity in mammalian models was generally correlated with Lys at residue 627 of polymerase basic protein 2.",amantadine;antivirus agent;oseltamivir;sialidase;amino acid sequence;article;chicken;controlled study;gene sequence;Influenza A virus (H5N1);nonhuman;pathogenicity;phylogeny;poultry;virus isolation,"Lipatov, A. S.;Evseenko, V. A.;Yen, H. L.;Zaykovskaya, A. V.;Durimanov, A. G.;Zolotykh, S. I.;Netesov, S. V.;Drozdov, I. G.;Onishchenko, G. G.;Webster, R. G.;Shestopalov, A. M.",2007,,,0
1187,Viral surveillance and discovery,"The field of virus discovery has burgeoned with the advent of high throughput sequencing platforms and bioinformatics programs that enable rapid identification and molecular characterization of known and novel agents, investments in global microbial surveillance that include wildlife and domestic animals as well as humans, and recognition that viruses may be implicated in chronic as well as acute diseases. Here we review methods for viral surveillance and discovery, strategies and pitfalls in linking discoveries to disease, and identify opportunities for improvements in sequencing instrumentation and analysis, the use of social media and medical informatics that will further advance clinical medicine and public health. © 2013 Elsevier B.V. All rights reserved.",adaptive immunity;article;disease surveillance;DNA sequence;electron microscopy;high throughput sequencing;human;immunohistochemistry;immunoprecipitation;in situ hybridization;innate immunity;medical informatics;multiplex polymerase chain reaction;nonhuman;pathogenesis;priority journal;protein synthesis;serology;social media;tissue culture;vaccination;virus infection;virus transcription,"Lipkin, W. I.;Firth, C.",2013,,10.1016/j.coviro.2013.03.010,0
1188,Genetic characterization and mutation analysis of Qihe547 Aujeszky's disease virus in China,"Background: Aujeszky's disease virus (ADV) can cause neurologic disease in young pigs, respiratory disease in older pigs and abortion or birth of mummified fetuses or stillborn neonates. The re-emergence of Aujeszky's disease (AD) in pig farms vaccinated with live vaccine (Bartha-K61) caused substantial economic losses to Chinese pig industry since late 2011. A field ADV, named Qihe547, was isolated from pigs that exhibited suspected AD clinical symptoms. To better understand the genetic characteristics and mutations of Qihe547 ADV, the whole genome was sequenced and analyzed. Results: The genomic length of Qihe547 ADV was 143,404 bp, with 73.59% G + C contents. Phylogenetic analysis based on the whole genome of ADV strains revealed that Chinese ADV strains were located to one group with three subgroups. Qihe547 ADV was closely related to these novel ADV strains isolated in China since 2012. Qihe547 presented numerous hypervariable regions compared with oversea ADV strains. In 34 genes of Qihe547 ADV, amino acid (AA) insertion or deletion were observed. In addition, numerous AA mutations were found in the main protective antigen genes (gB, gC and gD genes). The differences of potential antigenic peptides in the main protective antigens between Qihe547 ADV and ADV Bartha were discovered in the dominant antigenic regions of gB (AA59-AA126, AA507-AA734),the extracellular region of gC and gD. Conclusion: High diversity was observed between Qihe547 and foreign ADV isolates. The AA variations and the differences of potential antigenic peptides in the important functional regions of the main protective antigen (gB, gC and gD) of ADV Qihe547 may contribute to immune evasion of the virus and may be partial reason that the virus escapes from the vaccination of Bartha-K61 vaccine. In a word, the effect of the variations obviously requires further research.",virus antigen;amino acid sequence;animal cell;animal tissue;article;China;controlled study;cytopathogenic effect;DNA sequence;fluorescence microscopy;gB gene;gC gene;gD gene;gene;gene control;genetic analysis;herd;immune evasion;immunofluorescence;mutational analysis;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;pig;pseudorabies;Pseudorabies virus;Pseudorabies virus Qihe547;real time polymerase chain reaction;Sanger sequencing;virus identification;virus infectivity;virus isolation;virus replication;whole genome sequencing,"Liu, C.;Liu, Y.;Tian, Y.;Wei, X.;Zhang, Y.;Tian, F.",2018,,10.1186/s12917-018-1492-2,0
1189,"First report of feline bocavirus associated with severe enteritis of cat in Northeast China, 2015","Feline bocavirus (FBoV) is a newly identified bocavirus of cats in the family Parvoviridae. A novel FBoV HRB2015-LDF was first identified from the cat with severe enteritis in Northeast China, with an overall positive rate of 2.78% (1/36). Phylogenetic and homologous analysis of the complete genome showed that FBoV HRB2015-LDF was clustered into the FBoV branch and closely related to other FBoVs, with 68.7-97.5% identities. And the genes of VP1, NPA and NS1 shared 70.7-97.6, 72.4-98.6 and 67.2-98.0% nucleotide identities with other FBoVs, respectively. The results suggested that the FBoVs could be divided into two distinct lineages, and the difference of nucleotide identities was >20-30% between the lineages.",cat;China;enteritis;feline bocavirus (FBoV);genetic analysis;MINUTE VIRUS;BOVINE PARVOVIRUS;FECAL VIROME;CANINE BOCAVIRUSES;VIRAL;FLORA;IDENTIFICATION;DOGS;INFECTION;PREVALENT;SEQUENCE,"Liu, C. G.;Liu, F.;Li, Z. G.;Qu, L. D.;Liu, D. F.",2018,Apr,,0
1190,"Emerging multiple reassortant H5N5 avian influenza viruses in ducks, China, 2008","Three highly pathogenic H5N5 avian influenza viruses (HPAI), A/duck/Guangdong/wy11/2008 (WY11), A/duck/Guangdong/wy19/2008 (WY19), and A/duck/Guangdong/wy24/2008 (WY24) were isolated from ducks in southern China in April 2008. Here, we characterized these viruses by performing sequencing and phylogenetic analyses of their viral genes, assessing their virulence in ducks and mice, and performing cross-protection experiments in chickens. Sequence analysis revealed that the HA genes of these H5N5 viruses showed 97.1-97.8% homology to A/wild duck/Hunan/211/2005 (H5N1) influenza virus and that their NA genes showed 96.4-96.8% nucleotide identity to the NA gene of A/duck/Hunan/5613/2003 (H6N5) influenza virus, which belongs to the Eurasian lineage. Genotypic analysis indicated that these H5N5 viruses were multiple reassortants among H5N1, H5N2, H6N2, and H6N5 viruses. The analysis of HA clade showed that these H5N5 viruses are clustering into clade 2.3.4. In animal experiments, these H5N5 viruses caused 50% mortality in ducks and 100% mortality in chickens. In cross-protection experiments, the clade 2.3.2 avian influenza vaccine could provide only 75% protection with chickens against H5N5 virus challenge. Moreover, the H5N5 virus replicated efficiently in the lungs of mice, which suggested that the H5N5 viruses have the potential to infect mammalian hosts. Since ducks have served as reassortant vessels, playing pivotal roles in the generation of new subtypes of influenza viruses, it is important to monitor the emergence of this novel subtype of influenza viruses in waterfowl to understand their ecology and evolution and to control the spread of new viruses. © 2013 Elsevier B.V.",animal experiment;animal tissue;antibody titer;article;avian influenza virus;avian influenza virus H5N5;chicken;China;cladistics;controlled study;cross protection;duck;gene sequence;genetic reassortment;genotype;histochemistry;Influenza A virus (H5N1);Influenza A virus (H5N2);Influenza virus A H6N2;Influenza virus A H6N5;mortality;mouse;nonhuman;nucleotide sequence;pathogenicity;phylogeny;protein motif;sequence analysis;virus gene;virus replication;virus virulence,"Liu, C. G.;Liu, M.;Liu, F.;Lv, R.;Liu, D. F.;Qu, L. D.;Zhang, Y.",2013,,10.1016/j.vetmic.2013.09.004,0
1191,Development of reverse genetics system for small ruminant morbillivirus: Rescuing recombinant virus to express Echinococcus granulosus EG95 antigen,"Peste des petits ruminants and cystic hydatidosis may be simultaneously endemic in a given area. Their pathogens are small ruminant morbillivirus (SRMV) and Echinococcus granulosus (E. granulosus), respectively. The SRMV, formerly called peste-des-petits-ruminants virus (PPRV), is classified into the genus Morbillivirus in the family Paramyxoviridae. This virus is an ideal vaccine vector to deliver immunogenic proteins. In this study, a reverse genetics system was developed to rescue a recombinant SRMV (Nigeria 75/1 strain) expressing E. granulosus EG95 antigen in vitro. The recombinant SRMV, albeit replicating more slowly than its parental virus, could effectively express the EG95 antigen in cells by analyses of Western blot, indirect immunofluorescence and mass spectrometry. An EG95 subunit vaccine has been widely used for prevention of cystic hydatidosis in some areas of China. The EG95-expressing SRMV, if proven to induce effective immune responses against both diseases in a future animal experiment, would become a potential candidate of bivalent vaccine.",antigen;Echinococcus granulosus antigen;unclassified drug;agar gel electrophoresis;amino acid sequence;antigen expression;article;controlled study;echinococcosis;genetic transfection;immunofluorescence;in vitro study;mass spectrometry;Morbillivirus;nonhuman;peste des petits ruminants;phenotype;priority journal;reverse genetics;reverse transcription polymerase chain reaction;Sanger sequencing;small ruminant morbillivirus;virus recombinant;Western blotting,"Liu, F.;Li, L.;Liu, Y.;Sun, C.;Liu, C.;Wu, X.;Wang, Z.",2019,,10.1016/j.virusres.2018.12.008,0
1192,Rescue of eGFP-expressing small ruminant morbillivirus for identifying susceptibilities of eight mammalian cell lines to its infection,"Small ruminant morbillivirus (SRMV), formerly called peste-des-petits-ruminants virus (PPRV), is classified into the genus Morbillivirus in the family Paramyxoviridae. If genetically modified using reverse genetics, the SRMV would be a useful vector to express foreign proteins in vitro and in vivo. In this study, a recombinant SRMV was rescued by reverse genetics for efficiently expressing an enhanced green fluorescent protein (eGFP) in vitro. Based on green fluorescence-tracked characteristics of the recombinant SRMV, eight mammalian cell lines (BHK-21, F81, MDBK, RK13, MDCK, PK15, Vero and GT) were selected for identifying their susceptibilities to SRMV infection. The result showed that all cell lines could be infected with the recombinant SRMV but at different efficiencies. The Vero and PK15 cell lines showed the highest and lowest susceptibilities to its infection, respectively, if merely comparing the proportions of green fluorescence-emitting cells among eight cell monolayers.",enhanced green fluorescent protein;animal cell;article;BHK-21 cell line;cell line;controlled study;F81 cell line;gene expression;GT cell line;in vitro study;infection sensitivity;mammal cell;MDBK cell line;MDCK cell line;nonhuman;peste des petits ruminants;Peste-des-petits-ruminants virus;PK-15 cell line;priority journal;reverse genetics;RK 13 cell line;small ruminant morbillivirus;Vero cell line;virus recombinant,"Liu, F.;Zhang, Y.;Li, L.;Zuo, Y.;Sun, C.;Xiaodong, W.;Wang, Z.",2019,,10.1016/j.virusres.2018.12.011,0
1193,Identification and analysis of novel viral and host dysregulated MicroRNAs in variant pseudorabies virus-infected PK15 cells,"Pseudorabies (PR) is one of the most devastating diseases in the pig industry. To identify changes in microRNA(miRNA) expression and post-transcriptional regulatory responses to PRV infection in porcine kidney epithelial (PK15) cells, we sequenced a small RNA (sRNA) library prepared from infected PK15 cells and compared it to a library prepared from uninfected cells using Illumina deep sequencing. Here we found 25 novel viral miRNAs by high throughput sequencing and 20 of these miRNAs were confirmed through stem-loop RT-qPCR. Intriguingly, unlike the usual miRNAs encoded by the α-herpesviruses, which are found clustered in the large latency transcript (LLT), these novel viral miRNAs are throughout the PRV genome like β-herpesviruses. Viral miRNAs are predicted to target multiple genes and form a complex regulatory network. GO analysis on host targets of viral miRNAs were involved in complex cellular processes, including the metabolic pathway, biological regulation, stimulus response, signaling process and immune response. Moreover, 13 host miRNAs were expressed with significant difference after infection with PRV: 8 miRNAs were up-regulated and 5 miRNAs were down-regulated, which may affect viral replication in host cell. Our results provided new insight into the characteristic of miRNAs in response to PRV infection, which is significant for further study of these miRNAs function.",microRNA;article;controlled study;down regulation;epithelium cell;gene regulatory network;gene sequence;genetic code;Herpesviridae;high throughput sequencing;host cell;immune response;kidney epithelium;nonhuman;polymerase chain reaction;Pseudorabies virus;stimulus response;upregulation;virus cell interaction;virus replication,"Liu, F.;Zheng, H.;Tong, W.;Li, G. X.;Tian, Q.;Liang, C.;Li, L. W.;Zheng, X. C.;Tong, G. Z.",2016,,10.1371/journal.pone.0151546,0
1194,Genetic diversity of the VP1 gene of duck hepatitis virus type I (DHV-I) isolates from southeast China is related to isolate attenuation,"The complete sequence of an isolate (ZJ-V) of Duck hepatitis virus I (DHV-I), originally taken from the field in southeast China was determined. It was 7691 nucleotides long and had 5′- and 3′-terminal non-coding regions of 626 and 315 nucleotides, respectively. The poly(A) tail contained at least 22 residues and the single open reading frame encoded a polypeptide of 2249 amino acids. The VP1 gene was also sequenced from nine southeast China field isolates and three attenuated DHV-I vaccine strains. In phylogenetic analysis of the isolates and other published sequences, attenuated and tissue-adapted isolates (including ZJ-V) clustered as genotypes significantly different from the field isolates that had not been passaged in chicken/duck embryos. There were two consistent amino acid substitutions (E129 → V129 and A142 → S142) between all the field isolates and all the tissue-adapted ones. The carboxyl terminal region was generally the most variable and here the four attenuated Chinese isolates showed six consistent differences from the field isolates (S181 → L181, H183K184 → R183G1841, N193 → D193, E205 → K205, R217 → K217, N235 → D235). It seems likely that at least some of these differences result from mutations leading to isolate attenuation. © 2008 Elsevier B.V. All rights reserved.",polypeptide;protein VP1;amino acid sequence;amino acid substitution;animal tissue;article;carboxy terminal sequence;China;controlled study;gene mutation;genetic variability;hepatitis virus;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal,"Liu, G.;Wang, F.;Ni, Z.;Yun, T.;Yu, B.;Huang, J.;Chen, J.",2008,,10.1016/j.virusres.2008.04.030,0
1195,Complete genomic sequence of a Chinese isolate of Duck hepatitis virus,"The complete genomic sequence of Duck hepatitis virus 1 (DHV-1) ZJ-V isolate was sequenced and determined to be 7 691 nucleotides (nt) in length with a 5′-terminal un-translated region (UTR) of 626 nt and a 3′-terminal UTR of 315 nt (not including the poly(A) tail). One large open reading frame (ORF) was found within the genome (nt 627 to 7 373) coding for a polypeptide of 2 249 amino acids. Our data also showed that the poly (A) tail of DHV-1 has at least 22 A's. Sequence comparison revealed significant homology (from 91.9% to 95.7%) between the protein sequences of the ZJ-V isolate and those of 21 reference isolates. Although DHV-1 has been classified as an unassigned virus in the Picornaviridae family, its genome showed some unique characteristics. DHV-1 contains 3 copies of the 2A gene and only 1 copy of the 3B gene, and its 3′-NCR is longer than those of other picornaviruses. Phylogenetic analysis to do sequence homology based on the VP1 protein sequences showed that the ZJ-V isolate shares high sequence homology with the reported DHV-1 isolates (from 92.9% to 99.2%), indicating that DHV-1 is genetically stable.",amino acid derivative;nucleotide;polyadenylic acid;polypeptide;protein VP1;3' untranslated region;5' untranslated region;amino acid sequence;amino terminal sequence;article;Chinese;controlled study;gene sequence;genetic code;genetic stability;hepatitis virus;multigene family;nonhuman;nucleotide sequence;open reading frame;phylogeny;Picornaviridae;sequence homology;virus classification;virus genome;virus isolation,"Liu, G. Q.;Wang, F.;Ni, Z.;Yun, T.;Yu, B.;Huang, J. G.;Chen, J. P.",2007,,,0
1196,Genomic characterization of the first class I Newcastle disease virus isolated from the mainland of China,"The complete genomic sequence of Newcastle disease virus (NDV) strain NDV08-004, isolated from domestic ducks in China, was determined in this study. The genome is 15198 nucleotides (nt) in length, follows the ""rule of six"" and contains a 55-nt leader sequence at the 3′ end and a 114-nt trailer sequence at the 5′ end. Compared with the full genome sequences of Class II NDV strains, the NDV08-004 isolate has a 12-nt insertion (TGGGA GACGGGG) in the phosphoprotein gene between nucleotides 2381 and 2382 of the genome (numbered according to the genomic sequence of the La Sota strain, which consists of 15186 nt). Strain NDV08-004 has the motif 112E-Q-Q-E-R- L117 at the cleavage site of the fusion protein, which is typical of lentogenic NDV strains, and this is in agreement with the results of pathogenic tests based on the mean death time (MDT) and the intracerebral pathogenicity index (ICPI). Phylogenetic analysis based on the full genome revealed that all the NDV strains studied could be divided into two distinct clades, namely class I and class II, and the NDV08-004 isolate characterized in this study was grouped in class I. Further phylogenetic analysis based on a 374-bp fragment of the F gene in class I strains of NDV demonstrated that NDV08-004 belongs to genotype 3, and should be therefore similar to strains obtained from live bird markets in Hong Kong in recent years. © Springer Science+Business Media, LLC 2010.",fusion protein;nucleotide;phosphoprotein;article;binding site;China;controlled study;duck;gene insertion;gene sequence;genetic trait;genomics;genotype;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;priority journal;protein binding;protein motif;unindexed sequence;virus genome;virus isolation;virus strain;virus virulence,"Liu, H.;Chen, F.;Zhao, Y.;Zheng, D.;Li, J.;Xu, T.;Qi, L.;Wang, Z.",2010,,10.1007/s11262-010-0452-0,0
1197,Isolation and molecular and phylogenetic analyses of encephalomyocarditis virus from wild boar in central China,"Encephalomyocarditis virus (EMCV) can infect many host species and cause acute myocarditis and respiratory failure in piglets, reproductive failure in pregnant sows. In this study, an EMCV strain, designated JZ1202, was isolated from semi-captive wild boars that presented with acute myocarditis and sudden death in central China. It was identified by hemagglutination inhibition (HI) assay, reverse transcription polymerase chain reaction (RT-PCR) and genome sequencing. The subsequent results showed that the virus could produce a specific cytopathic effect on BHK cells and could cause clinical symptoms and pathological changes in mice. Complete genome sequencing and multiple sequence alignment indicated that JZ1202 strain was 81.3%-99.9% identical with other isolates worldwide. Phylogenetic analysis of the whole genome, ORF, VP3/VP1 and 3D genes using neighbor-joining method revealed that JZ1202 isolate was grouped into lineage 1. The results of this study confirmed that an EMCV strain JZ 1202 isolated from wild boar in central China was fatal to mice and provided new epidemiologic data on EMCV in China.",animal experiment;animal model;animal tissue;article;Cardiovirus infection;cell infiltration;controlled study;Encephalomyocarditis virus;gene amplification;gene sequence;cardiac muscle;hemagglutination inhibition;histopathology;molecular phylogeny;mouse;nonhuman;nucleotide sequence;open reading frame;priority journal;rat;reverse transcription polymerase chain reaction;sequence alignment;virus isolation;virus strain;European wild boar,"Liu, H.;He, X.;Song, X.;Xu, L.;Zhang, Y.;Zhou, G.;Zhu, W.;Chang, C.;Yin, Z.;Shi, Y.;Wang, C.;Chang, H.",2016,,10.1016/j.meegid.2016.02.025,0
1198,Complete genome sequences and phylogenetic analysis of encephalomyocarditis virus strains isolated from pigs and rats origin,"In order to evaluate the genetic variability of encephalomyocarditis virus (EMCV), the whole genomes of six EMCV field isolates originating from pigs and rats origin in different regions of central China, were phylogenetically and comparatively analyzed. Phylogenetic analysis of whole genome sequences, open reading frame (ORF), capsid coding region (CCR) and VP3/VP1 using neighbor-joining analysis revealed that these isolates belonged to lineage 1. Nucleotide sequences of six isolates showed more than 99% pairwise identity rates, and the sequences of isolates from pig and boar in the same region were completely identical with each other, without any genetic deletion or insertion. From comparative analysis of variability of each EMCV protein coding region, 3D and VP3 regions showed that the highest average identity rates, and was confirmed as highly conserved. In contrast, the protein coding regions 3A and 3B was confirmed to be highly variable region with the lowest average identity rate. Our data confirmed that the EMCV strains isolated from pigs and rats origin had high homology with each other, which implied rats may play an important role in EMCV transmission between domestic pigs and wild boars.",Encephalomyocarditis virus protein;unclassified drug;viral protein;article;capsid coding region;cell lineage;China;Encephalomyocarditis virus;gene deletion;gene insertion;gene sequence;genetic variability;nonhuman;nucleotide sequence;open reading frame;phylogeny;pig;priority journal;promoter region;virus capsid;virus genome;virus isolation,"Liu, H.;Li, Y.;Zhang, G.;Sang, S.;Wang, C.;Chang, H.",2017,,10.1016/j.meegid.2017.09.032,0
1199,"Japanese encephalitis virus in mosquitoes and swine in Yunnan province, China 2009–2010",,,"Liu, H.;Lu, H. J.;Liu, Z. J.;Jing, J.;Ren, J. Q.;Liu, Y. Y.",2013,,,0
1200,Characterization of Newcastle disease virus isolated from waterfowl in China,"Ten representative isolates of Newcastle disease virus (NDV) obtained from outbreaks in waterfowl (geese and ducks) in China since 1997 were characterized both pathotypically and genotypically. The mean death time and intracerebral pathogenicity index were used to evaluate the virulence of the isolates. Pathogenicity tests showed that all 10 isolates were velogenic strains. The main functional region of the F gene made up of 535 nucleotides was amplified by reverse transcription-polymerase chain reaction and sequenced. The deduced amino acid sequence of the fusion protein cleavage site in all 10 isolates was 112RRQKRF117, which is a typical sequence of velogenic strains and is in agreement with the results of in vivo pathogenicity tests. For genotyping, a phylogenetic tree based on nucleotides 47-435 of the F gene was constructed. Phylogenetic analysis showed that most of the isolates were of the genotype VII virus. Only one strain, WG, was found to be of the genotype IX virus. This strain was closest to F48E9, which was isolated in China in 1946 and has been used as a standard challenge strain in vaccine evaluation in China. So, genotype IX virus still causes sporadic infections in geese in China. Further phylogenetic analyses on the genotype VII strains found that all these strains can be subdivided into 5 subgenotypes, and most of the isolates (8 strains) were classified as VIId, a predominant genotype responsible for most Newcastle disease (ND) outbreaks since the end of the past century in China. Only 1 strain, NDV03-053, was shown to be of genotype VIIc virus. Results indicate that the strains of genotype VIId NDV have been the major pathogen, responsible for most epizootic ND outbreaks in waterfowl in China since 1997.",amino acid sequence;animal;animal disease;article;bird disease;chick embryo;China;duck;epidemic;genetics;germfree animal;goose;isolation and purification;Newcastle disease virus;nucleotide sequence;pathogenicity;phylogeny;randomization;reverse transcription polymerase chain reaction;virology;virulence,"Liu, H.;Wang, Z.;Wang, Y.;Sun, C.;Zheng, D.;Wu, Y.",2008,,10.1637/8030-061507-Reg,0
1201,Molecular characterization and phylogenetic analysis of new Newcastle disease virus isolates from the mainland of China,"Seventy-nine velogenic Newcastle disease virus (NDV) isolates were obtained from infected chicken flocks during the outbreaks of Newcastle disease (ND) in various regions of the mainland of China in 2006. The F gene fragment (535 bp, from nt 47 to 581 of the F gene) which codes the main functional region of the F protein was obtained by RT-PCR and sequenced. All sequences obtained in this study have been submitted to GenBank. All the isolates have the motif 112R-R-Q/R-K/R-R-F117 at the cleavage site of the fusion protein, which is typical of velogenic NDV isolates. For genotyping, a phylogenetic tree based on nucleotides 47-435 of the F gene was constructed, and the 79 isolates could be divided into two genotypes, namely VIId and III. Most of the isolates proved to be of genotype VIId; only two isolates were of genotype III. Genotype VIId NDV has been the predominant pathogen responsible for most Newcastle disease outbreaks in China. The proportion of isolates of genotype VIId NDV shows an increasing trend, according to studies on the molecular epidemiology of NDV in China from 2002 to 2006. © 2008 Elsevier Ltd. All rights reserved.",F protein;fusion protein;viral protein;article;base pairing;bird disease;chicken;China;epidemic;gene construct;gene sequence;genome analysis;genotype;molecular epidemiology;Newcastle disease virus;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;protein degradation;protein motif;reverse transcription polymerase chain reaction;RNA virus infection;sequence analysis;trend study;virus characterization;virus isolation,"Liu, H.;Wang, Z.;Wu, Y.;Wu, Y.;Sun, C.;Zheng, D.;Xu, T.;Li, J.",2008,,10.1016/j.rvsc.2008.02.013,0
1202,Molecular epidemiological analysis of Newcastle disease virus isolated in China in 2005,"Eighty-three strains of Newcastle disease virus (NDV) were obtained from outbreaks in chickens, pigeons, geese, and ducks in China in 2005 and characterized genotypically. The main functional region of the F gene (535 nucleotides) was amplified and sequenced. A phylogenetic tree based on nucleotides 47-435 of the F gene was created using sequences from 83 isolates and representative NDV sequences obtained from GenBank. Phylogenetic analysis showed that all newly characterized strains belonged to six genetic groups: I, II, III, VIb, VIIc, and VIId. All the isolates belonging to groups I and II (14 total) were lentogenic according to the amino acid sequences of the fusion protein cleavage site, and either V4 or LaSota-type, depending on the vaccines that were used. Most isolates (64 total) were classified in group VIId, a predominant genotype responsible for most Newcastle disease outbreaks since the end of the last century. One strain, NDV05-055, was in group VIIc, three pigeon strains were in group VIb, and one isolate, NDV05-041, was in group III, and characterized as a velogenic strain. This study revealed that genotype VIId was the major NDV strain responsible for the 2005 ND epizoonosis that occurred in China. © 2006 Elsevier B.V. All rights reserved.",amino acid sequence;article;bird disease;chicken;China;duck;epidemic;gene amplification;gene sequence;genotype;goose;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;Columbidae;priority journal;protein degradation;virus isolation;virus strain,"Liu, H.;Wang, Z.;Wu, Y.;Zheng, D.;Sun, C.;Bi, D.;Zuo, Y.;Xu, T.",2007,,10.1016/j.jviromet.2006.10.012,0
1203,Phylogenetic characterization and virulence of two Newcastle disease viruses isolated from wild birds in China,"Wild birds are considered as a natural reservoir of Newcastle disease virus (NDV). However, there is no information about genotype IX NDV from wild birds, especially from Columbiformes. In this study, two genotype IX NDV viruses were isolated from wild birds. One was from Eurasian Blackbird, while the other was from Spotted-necked dove. After purification by plaque technique, complete genomes of both viruses were sequenced. Phylogenetic analysis of partial fusion (F) gene and complete genome indicated both strains belonged to genotype IX. Based on intracerebral pathogenicity index (ICPI), the virus from Eurasian Blackbird was velogenic virus, while the strain from Spotted-necked dove was lentogenic virus. However, both strains showed one of velogenic cleavage sites. In addition, the strain from Eurasian Blackbird showed greater replication ability and generated larger fusion foci in vitro than that of strain from Spotted-necked dove. Comparing all the corresponding protein sequences of both strains, there were only 9 different amino acid residues between them. Furthermore, after analysis of these differences, the information about lentogenic NDV with multi-basic cleavage site was presented.","Amino Acid Sequence;Animals;Animals, Wild/vi [Virology];Base Sequence;Chickens/im [Immunology];Chickens/vi [Virology];China;*Columbiformes/vi [Virology];Genome, Viral/ge [Genetics];Immunization;Newcastle Disease/pc [Prevention & Control];*Newcastle Disease/vi [Virology];*Newcastle disease virus/cl [Classification];Newcastle disease virus/ge [Genetics];*Newcastle disease virus/py [Pathogenicity];Nucleoproteins/ge [Genetics];Phylogeny;Poultry Diseases/im [Immunology];Poultry Diseases/vi [Virology];Sequence Alignment;Sequence Analysis, RNA/ve [Veterinary];Viral Fusion Proteins/ge [Genetics];Viral Proteins/ge [Genetics];Viral Vaccines/im [Immunology];0 (L protein, paramyxoviridae);0 (Nucleoproteins);0 (V protein, Paramyxovirus);0 (Viral Fusion Proteins);0 (Viral Proteins);0 (Viral Vaccines);0 (nucleoprotein, Newcastle disease virus)","Liu, H.;Zhang, P.;Wu, P.;Chen, S.;Mu, G.;Duan, X.;Hao, H.;Du, E.;Wang, X.;Yang, Z.",2013,Dec,,0
1204,"Rapid characterization of avian reoviruses using phylogenetic analysis, reverse transcription-polymerase chain reaction and restriction enzyme fragment length polymorphism","A reverse transcription-polymerase chain reaction is described, which amplified the full-length sigmaC-encoding and sigmaNS-encoding genes of avian reovirus (ARV). DNA fragments of 1022 and 1152 base pairs were amplified among ARV isolates, respectively, indicating that there were no apparent deletions or insertions in these regions. Fragments amplified from vaccine strains and field isolates were digested with five different restriction enzymes Bcn I, Hae III, Taq I, Dde I, and Hinc II, respectively. Restriction fragment profiles observed on polyacrylamide gels showed heterogeneity between vaccine and Taiwanese isolates. All ARV isolates tested showed different restriction enzyme cleavage patterns and could be clearly distinguished. The strain-typing based on the cleavage sites in the sigmaC-encoding gene of ARV showed that viruses could be classified into four distinct groups. A phylogenetic tree based on the nucleotide sequences of the sigmaC-encoding gene revealed that Taiwanese ARV isolates were classified into four distinct groups, indicating that the genotyping is consistent with typing based on restriction enzyme fragment length polymorphism of the sigmaC-encoding gene of ARV. The results suggested that polymerase chain reaction followed by restriction enzyme analysis provided a simple and rapid approach for characterization of ARV isolates. Also, it is possible to determine whether a new variant strain has been introduced into a flock or a given virus strain has spread from one flock to another.",LINKED-IMMUNOSORBENT-ASSAY;PROTEIN SIGMA-A;GENOME SEGMENT;INVIVO;CHARACTERIZATION;ENDONUCLEASE ANALYSIS;STRAIN S1133;VIRUS;CHICKENS;NEUTRALIZATION;IDENTIFICATION,"Liu, H. J.;Lee, L. H.;Shih, W. L.;Li, Y. J.;Su, H. Y.",2004,Apr,,0
1205,Complete genome sequence of goose parvovirus Y strain isolated from Muscovy ducks in China,"A goose parvovirus (GPV) Y strain was isolated from Muscovy ducks in Anhui Province of China. By polymerase chain reaction method, its complete genomic sequence was found to be 5,106 bp in length, consisting of 444-bp inverted terminal repeat, 1,844-bp non-structural protein and 2,199-bp capsid protein (VP) regions. Then its sequence was aligned with the sequences of GPV and Muscovy duck parvovirus published in the GenBank using the neighbor-joining method. The phylogenetic analyses based on the VP3 gene sequences revealed that the GPV Y strain along with those from Taiwan belonged to the subgroup IIb, while other GPV strains from Muscovy ducks belonged to the subgroup Ib and most of other GPV strains isolated in China mainland were clustered in the subgroup IIa. The absence of the deduced 703-705NRT glycosylation site in VP region may explain the host specificity of the GPV Y strain. The complete genomic sequence of the GPV Y strain from Muscovy ducks will help to understand the molecular and evolutionary characteristics of GPV. © Springer Science+Business Media 2013.",capsid protein;viral protein;article;China;duck;evolutionary adaptation;gene cluster;gene sequence;gene structure;glycosylation;goose parvovirus Y;host range;inverted terminal repeat;Cairina moschata;neighbor joining method;nonhuman;nucleotide sequence;Parvoviridae;phylogeny;polymerase chain reaction;priority journal;sequence alignment;Taiwan;virus classification;virus gene;virus genome;virus isolation;virus strain;VP3 gene,"Liu, H. M.;Wang, H.;Tian, X. J.;Zhang, S.;Zhou, X. H.;Qi, K. Z.;Pan, L.",2014,,10.1007/s11262-013-1001-4,0
1206,Construction of phylogenetic tree and sequence analysis on BDV p24 gene in both livestock and host in Ningxia,,,"Liu, J.;Liu, Y.;Wang, Z. H.;Xie, P.",2010,,,0
1207,Interregional transmission of the internal protein genes of H2 influenza virus in migratory ducks from North America to Eurasia,"H2 influenza virus caused a pandemic in 1957 and has the possibility to cause outbreaks in the future. To assess the evolutionary characteristics of H2 influenza viruses isolated from migratory ducks that congregate in Hokkaido, Japan, on their flyway of migration from Siberia in 2001, we investigated the phylogenetic relationships among these viruses and avian and human viruses described previously. Phylogenetic analysis showed that the PB2 gene of Dk/Hokkaido/107/01 (H2N3) and the PA gene of Dk/Hokkaido/95/01 (H2N2) belonged to the American lineage of avian virus and that the other genes of the isolates belonged to the Eurasian lineage. These results indicate that the internal protein genes might be transmitted from American to Eurasian avian host. Thus, it is further confirmed that interregional transmission of influenza viruses occurred between the North American and Eurasian birds. The fact that reassortants could be generated in the migratory ducks between North American and Eurasian avian virus lineage further stresses the importance of global surveillance among the migratory ducks.",article;controlled study;duck;genetic analysis;Influenza virus;internal protein gene;nonhuman;North America;nucleotide sequence;phylogeny;priority journal;species comparison;viral genetics;virus gene;virus isolation;virus strain;virus transmission,"Liu, J.;Okazaki, K.;Bai, G.;Shi, W.;Mweene, A.;Kida, H.",2004,,10.1023/B:VIRU.0000032791.26573.f1,0
1208,"Recombination in lineage 1, 3, 5 and 8 of porcine reproductive and respiratory syndrome viruses in China","Porcine reproductive and respiratory syndrome (PRRS) is one of the most important viral swine diseases, resulting in immense economic losses in Chinese pig industry. Currently, four major lineages: lineage 1 (NADC30-like), 3 (QYYZ-like), 5.1 (VR2332-like) and 8.7 (JXA1-like) of type 2 PRRSV (North American type) have been circulating in China based on classification system, which have caused concern about the potential of virus recombination. In the present study, a novel variant of PRRSV strain named FJLIUY-2017 was isolated from abortion rate (25%) in pregnant gilts in Fujian Province in China in 2017. To further our knowledge about the novel virus strain, we characterized the complete genome of FJLIUY-2017. Comparison to PRRS sequences in GenBank confirmed the absence of close relatives (<92%), but indicated FJLIUY-2017 belonged to NADC30-like PRRSV. The full length of FJLIUY-2017 was determined to be 15017 nucleotides (nt), excluding the poly(A) tail, shared 86.2–86.6% identity with JXA1-like strains (JXA1, TJ and FJYR), 88.9–90.6% with NADC30-like PRRSVs (NADC30, FJZ03 and CHsx1401), 86.4–86.5% with VR2332-like (VR2332, RespPRRS MLV and BJ-4) and only 60.8% with LV (European type). Recombination analyses revealed genomic breakpoints in structural (ORF3, ORF4 and ORF7) and nonstructural (Nsp1, Nsp2, Nsp6, Nsp9, Nsp11 and Nsp12) regions of the genomes with evidence for recombination events between lineages 1, 3, 5.1 and 8.7. Taken altogether, the results of our study provide further confirmation that PRRSV is prone to undergo recombination events. Thus, it is critical to monitor PRRSV evolution in China and establish an effective strategy for the control of PRRS.",animal cell;animal tissue;article;China;DNA determination;female;gene structure;gilt (swine);infection control;nonhuman;Nsp1 gene;Nsp11 gene;Nsp12 gene;Nsp2 gene;Nsp6 gene;Nsp9 gene;ORF3 gene;ORF4 gene;ORF7 gene;porcine reproductive and respiratory syndrome;Porcine reproductive and respiratory syndrome virus;Porcine reproductive and respiratory syndrome virus FJLIUY 2017;Porcine reproductive and respiratory syndrome virus JXA1;Porcine reproductive and respiratory syndrome virus NADC30;Porcine reproductive and respiratory syndrome virus QYYZ;Porcine reproductive and respiratory syndrome virus VR2332;priority journal;virus classification;virus gene;virus isolation;virus recombination;virus strain,"Liu, J.;Wei, C.;Lin, Z.;Fan, J.;Xia, W.;Dai, A.;Yang, X.",2019,,10.1016/j.meegid.2018.12.006,0
1209,"Genetic characterization of VP4-VP2 of two coxsackievirus A4 isolated from patients with hand, foot and mouth disease","OBJECTIVE: To study the genetic characteristic of VP4-VP2 of Coxsackievirus A4 (CVA4) isolated from clinical specimens of patients with Hand, foot and mouth disease (HFMD) in Gansu in 2008. METHODS: Two clinical samples were collected from HFMD patients in outpatient service, and then viral isolation was performed by inoculating RD cells. VP4-VP2 region of two viral isolates were amplified by using reverse transcription-polymerase chain reaction methods, and then the PCR products were sequenced; molecular typing was used to identify the serotype of these two viral isolates. Finally phylogenetic tree was constructed among these two Gansu viral isolates and 16 CVA4 strains downloaded from GenBank database. RESULTS: Two Viruses were isolated from the clinical specimens collected from two HFMD patients by inoculating RD cells, and were identified as CVA4 by using molecular typing methods. The homology of the nucleotide sequences in VP4-VP2 region between the two Gansu CVA4 strains was 94.6%, and the homology of the amino acid sequences was 100%. Compared with the prototype strain of CVA4 (Strain High Point/USA/1948), the homologies of nucleotide sequences and amino acid sequences were 85.5%-85.8% and 99.3%, respectively. It revealed that two Gansu CVA4 strains lie in the independence group. CONCLUSION: Compared with CVA4 strains isolated in Japan and Mongolia downloaded from GenBank database, two Gansu CVA4 were found to have great difference on VP4-VP2 region, and phylogenetic analysis revealed that they belong to an independence evolution lineage.",viral protein;article;case report;chemistry;classification;Enterovirus;genetics;hand foot and mouth disease;human;infant;isolation and purification;molecular genetics;sequence alignment;virology,"Liu, J. F.;Zhang, Y.;Li, H.",2009,,,0
1210,Phylogenetic Analysis of Hemagglutinin and Neuraminidase Genes of H9N2 Viruses Isolated from Migratory Ducks,"Genetic analysis indicated that the pandemic influenza strains derived from wild aquatic birds harbor viruses of 15 hemagglutinin (HA) and 9 neuraminidase (NA) antigenic subtypes. Surveillance studies have shown that H9N2 subtype viruses are worldwide in domestic poultry and could infect mammalian species, including humans. Here, we genetically analyzed the HA and NA genes of five H9N2 viruses isolated from the migratory ducks in Hokkaido, Japan, the flyway of migration from Siberia during 1997-2000. The results showed that HA and NA genes of these viruses belong to the same lineages, respectively. Compared with those of A/quail/Hong Kong/G1/97-like and A/duck/Hong Kong/Y280/97-like viruses, HA and NA of the migratory duck isolates had a close relationship with those of H9N2 viruses isolated from the chicken in Korea, indicating that the Korea H9N2 viruses might be derived from the migratory ducks. The NA genes of the five isolates were located in the same cluster as those of N2 viruses, which had caused a human pandemic in 1968, indicating that the NA genes of the previous pandemic strains are still circulating in waterfowl reservoirs. The present results further emphasize the importance of carrying out molecular epidemiological surveillance of H9N2 viruses in wild ducks to obtain more information for the future human influenza pandemics preparedness.",hemagglutinin;sialidase;article;duck;genetic analysis;Influenza virus;Japan;Korea;nonhuman;nucleotide sequence;phylogeny;priority journal;Russian Federation;virus gene;virus isolation,"Liu, J. H.;Okazaki, K.;Shi, W. M.;Kida, H.",2003,,10.1023/a:1026304117797,0
1211,Identification of a novel bufavirus in domestic pigs by a viral metagenomic approach,"Bufavirus is a single-stranded DNA virus belonging to the genus Protoparvovirus. This study reports the identification and characterization of a porcine bufavirus by a metagenomic approach, and a limited epidemiology investigation of bufavirus in six swine farms. A comparative genome analysis showed a similarity of 93% to a Hungarian porcine bufavirus. Bayesian and maximumlikelihood analyses of genome sequences showed a close relationship of porcine bufaviruses to human and monkey bufaviruses. Molecular dating of the most recent common ancestors supported a recent introduction of bufaviruses into human and pig populations, respectively. A real-time PCR method was developed to screen 60 faecal samples for the porcine bufavirus DNA, and eight positive samples were found in two neighbouring farms, suggesting a relatively low prevalence (13.3 %). No direct transmission of porcine bufaviruses between two neighbouring farms was found, suggesting that bufaviruses may have spread widely in different geographical regions.",protein VP1;protein VP2;virus DNA;animal experiment;article;Bayesian learning;bootstrapping;bufavirus;domestic pig;feces analysis;gene sequence;metagenomics;nonhuman;nucleotide sequence;priority journal;Protoparvovirus;real time polymerase chain reaction;virus genome;virus transmission,"Liu, L.;Schwarz, L.;Ullman, K.;Ahola, H.;Qiu, Y.;Ma, Z.;Hennig-Pauka, I.",2016,,10.1099/jgv.0.000476,1
1212,"Phylogeny, classification and evolutionary insights into pestiviruses","The genus Pestivirus comprises four established species: Bovine viral diarrhoea viruses 1 (BVDV-1) and 2 (BVDV-2), Border disease virus (BDV), and Classical swine fever virus (CSFV); and a tentative species, Pestivirus of giraffe. Additional pestiviruses have been identified and suggested for recognition as novel subgroups/species. To achieve a reliable phylogeny as the basis for classification of pestiviruses, a molecular dataset of 56 pestiviruses and 2089 characters, comprising the 5′UTR, complete Npro and E2 gene regions was analysed by Maximum likelihood and Bayesian approach. An identical, robust tree topology was inferred, where seven well-supported monophyletic clades and two highly divergent lineages were identified. Dating most recent common ancestor was estimated for major pestivirus lineages and their evolutionary histories were revealed. Accordingly, a new proposal is presented for the classification of pestiviruses into nine species: BVDV-1, BVDV-2, BVDV-3 (atypical bovine pestiviruses), Pestivirus of giraffe, CSFV, BDV, Tunisian sheep virus (TSV; previously termed ""Tunisian isolates""), Antelope and Bungowannah. © 2008 Elsevier Inc. All rights reserved.",n terminal autoprotease;proteinase;unclassified drug;virus glycoprotein;5' untranslated region;antelope;article;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;Bovine viral diarrhea virus 3;cladistics;controlled study;data base;genetic line;genetic variability;molecular evolution;molecular phylogeny;nonhuman;nucleotide sequence;Pestivirus;Pestivirus of giraffe;priority journal;Tunisian sheep virus;unindexed sequence;virus classification,"Liu, L.;Xia, H.;Wahlberg, N.;Belák, S.;Baule, C.",2009,,10.1016/j.virol.2008.12.004,0
1213,Characterization of Clade 7.2 H5 Avian Influenza Viruses That Continue To Circulate in Chickens in China,"The H5N1 avian influenza viruses emerged in Southeast Asia in the late 20th century and have evolved into multiple phylogenetic clades based on their hemagglutinin (HA)-encoding genes. The clade 7.2 viruses were first detected in chickens in northern China in 2006, and vaccines specifically targeted to the clade were developed and have been used in poultry in China since 2006. During routine surveillance and disease diagnosis, we isolated seven H5 viruses between 2011 and 2014 that bear the clade 7.2 HA genes. Here, we performed extensive studies to understand how the clade 7.2 H5 viruses have evolved in chickens in China. Full genome sequence analysis revealed that the seven viruses formed two subtypes (four H5N1 viruses and three H5N2 viruses) and four genotypes by deriving genes from other influenza viruses. All of the viruses had antigenically drifted from the clade 7.2 viruses that were isolated in 2006. Pathogenicity studies of four viruses, one from each genotype, revealed that all of the viruses are highly pathogenic in chickens, but none of them could replicate in ducks. The four viruses exclusively bound to avian-type receptors and replicated only in the turbinates and/or lungs of mice; none of them were lethal to mice at a dosage of 10<sup>6</sup> 50% egg infective doses (EID<sub>50</sub>). Our study indicates that although the clade 7.2 viruses have not been eradicated from poultry through vaccination, they have not become more dangerous to other animals (e.g., ducks and mice) and humans. IMPORTANCE: Animal influenza viruses can acquire the ability to infect and kill humans. The H5N1 viruses have been a concern in recent decades because of their clear pandemic potential. We sorted H5N1 influenza viruses into different phylogenetic clades based on their HA genes. The clade 7.2 viruses were detected in chickens in several provinces of northern China in 2006. Vaccines for these viruses were subsequently developed and have been used ever since to control infection of poultry. Here, we analyzed the genetic and biologic properties of seven clade 7.2 viruses that were isolated from chickens between 2011 and 2014. We found that after nearly 9 years of circulation in chickens, the clade 7.2 viruses still exclusively bind to avian-type receptors and are of low pathogenicity to mice, suggesting that these H5 viruses pose a low risk to human public health.","Animals;Chickens;China/ep [Epidemiology];Ducks/vi [Virology];Genome, Viral/ge [Genetics];Genotype;Hemagglutinin Glycoproteins, Influenza Virus/me [Metabolism];*Influenza A Virus, H5N1 Subtype/ge [Genetics];Influenza A Virus, H5N1 Subtype/im [Immunology];*Influenza A Virus, H5N2 Subtype/ge [Genetics];Influenza A Virus, H5N2 Subtype/im [Immunology];Influenza Vaccines/im [Immunology];*Influenza in Birds/ep [Epidemiology];Influenza in Birds/im [Immunology];*Influenza in Birds/vi [Virology];Phylogeny;Poultry;Vaccination/mt [Methods];0 (Hemagglutinin Glycoproteins, Influenza Virus);0 (Influenza Vaccines)","Liu, L.;Zeng, X.;Chen, P.;Deng, G.;Li, Y.;Shi, J.;Gu, C.;Kong, H.;Suzuki, Y.;Jiang, Y.;Tian, G.;Chen, H.",2016,Nov 01,,0
1214,Genotypic and pathotypic characterization of Newcastle disease virus isolated from racing pigeons in China,"A Newcastle disease virus (NDV) isolated from an outbreak in racing pigeons in China was characterized in this study. Complete gene of the NDV isolate was sequenced and phylogenetic analysis. Pathogenicity experiment was carried out in pigeons, chickens, and ducks. Phylogenetic analysis revealed that the strain clustered with the Class II viruses, has highly phylogenetically similar to NDV strains isolated from pigeons in China, but was distant from the viruses prevalence in chickens and vaccine strains used in China. The deduced amino acid sequence of the cleavage site of the fusion (F) protein confirmed that the isolate contained the virulent motif (112)RRQKRF(117) at the cleavage site, but it caused no appearance disease in chickens and ducks. However, the isolate had virulence in pigeons, resulting in severe nervous signs and highly mortality. Pigeons were considered as a potential source of NDV infection and disease for commercial poultry flocks. Therefore, new vaccines to prevent the NDV infection in the pigeon flocks should be developed as soon as possible, and strict biosecurity measures should be taken to reduce the risk of pigeon Newcastle disease outbreaks.",animal;China;genetics;isolation and purification;molecular genetics;Newcastle disease;Newcastle disease virus;pathogenicity;phylogeny;physiology;Columbidae;sequence analysis;virology;virulence,"Liu, M.;Qu, Y.;Wang, F.;Liu, S.;Sun, H.",2015,,10.3382/ps/pev106,0
1215,High reversion potential of a cell-adapted vaccine candidate against highly pathogenic porcine reproductive and respiratory syndrome,"Modified live vaccine (MLV) based on highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) is prone to quick reversion of virulence upon circulating in host animals. The objective of this study was to evaluate the virulence reversion potential of HP-PRRSV MLV and to identify elements within the HP-PRRSV genome contributing to this phenomenon. A blind passage, cell-adaptation strategy was attempted to attenuate a HP-PRRSV strain JX143, which was isolated during the atypical PRRS outbreak in 2006. Two attenuated candidates passage 87 (JXM87) and passage 105 (JXM105) used as MLVs showed the best balance of safety and efficacy in 4 week-old piglets (unpublished data). Two studies were performed during which the candidates were assessed for reversion to virulence through five back passages in susceptible piglets (21 +/- 3 days of age). Both study results showed increase in clinical signs, pyrexia and lung lesions as well as decreased average daily weight gain as of passage 3 in susceptible pigs clearly, and it indicated that both candidates regained virulence, irrespective of the passage level. Increase in respective parameters was accompanied by increase in viremia in piglets: JXM87 virus titer increased from Passage 1 (P1) 4.40 Lg TCID<sub>50</sub>/mL to P4 5.75 Lg TCID<sub>50</sub>/mL, and JXM105 virus titer increased from P1 3.78 Lg TCID<sub>50</sub>/mL to P4 6.42 Lg TCID<sub>50</sub>/mL. Next generation sequencing (NGS) was performed on clinical samples (serum, lung tissue) from P4 animals. Sequence analysis comparing P4 materials with their parental strains revealed 10 amino acid mutations in 4 proteins for JXM87 and 14 amino acid mutations in 9 proteins for JXM105, respectively. Interestingly, five amino acid mutations were identical for the two candidates, which were located in nsp1beta, GP5a and nsp10 coding regions, suggesting nsp1beta, GP5a and nsp10 could contribute to virulence in HP-PRRSV.","Age Factors;Amino Acid Sequence/ge [Genetics];Animals;Antibodies, Viral/bl [Blood];Cell Line;Genome, Viral;High-Throughput Nucleotide Sequencing;*Mutation;*Porcine Reproductive and Respiratory Syndrome/pc [Prevention & Control];Porcine respiratory and reproductive syndrome virus/ge [Genetics];*Porcine respiratory and reproductive syndrome virus/py [Pathogenicity];Porcine respiratory and reproductive syndrome virus/ph [Physiology];Swine;Vaccines, Attenuated/ge [Genetics];*Vaccines, Attenuated/im [Immunology];Viral Load;*Viral Vaccines/ge [Genetics];Viremia;Virulence/ge [Genetics];*Virulence Factors/ge [Genetics];0 (Antibodies, Viral);0 (Vaccines, Attenuated);0 (Viral Vaccines);0 (Virulence Factors)","Liu, P.;Bai, Y.;Jiang, X.;Zhou, L.;Yuan, S.;Yao, H.;Yang, H.;Sun, Z.",2018,Dec,,0
1216,Phylogenetic analysis of 626 hepatitis E virus (HEV) isolates from humans and animals in China (1986-2011) showing genotype diversity and zoonotic transmission,"Hepatitis E is considered as a public health problem in China. To determine the overall molecular epidemiology of hepatitis E virus (HEV) and analyze the situation of cross-species transmission between humans and swine in China over the last 25. years (1986-2011), 626 HEV complete and partial sequences (89 isolates identified by our group) isolated from humans and animals in China were retrieved from GenBank and subjected to phylogenetic analysis. There were three genotypes and 11 sub-genotypes of HEV prevailing in China. Furthermore, rabbit HEVs, of which the genotype is controversial, are also widespread in China. Genotype 1 was the most isolated genotype prior to 2000 and mainly detected in Xinjiang, Beijing and East China. However, genotype 4, which was identified in most regions of China during the last 10. years, has overtaken genotype 1 in frequency of isolation nationwide. Genotype 3 HEV strains have been found only in eastern China and were thought to be imported from Japan. Both genotypes 3 and 4 were found in humans and swine and cross-species transmission from pigs to humans of the two genotypes may have occurred in Northeast, Northwest, North, East and South China. These results indicate that HEV strains with considerable genetic diversity are widespread and the zoonotic transmission between swine and humans appears ubiquitous in China. © 2012 Elsevier B.V.",article;China;gene frequency;gene isolation;gene sequence;genetic variability;genotype;Hepatitis E virus;human;infection rate;molecular epidemiology;nonhuman;nucleotide sequence;phylogeny;priority journal;Leporidae;pig;virus isolation;virus strain;virus transmission;zoonosis,"Liu, P.;Li, L.;Wang, L.;Bu, Q.;Fu, H.;Han, J.;Zhu, Y.;Lu, F.;Zhuang, H.",2012,,10.1016/j.meegid.2012.01.017,0
1217,Characterization of a highly pathogenic avian influenza H5N1 clade 2.3.4 virus isolated from a tree sparrow,"The spread of H5N1 virus into a wide range of avian and mammalian species may facilitate the adaptation of the virus to human populations. In the present study, a survey of avian influenza virus in tree sparrows was performed and a HPAI H5N1 virus (A/tree sparrow/Jiangsu/1/08) was isolated. The H5N1 virus was found to be a genotype V variant belonging to clade 2.3.4, which had newly emerged in southern China in 2005. Genetic analysis showed that it had a close relation with A/Jiangsu/1/07 (H5N1), which was thought to be responsible for a probable limited person-to-person transmission in a family cluster in China in 2007. Pathogencity studies showed that the virus was highly virulent when experimentally inoculated into the chickens, tree sparrow, and mouse. As clade 2.3.4, genotype V variant of H5N1 virus has been accounted for the most of human fatal cases in China during 2005-2008, the existence of such H5N1 variants in the tree sparrows highlights the potential threat of this type of wild bird infection to veterinary and public health. © 2009 Elsevier B.V. All rights reserved.",animal experiment;article;avian influenza;China;cladistics;controlled study;female;genetic analysis;genetic variability;genotype;Influenza A virus (H5N1);mouse;nonhuman;nucleotide sequence;phylogeny;priority journal;sparrow;viral genetics;virus identification;virus isolation;virus transmission;virus virulence,"Liu, Q.;Ma, J.;Kou, Z.;Pu, J.;Lei, F.;Li, T.;Liu, J.",2010,,10.1016/j.virusres.2009.09.014,0
1218,"Systematic review of severe fever with thrombocytopenia syndrome: Virology, epidemiology, and clinical characteristics","SUMMARY: Severe fever with thrombocytopenia syndrome (SFTS) was firstly discovered in China in 2010, followed by several reports from many other countries worldwide. SFTS virus (SFTSV) has been identified as the causative agent of the disease and has been recognized as a public health threat. This novel Bunyavirus belongs to the Phlebovirus genus in the family Bunyaviridae. This review also describes the different aspects of virology, pathogenesis, epidemiology, and clinical symptoms on the basis of the published article surveillance data and phylogenetic analyses of viral sequences of large, medium, and small segments retrieved from database using mega 5.05, simplot 3.5.1, network 4.611, and epi information system 3.5.3 software. SFTS presents with fever, thrombocytopenia, leukocytopenia, and considerable changes in several serum biomarkers. The disease has 10~15% mortality rate, commonly because of multiorgan dysfunction. SFTSV is mainly reported in the rural areas of Central and North-Eastern China, with seasonal occurrence from May to September, mainly targeting those of ≥50years of age. A wide range of domesticated animals, including sheep, goats, cattle, pigs, dogs, and chickens have been proven seropositive for SFTSV. Ticks, especially Haemaphysalis longicornis, are suspected to be the potential vector, which have a broad animal host range in the world. More studies are needed to elucidate the vector-animal-human ecological cycle, the pathogenic mechanisms in high level animal models and vaccine development. © 2013 The Authors. Reviews in Medical Virology published by John Wiley & Sons, Ltd..",biological marker;receptor;age distribution;article;Bunyaviridae;bovine;cell culture;chicken;China;clinical feature;dog;evolution;fever;genome;goat;Haemaphysalis longicornis;host;human;leukopenia;mortality;multiple organ failure;nonhuman;nucleotide sequence;pathogenesis;population distribution;rural area;seasonal variation;serology;sheep;pig;systematic review;thrombocytopenia;tick;virology,"Liu, S.;Chai, C.;Wang, C.;Amer, S.;Lv, H.;He, H.;Sun, J.;Lin, J.",2014,,10.1002/rmv.1776,0
1219,Identification of the avian infectious bronchitis coronaviruses with mutations in gene 3,"The sequence of a 6.0-kb fragment was compared in the 3′-encoding region of the genome in 27 infectious bronchitis virus (IBV) strains. All these strains have the same S-3-M-5-N gene order, as is the case for other IBVs. However, the sizes of the corresponding open reading frames (ORFs) of some genes varied among the virus strains. Phylogenetic analysis and sequence alignments demonstrated that recombination events had occurred in the origin and evolution of the strains CK/CH/LSD/03I and CK/CH/LLN/98I and the possible recombinant junction sites might be located at the 3c and M genes, respectively. The normal product of ORF 3a is 57 amino acids long, whereas a 43-bp deletion at the 3′-end of the CK/CH/LSD/03I 3a gene was detected, resulting in a frameshift event and C-terminally truncated protein with 47 amino acids. Comparison of the growth ability in embryos and replication and pathogenicity in chickens with IBV carrying the normal 3a gene indicated that this deleted sequence in the 3a gene of CK/CH/LSD/03I was not necessary for viral pathogenesis and replication either in vitro or in vivo. Occurrence of a mutation at the corresponding position of the CK/CH/LLN/98I start codon in the 3a gene led to the absence of ORF 3a in this virus, resulting in a novel genomic organization at the 3′-encoding regions: S-3b, 3c-M-5a, 5b-N. Comparison with other viruses carrying the normal 3a gene revealed that CK/CH/LLN/98I had replication and pathogenicity abilities in vivo similar to those of other IBVs; however, its growth ability in embryos was lower, although the relationship between the lower growth ability and the ORF 3a defect requires further confirmation. © 2008 Elsevier B.V. All rights reserved.",animal cell;animal tissue;article;Avian infectious bronchitis virus;chicken;embryo;gene mutation;gene order;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;sequence alignment;virus identification;virus pathogenesis;virus replication;virus strain,"Liu, S.;Zhang, Q.;Chen, J.;Han, Z.;Shao, Y.;Kong, X.;Tong, G.",2008,,10.1016/j.gene.2008.01.004,0
1220,Porcine Epidemic Diarrhea Virus Infection Induced the Unbalance of Gut Microbiota in Piglets,"Porcine epidemic diarrhea (PED) is a devastating disease in livestock industry. Most of the previous studies related to the PED were focused on the pathology and etiology of porcine epidemic diarrhea virus (PEDV). A little was known regarding the status of gut microbiota after piglets infected by PEDV. In this study, aided by metagenome sequencing technology, gut microbiota profiles in feces of viral diarrhea (VD) and viral control (VC) piglets were investigated. The results showed that the abundance of four dominant phyla (Fusobacteria, Actinobacteria, Verrucomicrobia, and Proteobacteria) in feces was affected greatly by porcine epidemic diarrhea. Especially, the abundance of Fusobacteria was higher in VD piglets (36 %) than in VC piglets (5 %). On the contrary, the Verrucomicrobia was detected in lower distribution proportion in VD piglets (around 0 %) than in VC piglets (20 %). Furthermore, 25 genera were significantly different between VC and VD piglets at the genus level. Among the 25 genera, Leptotrichia belonging to Fusobacteria was remarkably lower in VC piglets than in VD piglets. Akkermansia belonging to Verrucomicrobia was higher in VC piglets than in VD piglets. Our findings implicated that the gut microbiota associated with PED significantly provided an insight into the pathology and physiology of PED.",Actinobacteria;Akkermansia;article;controlled study;feces;Fusobacteria;gene sequence;intestine flora;Leptotrichia;metagenome;nonhuman;piglet;porcine epidemic diarrhea;Porcine epidemic diarrhea virus;priority journal;Proteobacteria;Verrucomicrobia;virus identification,"Liu, S.;Zhao, L.;Zhai, Z.;Zhao, W.;Ding, J.;Dai, R.;Sun, T.;Meng, H.",2015,,10.1007/s00284-015-0895-6,0
1221,Identification of natural recombination in duck hepatitis B virus,"Due to its high similarity to human hepatitis B virus (HBV), duck HBV (DHBV) is often used as an important model for HBV research. While inter-genotypic recombination of HBV is common, it has not been reported with DHBV. In this study, 32 non-redundant DHBV complete genomes were analyzed using phylogenetic methods and classified into two clusters, corresponding to the 'Chinese' and 'Western country' branches previously reported based on geographical distribution. One 'Chinese' branch strain was isolated in Australia and three 'Western country' branch strains were isolated in China, suggesting cross-geographical distribution of both branches. Recombination analyses of the 32 DHBV genomes identified two possible inter-genotypic recombination events with high confidence value. These recombination events occurred between the lineages represented, respectively, by the Chinese isolate GD3 (AY536371, 'Chinese' branch) and the American isolate DHBV16 (K01834, 'Western country' branch), giving rise to two Chinese recombinant isolates CH4 (EU429324) and CH6 (EU429326). The identification of inter-genotypic recombination among circulating DHBV isolates suggests the usefulness of DHBV as a model for studying the mechanism of HBV recombination. © 2010 Elsevier B.V.",article;Australia;China;genome analysis;genotype;geographic distribution;Hepatitis B virus;nonhuman;nucleotide sequence;phylogeny;priority journal;virus genome;virus recombinant;virus recombination;virus strain,"Liu, W.;Zhai, J.;Liu, J.;Xie, Y.",2010,,10.1016/j.virusres.2010.02.002,0
1222,"Genome sequencing and analysis of a peste des petits ruminants virus isolate, China/Tib/07","Peste des petits ruminants virus is a member of Morbillivirus Paramyxoviridae. The complete genome of a Peste des petits ruminants virus (PPRV) isolate, China/Tib/07 was sequenced and molecular characteristics was analyzed. The internal sequences of the virus genome were amplified by RT-PCR with primers designed according to the published data in GenBank, while the sequences of the 3' and 5' ends of the genome were determined by RACE. Amplification products were directly sequenced,assembled and analyzed with DNAStar4.0. Results showed that China/Tib/07 genome consisted of 15 948 nucleotides in length, encoding six structural proteins and two non-structural proteins just like other known PPRV genomes. Phylogenetically, the virus genome shared homology of 91.6%-98.1% with Southwest Asian isolates among PPRV strains and the highest homology of 64.3% with rinderpest virus among morbillivirus members.",viral protein;animal;animal disease;article;Cercopithecus;China;classification;DNA sequence;genetics;isolation and purification;Measles virus;molecular genetics;nucleotide sequence;peste des petits ruminants;phylogeny;sequence alignment;sheep;sheep disease;Vero cell line;virology;virus genome,"Liu, W. H.;Bao, J. Y.;Wu, X. D.;Wang, Z. L.",2010,,,0
1223,Molecular phylogenetic and positive selection analysis of Japanese encephalitis virus strains isolated from pigs in China,"Japanese encephalitis virus (JEV) is one of the most important virus which causes encephalitis. This disease is most prevalent in the south, southeast and the east region of Asia. In this study, two JEV strains, named JEV/SW/GD/01/2009 and JEV/SW/GZ/09/2004, were isolated from aborted fetuses and seminal fluid of pigs in China. To determine the characteristic of these virus isolates, the virulence of two newly JEV isolates was investigated, the result evidenced that the JEV/SW/GD/01/2009 did not kill mice, while the JEV/SW/GZ/09/2004 displayed neurovirulence with 0.925log10 p.f.u./LD50. Additionally, the full genome sequences of JEV were determined and compared with other known JEV strains. Results demonstrated that the genome of two JEV isolates was 10,976 nucleotides (nt) in length. As compared to the Chinese vaccine strain SA14-14-2, the JEV/SW/GD/01/2009 and the JEV/SW/GZ/09/2004 showed 99.7% and 97.5% identity at the nucleotide level, 99.6% and 96.7% identity at the amino acid level, respectively. Phylogenetic analysis, based on the full-length genome revealed that two JEV isolates were all clustered into genotype III compared to the reference strains. Furthermore, selection analyses revealed that dominant selective pressure acting on the JEV genome was purifying selection. Four sites under positive selection were identified: codon 521 (amino acid E-227), 2296 (amino acid NS4b-24), 3048 (amino acid NS5-521) and 3055 (amino acid NS5-528). Amino acid E-227 was proved to be related to neurovirulence. Taken together, the molecular epidemiology and functional of positively selected amino acid sites of two newly JEV isolates were fully understood, which might be helpful to predict possible changes in virulence. © 2013 Elsevier B.V.",amino acid;animal tissue;article;China;codon;fetus;fetus death;genetic selection;genotype;Japanese encephalitis virus;molecular epidemiology;molecular phylogeny;mouse;nonhuman;nucleotide sequence;phylogenetic tree;positive selection;priority journal;purifying selection;seminal plasma;sequence analysis;pig;virus genome;virus isolation;virus virulence,"Liu, W. J.;Zhu, M.;Pei, J. J.;Dong, X. Y.;Liu, W.;Zhao, M. Q.;Wang, J. Y.;Gou, H. C.;Luo, Y. W.;Chen, J. D.",2013,,10.1016/j.virusres.2013.09.002,0
1224,Identification and analysis of the porcine MicroRNA in porcine cytomegalovirus- infected macrophages using deep sequencing,"Porcine cytomegalovirus (PCMV; genus Cytomegalovirus, subfamily Betaherpesvirinae, family Herpesviridae) is an immunosuppressive virus that mainly inhibits the immune function of T lymphocytes and macrophages, which has caused substantial damage in the farming industry. In this study, we obtained the miRNA expression profiles of PCMV-infected porcine macrophages via high-Throughput sequencing. The comprehensive analysis of miRNA profiles showed that 239 miRNA database-Annotated and 355 novel pig-encoded miRNAs were detected. Of these, 130 miRNAs showed significant differential expression between the PCMV-infected and uninfected porcine macrophages. The 10 differentially expressed pig-encoded miRNAs were further determined by stem-loop reverse-Transcription polymerase chain reaction, and the results were consistent with the high-Throughput sequencing. Gene Ontology analysis of the target genes of miRNAs in PCMV-infected porcine macrophages showed that the differentially expressed miRNAs are mainly involved in immune and metabolic processes. This is the first report of the miRNA transcriptome in porcine macrophages and an analysis of the miRNA regulatory mechanisms during PCMV infection. Further research into the regulatory mechanisms of miRNAs during immunosuppressive viral infections should contribute to the treatment and prevention of immunosuppressive viruses.",microRNA;microRNA 1;microRNA 101;microRNA 10a 3p;microRNA 125b;microRNA 128;microRNA 1307;microRNA 139 5p;microRNA 142 3p;microRNA 143 3p;microRNA 148a 3p;microRNA 148b 3p;microRNA 155 5p;microRNA 192;microRNA 194a;microRNA 194b 5p;microRNA 196b 5p;microRNA 20a;microRNA 210;microRNA 215;microRNA 27b 3p;microRNA 29c;microRNA 30c 3p;microRNA 32;microRNA 361 3p;microRNA 378;microRNA 7;microRNA 744;microRNA 769 5p;unclassified drug;unindexed drug;article;controlled study;Cytomegalovirus;down regulation;gene control;gene expression profiling;gene identification;gene ontology;gene targeting;genetic analysis;genetic transcription;genetic variability;high throughput sequencing;macrophage;molecular genetics;nonhuman;open reading frame;pig;reverse transcription polymerase chain reaction;sequence alignment;upregulation,"Liu, X.;Liao, S.;Xu, Z.;Zhu, L.;Yang, F.;Guo, W.",2016,,10.1371/journal.pone.0150971,0
1225,MicroRNA transcriptome analysis of porcine vital organ responses to immunosuppressive porcine cytomegalovirus infection,"Background: Porcine cytomegalovirus (PCMV) is an immunosuppressive virus that mainly inhibits T-lymphocyte and macrophage immune functions; it has significantly damaged the farming industry. Although recent studies have shown that miRNAs play important roles in immune responses, the regulatory mechanisms of miRNAs during immunosuppressive virus infection remain unclear. Methods: In this study, porcine small-RNA transcriptomes of PCMV-infected and uninfected vital organs were first characterised by high-throughput sequencing. miRDeep2 software was used to predict novel pig-encoded miRNAs. To verify the accuracy of the high-throughput sequencing results, stem-loop qRT-PCR was performed on 12 significantly DE miRNAs. The physical and functional interactions between the immune-related target genes of the DE miRNAs in PCMV-infected organs were analysed using the STRING database. Results: In total, 306 annotated and 295 novel miRNAs were identified from PCMV-infected and uninfected porcine organs, respectively, through alignment with known Sus scrofa pre-miRNAs. Overall, 92, 107, 95, 77 and 111 miRNAs were significantly differentially expressed in lung, liver, spleen, kidney and thymus after PCMV infection, respectively. According to Gene Ontology enrichment analysis, target genes of the differentially expressed miRNAs associated with immune system processes, regulation of biological processes and metabolic processes were enriched in every sample. Integrated expression analysis of the differentially expressed miRNAs and their target mRNAs in PCMV-infected thymus showed that the significant differential expression of specific miRNAs under the pressure of PCMV infection in central immune organs interfered with the expression of genes involved in important immune-related signalling pathways, thus promoting the viral infection. Conclusions: This is the first comprehensive analysis of the responses of host small-RNA transcriptomes to PCMV infection in vital porcine organs. It provides new insights into the regulatory mechanisms of miRNAs during infection by immunosuppressive viruses.",microRNA;transcriptome;animal experiment;animal model;animal tissue;article;controlled study;cytomegalovirus infection;gene expression profiling;gene expression regulation;gene ontology;genetic association;high throughput sequencing;immunosuppressive treatment;measurement accuracy;nonhuman;quantitative analysis;reverse transcription polymerase chain reaction;sequence alignment;signal transduction,"Liu, X.;Wei, H.;Liao, S.;Ye, J.;Zhu, L.;Xu, Z.",2018,,10.1186/s12985-018-0922-x,0
1226,"Characterisation of a highly pathogenic H5N1 clade 2.3.2 influenza virus isolated from swans in Shanghai, China","In spring 2009, one strain of H5N1 clade 2.3.2 virus was isolated from wild swans in Shanghai, indicating the importance of the wild swan in the ecology of this highly pathogenic avian influenza virus (HPAIV) in Eastern China. Pathogenicity experiments conducted in this study indicated that the virus was highly pathogenic for chickens but lowly pathogenic for mammalian hosts, as evidenced by reduced infection of mice. The analysis of complete genome sequences and genetic evolution showed that A/Swan/Shanghai/10/09 (SW/SH/09) may be derived from the strain A/silky chicken/Shantou/475/2004 (CK/ST/04), which is homologous to the influenza viruses isolated from chicken, duck, pika, little egret, swan, mandarin duck and bar-headed goose in China Hunan, China Qinghai, Mongolia, Russia, Japan, Korea, Laos and Hong Kong during 2007-2011, indicating that the virus has retroinfected diverse wild birds from chicken, and significant spread of the virus is still ongoing through overlapping migratory flyways. On the basis of the molecular analysis, we also found that there was a deletion of the glycosylation site (NSS) in amino acid 156 of the hemagglutinin (HA) protein when compared with that of the other Clade 2.3.2 viruses isolated between 2007 and 2011. More importantly, the sequence analysis of SW/SH/09 virus displayed the drug-resistant mutations on the matrix protein (M2) and neuraminidase (NA) genes. © Springer Science+Business Media, LLC 2011.",amino acid;hemagglutinin;matrix protein;sialidase;animal experiment;animal model;article;avian influenza virus;China;cladistics;cob (swan);ecology;evolutionary homology;gene deletion;gene sequence;genetic analysis;glycosylation;Influenza A virus (H5N1);migratory species;molecular evolution;mouse;nonhuman;nucleotide sequence;pathogenicity;pen (swan);priority journal;sequence analysis;virus characterization;virus genome;virus isolation;virus mutation;virus strain,"Liu, X.;Zhao, G.;Zhong, L.;Lu, X.;Hu, J.;Gu, X.;Kai, Y.;Song, Q.;Sun, Q.;Liu, J.;Peng, D.;Wang, X.;Liu, X.",2012,,10.1007/s11262-011-0667-8,0
1227,The porcine microRNA transcriptome response to transmissible gastroenteritis virus infection,"Transmissible gastroenteritis virus (TGEV; Coronaviridae family) causes huge economic losses to the swine industry. MicroRNAs (miRNAs) play a regulatory role in viral infection and may be involved in the mammalian immune response. Here, we report a comprehensive analysis of host miRNA expression in TGEV-infected swine testis (ST) cells. Deep sequencing generated 3,704,353 and 2,763,665 reads from uninfected ST cells and infected ST cells, respectively. The reads were aligned to known Sus scrofa pre-miRNAs in miRBase 19, identifying 284 annotated miRNAs. Certain miRNAs were differentially regulated during TGEV infection. 59 unique miRNAs displayed significant differentially expression between the normal and TGEV-infected ST cell samples: 15 miRNAs were significantly upregulated and 44 were significantly down-regulated. Stem-loop RT-PCR was carried out to determine the expression levels of specific miRNAs in the two samples, and the results were consistent with those of sequencing. Gene ontology enrichment analysis of host target genes demonstrated that the differentially expressed miRNAs are involved in regulatory networks, including cellular process, metabolic process, immune system process. This is the first report of the identification of ST cell miRNAs and the comprehensive analysis of the miRNA regulatory mechanism during TGEV infection, which revealed the miRNA molecular regulatory mechanisms for the viral infection, expression of viral genes and the expression of immune-related genes. The results presented here will aid research on the prevention and treatment of viral diseases.",microRNA;microRNA 146;microRNA 155;transcriptome;unclassified drug;animal cell;article;controlled study;enrichment culture;gene control;gene expression regulation;gene identification;gene ontology;gene regulatory network;gene sequence;gene targeting;high throughput sequencing;host;immune response;male;nonhuman;reverse transcription polymerase chain reaction;sequence alignment;pig;testis cell;transmissible gastroenteritis of swine;Transmissible gastroenteritis virus;virus gene,"Liu, X.;Zhu, L.;Liao, S.;Xu, Z.;Zhou, Y.",2015,,10.1371/journal.pone.0120377,0
1228,Complete genome sequence analysis of a predominant infectious bronchitis virus (IBV) strain in China,"Infectious bronchitis (IB) is one of the major diseases in poultry flocks all over the world caused by infectious bronchitis virus (IBV). In the study, the complete genome sequence of strain A2 was sequenced and analyzed, which was a predominant IBV strain in China. The results indicated that there were mutations, insertions, and deletions distributed in the whole genome. The A2 virus had the highest identity to S14 and BJ in terms of full genome, whereas had a further distance to Massachusetts strains. Phylogenetic analysis showed that A2 isolate clustered together with most Chinese strains. The results of this study suggest that strain A2 may play an important role in IBV's evolution and A2-like IBVs are predominant strains in China. © 2008 Springer Science+Business Media, LLC.",animal experiment;article;Avian infectious bronchitis virus;China;embryo;gene deletion;gene insertion;gene mutation;gene sequence;nonhuman;nucleotide sequence;phylogeny;priority journal;sequence analysis;unindexed sequence;virus identification;virus isolation;virus strain,"Liu, X. L.;Su, J. L.;Zhao, J. X.;Zhang, G. Z.",2009,,10.1007/s11262-008-0282-5,0
1229,Phylogenetic diversity and genotypic complexity of H1N1 subtype swine influenza viruses isolated in Mainland China,"Background: After the occurrence of 2009 pandemic H1N1, close attention has been paid to the H1N1 subtype swine influenza viruses (H1N1 SIV) by scientific communities in many countries. A large-scale sequence analysis of the NCBI Influenza Virus Resource Database on H1N1 SIVs submitted primarily by scientists in China during 1992 to 2011 was performed. The aims of this study were to elucidate the genetic and evolutionary characteristics of H1N1 SIVs, to identify and unify the lineages and genetic characteristics of the H1N1 SIVs isolated in mainland China. Results: Most of the strains were isolated during the period of 2008 to 2010 from Guangdong and Shandong provinces, China. Based on the phylogenetic and genotypic analyses, all of the H1N1 SIV strains can be classified into 8 lineages and 10 genotypes. All strains were of the characteristics of low pathogenic influenza viruses. The viruses of different lineage are characterized with different amino acid residues at the receptor-binding sites. Viruses containing PB2 genes of the classical swine, early seasonal human and recent seasonal human lineage might be more infectious to human. Some genotypes were directly related with human influenza viruses, which include strains that harbored genes derived from human influenza viruses. Conclusions: Phylogenetic diversity and complexity existed in H1N1 SIVs isolated in mainland China. These H1N1 SIV strains were closely related to other subtype influenza viruses, especially to human influenza viruses. Moreover, it was shown that, novel lineages and genotypes of H1N1 SIVs emerged recently in mainland China. These findings provided new and essential information for further understanding of the genetic and evolutionary characteristics and monitoring the H1N1 SIVs in mainland China. © 2012 Liu et al; licensee BioMed Central Ltd.",article;China;evolution;genetic line;genetic variability;genotype;Influenza A virus (H1N1);nonhuman;phylogeny;swine influenza virus;viral genetics;virus gene;virus identification;virus isolation;virus strain,"Liu, Y.;Wang, J.;Ji, J.;Chang, S.;Xue, C.;Ma, J.;Bi, Y.;Xie, Q.",2012,,10.1186/1743-422x-9-289,0
1230,Application of a Molecular Method for the Classification of Human Enteroviruses and its Correlation with Clinical Manifestations,"Background/Purpose: A new molecular classification scheme has recently been adopted that groups all enteroviruses into four species, designated human enterovirus A (HEV-A) through D. In this study, we tried to demonstrate the correlation between this molecular classification scheme and clinical manifestations in patients. Methods: We retrospectively reclassified the clinical isolates of enteroviruses from the preceding 4.5 years in our virology laboratory using reverse transcription-polymerase chain reaction, and reviewed the clinical manifestations of 138 pediatric patients. Results: We reclassified 23 isolates of the five serotypes into the HEV-A group, 110 isolates of 16 sero-types into the HEV-B group, five isolates into the HEV-C group, and no isolate of the HEV-D group. HEV-A species caused significantly more hand-foot-and-mouth disease (p < 0.001), herpangina (p = 0.029), and myoclonic jerks (p < 0.001) compared with HEV-B species. However, HEV-B species caused significantly more pharyngitis (p = 0.043), respiratory tract infections (p = 0.046), nausea and vomiting (p = 0.007), and aseptic meningitis (p = 0.001). The only death in our report was caused by coxsackievirus A16, which belonged to the HEV-A group. Conclusion: The association between the molecular classification of enteroviruses and related disease patterns is an important finding. We suggest that this molecular classification could be applied in a clinical laboratory as an alternative method under certain circumstances, such as limited availability of antisera or questionable serotyping results, to identify the untypeable isolates. © 2010 Taiwan Society of Microbiology.",article;aseptic meningitis;controlled study;convulsion;Enterovirus;diarrhea;encephalitis;female;hand foot and mouth disease;herpangina;human;male;nausea and vomiting;nonhuman;pharyngitis;respiratory tract infection;retrospective study;reverse transcription polymerase chain reaction;serotype;tendon reflex;virus classification,"Lo, C. W.;Wu, K. G.;Lin, M. C.;Chen, C. J.;Ho, D. M. T.;Tang, R. B.;Chan, Y. J.",2010,,10.1016/s1684-1182(10)60056-4,0
1231,Origin and evolution of Nipah virus,"Nipah virus, member of the Paramyxoviridae family, is classified as a Biosafety Level-4 agent and category C priority pathogen. Nipah virus disease is endemic in south Asia and outbreaks have been reported in Malaysia, Singapore, India, and Bangladesh. Bats of the genus Pteropus appear to be the natural reservoir of this virus. The aim of this study was to investigate the genetic diversity of Nipah virus, to estimate the date of origin and the spread of the infection. The mean value of Nipah virus N gene evolutionary rate, was 6.5×10-4 substitution/site/year (95% HPD: 2.3×10-4-1.18×10-3). The time-scaled phylogenetic analysis showed that the root of the tree originated in 1947 (95% HPD: 1888-1988) as the virus entered in south eastern Asiatic regions. The segregation of sequences in two main clades (I and II) indicating that Nipah virus had two different introductions: one in 1995 (95% HPD: 1985-2002) which correspond to clade I, and the other in 1985 (95% HPD: 1971-1996) which correspond to clade II. The phylogeographic reconstruction indicated that the epidemic followed two different routes spreading to the other locations. The trade of infected pigs may have played a role in the spread of the virus. Bats of the Pteropus genus, that are able to travel to long distances, may have contributed to the spread of the infection. Negatively selected sites, statistically supported, could reflect the stability of the viral N protein.",article;bat;cladistics;evolution;evolutionary rate;gene segregation;genetic variability;Nipah virus;Nipah virus infection;nonhuman;phylogenetic tree root;phylogeny;phylogeography;pig;Southeast Asia,"Lo Presti, A.;Cella, E.;Giovanetti, M.;Lai, A.;Angeletti, S.;Zehender, G.;Ciccozzi, M.",2016,,10.1002/jmv.24345,0
1232,Comparative genomics reveals multiple pathways to mutualism for tick-borne pathogens,"BACKGROUND: Multiple important human and livestock pathogens employ ticks as their primary host vectors. It is not currently known whether this means of infecting a host arose once or many times during evolution. RESULTS: In order to address this question, we conducted a comparative genomics analysis on a set of bacterial pathogens from seven genera - Borrelia, Rickettsia, Anaplasma, Ehrlichia, Francisella, Coxiella, and Bartonella, including species from three different host vectors - ticks, lice, and fleas. The final set of 102 genomes used in the study encoded a total of 120,046 protein sequences. We found that no genes or metabolic pathways were present in all tick-borne bacteria. However, we found some genes and pathways were present in subsets of tick-transmitted organisms while absent from bacteria transmitted by lice or fleas. CONCLUSION: Our analysis suggests that the ability of pathogens to be transmitted by ticks arose multiple times over the course of evolution. To our knowledge, this is the most comprehensive study of tick transmissibility to date.",Animals;Bacteria/cl [Classification];Bacteria/ge [Genetics];Bacteria/me [Metabolism];Cluster Analysis;Computational Biology/mt [Methods];Humans;Metabolic Networks and Pathways;*Metagenome;Metagenomics/mt [Methods];*Metagenomics;Phthiraptera/mi [Microbiology];Phylogeny;Siphonaptera/mi [Microbiology];*Tick-Borne Diseases/mi [Microbiology];Tick-Borne Diseases/tm [Transmission],"Lockwood, S.;Brayton, K. A.;Broschat, S. L.",2016,07 02,,0
1233,A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq,"BACKGROUND: Next-Generation Sequencing (NGS) is revolutionizing molecular epidemiology by providing new approaches to undertake whole genome sequencing (WGS) in diagnostic settings for a variety of human and veterinary pathogens. Previous sequencing protocols have been subject to biases such as those encountered during PCR amplification and cell culture, or are restricted by the need for large quantities of starting material. We describe here a simple and robust methodology for the generation of whole genome sequences on the Illumina MiSeq. This protocol is specific for foot-and-mouth disease virus (FMDV) or other polyadenylated RNA viruses and circumvents both the use of PCR and the requirement for large amounts of initial template. RESULTS: The protocol was successfully validated using five FMDV positive clinical samples from the 2001 epidemic in the United Kingdom, as well as a panel of representative viruses from all seven serotypes. In addition, this protocol was successfully used to recover 94% of an FMDV genome that had previously been identified as cell culture negative. Genome sequences from three other non-FMDV polyadenylated RNA viruses (EMCV, ERAV, VESV) were also obtained with minor protocol amendments. We calculated that a minimum coverage depth of 22 reads was required to produce an accurate consensus sequence for FMDV O. This was achieved in 5 FMDV/O/UKG isolates and the type O FMDV from the serotype panel with the exception of the 5' genomic termini and area immediately flanking the poly(C) region. CONCLUSIONS: We have developed a universal WGS method for FMDV and other polyadenylated RNA viruses. This method works successfully from a limited quantity of starting material and eliminates the requirement for genome-specific PCR amplification. This protocol has the potential to generate consensus-level sequences within a routine high-throughput diagnostic environment.","Foot-and-Mouth Disease Virus/cl [Classification];*Foot-and-Mouth Disease Virus/ge [Genetics];Genome, Viral;High-Throughput Nucleotide Sequencing;Molecular Sequence Data;Polyadenylation;RNA Viruses/cl [Classification];*RNA Viruses/ge [Genetics];*Sequence Analysis, RNA/mt [Methods]","Logan, G.;Freimanis, G. L.;King, D. J.;Valdazo-Gonzalez, B.;Bachanek-Bankowska, K.;Sanderson, N. D.;Knowles, N. J.;King, D. P.;Cottam, E. M.",2014,Sep 30,,0
1234,Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing,"Understanding mosquito host choice is important for assessing vector competence or identifying disease reservoirs. Unfortunately, the availability of an unbiased method for comprehensively evaluating the composition of insect blood meals is very limited, as most current molecular assays only test for the presence of a few pre-selected species. These approaches also have limited ability to identify the presence of multiple mammalian hosts in a single blood meal. Here, we describe a novel high-throughput sequencing method that enables analysis of 96 mosquitoes simultaneously and provides a comprehensive and quantitative perspective on the composition of each blood meal. We validated in silico that universal primers targeting the mammalian mitochondrial 16S ribosomal RNA genes (16S rRNA) should amplify more than 95% of the mammalian 16S rRNA sequences present in the NCBI nucleotide database. We applied this method to 442 female Anopheles punctulatus s.l. mosquitoes collected in Papua New Guinea (PNG). While human (52.9%), dog (15.8%) and pig (29.2%) were the most common hosts identified in our study, we also detected DNA from mice, one marsupial species and two bat species. Our analyses also revealed that 16.3% of the mosquitoes fed on more than one host. Analysis of the human mitochondrial hypervariable region I in 102 human blood meals showed that 5 (4.9%) of the mosquitoes unambiguously fed on more than one person. Overall, analysis of PNG mosquitoes illustrates the potential of this approach to identify unsuspected hosts and characterize mixed blood meals, and shows how this approach can be adapted to evaluate inter-individual variations among human blood meals. Furthermore, this approach can be applied to any disease-transmitting arthropod and can be easily customized to investigate non-mammalian host sources.",PAPUA-NEW-GUINEA;LENGTH POLYMORPHISM ANALYSIS;HOST-FEEDING PATTERNS;CYTOCHROME-B GENE;WEST-NILE-VIRUS;MOLECULAR-IDENTIFICATION;SPECIES;IDENTIFICATION;MALARIA VECTORS;COMPLEX DIPTERA;INSECT VECTORS,"Logue, K.;Keven, J. B.;Cannon, M. V.;Reimer, L.;Siba, P.;Walker, E. D.;Zimmerman, P. A.;Serre, D.",2016,Mar,,0
1235,Virus particles in the cochlear spiral ganglion of guinea pigs,"All examined spiral ganglions of several guinea pig populations from different breeds showed intracytoplasmic viruses in some granular spiral ganglion cells. According to their localization and morphology, we classify these viruses with the oncorna group. This is not in agreement with the classification of other authors. Apparently there is a world-wide latent viral infection in guinea pigs. Beside the virus particles we found an accumulation of lysosomes which indicate a local increased lysosomal activity of the infected ganglion cells. Further influences on the infected cells can neither be demonstrated nor denied.",auditory system;cochlea;electron microscopy;guinea pig;lysosome;Orthoretrovirinae;Retroviridae;spiral ganglion;virus particle,"Lohle, E.;Kistler, G. S.;Riede, U. N.;Merck, W.",1982,,,0
1236,Columbid circoviruses detected in free ranging pigeons from Southern Brazil: insights on PiCV evolution,"Pigeon circovirus (PiCV) is taxonomically classified as a member of the Circovirus genus, family Circoviridae. The virus contains a single stranded DNA genome of approximately 2 kb, with minor length variations among different isolates. The occurrence of PiCV infections in pigeons (Columba livia) has been documented worldwide over the past 20 years; however, in Brazil there were still no reports on PiCV detection. This study identifies seven PiCV genomes recovered from domestic pigeons of South Brazil through high-throughput sequencing and shows a high frequency of PiCV infection, through quantitative real-time PCR. Phylogenetic classification was performed by maximum likelihood analysis of the full genomes, ORF V1 (Rep) and ORF C1 (Cap). The results show that either full genome or Cap based analysis allowed PiCV classification into five major clades (groups A to E), where Brazilian sequences were classified as A, C or D. Recombination analyses were carried out with Simplot and RDP4 and the results show that both Rep and Cap ORFs contain several recombination hotspots, pointing to an important role for such events in PiCV evolution.",animal;bird disease;Brazil;Circoviridae infection;Circovirus;classification;Columbidae;genetics;high throughput sequencing;isolation and purification;molecular evolution;open reading frame;phylogeny;veterinary medicine;virology,"Loiko, M. R.;Junqueira, D. M.;Varela, A. P. M.;Tochetto, C.;Scheffer, C. M.;Lima, D. A.;Morel, A. P.;Cerva, C.;Paim, W. P.;Mayer, F. Q.;Roehe, P. M.",2018,,10.1007/s00705-018-3990-8,0
1237,Faecal virome of red foxes from peri-urban areas,"Red foxes (Vulpes vulpes) are the most abundant carnivore species in the Northern Hemisphere. Since their populations are well established in peri-urban and urban areas, they represent a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. In this study, we evaluated the faecal virome of juvenile and adult foxes from peri-urban areas in central Croatia. The dominating mammalian viruses were fox picobirnavirus and parvovirus. The highest number of viral reads (N = 1412) was attributed to a new fox circovirus and complete viral genome was de novo assembled from the high-throughput sequencing data. Fox circovirus is highly similar to dog circoviruses identified in diseased dogs in USA and Italy, and to a recently discovered circovirus of foxes with neurologic disease from the United Kingdom. Our fox picobirnavirus was more closely related to the porcine and human picobirnaviruses than to known fox picobirnaviruses.",adult;animal tissue;article;Circovirus;Croatia;feces analysis;juvenile animal;nonhuman;nucleotide sequence;Picobirnavirus;urban area;virus detection;virus genome;Vulpes vulpes,"Lojkić, I.;Bidin, M.;Prpić, J.;Šimić, I.;Krešić, N.;Bedeković, T.",2016,,10.1016/j.cimid.2016.01.005,0
1238,The study of the nonpathogenic influenza virus A/gull/Moscow/3100/2006 (H6N2) isolated in Moscow,"The influenza virus A/gull/Moscow/3100/2006 (H6N2) was isolated from gull feces within the precincts of Moscow in autumn 2006. The nucleotide sequence of the complete genome (GenBank, EU152234-EU152241) and genotype (K, G, D, 6B, F, 2D, F, 1E) for this virus were determined. Phylogenetic analysis suggests that the H6N2 virus derived by numerous reassortment between viruses that have been circulating among different birds in Europe since 1999 and in South-East Asia (NA gene) for last years. Migratory birds probably introduced some of these viruses from South-East Asia earlier. The strain A/gull/Moscow/3100/2006 is nonpathogenic for chicken embryos and mice and induces specific antibody production in mice. Similar to all avian influenza viruses A/gull/Moscow/3100/ 2006 it binds to Neu5Ac(2-3Gal receptors, but reveals higher affinity for fucosylated sialosugars (SLex) in contrast to the duck viruses, as was shown in receptor specificity assay and clarified due to modeling the accommodation of SLex into receptor binding site of duck and gull influenza virus hemagglutinin.",animal;article;Bagg albino mouse;chick embryo;DNA sequence;duck;genetics;human;Influenza A virus;isolation and purification;molecular genetics;mouse;nucleotide sequence;pathogenicity;phylogeny;Russian Federation;virology;virus genome,"Lomakina, N. F.;Gambarian, A. S.;Boravleva, E. I.;Kropotkina, E. A.;Kirillov, I. M.;Lavrent'ev, M. V.;Iamnikova, S. S.",2009,,,0
1239,"Character of apathogenic influenza a viruses found in Moscow, Russia","An influenza virus A/gull/Moscow/3100/2006 (H6N2) was isolated from gull' faeces within the precincts of Moscow in autumn 2006. Nucleotide sequence of complete genome (GenBank, EU152234-EU152241) and genotype (K, G, D, 6B, F, 2D, F, 1E) for this virus were determined. Phylogenetic analysis suggests that the H6N2 virus derived by numerous reassortment between viruses, which have been circulating among different birds in Europe since 1999 and in South-East Asia (NA gene) for last years. Some of these viruses probably were introduced by migratory birds from South-East Asia earlier. The strain A/gull/Moscow/3100/2006 is nonpathogenic for chicken embryos and mice and induces specific antibody production in mice. Similar to all avian influenza viruses A/gull/Moscow/3100/2006 binds to Neu5Ac alpha 2-3Gal receptors but reveals higher affinity for fucosylated sialosugars (SLex) in contrast to the duck viruses, as was shown in receptor specificity assay and clarified due to modeling the accommodation of SLex into receptor binding site of duck and gull influenza virus hemagglutinin.",HONG-KONG;RECEPTOR SPECIFICITY;MOLECULAR-BASIS;SOUTHERN CHINA;H5N1;H6N2;REPLICATION;CALIFORNIA;EVOLUTION;BIRDS,"Lomakina, N. F.;Gambaryan, A. C.;Boravleva, E. Y.;Kropotkina, E. A.;Kirillov, I. M.;Lavrient'ev, M. V.;Yamnikova, S. S.",2009,Mar,,0
1240,Specificity of antibody to the RD 114 viral polymerase,"The use of antiserum against the RNA dependent DNA polymerase (RDP) of type C viruses has permitted the distinction of these enzymes from cellular enzymes which are capable of utilizing RNA templates for DNA syntheses. Such sera have also permitted some degree of subclassification of the viruses themselves and also distinction between other RDP containing viruses. Thus, within the type C family, viper, chicken and mammalian viruses are readily distinguished, whereas, within the mammalian group, the polymerases of two new primate isolates, woolly monkey and gibbon ape appear distinct from the viruses of lower mammals. The newly described RD 114 virus, which is currently under consideration as a human candidate virus, was also distinguished from the viruses of lower mammals by polymerase inhibition tests. The major internal protein of the RD 114 virus is distinct from all other type C viruses both antigenically, and by virtue of a unique isoelectric point. In the absence of other criteria for species classification, it was suggested that polymerase inhibition tests might provide evidence for a primate virus group which would hopefully include RD 114. If so, this would provide strong circumstantial evidence for the human origin of RD 114. In this report experiments with a hyperimmune guinea pig antiserum prepared against purified RD 114 RDP are described. The RD 114 RDP seems to be more closely related to the RDP of two primate viruses than to the RDP of viruses from lower mammals and non mammalian species. The enzyme is also distinct from an RD cellular activity which can utilize RNA templates.",enzyme antibody;transcriptase;biochemistry;electron microscopy;leukemia virus;microorganism;theoretical study;virus classification,"Long, C.;Sachs, R.;Norvell, J.",1973,,,0
1241,Naturally occurring picornavirus infection of domestic mink,"The isolation and preliminary characterization of a virus from domestic mink are reported. The virus was tentatively classified as a member of the family Picornaviridae on the basis of its physicochemical properties. The mink virus was not neutralized by antiserum to some known members of the calicivirus genus, which included the nine serotypes of vesicular exanthema of swine virus, ten serotypes of San Miguel sea lion virus and feline calicivirus. Seroepidemiological studies indicated that the incidence of mink virus infection was widespread in domestic mink populations. Although the virus was isolated from mink on ranches with a history of hemorrhagic pneumonia (pseudomonas pneumonia), no specific disease process could be attributed to the virus infection.",animal experiment;in vitro study;mammal;Picornaviridae;virus infection,"Long, G. G.;Evermann, J. F.;Gorham, J. R.",1980,,,0
1242,"Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations","Disturbance of the beneficial gut microbial community is a potential collateral effect of antibiotics, which have many uses in animal agriculture (disease treatment or prevention and feed efficiency improvement). Understanding antibiotic effects on bacterial communities at different intestinal locations is essential to realize the full benefits and consequences of in-feed antibiotics. In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and large intestine (cecum and colon) plus feces, and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine and penicillin (ASP250)) on these communities. 16S rRNA gene sequence and metagenomic analyses of bacterial membership and functions revealed dramatic differences between small and large intestinal locations, including enrichment of Firmicutes and phage-encoding genes in the ileum. The large intestinal microbiota encoded numerous genes to degrade plant cell wall components, and these genes were lacking in the ileum. The mucosa-associated ileal microbiota harbored greater bacterial diversity than the lumen but similar membership to the mucosa of the large intestine, suggesting that most gut microbes can associate with the mucosa and might serve as an inoculum for the lumen. The collateral effects on the microbiota of antibiotic-fed animals caused divergence from that of control animals, with notable changes being increases in Escherichia coli populations in the ileum, Lachnobacterium spp. in all gut locations, and resistance genes to antibiotics not administered. Characterizing the differential metabolic capacities and response to perturbation at distinct intestinal locations will inform strategies to improve gut health and food safety.",antiinfective agent;animal;animal food;bacteriophage;bacterium;classification;drug effect;female;genetics;intestine;isolation and purification;large intestine;male;microbiology;microflora;pig;small intestine,"Looft, T.;Allen, H. K.;Cantarel, B. L.;Levine, U. Y.;Bayles, D. O.;Alt, D. P.;Henrissat, B.;Stanton, T. B.",2014,,10.1038/ismej.2014.12,0
1243,The swine intestinal microbiota: localized adaptations and responses to in-feed antibiotics,,,"Looft, T. P.",2012,,,0
1244,Automated classification of tailed bacteriophages according to their neck organization,"Background: The genetic diversity observed among bacteriophages remains a major obstacle for the identification of homologs and the comparison of their functional modules. In the structural module, although several classes of homologous proteins contributing to the head and tail structure can be detected, proteins of the head-to-tail connection (or neck) are generally more divergent. Yet, molecular analyses of a few tailed phages belonging to different morphological classes suggested that only a limited number of structural solutions are used in order to produce a functional virion. To challenge this hypothesis and analyze proteins diversity at the virion neck, we developed a specific computational strategy to cope with sequence divergence in phage proteins. We searched for homologs of a set of proteins encoded in the structural module using a phage learning database. Results: We show that using a combination of iterative profile-profile comparison and gene context analyses, we can identify a set of head, neck and tail proteins in most tailed bacteriophages of our database. Classification of phages based on neck protein sequences delineates 4 Types corresponding to known morphological subfamilies. Further analysis of the most abundant Type 1 yields 10 Clusters characterized by consistent sets of head, neck and tail proteins. We developed Virfam, a webserver that automatically identifies proteins of the phage head-neck-tail module and assign phages to the most closely related cluster of phages. This server was tested against 624 new phages from the NCBI database. 93% of the tailed and unclassified phages could be assigned to our head-neck-tail based categories, thus highlighting the large representativeness of the identified virion architectures. Types and Clusters delineate consistent subgroups of Caudovirales, which correlate with several virion properties. Conclusions: Our method and webserver have the capacity to automatically classify most tailed phages, detect their structural module, assign a function to a set of their head, neck and tail genes, provide their morphologic subtype and localize these phages within a ""head-neck-tail"" based classification. It should enable analysis of large sets of phage genomes. In particular, it should contribute to the classification of the abundant unknown viruses found on assembled contigs of metagenomic samples.",Bacteriophage;Profile-profile comparison;Virion;Gene organization;Evolution;PROTEIN HOMOLOGY DETECTION;STRUCTURE PREDICTION;COMPARATIVE GENOMICS;TERMINATOR PROTEIN;PORTAL PROTEIN;PHAGE;LAMBDA;BACTERIAL;GENES;EVOLUTIONARY,"Lopes, A.;Tavares, P.;Petit, M. A.;Guerois, R.;Zinn-Justin, S.",2014,Nov,,0
1245,Mapping the subgroup epitopes of rotavirus protein VP6,"VP6, the most abundant protein of rotaviruses, contains epitopes that allow the classification of these viruses into four subgroups (SG), depending on the presence or absence of two epitopes called I and II. The subgroup-specific epitopes are conformational and appear to be present on trimeric but not monomeric VP6. We have identified on VP6 some of the amino acids that determine the reactivity of the subgroup-specific mAbs 255/60 and 631/9. A single amino acid mutation at positions 172 (Met to Ala) or 305 (Asn to Ala) was sufficient to change the subgroup specificity of the human rotavirus Wa VP6 protein from SGII to SGI/II, since either of these mutations allowed the protein to be recognized by the SGI mAb 255/60, while retaining its capacity to interact with the SGII mAb 631/9. In the case of the SGII epitope, the mutation of two contiguous amino acids (Ala305 Asn306 to Asn305 Ala306) in the porcine rotavirus YM VP6 protein (SGI) enabled the protein to be efficiently recognized by the SGII mAb 631/9, while causing the YM VP6 protein to rose its capacity to interact with mAb 255/60. These results suggest that both subgroup mAbs interact with an antigenic domain in VP6 that is composed of at least two regions of the protein that, although distant in the linear sequence, might be in close proximity in the structured VP6 trimer.",viral protein;article;controlled study;epitope mapping;immunoprecipitation;nonhuman;priority journal;Rotavirus;virus classification,"Lopez, S.;Espinosa, R.;Greenberg, H. B.;Arias, C. F.",1994,,10.1006/viro.1994.1519,0
1246,First detection and analysis of a fish circovirus,"Circoviruses are present worldwide in birds and pigs but their occurrence in fish has not yet been reported. Recently, increased mortality was observed in barbel fry (Barbus barbus) in Hungary. This paper reports the detection of previously unknown circular viral DNA genomes in barbels by the use of a circovirus-specific wide-range nested PCR. The analysis of two complete genomes (Barbel circovirus, BaCV1 and BaCV2) indicated that they belonged into a new genetic group within the family Circoviridae, distinct from known circoviruses and circovirus-like genomes. Their genome size was 1957 bases and contained two major ORFs similar to the capsid and replication-associated protein genes of circoviruses. A connection between the presence of the virus and clinical manifestations of the infection could not be proved.",SINGLE-STRANDED-DNA;PORCINE CIRCOVIRUSES;DISEASE;METAGENOMICS;DATABASE;VIRUSES,"Lorincz, M.;Csagola, A.;Farkas, S. L.;Szekely, C.;Tuboly, T.",2011,Aug,,0
1247,Bluetongue virus serotypes 1 and 4 in Sardinia during autumn 2012: New incursions or re-infection with old strains?,"Since 2000 several bluetongue virus (BTV) incursions have occurred in Sardinia (Italy) involving serotypes 1, 2, 4, 8 and 16. In October 2012, new BT outbreaks caused by BTV-1 and BTV-4 were reported. Nearly 500 flocks were infected and 9238 sheep died because of the infection. When sequenced, Seg-10 of both strains shared 99% similarity at nucleotide level with BTV strains that have circulated in the Mediterranean basin in the last few years. Similarly, Seg-5 sequences of BTV-1 and BTV-4 newly isolated Sardinian strains are identical and cluster together with recent BTV-1 circulating in the Mediterranean Basin and the BTV-4 strains isolated in Tunisia in 2007 and 2009. These BTV-4 strains differ from the ones that circulated in Europe from 2003 to 2005 and appear to be reassortant strains. © 2013 Elsevier B.V.",virus RNA;animal cell;animal tissue;article;autumn;Bluetongue orbivirus;Bluetongue virus serotype 1;Bluetongue virus serotype 4;controlled study;gene amplification;gene cluster;genetic reassortment;herd;Italy;molecular phylogeny;mortality;nonhuman;nucleotide sequence;priority journal;reinfection;reovirus infection;sequence analysis;sequence homology;sheep;Southern Europe;strain difference;Tunisia;virus cell interaction;virus isolation;virus strain,"Lorusso, A.;Sghaier, S.;Carvelli, A.;Di Gennaro, A.;Leone, A.;Marini, V.;Pelini, S.;Marcacci, M.;Rocchigiani, A. M.;Puggioni, G.;Savini, G.",2013,,10.1016/j.meegid.2013.06.028,0
1248,Innate immune recognition of poxviral vaccine vectors,"The study of poxviruses pioneered the field of vaccinology after Jenner's remarkable discovery that 'vaccination' with the phylogenetically related cowpox virus conferred immunity to the devastating disease of smallpox. The study of poxviruses continues to enrich the field of virology because the global eradication of smallpox provides a unique example of the potency of effective immunization. Other poxviruses have since been developed as vaccine vectors for clinical and veterinary applications and include modified vaccinia virus strains such as modified vaccinia Ankara and NYVAC as well as the avipox viruses, fowlpox virus and canarypox virus. Despite the empirical development of poxvirus-based vectored vaccines, it is only now becoming apparent that we need to better understand how the innate arm of the immune system drives adaptive immunity to poxviruses, and how this information is relevant to vaccine design strategies, which are the topics addressed in this article. © 2011 Expert Reviews Ltd.",beta interferon;canarypox virus vaccine;CD40 antigen;CD69 antigen;fowlpox virus vaccine;gamma interferon;Human immunodeficiency virus vaccine;immunoglobulin enhancer binding protein;immunoglobulin G1 antibody;immunoglobulin G2a antibody;inflammasome;interleukin 12;interleukin 1beta;interleukin 6;modified from copenhagen strain of vaccinia virus vaccine;modified vaccinia virus Ankara 5T4 vaccine;monocyte chemotactic protein 1;myeloid differentiation factor 88;pattern recognition receptor;toll like receptor 2;toll like receptor 3;toll like receptor 6;toll like receptor 7;toll like receptor 8;toll like receptor 9;tumor necrosis factor;unclassified drug;vaccinia vaccine;viral protein;virus protein n1;virus vaccine;adaptive immunity;adjuvant therapy;antigen expression;antigen presentation;antiviral activity;apoptosis;bone marrow cell;Canarypox virus;CD4+ T lymphocyte;CD8+ T lymphocyte;cell activation;cell infiltration;cell maturation;cell migration;clinical trial (topic);cytokine production;cytokine release;cytomegalovirus infection;dendritic cell;DNA modification;equine influenza;fever;Fowlpox virus;fowlpox virus infection;gene expression;gene synthesis;gene targeting;human;Human immunodeficiency virus infection;immunization;immunopathogenesis;immunotherapy;inflammation;innate immunity;lymphadenopathy;lymphocyte proliferation;macrophage;natural killer cell;neoplasm;nonhuman;open reading frame;persistent virus infection;Poxviridae;priority journal;protein phosphorylation;protein protein interaction;rash;review;signal transduction;single drug dose;smallpox;T lymphocyte activation;upregulation;Vaccinia virus;vaccinia virus infection;viral clearance;viral gene delivery system;virus detection;virus infection;virus inhibition;virus replication,"Lousberg, E. L.;Diener, K. R.;Brown, M. P.;Hayball, J. D.",2011,,10.1586/erv.11.121,0
1249,Classical swine fever virus diversity and evolution,"By analysing the nucleotide sequence data generated from both the E2 (gp55) and the NS5B genes of classical swine fever virus (CSFV), in addition to previously published data from the 5'NCR, we were able to divide 115 CSFV isolates into two major groups, five subgroups and two disparate isolates. Further discrimination was possible by analysis of sequence data from the E2 region. The three sequencing based methods were compared to monoclonal antibody (MAb) typing and to limited restriction enzyme (RE) mapping. Although both MAb and RE methods confirmed the previous classification the resolution was inferior. We estimated an approximate evolution rate for CSFV from an analysis of the virus variation observed in a single geographical area over a 6 year period. Applying this proposed rate to each of our deduced CSFV subgroups enabled us to calculate the approximate dates of divergence for each subgroup.",monoclonal antibody;article;evolution;genetic variability;nonhuman;nucleotide sequence;Pestivirus;priority journal;restriction mapping;virus classification;virus typing,"Lowings, P.;Ibata, G.;Needham, J.;Paton, D.",1996,,,0
1250,The evaluation of a monoclonal antibody panel for Lyssavirus typing in Mexico,"The purpose of this study was to evaluate the ability of a panel of eight antinucleocapsid monoclonal antibodies developed in Europe to identify different strains of rabies virus isolated from a variety of animal species from diverse geographic areas in Mexico. Fifty-one virus-positive samples of brain tissue from various animal species and humans were studied. Material from these samples was used to infect mice, whose brains were later tested by indirect immunofluorescence, using the monoclonal antibodies described above. Strains of the virus that showed antigenic variations were sent to the Pasteur Institute in Paris for confirmation of the results. No mouse brain sample showed a pattern of antigenic reactivity that indicated the presence of a Lyssavirus other than the classic rabies virus. However, four antigenic variations from serotype 1 of classic rabies were found. The panel of antibodies was judged to be useful for the rapid classification of rabies virus in Mexico. It is possible that autochthonous antigenic variations are appearing among strains circulating in that country, a scenario that could explain some of the failures observed with certain vaccines. For this reason, there is a need to produce antinucleocapsid monoclonal antibodies with strains of rabies virus indigenous to the area.",core protein;diagnostic agent;monoclonal antibody;animal;article;brain;cat;bovine;classification;comparative study;dog;goat;horse;human;immunology;isolation and purification;methodology;Mexico;Rabies virus;serotyping;pig;virology;virus capsid,"Loza-Rubio, E.;Vargas, R.;Hernández, E.;Batalla, D.;Aguilar-Setién, A.",1995,,,0
1251,"Novel bovine hepacivirus in dairy cattle, China",,,"Lu, G.;Jia, K.;Ping, X.;Huang, J.;Luo, A.",2018,,,0
1252,In vitro and in vivo identification of structural and sequence elements in the 5 ' untranslated region of Ectropis obliqua picorna-like virus required for internal initiation,"Ectropis obliqua picorna-like virus (EoPV) is a newly described insect virus that is classified as a putative member of the genus Iflavirus, The virus possesses a large, positive-sense RNA genome encoding a single polyprotein that shares physicochemical properties with those of members of the family Picornaviridae. The 5' untranslated region (5' UTR) plays an important role in picornavirus translation initiation, as it contains an internal ribosome entry site (IRES) that mediates cap-independent translation. To investigate translation in EoPV, an extensive range of mutations were engineered within the 5' UTR and the effects of these changes were examined in vitro and in vivo by using a bicistronic construct. Results showed that deletions within the first 63 nt had little impact on IRES activity, whilst core IRES function was contained within stem-loops C and D, as their removal abrogated IRES activity significantly. In contrast to these findings, removal of stem-loop G containing two cryptic AUGs caused a remarkable increase in IRES activity, which was further investigated by site-directed mutagenesis at these two positions. It was also confirmed that initiation of protein synthesis occurs at AUG6 (position 391-394) and not at the AUG immediately downstream of the polypyrimidine tract. Mutation of the polypyrimidine tract (CCTTTC) had a slight effect on EoPV IRES activity. Furthermore, mutations of the RAAA motif led to a decrease in IRES activity of approximately 40 % in vitro, but these results were not supported by in vivo experiments. In conclusion, this study reveals that the EoPV IRES element is unique, although it has features in common with the type II IRESs.",RIBOSOMAL ENTRY SITE;CAP-INDEPENDENT TRANSLATION;MOUTH-DISEASE VIRUS;HEPATITIS-C VIRUS;PORCINE TESCHOVIRUS-1 TALFAN;INFECTIOUS FLACHERIE;VIRUS;RNA SECONDARY STRUCTURE;ENCEPHALOMYOCARDITIS VIRUS;NONTRANSLATED REGION;A VIRUS,"Lu, J.;Zhang, J. M.;Wang, X. C.;Jiang, H.;Liu, C. F.;Hu, Y. Y.",2006,Dec,,0
1253,Phylogenetic analysis of eight genes of H9N2 subtype influenza virus: A mainland China strain possessing early isolates' genes that have been circulating,"H9N2 subtype influenza virus has become worldwide and prevalent in China. Previous studies illustrated that at least three sublineages had been established in terrestrial poultry of Eurasian avian. In this presentation, eight full-length genes of an H9N2 strain, A/Chicken/Shanghai/F/98 (Ck/SH/F/98) were obtained. Sequence analysis and phylogenetic studies were conducted by comparing eight genes with those of all the available H9N2 strains from the GenBank. The results showed that four genes (HA, NA, M and NS genes) of Ck/SH/F/98 were incorporated into the sublineage represented by the early mainland China strain, Ck/BJ/1/94. However, the other four of RNP genes of Ck/SH/F/98 did not show close relationship with those of the three known sublineages' viruses. Therefore, Ck/SH/F/98 was a natural reassortant between different sublineages. In addition, comparison showed that Ck/SH/F/98 could be a putative precursor of a later isolate from southern China, Dk/ST/1605/01, with at least six genes of both closely related, indicating genes of Ck/SH/F/98 and early isolates had ever been circulating. Further comparison in terms of molecular markers of species specificity of HA1 revealed that DK/ST/1605/01 also resembled Ck/SH/F/98 more than a common earlier duck strain. The results supported the idea of two-way transmission between terrestrial and aquatic birds that emphasized the importance to raise concerns on the natural evolution of all the eight genes of H9N2 avian influenza viruses. © 2005 Springer Science+Business Media, Inc.",article;bird;chicken;comparative study;evolution;GenBank;gene isolation;genetic analysis;Influenza virus;molecular biology;nonhuman;nucleotide sequence;phylogeny;prevalence;priority journal;sequence analysis;species difference;viral genetics;virus strain;virus transmission,"Lu, J. H.;Liu, X. F.;Shao, W. X.;Liu, Y. L.;Wei, D. P.;Liu, H. Q.",2005,,10.1007/s11262-005-1790-1,0
1254,Turkey Fecal Microbial Community Structure and Functional Gene Diversity Revealed by 16S rRNA Gene and Metagenomic Sequences,"The primary goal of this study was to better understand the microbial composition and functional genetic diversity associated with turkey fecal communities. To achieve this, 16S rRNA gene and metagenomic clone libraries were sequenced from turkey fecal samples. The analysis of 382 16S rRNA gene sequences showed that the most abundant bacteria were closely related to Lactobacillales (47%), Bacillales (31%), and Clostridiales (11%). Actinomycetales, Enterobacteriales, and Bacteroidales sequences were also identified, but represented a smaller part of the community. The analysis of 379 metagenomic sequences showed that most clones were similar to bacterial protein sequences (58%). Bacteriophage (10%) and avian viruses (3%) sequences were also represented. Of all metagenomic clones potentially encoding for bacterial proteins, most were similar to low G+C Gram-positive bacterial proteins, particularly from Lactobacillales (50%), Bacillales (11%), and Clostridiales (8%). Bioinformatic analyses suggested the presence of genes encoding for membrane proteins, lipoproteins, hydrolases, and functional genes associated with the metabolism of nitrogen and sulfur containing compounds. The results from this study further confirmed the predominance of Firmicutes in the avian gut and highlight the value of coupling 16S rRNA gene and metagenomic sequencing data analysis to study the microbial composition of avian fecal microbial communities.",metagenomics;16S rRNA gene;Turkey Feces;BACTERIAL COMMUNITY;GENOMIC SEQUENCES;SP NOV.;CHICKENS;IDENTIFICATION;DIOXYGENASE;SUCCESSION;INTESTINE;LIBRARIES;ECOLOGY,"Lu, J. R.;Domingo, J. S.",2008,Oct,,0
1255,The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver,"Background: Geese were domesticated over 6,000years ago, making them one of the first domesticated poultry. Geese are capable of rapid growth, disease resistance, and high liver lipid storage capacity, and can be easily fed coarse fodder. Here, we sequence and analyze the whole-genome sequence of an economically important goose breed in China and compare it with that of terrestrial bird species. Results: A draft sequence of the whole-goose genome was obtained by shotgun sequencing, and 16,150 protein-coding genes were predicted. Comparative genomics indicate that significant differences occur between the goose genome and that of other terrestrial bird species, particularly regarding major histocompatibility complex, Myxovirus resistance, Retinoic acid-inducible gene I, and other genes related to disease resistance in geese. In addition, analysis of transcriptome data further reveals a potential molecular mechanism involved in the susceptibility of geese to fatty liver disease and its associated symptoms, including high levels of unsaturated fatty acids and low levels of cholesterol. The results of this study show that deletion of the goose lep gene might be the result of positive selection, thus allowing the liver to adopt energy storage mechanisms for long-distance migration. Conclusions: This is the first report describing the complete goose genome sequence and contributes to genomic resources available for studying aquatic birds. The findings in this study are useful not only for genetic breeding programs, but also for studying lipid metabolism disorders.",apolipoprotein B;cholesterol;fatty acid transporter 4;glucose;major histocompatibility antigen;retinoic acid inducible protein I;triacylglycerol;unsaturated fatty acid;acc gene;acly gene;animal tissue;Anser cygnoides;apoB gene;article;China;controlled study;copy number variation;cs gene;dgat2 gene;disease predisposition;elovl6 gene;evolution;fads1 gene;fads2 gene;fasn gene;fatp gene;fatty liver;gene;gene deletion;gene expression;gene function;gene ontology;gene sequence;genetic difference;genetic susceptibility;genome analysis;gpi gene;hk1 gene;lep gene;liver weight;lpl gene;male;mdh1 gene;me1 gene;MHC gene;Mx gene;nonhuman;Orthomyxoviridae;pdh gene;pfkm gene;phylogenetic tree;pksG gene;scd gene;sequence analysis;shotgun sequencing;species comparison;synteny;virus resistance,"Lu, L.;Chen, Y.;Wang, Z.;Li, X.;Chen, W.;Tao, Z.;Shen, J.;Tian, Y.;Wang, D.;Li, G.;Chen, L.;Chen, F.;Fang, D.;Yu, L.;Sun, Y.;Ma, Y.;Li, J.;Wang, J.",2015,,10.1186/s13059-015-0652-y,0
1256,Subtypes of genotype 3 hepatitis E virus in pigs,The prevalence of hepatitis E virus (HEV) RNA in faecal and bile samples from pigs in abattoirs in Eastern and South Western China from 2006 to 2011 was determined by reverse transcriptase PCR. HEV-3 was detected in 4/5952 (0.07%) pigs and HEV-4 was detected in 287/5952 (4.8%) pigs. Two HEV-3 subtype 3a strains from South Western China had 87.1-89.7% sequence identity. Two HEV-3 subtype 3b strains from Eastern China had 91.8-93.8% sequence identity and were similar to strains reported previously in Eastern and Central China. The distinct subtypes of HEV-3 in different regions of China suggested multiple origins of HEV infection. © 2012 Elsevier Ltd.,virus RNA;article;China;controlled study;feces analysis;gene sequence;genotype;hepatitis E;Hepatitis E virus;nonhuman;nucleotide sequence;phylogenetic tree;reverse transcription polymerase chain reaction;sequence analysis;pig;virus detection;virus genome,"Lu, Y. H.;Qian, H. Z.;Qin, X.;Jiang, Q. W.;Zheng, Y. J.",2013,,10.1016/j.tvjl.2012.12.023,0
1257,Beyond the whole genome consensus: unravelling of PRRSV phylogenomics using next generation sequencing technologies Review,"The highly heterogeneous porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent responsible for an economically important pig disease with the characteristic symptoms of reproductive losses in breeding sows and respiratory illnesses in young piglets. The virus can be broadly divided into the European and North American-like genotype 1 and 2 respectively. In addition to this intra-strains variability, the impact of coexisting viral quasispecies on disease development has recently gained much attention; owing very much to the advent of the next-generation sequencing (NGS) technologies. Genomic data produced from the massive sequencing capacities of NGS have enabled the study of PRRSV at an unprecedented rate and details. Unlike conventional sequencing methods which require knowledge of conserved regions, NGS allows de novo assembly of the full viral genomes. Evolutionary variations gained from different genotypic strains provide valuable insights into functionally important regions of the virus. Together with the advancement of sophisticated bioinformatics tools, ultra-deep NGS technologies make the detection of low frequency co-evolving quasispecies possible. This short review gives an overview, including a proposed workflow, on the use of NGS to explore the genetic diversity of PRRSV at both macro- and micro-evolutionary levels.","Animals;Evolution, Molecular;*Genetic Variation;*Genome, Viral;*High-Throughput Nucleotide Sequencing;*Phylogeny;Porcine Reproductive and Respiratory Syndrome/vi [Virology];*Porcine respiratory and reproductive syndrome virus/cl [Classification];*Porcine respiratory and reproductive syndrome virus/ge [Genetics];Porcine respiratory and reproductive syndrome virus/ip [Isolation & Purification];Swine","Lu, Z. H.;Archibald, A. L.;Ait-Ali, T.",2014,Dec 19,,0
1258,Genomic variation in macrophage-cultured European porcine reproductive and respiratory syndrome virus Olot/91 revealed using ultra-deep next generation sequencing,"BACKGROUND: Porcine Reproductive and Respiratory Syndrome (PRRS) is a disease of major economic impact worldwide. The etiologic agent of this disease is the PRRS virus (PRRSV). Increasing evidence suggest that microevolution within a coexisting quasispecies population can give rise to high sequence heterogeneity in PRRSV. FINDINGS: We developed a pipeline based on the ultra-deep next generation sequencing approach to first construct the complete genome of a European PRRSV, strain Olot/9, cultured on macrophages and then capture the rare variants representative of the mixed quasispecies population. Olot/91 differs from the reference Lelystad strain by about 5% and a total of 88 variants, with frequencies as low as 1%, were detected in the mixed population. These variants included 16 non-synonymous variants concentrated in the genes encoding structural and nonstructural proteins; including Glycoprotein 2a and 5. CONCLUSION: Using an ultra-deep sequencing methodology, the complete genome of Olot/91 was constructed without any prior knowledge of the sequence. Rare variants that constitute minor fractions of the heterogeneous PRRSV population could successfully be detected to allow further exploration of microevolutionary events.","Animals;Cluster Analysis;Evolution, Molecular;*Genetic Variation;*Genome, Viral;Genotype;High-Throughput Nucleotide Sequencing;*Macrophages/vi [Virology];Molecular Sequence Data;Phylogeny;*Porcine respiratory and reproductive syndrome virus/cl [Classification];*Porcine respiratory and reproductive syndrome virus/ge [Genetics];Porcine respiratory and reproductive syndrome virus/gd [Growth & Development];Porcine respiratory and reproductive syndrome virus/ip [Isolation & Purification];*RNA, Viral/ge [Genetics];Sequence Analysis, DNA;Swine;Virus Cultivation;0 (RNA, Viral)","Lu, Z. H.;Brown, A.;Wilson, A. D.;Calvert, J. G.;Balasch, M.;Fuentes-Utrilla, P.;Loecherbach, J.;Turner, F.;Talbot, R.;Archibald, A. L.;Ait-Ali, T.",2014,Mar 04,,0
1259,Wuhan large pig roundworm virus identified in human feces in Brazil,"We report here the complete genome sequence of a bipartite virus, herein denoted WLPRV/human/BRA/TO-34/201, from a sample collected in 2015 from a two-year-old child in Brazil presenting acute gastroenteritis. The virus has 98–99% identity (segments 2 and 1, respectively) with the Wuhan large pig roundworm virus (unclassified RNA virus) that was recently discovered in the stomachs of pigs from China. This is the first report of a Wuhan large pig roundworm virus detected in human specimens, and the second genome described worldwide. However, the generation of more sequence data and further functional studies are required to fully understand the ecology, epidemiology, and evolution of this new unclassified virus.",complementary DNA;acute gastroenteritis;amino acid sequence;article;Brazil;child;clinical article;DNA synthesis;feces analysis;female;food contamination;gene sequence;genetic analysis;genetic distance;human;next generation sequencing;nonhuman;open reading frame;phylogenetic tree;preschool child;priority journal;RNA virus;sequence alignment;virus detection;Wuhan large pig roundworm virus,"Luchs, A.;Leal, E.;Komninakis, S. V.;de Pádua Milagres, F. A.;Brustulin, R.;da Aparecida Rodrigues Teles, M.;Gill, D. E.;Deng, X.;Delwart, E.;Sabino, E. C.;da Costa, A. C.",2018,,10.1007/s11262-018-1557-0,0
1260,Identification of viruses with bi- and trisegmented double-stranded RNA genome in faeces of children with gastroenteritis,"Polyacrylamide gel electrophoresis of nucleic acid extracted from faecal samples of diarrhoeic children revealed the presence of group A rotavirus in 50 (23.4%) samples and group C rotavirus in 1 (0.5%) sample out of 214 tested. One other sample showed the presence of three bands (with apparent length of 2.92, 2.37 and 1.32 kbp) which by enzymatic digestion analysis, were shown to consist of double-stranded RNA (dsRNA). The sample was shown by electron microscopy to contain virus particles with a diameter of 32-34 nm. On the basis of morphology and genomic characteristics, this virus closely resembles a virus hitherto described only in chickens by Leite et al. in 1990 and tentatively named 'picotrirnavirus'. From the same group of 214, one sample containing a 'picobirnavirus' was also identified. Thus, small icosahedral viruses with either a bi- or trisegmented dsRNA genome appear to infect humans. However, their pathogenic potential remains to be established.",article;child;controlled study;feces analysis;gastroenteritis;human;major clinical study;priority journal;RNA virus;Rotavirus;Venezuela;virus characterization;virus classification,"Ludert, J. E.;Liprandi, F.",1993,,,0
1261,Serotype Diversity of Foot-and-Mouth-Disease Virus in Livestock without History of Vaccination in the Far North Region of Cameroon,"Little information is available about the natural cycle of foot-and-mouth disease (FMD) in the absence of control measures such as vaccination. Cameroon presents a unique opportunity for epidemiological studies because FMD vaccination is not practiced. We carried out a prospective study including serological, antigenic and genetic aspects of FMD virus (FMDV) infections among different livestock production systems in the Far North of Cameroon to gain insight into the natural ecology of the virus. We found serological evidence of FMDV infection in over 75% of the animals sampled with no significant differences of prevalence observed among the sampled groups (i.e. market, sedentary, transboundary trade and mobile). We also found antibodies reactive to five of the seven FMDV serotypes (A, O, SAT1, SAT2 and SAT3) among the animals sampled. Finally, we were able to genetically characterize viruses obtained from clinical and subclinical FMD infections in Cameroon. Serotype O viruses grouped into two topotypes (West and East Africa). SAT2 viruses grouped with viruses from Central and Northern Africa, notably within the sublineage causing the large epidemic in Northern Africa in 2012, suggesting a common origin for these viruses. This research will guide future interventions for the control of FMD such as improved diagnostics, guidance for vaccine formulation and epidemiological understanding in support of the progressive control of FMD in Cameroon.",virus antibody;animal;blood;bovine;Cameroon;cattle disease;classification;enzyme linked immunosorbent assay;Foot and mouth disease virus;foot and mouth disease;genetics;immunology;livestock;prevalence;prospective study;serotype;veterinary medicine;virology,"Ludi, A.;Ahmed, Z.;Pomeroy, L. W.;Pauszek, S. J.;Smoliga, G. R.;Moritz, M.;Dickmu, S.;Abdoulkadiri, S.;Arzt, J.;Garabed, R.;Rodriguez, L. L.",2016,,10.1111/tbed.12227,0
1262,Close genetic relatedness of picornaviruses from European and Asian bats,"Our investigation of 1004 faecal specimens from European bats for picornaviruses by broadly reactive nested reverse transcription-PCR found picornaviral RNA in 28 samples (2.8 %). Phylogenetic analysis of the partial 3D genomic region suggested that one bat virus belonged to the species Enterovirus G (EV-G, formerly Porcine enterovirus B). Bat infection was supported by relatively high EV-G concentrations of 1.1×106RNA copies per gram of faeces. All other bat viruses belonged either to the bat-associated genus Mischivirus, or to an unclassified Picornaviridae group distantly related to the genus Sapelovirus. Members of this unclassified sapelovirus-related group had RNA secondary structures in their 3′-nontranslated regions that were typical of enteroviruses and that resembled structures that occur in bat-associated coronaviruses, suggesting ancient recombination events. Based on sequence distances, several picornaviruses from European and Chinese bats were likely conspecific, suggesting connectivity of virus populations. Due to their high mutation rates and their diversity, picornaviruses may be useful tools for studies of bat and virus ecology.",virus RNA;3' untranslated region;article;bat;Chinese;Coronaviridae;Enterovirus;European;nonhuman;phylogeny;Picornaviridae;priority journal;protein secondary structure;reverse transcription polymerase chain reaction;Teschovirus,"Lukashev, A. N.;Corman, V. M.;Schacht, D.;Gloza-Rausch, F.;Seebens-Hoyer, A.;Gmyl, A. P.;Drosten, C.;Drexler, J. F.",2017,,10.1099/jgv.0.000760,0
1263,Evolutionary relationships among parvoviruses: Virus-host coevolution among autonomous primate parvoviruses and links between adeno-associated and avian parvoviruses,"The current classification of parvoviruses is based on virus host range and helper virus dependence, while little data on evolutionary, relationships among viruses are available. We identified and analyzed 472 sequences of parvoviruses, among which there were (virtually) full-length genomes of all 41 viruses currently recognized as individual species within the family Parvoviridae. Our phylogenetic analysis of full-length genomes as well as open reading frames distinguished three evolutionary groups of parvoviruses from vertebrates: (i) the human helper-dependent adeno-associated virus (AAV) serotypes 1 to 6 and the autonomous avian parvoviruses; (ii) the bovine, chipmunk, and autonomous primate parvoviruses, including human viruses B19 and V9; and (iii) the parvoviruses from rodents (except for chipmunks), carnivores, and pigs. Each of these three evolutionary groups could be further subdivided, reflecting both virus-host coevolution and multiple cross-species transmissions in the evolutionary history of parvoviruses. No parvoviruses from invertebrates clustered with vertebrate parvoviruses. Our analysis provided evidence for negative selection among parvoviruses, the independent evolution of their genes, and recombination among parvoviruses from rodents. The topology of the phylogenetic tree of autonomous human and simian parvoviruses matched exactly the topology of the primate family tree, as based on the analysis of primate mitochondrial DNA. Viruses belonging to the AAV group were not evolutionarily linked to other palmate parvoviruses but were linked to the parvoviruses of birds. The two lineages of human parvoviruses may have resulted from independent ancient zoonotic infections. Our results provide an argument for reclassification of Parvovirinae based on evolutionary relationships among viruses.",Adeno associated virus;article;DNA determination;evolution;fowl;genetic analysis;nonhuman;nucleotide sequence;open reading frame;Parvoviridae;phylogeny;priority journal;species difference;unindexed sequence;virus cell interaction;virus classification,"Lukashov, V. V.;Goudsmit, J.",2001,,10.1128/jvi.75.6.2729-2740.2001,0
1264,Evolutionary relationships among Astroviridae,"To study the evolutionary relationships among astroviruses, all available sequences for members of the family Astroviridae were collected. Phylogenetic analysis distinguished two deep-rooted groups: one comprising mammalian astroviruses, with ovine astrovirus being an outlier, and the other comprising avian astroviruses. All virus species as well as serotypes of human astroviruses represented individual lineages within the tree. All human viruses clustered together and separately from non-human viruses, which argue for their common evolutionary origin and against ongoing animal-to-human transmissions. The branching order of mammalian astroviruses was exactly the opposite of that of their host species, suggesting at least two cross-species transmissions involving pigs, cats and humans, possibly through intermediate hosts. Analysis of synonymous (Ds) versus non-synonymous (Da) distances revealed that negative selection is dominating in the evolution of astroviruses, with the Ds: Da ratios being up to 46 for the comparisons of the most closely related viruses. Phylogenetic analyses of all open reading frames (ORFs) based on Ds resulted in the loss of tree structures, with virus species - and in ORF2, even serotypes of human astroviruses - branching out from virtually a single node, suggesting their ancient separation. The strong selection against non-synonymous substitutions, the low number of which is, therefore, not proof of a recent separation between lineages, together with the position of the oldest available human astrovirus strain (1971) far from the common node of its serotype 4, suggest that intraserotype diversification-originates from an earlier date.",article;Astroviridae;cat;controlled study;genetic variability;host;human;intermediate host;mammal;molecular evolution;nonhuman;nucleotide sequence;open reading frame;phylogenetic tree;priority journal;sequence analysis;serotype;species difference;pig;virus classification;virus strain;virus transmission,"Lukashov, V. V.;Goudsmit, J.",2002,,,0
1265,In Silico Identification of Plant miRNAs in Mammalian Breast Milk Exosomes - A Small Step Forward?,"MicroRNAs (miRNAs) are a class of small RNA molecules that regulate gene expression by inhibiting the protein translation or targeting the mRNA cleavage. They play many important roles in living organism cells; however, the knowledge on miRNAs functions has become more extensive upon their identification in biological fluids and recent reports on plant-origin miRNAs abundance in human plasma and serum. Considering these findings, we performed a rigorous bioinformatics analysis of publicly available, raw data from high-throughput sequencing studies on miRNAs composition in human and porcine breast milk exosomes to identify the fraction of food-derived miRNAs. Several processing and filtering steps were applied to increase the accuracy, and to avoid false positives. Through aforementioned analysis, 35 and 17 miRNA species, belonging to 25 and 11 MIR families, were identified, respectively. In the human samples the highest abundance levels yielded the ath-miR166a, pab-miR951, ptc-miR472a and bdi-miR168, while in the porcine breast milk exosomes, the zma-miR168a, zma-miR156a and ath-miR166a have been identified in the largest amounts. The consensus prediction and annotation of potential human targets for select plant miRNAs suggest that the aforementioned molecules may interact with mRNAs coding several transcription factors, protein receptors, transporters and immune-related proteins, thus potentially influencing human organism. Taken together, the presented analysis shows proof of abundant plant miRNAs in mammal breast milk exosomes, pointing at the same time to the new possibilities arising from this discovery.",RNA EDITING SITES;MICRORNA TARGETS;ACCESSORY PROTEIN;GENE-EXPRESSION;SEQUENCING DATA;MEASLES-VIRUS;CANCER-CELLS;BODY-FLUIDS;RECEPTOR;DISEASE,"Lukasik, A.;Zielenkiewicz, P.",2014,Jun,,0
1266,Infectious bursal disease virus: growth and characterization in cell cultures,"The infectious bursal disease virus (IBDV) was adapted to chicken embryo bursal (CEB) and kidney (CEK) cells. The virus did not replicate in the kidney cells until 4 serial passages of the virus were made in bursal cells. The virus produced plaques in CEK cells in 3 to 5 days. The replication of the virus was unaltered by 5 iodo 2' deoxyuridine, indicating that it is a ribovirus. The infectivity of the virus was not destroyed with chloroform and was stable at 56 C for 90 min. The virus attached to the CEK cell monolayer maximally in 75 min and had an eclipse period of 9 to 10 hours before virus maturation and release. Immunofluorescent studies of infected cells showed that the first antigen was detected 6 hr postinfection and all fluorescing antigen was confined to the cytoplasm. All of these characteristics lend support to the classification of IBDV in the diplornavirus group of riboviruses.",virus antigen;bursitis;cell culture;immunofluorescence test;in vitro study;microorganism;theoretical study;virogenesis;virus characterization;virus classification;virus infection,"Lukert, P. D.;Davis, R. B.",1974,,10.2307/1589133,0
1267,Phylogenetic position of an uncharacterized Brazilian strain of bovine papillomavirus in the genus Xipapillomavirus based on sequencing of the L1 open reading frame,"The use of PCR assays with degenerate primers has suggested the existence of numerous as yet uncharacterized bovine papillomaviruses (BPV). Despite the endemic nature of BPV infections, the identification of BPV types in Brazilian cattle is still only sporadic. However, in a recent analysis of a partial segment of the L1 gene, we observed notable diversity among the BPV types detected. The aim of this study was to determine the phylogenetic position of the previously identified wild strain BPV/BR-UEL2 detected in the state of Paraná in Brazil. Since previous analysis of the partial L1 sequence had shown that this strain was most closely related to BPV type 4, genus-specific primers were designed. Phylogenetic analysis using complete L1 ORF sequences revealed that BPV/BR-UEL2 was related to BPV types classified in the genus Xipapillomavirus and shared the highest L1 nucleotide sequence similarity with BPV type 4 (78%). This finding suggests that BPV/BR-UEL2 should be classified as a potential new type of BPV in the genus Xipapillomavirus. © 2010, Sociedade Brasileira de Genética.",virus DNA;article;Bovine papillomavirus type 4;Brazil;controlled study;genetic variability;long interspersed repeat;molecular dynamics;molecular phylogeny;new species;nonhuman;nucleotide sequence;open reading frame;organisms by phylogenetic position;phylogenetic tree;polymerase chain reaction;sequence analysis;sequence homology;virus characterization;virus classification;virus detection;virus identification;virus isolation;virus strain;virus typing;wild type,"Lunardi, M.;Claus, M. P.;Alfieri, A. A.;Fungaro, M. H. P.;Alfieri, A. F.",2010,,,0
1268,Outbreak of acute bovine viral diarrhea in Brazilian beef cattle: Clinicopathological findings and molecular characterization of a wild-type BVDV strain subtype 1b,"When first described in 1946, bovine viral diarrhea (BVD) was characterized as an acute transmissible disease associated with severe leucopenia, high fever, depression, diarrhea, gastrointestinal erosions, and hemorrhages. Recently the severe acute form has been related only to some hypervirulent BVDV-2 strains. This article reports the detection of BVDV-1b associated with an acute and fatal outbreak of BVD in a Brazilian beef cattle herd. Depression, anorexia, watery diarrhea, sialorrhea, and weakness were observed in six steers. One of these animals was evaluated for laboratorial, clinical, and pathological alterations. Laboratory findings were non-specific; clinically, the animal was weak, with dehydration and erosive oral lesions. Pathological alterations were predominant at the tongue, esophagus, and rumen. A RT-PCR assay using primers to partially amplify the 5′ untranslated region (5′UTR) of the BVDV genome was performed and identified BVDV in all clinical samples analyzed. Phylogenetic analysis of BVDV derived from lymph node revealed that this strain was clustered within the BVDV subtype 1b. This differentiating was only possible to be performed by molecular characterization since both clinical presentation and pathologic findings were similar to BVDV-2 infection. © 2008 Elsevier Ltd. All rights reserved.",5' untranslated region;acute diarrhea;animal tissue;anorexia;article;beef cattle;Brazil;bullock;cattle disease;clinical feature;cluster analysis;controlled study;dehydration;depression;disease association;disease severity;epidemic;esophagus;fatality;gene amplification;genome analysis;histopathology;hypersalivation;lymph node;molecular mechanics;mouth lesion;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;ruminant stomach;tissue distribution;tongue;virus characterization;virus detection;virus identification;virus infection;virus strain;virus virulence;weakness;wild type,"Lunardi, M.;Headley, S. A.;Lisbôa, J. A. N.;Amude, A. M.;Alfieri, A. A.",2008,,10.1016/j.rvsc.2008.01.002,0
1269,Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing,"Here we demonstrate the use of short-read massive sequencing systems to in effect achieve longer read lengths through hierarchical molecular tagging. We show how indexed and PCR-amplified targeted libraries are degraded, sub-sampled and arrested at timed intervals to achieve pools of differing average length, each of which is indexed with a new tag. By this process, indices of sample origin, molecular origin, and degree of degradation is incorporated in order to achieve a nested hierarchical structure, later to be utilized in the data processing to order the reads over a longer distance than the sequencing system originally allows. With this protocol we show how continuous regions beyond 3000 bp can be decoded by an Illumina sequencing system, and we illustrate the potential applications by calling variants of the lambda genome, analysing TP53 in cancer cell lines, and targeting a variable canine mitochondrial region.","oligonucleotide;protein p53;TP53 protein, human;animal;article;Enterobacteria phage lambda;chemistry;DNA barcoding;DNA sequence;dog;genetics;high throughput sequencing;human;methodology;mitochondrion;polymerase chain reaction;tumor cell line","Lundin, S.;Gruselius, J.;Nystedt, B.;Lexow, P.;Käller, M.;Lundeberg, J.",2013,,,0
1270,Phylogenetic analysis of the S1 glycoprotein gene of infectious bronchitis viruses isolated in China during 2009-2010,"As part of our ongoing surveillance program, 40 field strains of avian infectious bronchitis virus (IBV) were isolated from dead or diseased chicken flocks in different areas of China between 2009 and 2010. S1 glycoprotein genes of these strains were sequenced and analyzed with 38 strains published in GenBank. S1 genes of these isolated strains and the vaccine strains showed nucleotide homologies ranging from 65.2 to 82% and amino acid homologies ranging from 58.4 to 81.9%. Meanwhile, Chinese IBV strains isolated in this study, which were mainly nephropathogenic, could be separated into six variant lineages (CH I-CH VI), and current vaccine strains used in China formed Mass variant lineage that is evolutionarily distant from Chinese isolates. Moreover, CK/CH/GD/NC10, CK/CH/GD/KP10, and our previous isolates TC07-2 formed the CH VI lineage, showing larger evolutionary distances from other strains. Taken together, these findings suggested that various variant lineages were co-circulating in China now, and appeared to be continuously evolving, alternative indigenous vaccines indeed need for effective control of IB in China. © Springer Science+Business Media, LLC 2011.",amino acid sequence;article;Avian infectious bronchitis virus;China;Chinese;evolutionary homology;genetic analysis;genetic distance;genetic variability;nonhuman;nucleotide sequence;phylogeny;priority journal;promoter region;S1 glycoprotein gene;virus gene;virus isolation;virus strain,"Luo, H.;Qin, J.;Chen, F.;Xie, Q.;Bi, Y.;Cao, Y.;Xue, C.",2012,,10.1007/s11262-011-0657-x,0
1271,"Serological evidence for high prevalence of Influenza D viruses in cattle, Nebraska, United States, 2003–2004",,,"Luo, J.;Ferguson, L.;Smith, D. R.;Woolums, A. R.",2017,,,0
1272,Phylogenetic analysis of the E2 gene of classical swine fever virus from the Guangxi Province of southern China,"In this study, suspected classical swine fever (CSF) samples from the Guangxi Province of China were obtained from pigs with acute CSF, aborted fetuses, newborn pigs that died at 1-2 days of age, tonsils of healthy pigs, and leukocytes of immunized sows during 2001-2009. About 92 of 775 samples were found to be positive by RT-PCR, and 41 isolates were obtained. Phylogenetic analysis was performed on the 31 isolates by sequencing the E2 gene, and the isolates were found to cluster into two groups: (1) isolates from aborted fetuses (except GXGZ02), deceased newborn baby pigs, tonsils of healthy pigs, and leukocytes of immunized sows belonged to group 1.1, along with vaccine strain, HCLV, and standard virulent strain, Shimen, of China, and (2) 20 isolates from pigs with acute CSF belonged to group 2.1, 13 of which were clustered into subgroup 2.1b with isolates from other provinces of China, and 7 of which were clustered into subgroup 2.1a with isolates from Italy and Germany. © 2011 Springer Science+Business Media, LLC.",animal cell;article;China;classical swine fever;cluster analysis;E2 gene;fetus;gene sequence;Germany;Italy;leukocyte;newborn;nonhuman;nucleotide sequence;Pestivirus;phylogeny;priority journal;tonsil;virus gene;virus isolation;virus strain,"Luo, T. R.;Liao, S. H.;Wu, X. S.;Feng, L.;Yuan, Z. X.;Li, H.;Liang, J. J.;Meng, X. M.;Zhang, H. Y.",2011,,10.1007/s11262-011-0578-8,0
1273,Pathogenicity and genomic characterization of a pseudorabies virus variant isolated from Bartha-K61-vaccinated swine population in China,"Pseudorabies (PR) or Aujeszky's disease (AD), caused by pseudorabies virus (PRV), is an economically important viral disease worldwide. Recently, PR outbreaks occurred in a large number of Bartha-K61-vaccinated swine herds in many regions of China. Here, we isolated a PRV variant, named TJ strain, from a Bartha-K61-vaccinated pig farm in China, evaluated the pathogenicity of the TJ strain in susceptible animals and analyzed its complete genomic sequence obtained by 454 pyrosequencing. Vaccination-challenge experiment in sheep showed that the classical Bartha-K61 vaccine could not provide complete protection against the challenge with the PRV TJ strain. In mice, the 50% lethal dose (LD<inf>50</inf>) of the TJ strain (10<sup>2.3</sup> TCID<inf>50</inf>) was lower than that of the classical PRV SC strain (10<sup>3.0</sup> TCID<inf>50</inf>). Furthermore, the TJ strain displayed higher mortality for pigs, as compared with the SC strain. The PRV TJ strain genome was determined to be 143,642bp in length, encoding 67 open reading frames. The TJ strain was clustered to an independent branch together with some recent PRV isolates in China in the phylogenetic tree, which was relatively distant from previous PRV isolates. The TJ strain showed unique variations in the viral proteins that play key roles in the viral replication cycle. Taken together, the TJ strain is a highly pathogenic PRV variant with unique molecular signatures. Further studies are needed to explore the relevance of the sequence differences to the virulence alteration of the PRV variant.",bartha k61 vaccine;pseudorabies vaccine;unclassified drug;animal experiment;animal model;animal tissue;article;China;controlled study;experimental infection;genetic variability;high throughput sequencing;lethal dose;mouse;nonhuman;nucleotide sequence;open reading frame;phylogenetic tree;polymerase chain reaction;pseudorabies;Pseudorabies virus;pig;vaccination;virus genome;virus identification;virus isolation;virus replication;virus strain;virus virulence,"Luo, Y.;Li, N.;Cong, X.;Wang, C. H.;Du, M.;Li, L.;Zhao, B.;Yuan, J.;Liu, D. D.;Li, S.;Li, Y.;Sun, Y.;Qiu, H. J.",2014,,10.1016/j.vetmic.2014.09.003,0
1274,A molecular epidemiology study based on VP2 gene sequences reveals that a new genotype of infectious bursal disease virus is dominantly prevalent in Italy,"A distinctive infectious bursal disease (IBD) virus genotype (ITA) was detected in IBD-live vaccinated broilers in Italy without clinical signs of IBD. It was isolated in specific-pathogen-free eggs and molecularly characterized in the hypervariable region of the virus protein (VP) 2. Phylogenetic analysis showed that ITA strains clustered separately from other homologous reference sequences of IBDVs, either classical or very virulent, retrieved from GenBank or previously reported in Italy, and from vaccine strains. The new genotype shows peculiar molecular characteristics in key positions of the VP2 hypervariable region, which affect charged or potentially glycosylated amino acids virtually associated with important changes in virus properties. Characterization of 41 IBDV strains detected in Italy between 2013 and 2014 showed that ITA is emergent in densely populated poultry areas of Italy, being 68% of the IBDV detections made during routine diagnostic activity over a two-year period, in spite of the immunity induced by large-scale vaccination. Four very virulent strains (DV86) and one classical strain (HPR2), together with eight vaccine strains, were also detected. The currently available epidemiological and clinical data do not allow the degree of pathogenicity of the ITA genotype to be defined. Only in vivo experimental pathogenicity studies conducted in secure isolation conditions, through the evaluation of clinical signs and macro/microscopic lesions, will clarify conclusively the virulence of the new Italian genotype.","viral protein;VP2 protein, infectious bursal disease virus;amino acid sequence;animal;birnavirus infection;chicken;classification;DNA sequence;female;genetics;genotype;germfree animal;infectious bursal disease virus;isolation and purification;Italy;longitudinal study;molecular epidemiology;ovum;pathogenicity;phylogeny;bird disease;prevalence;sequence alignment;veterinary medicine;virology;virulence","Lupini, C.;Giovanardi, D.;Pesente, P.;Bonci, M.;Felice, V.;Rossi, G.;Morandini, E.;Cecchinato, M.;Catelli, E.",2016,,10.1080/03079457.2016.1165792,0
1275,Accurate and precise real-time RT-PCR assays for the identification of astrovirus associated encephalitis in cattle,,,"Lüthi, R.;Boujon, C. L.;Kauer, R.;Koch, M. C.;Bouzalas, I. G.",2018,,,0
1276,Genetic evolution of Gallid herpesvirus 2 isolated in China,"Gallid herpesvirus 2 (GaHV-2), which causes Marek's disease in chickens and has caused extensive economic losses, has recently evolved increased virulence in China. To better understand the genetic basis of the pathogenic characteristics changed and increased virulence, we sequenced the genomes of six new GaHV-2 strains (LCC, LTS, WC/1203, JL/1404, CC/1409, and HS/1412) isolated from chickens with failed immunisation as well as one previously isolated Chinese GaHV-2 strain, J-1. Based on a multiple sequence alignment, several characteristic point mutations were detected in the open reading frames of the Chinese isolates. In addition, two deletions and an insertion were identified at the unique short region and terminal repeat short region junctions in Chinese isolates, and the insertion was a characteristic of the new Chinese isolates. According to a phylogenetic analysis, the GaHV-2 genome diverged substantially over the last two decades in China. Based on the internal repeat long region, the new isolates were closely related to very virulent or very virulent plus strains. Additionally, the new Chinese isolates diverged from the previously isolated strains J-1 and 814. In conclusion, our results provide evidence that Chinese GaHV-2 strains contain characteristic sequences, especially the new isolates. The observed genetic divergence in the new Chinese GaHV-2 strains over the last two decades may be related to observed changes in pathogenic characteristics and virulence.",amino acid substitution;animal cell;article;China;gene deletion;genome size;high throughput sequencing;Gallid alphaherpesvirus 2;mec gene;nonhuman;open reading frame;phylogeny;point mutation;priority journal;sequence alignment;sequence analysis;single nucleotide polymorphism;UL36 gene;virus gene;virus genome;virus isolation;virus strain;virus virulence,"Lv, H.;Zhang, Y.;Sun, G.;Bao, K.;Gao, Y.;Qi, X.;Cui, H.;Wang, Y.;Li, K.;Gao, L.;Pan, Q.;Wang, X.;Liu, C.",2017,,10.1016/j.meegid.2016.04.027,0
1277,Gene expression analysis of porcine whole blood cells infected with foot-and-mouth disease virus using high-throughput sequencing technology,"Foot-and-mouth disease virus (FMDV) is a single-stranded positive RNA virus that belongs to the family Picornaviridae. FMDV infects cloven-hoofed animals, such as pigs, sheep, goats, cattle and diverse wildlife species, and remains a major threat to the livestock industry worldwide. In this study, a transcriptome analysis of whole blood from pigs infected with FMDV was performed using the paired-end Illumina sequencing technique to understand the interactions between the pathogen and its host cells. During infection with FMDV, a total of 120 differentially expressed genes (DEGs) were identified, including 110 up-regulated genes and 10 down-regulated genes. To further investigate the DEGs involved in interactions between the virus and its host, gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were conducted. GO annotation indicated that a number of DEGs were enriched in categories involved in host-virus interactions, such as response to stimulus, immune system process and regulation of biological process. KEGG enrichment analysis indicated that the DEGs were primarily involved in the ribosome signaling pathway and immune-related signaling pathways. Ten DEGs, including the immune-related genes BTK1, C1QB, TIMD4 and CXCL10, were selected and validated using quantitative PCR, which showed that the expression patterns of these genes are consistent with the results of the in silico expression analysis. In conclusion, this study presents the first transcriptome analysis of pig whole blood cells infected with FMDV, and the results obtained in this study improve our understanding of the interactions between FMDV and host cells as well as the diagnosis and control of FMD.",gamma interferon inducible protein 10;animal cell;animal experiment;animal model;article;blood cell;BTK1 gene;C1QB gene;computer model;controlled study;CXCL10 gene;disease control;down regulation;foot and mouth disease;gene;gene expression;gene identification;gene ontology;genetic analysis;high throughput sequencing;host cell;host pathogen interaction;immunity;immunoregulation;nonhuman;pig;polymerase chain reaction;ribosome;signal transduction;TIMD4 gene;transcriptomics;upregulation;virus cell interaction,"Lv, J.;Ding, Y.;Liu, X.;Pan, L.;Zhang, Z.;Zhou, P.;Zhang, Y.;Hu, Y.",2018,,10.1371/journal.pone.0200081,0
1278,"[Taxonomic status of the Burana virus (BURV) (Bunyaviridae, Nairovirus, Tamdy group) isolated from the ticks Haemaphysalis punctata Canestrini et Fanzago, 1877 and Haem. concinna Koch, 1844 (Ixodidae, Haemaphysalinae) in Kyrgyzstan]",,animal;bovine;Bunyaviridae;genetics;high throughput sequencing;Ixodidae;Kyrgyzstan;molecular genetics;phylogeny;tick;virology;virus genome,"L'Vov D, K.;Al'khovskiĭ, S. V.;Shchelkanov, M. Iu;Shchetinin, A. M.;Deriabin, P. G.;Gitel'man, A. K.;Aristova, V. A.;Botikov, A. G.",2014,,,0
1279,West Nile virus and other zoonotic viruses in Russia: examples of emerging-reemerging situations,"Studies of the interactions of vertebrates, viruses and arthropod vectors of these viruses were monitored in terms of different ecological groups of viruses transmitted by mosquitoes and ticks in Northern Eurasia in an area encompassing more than 15 million km2. About 90 viruses were isolated, including 24 new to science. Newly recognized infections of vertebrates, including humans, were described. Many unusual epidemic situations were analysed. Permanent efforts were established to prevent bioterrorist activities and their consequences. Extensive epidemic outbreaks of West Nile fever (WNF; i.e., fever caused by West Nile virus) and Crimean-Congo hemorrhagic fever (CCHF) with unusual high mortality appeared in the last four years in southern Russia. We determined infection rates in humans, domestic and wild animals, mosquitoes and ticks from natural and synanthropic biocenoses [Editorial note: ""synanthropic"" means, roughly, all species living with (c.f. lice, fleas) or near people, such as in houses (c.f. house mice), parks (c.f. Rattus spp.), and the like, rather like ""peridomestic"", but not strictly so; ""biocenosis"" is the biome, the ""totality of living populations in a particular habitat, which itself is only a part of the ecosystem"".]. CCHF virus strains were phylogenetically similar to strains isolated in this area 35 years ago but different from Central-South-Asian and African strains. Before the outset of the current emergence of epidemic WNF, three genetic variants of this virus had been isolated in USSR, two African and one Indian. Phylogenetic analysis of complete genome sequences of epidemic strains demonstrated considerable similarity to strains from USA and Israel and differences from strains isolated in the same USSR areas 20-30 years before. In addition to strains of genotype 1, we isolated strains of second and third lineages and a strain of a fourth genetic variant. Nucleotide differences of these strains from all three genotypes was about 30%. The emerging WNF situation in Russia for the last 4 years probably has been the result of not only natural and social factors, but also to introduction of more virulent strains or by evolution of the virus.",animal;article;disease transmission;domestic animal;ecosystem;genetic variability;genetics;geography;human;isolation and purification;mammal;mosquito;pathogenicity;rat;Russian Federation;tick;virology;virus infection;West Nile virus;zoonosis,"Lvov, D. K.;Butenko, A. M.;Gromashevsky, V. L.;Kovtunov, A. I.;Prilipov, A. G.;Kinney, R.;Aristova, V. A.;Dzharkenov, A. F.;Samokhvalov, E. I.;Savage, H. M.;Shchelkanov, M. Y.;Galkina, I. V.;Deryabin, P. G.;Gubler, D. J.;Kulikova, L. N.;Alkhovsky, S. K.;Moskvina, T. M.;Zlobina, L. V.;Sadykova, G. K.;Shatalov, A. G.;Lvov, D. N.;Usachev, V. E.;Voronina, A. G.",2004,,,0
1280,"Razdan virus, a new ungrouped bunyavirus isolated from Dermacentor marginatus ticks in Armenia","A virus, designated Razdan, was isolated from Dermacentor marginatus ticks in the Armenian S.S.R. in 1973. The complement fixation tests revealed no antigenic relationships to 74 tick-borne arboviruses. The size of the virus is about 100 nm; it agglutinates goose erythrocytes at pH 5.5--7.0, is pathogenic for newborn, 14-day-old and adult white mice and multiplies in primary and continuous cell cultures. Morphological properties of the virus permit its classification as a member of the family Bunyaviridae.","Animals;Antigens, Viral/an [Analysis];*Arboviruses/cl [Classification];Armenia;*Bunyamwera virus/cl [Classification];Bunyamwera virus/ip [Isolation & Purification];Bunyamwera virus/ph [Physiology];Complement Fixation Tests;*Dermacentor/mi [Microbiology];*Sheep/ps [Parasitology];Terminology as Topic;*Ticks/mi [Microbiology];0 (Antigens, Viral)","Lvov, D. K.;Gromashevsky, V. L.;Zakaryan, V. A.;Skvortsova, T. M.;Berezina, L. K.;Gofman, Y. P.;Klimenko, S. M.;Chubkova, A. L.",1978,Nov,,0
1281,"Batken virus, a new arbovirus isolated from ticks and mosquitoes in Kirghiz S.S.R. Brief report","Three virus strains were isolated in 1970. Two of these (LEIV 300 K and LEIV 306 K) were isolated from Hyalomma plumbeum plumbeum Panz., 1795, ticks were collected from sheep in the Batken Region, Oshsk Province, and one virus strain from mixed pools of Aedes caspius caspius Pallas, 1771, and Culex (Neoculex) hortensis Ficalb, 1889, mosquitoes were caught in the Leninsk Region, Oshsk Province, Kirghiz USSR. The ticks were collected in the semidesert foothills of the Turkestan Mountains near the village of Batken, 700 M above sea level (40° 04' N, 70° 51' E). A total of 146 ticks was examined by virological methods. The mosquitoes were collected in the rice fields in the valley of the Naryn river, 650 M above sea level (41° N, 72° E). A total of 20,000 mosquitoes of the two species were examined by virological methods. Virus isolation attempts were made in 1-2 day old white suckling mice. Antigens were prepared from the brains of sickened suckling mice by the sucrose acetone method. Immune ascitic fluids (IAF) were prepared. Serological identification of the isolates was performed in complement fixation tests (CFT) by a macromethod with a set of 57 IAF to arboviruses. Since all isolates were found to be serologically identical, the prototype strain LEIV 306 K could be studied in detail. An examination of the virus antigen in CF tests revealed that it reacted with none of the IAFs used. The data collected, along with the isolation of the virus from ticks and mosquitoes, suggest that the virus is a new ungrouped arbovirus. It is named Batken virus after the site of its first isolation.",Arbovirus;arthropod;classification;in vitro study;microorganism;mosquito;theoretical study;tick;virogenesis;virus classification;virus isolation,"Lvov, D. K.;Karas, F. R.;Tsyrkin, Y. M.",1974,,,0
1282,"Antigenic cross-reactivity among avian pneumoviruses of subgroups A, B, and C at the matrix but not nucleocapsid proteins","Earlier findings from our laboratory based on analysis of nucleotide and predicted amino acid sequence identities of 15 avian pneumoviruses (APVs) isolated from the United States (subgroup C) demonstrated that the viruses were phylogenetically separated from the European subgroup A and subgroup B viruses. Here, we investigated whether viruses from the three subgroups were cross-reactive by testing field sera positive for each of the APV subgroups in an enzyme-linked immunosorbent assay (ELISA) test with recombinant matrix (M) and nucleoprotein (N) proteins generated from a Minnesota APV isolate (APV/ MN2A). Sera from turkeys infected with APV subgroup A, B, or C reacted with recombinant M protein derived from APV/MN2A. In contrast, recombinant N protein from APV/MN2A virus was reactive with sera from subtypes A and C viruses but not from subtype B virus. The results illustrate that viruses from the three APV subtypes share antigenic homology, and the M protein--based ELISA is adequate for monitoring APV outbreaks but not for distinguishing between different subtypes.",matrix protein;recombinant protein;virus antibody;virus antigen;animal;animal disease;article;bacterium identification;classification;cross reaction;enzyme linked immunosorbent assay;genetics;immunology;isolation and purification;methodology;phylogeny;Pneumovirinae;turkey (bird);virus nucleocapsid,"Lwamba, H. C. M.;Halvorson, D. A.;Nagaraja, K. V.;Turpin, E. A.;Swayne, D.;Seal, B. S.;Kariuki Njenga, M.",2002,,,0
1283,Investigations of porcine circovirus type 1 (PCV1) in vaccine-related and other cell lines,"Porcine circovirus type 1 (PCV1) is highly prevalent in swine and was recently reported in some rotavirus vaccines. Since animal-derived raw materials, such as cells, trypsin, and serum, can be a major source of introducing virus contamination in biological products, we have investigated PCV1 in several cell lines obtained from ATCC that have broad use in research, diagnostics, or vaccine development. It is expected that these cell lines have been exposed to bovine and porcine viruses during their establishment and passage history due to the use of serum and trypsin that was not qualified according to current testing guidances or processed using new virus-inactivation methods. This study showed that Vero, MRC-5, and CEFs, which represent cell substrates used in some U.S. licensed vaccines, and other cell lines used in investigational vaccines, such as MDCK, HEK-293, HeLa, and A549, were negative for PCV1 using a nested PCR assay: some were also confirmed negative by infectivity analysis. However, MDBK cells, which are used for some animal vaccines, contained PCV1 sequences, although no virus was isolated. Although the results showed that PCV infection may not have occurred under previous culture conditions, the recent cases of vaccine contamination emphasizes the need for continued efforts to reduce the likelihood of introducing viruses from animal-derived materials used in product manufacture. Published by Elsevier Ltd.",Porcine circovirus;PCR assay;Infectivity assays;Vaccine-related cell;lines;Animal-derived raw materials;ANTIBODIES;VIRUS;REPLICATION;INFECTION;DNA;AMPLIFICATION;PAPOVAVIRUS;PIGS;METAGENOMICS;CULTURES,"Ma, H. L.;Shaheduzzaman, S.;Willliams, D. K.;Gao, Y. M.;Khan, A. S.",2011,Oct,,0
1284,Identification and phylogenetic analysis of Coxsackie-virus B5 that caused an outbreak of viral encephalitis in Henan area,"Objective: To identify the pathogen that caused an outbreak of viral encephalitis in Henan area in 2011. Phylogenic analysis was carried out on Coxsackie-virus B5 (CVB5) which was isolated during this outbreak. Methods: Five throat swab, 21 stool and 14 cerebrospinal fluid (CSF) specimens were collected from 29 inpatients during this outbreak. Viral isolation and real time RT-PCR were then performed for all specimens. Viral nucleic acid of enterovirus 71 (EV71), coxsackievirus A 16 (CA16) and pan-enterovirus (PE) were detected by real time RT-PCR. Phylogenetic tree based on entire VP1 sequences was constructed among CVB5 isolates from 2 stool and 3 CSF specimens of 5 inpatients and others published data retrieved from GenBank. Results: The real time RT-PCR results showed that the PE nucleic acid positive rates of throat swab, stool and CSF specimens were 60.0% (3/5), 61.9% (13/21) and 85.7% (12/14) respectively. All of these specimens were negative for EV71 and CA16. The isolation rates of throat swab, stool and CSF specimens were 20.0% (1/5), 25.0% (5/21) and 29.0% (4/14), respectively. BLAST with both VP1 and 5'-UTR sequences and molecular typing indicated that CVB5 was the main pathogen. Analysis among the 5 positve isolates based on the complete VP1 sequences showed 97.9% - 99.5% homology. Data from homologous comparisons indicated that these isolates had the highest nucleotide acid identity with the Changchun CVB5 CC10/10/Changchun strain (97.1% - 98.1%) which caused hand, foot, and mouth disease (HFMD) outbreak in Changchun in 2010, and lower identity (89.0% - 89.6% and 91.8% - 92.5%) with the COXB5/Henan/2010 and 03001N strain isolated from Pingdingshan, Henan in 2010 and 2012, respectively. Phylogenetic tree in VP1 region showed that isolates of this outbreak belonged to genotype D, the same clade with Changchun strain. Conclusion: CVB5 was the major etiological agent correlated with this outbreak. The shift of predominant genotype might serve as one of the causes that associated with this outbreaks. Copyright © 2012 by the Chinese Medical Association.",protein VP1;article;cerebrospinal fluid examination;Enterovirus;Coxsackievirus B5;Enterovirus A71;epidemic;feces analysis;human;human tissue;nonhuman;phylogenetic tree;phylogeny;real time polymerase chain reaction;throat culture;virus encephalitis;virus identification;virus isolation;virus strain,"Ma, H. X.;Mu, Y. J.;Li, X. L.;Kang, K.;Huang, X. Y.;Tang, X. Y.;Wei, W.;Xu, B. L.",2012,,10.3760/cma.j.issn.0254-5101.2012.07.009,0
1285,A nanoparticle-assisted PCR assay to improve the sensitivity for rapid detection and differentiation of wild-type pseudorabies virus and gene-deleted vaccine strains,"Nanoparticle-assisted polymerase chain reaction (nanoPCR) is a novel method for the rapid amplification of DNA and has been adopted for the detection of virus because of its simplicity, rapidity, and specificity. A nanoPCR assay was developed to detect and differentiate wild-type and gene-deleted pseudorabies virus (PRV). Three pairs of primers for nanoPCR developed in this study were selected from conserved regions of PRV, producing specific amplicons of 431. bp (gB), 316. bp (gE), and 202. bp (gG). The sensitivity of this assay using purified plasmid constructs containing the specific gene fragments was 100-1000 fold higher than conventional PCR. The PRV nanoPCR assay did not amplify porcine parvovirus, porcine circovirus type 2, porcine reproductive and respiratory syndrome virus, porcine teschovirus, or African swine fever virus but produced three bands of expected size with PRV and two bands of expected size with the gene-deleted PRV-Bartha-K61. Of 110 clinical samples collected from seven provinces in China, 53% and 48% were positive for wild-type PRV according to the nanoPCR assay and virus isolation, respectively. © 2013 Elsevier B.V.",nanoparticle;plasmid vector;primer DNA;African swine fever virus;amplicon;Arterivirus;article;Circovirus;gene amplification;gene deletion;genetic conservation;intermethod comparison;nanoparticle assisted polymerase chain reaction;nonhuman;nucleotide sequence;polymerase chain reaction;Porcine parvovirus;priority journal;Pseudorabies virus;sensitivity analysis;Teschovirus;virus classification;virus detection;virus gene;virus strain;wild type,"Ma, X.;Cui, Y.;Qiu, Z.;Zhang, B.;Cui, S.",2013,,10.1016/j.jviromet.2013.07.018,0
1286,Completion of the sequence analysis and comparisons of genome segment 2 (encoding outer capsid protein VP2) from representative isolates of the 24 bluetongue virus serotypes,"Bluetongue (BT) is a non-contagious, arthropod-transmitted viral disease of domestic and wild ruminants. It is caused by bluetongue virus (BTV), a double-stranded (ds) RNA virus that is classified within the genus Orbivirus, family Reoviridae. There are at least twenty-four serotypes of BTV worldwide, five of which (1, 2, 4, 9 and 16) have been identified recently in Europe. BTV infects ruminants and its distribution throughout temperate and tropical regions of the world is dependent on the activity and abundance of certain vector-competent species of Culicoides midge. The outer capsid protein VP2 of BTV is a major protective antigen and the primary determinant of virus serotype. For the first time, the authors have completed the sequence analysis of full-length VP2 genes from the reference strains of each of the 24 BTV serotypes and their amino acid sequences were deduced. Multiple alignment of the VP2 gene (protein) sequences revealed that the level of nucleotide (amino acid) sequence variation between serotypes ranged from 29% (23%) to 59% (73%), confirming that segment 2/VP2 is the most variable BTV gene/protein. Phylogenetic analysis of VP2 grouped together the BTV types that are known to cross-react serologically. Low identity between types was demonstrated for specific regions within the VP2 amino acid sequences that have been shown to be antigenic and play a role in virus neutralisation. The sequence data represent the completion of an important step in the creation of a comprehensive BTV sequence database, which will support more rapid molecular methods for diagnosis and identification of BTV 'types', as well as continuing molecular epidemiology and surveillance studies of BTV.",,"Maan, S.;Maan, N. S.;Samuel, A. R.;O'Hara, R.;Meyer, A. J.;Rao, S.;Mertens, P. P.",2004,Oct-Dec,,0
1287,Development of reverse transcriptase-polymerase chain reaction-based assays and sequencing for typing European strains of bluetongue virus and differential diagnosis of field and vaccine strains,"Bluetongue virus (BTV) is a double-stranded (ds) RNA virus, classified within the genus Orbivirus, family Reoviridae, which causes bluetongue (BT), an infectious, non-contagious disease of ruminants. The virus exists as 24 distinct serotypes, which are currently identified by virus isolation and serum neutralisation assays. The most variable outer capsid protein VP2 (encoded by genome segment 2), is the primary determinant of BTV serotype. Reverse transcriptase-polymerase chain reaction (RT-PCR) assays, based on amplification of segment 2, have been developed for identification of the five European BTV types (BTV-1, BTV-2, BTV-4, BTV-9 and BTV-16). Primer pairs were designed that are specific for each BTV serotype. The resulting RT-PCR assay was both sensitive and specific, providing BTV typing within 24 h. Perfect agreement was recorded between the RT-PCR and virus neutralisation assays. The primers for each serotype could successfully amplify the BTV isolates of that serotype from different regions and showed no cross-amplification of the most closely related BTV serotypes. RT-PCR primers were also developed for the discrimination of field and vaccine strains of BTV serotypes currently circulating in Europe. The primer pairs which could amplify field and vaccine strains of BTV-1, BTV-2, BTV-4 and BTV-9 were validated with several isolates of each serotype from various geographic origins around the world and their type specificity was again tested with the most closely related serotypes. Overall, these RT-PCR assays provide a rapid and reliable method for the identification and differentiation of field and vaccine strains of different BTV types. The primers used in this study are listed on the website of the Institute for Animal Health, Pirbright.",,"Maan, S.;Maan, N. S.;Singh, K. P.;Samuel, A. R.;Mertens, P. P.",2004,Oct-Dec,,0
1288,Genome-Wide Identification and Quantification of cis- and trans-Regulated Genes Responding to Marek's Disease Virus Infection via Analysis of Allele-Specific Expression,"Marek's disease (MD) is a commercially important neoplastic disease of chickens caused by Marek's disease virus (MDV), a naturally occurring oncogenic alphaherpesvirus. Selecting for increased genetic resistance to MD is a control strategy that can augment vaccinal control measures. To identify high-confidence candidate MD resistance genes, we conducted a genome-wide screen for allele-specific expression (ASE) amongst F(1) progeny of two inbred chicken lines that differ substantially in MD resistance. High throughput sequencing was initially used to profile transcriptomes from pools of uninfected and infected individuals at 4 days post-infection to identify any genes showing ASE in response to MDV infection. RNA sequencing identified 22,655 single nucleotide polymorphisms (SNPs) of which 5,360 in 3,773 genes exhibited significant allelic imbalance. Illumina GoldenGate assays were subsequently used to quantify regulatory variation controlled at the gene (cis) and elsewhere in the genome (trans) by examining differences in expression between F(1) individuals and artificial F(1) RNA pools over six time periods in 1,536 of the most significant SNPs identified by RNA sequencing. Allelic imbalance as a result of cis-regulatory changes was confirmed in 861 of the 1,233 GoldenGate assays successfully examined. Furthermore we have identified seven genes that display trans-regulation only in infected animals and ~500 SNP that show a complex interaction between cis- and trans-regulatory changes. Our results indicate ASE analyses are a powerful approach to identify regulatory variation responsible for differences in transcript abundance in genes underlying complex traits. And the genes with SNPs exhibiting ASE provide a strong foundation to further investigate the causative polymorphisms and genetic mechanisms for MD resistance. Finally, the methods used here for identifying specific genes and SNPs have practical implications for applying marker-assisted selection to complex traits that are difficult to measure in agricultural species, when expression differences are expected to control a portion of the phenotypic variance.",,"Maceachern, S.;Muir, W. M.;Crosby, S. D.;Cheng, H. H.",2011,,,0
1289,"Potential strategies for control of bluetongue, a globally emerging, Culicoides-transmitted viral disease of ruminant livestock and wildlife","Bluetongue (BT) is a non-zoonotic arboviral disease of certain wild and domestic species of cloven-hoofed ungulates. The causative agent, bluetongue virus (BTV), is spread through temperate and tropical regions of the world by biting Culicoides midges. Control of BTV infection is complicated by the plurality of virus serotypes and the ubiquity and opportunistic feeding behavior of its midge vector. The global distribution of BTV infection has recently altered, perhaps driven in part by climatic influences on midge species resident in different regions. The goal of this review is to evaluate realistic strategies that might be utilized to control or prevent future outbreaks of BT and other Culicoides-transmitted diseases. Importantly, optimal control of emerging, rapidly evolving arbovirus diseases such as BT will require integrated countermeasures that mitigate all aspects of the virus's transmission cycle. This will best be accomplished using preventative, rather than purely reactive strategies. © 2013 Elsevier B.V.",arthropod;autumn;bluetongue;bovid;climate change;Culicoides;epidemic;genetic drift;genetic heterogeneity;geographic distribution;global climate;human;livestock;nonhuman;phenotype;priority journal;reverse transcription polymerase chain reaction;review;seasonal variation;sensitivity and specificity;serotype;summer;vaccination;vector control;virus classification;virus detection;virus strain;virus transmission;virus virulence;waste water;wildlife,"Maclachlan, N. J.;Mayo, C. E.",2013,,10.1016/j.antiviral.2013.04.021,0
1290,Sequence analysis of porcine reproductive and respiratory syndrome virus of the American type collected from Danish swine herds,"Vaccine-like viruses of American type of porcine reproductive and respiratory syndrome virus (PRRSV) were detected in serum samples by RTPCR. The viruses were analysed by nucleotide sequencing of the genomic region encoding open reading frames 2 to 7. During the ongoing study of Danish isolates of PRRSV by means of nucleotide sequencing, RT-PCR reactions and subsequent nucleotide sequencing showed the presence of American type PRRSV in Danish breeding herds. Most likely, these atypical viruses originated from boars vaccinated with live vaccine of American type (MLV RespPRRS), which were taken to artificial insemination centres and there brought together with unvaccinated boars already at the centres. The nucleotide sequences of three Danish viruses of American type PRRSV were compared to those of known PRRSV isolates. The nucleotide sequence identities of the atypical Danish isolates were between 99.299.5% to the vaccine virus RespPRRS and 99.0-99.3% to VR2332 which are the parental virus to the vaccine virus. Phylogenetic analysis including field isolates of American type supports the conclusion that the introduction of American type PRRSV in Denmark was due to spread of vaccine virus.",,"Madsen, K. G.;Hansen, C. M.;Madsen, E. S.;Strandbygaard, B.;Bøtner, A.;Sørensen, K. J.",1998,,10.1007/s007050050409,0
1291,New molecular mechanisms of virus-mediated carcinogenesis: oncogenic transformation of cells by retroviral structural protein Envelope,"RNA tumor viruses as classified in Retroviruses have been isolated and identified to induce tumors in a variety of animals including chickens, mice, and rats, or even in human in the last 100 years, since the first one has been reported in 1908. The RNA tumor viruses have been historically classified into two groups, acute transforming RNA tumor viruses and nonacute RNA tumor viruses. Acute transforming RNA tumor viruses are basically replication-defective and rapidly induce tumors by expressing the viral oncogenes captured from cellular genome in host cells. The first oncogene derived from Rous sarcoma virus was the src non-receptor tyrosine kinase, which has been identified to play the significant roles for signal transduction. On the other hand, nonacute RNA tumor viruses, which consist of only gag, pro, pol, and env regions but do not carry oncogenes, are replication-competent and could activate the cellular proto-oncogenes by inserting the viral long terminal repeat close to the proto-oncogenes to induce tumors with a long incubation period, as is termed a promoter insertion. These molecular mechanisms have been thought to induce tumors. However, very recently several reports have described that the retroviral structural protein Envelope could directly induce tumors in vivo and transform cells in vitro. These are very unusual examples of native retroviral structural proteins with transformation potential. In this review we look back over the history of oncogenic retrovirus research and summarize recent progress for our understanding of the molecular mechanisms of oncogenic transformation by retrovirus Envelope proteins.",protein tyrosine kinase;virus envelope protein;animal;cell transformation;chicken;gene expression regulation;genetics;human;mouse;physiology;promoter region;rat;Retroviridae;review,"Maeda, N.;Yoshikai, Y.",2007,,10.2222/jsv.57.159,0
1292,"Molecular characterization of Orf virus in goats in Gabon, Central Africa","Background: Orf or contagious ecthyma is a zoonotic viral infection with a potential serious health threat for the small ruminants industry as well as humans. It is currently emerging in new territories. Results: Eight suspected clinical cases of pustular dermatitis in goats occurred in the rural area of Tebe, in southeastern Gabon, in January 2013. The orf virus (ORFV) was detected by high-throughput sequencing on sera, buccal swabs and scab pool samples. It was confirmed in six out of eight sick goats by using specific PCR targeting the major envelope protein (B2L) and the orf virus interferon resistance (VIR) genes. Phylogenetic analysis revealed that the Gabonese strain and South Korean strains evolved from a common ancestor, suggesting an Asian origin of the ORFV' Gabonese strain. Conclusions: This study provides the molecular detection of the ORFV strain involved in the cases of pustular dermatitis in goats and highlights its circulation in Gabon.",animal tissue;article;B2L gene;controlled study;dermatitis;female;Gabon;goat;high throughput sequencing;last common ancestor;male;nonhuman;Orf virus;phylogeny;polymerase chain reaction;pustular dermatitis;VIR gene;virus characterization;virus detection;virus gene;virus strain,"Maganga, G. D.;Relmy, A.;Bakkali-Kassimi, L.;Ngoubangoye, B.;Tsoumbou, T.;Bouchier, C.;N'Dilimabaka, N.;Leroy, E. M.;Zientara, S.;Berthet, N.",2016,,10.1186/s12985-016-0535-1,1
1293,"Spillover of Peste des Petits Ruminants Virus from Domestic to Wild Ruminants in the Serengeti Ecosystem, Tanzania","We tested wildlife inhabiting areas near domestic livestock, pastures, and water sources in the Ngorongoro district in the Serengeti ecosystem of northern Tanzania and found 63% seropositivity for peste des petits ruminants virus. Sequencing of the viral genome from sick sheep in the area confirmed lineage II virus circulation.","Animals;Animals, Domestic/bl [Blood];Animals, Domestic/vi [Virology];Animals, Wild/bl [Blood];Animals, Wild/vi [Virology];Goat Diseases/vi [Virology];Goats/ge [Genetics];Goats/vi [Virology];Humans;Peste-des-Petits-Ruminants/ep [Epidemiology];Peste-des-Petits-Ruminants/vi [Virology];Peste-des-petits-ruminants virus/ge [Genetics];*Peste-des-petits-ruminants virus/py [Pathogenicity];Phylogeny;Sheep/ge [Genetics];Sheep/vi [Virology];Sheep Diseases/vi [Virology];Tanzania/ep [Epidemiology]","Mahapatra, M.;Sayalel, K.;Muniraju, M.;Eblate, E.;Fyumagwa, R.;Shilinde, L.;Mdaki, M.;Keyyu, J.;Parida, S.;Kock, R.",2015,Dec,,0
1294,"Surveillance of avian influenza virus of H5N1 subtype in backyard animals and its introduction in Bali, Indonesia","Epidemiological studies of the highly pathogenic avian influenza virus H5N1 (HPAIV-H5N1) in pet and backyard animals are limited. Here we provide serological and virological evidences of infection in various animals in households in Bali, Indonesia in 2005 and 2006. Serum and swab samples from poultry, pigs, dogs, and cats were collected using a stratified random sampling design. Antibodies against HPAIV-H5 were detected in sera using the standard hemagglutination inhibition assay, and the presence of HPAIV-H5N1 in swabs was confirmed by using egg inoculation technique, a hemagglutination assay, and molecular methods. The phylogeny and virus dispersal were inferred using BEAST and SPREAD software. The results showed that the seroprevalence of village chickens to waterfowl, poultry to pigs, and year of study varied significantly in the province (P < 0.001). The seroprevalences in dogs and cats were 1.85% and 7.50%, respectively. Moreover, HPAIV-H5N1 was isolated in all species except cats. The isolation rates varied between species and between the years of surveillance, too. Virus dispersal analysis showed that isolates from Bali grouped into two major clades with good statistical support. In light of these findings, surveillance of HPAIV should be extended to all poultry and mammalian species present in backyard environment.",virus antibody;antibody detection;article;avian influenza (H5N1);chicken;cross-sectional study;disease surveillance;DNA sequence;dog;geographic distribution;hemagglutination inhibition test;highly pathogenic avian influenza virus;Indonesia;nonhuman;nucleotide sequence;phylogeny;pig;poultry;reverse transcription polymerase chain reaction;seroprevalence;waterfowl,"Mahardika, G. N.;Adi, A. A. A. M.;Besung, N. K.;Dharmawan, N. S.;Kencana, G. A. Y.;Rompis, A. L. T.;Sampurna, P.;Setiasih, L. E.;Suardana, W.;Suardana, I. B. K.;Suarjana, G. K.;Suartha, N.;Suartini, G. A. A.;Suwiti, N. K.;Utama, I. H.",2018,,10.229261/pakvetj/2018.002,0
1295,Genetic analysis of bovine viral diarrhoea viruses from Australia,"Eighty-nine bovine viral diarrhoea viruses (BVDV) from Australia have been genetically typed by sequencing of the 5′ untranslated region (5′-UTR) and for selected isolates the Npro region of the viral genome. Phylogenetic reconstructions indicated that all of the samples examined clustered within the BVDV type 1 genotype. Of the 11 previously described genetic groups of BVDV-1, 87 of the samples examined in this study clustered with the BVDV-1c, while two samples clustered with the BVDV-1a. Based on these analyses there appears to be limited genetic variation within the Australian BVDV field isolates. In addition, the phylogenetic reconstructions indicate that the clustering of Australian BVDV in the phylogenetic trees is not a result of geographic isolation. © 2005 Elsevier B.V. All rights reserved.",5' untranslated region;article;Australia;Bovine viral diarrhea virus 1;cluster analysis;gene sequence;genetic analysis;genotype;geography;nonhuman;nucleotide sequence;phylogeny;viral genetics;virus isolation,"Mahony, T. J.;McCarthy, F. M.;Gravel, J. L.;Corney, B.;Young, P. L.;Vilcek, S.",2005,,10.1016/j.vetmic.2004.10.024,0
1296,Introduction and history of foot-and-mouth disease virus,"Foot-and-mouth disease (FMD) has been recognized as a significant epidemic disease threatening the cattle industry since the sixteenth century, and in the late nineteenth century it was shown by Loeffler and Frosch to be caused by a submicroscopic, filterable transmissible agent, smaller than any known bacteria. The agent causing FMD was thus the first virus of vertebrates to be discovered, soon after the discovery of tobacco mosaic virus of plants. It was not until 1920 that a convenient animal model for the study of FMD virus was established by Waldmann and Pape, using guinea-pigs, and with the later development of in vitro cell culture systems for the virus, the chemical and physical properties of FMD virus were elucidated during the remainder of the twentieth century, culminating in 1989 with a complete description of the three-dimensional structure of the virion. FMD virus is classified as a species in the Aphthovirus genus of the family Picornaviridae. The virus is acid labile, and the genome RNA contains a characteristic tract of polyC located about 360 nucleotides from the 5′ terminus. Seven main serotypes exist throughout the world, as well as numerous subtypes. The World Reference Laboratory for FMD is located at Pirbright, Surrey, UK and undertakes surveillance of FMD epidemics by serotyping as well as by genotyping isolates of the virus. A major epidemic of FMD occurred in the UK in 2001 and was caused by a virulent strain of FMD virus with origins in Asia. The advantages and some disadvantages of controlling FMD outbreaks by vaccination are discussed.",aluminum hydroxide;foot and mouth disease vaccine;formaldehyde;mineral oil;nucleotide;polycytidylic acid;saponin;virus RNA;acidity;agriculture;Aphthovirus;Asia;cattle farming;cell culture;economic aspect;epithelium cell;foot and mouth disease;Foot and mouth disease virus;genotype;guinea pig;nonhuman;nucleotide sequence;nutritional science;Picornaviridae;plant;priority journal;protein localization;Psychodidae;rash;review;sequence analysis;serotype;pig;swine disease;Vesicular exanthema of swine virus;Tobacco mosaic virus;tongue;vaccination;Vesiculovirus;virion;virus detection;virus genome;virus morphology;virus strain;virus transmission;virus virulence;X ray crystallography,"Mahy, B. W. J.",2005,,,0
1297,"Detection and phylogenetic characterization of Columbid circoviruses in Chaharmahal va Bakhtiari province, Iran","The virus genus Circovirus belongs to the family Circoviridae and contains virus species with circular single-stranded DNA genomes. The viruses are known to infect vertebrate species, including pigs, dogs, pigeons and ducks. In this study a nested polymerase chain reaction (PCR) was applied to investigate prevalence of circoviruses in pigeons in the Chaharmahal va Bakhtiari province, Iran. A total of 50 faecal samples were subjected to nucleic acid extraction, PCR amplification and DNA sequencing. Nested PCR primers were designed to amplify a 508 base pair segment of the pigeon circovirus (PiCV) capsid gene. Of the 50 faecal samples examined, 12 (24%) produced the expected DNA amplicons with identical DNA sequences. Phylogenetic analysis has grouped the viruses with those classified as group A circoviruses. The viruses were closely related to PiCVs found in Poland, Northern Ireland, the USA, Nigeria and Hungary. To the authors' knowledge, this is the first report of molecular detection and genomic characterization of PiCV from Iran.",capsid protein;virus DNA;animal;bird disease;chemistry;Circoviridae infection;Circovirus;DNA sequence;feces;genetics;Iran;isolation and purification;molecular genetics;nucleotide sequence;phylogeny;Columbidae;polymerase chain reaction;veterinary medicine;virology,"Mahzounieh, M.;Heidari Khoei, H.;Ghasemi Shamsabadi, M.;Dastjerdi, A.",2014,,10.1080/03079457.2014.966648,0
1298,The detection and phylogenetic analysis of porcine deltacoronavirus from Guangdong Province in Southern China,"Porcine deltacoronavirus (PDCoV) is a newly discovered coronavirus that causes diarrhoea, vomiting and dehydration in sucking and nursing piglets. It was first reported in Hong Kong in 2012 and has since been discovered in the United States, Canada, South Korea, mainland China, Thailand and Laos. PDCoV has been experimentally proved to lead to diarrhoea in swine and it was detected positive in pigs in Guangdong, southern China. In our study, 252 faecal and intestinal samples from sucking piglets and sows with diarrhoea were surveyed for common enteric viruses. We found a prevalence of PDCoV (21.8%), porcine epidemic diarrhoea virus (65.5%), transmissible gastroenteritis virus (0%), rotavirus group A (25.0%) and porcine kobuvirus (68.7%). We isolated 13 PDCoV strains and discovered that PDCoV infections were often co-infections with kobuvirus rather than the commonly linked porcine epidemic diarrhoea virus. Phylogenetic analysis of S gene and N gene revealed that 11 of 13 PDCoV strains belonged to Chinese lineage. As for the left two strains, one single strain (CHN-GD16-05) belonged to American and Korean lineages while another strain (CHN-GD16-03) was similar to a Thai strain, but only in the S gene. This suggested a possible recombination event between the Thai and the newly described Chinese strain.",animal model;China;Coronavirus infection;human;intestine;Kobuvirus;major clinical study;mixed infection;nonhuman;phylogeny;piglet;Porcine epidemic diarrhea virus;prevalence;Rotavirus;spike;sucking;Transmissible gastroenteritis virus;virus nucleocapsid,"Mai, K.;Feng, J.;Chen, G.;Li, D.;Zhou, L.;Bai, Y.;Wu, Q.;Ma, J.",2018,,10.1111/tbed.12644,0
1299,[Virosphere and giruses],Novel findings and concepts in the field of virology particularly regarding virosphere and giruses--a group of large nuclear-cytoplasmic deoxyriboviruses are briefly summarized. In the context of novel understanding the major taxonomic features and virus pathogenicity including African swine plague are interpreted.,virus DNA;African swine fever;African swine fever virus;animal;cell nucleus;chemistry;cytoplasm;genetics;Iridovirus;Mimivirus;Picobirnavirus;review;pig;ultrastructure;virology;virus capsid,"Makarov, V. V.",2013,,,0
1300,Avian influenza virus Review,"Influenza viruses are classified as A, B, or C based on the antigenicity of their nucleoproteins and matrix proteins. Influenza A viruses are further categorized into subtypes based on the antigenicity of two of their surface proteins, the hemagglutinin and neuraminidase. All avian influenza viruses are type A viruses. While the majority of avian influenza viruses are avirulent, viruses of a limited number of subtypes cause severe disease in birds. This difference in pathogenicity among avian influenza viruses is primarily determined by the amino acid sequence at the viral hemagglutinin cleavage site. Since 1997, there have been multiple reports of human infection by highly pathogenic avian influenza viruses. Acquisition of the ability to cause human-to-human transmission by avian influenza viruses will confront the human population with an influenza pandemic crisis. Here we review the molecular basis of pathogenicity of avian influenza viruses in humans. [References: 8]",Animals;Birds;Humans;Influenza A virus/cl [Classification];Influenza A virus/py [Pathogenicity];*Influenza A virus;*Influenza in Birds/vi [Virology],"Makino, A.;Kawaoka, Y.",2005,Dec,,0
1301,"Human microRNAs profiling in response to influenza A viruses (subtypes pH1N1, H3N2, and H5N1)","MicroRNAs (miRNAs) play an important role in regulation of gene silencing and are involved in many cellular processes including inhibition of infected viral replication. This study investigated cellular miRNA expression profiles operating in response to influenza virus in early stage of infection which might be useful for understanding and control of viral infection. A549 cells were infected with different subtypes of influenza virus (pH1N1, H3N2 and H5N1). After 24 h post-infection, miRNAs were extracted and then used for DNA library construction. All DNA libraries with different indexes were pooled together with equal concentration, followed by high-throughput sequencing based on MiSeq platform. The miRNAs were identified and counted from sequencing data by using MiSeq reporter software. The miRNAs expressions were classified into up and downregulated miRNAs compared to those found in noninfected cells. Mostly, each subtype of influenza A virus triggered the upregulated responses in miRNA expression profiles. Hsa-miR-101, hsa-miR-193b, hsa-miR-23b, and hsa-miR-30e* were upregulated when infected with all three subtypes of influenza A virus. Target prediction results showed that virus infection can trigger genes in cellular process, metabolic process, developmental process and biological regulation. This study provided some insights into the cellular miRNA profiling in response to various subtypes of influenza A viruses in circulation and which have caused outbreaks in human population. The regulated miRNAs might be involved in virus-host interaction or host defense mechanism, which should be investigated for effective antiviral therapeutic interventions.",miRNAs;influenza A virus;expression profiles;next-generation;sequencing;SWINE-ORIGIN H1N1;IMMUNE-RESPONSE;CAENORHABDITIS-ELEGANS;CELLULAR;MICRORNAS;EPITHELIAL-CELLS;MESSENGER-RNA;LUNG-TISSUE;EXPRESSION;INFECTION;PROTEIN,"Makkoch, J.;Poomipak, W.;Saengchoowong, S.;Khongnomnan, K.;Praianantathavorn, K.;Jinato, T.;Poovorawan, Y.;Payungporn, S.",2016,Feb,,0
1302,Need for new technologies for detection of adventitious agents in vaccines and other biological products,"From an industrial perspective, the conventional in vitro and in vivo assays used for detection of viral contaminants have shown their limitations, as illustrated by the unfortunate detection of porcine circovirus contamination in a licensed rotavirus vaccine. This contamination event illustrates the gaps within the existing adventitious agent strategy and the potential use of new broader molecular detection methods. This paper serves to summarize current testing approaches and challenges, along with opportunities for the use of these new technologies.",biological product;biomaterial;inactivated vaccine;interferon;live vaccine;monoclonal antibody;recombinant DNA;Rotavirus vaccine;virus vaccine;bioinformatics;blood;Circovirus;conference paper;cytopathogenic effect;high throughput sequencing;human;nonhuman;product safety;risk assessment;Vesiculovirus;viral contamination;virus detection;virus infectivity,"Mallet, L.;Gisonni-Lex, L.",2014,,10.5731/pdajpst.2014.01012,0
1303,Nonspecific immunostimulation against viruses,"A trypsinized preparation from chromogenic selected strain of Mycobacterium phlei (NSI) stimulated the recipient immune system non-specifically against a variety of viruses viz. Rabies virus (RNA virus), Marek's disease (DNA virus) and Foot and Mouth disease virus (RNA virus) in phylogenetically different hosts like mice, chicks and guinea pigs respectively. Investigation into mechanisms of such nonspecific immunostimulation revealed that there was induction of strong cell mediated immune response (CMIR) against both specific as well as to nonspecific viral antigens as evinced by LMIT, lymphokine (LyIF) assay and lymphocyte transformation test etc. There was induction of appreciable quantity of 'infectivity inhibiting substance(s)' (IIS) which was not the classical antiody (Ig) in the serum of NSI inoculated animals and birds. This substance(s) neutralized FMD, IBR, rabies and Newcastle disease virus in cell culture, mice and in embryonated eggs. Electrophoretic separation of the NSI induced serum revealed an increase in β fraction of globulin.",Gallid alphaherpesvirus 2;cellular immunity;Foot and mouth disease virus;immunostimulation;lymphocyte transformation;Newcastle disease virus;Rabies virus;virus infection,"Mallick, B. B.;Kishore, S.;Das, S. K.;Garg, A.",1985,,10.1016/0147-9571(85)90054-2,0
1304,The evidence of occurrence of porcine circovirus 2 isolation and characterization in Kazakhstan,"This report describes the first isolation and characterization of porcine circovirus 2 (PCV2) in the Republic of Kazakhstan. The virus was isolated from a dead piglet that did not exhibit any typical clinical symptoms of porcine circovirus disease at a pig factory in North Kazakhstan oblast (region). The isolated virus belongs to genotype 2 (PCV2) and shares 96.6% sequence homology with one isolate and two strains from China and two French strains in group 1, cluster 1ab and 96.4% homology with two strains isolated in China and one strain from Hungary. Electron microscopy revealed the isolated virus had the typical morphological structure of PCV. This is the evidence of occurrence of porcine circovirus 2 isolation and characterization in Kazakhstan.",article;electron microscopy;Kazakhstan;nonhuman;piglet;Porcine circovirus 2;sequence homology;virus characterization;virus isolation;virus morphology,"Mambetaliyev, M.;Yesimbekova, N. B.;Strochkov, V. M.;Tabynov, K. K.;Sultankulova, K. T.;Abduraimov, Y. O.",2018,,10.1007/s13337-018-0436-6,0
1305,"Molecular characterization and phylogenetic analysis of Murray Valley encephalitis virus and West Nile virus (Kunjin subtype) from an arbovirus disease outbreak in horses in Victoria, Australia, in 2011","Virus was detected in the central nervous system (CNS) tissue of 11 horses from Victoria that died displaying neurological symptoms during an outbreak of disease in Australia in 2011. Five horses were identified as being infected with Murray Valley encephalitis virus (MVEV) and 6 as being infected with West Nile virus subtype Kunjin (WNVKUN). Analysis of partial sequence information from the NS5 and E genes indicated that the MVEVs within the samples were highly homogenous and all belonged to lineage I, which is enzootic to the tropical regions of northern Australia. Likewise, analysis of partial NS5 and E gene and full genome sequences indicated that the WNVKUN within the samples were also highly homogenous and clustered with WNV lineage 1, clade b, which is consistent with other WNVKUN isolates. Full genomes of 1 MVEV isolate and 2 WNVKUN isolates were sequenced and characterized. The genome sequences of Victorian WNVKUN are almost identical (3 amino acid differences) to that of the recently sequenced WNV isolate WNVNSW2011. Metagenome sequencing directly from CNS tissue identified the presence of WNVKUN and MVEV within infected CNS tissue. © 2013 The Author(s).","NS5 protein, flavivirus;viral protein;virus RNA;amino acid sequence;animal;animal disease;article;Australia;chemistry;DNA sequence;epidemic;epidemic encephalitis;genetics;horse;horse disease;isolation and purification;molecular genetics;Murray Valley encephalitis virus;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;sequence alignment;virology;West Nile fever;West Nile virus","Mann, R. A.;Fegan, M.;O'Riley, K.;Motha, J.;Warner, S.",2013,,10.1177/1040638712467985,0
1306,Investigating the diversity of the 18S SSU rRNA hyper-variable region of Theileria in cattle and Cape buffalo (Syncerus caffer) from southern Africa using a next generation sequencing approach,"Molecular classification and systematics of the Theileria is based on the analysis of the 18S rRNA gene. Reverse line blot or conventional sequencing approaches have disadvantages in the study of 18S rRNA diversity and a next-generation 454 sequencing approach was investigated. The 18S rRNA gene was amplified using RLB primers coupled to 96 unique sequence identifiers (MIDs). Theileria positive samples from African buffalo (672) and cattle (480) from southern Africa were combined in batches of 96 and sequenced using the GS Junior 454 sequencer to produce 825711 informative sequences. Sequences were extracted based on MIDs and analysed to identify Theileria genotypes. Genotypes observed in buffalo and cattle were confirmed in the current study, while no new genotypes were discovered. Genotypes showed specific geographic distributions, most probably linked with vector distributions. Host specificity of buffalo and cattle specific genotypes were confirmed and prevalence data as well as relative parasitemia trends indicate preference for different hosts. Mixed infections are common with African buffalo carrying more genotypes compared to cattle. Associative or exclusion co-infection profiles were observed between genotypes that may have implications for speciation and systematics: specifically that more Theileria species may exist in cattle and buffalo than currently recognized. Analysis of primers used for Theileria parva diagnostics indicate that no new genotypes will be amplified by the current primer sets confirming their specificity. T. parva SNP variants that occur in the 18S rRNA hypervariable region were confirmed. A next generation sequencing approach is useful in obtaining comprehensive knowledge regarding 18S rRNA diversity and prevalence for the Theileria, allowing for the assessment of systematics and diagnostic assays based on the 18S gene.","Africa, Southern/ep [Epidemiology];Animals;*Buffaloes/ps [Parasitology];Cattle/ps [Parasitology];Coinfection;*Genetic Variation;Genotype;High-Throughput Nucleotide Sequencing;Host Specificity;Parasitemia/ve [Veterinary];*RNA, Ribosomal, 18S/ge [Genetics];Sequence Alignment;*Theileria/ge [Genetics];Theileria/ip [Isolation & Purification];Theileria parva/ge [Genetics];Theileria parva/ip [Isolation & Purification];Theileriasis/ep [Epidemiology];*Theileriasis/ps [Parasitology];0 (RNA, Ribosomal, 18S)","Mans, B. J.;Pienaar, R.;Ratabane, J.;Pule, B.;Latif, A. A.",2016,07,,0
1307,Microbiomes Associated with Animals: Implications for Livestock and Animal Production,,,"Mantovani, H. C.;Lopes, D. R. G.;Bento, C. B. P.",2017,,,0
1308,"Infectious particles, stress, and induced prion amyloids: A unifying perspective","Transmissible encephalopathies (TSEs) are believed by many to arise by spontaneous conversion of host prion protein (PrP) into an infectious amyloid (PrP-res, PrPSc) without nucleic acid. Many TSE agents reside in the environment, with infection controlled by public health measures. These include the disappearance of kuru with the cessation of ritual cannibalism, the dramatic reduction of epidemic bovine encephalopathy (BSE) by removal of contaminated feed, and the lack of endemic scrapie in geographically isolated Australian sheep with susceptible PrP genotypes. While prion protein modeling has engendered an intense focus on common types of protein misfolding and amyloid formation in diverse organisms and diseases, the biological characteristics of infectious TSE agents, and their recognition by the host as foreign entities, raises several fundamental new directions for fruitful investigation such as: (1) unrecognized microbial agents in the environmental metagenome that may cause latent neurodegenerative disease, (2) the evolutionary social and protective functions of different amyloid proteins in diverse organisms from bacteria to mammals, and (3) amyloid formation as a beneficial innate immune response to stress (infectious and non-infectious). This innate process however, once initiated, can become unstoppable in accelerated neuronal aging. © 2013 Landes Bioscience.",amyloid;nanotube;nucleic acid;article;binding site;environmental stress;immune response;immunosurveillance;infection;infectious particle;innate immunity;latent period;metagenome;nerve degeneration;nonhuman;open reading frame;polymerase chain reaction;prediction;prion;protein aggregation;scrapie agent;transmissible mink encephalopathy agent;virulence;virus forms;virus strain,"Manuelidis, L.",2013,,10.4161/viru.24838,0
1309,"Phylogenic analysis of the M genes of influenza viruses isolated from free-flying water birds from their Northern Territory to Hokkaido, Japan","During 2000-2007, 218 influenza viruses of 28 different combinations of HA (H1-H13) and NA (N1-N9) subtypes were isolated from fecal samples of free-flying water birds at two distant lakes in Hokkaido, Japan. Phylogenic analysis of the matrix (M) genes of 67 strains, selected on the basis of their subtype combinations, revealed that A/duck/Hokkaido/W95/2006 (H10N8) was a reassortant whose M gene belonged to North American non-gull-avian and the other seven genes to Eurasian non-gull-avian lineages. The M genes of other 65 strains belonged to Eurasian non-gull-avian and the one to Eurasian-gull lineages. The M genes of 65 strains were grouped into three different sublineages, indicating that influenza viruses circulating in different populations of free-flying water birds have evolved independently in nature. © 2008 Springer Science+Business Media, LLC.",article;controlled study;feces analysis;gene expression;gene sequence;genetic analysis;Influenza virus;Japan;nonhuman;nucleotide sequence;phylogeny;priority journal;reverse transcription polymerase chain reaction;unindexed sequence;virus isolation;water bird,"Manzoor, R.;Sakoda, Y.;Mweene, A.;Tsuda, Y.;Kishida, N.;Bai, G. R.;Kameyama, K. I.;Isoda, N.;Soda, K.;Naito, M.;Kida, H.",2008,,10.1007/s11262-008-0248-7,0
1310,"Identification of Clade E Avipoxvirus, Mozambique, 2016",Analysis of scab samples collected from poultry during outbreaks of fowlpox in Mozambique in 2016 revealed the presence of clade E avipoxviruses. Infected poultry were from flocks that had been vaccinated against fowlpox virus. These findings require urgent reevaluation of the vaccine formula and control strategies in this country.,Animals;*Avipoxvirus/cl [Classification];Avipoxvirus/ge [Genetics];Avipoxvirus/ip [Isolation & Purification];DNA-Directed DNA Polymerase/ge [Genetics];DNA-Directed DNA Polymerase/me [Metabolism];*Fowlpox/ep [Epidemiology];Fowlpox/im [Immunology];Fowlpox/tm [Transmission];Fowlpox/vi [Virology];*Fowlpox virus/cl [Classification];Fowlpox virus/ge [Genetics];Fowlpox virus/ip [Isolation & Purification];Gene Expression;Genotype;Mozambique/ep [Epidemiology];Phylogeny;Poultry/vi [Virology];*Poultry Diseases/ep [Epidemiology];Poultry Diseases/im [Immunology];Poultry Diseases/tm [Transmission];Poultry Diseases/vi [Virology];Poxviridae Infections/ep [Epidemiology];Poxviridae Infections/tm [Transmission];*Poxviridae Infections/ve [Veterinary];Poxviridae Infections/vi [Virology];Treatment Failure;*Vaccination/ve [Veterinary];Viral Proteins/ge [Genetics];Viral Proteins/me [Metabolism];Viral Vaccines/ad [Administration & Dosage];0 (Viral Proteins);0 (Viral Vaccines),"Mapaco, L. P.;Lacerda, Z.;Monjane, I. V. A.;Gelaye, E.;Sussuro, A. H.;Viljoen, G. J.;Dundon, W. G.;Acha, S. J.",2017,09,,0
1311,Development of RT-qPCR assays for the specific identification of two major genotypes of avian infectious bronchitis virus,"Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus (27.6 kb) that causes one of the most persistent respiratory disease in poultry. The virus is classified in genotypes with different epidemiological relevance and clinical implications. The present study reports the development and validation of specific RT-qPCR assays for the detection of two major IBV genotypes: South America I (SAI) and Asia/South America II (A/SAII). The SAI genotype is an exclusive and widespread South American lineage while the A/SAII genotype is distributed in Asia, Europe and South America. Both identification assays employ TaqMan probes that hybridize with unique sequences in the spike glycoprotein gene. The assays successfully detected all the assessed strains belonging to both genotypes, showing high specificity and absence of cross-reactivity. Using serial dilutions of in vitro-transcribed RNA we obtained acceptable determination coefficients, PCR efficiencies and relatively small intra- and inter-assay variability. The assays demonstrated a wide dynamic range between 101-107 and 102-107 RNA copies/reaction for SAI and A/SAII strains, respectively. The possibility to characterize a large number of samples in a rapid, sensitive and reproducible way makes these techniques suitable tools for routine testing, IBV control, and epidemiological research in poultry.",virus spike protein;article;cross reaction;Gammacoronavirus;gene sequence;genotype;in vitro study;molecular epidemiology;nonhuman;priority journal;reproducibility;reverse transcription polymerase chain reaction;sensitivity analysis;validation study;virus strain,"Marandino, A.;Tomás, G.;Hernández, M.;Panzera, Y.;Craig, M. I.;Vagnozzi, A.;Vera, F.;Techera, C.;Grecco, S.;Banda, A.;Hernández, D.;Pérez, R.",2016,,10.1016/j.jviromet.2016.05.007,0
1312,Whole-genome characterization of Uruguayan strains of avian infectious bronchitis virus reveals extensive recombination between the two major South American lineages,"Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus that causes one of the most persistent respiratory diseases in poultry. The virus is classified in genotypes and lineages with different epidemiological relevance. Two lineages of the GI genotype (11 and 16) have been widely circulating for decades in South America. GI-11 is an exclusive South American lineage while the GI-16 lineage is distributed in Asia, Europe and South America. Here, we obtained the whole genome of two Uruguayan strains of the GI-11 and GI-16 lineages using Illumina high-throughput sequencing. The strains here sequenced are the first obtained in South America for the infectious bronchitis virus and provide new insights into the origin, spreading and evolution of viral variants. The complete genome of the GI-11 and GI-16 strains have 27,621 and 27,638 nucleotides, respectively, and possess the same genomic organization. Phylogenetic incongruence analysis reveals that both strains have a mosaic genome that arose by recombination between Euro Asiatic strains of the GI-16 lineage and ancestral South American GI-11 viruses. The recombination occurred in South America and produced two viral variants that have retained the full-length S1 sequences of the parental lineages but are extremely similar in the rest of their genomes. These recombinant virus have been extraordinary successful, persisting in the continent for several years with a notorious wide geographic distribution. Our findings reveal a singular viral dynamics and emphasize the importance of complete genomic characterization to understand the emergence and evolutionary history of viral variants.",article;Avian infectious bronchitis virus;high throughput sequencing;human;nucleotide sequence;phylogeny;priority journal;South America;South American;virus genome;virus particle;virus recombinant;virus recombination;virus strain,"Marandino, A.;Tomás, G.;Panzera, Y.;Greif, G.;Parodi-Talice, A.;Hernández, M.;Techera, C.;Hernández, D.;Pérez, R.",2017,,10.1016/j.meegid.2017.07.009,0
1313,"A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection","BACKGROUND: Polymicrobial infections represent a great challenge for the clarification of disease etiology and the development of comprehensive diagnostic or therapeutic tools, particularly for fastidious and difficult-to-cultivate bacteria. Using bovine digital dermatitis (DD) as a disease model, we introduce a novel strategy to study the pathogenesis of complex infections. RESULTS: The strategy combines meta-transcriptomics with high-density peptide-microarray technology to screen for in vivo-expressed microbial genes and the host antibody response at the site of infection. Bacterial expression patterns supported the assumption that treponemes were the major DD pathogens but also indicated the active involvement of other phyla (primarily Bacteroidetes). Bacterial genes involved in chemotaxis, flagellar synthesis and protection against oxidative and acidic stress were among the major factors defining the disease. CONCLUSIONS: The extraordinary diversity observed in bacterial expression, antigens and host antibody responses between individual cows pointed toward microbial variability as a hallmark of DD. Persistence of infection and DD reinfection in the same individual is common; thus, high microbial diversity may undermine the host's capacity to mount an efficient immune response and maintain immunological memory towards DD. The common antigenic markers identified here using a high-density peptide microarray address this issue and may be useful for future preventive measures against DD.","Animals;Bacteroidetes/cl [Classification];Bacteroidetes/ge [Genetics];Bacteroidetes/ip [Isolation & Purification];Cattle;*Cattle Diseases/ge [Genetics];Cattle Diseases/mi [Microbiology];Cattle Diseases/pa [Pathology];*Coinfection/ge [Genetics];Coinfection/mi [Microbiology];Coinfection/pa [Pathology];*Digital Dermatitis/ge [Genetics];Digital Dermatitis/mi [Microbiology];Digital Dermatitis/pa [Pathology];Disease Models, Animal;Genetic Variation;High-Throughput Nucleotide Sequencing;*Host-Pathogen Interactions/ge [Genetics];Immunoglobulins/ge [Genetics];Immunoglobulins/me [Metabolism];Phylogeny;Protein Array Analysis;RNA/ch [Chemistry];RNA/ip [Isolation & Purification];RNA/me [Metabolism];RNA, Ribosomal, 16S/ge [Genetics];RNA, Ribosomal, 16S/me [Metabolism];Sequence Analysis, RNA;Transcriptome;Virulence Factors/ge [Genetics];0 (Immunoglobulins);0 (RNA, Ribosomal, 16S);0 (Virulence Factors);63231-63-0 (rna)","Marcatili, P.;Nielsen, M. W.;Sicheritz-Ponten, T.;Jensen, T. K.;Schafer-Nielsen, C.;Boye, M.;Nielsen, M.;Klitgaard, K.",2016,12 01,,0
1314,Characterization of the h5n1 influenza virus isolated during an outbreak among wild birds in russia (tuva republic) in 2010,"A study of the basic biological properties of H5N1 subtype strain isolated during an outbreak among wild birds in Russia in 2010 is presented. The study was carried out using conventional methods according to the WHO recommendations. H5N1 influenza virus isolated in Siberia belonged to clade 2.3.2 of the hemagglutinin gene, and phylogenetic analysis was performed. The antigenic characteristics and the basic genetic markers of biological properties were studied. It was shown that all strains were highly pathogenic for chickens and white mice. Thus, it was shown that, in Russia, the 2010 H5N1 virus phylogenetically closely related to Asian variants caused epizootic among wild birds. The potential danger of this variant of the virus for humans was confirmed by different methods. We discussed the possibility of formulating the natural focus of H5N1 influenza. © 2011 Allerton Press, Inc.",Influenza virus hemagglutinin;animal experiment;animal model;antigenicity;bird;cladistics;epidemic;epizootiology;genetic marker;hemagglutination;Influenza A virus (H5N1);lethal dose;mouse;nonhuman;nucleotide sequence;pathogenicity;phylogeny;priority journal;review;Russian Federation;virus characterization;virus isolation,"Marchenko, V. Yu;Sharshov, K. A.;Silko, N. Yu;Susloparov, I. M.;Durymanov, A. G.;Zaykovskaya, A. V.;Alekseev, A. Yu;Smolovskaya, O. V.;Stefanenko, A. P.;Malkova, E. M.;Shestopalova, A. M.",2011,,10.3103/s0891416811040057,0
1315,"Nairobi sheep disease virus, an important tick-borne pathogen of sheep and goats in Africa, is also present in Asia","Nairobi sheep disease (NSD) virus is the prototype of the tick-borne NSD serogroup, genus Nairovirus, family Bunyaviridae. It is highly pathogenic for sheep and goats, causes disease in humans, and is widespread throughout East Africa. Ganjam virus has caused disease in goats and humans in India. Due to their occurrence on different continents and association with different ticks, these viruses were considered distinct despite serologic cross-reactivity. Their S RNA genome segments and encoded nucleocapsid proteins were found to be 1590 nucleotides and 482 amino acids in length and differed by only 10 and 3% at nucleotide and amino acid levels, respectively. Genetic and serologic data demonstrate that Ganjam virus is an Asian variant of NSD virus. These viruses were phylogenetically more closely related to Hazara virus than Dugbe virus. © 2002 Elsevier Science (USA).",amino acid;M protein;nucleoside;transfer RNA;Africa;article;Asia;blood group typing;developed country;Dugbe virus;epidemic;genetic code;genetic database;genetics;goat;hazara virus;India;Nairobi sheep disease virus;nonhuman;nucleotide sequence;pathogenesis;phylogeny;priority journal;serology;sheep;tick borne disease;virus,"Marczinke, B. I.;Nichol, S. T.",2002,,10.1006/viro.2002.1514,0
1316,A very virulent genotype of infectious bursal disease virus predominantly associated with recurrent infectious bursal disease outbreaks in Tunisian vaccinated flocks,"Outbreaks of infectious bursal disease (IBD) still continue to afflict the Tunisian poultry industry even in those flocks where the vaccination program is strictly applied. To characterize the viruses that circumvent protection provided by vaccination, field isolates of infectious bursal disease virus (IBDV) obtained from vaccinated flocks that have repeatedly experienced IBDV outbreak episodes were analyzed from bursal samples by reverse transcription coupled with polymerase chain reaction and dideoxynucleotide sequencing of the VP2 hypervariable region. Although sequence data were obtained from samples collected from three distinct flocks over a period of 3 years, only limited sequence variation has been observed. The few nucleotide changes were silent and the deduced amino acid sequences were identical. Thus, the virus population that predominates in the field seems to represent a homogeneous antigenic pool. Compared with the VP2 sequences of several IBDV strains, this predominant pool was found to be closely related to the very virulent (vv) IBDV viruses described in Europe and Asia. Sequence and phylogenetic analysis of the precursor polyprotein coding sequence of a representative Tunisian isolate further confirmed its assignment to the vv genotype. The deduced amino acid sequence of the whole polyprotein of the Tunisian isolate was found to be identical to a South Korean IBDV strain. Alignment of the polyprotein amino acid sequence of 35 IBDV strains identified additional mutations outside the VP2 variable domain and which occur frequently in vv strains. Based on this comparative analysis, the set of amino acid residues that should represent a typical vv profile involves Ala222, Ile242, Ile256, Ile294, Leu451, Tyr680, N685, Ser715, Asp751, Val990, and Ala1005. Such a combination of amino acid changes was observed for the majority of vvIBDV strains that define a distinct phylogroup.","viral protein;virus vaccine;VP2 protein, infectious bursal disease virus;amino acid sequence;animal;animal disease;article;bird disease;chicken;epidemic;genetics;infectious bursal disease virus;molecular genetics;nucleotide sequence;pathogenicity;phylogeny;recurrent disease;Tunisia;virulence;virus infection","Mardassi, H.;Khabouchi, N.;Ghram, A.;Namouchi, A.;Karboul, A.",2004,,,0
1317,Complete genome sequences of pigeon adenovirus 1 and duck adenovirus 2 extend the number of species within the genus Aviadenovirus,"Complete genomes of the first isolates of pigeon adenovirus 1 (PiAdV-1) and Muscovy duck adenovirus (duck adenovirus 2, DAdV-2) were sequenced. The PiAdV-1 genome is 45,480. bp long, and has a gene organization most similar to turkey adenovirus 1. Near the left end of the genome, it lacks ORF0, ORF1A, ORF1B and ORF1C, and possesses ORF52, whereas six novel genes were found near the right end. The DAdV-2 genome is 43,734. bp long, and has a gene organization similar to that of goose adenovirus 4 (GoAdV-4). It lacks ORF51, ORF1C and ORF54, and possesses ORF55A and five other novel genes. PiAdV-1 and DAdV-2 genomes contain two and one fiber genes, respectively. Genome organization, G+C content, molecular phylogeny and host type confirm the need to establish two novel species (Pigeon aviadenovirus A and Duck aviadenovirus B) within the genus Aviadenovirus. Phylogenetic data show that DAdV-2 is most closely related to GoAdV-4. © 2014 Elsevier Inc.",animal cell;article;Aviadenovirus;DNA base composition;Duck adenovirus 2;Duck aviadenovirus B;gene sequence;genetic organization;genus;Goose adenovirus 4;high throughput sequencing;nonhuman;nucleotide sequence;open reading frame;phylogeny;Pigeon adenovirus 1;Pigeon aviadenovirus A;priority journal;unindexed sequence;virus genome,"Marek, A.;Kaján, G. L.;Kosiol, C.;Harrach, B.;Schlötterer, C.;Hess, M.",2014,,10.1016/j.virol.2014.04.033,0
1318,Two fiber genes of nearly equal lengths are a common and distinctive feature of Fowl adenovirus C members,The complete genome or the genome region containing the two fiber genes of two reference strains and one field isolate representing both serotypes of Fowl adenovirus C were sequenced. Two fiber genes were revealed in the genomes of all three isolates. Fiber-1 and fiber-2 genes of several Fowl adenovirus C isolates were sequenced as well. Both serotypes 4 and 10 have two fiber genes. The genome region containing the fiber gene was also sequenced for the reference strain of Fowl adenovirus B. Just one fiber gene was revealed in this strain. Predicted amino acid sequences were compared to already published fiber sequences of different adenovirus isolates and one amino acid substitution within fiber-2 was detected in all of the Fowl adenovirus C isolates that were isolated from chickens with hepatitis-hydropericardium syndrome in comparison to apathogenic isolates. Phylogenetic analyses provided insights about the evolution of fiber genes in avian adenoviruses and their genetic relationships.,"*Adenoviridae Infections/ve [Veterinary];Adenoviridae Infections/vi [Virology];Amino Acid Sequence;Amino Acid Substitution;Animals;*Aviadenovirus/ge [Genetics];Base Sequence;*Bird Diseases/vi [Virology];Chickens/vi [Virology];DNA, Viral/ge [Genetics];*Genes, Viral;High-Throughput Nucleotide Sequencing;Molecular Sequence Data;Phylogeny;0 (DNA, Viral)","Marek, A.;Nolte, V.;Schachner, A.;Berger, E.;Schlotterer, C.;Hess, M.",2012,May 04,,0
1319,When african swine fever plays at home - Description of an outbreak in Namibia,"Introduction - African swine fever (ASF) is regarded as the most serious health threat to the global pig industry and is caused by a complex linear double-stranded DNA virus (ASF virus, ASFV), currently classified as the only member of the family Asfarviridae. Aim - To describe an outbreak of ASF, which occurred in Namibia and was managed during international co-operation therein carried out by the Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise ""G. Caporale"" (Teramo, Italy). Materials and methods - The ASF outbreak occurred in the district of Omaruru (Namibia) and affected a small swine herd consisting of about 100 pigs. The herd was part of a hunting farm and was very close to a small abattoir, where warthogs had been recently slaughtered. Clinical signs suddenly onset and affected pigs of different classes of age. Two pigs were necropsied for diagnostic purpose: histopathology, direct immunofluorescence and polymerase chain reaction. Results - At necropsy, all pigs under investigation showed generalized hemorrhagic lesions. Microscopically, recently occurred hemorrhages were mainly observed, along with a severe lymphocytolysis in all lymphoid tissues. Laboratory investigations confirmed the diagnosis of ASF. The outbreak was finally solved by stamping out. Discussion - In Africa, ASFV infection strictly depends upon the ""sylvatic cycle"", which involves warthogs and ticks of the Ornithodoros moubata complex. The mechanisms of transmission from wildlife and domestic pigs are still unclear, but ticks most likely play a key role. Therefore, the ASF outbreak described herein could represent the prototype of ASF in southern Africa. In that region, ASFV eradication seems not achievable and ASF control should focus on biosecurity measures. As in the present report, acute ASF usually occurs with very high morbidity and mortality, at least in previously unexposed pigs. On the contrary, sub-clinical and chronic infections are more frequent in endemic areas. Pathological findings are extremely useful to diagnose and counteract ASF. A number of hemorrhagic diseases should be considered in differential diagnoses. Anamnestic and epidemiological data prove to be helpful to correctly address the diagnostic process. Conclusions - The recent outbreak in Eastern Europe further confirms that ASF that is a serious transboundary disease, which still negatively impacts the pig industry worldwide. Epidemiological and pathological features described herein are of diagnostic value and of relevance to promptly counteract the spreading and the economic impact of the disease.",Pig;african swine fever;pathology;epidemiology;VIRUS,"Marruchella, G.;Maseke, M.;Scacchia, M.",2014,Dec,,0
1320,Phylogenetic analysis of rabies viruses from Sudan provides evidence of a viral clade with a unique molecular signature,"Rabies is endemic in Sudan and remains a continual threat to public health as transmission to humans is principally dog-mediated. Additionally, large-scale losses of livestock occur each year causing economic and social dilemmas. In this study, we analysed a cohort of 143 rabies viruses circulating in Sudan collected from 10 different animal species between 1992 and 2006. Partial nucleoprotein sequence data (400 bp) were obtained and compared to available sequence data of African classical rabies virus (RABV) isolates. The Sudanese sequences formed a discrete cluster within the Africa 1a group, including a small number of sequences that clustered with sequences from Ethiopian RABV. These latter sequences share an Aspartic Acid at position 106 (Asp106) with all other Africa 1a group members, in contrast to the remaining Sudanese strains, which encode Glutamic Acid at this position (Glu106). Furthermore, when representatives of other African and European lineages were aligned, Glu106 is unique to Sudan, which supports the concept of a single distinct virus strain circulating in Sudan. The high sequence identity in all Sudanese isolates studied, demonstrates the presence of a single rabies virus biotype for which the principal reservoir is the domestic dog. Crown Copyright © 2009.",aspartic acid;glutamic acid;virus nucleoprotein;amino acid sequence;article;biotype;cladistics;cluster analysis;cohort analysis;controlled study;gene cluster;genetic difference;nonhuman;nucleotide sequence;phylogeny;priority journal;Rabies virus;sequence analysis;Sudan;virus carrier;virus isolation;virus strain,"Marston, D. A.;McElhinney, L. M.;Ali, Y. H.;Intisar, K. S.;Ho, S. M.;Freuling, C.;Müller, T.;Fooks, A. R.",2009,,10.1016/j.virusres.2009.07.010,0
1321,Zoonotic aspects of rotaviruses,"Rotaviruses are important enteric pathogens of humans and animals. Group A rotaviruses (GARVs) account for up to 1 million children deaths each year, chiefly in developing countries and human vaccines are now available in many countries. Rotavirus-associated enteritis is a major problem in livestock animals, notably in young calves and piglets. Early in the epidemiological GARV studies in humans, either sporadic cases or epidemics by atypical, animal-like GARV strains were described. Complete genome sequencing of human and animal GARV strains has revealed a striking genetic heterogeneity in the 11 double stranded RNA segments across different rotavirus strains and has provided evidence for frequent intersections between the evolution of human and animal rotaviruses, as a result of multiple, repeated events of interspecies transmission and subsequent adaptation. © 2009 Elsevier B.V. All rights reserved.",double stranded RNA;lanzhou lamb rotavirus vaccine;Rotavirus vaccine;unclassified drug;virus vaccine;adaptation;animal disease;antigen detection;child death;clinical trial;drug efficacy;drug safety;epidemic;genetic heterogeneity;genetic reassortment;genome analysis;human;intussusception;nonhuman;review;RNA virus infection;Rotavirus;viral gastroenteritis;viral genetics;virus cell interaction;virus classification;virus identification;virus strain;virus transmission;virus virulence;zoonosis;rotarix;rotashield;rotateq,"Martella, V.;Bányai, K.;Matthijnssens, J.;Buonavoglia, C.;Ciarlet, M.",2010,,10.1016/j.vetmic.2009.08.028,0
1322,Enteric viral infections in lambs or kids,"Diarrhoea in lambs and kids is often a complex, multi-factorial syndrome. Common infectious causes of diarrhoea in lambs and kids during the first month of life are of bacterial or parasite nature. However, despite appreciable improvements in management practices and prevention and treatment strategies over the last decades, diarrhoea is still a common and costly syndrome affecting newborn small ruminants. Recent advances in the diagnostics and metagenomic investigations of the enteric environment have allowed discovering a number of novel viruses, although their pathobiological properties remain largely unknown. Assessing more in depth the impact of these viruses on the health and productions of these livestock animals is necessary and requires the development of accurate diagnostic tools and updating of the diagnostic algorithms of enteric pathological conditions.",Adenoviridae;article;Astroviridae;Bunyaviridae;Caliciviridae;Coronaviridae;intestine infection;kid (goat);lamb;nonhuman;Picornaviridae;Rotavirus;virus infection,"Martella, V.;Decaro, N.;Buonavoglia, C.",2015,,10.1016/j.vetmic.2015.08.006,0
1323,Novel Parvovirus Related to Primate Bufaviruses in Dogs,"A novel protoparvovirus species, related genetically to human bufaviruses, was identified in dogs with respiratory signs. The canine bufavirus was distantly related to the wellknown canine protoparvovirus, canine parvovirus type 2, sharing low amino acid identities in the nonstructural protein 1 (40.6%) and in the capsid protein 1 (33.4%). By screening collections of fecal, nasal, and oropharyngeal samples obtained from juvenile dogs (<= 1 year of age), canine bufavirus DNA appeared as a common component of canine virome. The virus was common in the stool samples of dogs with or without enteric disease and in the nasal and oropharyngeal swab samples of dogs with respiratory signs. However, the virus was not detected in nasal and oropharyngeal swab samples from animals without clinical signs.",INFECTIOUS RESPIRATORY-DISEASE;EQUI SUBSP ZOOEPIDEMICUS;CANINE;PARVOVIRUS;INFLUENZA-VIRUS;ACUTE DIARRHEA;DOMESTIC PIGS;IDENTIFICATION;FECES;ASSOCIATION;BOCAVIRUSES,"Martella, V.;Lanave, G.;Mihalov-Kovacs, E.;Marton, S.;Varga-Kugler, R.;Kaszab, E.;Di Martino, B.;Camero, M.;Decaro, N.;Buonavoglia, C.;Banyai, K.",2018,Jun,,0
1324,"Rapid detection, complete genome sequencing, and phylogenetic analysis of porcine deltacoronavirus","In February 2014, porcine deltacoronavirus (PDCoV) was identified in the United States. We developed a PDCoV real-time reverse transcription PCR that identified PDCoV in 30% of samples tested. Four additional PDCoV genomes from the United States were sequenced; these had =99%-100% nt similarity to the other US PDCoV strains.","Animals;*Coronaviridae/cl [Classification];*Coronaviridae/ge [Genetics];*Coronaviridae Infections/di [Diagnosis];*Coronaviridae Infections/vi [Virology];Genetic Variation;*Genome, Viral;Open Reading Frames;*Phylogeny;Swine","Marthaler, D.;Raymond, L.;Jiang, Y.;Collins, J.;Rossow, K.;Rovira, A.",2014,Aug,,0
1325,"Widespread rotavirus H in commercially raised pigs, United States","We investigated the presence in US pigs of rotavirus H (RVH), identified in pigs in Japan and Brazil. From 204 samples collected during 2006-2009, we identified RVH in 15% of fecal samples from 10 US states, suggesting that RVH has circulated in the United States since 2002, but probably longer.","Animals;Feces/vi [Virology];Japan;Phylogeny;*Rotavirus/ge [Genetics];*Rotavirus Infections/vi [Virology];Sequence Analysis, DNA/mt [Methods];*Swine/vi [Virology];*Swine Diseases/vi [Virology];United States","Marthaler, D.;Rossow, K.;Culhane, M.;Goyal, S.;Collins, J.;Matthijnssens, J.;Nelson, M.;Ciarlet, M.",2014,Jul,,0
1326,"VP6 genetic diversity, reassortment, intragenic recombination and classification of rotavirus B in American and Japanese pigs","Rotavirus B (RVB) has been identified as a causative agent of diarrhea in rats, humans, cattle, lambs, and swine. Recently, 20 RVB VP7 genotypes were determined based on an 80% nucleotide percent cut-off value. In this study, we sequenced the RVB VP6 gene segment from 80 RVB positive swine samples from the United States and Japan. Phylogenetic analyses, using the 30 available RVB VP6 sequences from GenBank and our 80 novel RVB VP6 sequences, revealed a large genetic diversity of RVB strains, mainly in pigs. For classification purposes, pairwise identity frequency analyses suggested an 81% nucleotide percent cut-off value, resulting in 13 RVB VP6 (I) genotypes. In addition, an intragenic recombinant RVB VP6 segment was identified from Japan. Furthermore, the data indicates frequent reassortment events occurred between the porcine RVB VP7 and VP6 gene segments. © 2014 The Authors.",nucleotide;protein VP6;article;gene sequence;genetic reassortment;genetic recombination;genetic variability;genotype;Japan;nonhuman;phylogeny;Rotavirus;Rotavirus B;sequence alignment;pig;United States;virus classification;virus strain,"Marthaler, D.;Suzuki, T.;Rossow, K.;Culhane, M.;Collins, J.;Goyal, S.;Tsunemitsu, H.;Ciarlet, M.;Matthijnssens, J.",2014,,10.1016/j.vetmic.2014.05.015,0
1327,Pestiviruses infections at the wild and domestic ruminants interface in the French Southern Alps,"In alpine pasture, interspecies transmission has recently been incriminated in the epidemiology of pestivirus infection. The aim of this study was to investigate pestivirus infections in wild and domestic ruminants sharing pastures in the French Southern Alps. Animal sera were screened for pestivirus antibodies against the pestivirus NS3 protein by a commercial blocking enzyme linked immunosorbent assay (ELISA). All 38 domestic herds tested were positive for pestivirus-specific antibodies. Individual sero-prevalence reached 76.5% (95% confidence interval [95% CI]: [74.2-78.8%]) of the 1383 sheep tested. For wild ruminants, 38.7% (95% CI: [33.8-43.9%]) of the 369 chamois tested, 28.7% (95% CI: [17.4-38.1%]) of the 72 roe deer, and 22.2% (95% CI: [6.5-37.9%]) of the 27 mouflons were seropositive. Virus screening was carried out on spleen samples from hunted wild animals (. n=. 160) and from 15 domestic ruminants (clinically suspected to be persistently infected animals), by a conventional reverse transcription-polymerase chain reaction (RT-PCR). Three pestivirus strains were isolated from the sheep samples positive by RT-PCR. The viruses were classified in the BDV-3, BDV-Tunisian and BDV-6 genotypes. For the first time, one strain (RUPI-05 strain) was isolated from an alpine chamois and clustered in the BDV-6 genotype, showing in the 5'-UTR region 92% of identity with the ovine isolate from the same area. Thus, an active circulation of pestiviruses was demonstrated in both wild and domestic ungulates from the French Southern Alps. The results suggest that interspecies transmission between sheep and chamois probably occur.",nonstructural protein 3;virus antibody;animal tissue;article;bovid;domestic animal;enzyme linked immunosorbent assay;female;France;male;mouflon;nonhuman;pasture;Pestivirus;Pestivirus infection;phylogeny;reverse transcription polymerase chain reaction;roe deer;Rupicapra;seroprevalence;sheep;virus neutralization;virus strain;wild animal,"Martin, C.;Duquesne, V.;Adam, G.;Belleau, E.;Gauthier, D.;Champion, J. L.;Saegerman, C.;Thiéry, R.;Dubois, E.",2015,,10.1016/j.vetmic.2014.11.025,0
1328,Recombination in eukaryotic single stranded DNA viruses,"Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution. © 2011 by the authors; licensee MDPI, Basel, Switzerland.",single stranded DNA;viral protein;DNA replication;DNA replication origin;DNA structure;DNA transcription;DNA virus;eukaryote;evolutionary adaptation;evolutionary homology;gene interaction;genetic epidemiology;genetic recombination;genome analysis;geographic distribution;homologous recombination;host range;metagenomics;minichromosome;nonhuman;oligomerization;phylogenetic tree;protein folding;protein secondary structure;review;sequence homology;viral tropism;virus gene;virus genome;virus infectivity;virus recombination;virus replication,"Martin, D. P.;Biagini, P.;Lefeuvre, P.;Golden, M.;Roumagnac, P.;Varsani, A.",2011,,10.3390/v3091699,0
1329,Course of BVDV-2 infection in a dairy herd. A case study,"Objective: A case of severe, acute clinical disease following infection with BVDV-2 and causing high economic losses in a dairy herd is described and the course of infection followed. Material and methods: The affected herd consisted of 25 Deutsch Fleckvieh cows and their offspring. The farm was BHV-1 free and yearly milk production averaged 6500 kg. Cases of disease and clinical findings from September 2002 through to April 2003 were collected and analyzed. Proof of BVDV-antibodies was carried out with indirect antibody-ELISA. BVDV-antigenes were detected by means of antigen-ELISA and immunofluorecense flow cytometry. The isolated viruses were classified as BVDV-2 using monoclonal antibodies and PCR. Results: Six cows and one heifer came down with haemorrhagic enteritis. Two of these cows were euthanized and one cow died in the course of the disease. Six cows aborted or calved prematurely. Furthermore, four calves died and three calves, which were born weaklings or suffered from profuse diarrhoea, were euthanized. Two calves remained persistenly infected. As reason for the disease, an infection of the herd with BVDV-2 was diagnosed. Conclusion and clinical relevance: The results indicate that the herd was BVDV-2 naiv before infection. The virus must have circulated in the herd for some time, even without the presence of persistently infected animals.",pestivirus;bovine viral diarrhoea;BVDV-2;cattle;herd infection;BOVINE VIRAL DIARRHEA;VIRUS DIARRHEA;FETAL PROTECTION;5'-UNTRANSLATED;REGION;PHYLOGENETIC ANALYSIS;INACTIVATED VACCINE;MUCOSAL DISEASE;CATTLE;STRAINS;TYPE-2,"Martin, R.;Kuhne, S.;Mansfeld, R.",2005,,,0
1330,Genomic characterization of a rotavirus G8P[1] detected in a child with diarrhea reveal direct animal-to-human transmission,"Group A rotavirus is a major cause of severe gastroenteritis in children and young animals. During a retrospective analysis of samples collected from Paraguayan children under 5. years old with diarrhea, and previously negative for rotavirus and norovirus, we detected the presence of bovine rotavirus sequences by viral metagenomics. Nucleic acid was extracted direct from stool sample and determined to be G8P[1]. The genomic analyzes revealed that the strain presents an Artiodactyl-like genome (G8-P[1]-I2-R2-C2-M1-Ax-N2-T6-E12-H3) suggesting a direct animal-to-human transmission.",article;controlled study;genome analysis;human;metagenomics;molecular phylogeny;nonhuman;nucleotide sequence;phylogenetic tree;Rotavirus;virus detection;virus genome;virus strain;virus transmission,"Martinez, M.;Phan, T. G.;Galeano, M. E.;Russomando, G.;Parreno, V.;Delwart, E.;Parra, G. I.",2014,,10.1016/j.meegid.2014.08.015,0
1331,Molecular and phylogenetic analysis of bovine coronavirus based on the spike glycoprotein gene,"Bovine coronavirus has been associated with diarrhoea in newborn calves, winter dysentery in adult cattle and respiratory tract infections in calves and feedlot cattle. In Cuba, the presence of BCoV was first reported in 2006. Since then, sporadic outbreaks have continued to occur. This study was aimed at deepening the knowledge of the evolution, molecular markers of virulence and epidemiology of BCoV in Cuba. A total of 30 samples collected between 2009 and 2011 were used for PCR amplification and direct sequencing of partial or full S gene. Sequence comparison and phylogenetic studies were conducted using partial or complete S gene sequences as phylogenetic markers. All Cuban bovine coronavirus sequences were located in a single cluster supported by 100% bootstrap and 1.00 posterior probability values. The Cuban bovine coronavirus sequences were also clustered with the USA BCoV strains corresponding to the GenBank accession numbers EF424621 and EF424623, suggesting a common origin for these viruses. This phylogenetic cluster was also the only group of sequences in which no recombination events were detected. Of the 45 amino acid changes found in the Cuban strains, four were unique. © 2012 Elsevier B.V.",amino acid;article;beef cattle;controlled study;Coronavirinae;Cuba;dairy cattle;gene amplification;gene cluster;gene sequence;genetic marker;molecular epidemiology;molecular evolution;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;polymerase chain reaction;priority journal;spike glycoprotein gene;unindexed sequence;virus gene;virus strain;virus virulence,"Martínez, N.;Brandão, P. E.;de Souza, S. P.;Barrera, M.;Santana, N.;de Arce, H. D.;Pérez, L. J.",2012,,10.1016/j.meegid.2012.05.007,0
1332,Porcine Reproductive and Respiratory Syndrome Virus isolates differ in their susceptibility to neutralization,"Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is highly heterogenic. This heterogeneity has an effect on antigenic composition of PRRSV and might create differences in sensitivity to neutralization between isolates. The sensitivity to neutralization could be an important feature of PRRSV isolates because it is likely that isolates resistant to neutralization pose a significant challenge for the development of vaccines that elicit broad protective immunity. Nonetheless, little information is available for understanding or categorizing the viral neutralization phenotype of PRRSV isolates. Consequently, the main purpose of this study was to determine whether PRRSV isolates differ in their susceptibility to neutralization and if they can be classified in different categories based on their neutralization phenotype. For this purpose, a panel of 39 PRRSV isolates and a set of 30 hyperimmune monospecific sera were used in cross-neutralization assays. The results of this study indicate that PRRSV isolates differ in their sensitivity to neutralization and k-means clustering system allowed classifying the isolates in four different categories according to their neutralization phenotype: highly sensitive, sensitive, moderately sensitive and resistant to neutralization. Further analyses using two additional clustering systems that considered individual data for the classification of the isolates confirmed that classification obtained by k-means is accurate in most cases and that only in a few instances classification is less stringent. Sequences of GP3, GP4 and GP5 were analyzed but no correlation could be found between the sequence of previously identified neutralizing epitopes or the number of N-linked glycosylation sites in different proteins and the neutralization phenotype of the isolates. These data provide the first systematic assessment of overall neutralization sensitivities of a panel of diverse PRRSV isolates. The classification of the isolates provides a useful tool to facilitate the systematic characterization of neutralizing antibody production elicited by new vaccine candidates. © 2011 Elsevier Ltd.",hyperimmune globulin;amino acid sequence;Arterivirus;article;Belgium;cluster analysis;cross reaction;Czech Republic;Germany;glycosylation;Hungary;Italy;Netherlands;nonhuman;nucleotide sequence;open reading frame;phenotype;Poland;priority journal;sequence analysis;Spain;virus classification;virus neutralization,"Martínez-Lobo, F. J.;Díez-Fuertes, F.;Simarro, I.;Castro, J. M.;Prieto, C.",2011,,10.1016/j.vaccine.2011.07.076,0
1333,Whole genome sequencing of a rare rotavirus from archived stool sample demonstrates independent zoonotic origin of human G8P[14] strains in Hungary,"Genotype P[14] rotaviruses in humans are thought to be zoonotic strains originating from bovine or ovine host species. Over the past 30 years only few genotype P[14] strains were identified in Hungary totaling <0.1% of all human rotaviruses whose genotype had been determined. In this study we report the genome sequence and phylogenetic analysis of a human genotype G8P[14] strain, RVA/Human-wt/HUN/182-02/2001/G8P[14]. The whole genome constellation (G8-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3) of this strain was shared with another Hungarian zoonotic G8P[14] strain, RVA/Human-wt/HUN/BP1062/2004/G8P[14], although phylogenetic analyses revealed the two rotaviruses likely had different progenitors. Overall, our findings indicate that human G8P[14] rotavirus detected in Hungary in the past originated from independent zoonotic events. Further studies are needed to assess the public health risk associated with infections by various animal rotavirus strains.",complementary DNA;virus DNA;virus RNA;acute gastroenteritis;article;case report;child;DNA library;feces;gene amplification;gene sequence;genetic similarity;genotype;human;Human rotavirus;Hungary;male;molecular phylogeny;nonhuman;nucleotide sequence;phylogeny;preschool child;priority journal;Rotavirus infection;ruminant;sequence analysis;viral gastroenteritis;virus classification;virus detection;virus genome;virus strain;whole genome sequencing;zoonosis,"Marton, S.;Dóró, R.;Fehér, E.;Forró, B.;Ihász, K.;Varga-Kugler, R.;Farkas, S. L.;Bányai, K.",2017,,10.1016/j.virusres.2016.09.012,0
1334,Characterization of H9N2 influenza A viruses isolated from chicken products imported into Japan from China,"We characterized eleven H9N2 influenza A viruses isolated from chicken products imported from China. Genetically they were classified into six distinct genotypes, including five already known genotypes and one novel genotype. This suggested that such multiple genotypes of the H9N2 virus have possibly already become widespread and endemic in China. Two isolates have amino-acid substitutions that confer resistance to amantadine in the M2 region, and this supported the evidence that this mutation might be a result of the wide application of amantadine for avian influenza treatment in China. These findings emphasize the importance of surveillance for avian influenza virus in this region, and of quarantining imported chicken products as potential sources for the introduction of influenza virus. © 2006 Cambridge University Press.",amantadine;amino acid substitution;animal tissue;article;avian influenza;chicken;China;controlled study;disease surveillance;genotype;infection control;Influenza A virus (H9N2);Japan;nonhuman;nucleotide sequence;viral genetics;virus classification;virus isolation;virus mutation;virus resistance,"Mase, M.;Eto, M.;K, I. Mai;Tsukamoto, K.;Yamaguchi, S.",2007,,10.1017/s0950268806006728,0
1335,Genetic diversity of avian infectious bronchitis viruses in Japan based on analysis of S2 glycoprotein gene,"To understand the genetic diversity of the S2 gene of infectious bronchitis viruses (IBV) isolated in Japan, we determined the nucleotide sequences of these IBVs using the reverse transcriptase polymerase chain reaction method coupled with direct sequencing. IBV isolated in Japan were classified into six different groups by phylogenetic analysis based on the S2 gene. However, the classification based on the S2 gene of IBV isolated in Japan was different for some of the strains from those obtained with our previous analysis of the S1 gene. This suggested that genetic recombination between the virus strains classified into different genetic groups had occurred in poultry, and that recombinant viruses might be epidemic in Japan.",viral protein;animal;animal disease;article;Avian infectious bronchitis virus;chicken;classification;genetic variability;genetics;Japan;phylogeny;virology;virus infection,"Mase, M.;Inoue, T.;Yamaguchi, S.;Imada, T.",2009,,10.1292/jvms.71.287,0
1336,Genetic comparison of H5N1 influenza A viruses isolated from chickens in Japan and Korea,"Outbreaks of highly pathogenic avian influenza (HPAI) caused by H5N1 virus occurred during 2003 to 2004 in Korea and Japan. The H5N1 viruses isolated in both countries were genetically similar at >99% identity in the nucleotide sequences of all eight RNA segments, indicating that they belong to genotype V and are distinct from HPAI viruses prevalent in southeast Asia that belong to genotype Z. These findings indicate that the H5N1 viruses that caused the HPAI outbreaks in both Korea and Japan were derived from a common ancestor.",RNA;article;avian influenza;chicken;controlled study;genetic identification;genotype;Influenza A virus;Japan;Korea;nonhuman;nucleotide sequence;prevalence;sequence homology;Southeast Asia;species comparison;viral genetics;virus isolation;virus strain,"Mase, M.;Kim, J. H.;Lee, Y. J.;Tsukamoto, K.;Imada, T.;Imai, K.;Yamaguchi, S.",2005,,,0
1337,Analysis of the fusion protein gene of newcastle disease viruses isolated in Japan,"The complete nucleotide sequences of the fusion (F) protein gene of Newcastle disease viruses (NDV) isolated in Japan from 1930 to 2007 (45 strains total) were determined and genetically analyzed. In the deduced amino acid sequences of fusion protein, the 5 potential asparagine-linked glycosylation sites and 10 cysteine residues were all conserved in the NDV examined in this study. The major epitopes involved in virus neutralization are conserved in most of the NDV strains isolated in Japan except a few strains. By virus neutralization test, no major antigenic differences were observed among representative strains of each genotype in Japan. All chickens vaccinated with the B1 strain survived without clinical signs after challenge with 2 NDV strains isolated in Japan (velogenic strains, JP/ Ibaraki/2000 and JP/Kagoshima/91), which possess amino acids substitutions involved in virus neutralization in the F protein gene.",virus fusion protein;animal;article;gene expression regulation;genetics;genotype;Japan;metabolism;Newcastle disease;Newcastle disease virus;phylogeny;physiology;poultry;virology,"Mase, M.;Murayama, K.;Karino, A.;Inoue, T.",2011,,10.1292/jvms.10-0281,0
1338,Viral metagenomics demonstrates that domestic pigs are a potential reservoir for Ndumu virus,"Background: The rising demand for pork has resulted in a massive expansion of pig production in Uganda. This has resulted in increased contact between humans and pigs. Pigs can act as reservoirs for emerging infectious diseases. Therefore identification of potential zoonotic pathogens is important for public health surveillance. In this study, during a routine general surveillance for African swine fever, domestic pigs from Uganda were screened for the presence of RNA and DNA viruses using a high-throughput pyrosequencing method. Findings. Serum samples from 16 domestic pigs were collected from five regions in Uganda and pooled accordingly. Genomic DNA and RNA were extracted and sequenced on the 454 GS-FLX platform. Among the sequences assigned to a taxon, 53% mapped to the domestic pig (Sus scrofa). African swine fever virus, Torque teno viruses (TTVs), and porcine endogenous retroviruses were identified. Interestingly, two pools (B and C) of RNA origin had sequences that showed 98% sequence identity to Ndumu virus (NDUV). None of the reads had identity to the class Insecta indicating that these sequences were unlikely to result from contamination with mosquito nucleic acids. Conclusions: This is the first report of the domestic pig as a vertebrate host for Ndumu virus. NDUV had been previously isolated only from culicine mosquitoes. NDUV therefore represents a potential zoonotic pathogen, particularly given the increasing risk of human-livestock-mosquito contact. © 2012 Masembe et al.; licensee BioMed Central Ltd.",genomic DNA;genomic RNA;nucleic acid;African swine fever;animal experiment;article;blood sampling;DNA extraction;DNA sequence;domestic pig;endogenous retrovirus;metagenomics;mosquito;ndumu alphavirus;nonhuman;nucleotide sequence;RNA extraction;RNA sequence;taxon;Torque teno virus 1;Uganda;virus;virus carrier,"Masembe, C.;Michuki, G.;Onyango, M.;Rumberia, C.;Norling, M.;Bishop, R. P.;Djikeng, A.;Kemp, S. J.;Orth, A.;Skilton, R. A.;Ståhl, K.;Fischer, A.",2012,,10.1186/1743-422x-9-218,1
1339,The molecular biology of swinepox virus. II. The infectious cycle,"Studies based on low-stringency hybridizations of radiolabeled swinepox virus (SPV) DNA to Southern blots containing DNA of representative members of the Orthopoxvirus, Leporipoxvirus, and Avipoxvirus genera and the Entomopoxvirus subfamily have revealed no DNA homology at this level of resolution. Antigenic relatedness between SPV and vaccinia was also analyzed using immunoprecipitations and revealed little if any cross-reactivity. The growth characteristics of SPV in tissue culture were examined by light microscopy and revealed both a delayed and a different cytopathology than that of vaccinia virus. SPV causes foci in pig kidney cells that are not evident until at least 4 days postinfection, whereas vaccinia rapidly generates plaques on these cells. The kinetics of DNA accumulation, protein expression, and RNA transcription of SPV have been examined and indicate that each of these facets of the SPV growth cycle is also considerably delayed when compared to vaccinia virus. Our data indicate that swinepox virus is unique from other poxviruses characterized to date and supports the classification of swinepox virus into a separate genus, Suipoxvirus, within the poxvirus family.",animal cell;article;gene expression;immunoprecipitation;molecular biology;nonhuman;Poxviridae;priority journal;pig;virus characterization;virus infection;virus infectivity;virus replication,"Massung, R. F.;Moyer, R. W.",1991,,10.1016/0042-6822(91)90040-i,0
1340,Identification of novel bovine group A rotavirus G15P[14] strain from epizootic diarrhea of adult cows by de novo sequencing using a next-generation sequencer,"There are few reports describing diarrhea of adult cattle caused by group A rotaviruses. Here, we report the identification of a novel bovine group A rotavirus from diarrhea of adult cows. A group A rotavirus was detected from an epizootic outbreak of diarrhea in adult cows with a decrease in milk production in Japan in 2013. The comprehensive genomic analyses from fecal samples by viral metagenomics using a next-generation sequencer revealed that it had an unreported genotype combination G15P[14]. The genome constellation of this strain, namely, RVA/Cow-wt/JPN/Tottori-SG/2013/G15P[14] was G15-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3 representing VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5, respectively. Each gene segment of Tottori-SG was most closely related to Japanese bovine group A rotaviruses suggesting that Tottori-SG might have derived from multiple reassortment events from group A rotavirus strains circulating among Japanese cattle. No other diarrhea pathogen of adult cattle was detected by routine diagnosis and metagenomics. Viral metagenomics, using a next-generation sequencer, is useful to characterize group A rotaviruses from fecal samples and offers unbiased comprehensive investigations of pathogen. © 2014 Elsevier B.V.",adult;article;bovine viral diarrhea;gene sequence;genetic reassortment;genotype;Japan;metagenomics;milk production;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;Rotavirus;Rotavirus group A;virus identification;virus strain,"Masuda, T.;Nagai, M.;Yamasato, H.;Tsuchiaka, S.;Okazaki, S.;Katayama, Y.;Oba, M.;Nishiura, N.;Sassa, Y.;Omatsu, T.;Furuya, T.;Koyama, S.;Shirai, J.;Taniguchi, K.;Fujii, Y.;Todaka, R.;Katayama, K.;Mizutani, T.",2014,,10.1016/j.vetmic.2014.03.009,1
1341,Whole genome analysis of a novel picornavirus related to the Enterovirus/Sapelovirus supergroup from porcine feces in Japan,"A novel virus related to the Enterovirus/Sapelovirus supergroup in the family Picornaviridae was identified in healthy porcine feces in Japan by using a metagenomics approach. The genome of the virus, named Sapelo-like porcine picornavirus Japan (SPPVJ) Pig/Isi-Im1/JPN/2016, had a type-IV internal ribosomal entry site and carried a 6978-nucleotide-long single open reading frame encoding a 2326 amino acids (aa) polyprotein precursor. The coding sequence region consisted of leader protein (68 aa), a structural protein region P1 (824 aa), and the non-structural protein regions P2 (672 aa) and P3 (762 aa). Among representative picornaviruses, the P1, 2C, and 3CD regions of SPPVJ had the highest aa identities of 64.4%, 61.9%, and 73.3%, respectively, with the corresponding regions of sapelo-like bat picornavirus BtVs-PicoV/SC2013. Sequencing analysis of the RT-PCR products derived from the 5’ untranslated and 3D regions revealed the presence of SPPVJ in 17.8% (19/107) of the feces from healthy and diarrheal pigs in 12 farms in 2015–2016. Further studies are needed to determine the origin and pathogenic potential of SPPJV in pigs and other mammals.",genomic RNA;nonstructural protein 2;5' untranslated region;animal experiment;article;bat;codon;DNA library;Enterovirus;feces microflora;genome analysis;internal ribosome entry site;Japan;nonhuman;nucleotide sequence;open reading frame;phylogeny;Picornaviridae;piglet;priority journal;reverse transcription polymerase chain reaction;Sapelovirus;Sapelovirus A;virus genome,"Masuda, T.;Sunaga, F.;Naoi, Y.;Ito, M.;Takagi, H.;Katayama, Y.;Omatsu, T.;Oba, M.;Sakaguchi, S.;Furuya, T.;Yamasato, H.;Shirai, J.;Makino, S.;Mizutani, T.;Nagai, M.",2018,,10.1016/j.virusres.2018.09.003,1
1342,Genomic integration of lambda EG10 transgene in gpt delta transgenic rodents,"Background: Transgenic gpt delta mouse and rat models were developed to perform gpt and Spi- assays for in vivo mutagenicity tests. The animals were established by integration of lambda EG10 phage DNA as a transgene into the genome. The inserted position of the transgene on chromosome was determined by fluorescent in situ hybridization and Southern blot analyses; however, the exact position and sequence of the inserted junction were not known. To identify the site and pattern of genomic integration of the transgene copies, genomic DNAs extracted from C57BL/6J gpt delta mice and F344 gpt delta rats were applied to whole genome sequencing and mate-pair analysis. Results: The result confirmed that multi-copy lambda EG10 transgenes are inserted at a single position in the mouse chromosome 17. The junction contains 70 bp of overlapped genomic sequences, and it has short homology at both ends. A copy number analysis suggested that the inserted transgenes may contain 41 head-to-tail junctions and 16 junctions of other types such as rearranged abnormal junctions. It suggested that the number of intact copies could be approximately 40 at maximum. In the F344 gpt delta rats, transgenes are inserted at a single position in the rat chromosome 4. The junction contains no overlapped sequence but 72-kb genomic sequence including one gene was deleted. The inserted transgenes may contain 15 head-to-tail junctions and two rearranged junctions. It suggested that the number of intact copies could be 14 at maximum. One germline base substitution in the gpt gene rescued from gpt delta rats was characterized. Conclusions: The exact inserted positions of the lambda EG10 transgene in the genome of gpt delta transgenic rodents were identified. The copy number and arrangement of the transgene were analyzed. PCR primers for quick genotyping of gpt delta mice and rats have been designed.",genomic DNA;article;chromosome 17;chromosome 4;controlled study;copy number variation;DNA sequence;Enterobacteria phage lambda;gene deletion;gene insertion;gene insertion sequence;gene rearrangement;gene sequence;genomic integration;genomics;germline mutation;gpt delta mouse;high throughput sequencing;microbial genome;mutation rate;nonhuman;nucleic acid base substitution;overlapping gene;real time polymerase chain reaction;transgene,"Masumura, K.;Sakamoto, Y.;Kumita, W.;Honma, M.;Nishikawa, A.;Nohmi, T.",2015,,10.1186/s41021-015-0024-6,0
1343,"A new duck circovirus sequence, detected in velvet scoter (Melanitta fusca) supports great diversity among this species of virus","Background: The aim of this study was to investigate the presence of circoviruses in wild bird populations, in Poland. Circoviruses possess immuno-suppressive properties and might interfere with the health of wild birds. Method: 83 birds, which belonged to 23 species, were tested with broad-range, nested PCR. The obtained PCR products were sequenced and new primers designed, to analyse the full-length, viral genome. A phylogenetic analysis was conducted, to find any relationship to known circoviruses. Results: The circovirus DNA sequence was found in 4 birds. All samples originated from the velvet scoter (Melanitta fusca) a marine duck from the Merginae sub-family. Birds which tested positive for the circovirus were found dead in fishing nets, off the Baltic coast. During post-mortem examination, carcasses of two of the scoters showed only light emaciation, while the two other birds appeared healthy. The obtained, full-length, circovirus sequence revealed 1,988 nucleotides and the presence of typical features (i.e. Cap, Rep and ORF3). Nucleotide similarity to other duck circoviruses was 84 to 86 %. Phylogenetic analysis of the complete genome and cap gene, indicated that the new circovirus is related to known duck circoviruses, especially to sub-types sometimes referred to as duck circovirus genotype 1, but not genotype 2. Conclusions: In this study, we have reported a new duck circovirus sequence detected in the velvet scoter, a species of marine duck. Sequence comparison and phylogenetic analysis of the new virus sequence support previous reports that duck circovirus (DuCV) is a species with a high degree of diversity. The viral sequence obtained from the velvet scoter suggests that DuCV may infect birds from the Anatinae sub-family. More studies are needed to prove if the velvet scoter and other marine ducks act as a reservoir for DuCV.",DNA;nucleotide;article;autopsy;Baltic Sea;bird;carcass;Circovirus;controlled study;DNA sequence;duck;gene sequence;genetic variability;genotype;Melanitta fusca;nonhuman;nucleotide sequence;open reading frame;phylogeny;polymerase chain reaction;species difference;virus genome,"Matczuk, A. K.;Krawiec, M.;Wieliczko, A.",2015,,10.1186/s12985-015-0352-y,0
1344,B-cell epitopes of African horse sickness virus serotype 4 recognised by immune horse sera,"Identifying antigenic proteins and mapping their epitopes is important for the development of diagnostic reagents and recombinant vaccines. B-cell epitopes of African horse sickness virus (AHSV) have previously been mapped on VP2, VP5, VP7 and NS1, using mouse, rabbit and chicken monoclonal antibodies. A comprehensive study of the humoral immune response of five vaccinated horses to AHSV-4 antigenic peptides was undertaken. A fragmented-genome phage display library expressing a repertoire of AHSV-4 peptides spanning the entire genome was constructed. The library was affinity selected for binders on immobilised polyclonal immunoglobulin G (IgG) isolated from horse sera collected pre- and post-immunisation with an attenuated AHSV-4 monovalent vaccine. The DNA inserts of binding phages were sequenced with Illumina high-throughput sequencing. The data were normalised using preimmune IgG-selected sequences. More sequences mapped to the genes coding for NS3, VP6 and VP5 than to the other genes. However, VP2 and VP5 each had more antigenic regions than each of the other proteins. This study identified a number of epitopes to which the horse's humoral immune system responds during immunisation with AHSV-4.",antiserum;epitope;immunoglobulin G;monoclonal antibody;virus vaccine;African horse sickness;African horse sickness virus;animal;blood;enzyme linked immunosorbent assay;horse;immunology;vaccination;veterinary medicine;virology,"Mathebula, E. M.;Faber, F. E.;Van Wyngaardt, W.;Van Schalkwyk, A.;Pretorius, A.;Fehrsen, J.",2017,,10.4102/ojvr.v84i1.1313,0
1345,Human parvovirus 4 'PARV4' remains elusive despite a decade of study,"Human parvovirus 4 ('PARV4') is a small DNA tetraparvovirus, first reported in 2005. In some populations, PARV4 infection is uncommon, and evidence of exposure is found only in individuals with risk factors for parenteral infection who are infected with other blood-borne viruses. In other settings, seroprevalence studies suggest an endemic, age-associated transmission pattern, independent of any specific risk factors. The clinical impact of PARV4 infection remains uncertain, but reported disease associations include an influenza-like syndrome, encephalitis, acceleration of HIV disease, and foetal hydrops. In this review, we set out to report progress updates from the recent literature, focusing on the investigation of cohorts in different geographical settings, now including insights from Asia, the Middle East, and South America, and discussing whether attributes of viral or host populations underpin the striking differences in epidemiology. We review progress in understanding viral phylogeny and biology, approaches to diagnostics, and insights that might be gained from studies of closely related animal pathogens. Crucial questions about pathogenicity remain unanswered, but we highlight new evidence supporting a possible link between PARV4 and an encephalitis syndrome. The unequivocal evidence that PARV4 is endemic in certain populations should drive ongoing research efforts to understand risk factors and routes of transmission and to gain new insights into the impact of this virus on human health.",microRNA;acquired immune deficiency syndrome;Asia;blood donor;blood transfusion;Bocaparvovirus;cohort analysis;disease association;disease course;enzyme linked immunosorbent assay;fetus hydrops;flu like syndrome;gastroenteritis;genotype;geographic distribution;graft recipient;hepatitis;human;Human immunodeficiency virus infection;Human parechovirus;Human parvovirus 4;Human parvovirus B19;livestock;men who have sex with men;microbiology;Middle East;nonhuman;organ transplantation;parvovirus infection;pathophysiology;phylogeny;polymerase chain reaction;Porcine parvovirus;Porcine parvovirus 6;public health;rash;respiratory tract infection;review;risk factor;seroprevalence;South America;species endemicity;vertical transmission;virus cell interaction;virus encephalitis;virus immunity;virus transmission;virus virulence,"Matthews, P. C.;Sharp, C.;Simmonds, P.;Klenerman, P.",2017,,10.12688/f1000research.9828.1,0
1346,Full genome-based classification of rotaviruses reveals a common origin between human wa-like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains,"Group A rotavirus classification is currently based on the molecular properties of the two outer layer proteins, VP7 and VP4, and the middle layer protein, VP6. As reassortment of all the 11 rotavirus gene segments plays a key role in generating rotavirus diversity in nature, a classification system that is based on all the rotavirus gene segments is desirable for determining which genes influence rotavirus host range restriction, replication, and virulence, as well as for studying rotavirus epidemiology and evolution. Toward establishing such a classification system, gene sequences encoding VP1 to VP3, VP6, and NSP1 to NSP5 were determined for human and animal rotavirus strains belonging to different G and P genotypes in addition to those available in databases, and they were used to define phylogenetic relationships among all rotavirus genes. Based on these phylogenetic analyses, appropriate identity cutoff values were determined for each gene. For the VP4 gene, a nucleotide identity cutoff value of 80% completely correlated with the 27 established P genotypes. For the VP7 gene, a nucleotide identity cutoff value of 80% largely coincided with the established G genotypes but identified four additional distinct genotypes comprised of murine or avian rotavirus strains. Phylogenetic analyses of the VP1 to VP3, VP6, and NSP1 to NSP5 genes showed the existence of 4, 5, 6, 11, 14, 5, 7, 11, and 6 genotypes, respectively, based on nucleotide identity cutoff values of 83%, 84%, 81%, 85%, 79%, 85%, 85%, 85%, and 91%, respectively. In accordance with these data, a revised nomenclature of rotavirus strains is proposed. The novel classification system allows the identification of (i) distinct genotypes, which probably followed separate evolutionary paths; (ii) interspecies transmissions and a plethora of reassortment events; and (iii) certain gene constellations that revealed (a) a common origin between human Wa-like rotavirus strains and porcine rotavirus strains and (b) a common origin between human DS-1-like rotavirus strains and bovine rotaviruses. These close evolutionary links between human and animal rotaviruses emphasize the need for close simultaneous monitoring of rotaviruses in animals and humans. Copyright © 2008, American Society for Microbiology. All Rights Reserved.",nonstructural protein 1;nonstructural protein 5;protein VP1;protein VP3;protein VP6;protein VP7;article;Avian rotavirus;biological monitoring;bovine rotavirus;controlled study;correlation analysis;data base;gene sequence;genetic reassortment;genotype;Human DS 1 like rotavirus;Human rotavirus;Human Wa like rotavirus;interspecific relationship;molecular evolution;Murine rotavirus;nonhuman;nucleotide sequence;phylogeny;porcine rotavirus;priority journal;Rotavirus;unindexed sequence;virus classification;virus genome;virus strain;virus typing,"Matthijnssens, J.;Ciarlet, M.;Heiman, E.;Arijs, I.;Delbeke, T.;McDonald, S. M.;Palombo, E. A.;Iturriza-Gómara, M.;Maes, P.;Patton, J. T.;Rahman, M.;Van Ranst, M.",2008,,10.1128/jvi.02257-07,0
1347,Complete molecular genome analyses of equine rotavirus a strains from different continents reveal several novel genotypes and a largely conserved genotype constellation,"In this study, the complete genome sequences of seven equine group A rotavirus (RVA) strains (RVA/Horse-tc/GBR/L338/1991/G13P[18], RVA/Horse-wt/IRL/03V04954/2003/G3P[12] and RVA/Horse-wt/IRL/04V2024/2004/G14P[12] from Europe; RVA/Horse-wt/ARG/E30/1993/ G3P[12], RVA/Horse-wt/ARG/E403/2006/G14P[12] and RVA/Horse-wt/ARG/E4040/2008/ G14P[12] from Argentina; and RVA/Horse-wt/ZAF/EqRV-SA1/2006/G14P[12] from South Africa) were determined. Multiple novel genotypes were identified and genotype numbers were assigned by the Rotavirus Classification Working Group: R9 (VP1), C9 (VP2), N9 (NSP2), T12 (NSP3), E14 (NSP4), and H7 and H11 (NSP5). The genotype constellation of L338 was unique: G13-P[18]-I6- R9-C9-M6-A6-N9-T12-E14-H11. The six remaining equine RVA strains showed a largely conserved genotype constellation: G3/G14-P[12]-I2/I6-R2-C2-M3-A10-N2-T3-E2/E12-H7, which is highly divergent from other known non-equine RVA genotype constellations. Phylogenetic analyses revealed that the sequences of these equine RVA strains are related distantly to nonequine RVA strains, and that at least three lineages exist within equine RVA strains. A small number of reassortment events were observed. Interestingly, the three RVA strains from Argentina possessed the E12 genotype, whereas the three RVA strains from Ireland and South Africa possessed the E2 genotype. The unusual E12 genotype has until now only been described in Argentina among RVA strains collected from guanaco, cattle and horses, suggesting geographical isolation of this NSP4 genotype. This conserved genetic configuration of equine RVA strains could be useful for future vaccine development or improvement of currently used equine RVA vaccines. © 2012 SGM.",article;genetic reassortment;genome analysis;genotype;nonhuman;phylogeny;priority journal;Rotavirus;Rotavirus A;virus classification;virus genome;virus strain,"Matthijnssens, J.;Miño, S.;Papp, H.;Potgieter, C.;Novo, L.;Heylen, E.;Zeller, M.;Garaicoechea, L.;Badaracco, A.;Lengyel, G.;Kisfali, P.;Cullinane, A.;Collins, P. J.;Ciarlet, M.;O'Shea, H.;Parreño, V.;Bányai, K.;Barrandeguy, M.;van Ranst, M.",2012,,10.1099/vir.0.039255-0,0
1348,Pathogenic properties of six bovine picornavirus isolates in mice,"Six bovine picornavirus isolates were classified according to mouse pathogenicity. Of the 6 isolates, 4 (6727 sm, 4155 sm, 3039, and 7109) produced lesions, and 3 (6727 sm, 4155 sm, and 3039) caused death in suckling mice. Microscopic lesions included necrosis in brain, heart, lung, liver, and kidney. A correlation between mouse pathogenicity and hemagglutination was found, indicating that hemagglutination properties may be helpful in classifying picornaviruses.",autopsy;brain necrosis;bovine;Enterovirus;Enterovirus B;etiology;heart muscle necrosis;histology;inoculation;kidney necrosis;liver necrosis;lung necrosis;methodology;microorganism;mouse;Picornaviridae;pregnancy;theoretical study;virus;virus classification;virus hemagglutination;virus isolation;virus pathogenesis,"Mattson, J. M.;Vorhies, M. W.;Reed, D. E.",1974,,,0
1349,Cowpox virus: What’s in a name?,"Traditionally, virus taxonomy relied on phenotypic properties, however, a sequence-based virus taxonomy has become essential since the recent requirement of a species to exhibit monophyly. The species Cowpox virus has failed to meet this requirement, necessitating a reexamination of this species. Here, we report the genomic sequences of nine Cowpox viruses and, by combining them with the available data of 37 additional genomes, confirm polyphyly of Cowpox viruses and find statistical support based on genetic data for more than a dozen species. These results are discussed in light of the current International Committee on Taxonomy of Viruses species definition, as well as immediate and future implications for poxvirus taxonomic classification schemes. Data support the recognition of five monophyletic clades of Cowpox viruses as valid species.",article;controlled study;Cowpox virus;fluorometry;gene library;genetic distance;genetic heterogeneity;genetic recombination;nonhuman;nucleotide sequence;phylogenetic tree;phylogeography;polyphyly;protein assembly;sequence analysis;species identification;taxonomic identification;virus culture;virus genome,"Mauldin, M. R.;Antwerpen, M.;Emerson, G. L.;Li, Y.;Zoeller, G.;Carroll, D. S.;Meyer, H.",2017,,10.3390/v9050101,0
1350,Molecular evolution and epidemiological links study of Newcastle disease virus isolates from 1995 to 2016 in Iran,"In the case of Newcastle disease virus, multiple factors such as host adaptation, immune response evasion, and selective pressures have been suggested to result in evolution of viruses and the emergence of genetic variants. Multiple studies on virus classification and global epidemiological links have yielded consistent data. Here, we have performed a molecular analysis study of circulating Newcastle disease viruses in Iran (1995-2016). According to evolutionary divergences, subgenotype VIg, VIj, VIIj, VIId, XIIIa and XIIId isolates have been circulating in the country during a 21-year period. Based on data analysis, VIg isolates shared highest sequence identity with Russian and Polish isolates of the VIg subgenotype, while VIj subgenotype isolates (2012) were most similar to a virus isolated in 2015 in India. Analysis of the evolutionary divergence of subgenotype VIIj suggests that Chinese and Ukrainian viruses may have played a crucial role in the emergence of VIIj isolates. Evolutionary difference studies also indicated that XIIIa isolates circulating in Iran may have caused the emergence of adapted variants of subgenotype XIIId. Therefore, we propose that the evolutionary and epidemiological study of virulent Newcastle disease viruses could help to provide accurate molecular data about variants circulating in the region, thus aiding in the design of more efficient recombinant vaccines.",animal;classification;genetic variation;genetics;genotype;Iran;isolation and purification;molecular epidemiology;molecular evolution;Newcastle disease;Newcastle disease virus;phylogeny;poultry;sequence homology;virology,"Mayahi, V.;Esmaelizad, M.",2017,,10.1007/s00705-017-3536-5,0
1351,Protective efficacy of a recombinant bacterial artificial chromosome clone of a very virulent Marek's disease virus containing a reticuloendotheliosis virus long terminal repeat,"Marek's disease virus (MDV), an alphaherpesvirus, causes Marek's disease (MD), a lymphoproliferative disease in poultry characterized by T-cell lymphomas, nerve lesions, and mortality. Vaccination is used worldwide to control MD, but increasingly virulent field strains can overcome this protection, driving a need to create new vaccines. Previous studies revealed that insertion of reticuloendotheliosis virus (REV) long terminal repeat (LTR) into a bacterial artificial chromosome (BAC) clone of a very virulent strain of MDV, Md5, rendered the resultant recombinant virus, rMd5 REV-LTR BAC, fully attenuated in maternal antibody positive (Mab+) chickens at passage 40. In the current study, the protective efficacy of rMd5 REV-LTR BAC was evaluated. First, passage 70 was identified as being fully attenuated in maternal antibody negative chickens and chosen as the optimal passage level for use in protective efficacy studies. Second, three protective efficacy trials were conducted comparing the rMd5 REV-LTR p70 BAC to the CVI988/Rispens vaccine. Groups of Mab+ and Mab- 15I5 × 71 chickens were vaccinated in ovo at 18 days of embryonation or intra-abdominally at day of hatch, and challenged at 5 days post-hatch with the vv+MDV strain 686. Vaccination at day of hatch and in ovo with rMd5 REV-LTR p70 BAC protected chickens against MDV-induced bursa and thymic atrophy, but did not provide the same level of protection against MD tumours as that afforded by the commercial vaccine, CVI988/Rispens.",Marek disease vaccine;recombinant DNA;virus antibody;animal;bacterial artificial chromosome;bird disease;blood;cell culture;chicken;DNA sequence;duck;female;Gallid alphaherpesvirus 2;genetics;high throughput sequencing;immunology;long terminal repeat;male;Marek disease;pathogenicity;Reticuloendotheliosis virus;vaccination;veterinary medicine;virology,"Mays, J. K.;Black-Pyrkosz, A.;Spatz, S.;Fadly, A. M.;Dunn, J. R.",2016,,,0
1352,Comparison of sample sequences of the Salmonella typhi genome to the sequence of the complete Escherichia coli K-12 genome,"Raw sequence data representing the majority of a bacterial genome can be obtained at a tiny fraction of the cost of a completed sequence. To demonstrate the utility of such a resource, 870 single-stranded M13 clones were sequenced from a shotgun library of the Salmonella typhi Ty2 genome. The sequence reads averaged over 400 bases and sampled the genome with an average spacing of once every 5,000 bases. A total of 339,243 bases of unique sequence was generated (approximately 7% representation). The sample of 870 sequences was compared to the complete Escherichia coli K-12 genome and to the rest of the GenBank database, which can also be considered a collection of sampled sequences. Despite the incomplete S. typhi data set, interesting categories could easily be discerned. Sixteen percent of the sequences determined from S. typhi had close homologs among known Salmonella sequences (P < 1e-40 in BlastX or BlastN), reflecting the proportion of these genomes that have been sequenced previously; 277 sequences (32%) had no apparent orthologs in the complete E. coli K-12 genome (P > 1e-20), of which 155 sequences (18%) had no close similarities to any sequence in the database (P > 1e-5). Eight of the 277 sequences had similarities to genes in other strains of E. coli or plasmids, and six sequences showed evidence of novel phage lysogens or sequence remnants of phage integrations, including a member of the lambda family (P < 1e-15). Twenty-three sample sequences had a significantly closer similarity a sequence in the database from organisms other than the E. coli/Salmonella clade (which includes Shigella and Citrobacter). These sequences are new candidate lateral transfer events to the S. typhi lineage or deletions on the E. coli K-12 lineage. Eleven putative junctions of insertion/deletion events greater than 100 bp were observed in the sample, indicating that well over 150 such events may distinguish S. typhi from E. coli K-12. The need for automatic methods to more effectively exploit sample sequences is discussed.","Bacteriophages/ge [Genetics];Databases, Factual;Enterobacteriaceae/ge [Genetics];*Escherichia coli/ge [Genetics];*Genome, Bacterial;Mutagenesis;*Salmonella typhi/ge [Genetics]","McClelland, M.;Wilson, R. K.",1998,Sep,,0
1353,Evaluation of cells and biological reagents for adventitious agents using degenerate primer PCR and massively parallel sequencing,"We employed a massively parallel sequencing (MPS)-based approach to test reagents and model cell substrates including Chinese hamster ovary (CHO), Madin-Darby canine kidney (MDCK), African green monkey kidney (Vero), and High Five insect cell lines for adventitious agents. RNA and DNA were extracted either directly from the samples or from viral capsid-enriched preparations, and then subjected to MPS-based non-specific virus detection with degenerate oligonucleotide primer (DOP) PCR. MPS by 454, Illumina MiSeq, and Illumina HiSeq was compared on independent samples. Virus detection using these methods was reproducibly achieved. Unclassified sequences from CHO cells represented cellular sequences not yet submitted to the databases typically used for sequence identification. The sensitivity of MPS-based virus detection was consistent with theoretically expected limits based on dilution of virus in cellular nucleic acids. Capsid preparation increased the number of viral sequences detected. Potential viral sequences were detected in several samples; in each case, these sequences were either artifactual or (based on additional studies) shown not to be associated with replication-competent viruses. Virus-like sequences were more likely to be identified in BLAST searches using virus-specific databases that did not contain cellular sequences. Detected viral sequences included previously described retrovirus and retrovirus-like sequences in CHO, Vero, MDCK and High Five cells, and nodavirus and endogenous bracovirus sequences in High Five insect cells. Bovine viral diarrhea virus, bovine hokovirus, and porcine circovirus sequences were detected in some reagents. A recently described parvo-like virus present in some nucleic acid extraction resins was also identified in cells and extraction controls from some samples. The present study helps to illustrate the potential for MPS-based strategies in evaluating the presence of viral nucleic acids in various sample types, including cell culture substrates and vaccines.","Animals;*Biological Products;*Cell Line;*Drug Contamination/pc [Prevention & Control];*High-Throughput Nucleotide Sequencing/mt [Methods];*Indicators and Reagents;*Polymerase Chain Reaction/mt [Methods];*Technology, Pharmaceutical/mt [Methods];0 (Biological Products);0 (Indicators and Reagents)","McClenahan, S. D.;Uhlenhaut, C.;Krause, P. R.",2014,Dec 12,,0
1354,Interruption of Cytokine Networks by Poxviruses - Lessons from Myxoma Virus,"Myxoma virus is an infectious poxvirus pathogen that induces a virulent systemic disease called myxomatosis in European rabbits, The disease is rapidly and uniformly fatal to susceptible rabbits and is characterized by generalized dysfunction of cellular immunity and multiple interruptions of the host cytokine network, A number of virus genes are classified as virulence factors because virus constructs bearing targeted gene disruptions induce attenuated disease symptoms, Many of these genes encode proteins that interact directly with effector elements of the host immune system. Included among these immunosubversive viral proteins are secreted mimics of host ligands or regulators (virokines) and homologues of cellular cytokine receptors (viroceptors). Five examples of these immune modulator proteins encoded by myxoma virus are reviewed: (1) myxoma growth factor, a member of the epidermal growth factor ligand superfamily; (2) SERF-1, a secreted serine proteinase inhibitor; (3) M11L, a receptor-like surface protein; (4) T2, a tumor necrosis factor receptor homologue; and (5) T7, an interferon-gamma receptor homologue, The origin of viral strategies designed to subvert immune regulation by host cytokines is considered in the context of the biology of myxoma virus within immunocompetent hosts.",TNF;SERPINS;IFN-GAMMA;VIROKINES;VIROCEPTORS;SHOPE FIBROMA VIRUS;EPIDERMAL GROWTH-FACTOR;SERINE PROTEASE INHIBITOR;VACCINIA VIRUS;DNA-SEQUENCE;COWPOX VIRUS;TUMORIGENIC POXVIRUSES;FACTOR-ALPHA;INFLAMMATORY RESPONSE;PROTEINASE-INHIBITOR,"McFadden, G.;Graham, K.;Ellison, K.;Barry, M.;Macen, J.;Schreiber, M.;Mossman, K.;Nash, P.;Lalani, A.;Everett, H.",1995,May,,0
1355,Sequence analysis of the gene coding for the S1 glycoprotein of infectious bronchitis virus (IBV) strains from New Zealand,"Four new infectious bronchitis virus (IBV) strains (T6, K32, K43, and K87) were isolated from clinically infected chickens in New Zealand. These strains were compared with four strains (A, B, C, and D), which had circulated 25 years previously, by sequencing the gene coding for the S1 subunit of the spike glycoprotein. Analysis of the nucleotide and deduced amino acid sequences revealed that the eight strains from New Zealand are genetically related and share greater than 82.8% nucleotide and 79% amino acid homology within the S1 region. Strains T6, K43, and K87 were more than 99% homologous to previously described strains C and D. A fourth new strain (K32) was most closely related to the previously described B strain. Phylogenetic analysis of strains revealed that New Zealand strains were more closely related to Australian than European or North American strains. The New Zealand A strain shared 99.5% nucleotide and 98.7% amino acid homology with the Australian Vic S strain. Deduced amino acid sequence of the S1 glycoprotein indicated differences between strains that were, in general, consistent with virus neutralization patterns. © 2008 Springer Science+Business Media, LLC.",glycoprotein;glycoprotein s1;unclassified drug;amino acid sequence;article;Avian infectious bronchitis virus;comparative study;controlled study;gene sequence;New Zealand;nonhuman;nucleotide sequence;phylogeny;priority journal;sequence analysis;sequence homology;virus neutralization;virus strain,"McFarlane, R.;Verma, R.",2008,,10.1007/s11262-008-0273-6,0
1356,Tracing the origins of louping ill virus by molecular phylogenetic analysis,"The nucleotide and deduced amino acid sequences of louping ill (LI) virus isolates, collected from representative regions of the British Isles and Norway, were determined for either the entire envelope gene (20 isolates) or for a portion of the envelope gene that spans a hypervariable region and includes an LI virus specific marker sequence (53 isolates). Phylogenetic analysis reveals the presence of three major geographical populations of LI virus in the British Isles, viz. Irish, Welsh and British LI viruses, which all cause encephalomyelitis in animals, predominantly sheep, and co-habit the same tick population. British LI virus occurs throughout Scotland, England, Ireland and Norway. Irish and Welsh LI viruses occur only in Ireland and Wales, respectively. Phylogenetic analysis also predicts that LI virus initially emerged in Ireland and that a descendant was introduced into Great Britain via Wales and was subsequently transported to the borders of Scotland, from where it was dispersed throughout Scotland, northern England and Norway. More recently, the British LI virus was reintroduced into Ireland and also into south-west England. Dates of lineage divergence, calculated from the synonymous substitution rate, indicate that LI virus emerged in the British Isles less than 800 years ago and most LI virus dispersal occurred during the last 300 years. By combining these data with historical records it appears that livestock movement can be implicated in the dispersal of LI virus.",amino acid sequence;article;envelope gene;Ireland;nonhuman;Norway;nucleotide sequence;phylogeny;priority journal;sheep;sheep disease;tick;Tick borne encephalitis virus;United Kingdom;viral genetics,"McGuire, K.;Holmes, E. C.;Gao, G. F.;Reid, H. W.;Gould, E. A.",1998,,,0
1357,Type-specific antigenicity of avian reoviruses,"The type-specificity of the neutralizing activity in chicken antiserum to avian reoviruses was affected by the method of antiserum production. The neutralizing activity produced in response to virus infection had higher type-specificity than that produced by immunization with inactivated virus emulsified in adjuvant. By using reassortant viruses the induction of type-specific neutralizing activity was shown to be associated with the sigma C (sigmaC) virion protein. Antigenic classification of virus strains based on immunoprecipitation of the sigmaC protein by chicken antiserum was attempted and the results were similar to those obtained by reciprocal serum neutralization tests. One-way immunoprecipitation of the sigmaC protein by antisera to some heterologous viruses, similar to that reported in reciprocal neutralization tests, made it difficult to assign individual viruses to serogroups and showed that the type-specificity of the sigmaC protein was not absolute. The neutralization activity of monoclonal antibodies to the sigmaC protein of the RAM1 strain of avian reovirus suggested there were separate type- and group-specific antigenic domains on the sigmaC protein, and that the group-specific domains may be associated with the induction of antibody against heterologous viruses.",,"Meanger, J.;Wickramasinghe, R.;Enriquez, C. E.;Robertson, M. D.;Wilcox, G. E.",1995,Mar,,0
1358,Canine distemper virus infection in a lesser grison (Galictis cuja): first report and virus phylogeny,"Megid J., Teixeira C.R., Cortez A., Heinemann M.B., Antunes J.M.A.P., Fornazari F., Rassy F.B. & Richtzenhaim L.J. 2013. Canine distemper virus infection in a lesser grison (Galictis cuja): first report and virus phylogeny. Pesquisa Veterinaria Brasileira 33(2):247-250. Departamento de Higiene Veterinaria e Saude Publica, Faculdade de Medicina Veterinariae Zootecnia, Universidade Estadual Paulista, Distrito de Rubiao Jr s/n, Botucatu, SP 18618-970, Brazil. E-mail: jane@fmvz.unesp.br Infectious diseases in wild animals have been increasing as a result of their habitat alterations and closer contact with domestic animals. Canine distemper virus (CDV) has been reported in several species of wild carnivores, presenting a threat to wildlife conservation. We described the first case of canine distemper virus infection in lesser grison (Galictis cuja). A free-ranging individual, with no visible clinical sigs, presented sudden death after one day in captivity. Molecular diagnosis for CDV infection was performed using whole blood collected by postmortem intracardiac puncture, which resulted positive. The virus phylogeny indicated that domestic dogs were the probable source of infection.",Canine distemper virus;Galictis cuja;Lesser grison;nucleoprotein;phylogeny;ARGENTINA;BRAZIL,"Megid, J.;Teixeira, C. R.;Cortez, A.;Heinemann, M. B.;Antunes, Jmap;Fornazari, F.;Rassy, F. B.;Richtzenhain, L. J.",2013,Feb,,0
1359,Localization of VZV in saliva of zoster patients,"Varicella zoster virus (VZV) in saliva from six herpes zoster patients and one chickenpox patient was found to be exclusively associated with epithelial cells by confocal microscopy. VZV localization with antibody specific to the VZV glycoprotein E was detected primarily on the membrane but was also inside the cell. Epithelial cells with VZV were still present in saliva in one out of two tested zoster patients after 10 months of recovery. Saliva from healthy controls (non-shingles patients, n = 5) did not show any sign of VZV by polymerase chain reaction or by confocal microscopy. No VZV was found in the liquid fraction of saliva. Further work is required to understand the movement of VZV in the saliva cells of infected patients.",glycoprotein E;valaciclovir;adult;aged;article;chickenpox;clinical article;confocal microscopy;controlled study;epithelium cell;female;herpes zoster;human;human cell;male;middle aged;polymerase chain reaction;saliva analysis;Varicella zoster virus;very elderly,"Mehta, S. K.;Nelman-Gonzalez, M.;Tyring, S. K.;Tong, Y.;Beitman, A.;Crucian, B. E.;Renner, A. N.;Pierson, D. L.",2017,,10.1002/jmv.24807,0
1360,"Antibody titer against bovine viral diarrhea virus (BVDV) in bulk milk samplers from Bavaria, Germany","A total of 5204 bulk milk samples were tested for antibodies against bovine viral diarrhea virus (BVDV) classified according to the scheme after Alenius. Fortyfive percent of the samples from 2002 were classified as class 0 and class 1, 55% as class 2 and 3. 6420 bulk milk samples from 1997 were classified in an independent study in 65,6% class 0 and 1 and 34,4% in class 2 and 3. In class 0 and class 1 farms only very rarely persistent viremic animals have been found, whereas in class 2 and 3 their presence is highly likely. Our studies with non-selected sera defined the serological screening of bulk milk samples as a promising tool for a possible BVDV eradication program in Bavaria.",,"Meier, N.;Meier, B.;Banzhaf, K.;Wittkowski, G.;Schmitt, D.;Truyen, U.",2003,,,0
1361,Molecular epidemiological survey and phylogenetic analysis of bovine influenza D virus in Japan,"The influenza D virus, a new member of the Orthomyxoviridae family, is predominantly found in cattle. Although viral pathology and clinical disease in cattle appear mild, this virus plays an important role as a trigger of bovine respiratory disease (BRD). BRD is a costly illness worldwide. Thus, epidemiological surveys of the influenza D virus are necessary. Here, we conducted a molecular epidemiological survey for the influenza D virus in healthy and respiratory-diseased cattle in Japan. We found that 2.1% (8/377) of the cattle were infected with influenza D. The cattle with and without respiratory symptoms had approximately equal amounts of the virus. A full-genome sequence analysis revealed that the influenza D virus that was isolated in Japan formed an individual cluster that was distinct from the strains found in other countries. These results suggest that this virus might have evolved uniquely in Japan over a long period of time and that the viral pathology of Japanese strains might be different from the strains found in other countries. Continuous surveillance is required to determine the importance of this virus and to characterize its evolution.",animal experiment;animal model;article;bootstrapping;bovine model;centrifugation;controlled study;epidemiological monitoring;evolution;evolutionary adaptation;health survey;Human parainfluenza virus 1;Japan;limit of quantitation;molecular biology;next generation sequencing;nonhuman;nose smear;nucleotide sequence;observational study;pathology;phylogenetic tree;quantitative analysis;real time polymerase chain reaction;respiratory tract disease;reverse transcription polymerase chain reaction;RNA extraction;sequence analysis;serology;virus isolation,"Mekata, H.;Yamamoto, M.;Hamabe, S.;Tanaka, H.;Omatsu, T.;Mizutani, T.;Hause, B. M.;Okabayashi, T.",2018,,10.1111/tbed.12765,1
1362,The discovery of the enteroviruses and the classification of poliovirus among them,"The history of the enteroviruses is described, and how poliovirus came to be recognized as the prototype species of the genus, a subdivision of the family Picornaviridae. Albert Sabin was one of the main contributors. He isolated several enterovirus types and established them as causative agents of human disease. The enteroviruses were discovered only after new methods were introduced for working with viruses. They are now recognized as constituting one of the genera of the picornavirus family. Pico-rna-virus stands for viruses which are small (pico), and have an RNA genome. The enterovirus genus includes the polioviruses, the coxsackieviruses and the echoviruses of humans, plus a number of enteroviruses of lower animals (e.g., monkeys, cattle, pigs, mice). Over 100 serotypes are now recognized, the first having been the polioviruses.",bovine;Enterovirus;Enterovirus B;genome;history;human;Haplorhini;mouse;nonhuman;Picornaviridae;Poliomyelitis virus;priority journal;serotype;short survey;pig;virus classification;virus isolation,"Melnick, J. L.",1993,,10.1006/biol.1993.1088,0
1363,Phylogenetic classification and clinical aspects of a new putative Deltapapillomavirus associated with skin lesions in cattle,"Bovine papillomaviruses (BPVs) are recognized as causal agents of benign and malignant tumors in cattle. Thirteen types of BPVs have already been described and classified into 3 distinct genera. Divergences in the nucleotide sequence of the L1 gene are used to identify new viral types through the employment of PCR assays with degenerated primers. In the present study, a method for identifying BPVs based on PCR-RFLP and DNA sequencing allowed the identification of a new putative Deltapapillomavirus, designated JN/3SP (JQ280500.1). The analysis of the L1 gene showed that this strain was most closely related to the BPVs -1, -2, -13, and OaPV1 (71-73% genetic similarity). In this study, we describe the detection of this new putative Deltapapillomavirus type and verify its phylogenetic position within the genus. © FUNPEC-RP.",acanthosis;animal cell;animal experiment;animal tissue;article;Bovine papillomavirus type 1;Bovine papillomavirus type 13;Bovine papillomavirus type 2;bovine;cattle disease;controlled study;cow;Deltapapillomavirus;Deltapapillomavirus (strain JN 3SP);dermis;DNA sequence;epidermal koilocytosis;epidermis;gene;genetic variability;genome analysis;histopathologic skin reaction;histopathology;Human papillomavirus type 16;hyperkeratosis;inflammatory infiltrate;L1 gene;new species;nonhuman;nucleotide sequence;papilloma;Papillomaviridae;papillomatosis;papillomavirus infection;phylogeny;polymerase chain reaction;restriction fragment length polymorphism;sequence homology;skin defect;skin infection;species comparison;species identification;strain identification;virus classification;virus detection;virus genome;virus strain,"Melo, T. C.;Carvalho, R. F.;Mazzucchelli-de-Souza, J.;Diniz, N.;Vasconcelos, S.;Assaf, S. L. M. R.;Araldi, R. P.;Ruiz, R. M.;Kerkis, I.;Beçak, W.;Stocco, R. C.",2014,,10.4238/2014.April.3.18,0
1364,"Whole genome sequencing and biological characterization of Duck/JS/10, a new lentogenic class I Newcastle disease virus","A lentogenic Newcastle disease virus (NDV), Duck/JS/10 (JS10), was isolated from an unvaccinated duck in China. The complete genome of the virus contained 15,198 nucleotides. Based on length of the genome and a partial sequence of the F gene, the virus was classified as a class I genotype 4 NDV. The antigenicity of the virus was compared with that of NDV strain La Sota via hemagglutination inhibition (HI), virus neutralization (VN) assay and animal experiments. Our results show that JS10 generates higher HI and VN titers than La Sota against both class I and II virulent NDV strains. Experiments on animals demonstrate that virus shedding from chickens vaccinated with JS10 is significantly reduced when compared to those vaccinated with La Sota. Overall, this study strongly suggests that JS10 may qualify as a new vaccine candidate against Newcastle disease. © 2012 Springer-Verlag.",virus antibody;viral protein;amino acid sequence;animal;article;bird disease;chemistry;chicken;China;classification;DNA sequence;duck;genetics;immunology;isolation and purification;molecular genetics;Newcastle disease;Newcastle disease virus;phylogeny;sequence alignment;virology;virus genome,"Meng, C.;Qiu, X.;Jin, S.;Yu, S.;Chen, H.;Ding, C.",2012,,10.1007/s00705-012-1248-4,0
1365,Potential of genotype VII Newcastle disease viruses to cause differential infections in chickens and ducks,"Newcastle disease (ND), caused by ND virus (NDV), is one of the most infectious and economically important diseases of the poultry industry worldwide. While infections are reported in a wide range of avian species, the pathogenicity of chicken-origin virulent NDV isolates in ducks remains elusive. In this study, two NDV strains were isolated and biologically and genetically characterized from an outbreak in chickens and apparently healthy ducks. Pathogenicity assessment indices, including the mean death time (MDT), intracerebral pathogenicity index (ICPI) and cleavage motifs in the fusion (F) protein, indicated that both isolates were velogenic in nature. While these isolates carried pathogenic characteristics, interestingly they showed differential pathogenicity in ducks. The chicken-origin isolate caused high (70%) mortality, whereas the duck-origin virus resulted in low (20%) mortality in 4-week-old ducks. Intriguingly, both isolates showed comparable disease pathologies in chickens. Full-genome sequence analysis showed that the virus genome contains 15 192 nucleotides and carried features that are characteristic of velogenic strains of NDV. A phylogenetic analysis revealed that both isolates clustered in class II and genotype VII. However, there were several mutations in the functionally important regions of the fusion (F) and haemagglutinin-neuraminidase (HN) proteins, which may be responsible for the differential pathogenicity of these viruses in ducks. In summary, these results suggest that NDV strains with the same genotype show differential pathogenicity in chickens and ducks. Furthermore, chicken-origin virulent NDVs are more pathogenic for ducks than duck-origin viruses. These findings propose a role for chickens in the evolution of viral pathogenicity and the potential genetic resistance of ducks to poultry viruses.",fibrin;hemagglutinin;virus RNA;virus sialidase;amino acid sequence;amnion fluid;animal experiment;animal tissue;article;cell infiltration;chicken;controlled study;duck;enteritis;gene mutation;gene sequence;genetic analysis;genotype;histopathology;ID50 (median infectious dose);lymphocyte depletion;lymphocytic infiltration;necrosis;Newcastle disease;Newcastle disease virus;nonhuman;nucleotide sequence;pathogenicity;phylogenetic tree;phylogeny;polymerase chain reaction;reverse transcription polymerase chain reaction;RNA extraction;sequence analysis;survival rate;virogenesis;virus hemagglutination;virus isolation;virus load;virus virulence,"Meng, C.;Rehman, Z. U.;Liu, K.;Qiu, X.;Tan, L.;Sun, Y.;Liao, Y.;Song, C.;Yu, S.;Ding, Z.;Nair, V.;Munir, M.;Ding, C.",2018,,10.1111/tbed.12965,0
1366,"Virome analysis of tick-borne viruses in Heilongjiang Province, China","Ticks are implicated in the transmission of various human and livestock pathogens worldwide. This study aimed to understand the geographical distribution of tick species, along with tick-associated viruses, in Heilongjiang Province, northeast China. Molecular methods were used to classify tick species, with next-generation sequencing and polymerase chain reaction-based analyses used to assess the viromes of ticks from four representative sampling locations in the Greater Khingan Mountains. Five species of ixodid ticks were identified, including Ixodes persulcatus, Dermacentor nuttalli, Dermacentor silvarum, Haemaphysalis longicornis, and Haemaphysalis concinna. From the 1102 ticks, 3,568,561 high-quality reads were obtained by next-generation sequencing. Following trimming, 302,540 reads were obtained, of which 6577 (2.16%) reads were annotated to viruses. Phylogenetic analysis revealed that the viral sequences shared a close relationship with Orthonairovirus, Phlebovirus, deer tick Mononegavirales-like virus, and Jingmen tick virus sequences, but the significance of these newly-identified tick-borne viruses to human and animal health requires further investigation. The results of this study provide a basis not only for further studies on the relationship between ticks and tick-borne viruses, but also for preventing future tick-borne epidemic outbreaks by means of vector control.",article;China;Dermacentor nuttalli;Dermacentor silvarum;epidemic;geographic distribution;geography;Haemaphysalis concinna;Haemaphysalis longicornis;human;Ixodes persulcatus;Ixodidae;Jingmenvirus;Mononegavirales;next generation sequencing;nonhuman;Orthonairovirus;Phlebovirus;phylogeny;polymerase chain reaction;priority journal;RNA virus;species distribution;tick;tick borne disease;vector control;virulence,"Meng, F.;Ding, M.;Tan, Z.;Zhao, Z.;Xu, L.;Wu, J.;He, B.;Tu, C.",2019,,10.1016/j.ttbdis.2018.12.002,0
1367,A deep sequencing reveals significant diversity among dominant variants and evolutionary dynamics of avian leukosis viruses in two infectious ecosystems,"BACKGROUND: As a typical retrovirus, the evolution of Avian leukosis virus subgroup J (ALV-J) in different infectious ecosystems is not characterized, what we know is there are a cloud of diverse variants, namely quasispecies with considerable genetic diversity. This study is to explore the selection of infectious ecosystems on dominant variants and their evolutionary dynamics of ALV-J between DF1 cells and specific-pathogen-free (SPF) chickens. High-throughput sequencing platforms provide an approach for detecting quasispecies diversity more fully. RESULTS: An average of about 20,000 valid reads were obtained from two variable regions of gp85 gene and LTR-U3 region from each sample in different infectious ecosystems. The top 10 dominant variants among ALV-J from chicken plasmas, DF1 cells and liver tumor were completely different from each other. Also there was a difference of shannon entropy and global selection pressure values (ω) in different infectious ecosystems. In the plasmas of two chickens, a large portion of quasispecies contained a 3-peptides ""LSD"" repeat insertion that was only less than 0.01% in DF1 cell culture supernatants. In parallel studies, the LTR-U3 region of ALV-J from the chicken plasmas demonstrated more variants with mutations in their transcription regulatory elements than those from DF1 cells. CONCLUSIONS: Our data taken together suggest that the molecular epidemiology based on isolated ALV-J in cell culture may not represent the true evolution of virus in chicken flocks in the field. The biological significance of the ""LSD"" insert and mutations in LTR-U3 needs to be further studied.",animal;avian leukosis;Avian leukosis virus;bird disease;cell line;chicken;ecosystem;evolution;genetic variation;genetics;germfree animal;molecular epidemiology;mutation;virology,"Meng, F.;Dong, X.;Hu, T.;Chang, S.;Fan, J.;Zhao, P.;Cui, Z.",2016,,,0
1368,Analysis of Quasispecies of Avain Leukosis Virus Subgroup J Using Sanger and High-throughput Sequencing,"BACKGROUND: Avian leukosis viruses subgroup J (ALV-J) exists as a complex mixture of different, but closely related genomes named quasispecies subjected to continuous change according to the Principles of Darwinian evolution. METHOD: The present study seeks to compare conventional Sanger sequencing with deep sequencing using MiSeq platform to study quasispecies dynamics of ALV-J. RESULTS: The accuracy and reproducibility of MiSeq sequencing was determined better than Sanger sequencing by running each experiment in duplicate. According to the mutational rate of single position and the ability to distinguish dominant quasispecies with two sequencing methods, conventional Sanger sequencing technique displayed high randomness due to few sequencing samples, while deep sequencing could reflect the composition of the quasispecies more accurately. In the mean time, the research of quasispecies via Sanger sequencing was simulated and analyzed with the aid of re-sampling strategy with replacement for 1000 times repeat from high-throughput sequencing data, which indicated that the higher antibody titer, the higher sequence entropy, the harder analyzing with the conventional Sanger sequencing, resulted in lower ratios of dominant variants. CONCLUSIONS: In sum, deep sequencing is better suited for detecting rare variants comprehensively. The simulation of Sanger sequencing that we propose here will also help to standardize quasispecies researching under different selection pressure based on next-generation sequencing data.",Amino Acid Sequence;Animals;*Avian Leukosis/vi [Virology];Avian Leukosis Virus/cl [Classification];Avian Leukosis Virus/ge [Genetics];*Avian Leukosis Virus/ip [Isolation & Purification];Chickens;Genetic Variation;High-Throughput Nucleotide Sequencing/is [Instrumentation];*High-Throughput Nucleotide Sequencing/mt [Methods];Molecular Sequence Data;Mutation;Phylogeny;*Poultry Diseases/vi [Virology],"Meng, F.;Dong, X.;Hu, T.;Liu, Y.;Zhao, Y.;Lv, Y.;Chang, S.;Zhao, P.;Cui, Z.",2016,06 27,,0
1369,Characterization of subgroup J avian Leukosis virus isolated from Chinese indigenous chickens,"Background: In spite of the purification of the laying hens and broilers of avian leukosis virus (ALV) has made remarkable achievements, the infection of ALV was still serious in Chinese indigenous chickens. Methods: In order to assess the epidemic state of avian leukosis virus in indigenous chickens in China, 10 novel strains of ALV subgroup J (ALV-J), named JS16JH01 to JS16JH10, were isolated and identified by virus isolation and immunofluorescence antibody assays from a Chinese local breed farm with a sporadic incidence of tumors. To understand their virological characteristics further, the proviral genome of ENV-LTR was sequenced and compared with the reference strains. Results: The homology of the gp85 gene between the ten ALV-J strains and NX0101 was in the range from 89.7-94.8% at the nuclear acid level. In addition, their gp85 genes were quite varied, with identities of 92-98% with themselves at the nuclear acid level. There were several snp and indel sites in the amino acid sequence of gp85 genes after comparison with other reference strains of ALV. Interestingly, a novel insertion in the gp85 region was found in two strains, JS16JH01 and JS16JH07, compared with NX0101 and HPRS-103. Discussion: At present, owing to the large-scale purification of ALV in China, laying hens and broiler chickens with ALV infection are rarely detected, but ALVs are still frequently detected in the local chickens, which suggests that more efforts should be applied to the purification of ALV from indigenous chickens.",nucleic acid;amino acid sequence;animal cell;animal tissue;article;avian leukosis;Avian leukosis virus;biodiversity;cancer incidence;chicken;Chinese;comparative study;controlled study;epidemic;gene insertion;gene sequence;genetic variability;gp85 gene;immunofluorescence test;native species;nonhuman;sequence analysis;sequence homology;virus characterization;virus classification;virus gene;virus genome;virus identification;virus isolation;virus purification;virus strain,"Meng, F.;Li, Q.;Zhang, Y.;Zhang, Z.;Tian, S.;Cui, Z.;Chang, S.;Zhao, P.",2018,,10.1186/s12985-018-0947-1,0
1370,"[Isolation and identification of arboviruses from mosquito pools in some regions of Liaoning province, China]","To isolate and identify arboviruses from mosquito pools in some regions of Liaoning province. Mosquitoes were collected from Shenyang, Yingkou, Panjin, Jinzhou and Dandong cities of Liaoning province in 2006. Viruses were isolated by inoculating the specimens onto C6/ 36 and BHK-21cells. The new isolates were identified using serological and molecular biological methods. 5410 mosquitoes were collected from the five cities in total. Three isolates produced CPE in C6/ 36 cell and five isolates produced CPE in both C6/36 and BHK-21 cell. Three isolates (LN0684, LN0688 and LN0689) were identified as Banna virus and one isolate (LN0636) was identified as Getah virus. Phylogenetic analysis showed that the three Banna virus strains were clustered into the same evolution branch as the other Chinese isolates. The identity of nucleotide sequence was between 91.2% and 94.7%, compared with other Banna virus strains. The new isolated Getah virus was clustered into the same branch with the strain of South Korea (swine). The identity of nucleotide sequence was 99.2%, when comparing with the strain of South Korea and was 95% to 99% with the strains from Russia, mainland of China and Taiwan region. Conclusion Eight virus isolates, including three Banna virus, one Getah virus and four unknown virus strains were isolated from mosquitoes in Liaoning province. Banna virus and Getah virus were reported for the first time in Liaoning province, while Getah virus showed the highest nucleotide homology with the South Korea strains.",virus RNA;Alphavirus;animal;Arbovirus;article;cell line;China;classification;Coltivirus;DNA sequence;genetics;isolation and purification;mosquito;phylogeny;sequence analysis;virology,"Meng, W. S.;Zhang, J. B.;Sun, X. H.;Liu, Q. N.;Chen, Z.;Zhai, Y. G.;Fu, S. H.;Cao, Y. X.;Wang, H. Y.;Ding, J.;Chu, F. J.;Li, Z.;Zhang, L. T.;Zhao, Y. J.;Liang, G. D.",2009,,,0
1371,Swine hepatitis E virus: Cross-species infection and risk in xenotransplantation,"Swine hepatitis E Virus (swine HEV), a ubiquitous agent recently discovered in pigs, is antigenically and genetically closely related to the human HEV. Swine HEV infection in pigs generally occurs at about 2-3 months of age, and about 80%-100% of the pigs in commercial farms in the USA were infected. Swine HEV infections have now been recognized in pigs in many other countries of the world. Interspecies transmission has been documented, as swine HEV infects nonhuman primates and some strains of human HEV infect pigs. Recent seroepidemiological studies showed that swine veterinarians and other pig handlers are at higher risk of HEV infection compared to normal blood donors. In addition, novel strains of human HEV recovered from hepatitis patients in the USA, Japan and Taiwan are genetically more closely related to strains of swine HEV from respective countries than to other strains of human HEV. The ubiquitous nature of the virus in pigs and the demonstrated ability of cross-species infection raise a potential concern for swine HEV infection in xenotransplantation with pig organs. This chapter discusses the recent advances in HEV research with emphases on potential zoonosis and xenozoonosis.",antibody titer;antigenicity;gene identification;genetic heterogeneity;genome analysis;genotype;hepatitis E;Hepatitis E virus;high risk population;human;infection risk;Japan;nonhuman;nucleotide sequence;organ donor;pathophysiology;phylogeny;priority journal;protein domain;review;risk assessment;sequence analysis;sequence homology;serodiagnosis;seroprevalence;species difference;strain difference;swine disease;Taiwan;United States;veterinary medicine;virus classification;virus detection;virus replication;virus strain;virus transmission;xenotransplantation;zoonosis,"Meng, X. J.",2003,,,0
1372,Molecular cloning and nucleotide sequencing of the 3'-terminal genomic RNA of the porcine reproductive and respiratory syndrome virus,"The genomic RNA of a porcine reproductive and respiratory syndrome virus (PRRSV) isolate from the U.S.A., VR 2385 (ATCC), was copied into cDNA after priming with oligo(dT) and cloned into phage lambda. The cDNA clones representing the 3'-terminal genomic RNA of the virus were isolated and sequenced. The genome is a positive-stranded, polyadenylated RNA with an estimated size of 15 kb. Analysis of the resulting sequence identified three complete open reading frames (ORFs) with the potential to encode polypeptides with predicted M(r)s of 22.2K (ORF 5), 19.1K (ORF 6) and 13.6K (ORF 7). ORF 7, which is closest to the 3' end, is predicted to encode a highly basic nucleocapsid protein displaying 58% amino acid identity to the corresponding protein of the Lelystad virus (LV), a European PRRSV isolate. ORFs 6 and 5, preceding ORF 7, are each predicted to encode proteins containing several hydrophobic domains that are thought to be membrane-associated. The VR 2385 ORF 6 protein is the most conserved structural protein. It has 78% amino acid identity to the equivalent LV protein, and ORF 5 shares only 54% of its amino acid sequence. Northern blot analysis revealed a 3'-coterminal nested set of six subgenomic RNAs in VR 2385 virus-infected CRL 11171 cells. Our results indicate that VR 2385, like LV, is a member of the newly proposed arterivirus group. However, the striking genetic variation and the difference in pathogenicity between LV and VR 2385 suggest that the viruses causing PRRS in the U.S.A. and Europe are highly variable and they may represent different genotypes.",complementary DNA;virus RNA;amino acid sequence;animal tissue;article;Enterobacteria phage lambda;controlled study;gene structure;molecular cloning;nonhuman;Northern blotting;nucleotide sequence;open reading frame;priority journal;RNA virus;sequence homology;swine disease;virus classification;virus genome;virus infection;virus nucleocapsid,"Meng, X. J.;Paul, P. S.;Halbur, P. G.",1994,,,0
1373,Sequence comparison of open reading frames 2 to 5 of low and high virulence United States isolates of porcine reproductive and respiratory syndrome virus,"The sequences of ORFs 2 to 5 of five United States (US) porcine reproductive and respiratory syndrome virus (PRRSV) isolates with differing virulence were determined. The nucleotide and deduced amino acid sequences of these isolates were compared with those of other known PRRSV isolates. The amino acid sequence identity between seven US PRRSV isolates was 91-99% in ORF 2, 86-98% in ORF 3, 92-99% in ORF 4 and 88-97% in ORF 5. The low virulence US isolate had highest sequence variation in ORFs 2 to 4 compared to the other US isolates. A hypervariable region with antigenic potential was identified within the major envelope glycoprotein. Phylogenetic analysis of ORFs 2 to 7 indicated the existence of at least three minor genotypes within the major US genotype. The low virulence US isolate formed a branch distinct from the other US isolates. The results of this study have implications for both the taxonomy of PRRSV and vaccine development.",envelope protein;virus glycoprotein;amino acid sequence;animal cell;Arterivirus;article;genotype;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;sequence homology;pig;United States;virus classification;virus genome;virus virulence,"Meng, X. J.;Paul, P. S.;Halbur, P. G.;Morozov, I.",1995,,,0
1374,Oncorna like virus particles in the cochlear spiral ganglion of guinea pigs,"Virus particles in spiral ganglion cells of the guinea pig are mostly grouped with the herpes viruses. The purpose of this study was to evaluate this classification of the viruses and their influence on cell morphology. Healthy, adult guinea pigs were studied. The spiral ganglion was serially sectioned and examined electron microscopically. All spiral ganglia examined of several guinea pig populations from different breeds showed intracytoplasmic viruses in some granular spiral ganglion cells. According to their localization and morphology these viruses are classified with the oncorna virus group, which is not in agreement with the classification of other authors. Apparently there is a world-wide latent viral infection in guinea pigs. The accumulation of lysosomal-like vacuoles in The vicinity of the virus indicates an increased local lysosomal activity of the infected ganglion cells. Considering the otherwise normal ultrastructure of the infected cells an additional influence of these viruses on the intracellular metabolism can neither be demonstrated nor denied.",cell inclusion;cell metabolism;cell vacuole;electron microscopy;experimental animal;guinea pig;inner ear;latent virus infection;methodology;microorganism;nerve cell;Orthoretrovirinae;spiral ganglion;theoretical study,"Merck, W.;Kistler, G. S.;Riede, U. N.",1977,,,0
1375,"Characterization of Newcastle disease viruses isolated from chicken, gamefowl, pigeon and quail in Mexico","Velogenic Newcastle disease has threatened the Mexican poultry industry since 1946. Seven strains of velogenic Newcastle disease virus were isolated from poultry and other avian species in central and northern Mexico from 1998 to 2006 and subjected to phylogenetic analysis and biological characterization using standard pathogenicity tests and challenge studies. Phylogenetic analysis showed that all velogenic strains belonged to genetic group V and are clearly divided in two lineages, since phylogenetic similarities between groups are of only 93-94%. Isolates from 1998 to 2001 are closely related to the strain responsible for the 2000 year outbreak raised in La Laguna region (Torreon strain), and are phylogenetically distinct from viruses isolated between 2004 and 2006 that are genetically related to the Chimalhuacan strain isolated in 1973. All the viruses of both, the Chimalhuacan and the Torreon groups, contained a virulent fusion protein cleavage site represented by the motif ""GGRRQKRF"", revealing that evolutionary changes occurred at a different site. Chicken embryo mean death time value was shorter for the Chimalhuacan-like viruses (43.9 hours), when compared with the 1998-2001 average (54.3 hours). ICPI average value was higher (1.92) for viruses isolated during 2004-2006 than that for viruses isolated before 2001 (1.74). Microscopic evaluation of bursa of Fabricius and thymus of 5w-o broiler chickens challenged with 106 LD50/0.2 ml showed that Chimalhuacan-like isolate caused more severe lesions at 48 hpi in bursa and 72 and 96 hpi in thymus than Torreon-like isolate. Along with the MDT, ICPI and microscopic results, our findings suggest that some distinct selective pressure on the very virulent Chimalhuacan strain isolated in early 1970's may have led to the appearance of the still velogenic but less virulent new group (Torreon-like) in the middle of 1990's. © 2009 Springer Science+Business Media B.V.",article;bursa Fabricii;chicken;embryo;Mexico;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;Columbidae;protein cleavage;protein motif;quail;thymus;virus characterization;virus identification;virus isolation;virus strain;virus virulence,"Merino, R.;Villegas, H.;Quintana, J. A.;Calderon, N.",2009,,10.1007/s11259-009-9321-5,0
1376,Evaluation of phenotypic markers in full genome sequences of avian influenza isolates from California,"We evaluated phenotypic markers in full-genome sequences of avian influenza isolates to identify avian strains with increased potential for transmission and pathogenicity in mammals. Of 149 markers examined, 67 were positive in the consensus sequences from 206 avian isolates. Analysis of deep sequencing data in a subset of 24 isolates revealed that 344 subpopulations occurred at marker positions. Markers in subpopulations were significantly more likely to be negative (258/344) than positive (86/344), but nearly all of the marker-positive subpopulations (78/86) were associated with marker-negative consensus sequences. Our analysis revealed significant variation in important markers among avian isolates, and showed that consensus sequences do not fully convey an isolate's potential for increased transmissibility and pathogenicity in mammals.","Amino Acid Sequence;Animals;Birds;California;Genetic Markers;Genetic Variation;*Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];High-Throughput Nucleotide Sequencing;*Influenza A Virus, H1N1 Subtype/ge [Genetics];Influenza A Virus, H1N1 Subtype/ip [Isolation & Purification];*Influenza A Virus, H5N1 Subtype/ge [Genetics];Influenza A Virus, H5N1 Subtype/ip [Isolation & Purification];*Influenza in Birds/ge [Genetics];Influenza in Birds/tm [Transmission];Molecular Sequence Data;Sequence Analysis, RNA;0 (Genetic Markers);0 (Hemagglutinin Glycoproteins, Influenza Virus)","Mertens, E.;Dugan, V. G.;Stockwell, T. B.;Lindsay, L. L.;Plancarte, M.;Boyce, W. M.",2013,Sep,,0
1377,"The First ""Virus Hunters""","The history of virology is a history of conceptual and technological inventions and breakthroughs. The development of filters made of porcelain or kieselgur by the end of the 19th century which withheld bacteria allowed the identification of infectious agents smaller than bacteria and noncultivable on the media known at that time and used to grow bacteria. Even finer-grain filters resulted in the observation that the ultravisible novel infectious agents are in fact of particulate nature. Infections of plants and animals were the first to be attributed to these tiny entities. Proof resulted from experimental infection of the natural hosts (including humans). Thus, of the first 30 viruses identified, 20 are veterinary viruses, i.e. infectious agents of poultry and livestock. The discovery that bacteria also have viruses in the 1910s expanded the viral universe which continues today. Filterability and ultravisibility remained a hallmark for the identification of viruses until the advent of the electron microscope in the late 1930s marking another technological breakthrough in virology. Cell culture techniques allowed virus propagation outside the infected organism. In the past decades, the advent and development of molecular biology has brought more innovations culminating in the rapid and accurate determination of genomic material of a variety of living beings including viruses in a hitherto unknown speed and depth using next-generation sequencing and metagenomic analyses. Thus, it is no surprise that new viruses are detected constantly including specimens of unprecedented size and shape. Virologists agree that the viral universe is immense, and only a small fraction has been explored yet.",animal;bacterium;electron microscopy;history;isolation and purification;molecular biology;plant;procedures;virology;virus;virus culture,"Mettenleiter, T. C.",2017,,10.1016/bs.aivir.2017.07.005,0
1378,Inter-species transmission of the influenza virus,"Influenza is an infection of human beings and several animal species. It is caused by influenza viruses which belong to the Orthomyxoviridae family. Type A influenza viruses are the most important as they cause severe epidemics and are responsible of important pathological troubles. Type A influenza viruses are classified in different sub-types depending of the nature of their surface glycoproteins: haemagglutinin (H) and neuraminidase (N). The nature of the genome and the mode of replication of influenza viruses account for the high variability of these two proteins which are responsible for the immunity to the virus. The continuous appearance of point mutations in the gene coding for the H protein, leads to the progressive emergence of new viral strains. This event which is called antigenic drift makes it necessary to annually assess the composition of the human flue vaccine. Genetic reassortment is another mechanism of antigenic variation. When the gene coding for the H protein, or when both genes coding for H and N proteins are involved in genetic reassortment, a new viral sub-type occurs which replace the precedent. This event, which is termed antigenic shift, occurs occasionally every 10 to 30 years, and it is responsible of the great human pandemics. The role of the animals and particularly the importance of pigs and poultry in the emergence of these new viruses is discussed.",hemagglutinin;membrane antigen;sialidase;virus antigen;animal;antigenic variation;article;classification;disease transmission;epidemic;genetics;human;immunology;influenza;Influenza A virus;mutation;poultry;pig;virus capsid;virus genome;virus replication;zoonosis,"Meulemans, G.",1999,,,0
1379,Isolation of orthoreoviruses from psittacine birds,"Orthoreoviridae were regularly isolated from imported psittacine birds in the absence of other pathogens or in combination with salmonella. These viruses grew in embryonated eggs, in chicken embryo fibroblasts and in hepatic cell cultures. The viral isolates were classified as orthoreoviridae on the basis of their morphological and physico-chemical properties.","Animals;Chick Embryo;Cytopathogenic Effect, Viral;Liver/mi [Microbiology];Lung/mi [Microbiology];Microscopy, Electron;*Psittaciformes/mi [Microbiology];*Reoviridae/ip [Isolation & Purification];Reoviridae/ul [Ultrastructure]","Meulemans, G.;Dekegel, D.;Charlier, G.;Froyman, R.;Van Tilburg, J.;Halen, P.",1983,Jan,,0
1380,Characterization of proteins encoded by ORFs 2 to 7 of Lelystad virus,"The genome of Lelystad virus (LV), a positive-strand RNA virus, is 15 kb in length and contains 8 open reading frames (ORFs) that encode putative viral proteins. ORFs 2 to 7 were cloned in plasmids downstream of the Sp6 RNA polymerase promoter, and the translation of transcripts generated in vitro yielded proteins that could be immunoprecipitated with porcine anti-LV serum. Synthetic polypeptides of 15 to 17 amino acids were selected from the amino acid sequences of ORFs 2 to 7 and antipeptide sera were raised in rabbits. Antisera that immunoprecipitated the in vitro translation products of ORFs 2 to 5 and 7 were obtained. Sera containing antibodies directed against peptides from ORFs 3 to 7 reacted positively with LV-infected alveolar lung macrophages in the immunoperoxidase monolayer assay. Using these antipeptide sera and porcine anti-LV serum, we identified three structural proteins and assigned their corresponding genes. Virions were found to contain a nucleocapsid protein of 15 kDa (N), an unglycosylated membrane protein of 18 kDa (M), and a glycosylated membrane protein of 25 kDa (E). The N protein is encoded by ORF7, the M protein is encoded by ORF6, and the E protein is encoded by ORF5. The E protein in virus particles contains one or two N-glycans that are resistant to endo-β-N-acetyl-D-glucosaminidase H. This finding indicates that the high-mannose glycans are processed into complex glycans in the Golgi compartment. The protein composition of the LV virions further confirms that LV is evolutionarily related to equine arteritis virus, simian hemorrhagic fever virus, and lactate dehydrogenase-elevating virus.",article;controlled study;evolution;lelystad virus;nonhuman;open reading frame;priority journal;protein analysis;RNA virus;virion;virus classification,"Meulenberg, J. J. M.;Besten, A. P. D.;De Kluyver, E. P.;Moormann, R. J. M.;Schaaper, W. M. M.;Wensvoort, G.",1995,,10.1016/s0042-6822(95)80030-1,0
1381,Characterization of orthopoxviruses isolated from man and animals in Germany,"Fourteen orthopoxvirus strains isolated from humans, cats, a dog, a cow, and an elephant in Germany were characterized. All were classified as cowpox virus based on haemorrhagic lesions induced on the chorioallantoic membrane of chicken eggs and reactivity of a 160 kDa protein with anti-A-type inclusion protein hyperimmun serum in a Western blot. More detailed comparison of the isolates by restriction endonuclease mapping using HindIII and XhoI demonstrated a close relationship between all isolates and confirmed them as cowpox viruses. However, some minor differences between the isolates were detected which proved to be of epidemiological value. One group consisting of five closely related isolates contained a unique 4.0 kb HindIII fragment. In a Southern blot this fragment failed to hybridize with other cowpox virus isolates including the reference strain.",,"Meyer, H.;Schay, C.;Mahnel, H.;Pfeffer, M.",1999,,10.1007/s007050050520,0
1382,Comprehensive Phylogenetic Reconstructions of African Swine Fever Virus: Proposal for a New Classification and Molecular Dating of the Virus,"African swine fever (ASF) is a highly lethal disease of domestic pigs caused by the only known DNA arbovirus. It was first described in Kenya in 1921 and since then many isolates have been collected worldwide. However, although several phylogenetic studies have been carried out to understand the relationships between the isolates, no molecular dating analyses have been achieved so far. In this paper, comprehensive phylogenetic reconstructions were made using newly generated, publicly available sequences of hundreds of ASFV isolates from the past 70 years. Analyses focused on B646L, CP204L, and E183L genes from 356, 251, and 123 isolates, respectively. Phylogenetic analyses were achieved using maximum likelihood and Bayesian coalescence methods. A new lineage-based nomenclature is proposed to designate 35 different clusters. In addition, dating of ASFV origin was carried out from the molecular data sets. To avoid bias, diversity due to positive selection or recombination events was neutralized. The molecular clock analyses revealed that ASFV strains currently circulating have evolved over 300 years, with a time to the most recent common ancestor (TMRCA) in the early 18th century. © 2013 Michaud et al.",African swine fever virus;article;B646L gene;Bayes theorem;CP204L gene;E183L gene;gene sequence;genetic variability;maximum likelihood method;molecular clock;molecular evolution;phylogenetic tree construction method;phylogeny;virus classification;virus gene;virus nomenclature,"Michaud, V.;Randriamparany, T.;Albina, E.",2013,,10.1371/journal.pone.0069662,0
1383,Henipaviruses in their natural animal hosts,"Hendra virus (HeV) and Nipah virus (NiV) form a separate genus Henipavirus within the family Paramyxoviridae, and are classified as biosafety level 4 pathogens due to their high case fatality rate following human infection and because of the lack of effective vaccines or therapy. Both viruses emerged from their natural reservoir during the last decade of the twentieth century, causing severe disease in humans, horses and swine, and infecting a number of other mammalian species. The current review summarizes our up to date understanding of pathology and pathogenesis in the natural reservoir species, the Pteropus bat, and in the equine and porcine spill over species. © 2012 Springer-Verlag Berlin Heidelberg.",article;bat;clinical feature;disease carrier;disease course;disease severity;experimental infection;fatality;Hendra virus;Henipavirus;horse;host;immune response;mammal;Nipah virus;nonhuman;Paramyxoviridae;pathogenesis;priority journal;pig;virus cell interaction;virus classification;virus isolation;virus pathogenesis,"Middleton, D. J.;Weingartl, H. M.",2012,,10.1007/82-2012-210,0
1384,Rotavirus vaccines: An overview,"Rotavirus vaccine development has focused on the delivery of live attenuated rotavirus strains by the oral route. The initial 'Jennerian' approach involving bovine (RIT4237, WC3) or rhesus (RRV) rotavirus vaccine candidates showed that these vaccines were safe, well tolerated, and immunogenic but induced highly variable rates of protection against rotavirus diarrhea. The goal of a rotavirus vaccine is to prevent severe illness that can lead to dehydration in infants and young children in both developed and developing countries. These studies led to the concept that a multivalent vaccine that represented each of the four epidemiologically important VP7 serotypes might be necessary to induce protection in young infants, the target population for vaccination. Human-animal rotavirus reassortants whose gene encoding VP7 was derived from their human rotavirus parent but whose remaining genes were derived from the animal rotavirus parent were developed as vaccine candidates. The greatest experience with a multivalent vaccine to date has been gained with the quadrivalent preparation containing RRV (VP7 serotype 3) and human-RRV reassortants of VP7 serotype 1, 2, and 4 specificity. Preliminary efficacy trial results in the United States have been promising whereas a study in Peru has shown only limited protection. Human-bovine reassortant vaccines, including a candidate that contains the VP4 gene of a human rotavirus (VP4 serotype 1A), are also being studied.",Rotavirus vaccine;human;immunogenicity;nonhuman;review;Rotavirus;virus classification;virus immunity;virus infection;virus morphology,"Midthun, K.;Kapikian, A. Z.",1996,,,0
1385,The fecal virome of domesticated animals,"Next-generation sequencing is a new research tool in our hands helping us to explore still unknown fields of human and veterinary virology. Metagenomic analysis has enabled the discovery of putative novel pathogens and the identification of the etiologic agents of several diseases, solving long-standing mysteries caused by divergent viruses. This approach has been used in several studies investigating fecal samples of livestock, and companion animal species, providing information on the diversity of animal fecal virome, helping the elucidation of the etiology of diarrheal disease in animals and identifying potential zoonotic and emerging viruses.",article;Astroviridae;Avian orthoreovirus;Bocaparvovirus;Bornavirus;Canine parvovirus;Circovirus;Coronaviridae;dog;domestic animal;enteritis;Enterovirus;fecal virome;feces culture;feces microflora;Mustela putorius furo;Herpesviridae;horse;Kobuvirus;livestock;metagenomics;Myoviridae;next generation sequencing;nonhuman;Orthopoxvirus;parrot;Parvoviridae;Picornaviridae;pig;Podoviridae;Poxviridae;Leporidae;Rotavirus;Rotavirus A;Rotavirus C;Sapelovirus;Sapovirus;Siphoviridae;Teschovirus;turkey (bird);virus;virus detection,"Mihalov-Kovács, E.;Fehér, E.;Martella, V.;Bányai, K.;Farkas, S. L.",2014,,10.1007/s13337-014-0192-1,0
1386,Nyamanini and midway viruses define a novel taxon of RNA viruses in the order Mononegavirales,"Here, we report the sequencing and classification of Nyamanini virus (NYMV) and Midway virus (MIDWV), two antigenically related viruses that were first isolated in 1957 and 1966, respectively. Although these viruses have been cultured multiple times from cattle egrets, seabirds, and their ticks, efforts to classify them taxonomically using conventional serological and electron microscopic approaches have failed completely. We used a random shotgun sequencing strategy to define the genomes of NYMV and MIDWV. Contigs of 11,631 and 11,752 nucleotides, representing the complete genome of NYMV and the near-complete genome of MIDWV, respectively, were assembled. Each virus genome was predicted to carry six open reading frames (ORFs). BLAST analysis indicated that only two of the ORF proteins of each virus, the putative nucleocapsid and polymerase, had detectable sequence similarity to known viral proteins. Phylogenetic analysis of these ORF proteins demonstrated that the closest relatives of NYNV and MIDWV are negative-stranded-RNA viruses in the order Mononegavirales. On the basis of their very limited sequence similarity to known viruses, we propose that NYMV and MIDWV define a novel genus, Nyavirus, in this order. Copyright © 2009, American Society for Microbiology. All Rights Reserved.",DNA directed DNA polymerase alpha;nucleocapsid protein;animal cell;article;bovine;cell culture;controlled study;electron microscopy;Midway virus;Mononegavirales;nonhuman;Nyamanini virus;open reading frame;priority journal;RNA sequence;RNA virus;seabird;serology;taxon;tick;virus genome;virus isolation,"Mihindukulasuriya, K. A.;Nguyen, N. L.;Wu, G.;Huang, H. V.;Travassos Da Rosa, A. P. A.;Popov, V. L.;Tesh, R. B.;Wang, D.",2009,,10.1128/jvi.02667-08,0
1387,A first look at the Oxford Nanopore MinION sequencer,"Oxford Nanopore's third-generation single-molecule sequencing platform promises to decrease costs for reagents and instrumentation. After a 2-year hiatus following the initial announcement, the first devices have been released as part of an early access program. We explore the performance of this platform by resequencing the lambda phage genome, and amplicons from a snake venom gland transcriptome. Although the handheld MinION sequencer can generate more than 150 megabases of raw data in one run, at most a quarter of the resulting reads map to the reference, with less than average 10% identity. Much of the sequence consists of insertion/deletion errors, or is seemingly without similarity to the template. Using the lambda phage data as an example, although the reads are long, averaging 5 kb, at best 890 ± 1932 bases per mapped read could be matched to the reference without soft clipping. In the course of a 36 h run on the MinION, it was possible to resequence the 48 kb lambda phage reference at 16× coverage. Currently, substantially larger projects would not be feasible using the MinION. Without increases in accuracy, which would be required for applications such as genome scaffolding and phasing, the current utility of the MinION appears limited. Library preparation requires access to a molecular laboratory, and is of similar complexity and cost to that of other next-generation sequencing platforms. The MinION is an exciting step in a new direction for single-molecule sequencing, though it will require dramatic decreases in error rates before it lives up to its promise.",transcriptome;virus DNA;animal;chemistry;devices;DNA sequence;Enterobacteria phage lambda;evaluation study;exocrine gland;genetics;high throughput sequencing;procedures;snake,"Mikheyev, A. S.;Tin, M. M.",2014,,10.1111/1755-0998.12324,0
1388,Vaccine immune pressure influences viral population complexity of avian influenza virus during infection,"Vaccines are useful tools to control influenza A virus infection in poultry, but they need to be periodically reformulated to guarantee appropriate protection from infection and to limit viral replication and circulation, which could favour the emergence of new variants. In this study, a deep sequencing approach was used to characterize and follow the evolution of the hemagglutinin of the H5N1 highly pathogenic avian influenza viral population in infected animals vaccinated with two vaccines conferring different protection levels.","Animals;Genetic Variation;*Hemagglutinins/ge [Genetics];High-Throughput Nucleotide Sequencing/ve [Veterinary];*Influenza A Virus, H5N1 Subtype/ge [Genetics];Influenza A Virus, H5N1 Subtype/im [Immunology];Influenza A Virus, H5N1 Subtype/ip [Isolation & Purification];*Influenza Vaccines/im [Immunology];*Influenza in Birds/vi [Virology];Poultry;*Poultry Diseases/vi [Virology];*Vaccination/ve [Veterinary];0 (Hemagglutinins);0 (Influenza Vaccines)","Milani, A.;Fusaro, A.;Bonfante, F.;Zamperin, G.;Salviato, A.;Mancin, M.;Mastrorilli, E.;Hughes, J.;Hussein, H. A.;Hassan, M.;Mundt, E.;Terregino, C.;Cattoli, G.;Monne, I.",2017,May,,0
1389,Differential interactions among isolates of peanut stunt cucumovirus and its satellite RNA,"The interactions of seven isolates of peanut stunt cucumovirus (PSV) originating from North America, Europe and Africa, and two variants of PSV satellite RNA (sat RNA) were analysed. Electrophoretic and immunoblot analyses of the coat protein (CP) and Northern blot hybridization analyses of the viral RNAs showed that isolates PSV F352, 1339 and 1507 belonged to subgroup I, and isolates PSV W, Su and B to subgroup II. The seventh isolate, robinia mosaic virus (RoMV) clustered with subgroup isolates by CP analysis, but was related to both subgroups by RNA hybridization analysis. The ability to support the accumulation of two newly described sat RNA variants, P4 and P6 sat RNAs, was not related to PSV isolate classification: neither PSV W nor RoMV were helper viruses for these PSV sat RNAs. Symptom modulation by both sat RNAs was the same: the presence of sat RNA did not modify the symptoms induced by subgroup I isolates but exacerbated the symptoms induced by subgroup II isolates in both tobacco and cowpea. Sat RNAs P4 and P6 contained 393 nucleotides, and differed only in three nucleotide substitutions. This resulted in marked differences in infectivity, level of accumulation and relative encapsidation between both the sat RNAs. Accumulation levels and relative encapsidation of sat RNAs was also affected by the isolate of helper virus.",coat protein;satellite RNA;viral protein;virus RNA;article;controlled study;electrophoresis;helper virus;immunoblotting;plant virus;nonhuman;Northern blotting;nucleotide sequence;priority journal;symptom;virus classification;virus infectivity,"Militão, V.;Moreno, I.;Rodríguez-Cerezo, E.;García-Arenal, F.",1998,,,0
1390,Newcastle disease: Evolution of genotypes and the related diagnostic challenges,"Since the discovery of Newcastle disease virus (NDV) in 1926, nine genotypes of class I viruses and ten of class II have been identified, representing a diverse and continually evolving group of viruses. The emergence of new virulent genotypes from global epizootics and the year-to-year changes observed in the genomic sequence of NDV of low and high virulence implies that distinct genotypes of NDV are simultaneously evolving at different geographic locations across the globe. This vast genomic diversity may be favored by the large variety of avian species susceptible to NDV infection and by the availability of highly mobile wild bird reservoirs. The genomic diversity of NDV increases the possibility of diagnostic failures, resulting in unidentified infections. Constant epidemiological surveillance and pro-active characterization of circulating strains are needed to ensure that the immunological and PCR reagents are effective in identifying NDV circulating worldwide. For example, in the United States, the widely used real-time reverse transcription polymerase chain reaction (RRT-PCR) matrix gene assay for the identification of NDV often fails to detect low virulence APMV-1 from waterfowl, while the RRT-PCR fusion gene assay, used to identify virulent isolates, often fails to detect certain virulent NDV genotypes. A new matrix-polymerase multiplex test that detects most of the viruses currently circulating worldwide and a modified fusion test for the identification of virulent pigeon viruses circulating in the U.S. and Europe have recently been developed. For newly isolated viruses with unknown sequences, recently developed random priming sequencing methods need to be incorporated into the diagnostic arsenal. In addition, the current system of classifying NDV into genotypes or lineages is inadequate. Here, we review the molecular epidemiology and recent diagnostic problems related to viral evolution of NDV and explain why a new system, based on objective criteria, is needed to categorize genotypes.",glutamine;HN protein;fusion protein;lysine;matrix protein;Newcastle disease vaccine;nucleoprotein;phosphoprotein;RNA polymerase;Avulavirus;bird disease;disease carrier;gene sequence;genetic conservation;genetic variability;genotype;molecular epidemiology;Newcastle disease virus;nonhuman;nucleotide sequence;phylogenetic tree;priority journal;real time polymerase chain reaction;reverse transcription polymerase chain reaction;review;virus classification;virus detection;virus genome;virus identification;virus strain;virus virulence,"Miller, P. J.;Decanini, E. L.;Afonso, C. L.",2010,,10.1016/j.meegid.2009.09.012,0
1391,Common evolutionary origin of hepatitis B virus and retroviruses,"Hepatitis B virus (HBV), although classified as a double-stranded DNA virus, has been shown recently to replicate by reverse transcription of an RNA intermediate. Also, the putative viral polymerase has been found to share amino acid homology with reverse transcriptase of retroviruses. Using computer-assisted DNA and protein sequence analyses, we examined the genomes of 13 hepadnavirus isolates (nine human, two duck, one woodchuck, and one ground squirrel) and found that other conserved regions of the hepadnavirus genome share homology to corresponding regions of the genomes of type C retroviruses and retrovirus-like endogenous human DNA elements. Specifically, the most highly conserved sequence of the HBV genome, positioned at or near the initiation site for first-strand HBV DNA synthesis, is homologous over 67 nucleotides to the U5 region, a comparable region in retrovirus long terminal repeats. Within a highly conserved (i.e., 90%) 16-nucleotide sequence a heptanucleotide sequence CCTTGGG is 97% homologous between 27 virus isolates. Also, we found that the highly conserved HBV core, or nucleocapsid, protein shares 41% homology over 98 amino acids with the carboxyl-terminal region of the p30 gag nucleocapsid protein of type C retroviruses. In both cases, as with the previously reported polymerase homology, HBV is most homologous to the murine leukemia/sarcoma retroviruses. Further analysis revealed additional similarities between hepadnavirus and retroviral genomes. Taken together, our results suggest that HBV and retroviruses have a common evolutionary origin, with HBV arising through a process of deletion from a retrovirus, or retrovirus-like, progenitor.",double stranded DNA;radioisotope;RNA directed DNA polymerase;virus DNA;gene sequence;genetic engineering;Hepatitis B virus;heredity;liver;nonhuman;priority journal;Retroviridae;virus replication,"Miller, R. H.;Robinson, W. S.",1986,,,0
1392,"Detection of bovine group A rotavirus using rapid antigen detection kits, RT-PCR and next-generation DNA sequencing","We investigated the sensitivity of human rotavirus rapid antigen detection (RAD) kits, RT-PCR and next-generation DNA sequencing (NGS) for detection of bovine group A rotavirus (RVA). The Dipstick 'Eiken' Rota (Dipstick) showed the highest sensitivity out of the seven RAD kits against all selected strains in limited dilution analyses, which was consistent with the results for equine rotavirus previously reported. RT-PCR had 100-103-fold higher sensitivity than the Dipstick. NGS using thirteen RT-PCR-negative fecal samples revealed that all samples yielded RVA reads and especially that two of them covered all 11 genome segments. Moreover, mapping reads to reference sequences allowed genotyping. The NGS would be sensitive and useful for analysis of less dependent on specific primers and screening of genotypes. © 2013 The Japanese Society of Veterinary Science.",virus antigen;animal;animal disease;bovine;cattle disease;diagnostic kit;evaluation study;genetics;high throughput sequencing;immunology;isolation and purification;note;reverse transcription polymerase chain reaction;Rotavirus;Rotavirus infection;sensitivity and specificity;virology,"Minami-Fukuda, F.;Nagai, M.;Takai, H.;Murakami, T.;Ozawa, T.;Tsuchiaka, S.;Okazaki, S.;Katayama, Y.;Oba, M.;Nishiura, N.;Sassa, Y.;Omatsu, T.;Furuya, T.;Koyama, S.;Shirai, J.;Tsunemitsu, H.;Fujii, Y.;Katayama, K.;Mizutani, T.",2013,,10.1292/jvms.13-0265,0
1393,A systematic review of the natural Virome of Anopheles mosquitoes,,,"Minkeu, F. Nanfack;Vernick, K.",2018,,,0
1394,Rapid evolution of the human gut virome,,,"Minot, S.;Bryson, A.;Chehoud, C.",2013,,,0
1395,Conservation of Gene Cassettes among Diverse Viruses of the Human Gut,"Viruses are a crucial component of the human microbiome, but large population sizes, high sequence diversity, and high frequencies of novel genes have hindered genomic analysis by high-throughput sequencing. Here we investigate approaches to metagenomic assembly to probe genome structure in a sample of 5.6 Gb of gut viral DNA sequence from six individuals. Tests showed that a new pipeline based on DeBruijn graph assembly yielded longer contigs that were able to recruit more reads than the equivalent non-optimized, single-pass approach. To characterize gene content, the database of viral RefSeq proteins was compared to the assembled viral contigs, generating a bipartite graph with functional cassettes linking together viral contigs, which revealed a high degree of connectivity between diverse genomes involving multiple genes of the same functional class. In a second step, open reading frames were grouped by their co-occurrence on contigs in a database-independent manner, revealing conserved cassettes of co-oriented ORFs. These methods reveal that free-living bacteriophages, while usually dissimilar at the nucleotide level, often have significant similarity at the level of encoded amino acid motifs, gene order, and gene orientation. These findings thus connect contemporary metagenomic analysis with classical studies of bacteriophage genomic cassettes. Software is available at https://sourceforge.net/projects/optitdba/.",DE-NOVO ASSEMBLER;MODULAR EVOLUTION;PHAGE;DNA;BACTERIOPHAGES;PROTEINS;GENOMICS;SEQUENCE;FEATURES;LAMBDA,"Minot, S.;Wu, G. D.;Lewis, J. D.;Bushman, F. D.",2012,Aug,,0
1396,Phylogenetic evidence for a recent spread of two populations of human enterovirus 71 in European countries,"Human enterovirus 71 (EV-71) is a cause of seasonal epidemics of hand, foot and mouth disease, and of less common but severe neurological manifestations. Uncertainty persists regarding the circulation of virus populations in several geographical areas and the timescale of their dissemination. We determined EV-71 sequences at loci 1D (VP1 capsid protein) and 3CD (non-structural proteins) in 86 strains recovered in Austria, France and Germany and performed an evolutionary genetic study of extant virus populations. Phylogenetic analyses positioned 78 of the 86 sequences within two clades among subgenogroups C1 and C2. A minor sequence cluster was assigned to subgenogroup C4. Analyses incorporating the available sequences estimated the substitution rate in genogroup C at 3.66×10-3 and 4.46×10-3 substitutions per site year-1 for loci 1D and 3CD, respectively, assuming a relaxed molecular-clock model for sequence evolution. Most of the 'European' strains belonged to clades C1b and C2b, which originated in 1994 [95% confidence interval (CI), 1992.7-1995.8] and 2002 (95% CI, 2001.6-2003.8), respectively. Estimates of divergence times for locus 3CD were consistent with those measured for locus 1D. Intertwining between clades representing EV-71 subgenogroups and clades corresponding to other enterovirus types (notably early coxsackievirus A prototype strains) in the 3CD phylogeny is highly indicative of ancestral recombination events. Incongruent phylogenetic patterns estimated for loci 1D and 3CD show that a single tree cannot model the epidemic history of circulating EV-71 populations. The evolutionary timescale of genogroup C estimated for both loci was measured only in decades, indicating recent dissemination. © 2010 SGM.",protein VP1;article;Austria;comparative study;confidence interval;Enterovirus;DNA polymorphism;Enterovirus A71;epidemic;Europe;France;gene sequence;Germany;human;molecular model;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;priority journal;virus gene;virus strain,"Mirand, A.;Schuffenecker, I.;Henquell, C.;Billaud, G.;Jugie, G.;Falcon, D.;Mahul, A.;Archimbaud, C.;Terletskaia-Ladwig, E.;Diedrich, S.;Huemer, H. P.;Enders, M.;Lina, B.;Peigue-Lafeuille, H.;Bailly, J. L.",2010,,10.1099/vir.0.021741-0,0
1397,Genetic diversity of bovine diarrhea and mucosal disease virus,"Bovine viral diarrhea virus (BVDV) is classified as a member of the Pestivirus genus of the Flaviviridae family. BVDV is one of the most important viral pathogens of ruminants worldwide, causing severe economic losses. Infection results in a wide range of clinical manifestations, ranging from mild respiratory disease to fetal death and mucosal disease. The virus particles are small and contain a single-stranded, positive-sense RNA molecule of approximately 12.3 kb with one large open reading frame flanked by two untranslated regions (5’UTR and 3’UTR). The polyprotein is proteolytically cleaved by viral and host proteases resulting in the formation of mature viral proteins. It is well established that BVDV strains show considerable genetic diversity. BVD viruses are classified as two species: BVDV-1 and BVDV-2. Quite recently, a new putative species, BVDV-3, was detected. The viruses exist as one of two biotypes: cytopathic or non-cytopathic, based on their activity in cell cultures. The phylogenetic analysis of the 5’UTR and Npro region has revealed at least 21 distinct subtypes of BVDV-1 and 4 subtypes of BVDV-2. Genetic diversity of BVD viruses has serious clinical implications such as immune evasion, increase of virulence, host range alteration and also affects the efficacy of vaccination programmes and diagnostic methods.",viral protein;virus RNA;3' untranslated region;5' untranslated region;article;biotype;bovine viral diarrhea;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;Bovine viral diarrhea virus 3;Bovine viral diarrhea virus 4;genetic variability;nonhuman;phylogeny;virus particle,"Mirosław, P.;Antos, A.;Polak, M.",2017,,,0
1398,VARV B22R homologue as phylogenetic marker gene for Capripoxvirus classification and divergence time dating,"Sheeppox disease is associated with significant losses in sheep production world over. The sheep pox virus, the goatpox virus, and the lumpy skin disease virus cannot be distinguished by conventional serological tests. Identification of these pathogens needs molecular methods. In this study, seven genes viz. EEV maturation protein—F12L, Virion protein—D3R, RNA polymerase subunit—A5R, Virion core protein—A10L, EEV glycoprotein—A33R, VARV B22R homologue, and Kelch like protein—A55R that cover the start, middle, and end of the genome were selected. These genes were amplified from Roumanian-Fanar vaccine strain and Jaipur virulent strain, cloned, and sequenced. On analysis with the available database sequences, VARV B22R homologue was identified as a marker for phylogenetic reconstruction for classifying the sheeppox viruses of the ungulates. Further, divergence time dating with VARV B22R gene accurately predicted the sheeppox disease outbreak involving Jaipur virulent strain.",core protein;RNA polymerase;Sheeppox virus vaccine;unclassified drug;virus glycoprotein;virus vaccine;A10L gene;A33R gene;A55R gene;A5R gene;article;Capripoxvirus;controlled study;D3R gene;divergence time dating;F12L gene;gene amplification;gene sequence;genetic database;genetic variability;Lumpy skin disease virus;male;marker gene;molecular clock;molecular cloning;nonhuman;phylogeny;priority journal;sheeppox;VARV B22R gene;virion;virus classification;virus gene;virus identification;virus strain,"Mishra, B.;Mondal, P.;Patel, C. L.;Zafir, I.;Gangwar, R.;Singh, N.;Sonowal, J.;Bisht, D.;Sahu, A. R.;Baig, M.;Sajjanar, B.;Singh, R. K.;Gandham, R. K.",2019,,10.1007/s11262-018-1613-9,0
1399,Phylogenetic analysis of sheep pox virus (SPPV) virion core protein P4a gene revealed extensive sequence conservation among capripox viruses,"In the present study, virion core protein P4a gene was PCR amplified from sheep pox virus (SPPV) Jaipur isolate and Roumanian Fanar (RF) vaccine strain adapted and propagated in lamb testis/vero cells. Gene specific primers were designed for amplification of P4a gene. Amplified P4a gene fragment was sequence characterized and 808 bp sequence was compared across SPPV, GTPV and LSDV isolates available in GenBank database which revealed extensive sequence conservation of 97% to 100% within pox virus groups. Sheep pox virus Jaipur isolate was found closely placed with Roumaninan Fanar (RF) and TU isolates. Further, phylogenetic analysis of P4a gene sequence indicated three distinct clusters of Capripox viruses with GTPV interestingly placed closely to LSDV group.",core protein;roumaninan fanar vaccine;unclassified drug;vaccine;amino acid sequence;article;gene;gene insertion;gene sequence;goatpox;lumpy skin disease;nonhuman;nucleotide sequence;p4a gene;phylogenetic tree;phylogeny;polymerase chain reaction;sequence alignment;sheeppox,"Mishra, B.;Ravi Kumar, G.;Sonal;Patel, C. L.;Chaturvedi, V. K.",2018,,,0
1400,Molecular characterization of bovine viral diarrhea virus type 2 isolate originating from a native Indian sheep (Ovies aries),"The wide spread prevalence of bovine viral diarrhea virus type 1 (BVDV-1) in cattle and recent identification of BVDV-2 in goats in India warranted pestivirus surveillance in sheep. Nested reverse transcription-polymerase chain reaction (RT-PCR) was used to detect BVDV-2 in one of 1561 blood samples collected randomly from 78 sheep flocks in 11 states of India. Antigenic characterization of the isolated pestivirus using polyclonal and monoclonal antibodies typed the isolate as BVDV-2. When analyzed at genetic level in Npro (N-terminal autoprotease) and entire gene region coding structural proteins, namely capsid (C) protein and envelope proteins Erns (ribonuclease secreted), E1 and E2 genomic organization was the same for all pestiviruses, the nucleic acid and amino acid sequences showed highest similarity with those of BVDV-2. When compared with BVDV-2 isolate 890, the sequence homology was 83.7% for C, 84.6% for Erns and E1, and 81.5% for E2. The cleavage site C/Erns was found totally conserved while Npro/C was conserved only from C-terminus of Npro, Erns/E1 site was conserved only from C-terminus of Erns and E1/E2 site was conserved only from C-terminus of E1. Phylogenetic analysis of nucleotide sequences in 5′ untranslated regions (UTR), Npro, E2, NS3 and NS5B regions placed the sheep isolate in a separate clade within BVDV-2 subtype b. This was supported by the presence of unique mutations in the structural protein coding regions beside NS3 and NS5B. To our knowledge this is the first report on the sequence analysis of the entire structural gene coding region of a BVDV-2b isolate. This is also the first occurrence of BVDV-2 subtype b in sheep, providing the evidence that this subtype can also occur in species other than cattle. © 2008 Elsevier B.V. All rights reserved.",glycoprotein E;glycoprotein E1;glycoprotein E2;virus envelope protein;5' untranslated region;amino acid sequence;article;Bovine viral diarrhea virus 1;controlled study;gene mutation;genetic analysis;genetic trait;India;nonhuman;nucleotide sequence;Ovies aries;Pestivirus;phylogeny;reverse transcription polymerase chain reaction;sequence homology;sheep;virus capsid;virus characterization;virus detection;virus isolation;virus neutralization;virus typing,"Mishra, N.;Rajukumar, K.;Vilcek, S.;Tiwari, A.;Satav, J. S.;Dubey, S. C.",2008,,10.1016/j.vetmic.2008.01.005,0
1401,Metagenomic characterization of the virome associated with bovine respiratory disease in feedlot cattle identified novel viruses and suggests an etiologic role …,,,"Mitra, N.;Cernicchiaro, N.;Torres, S.;Li, F.",2016,,,0
1402,Metagenomic characterization of the virome associated with bovine respiratory disease in feedlot cattle identified novel viruses and suggests an etiologic role for influenza D virus,"Bovine respiratory disease (BRD) is the most costly disease affecting the cattle industry. The pathogenesis of BRD is complex and includes contributions from microbial pathogens as well as host, environmental and animal management factors. In this study, we utilized viral metagenomic sequencing to explore the virome of nasal swab samples obtained from feedlot cattle with acute BRD and asymptomatic pen-mates at six and four feedlots in Mexico and the USA, respectively, in April–October 2015. Twenty-one viruses were detected, with bovine rhinitis A (52.7%) and B (23.7%) virus, and bovine coronavirus (24.7%) being the most commonly identified. The emerging influenza D virus (IDV) tended to be significantly associated (P=0.134; odds ratio=2.94) with disease, whereas viruses commonly associated with BRD such as bovine viral diarrhea virus, bovine herpesvirus 1, bovine respiratory syncytial virus and bovine parainfluenza 3 virus were detected less frequently. The detection of IDV was further confirmed using a real-time PCR assay. Nasal swabs from symptomatic animals had significantly more IDV RNA than those collected from healthy animals (P=0.04). In addition to known viruses, new genotypes of bovine rhinitis B virus and enterovirus E were identified and a newly proposed species of bocaparvovirus, Ungulate bocaparvovirus 6, was characterized. Ungulate tetraparvovirus 1 was also detected for the first time in North America to our knowledge. These results illustrate the complexity of the virome associated with BRD and highlight the need for further research into the contribution of other viruses to BRD pathogenesis.",amino acid sequence;article;Bocaparvovirus;bovine adeno associated virus;Bovine coronavirus;Bovine herpesvirus 1;bovine nidovirus;Bovine parainfluenza virus 3;bovine parvovirus 3;Bovine respiratory syncytial virus;bovine rhinitis A virus;bovine rhinitis B virus;bovine torovirus;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;cattle disease;DNA virus;Enterovirus;enterovirus E;enterovirus F;genome analysis;genotype;Human parainfluenza virus 1;male;metagenomics;Musca domestica salivary gland hypetrophy virus;new species;nonhuman;nose smear;nucleotide sequence;phylogeny;Picobirnavirus;priority journal;real time polymerase chain reaction;Ungulate bocaparvovirus 6;Ungulate tetraparvovirus 1;virus detection;virus genome;virus identification,"Mitra, N.;Cernicchiaro, N.;Torres, S.;Li, F.;Hause, B. M.",2016,,10.1099/jgv.0.000492,1
1403,Molecular characterization of Indian isolates of infectious bursal disease virus from broiler chickens,"The present study was undertaken to characterize recent field isolates of infectious bursal disease virus (IBDV) by reverse transcription-polymerase chain reaction (RT-PCR) and partial sequencing of VP2 gene. The virus could be detected in 17 of 20 field samples from broiler chickens in Haryana state, India as well as in all the four vaccine strains. Nucleotide sequences of four field isolates and one vaccine strain were compared with 10 reported IBDV strains from different parts of the world. Nucleotide substitutions at 795G, 827T, 833C, 857C, 897A, 905T, 908T, 1011A and 1094G specific for very virulent (vv) strains, were maintained in all the four field isolates. However, unique nucleotide substitutions at 806A-G, 851C-T, 1010 T-C, 1019T-C and 1082T-C showed further divergence of these isolates from already reported vvIBDVs. Deduced amino acid substitutions at 222P-A, 256V-I, 279N-D, 294L-I and 299N-S specific for vvIBDV strains were also present in all the four isolates. The vaccine strain showed amino acid change 279D-N, a characteristic of attenuated vaccine strains. Phylogenetic analysis showed that all the field isolates in the present study were closely related to reported UK (UK661) and Japan (OKYM) field isolates. All the four field IBDV strains of the present study were closely related to each other but distinct from already reported vvIBDVs of India. On the basis of nucleotide sequencing and phylogenetic analysis, it is very likely that IBD causing strains in this part of India are of very virulent character and are still undergoing changes at genetic level. © 2006 Informa UK Ltd.",protein VP2;amino acid substitution;animal tissue;article;chicken;controlled study;gene sequence;India;infectious bursal disease virus;molecular phylogeny;nonhuman;nucleic acid base substitution;nucleotide sequence;priority journal;reverse transcription polymerase chain reaction;viral genetics;virus gene;virus isolation,"Mittal, D.;Jindal, N.;Gupta, S. L.;Kataria, R. S.;Singh, K.;Tiwari, A. K.",2006,,10.1080/10425170601017160,0
1404,Full-length genomic sequence analysis of new subtype 3k hepatitis E virus isolates with 99.97% nucleotide identity obtained from two consecutive acute hepatitis patients in a city in northeast Japan,"Full-length genomic sequences of hepatitis E virus (HEV) obtained from two consecutive cases of acute self-limiting hepatitis E in a city in northeast Japan were determined. Interestingly, two HEV isolates from each patient shared nucleotide identity of 99.97% in 7 225 nucleotides, and a phylogenetic analysis showed that they formed a cluster of Japanese isolates that is considered as a new HEV subtype 3k. The high similarity of HEV sequences of two isolates from these patients in this study suggested that a subtype 3k HEV strain had spread via a commonly distributed food in the city, possibly pig liver.",alanine aminotransferase;aspartate aminotransferase;immunoglobulin A;prednisolone;adult;alanine aminotransferase blood level;anamnesis;article;aspartate aminotransferase blood level;blood analysis;case report;convalescence;food contamination;food intake;gene cluster;gene sequence;hepatitis E;Hepatitis E virus;hospital admission;hospital discharge;human;Japan;liver tissue;loss of appetite;male;middle aged;nausea;nonhuman;nucleotide sequence;phylogeny;pig;sequence analysis;sequence homology;urine color;virus isolation;virus strain;virus transmission,"Miura, M.;Inoue, J.;Tsuruoka, M.;Nishizawa, T.;Nagashima, S.;Takahashi, M.;Shimosegawa, T.;Okamoto, H.",2017,,10.1002/jmv.24743,0
1405,"Isolation of Chuzan virus, a new member of the Palyam subgroup of the genus Orbivirus, from cattle and Culicoides oxystoma in Japan","Five virus strains with identical antigenic properties were isolated from 3 RBC suspensions obtained from 2 healthy sentinel calves and from 2 pools of Culicoides oxystoma in cultures of a hamster lung cell line (HmLu-1). The virus was tentatively named Chuzan virus. The Chuzan virus was classified as a new member of the Palyam subgroup of the genus Orbivirus on the basis of its physicochemical, morphologic, and antigenic properties.",animal;animal disease;article;bovine;cattle disease;Ceratopogonidae;isolation and purification;Japan;microbiology;Reoviridae;serotyping;virus infection,"Miura, Y.;Goto, Y.;Kubo, M.;Kono, Y.",1988,,,0
1406,Pestiviruses: a review Review,"Pestiviruses comprise a group of economically important animal pathogens, namely hog cholera, bovine viral diarrhoea and border disease viruses. The viruses are serologically closely related and share a common host spectrum, i.e. pigs and numerous domestic and wild living ruminants. Interspecies transmissions occur frequently. Despite some common features in their natural hosts, pathogenesis of pestivirus-induced disease is complex; especially some aspects of highly fatal mucosal disease of cattle are still enigmatic. Pestiviruses are amongst the smallest enveloped single-stranded RNA viruses with an icosaeder-shaped nucleocapsid. They are currently classified as Togaviridae. However, based on recent progress in the molecular characterisation of the viruses their taxonomic real-location seems inevitable. Viral RNAs studied so far display one large open reading frame and in infected cells no subgenomic RNA is demonstrable. Structural proteins are coded for by genes located at the 5' end of the RNA. The majority of the genome codes for 2-3 nonstructural proteins. Virions are composed of a major and one minor envelope glycoprotein with molecular weights of 53 and 48 kD respectively. The core is composed of a small protein with a molecular weight of 20 kD. Analysis of viral proteins with monoclonal antibodies has yielded detailed information about the antigenic composition of both structural and nonstructural proteins. [References: 102]","Animals;Antigens, Viral/an [Analysis];Pestivirus/ge [Genetics];Pestivirus/im [Immunology];*Pestivirus/ph [Physiology];RNA, Viral/an [Analysis];Togaviridae Infections/mi [Microbiology];*Togaviridae Infections/ve [Veterinary];Viral Proteins/an [Analysis];0 (Antigens, Viral);0 (RNA, Viral);0 (Viral Proteins)","Moenning, V.",1990,Jun,,0
1407,Defects in small intestinal epithelial barrier function and morphology associated with peri-weaning failure to thrive syndrome (PFTS) in swine,,,"Moeser, A. J.;Borst, L. B.;Overman, B. L.",2012,,,0
1408,Detection and genetic characterization of bovine kobuvirus from calves in Egypt,"Kobuviruses are small non-enveloped RNA viruses that probably cause diarrhea in cattle and swine. Since its discovery in 2003, few studies have addressed bovine kobuvirus (BKoV; a species of Aichivirus B) infections. BKoV has been reported in Europe, Asia, and South America, suggesting a worldwide distribution. To investigate the presence of BKoV in Egypt, 36 fecal specimens from diarrheic calves in two different Egyptian provinces (Cairo and Sharkia) were screened by RT-PCR and 24 (66.7%) were found positive for BKoV. RNA from one of the positive samples (BKoV/Egy-1/KY407744) was subjected to next-generation sequencing to determine the complete BKoV genome sequence. When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Additionally, five VP1 and seven 3D sequences were obtained from other samples by using RT-PCR and Sanger sequencing. A discrepancy in the phylogenetic topography of VP1 and 3D was observed, where the Egyptian VP1 sequences were classified as a distinct cluster within the proposed lineage 1 (genotype A), which also contained strains from the UK, Brazil, and Japan. While, the 3D sequences from Cairo were related to those of Chinese strains unlike Sharkia ones that were more closer to Korean  strains. To the best of our knowledge, this is the first detection and genomic characterization of BKoV in Egypt or indeed Africa.",polyprotein;virus RNA;amino acid sequence;amino acid substitution;animal;bovine;cattle disease;classification;diarrhea;Egypt;feces;genetics;genotype;high throughput sequencing;isolation and purification;Kobuvirus;nucleotide sequence;phylogeny;phylogeography;picornavirus infection;reverse transcription polymerase chain reaction;veterinary medicine;virology;virus genome,"Mohamed, F. F.;Mansour, S. M. G.;Orabi, A.;El-Araby, I. E.;Ng, T. F. F.;Mor, S. K.;Goyal, S. M.",2018,,10.1007/s00705-018-3758-1,0
1409,Effect of phylogenetic diversity of velogenic Newcastle disease virus challenge on virus shedding post homologous and heterologous DNA vaccination in chickens,"Newcastle disease (ND) is a highly devastating disease for the poultry industry as it causes high economic losses. In this present study, a DNA vaccine containing the F and HN surface antigens of a highly virulent Newcastle disease virus (NDV), NDV/1/Chicken/2005 (FJ939313), was successfully generated. Cell transfection test indicated that the vaccine expressed the F and HN genes in Hep-2 cells. The main objective of this study was to compare the extent of protection induced by DNA vaccination after homologous and heterologous NDV-challenge as determined by the amount of NDV shedding after challenge. NDV-antibody-negative chickens were vaccinated either once, twice or thrice intramuscularly at 7, 14 and 21 days old and were challenged 14 days post vaccination with either homologous virus (vaccine-matched velogenic viscerotropic Newcastle disease virus (vvNDV) strain, FJ939313), phylogenetically related to group VII, or a phylogenetically divergent heterologous virus (unmatched vvNDV strain, AY968809), which belongs to genogroup VI and shows 84.1% nucleotide similarity to the NDV-sequences of the DNA vaccine. Our data indicate that birds, which received a single dose of the DNA vaccine were poorly protected, and only 30-40% of these birds survived after challenge with high virus shedding titre. Multiple administration of the DNA vaccine induced high protection rates of 70-90% with reduced virus shedding compared to the non-vaccinated and challenged birds. Generally, homologous challenge led to reduced tracheal and cloacal shedding compared to the heterologous vvNDV strain. This study provides a promising approach for the control of ND in chickens using DNA vaccines, which are phylogenetically closely related to the circulating field strains.",live vaccine;virus antibody;virus fusion protein;virus vaccine;animal;chick embryo;chicken;female;genetics;genotype;germfree animal;immunology;isolation and purification;male;Newcastle disease;Newcastle disease virus;pathogenicity;phylogeny;bird disease;vaccination;veterinary medicine;virology;virus shedding,"Mohamed, M. H.;Abdelaziz, A. M.;Kumar, S.;Al-Habib, M. A.;Megahed, M. M.",2016,,10.1080/03079457.2016.1144870,0
1410,Complete genome sequence of a virulent Newcastle disease virus isolated from an outbreak in chickens in Egypt,"The complete genome sequence of a virulent Newcastle disease virus (NDV) isolated from chickens in Egypt was determined and compared to the sequence of NDV strains isolated from different parts of the world. The genome is 15,186 nucleotides (nt) long and consists of 6 genes in the order of 3′-N-P-M-F-HN-L-5′. The genome contains a 55-nt leader region at the 3′ end and a 114-nt trailer region at the 5′ end. Interestingly, the phylogenetic analysis showed that strain Egypt is closely related with the NDV strains isolated in China. In addition, the sequence of the fusion protein cleavage site of strain Egypt was identical to that of the NDV strain recently isolated in Mali. Determination of complete genome sequences of additional NDV strains from Africa is necessary to understand the epidemiology of currently circulating viruses in Africa. © 2009 Springer Science+Business Media, LLC.",fusion protein;Africa;article;chicken;China;Egypt;epidemic;gene sequence;Mali;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;priority journal;protein cleavage;virus genome;virus isolation;virus strain,"Mohamed, M. H. A.;Kumar, S.;Paldurai, A.;Megahed, M. M.;Ghanem, I. A.;Lebdah, M. A.;Samal, S. K.",2009,,10.1007/s11262-009-0385-7,0
1411,Application of molecular biological techniques for detection of epizootic hemorrhagic disease virus (EHDV-318) recovered from a sentinel calf in central Sudan,"Epizootic hemorrhagic disease virus (EHDV), isolate 318 (EHDV-318), an untyped virus recovered from a sentinel calf herd at the Khartoum University farm in central Sudan, was characterized using molecular biological techniques. With dot blot hybridization technique, a cDNA probe derived from genome segment 6 of EHDV-2 (Alberta strain) hybridized with RNA from EHDV-318. Application of serogroup-specific EHDV polymerase chain reaction (PCR) to EHDV-318 RNA resulted in specific amplification of a 387 bp PCR product. Amplification product was visualized on ethidium bromide-stained agarose gel. Specificity of the PCR products was confirmed by chemiluminescent hybridization with a non-radiolabelled internal probe. No amplification product or hybridization signal was detected when the serotype-specific EHDV-1 or EHDV-2 PCR-based assays were applied to RNA from EHDV-318. The scientific data presented in this study indicated that cDNA probes and serogroup-specific PCR-based assay can de used to classify the virus as a member of EHDV serogroup, and as serotypically distinct from EHDV-1 and EHDV-2.",complementary DNA;animal experiment;article;bovine epizootic fever virus;bovine;controlled study;DNA probe;nonhuman;polymerase chain reaction;Sudan;virus infection,"Mohammed, M. E. H.;Aradaib, I. E.;Mukhtar, M. M.;Ghalib, H. W.;Riemann, H. P.;Oyejide, A.;Osburn, B. I.",1996,,10.1016/s0378-1135(96)00073-9,0
1412,Analysis of the leader proteinase (Lpro) region of type A foot-and-mouth disease virus with due emphasis on phylogeny and evolution of the emerging VP359-deletion lineage from India,"Genotype inclusive grouping of Indian type A isolates as observed in 1D region based phylogeny was distorted at complete Lpro region, where the VP359-deletion group lineages of genotype VII clustered away from both genotypes VII and VI, confirming its uniqueness and independent evolution of Lpro and 1D region. Akin to the 1D region, this deletion group is gradually diverging genetically even at L region forming more number of lineages and inter-lineage distance at L region is considerably more than that for 1D region. The deletion group is restricted to India only as none of the exotic sequences clustered within this group. Notably, L protein exhibited variability comparable to external capsid proteins as evident from its high dN/dS ratio (0.105), number of variable amino acid positions (41%), low Ts/Tv ratio (3.47) and alignment revealed N-terminal region, β2 sheet and C-terminal extension to be extremely variable. Basic residues at P1, P3 and only leucine at P2 were predicted to provide an optimum autocatalytic cleavage site at L/P1 junction. All of the eight sites identified to be under positive selection revealed aa substitutions of varied physicochemical properties and at two positions lineage specific signatures were observed, which supports the contention that lineages are evolving under differential selection pressure to adapt to the varied ecological environment. © 2008 Elsevier B.V. All rights reserved.",amino acid;capsid protein;dihydrolipoamide dehydrogenase;leucine;protein VP3;proteinase;amino terminal sequence;article;carboxy terminal sequence;controlled study;Foot and mouth disease virus;gene deletion;genotype;India;nonhuman;nucleotide sequence;phylogeny;physical chemistry;priority journal;unindexed sequence,"Mohapatra, J. K.;Priyadarshini, P.;Pandey, L.;Subramaniam, S.;Sanyal, A.;Hemadri, D.;Pattnaik, B.",2009,,10.1016/j.virusres.2008.12.012,0
1413,"Genetic variability of VP6, VP7, VP4, and NSP4 genes of porcine rotavirus group H detected in Brazil","Rotaviruses (RV) are a common cause of viral gastroenteritis in humans and animals. Despite the seven groups/species of RV (A-G), recently it was proposed the creation of a new RV group/specie H (RVH) based on VP6 sequence analysis. In this study we determined the VP6, VP7, VP4, and NSP4 nucleotide and deduced amino acid sequences of 6 (BR59-BR64) RVH-positive stool specimens obtained from piglets with diarrhea in Mato Grosso do Sul, Central-West region of Brazil in 2012, using RT-PCR assay. Based on the high sequence identities (>99%) of the VP6, VP4, VP7, and NSP4 genes among 5 of the studied fecal specimens (BR59-BR63), they are considered the same local rotavirus strain denominated RVH/BRA-1. In contrast, once that the fecal sample BR64 showed a relatively high difference (81.6% nt identity and 83.4% aa identity) in the VP7 sequence when compared to the other 5 specimens it was named RVH/BRA-2 strain. Comparative phylogenetic analysis showed that the 6 RVH strains do not cluster together with any available sequences of members of the established RV groups (RVA-RVG), however, seem to be related to RVB and RVG. These results confirm the presence of RVH in Brazil, demonstrate their genetic diversity, and provide new data that will assist in understanding the viral phylogeny and epidemiology, as well as the explanation of patterns of viral evolution and biological properties of RVH.",nucleotide;protein VP4;protein VP6;protein VP7;Rotavirus nonstructural protein 4;amino acid sequence;article;Brazil;gene sequence;genetic variability;molecular evolution;nonhuman;phylogeny;porcine rotavirus;priority journal;Rotavirus;sequence analysis,"Molinari, B. L. D.;Alfieri, A. F.;Alfieri, A. A.",2015,,10.1016/j.virusres.2014.12.003,0
1414,"Phylogenetic Analysis of Pigeon Paramyxoviruses Type-1 Identified in Mourning Collared-doves ( Streptopelia decipiens) in Namibia, Africa","We generated the complete sequence of the fusion ( F) protein gene from six pigeon paramyxoviruses type 1 (PPMV-1) isolated from Mourning Collared-doves ( Streptopelia decipiens) in Namibia, Africa between 2016 and 2017. All of the isolates had an F gene cleavage site motif of 112RRQKRF117 characteristic of virulent viruses. A phylogenetic analysis using the full F gene sequence revealed that the viruses belonged to genotype VIa and were epidemiologically related to PPMV-1s from Asia, Europe, and North America.",viral protein;animal;Columbidae;gene expression regulation;genetics;genotype;metabolism;Namibia;Newcastle disease;Newcastle disease virus;phylogeny;virology,"Molini, U.;Aikukutu, G.;Khaiseb, S.;Cattoli, G.;Dundon, W. G.",2018,,10.7589/2017-10-246,0
1415,The genome of the chicken DT40 bursal lymphoma cell line,"The chicken DT40 cell line is a widely used model system in the study of multiple cellular processes due to the efficiency of homologous gene targeting. The cell line was derived from a bursal lymphoma induced by avian leukosis virus infection. In this study we characterized the genome of the cell line using whole genome shotgun sequencing and single nucleotide polymorphism array hybridization. The results indicate that wild-type DT40 has a relatively normal karyotype, except for whole chromosome copy number gains, and no karyotype variability within stocks. In a comparison to two domestic chicken genomes and the Gallus gallus reference genome, we found no unique mutational processes shaping the DT40 genome except for a mild increase in insertion and deletion events, particularly deletions at tandem repeats. We mapped coding sequence mutations that are unique to the DT40 genome; mutations inactivating the PIK3R1 and ATRX genes likely contributed to the oncogenic transformation. In addition to a known avian leukosis virus integration in the MYC gene, we detected further integration sites that are likely to de-regulate gene expression. The new findings support the hypothesis that DT40 is a typical transformed cell line with a relatively intact genome; therefore, it is well-suited to the role of a model system for DNA repair and related processes. The sequence data generated by this study, including a searchable de novo genome assembly and annotated lists of mutated genes, will support future research using this cell line.",animal cell;article;chicken;controlled study;copy number variation;Gallus gallus;gene deletion;gene insertion;gene mutation;gene sequence;gene targeting;genomics;karyotype;lymphoma cell line;nonhuman;sequence analysis;single nucleotide polymorphism;tandem repeat;tumor suppressor gene,"Molnár, J.;Póti, A.;Pipek, O.;Krzystanek, M.;Kanu, N.;Swanton, C.;Tusnády, G. E.;Szallasi, Z.;Csabai, I.;Szüts, D.",2014,,10.1534/g3.114.013482,0
1416,Altered virome and bacterial microbiome in human immunodeficiency virus-associated acquired immunodeficiency syndrome,,,"Monaco, C. L.;Gootenberg, D. B.;Zhao, G.;Handley, S. A.",2016,,,0
1417,Viruses isolated from reptiles: identification of three new members of the family Rhabdoviridae,"The growth of four viruses isolated from lizards in Brazil (Marco, Chaco, and Timbo viruses) and Australia (Almpiwar virus) was studied in a variety of continuous cell lines of mammalian, reptilian, amphibian, and piscine origin. Although replication was found in certain cell lines derived from the coldblooded species, cytopathic effect (CPE) was absent or minimal and growth was less than or equal to that in mammalian cells. These observations appear to limit the value of poikilothermic cells for primary isolation of viruses from field-collected, coldblooded vertebrates or arthropods that feed upon them. The four reptilian viruses were found to be naturally occuring temperature sensitive agents, with optima for growth of approximately 30° C. Electron microscope studies showed three of the virsues (Marco, Chaco, and Timbo) to be new members of the family Rhabdoviridae. Marco virus particles were conically shaped and resembled bovine ephemeral fever virus, and two lyssaviruses (Kotonkan and Obodhaing). Chaco and Timbo viruses were cylindrial viruses resembling other rhabdoviruses with particle lengths longer than the prototype VSV. No serologic relationships were found in cross complement fixation tests between these viruses, Marco virus, and 34 other rhabdoviruses.",animal experiment;cell culture;classification;geographic distribution;in vitro study;reptile;Rhabdoviridae;virus classification;virus isolation,"Monath, T. P.;Cropp, C. B.;Frazier, C. L.",1979,,,0
1418,Detection of orf virus from an outbreak in goats and its genetic relation with other parapoxviruses,,virus DNA;amplicon;article;controlled study;counter immunoelectrophoresis;epidemic;goat;herd;hyperthermia;lip disease;molecular cloning;morbidity;nipple;nonhuman;nose disease;nucleotide sequence;Parapoxvirus;polymerase chain reaction;Poxviridae;sequence analysis;skin defect;viral genetics;virus detection,"Mondal, B.;Bera, A. K.;Hosamani, M.;Tembhurne, P. A.;Bandyopadhyay, S. K.",2006,,10.1007/s11259-006-3270-z,0
1419,Comparison of four regions in the replicase gene of heterologous infectious bronchitis virus strains,"Infectious bronchitis virus (IBV) produces six subgenomic (sg) mRNAs, each containing a 64 nucleotide (nt) leader sequence, derived from the 5′ end of the genome by a discontinuous process. Several putative functional domains such as a papain-like proteinase (PLpro), main protease (M pro), RNA-dependent RNA polymerase (RdRp), and RNA helicase encoded by the replicase gene are important for virus replication. We have sequenced four regions of the replicase genes corresponding to the 5′-terminal sequence, PLpro, Mpro, and RdRp domains from 20 heterologous IBV strains, and compared them with previously published coronavirus sequences. All the coronavirus 5′-termini and PLpro domains were divergent, unlike the Mpro and the RdRp domains that were highly conserved with 28% and 48% conserved residues, respectively. Among IBV strains, the 5′ untranslated region including the leader sequence was highly conserved (>94% identical); whereas, the N-terminal coding region and the PLpro domains were highly variable ranging from 84.6% to 100%, and 77.6% to 100% identity, respectively. The IBV Mpro and RdRp domains were highly conserved with 82.7% and 92.7% conserved residues, respectively. The BJ strain was the most different from other IBVs in all four regions of the replicase. Phylogeny-based clustering based on replicase genes was identical to the antigen-based classification of coronaviruses into three groups. However, the IBV strain classification based on replicase gene domains did not correlate with that of the type-specific antigenic groups. The replicase gene sequences of many IBVs recovered from infected chickens were identical to those of vaccine viruses irrespective of serotype, suggesting that either there has been an exchange of genetic material among vaccine and field isolates or that there is a convergent evolution to a specific replicase genotype. There was no correlation between the genotype of any region of the replicase gene and pathotype, suggesting that the replicase is not the sole determinant of IBV pathogenicity. © 2004 Elsevier Inc. All rights reserved.",main protease;papain like proteinase;RNA directed RNA polymerase;RNA helicase;unclassified drug;virus enzyme;amino terminal sequence;antigenicity;article;Avian infectious bronchitis virus;chicken;controlled study;convergent evolution;gene sequence;gene structure;genetic conservation;genotype;molecular evolution;nonhuman;pathotype;phylogeny;priority journal;protein domain;sequence analysis;serotype;strain difference;virus classification;virus gene;virus genome;virus infection;virus strain;virus virulence,"Mondal, S. P.;Cardona, C. J.",2004,,10.1016/j.virol.2004.03.032,0
1420,"Molecular characterization of bovine rotavirus strains circulating in northern Italy, 2003-2005","A total of 232 stools collected from calves with rotavirus infection in herds located in northern Italy from 2003 to 2005 was investigated. Determination of the rotavirus G and P types was carried out using nested RT-PCR. G6 was the most prevalent genotype, accounting for 78.5% of samples, G10 accounted for 9.9% of samples and viruses of G8 type were found in 4.7% of samples. In 3% of samples, viruses were not classified due to concomitant infection with more G type strains, whereas viruses in 3.9% of samples could not be characterized with any of the G-specific primers used in this study. Most common P types were P[11] and P[5], accounting for 65.1% and 25%, respectively. In 2.6% of cases, samples reacted with multiple P-specific primers; no P[1] serotype was identified. The G6P[11] combination was predominant throughout the study period, i.e. 52.5% in 2003, 50% in 2004 and 40% in 2005. The incidence of G6P[5] increased from 13.1% in 2003 to 27% in 2004 and 25.5% in 2005. The G10P[11] combination decreased markedly from 18% in 2003 to 2.6% in 2004, rising again to 7.3% in 2005. G8P[11] viruses were similarly present in 2003 (5%) and 2004 (4.3%), declining slightly in 2005 (1.8%). © 2007 Elsevier B.V. All rights reserved.",article;concurrent infection;controlled study;DNA sequence;enzyme linked immunosorbent assay;feces analysis;genotype;nonhuman;real time polymerase chain reaction;Rotavirus;virus detection;virus infection;virus strain,"Monini, M.;Cappuccini, F.;Battista, P.;Falcone, E.;Lavazza, A.;Ruggeri, F. M.",2008,,10.1016/j.vetmic.2007.11.036,0
1421,"Reassortant avian influenza A(H5N1) viruses with H9N2-PB1 gene in poultry, Bangladesh",Bangladesh has reported a high number of outbreaks of highly pathogenic avian influenza (HPAI) (H5N1) in poultry. We identified a natural reassortant HPAI (H5N1) virus containing a H9N2-PB1 gene in poultry in Bangladesh. Our findings highlight the risks for prolonged co-circulation of avian influenza viruses and the need to monitor their evolution.,"Animals;Bangladesh/ep [Epidemiology];Chickens/vi [Virology];Cloaca/vi [Virology];*Disease Outbreaks;Evolution, Molecular;*Influenza A Virus, H5N1 Subtype/ge [Genetics];Influenza A Virus, H5N1 Subtype/ip [Isolation & Purification];*Influenza A Virus, H9N2 Subtype/ge [Genetics];Influenza A Virus, H9N2 Subtype/ip [Isolation & Purification];*Influenza in Birds/ep [Epidemiology];Influenza in Birds/vi [Virology];Phylogeny;*Reassortant Viruses/ge [Genetics];Reassortant Viruses/ip [Isolation & Purification];Recombination, Genetic;*Viral Proteins/ge [Genetics];0 (Viral Proteins);0 (influenza virus polymerase basic protein 1)","Monne, I.;Yamage, M.;Dauphin, G.;Claes, F.;Ahmed, G.;Giasuddin, M.;Salviato, A.;Ormelli, S.;Bonfante, F.;Schivo, A.;Cattoli, G.",2013,Oct,,0
1422,Immunomodulatory effects of heat stress and lipopolysaccharide on the bursal transcriptome in two distinct chicken lines,"BACKGROUND: Exposure to heat stress suppresses poultry immune responses, which can increase susceptibility to infectious diseases and, thereby, intensify the negative effects of heat on poultry welfare and performance. Identifying genes and pathways that are affected by high temperatures, especially heat-induced changes in immune responses, could provide targets to improve disease resistance in chickens. This study utilized RNA-sequencing (RNA-seq) to investigate transcriptome responses in the bursa of Fabricius, a primary immune tissue, after exposure to acute heat stress and/or subcutaneous immune stimulation with lipopolysaccharide (LPS) in a 2 x 2 factorial design: Thermoneutral + Saline, Heat + Saline, Thermoneutral + LPS and Heat + LPS. All treatments were investigated in two chicken lines: a relatively heat- and disease-resistant Fayoumi line and a more susceptible broiler line. RESULTS: Differential expression analysis determined that Heat + Saline had limited impact on gene expression (N = 1 or 63 genes) in broiler or Fayoumi bursa. However, Thermoneutral + LPS and Heat + LPS generated many expression changes in Fayoumi bursa (N = 368 and 804 genes). Thermoneutral + LPS was predicted to increase immune-related cell signaling and cell migration, while Heat + LPS would activate mortality-related functions and decrease expression in WNT signaling pathways. Further inter-treatment comparisons in the Fayoumi line revealed that heat stress prevented many of the expression changes caused by LPS. Although fewer significant expression changes were observed in the broiler bursa after exposure to Thermoneutral + LPS (N = 59 genes) or to Heat + LPS (N = 146 genes), both treatments were predicted to increase cell migration. Direct comparison between lines (broiler to Fayoumi) confirmed that each line had distinct responses to treatment. CONCLUSIONS: Transcriptome analysis identified genes and pathways involved in bursal responses to heat stress and LPS and elucidated that these effects were greatest in the combined treatment. The interaction between heat and LPS was line dependent, with suppressive expression changes primarily in the Fayoumi line. Potential target genes, especially those involved in cell migration and immune signaling, can inform future research on heat stress in poultry and could prove useful for improving disease resistance.",Animals;Birnaviridae Infections/dt [Drug Therapy];Birnaviridae Infections/im [Immunology];*Birnaviridae Infections/ve [Veterinary];Birnaviridae Infections/vi [Virology];Bursa of Fabricius/im [Immunology];Bursa of Fabricius/me [Metabolism];Bursa of Fabricius/vi [Virology];*Chickens/ge [Genetics];*Chickens/im [Immunology];Gene Expression Regulation;Gene Regulatory Networks;High-Throughput Nucleotide Sequencing;Hot Temperature;*Immunologic Factors/pd [Pharmacology];*Lipopolysaccharides/im [Immunology];*Poultry Diseases/ge [Genetics];Poultry Diseases/im [Immunology];Poultry Diseases/vi [Virology];Transcriptome;0 (Immunologic Factors);0 (Lipopolysaccharides),"Monson, M. S.;Van Goor, A. G.;Ashwell, C. M.;Persia, M. E.;Rothschild, M. F.;Schmidt, C. J.;Lamont, S. J.",2018,Aug 30,,0
1423,Genetic analysis of avian influenza virus from migratory waterfowl in Mexico,"This study describes the genetic characterization of avian influenza virus from waterfowl in Mexico. Partial sequences of two H5, one H6, and one H9 hemmaglutinin (HA) genes were determined. The deduced amino acid sequences showed that they were low-pathogenic viruses (LPAI). Phylogenetic analysis of H5 and H6 HA indicates a North American lineage, closely related to contemporary Californian isolates, and H9 HA was closer to the Korean-like lineage. These results demonstrate the introduction of a diverse genetic pool of subtypes to Sonora estuaries through circulation of bird species carriers from the Pacific flyway.","*Animal Migration;Animals;Anseriformes;Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];Influenza A virus/cl [Classification];*Influenza A virus/ge [Genetics];Influenza A virus/ip [Isolation & Purification];*Influenza in Birds/vi [Virology];Mexico;Molecular Sequence Data;Phylogeny;0 (Hemagglutinin Glycoproteins, Influenza Virus)","Montalvo-Corral, M.;Hernandez, J.",2010,,,0
1424,Genetic grouping of avian infectious bronchitis virus isolated in Brazil based on RT-PCR/RFLP analysis of the S1 gene,"Twelve Brazilian isolates and one reference vaccine strain of avian infectious bronchitis virus (IBV) were propagated in embryonating chicken eggs. The entire S1 glycoprotein gene of these viruses was analysed by reverse-transcriptase-polymerase chain reaction and restriction fragment length polymorphism (RT-PCR-RFLP), using the restriction enzymes HaeIII, XcmI and Bstyl. The RFLP patterns led to the classification of these isolates into five distinct genotypes: A, B, C, D and Massachusetts. Five of twelve isolates were grouped in Massachusetts genotype and the remaining seven viruses were classified into four distinct genotypes: A (2), B (2), C (2) or D (1). Such genotyping classification agreed with previous immunological analysis for most of these viruses, highlighting the occurrence of a relevant variability among the IBV strains that are circulating in Brazilian commercial poultry flocks.",avian infectious bronchitis virus;spike glycoprotein;genotyping and;RFLP;FRAGMENT-LENGTH-POLYMORPHISM;POLYMERASE CHAIN-REACTION;MOLECULAR;CHARACTERIZATION;UNITED-STATES;SEROTYPES;STRAIN;IBV,"Montassier, M. D. S.;Brentano, L.;Montassier, H. J.;Richtzenhain, L. J.",2008,Mar,,0
1425,Detection and genetic identification of pestiviruses in Brazilian lots of fetal bovine serum collected from 2006 to 2014,"The present study performed a genetic identification of pestiviruses contaminating batches of fetal bovine serum (FBS) produced in Brazil from 2006 to 2014. Seventy-three FBS lots were screened by a RT-PCR targeting the 5'untranslated region (UTR) of the pestivirus genome. Thirty-nine lots (53.4%) were positive for pestivirus RNA and one contained infectious virus. Nucleotide sequencing and phylogenetic analysis of the 5'UTR revealed 34 lots (46.6%) containing RNA of bovine viral diarrhea virus type 1 (BVDV-1), being 23 BVDV-1a (5' UTR identity 90.8-98.7%), eight BVDV-1b (93.9-96.7%) and three BVDV-1d (96.2- 97.6%). Six lots (8.2%) contained BVDV-2 (90.3-100% UTR identity) being two BVDV-2a; three BVDV-2b and one undetermined. Four FBS batches (5.5%) were found contaminated with HoBi-like virus (98.3 to 100%). Five batches (6.8%) contained more than one pestivirus. The high frequency of contamination of FBS with pestivirus RNA reinforce the need for systematic and updated guidelines for monitoring this product to reduce the risk of contamination of biologicals and introduction of contaminating agents into free areas.",bovine serum albumin;complementary DNA;5' untranslated region;animal cell;animal experiment;article;Bovine viral diarrhea virus 1;Brazil;controlled study;fetus;fluorescent antibody technique;genetic identification;high throughput sequencing;MDBK cell line;nonhuman;nucleotide sequence;observational study;Pestivirus;phylogeny;real time polymerase chain reaction;reverse transcription polymerase chain reaction;RNA extraction;sequence alignment;virus detection;virus isolation,"Monteiro, F. L.;Cargnelutti, J. F.;Braunig, P.;Folgueras-Flatschart, A. V.;Santos, N. C.;Pituco, E. M.;Weiblen, R.;Flores, E. F.",2018,,10.1590/1678-5150-pvb-5283,0
1426,Hepatitis E virus circulation in Italy: Phylogenetic and evolutionary analysis,"Background: Hepatitis E virus (HEV), a major cause of acute viral hepatitis in developing countries, has been classified into four main genotypes and a number of subtypes. New genotypes have been recently identified in various mammals, including HEV genotype 3, which has a worldwide distribution. It is widespread among pigs in developed countries. Objectives: This study investigated the genetic diversity of HEV among humans and swine in Italy. The date of origin and the demographic history of the HEV were also estimated. Materials and Methods: A total of 327 HEV sequences of swine and humans from Italy were downloaded from the national centre for biotechnology information. Three different data sets were constructed. The first and the second data set were used to confirm the genotype of the sequences analyzed. The third data set was used to estimate the mean evolutionary rate and to determine the time-scaled phylogeny and demographic history. Results: The Bayesian maximumclade credibility tree and the time of the mostcommonrecent ancestor estimates showed that the root of the tree dated back to the year 1907 (95% HPD: 1811 - 1975). Twomain clades were found, divided into two subclades. Skyline plot analysis, performed separately for human and swine sequences, demonstrated the presence of a bottleneck only in the skyline plot from the swine sequences. Selective pressure analysis revealed only negatively selected sites. Conclusions: This study provides support for the hypothesis that humans are probably infected after contact with swine sources. The findings emphasize the importance of checking the country of origin of swine and of improving sanitary control measures from the veterinary standpoint to prevent the spread of HEV infection in Italy.",animal experiment;biotechnology;cladistics;evolutionary rate;genetic variability;Hepatitis E virus;Italy;nonhuman;phylogeny;pig;prevention,"Montesano, C.;Giovanetti, M.;Ciotti, M.;Cella, E.;Lo Presti, A.;Grifoni, A.;Zehender, G.;Angeletti, S.;Ciccozzi, M.",2016,,10.5812/hepatmon.31951,0
1427,Viral interactions with the host and microbiota in the intestine,"This review explores the recent advances that have been made in our understanding of host viral interactions in the intestine. Technical advances have allowed the initial definition of intestinal viromes in a number of species including humans. Important advances in our knowledge of the host response to viral infection have shown that interferon lambda has a role that is unique from type I interferons in the intestine. Lastly, our understanding of virally induced phenotypes has expanded through new studies that show bacteria can play an important role in the outcome of viral infection in the intestine. © 2012 Elsevier Ltd.",bacterial DNA;caspase recruitment domain protein 15;caspase recruitment domain protein 4;interferon;interferon lambda;melanoma differentiation factor 5;mitochondrial antiviral signaling protein;pattern recognition receptor;protein;RIG I like receptor;single stranded RNA;toll like receptor;toll like receptor 3;type III interferon;unclassified drug;virus RNA;AIDS patient;antiviral activity;bacterial infection;bacteriophage;commensal;commensal microbiota;DNA sequence;enteritis;human;Human immunodeficiency virus infection;infection sensitivity;influenza;innate immunity;interferon production;intestinal virome;intestine epithelium cell;intestine flora;microbiome;Mouse mammary tumor virus;nonhuman;Paneth cell;plasma;protein expression;protein family;protein protein interaction;protein RNA binding;review;Rotavirus infection;secondary bacterial infection;virus cell interaction;virus detection;virus like agent,"Moon, C.;Stappenbeck, T. S.",2012,,10.1016/j.coi.2012.05.002,0
1428,Sequence comparison of avian infectious bronchitis virus S1 glycoproteins of the Florida serotype and five variant isolates from Georgia and California,"The infectious bronchitis virus (IBV) spike glycoprotein S1 subunit is required to initiate infection and contains virus-neutralizing and serotype-specific epitope(s). Reported are the S1 gene nucleotide and predicted amino acid sequences for the Florida 18288 strain and isolates GA-92, CV-56b, CV-9437, CV-1686, and 1013. These sequences were compared with previously published gene sequences of IBV strains, and phylogenetic relationships are reported. The SI amino acid sequence of Florida 18288 was 94.9% similar to the Connecticut strain, and GA-92 was 92.8% similar to the Arkansas 99 strain. S1 amino acid sequences of the California variants, CV-56b, CV-9437, and CV-1686, were 97.6-99.3% similar to one another and only 76.6%-76.8% similar to the Arkansas-type strains. Isolate 1013, also from California, was 84.0% similar to Ark DPI and 77.9% similar to CV-56b. When comparing 19 viruses isolated from the United States, sequence variations were observed between amino acids 55-96, 115-149, 255-309, and 378-395. Similar regions are reported to be involved in virus-neutralizing and/or serotype-specific epitopes. These data demonstrate that variant IBV strains continue to emerge, and unique variants may circulate among poultry in geographically isolated areas.",protein subunit;virus glycoprotein;amino acid sequence;article;Avian infectious bronchitis virus;nonhuman;nucleotide sequence;phylogeny;priority journal;serotype;United States;virus isolation;virus neutralization,"Moore, K. M.;Bennett, J. D.;Seal, B. S.;Jackwood, M. W.",1998,,10.1023/a:1008057118625,0
1429,Phylogenetic analysis of the hemagglutinin genes of 12 H9N2 influenza viruses isolated from chickens in Iran from 2003 to 2005,"In the present study, the hemagglutinin genes from 12 influenza viruses of the H9N2 subtype were isolated from chicken flocks in different provinces of Iran from 2003 to 2005, amplified and sequenced. All of the 12 isolates showed similar sequences at the cleavage site, RSSF/GLF, bearing eight potential glycosylation sites and sharing the characteristic deduced amino acid residues alanine-190, glutamine-226, and glutamine-227 at the receptor-binding site. Ten out of these 12 isolates possessed leucine at position 226, which prevails in the sequences found in human H2 and H3 strains. Overall, the presence in these Iranian poultry H9N2 viruses of the sequence known to bind to human-type receptors and the presence of antibodies in the human population of Iran to H9N2 showed that it is possible for circulating H9N2 avian influenza viruses in Iran to infect humans. Hence, extensive surveillance of H9N2 in this country is highly recommended. © 2010 American Association of Avian Pathologists.",hemagglutinin;animal;article;avian influenza;chicken;genetic variability;genetics;Influenza A virus (H9N2);Iran;phylogeny;time;virology,"Moosakhani, F.;Shoshtari, A. H.;Pourbakhsh, S. A.;Keyvanfar, H.;Ghorbani, A.",2010,,10.1637/9103-101309-Reg.1,0
1430,Detection and molecular characterization of Porcine astrovirus strains associated with swine diarrhea,"Astrovirus has been reported to be associated with diarrhea in pigs. The current study was conducted for the detection and molecular characterization of astroviruses in diarrheic pigs submitted to the Veterinary Diagnostic Laboratory, University of Minnesota. Intestinal contents from 269 pigs were examined by reverse transcription polymerase chain reaction (RT-PCR), and 62% were found positive for astroviruses. Of the positive samples, 20% were positive for astrovirus alone while astrovirus with rotavirus was detected in 58% of the samples. The remaining 22% revealed the presence of astrovirus along with Porcine hemagglutinating encephalomyelitis virus, Transmissible gastroenteritis virus, or Porcine circovirus-2. Sequencing the capsid gene of 56 randomly selected samples confirmed them to be Porcine astrovirus type 4 (PAstV-4) with 58-100% nucleotide identity within these viruses. Phylogenetic analysis revealed 2 possible subgroups. The results indicate that PAstV is present on swine farms in the United States and that it may be associated with diarrhea either alone or in combination with other enteric viruses. Further studies are needed to determine strain diversity among porcine astroviruses so that appropriate control strategies can be devised and implemented. © 2012 The Author(s).",animal;animal disease;article;Astroviridae;astrovirus infection;classification;diarrhea;genetics;intestine;pathology;phylogeny;stomach juice;pig;swine disease;virology,"Mor, S. K.;Chander, Y.;Marthaler, D.;Patnayak, D. P.;Goyal, S. M.",2012,,10.1177/1040638712458781,0
1431,Molecular characterization of L class genome segments of a newly isolated turkey arthritis reovirus,"Seven strains of turkey arthritis reovirus (TARV) isolated from cases of turkey arthritis were characterized on the basis of their L class genome segment sequences, which were then compared with those of turkey enteric reovirus (TERV) and chicken reovirus (CRV). All three L class gene segments of TARVs and TERVs and their encoded proteins λA, λB, and λC were similar in size to those of CRV reference strain S1133. The conserved motifs such as C2H2 zinc-binding motif and conserved polymerase region were present in λA and λB, respectively. A conserved motif for ATP/GTP-binding site and an S-adenosyl-. l-methionine (SAM)-binding pocket for methyltransferase were observed in λC protein of TARVs and TERVs with only one substitution as compared to that in CRV. We propose a new genotype classification system for avian reoviruses (ARVs) based on the nt identity cut-off value for each of the L class. Based on this new genotype classification, all ARVs were divided into six, seven and eight genotypes in L1, L2 and L3 genes, respectively. Interestingly TARVs and TERVs grouped with three CRVs (two arthritic strains from Taiwan and one enteritic strain from Japan) in genotype L1-I and formed a different genotypes (L2-I, L3-I) from CRVs in L2 and L3 genes. The maximum nucleotide divergence was observed in genotypes of L1 and L2 genes but less at amino acid level indicates mostly changes were synonymous type. Compared to L1 and L2 genes, the nonsynonymous changes were more in L3 gene. Point mutations and possible reassortments among TARVs, TERVs and CRVs were also observed. © 2014 Elsevier B.V.",adenosine triphosphate;CD79b antigen;guanosine triphosphate;immunoglobulin;immunoglobulin A;s adenosylmethionine;article;Avian orthoreovirus;gene sequence;genetic conservation;genetic reassortment;genome analysis;L class genome segment;L1 gene;L2 gene;L3 gene;nonhuman;nucleotide binding site;nucleotide sequence;phylogeny;point mutation;priority journal;sequence analysis;turkey arthritis reovirus;unindexed sequence;virus classification;virus gene;virus genome;zinc finger motif,"Mor, S. K.;Sharafeldin, T. A.;Porter, R. E.;Goyal, S. M.",2014,,10.1016/j.meegid.2014.07.012,0
1432,Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics,,,"Moreno, P. S.;Wagner, J.;Mansfield, C. S.;Stevens, M.",2017,,,0
1433,Concise and broadly applicable method for determining the genomic sequences of North-American-type porcine reproductive and respiratory syndrome viruses in various clusters,"We developed a concise and broadly applicable method for accurate genomic sequencing of North American genotype (NA-type) porcine reproductive and respiratory syndrome viruses (PRRSVs) that overcomes high genetic variability of the viruses. The method, designated ""combination of consensus oligonucleotide reverse transcription and multiple displacement amplification"" (CORT-MDA), involves reverse-transcription of viral RNA followed by shotgun sequencing after amplification using only 11 degenerate oligonucleotide primers; these primers were designed against consensus regions within the open reading frames of the 124 NA-type PRRSV strains with reported full-length genomic sequences. Sequencing of the 192 shotgun clones generated per virus showed 80% to 94% coverage on the reported PRRSV genomic sequence, such that only 2 or 3 unread regions had to be resequenced after PCR amplification using custom primers. Direct sequencing of RT-PCR products confirmed absolute consistency between sequences determined by the CORT-MDA method and those from RT-PCR. These results suggest that our method is applicable to diverse NA-type viruses.",virus RNA;animal;chemistry;DNA sequence;female;genetics;North America;phylogeny;pig;Porcine reproductive and respiratory syndrome virus;procedures;reverse transcription polymerase chain reaction;virus genome,"Morozumi, T.;Iseki, H.;Toki, D.;Takagi, M.;Tsunemitsu, H.;Uenishi, H.",2014,,,0
1434,"Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis","Chelonid alphaherpesvirus 5 (ChHV5) is a herpesvirus associated with fibropapillomatosis (FP) in sea turtles worldwide. Single-locus typing has previously shown differentiation between Atlantic and Pacific strains of this virus, with low variation within each geographic clade. However, a lack of multi-locus genomic sequence data hinders understanding of the rate and mechanisms of ChHV5 evolutionary divergence, as well as how these genomic changes may contribute to differences in disease manifestation. To assess genomic variation in ChHV5 among five Hawaii and three Florida green sea turtles, we used high-throughput short-read sequencing of long-range PCR products amplified from tumor tissue using primers designed from the single available ChHV5 reference genome from a Hawaii green sea turtle. This strategy recovered sequence data from both geographic regions for approximately 75% of the predicted ChHV5 coding sequences. The average nucleotide divergence between geographic populations was 1.5%; most of the substitutions were fixed differences between regions. Protein divergence was generally low (average 0.08%), and ranged between 0 and 5.3%. Several atypical genes originally identified and annotated in the reference genome were confirmed in ChHV5 genomes from both geographic locations. Unambiguous recombination events between geographic regions were identified, and clustering of private alleles suggests the prevalence of recombination in the evolutionary history of ChHV5. This study significantly increased the amount of sequence data available from ChHV5 strains, enabling informed selection of loci for future population genetic and natural history studies, and suggesting the (possibly latent) co-infection of individuals by well-differentiated geographic variants.",Green sea turtles;Fibropapillomatosis;Recombination;Protein;divergence;Viral genomics;High-throughput sequencing;Phylogeography;Chelonid alphaherpesvirus 5;SIMPLEX-VIRUS TYPE-1;CODON-SUBSTITUTION MODELS;VARICELLA-ZOSTER-VIRUS;COMPLETE DNA-SEQUENCE;MARINE TURTLES;PHYLOGENETIC ANALYSIS;NUCLEOTIDE;SUBSTITUTIONS;BOVINE HERPESVIRUS-1;NATURAL-POPULATIONS;MAXIMUM-LIKELIHOOD,"Morrison, C. L.;Iwanowici, L.;Work, T. M.;Fahsbender, E.;Breitbart, M.;Adams, C.;Iwanowiczi, D.;Sanders, L.;Ackermann, M.;Cornman, R. S.",2018,Feb,,0
1435,Myeloid and erythroid neoplastic responses to avian defective leukemia viruses in chickens and in quail,A comparative study of the oncogenic potential of two avian defective leukemia viruses (DLVs) shows that avian erythroblastosis virus induces myeloid leukemia in quail and confirms that E26 causes erythroid leukemia in chickens. These results indicate that the response of birds to these two DLVs depends on the host species and suggest that classification of DLVs based only on in vitro studies may not be definitive.,animal experiment;blood and hemopoietic system;chicken;defective virus;erythroleukemia;experimental infection;in vitro study;lymphatic system;myeloid leukemia;Orthoretrovirinae;virus classification,"Moscovici, C.;Samarut, J.;Gazzolo, L.;Moscovici, M. G.",1981,,10.1016/0042-6822(81)90205-1,0
1436,A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses,"Several biosafety level 3 and/or 4 (BSL-3/4) pathogens are high-consequence, single-stranded RNA viruses, and their genomes, when introduced into permissive cells, are infectious. Moreover, many of these viruses are select agents (SAs), and their genomes are also considered SAs. For this reason, cDNAs and/or their derivatives must be tested to ensure the absence of infectious virus and/or viral RNA before transfer out of the BSL-3/4 and/or SA laboratory. This tremendously limits the capacity to conduct viral genomic research, particularly the application of next-generation sequencing (NGS). Here, we present a sequence-independent method to rapidly amplify viral genomic RNA while simultaneously abolishing both viral and genomic RNA infectivity across multiple single-stranded positive-sense RNA (ssRNA +) virus families. The process generates barcoded DNA amplicons that range in length from 300 to 1,000 bp, which cannot be used to rescue a virus and are stable to transport at room temperature. Our barcoding approach allows for up to 288 barcoded samples to be pooled into a single library and run across various NGS platforms without potential reconstitution of the viral genome. Our data demonstrate that this approach provides full-length genomic sequence information not only from high-titer virion preparations but it can also recover specific viral sequence from samples with limited starting material in the background of cellular RNA, and it can be used to identify pathogens from unknown samples. In summary, we describe a rapid, universal standard operating procedure that generates high-quality NGS libraries free of infectious virus and infectious viral RNA. IMPORTANCE This report establishes and validates a standard operating procedure (SOP) for select agents (SAs) and other biosafety level 3 and/or 4 (BSL-3/4) RNA viruses to rapidly generate noninfectious, barcoded cDNA amenable for next-generation sequencing (NGS). This eliminates the burden of testing all processed samples derived from high-consequence pathogens prior to transfer from high-containment laboratories to lower-containment facilities for sequencing. Our established protocol can be scaled up for high-throughput sequencing of hundreds of samples simultaneously, which can dramatically reduce the cost and effort required for NGS library construction. NGS data from this SOP can provide complete genome coverage from viral stocks and can also detect virus-specific reads from limited start-ing material. Our data suggest that the procedure can be implemented and easily validated by institutional biosafety committees across research laboratories.",next-generation sequencing;West Nile virus;alphavirus;coronavirus;flavivirus;foot-and-mouth disease virus;genomics;picornavirus;rhinovirus;MOUTH-DISEASE VIRUS;WEST-NILE-VIRUS;SELECT AGENT;PATHOGENESIS;REPLICATION;INFECTIVITY;PERSISTENCE;VIROLOGY;DESIGN;MODEL,"Moser, L. A.;Ramirez-Carvajal, L.;Puri, V.;Pauszek, S. J.;Matthews, K.;Dilley, K. A.;Mullan, C.;McGraw, J.;Khayat, M.;Beeri, K.;Yee, A.;Dugan, V.;Heise, M. T.;Frieman, M. B.;Rodriguez, L. L.;Bernard, K. A.;Wentworth, D. E.;Stockwell, T. B.;Shabman, R. S.",2016,May-Jun,,0
1437,RNA2DMut: a web tool for the design and analysis of RNA structure mutations,"With the widespread application of high-throughput sequencing, novel RNA sequences are being discovered at an astonishing rate. The analysis of function, however, lags behind. In both the cis- and trans-regulatory functions of RNA, secondary structure (2D base-pairing) plays essential regulatory roles. In order to test RNA function, it is essential to be able to design and analyze mutations that can affect structure. This was the motivation for the creation of the RNA2DMut web tool. With RNA2DMut, users can enter in RNA sequences to analyze, constrain mutations to specific residues, or limit changes to purines/pyrimidines. The sequence is analyzed at each base to determine the effect of every possible point mutation on 2D structure. The metrics used in RNA2DMut rely on the calculation of the Boltzmann structure ensemble and do not require a robust 2D model of RNA structure for designing mutations. This tool can facilitate a wide array of uses involving RNA: for example, in designing and evaluating mutants for biological assays, interrogating RNA-protein interactions, identifying key regions to alter in SELEX experiments, and improving RNA folding and crystallization properties for structural biology. Additional tools are available to help users introduce other mutations (e.g., indels and substitutions) and evaluate their effects on RNA structure. Example calculations are shown for five RNAs that require 2D structure for their function: the MALAT1 mascRNA, an influenza virus splicing regulatory motif, the EBER2 viral noncoding RNA, the Xist lncRNA repA region, and human Y RNA 5. RNA2DMut can be accessed at https://rna2dmut.bb.iastate.edu/.","Animals;Base Pairing;Birds;*Computational Biology/mt [Methods];Female;High-Throughput Nucleotide Sequencing;Humans;Internet;Mice;*Mutation;*Nucleic Acid Conformation;RNA/ch [Chemistry];*RNA/ge [Genetics];RNA Folding;Sequence Analysis, RNA;*Software;Swine;63231-63-0 (rna)","Moss, W. N.",2018,03,,0
1438,Viral detection by high-throughput sequencing,"We applied a high-throughput sequencing platform, Ion PGM, for viral detection in fecal samples from adult cows collected in Hokkaido, Japan. Random RT-PCR was performed to amplify RNA extracted from 0.25 ml of fecal specimens (N = 8), and more than 5 μg of cDNA was synthesized. Unbiased highthroughput sequencing using the 318 v2 semiconductor chip of these eight samples yielded 57–580 K (average: 270 K, after data analysis) reads in a single run. As a result, viral genome sequences were detected in each specimen. In addition to bacteriophage, mammal- and insect-derived viruses, partial genome sequences of plant, algal, and protozoal viruses were detected. Thus, this metagenomic analysis of fecal specimens could be useful to comprehensively understand viral populations of the intestine and food sources in animals.",complementary DNA;virus RNA;adult;algal virus;article;bacteriophage;DNA synthesis;feces analysis;gene sequence;genome analysis;high throughput sequencing;insect virus;ion pgm benchtop sequencer;laboratory device;metagenomics;next generation sequencing;nonhuman;plant virus;priority journal;reverse transcription polymerase chain reaction;RNA extraction;semiconductor;virus detection;virus genome;Ion PGM,"Motooka, D.;Nakamura, S.;Hagiwara, K.;Nakaya, T.",2015,,10.1007/978-1-4939-1743-3_11,0
1439,Hepatitis E in three immunocompromized children in southeastern France,"Hepatitis E virus (HEV) causes an emerging autochthonous disease in developed countries where links with a viral porcine reservoir have been evidenced. Moreover, chronic HEV infection and associated-cirrhosis have been described in severely immunocompromized patients. Nonetheless, only few studies have focused on pediatric HEV infections worldwide and only four autochthonous cases have been reported in children in developed countries. We describe here acute hepatitis E in three immunocompromized children. Case no. 1 was a 9-year-old liver transplant recipient girl in whom H1N1 2009 flu infection was diagnosed concurrently with hepatitis E. Case no. 2 was a 12-year-old boy presenting early medullar relapse of lymphoblastic leukemia of type B and in whom HEV RNA was detected over a 29-week period. Case no. 3 was a 9-year-old boy with a rare primary immunodeficiency due to XIAP deficiency. HEV infections were all autochthonously acquired and involved different viruses classified as subtype f, c, and e of genotype 3, which are those described in autochthonous cases in Europe. These three observations prompt to consider HEV as a causative agent of hepatitis in children in developed countries, and to perform particularly HEV testing in those severely immunocompromized who may develop chronic hepatitis E. © 2011 Elsevier B.V.",asparaginase;cidofovir;clofarabine;cyclophosphamide;cyclosporine;dexamethasone;etoposide;fludarabine;foscarnet;immunoglobulin M antibody;mitoxantrone;mycophenolate mofetil;tacrolimus;virus antibody;virus RNA;X linked inhibitor of apoptosis;2009 H1N1 influenza;acute graft rejection;article;case report;child;concurrent infection;drug dose increase;female;France;genotype;graft recipient;graft versus host reaction;hepatitis E;hepatomegaly;herpes zoster;human;human tissue;hyperbilirubinemia;immune deficiency;immunocompromised patient;leukemia relapse;liver biopsy;liver transplantation;lymphatic leukemia;male;nucleotide sequence;priority journal;protein deficiency;school child,"Motte, A.;Roquelaure, B.;Galambrun, C.;Bernard, F.;Zandotti, C.;Colson, P.",2012,,10.1016/j.jcv.2011.11.012,0
1440,"The blood DNA virome in 8,000 humans",,,"Moustafa, A.;Xie, C.;Kirkness, E.;Biggs, W.;Wong, E.",2017,,,0
1441,Epidemiological survey of enteric viruses in wild boars in the Czech Republic: First evidence of close relationship between wild boar and human rotavirus A strains,"Population of wild boar is increasing in the whole Europe, the animals migrate close to human habitats which greatly increases the possibility of natural transmission between domestic animals or humans and wild boars. The aim of the study was to estimate in population of free-living wild boar in the Czech Republic the prevalence of enteric viral pathogens, namely rotavirus groups A and C (RVA and RVC), porcine reproductive and respiratory syndrome virus (PRRSV), and members of family Coronaviridae (transmissible gastroenteritis virus – TGEV, porcine epidemic diarrhea virus − PEDV, porcine respiratory coronavirus – PRCV, and porcine hemagglutination encephalomyelitis virus – PHEV) and Picornaviridae,(teschovirus A – PTV, sapelovirus A – PSV, and enterovirus G – EV-G). In our study, stool samples from 203 wild boars culled during hunting season 2014–2015 (from October to January) were examined by RT-PCR. RVA was detected in 2.5% of tested samples. Nucleotide analysis of VP7, VP4, and VP6 genes revealed that four RVA strains belong to G4P[25]I1, G4P[6]I5, G11P[13]I5, and G5P[13]I5 genotypes and phylogenetic analysis suggested close relation to porcine and human RVAs. The prevalence of RVC in wild boar population reached 12.8%, PTV was detected in 20.2%, PSV in 8.9%, and EV-G in 2.5% of samples. During our study no PRRSV or coronaviruses were detected. Our study provides the first evidence of RVC prevalence in wild boars and indicates that wild boars might contribute to the genetic variability of RVA and also serve as an important reservoir of other enteric viruses.",protein VP4;protein VP6;protein VP7;animal hunting;article;controlled study;Coronaviridae;Czech Republic;encephalitis virus;enteric virus;feces culture;genotype;molecular phylogeny;nonhuman;Picornaviridae;Porcine epidemic diarrhea virus;Porcine reproductive and respiratory syndrome virus;Porcine respiratory coronavirus;prevalence;reverse transcription polymerase chain reaction;Rotavirus A;Rotavirus C;Transmissible gastroenteritis virus;virus detection;virus gene;virus strain;European wild boar,"Moutelíková, R.;Dufková, L.;Kamler, J.;Drimaj, J.;Plhal, R.;Prodělalová, J.",2016,,10.1016/j.vetmic.2016.08.003,0
1442,Defining an emerging disease,"Defining an emerging disease is not straightforward, as there are several different types of disease emergence. For example, there can be a 'real' emergence of a brand new disease, such as the emergence of bovine spongiform encephalopathy in the 1980s, or a geographic emergence in an area not previously affected, such as the emergence of bluetongue in northern Europe in 2006. In addition, disease can emerge in species formerly not considered affected, e.g. the emergence of bovine tuberculosis in wildlife species since 2000 in France. There can also be an unexpected increase of disease incidence in a known area and a known species, or there may simply be an increase in our knowledge or awareness of a particular disease. What all these emerging diseases have in common is that human activity frequently has a role to play in their emergence. For example, bovine spongiform encephalopathy very probably emerged as a result of changes in the manufacturing of meat-and-bone meal, bluetongue was able to spread to cooler climes as a result of uncontrolled trade in animals, and a relaxation of screening and surveillance for bovine tuberculosis enabled the disease to re-emerge in areas that had been able to drastically reduce the number of cases. Globalisation and population growth will continue to affect the epidemiology of diseases in years to come and ecosystems will continue to evolve. Furthermore, new technologies such as metagenomics and high-throughput sequencing are identifying new microorganisms all the time. Change is the one constant, and diseases will continue to emerge, and we must consider the causes and different types of emergence as we deal with these diseases in the future.",animal;bluetongue;Bluetongue orbivirus;bovine;classification;communicable disease;disease carrier;bovine spongiform encephalopathy;health;Lyssavirus;pathology;rhabdovirus infection;transmission;bovine tuberculosis;virology,"Moutou, F.;Pastoret, P. P.",2015,,,0
1443,Stem-loop recognition by DDX17 facilitates miRNA processing and antiviral defense,"DEAD-box helicases play essential roles in RNA metabolism across species, but emerging data suggest that they have additional functions in immunity. Through RNAi screening, we identify an evolutionarily conserved and interferon-independent role for the DEAD-box helicase DDX17 in restricting Rift Valley fever virus (RVFV), a mosquito-transmitted virus in the bunyavirus family that causes severe morbidity and mortality in humans and livestock. Loss of Drosophila DDX17 (Rm62) in cells and flies enhanced RVFV infection. Similarly, depletion of DDX17 but not the related helicase DDX5 increased RVFV replication in human cells. Using crosslinking immunoprecipitation high-throughput sequencing (CLIP-seq), we show that DDX17 binds the stem loops of host pri-miRNA to facilitate their processing and also an essential stem loop in bunyaviral RNA to restrict infection. Thus, DDX17 has dual roles in the recognition of stem loops: in the nucleus for endogenous microRNA (miRNA) biogenesis and in the cytoplasm for surveillance against structured non-self-elements. © 2014 Elsevier Inc.",ddx17 protein;DEAD box protein;microRNA;unclassified drug;animal cell;antiviral activity;article;autoradiography;biogenesis;bunyavirus infection;cell granule;cell viability;controlled study;cross linking;Drosophila;genetic transfection;high throughput sequencing;human;human cell;immunofluorescence;immunoprecipitation;in vitro study;microscopy;nonhuman;Northern blotting;osteosarcoma cell line;priority journal;protein binding;protein depletion;protein expression;protein secondary structure;RNA processing;RNA replication;U2OS cell line;Vesiculovirus;virus replication,"Moy, R. H.;Cole, B. S.;Yasunaga, A.;Gold, B.;Shankarling, G.;Varble, A.;Molleston, J. M.;Tenoever, B. R.;Lynch, K. W.;Cherry, S.",2014,,10.1016/j.cell.2014.06.023,0
1444,Phylogeographic analysis of African swine fever virus based on the p72 gene sequence,"African swine fever virus (ASFV) outbreak has been considered as an emerging and re-emerging disease for almost a century. Diagnostically, simple polymerase chain reaction and sequencing-based molecular detection could be employed for both viral identification and genotyping. This study established a novel phylogenetic analysis and epidemiology comparison based on 205 bp of p72 gene sequences. Based on this partial p72 fragment, an updated list of 44 different genotypes from a total of 516 ASFV sequences compiled from GenBank was generated. Nucleotide diversity was 0.04325 ± 0.00231. The analysis of spatial genetic variation divided the ASFV populations of the African continent into four clades (clade A: central and upper eastern Africa; clade B: eastern Africa; clade C: eastern and southern Africa; and clade D: southern Africa). These results and the developed protocol could serve as useful molecular tools for ASFV diagnosis from degraded DNA or putrefied samples, and also provide the phylogeographic perspective to identify the origin of viral outbreaks, facilitating the decision planning to limit their spread.",protein p72;Africa;African swine fever virus;amino acid sequence;article;Burundi;cladistics;Congo;controlled study;Democratic Republic Congo;DNA degradation;gene sequence;genetic epidemiology;genetic variability;genotype;Kenya;neighbor joining method;nonhuman;p72 gene;phylogeny;phylogeography;polymerase chain reaction;sequence alignment;sequence analysis;Tanzania;Uganda;virus gene;virus transmission,"Muangkram, Y.;Sukmak, M.;Wajjwalku, W.",2015,,10.4238/2015.May.4.15,0
1445,‘Next-Generation’ Surveillance: An Epidemiologists’ Perspective on the Use of Molecular Information in Food Safety and Animal Health Decision-Making,"Advances in the availability and affordability of molecular and genomic data are transforming human health care. Surveillance aimed at supporting and improving food safety and animal health is likely to undergo a similar transformation. We propose a definition of ‘molecular surveillance’ in this context and argue that molecular data are an adjunct to rather than a substitute for sound epidemiological study and surveillance design. Specific considerations with regard to sample collection are raised, as is the importance of the relation between the molecular clock speed of genetic markers and the spatiotemporal scale of the surveillance activity, which can be control- or strategy-focused. Development of standards for study design and assessment of molecular surveillance system attributes is needed, together with development of an interdisciplinary skills base covering both molecular and epidemiological principles.",molecular marker;animal health;antibiotic resistance;article;bovine spongiform encephalopathy;cost effectiveness analysis;decision making;disease surveillance;food safety;genetic marker;genetic polymorphism;geographic origin;high throughput sequencing;influenza;methicillin resistant Staphylococcus aureus;molecular clock;molecular epidemiology;molecular surveillance;molecular typing;next generation sequencing;nonhuman;priority journal;pulsed field gel electrophoresis;risk assessment;Salmonella;sensitivity and specificity;sequence analysis;virus strain;whole genome sequencing,"Muellner, P.;Stärk, K. D. C.;Dufour, S.;Zadoks, R. N.",2016,,10.1111/zph.12230,0
1446,Molecular epidemiology and a loop-mediated isothermal amplification method for diagnosis of infection with rabies virus in Zambia,"The National Livestock Epidemiology and Information Center (NALEIC) in Zambia reported over 132 cases of canine rabies diagnosed by the direct fluorescent antibody test (DFAT) from 2004 to 2009. In this study, the lineage of rabies virus (RABV) in Zambia was determined by phylogenetic analysis of the nucleoprotein (N) and glycoprotein (G) gene sequences. Total RNA was extracted from 87-DFAT brain specimens out of which only 35 (40%) were positive on nested reverse transcription polymerase chain reaction (RT-PCR) for each gene, and 26 being positive for both genes. Positive specimens for the N (n= 33) and G (n= 35) genes were used for phylogenetic analysis. Phylogenetic analysis of the N gene showed two phylogenetic clusters in Zambia belonging to the Africa 1b lineage present in eastern and southern Africa. While one cluster exclusively comprised Zambian strains, the other was more heterogeneous regarding the RABV origins and included strains from Tanzania, Mozambique and Zambia. Phylogenetic analysis of the G gene revealed similar RABV strains in different hosts and regions of Zambia. We designed primers for reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay from the consensus sequence of the N gene in an attempt to improve the molecular diagnosis of RABV in Zambia. The specificity and reproducibility of the RT-LAMP assay was confirmed with actual clinical specimens. Therefore, the RT-LAMP assay presented in this study may prove to be useful for routine diagnosis of rabies in Zambia. © 2011 Elsevier B.V.",glycoprotein;nucleoprotein;RNA;Africa;animal experiment;animal tissue;article;controlled study;fluorescent antibody technique;gene sequence;human;loop mediated isothermal amplification;molecular epidemiology;Mozambique;nonhuman;nucleotide sequence;phylogeny;priority journal;rabies;Rabies virus;reverse transcription polymerase chain reaction;RNA extraction;Tanzania;Zambia,"Muleya, W.;Namangala, B.;Mweene, A.;Zulu, L.;Fandamu, P.;Banda, D.;Kimura, T.;Sawa, H.;Ishii, A.",2012,,10.1016/j.virusres.2011.09.010,0
1447,A polyoma-like virus associated with an acute disease of fledgling budgerigars (Melopsittacus undulatus),"A virus previously isolated from fledgling budgerigars (Melopsittacus undulatus) suffering from an acute disease, has been purified and the structural characteristics have been determined. The virions with a buoyant density of 1.34 g/ml are non-enveloped icosahedral particles with a diameter of about 46-48 nm. Their DNA genome has a molecular weight of about 3.3 x 106 d, and exists as supericoiled circular, relaxed circular, and linear molecules. There are eight structural proteins, the most abundant of which gas a molecular weight of about 42,000 d. Empty capsid shells with buoyant densities of 1.31 g/ml are similar in size and shape, but lack DNA and histone-like polypeptides. Virus replication in chicken embryo cells results in cytopathic changes characterized by rounding and enlargement of the nucleus, and formation of intranuclear inclusion bodies. All these properties justify classification of the virus as polyoma-like.",virus DNA;bird;cell culture;classification;diagnosis;electron microscopy;electrophoresis;in vitro study;nonhuman;Polyomavirus;priority journal;virus characterization;virus purification,"Muller, H.;Nitschke, R.",1986,,,0
1448,Genomic characterisation of the feline sarcoid-associated papillomavirus and proposed classification as Bos taurus papillomavirus type 14,"Feline sarcoids are rare mesenchymal neoplasms of domestic and exotic cats. Previous studies have consistently detected short DNA sequences from a papillomavirus (PV), designated feline sarcoid-associated papillomavirus (FeSarPV), in these neoplasms. The FeSarPV sequence has never been detected in any non-sarcoid sample from cats but has been amplified from the skin of cattle suggesting that feline sarcoids are caused by cross-species infection by a bovine papillomavirus (BPV). The aim of the present study was to determine the genome of the PV that contains the FeSarPV sequence. Using the circular nature of PV DNA, four specifically designed 'outward facing' primers were used to amplify two approximately 4,000 bp DNA segments from a feline sarcoid. The two PCR products were sequenced using next generation sequencing and the full genome of the PV, consisting 7,966 bp, was assembled and analysed. Phylogenetic analysis revealed the PV was closely related to the species 4 delta BPVs-1, -2, and -13, but distantly related to any carnivoran PV genus. These results are consistent with feline sarcoids being caused by a BPV type and we propose a classification of BPV-14 for this novel PV. Initial analysis suggests that, like other delta BPVs, the BPV-14 E5 protein could cause mesenchymal proliferation by binding to the platelet derived growth factor beta receptor. Interestingly BPV-14 has not been detected in any equine sarcoid suggesting that BPV-14 has a host range that is limited to bovids and felids.","Amino Acid Sequence;Animals;Base Sequence;Cat Diseases/dt [Drug Therapy];Cat Diseases/su [Surgery];*Cat Diseases/vi [Virology];Cats;Cattle;DNA, Viral/ch [Chemistry];DNA, Viral/ip [Isolation & Purification];*Deltapapillomavirus/cl [Classification];*Deltapapillomavirus/ge [Genetics];Euthanasia, Animal;Genome, Viral;Genomics;High-Throughput Nucleotide Sequencing;Molecular Sequence Data;Neoplasm Recurrence, Local/su [Surgery];*Neoplasm Recurrence, Local/ve [Veterinary];Open Reading Frames/ge [Genetics];Papillomavirus Infections/dt [Drug Therapy];Papillomavirus Infections/su [Surgery];*Papillomavirus Infections/ve [Veterinary];Papillomavirus Infections/vi [Virology];Phylogeny;Polymerase Chain Reaction/ve [Veterinary];Sequence Alignment/ve [Veterinary];Skin/vi [Virology];Skin Neoplasms/dt [Drug Therapy];Skin Neoplasms/su [Surgery];*Skin Neoplasms/ve [Veterinary];Skin Neoplasms/vi [Virology];0 (DNA, Viral)","Munday, J. S.;Thomson, N.;Dunowska, M.;Knight, C. G.;Laurie, R. E.;Hills, S.",2015,Jun 12,,0
1449,Transcriptome sequencing reveals a complete genome sequence of cowpea aphid-borne mosaic virus from passion fruit in Kenya,"Analysis of transcriptome sequencing (RNA-Seq) data revealed a complete Cowpea aphid-borne mosaic virus (CABMV) genome from virus-infected passion fruit in Kenya. We compared it with six complete CABMV genomes, one each from Zimbabwe and Uganda and two each from Brazil and India. The Zimbabwean isolate CABMV-Z was the closest, with 83.0% nucleotide identity.",contig;nucleotide;transcriptome;amino acid sequence;article;Brazil;cowpea aphid;Cowpea mosaic virus;gene sequence;high throughput sequencing;India;Kenya;nonhuman;nucleotide sequence;passion fruit;plant virus;RNA sequence;sequence homology;Uganda;virus genome;virus isolation;Zimbabwe,"Munguti, F.;Maina, S.;Nyaboga, E. N.;Kilalo, D.;Kimani, E.;Macharia, M.;Holton, T.",2019,,10.1128/mra.01607-18,0
1450,Transcriptional response of avian cells to infection with Newcastle disease virus,"Newcastle disease virus (NDV) causes widespread disease in poultry and wild-birds throughout the world. cDNA microarray analysis was used to examine the effect of NDV infection on host cell transcription. The results show that NDV infection causes an apparent suppression of the interferon response genes during the early stages of infection. In addition, the results reveal transcriptional silencing of cytoskeletal proteins such as the α, β, and γ types of actin, and a downregulation of the thioredoxin gene, a likely mediator of apoptosis with possible implications in NDV pathogenesis. Comparative analyses show that a majority of genes that were transcriptionally regulated during infection with another common respiratory pathogen of poultry, the avian pneumovirus, remained unaltered during NDV infection, suggesting that even phylogenetically related viruses elicit unique or ""signature"" patterns of host transcriptional profiles during infection of host cells. © 2004 Elsevier B.V. All rights reserved.",actin;alpha actin;beta actin;cytoskeleton protein;gamma actin;thioredoxin;unclassified drug;amino acid sequence;apoptosis;article;Avian metapneumovirus;comparative study;DNA microarray;down regulation;gene expression profiling;gene expression regulation;gene repression;gene silencing;molecular phylogeny;Newcastle disease virus;nonhuman;nucleotide sequence;priority journal;sequence homology;transcription initiation;transcription regulation;virus infectivity;virus pathogenesis,"Munir, S.;Sharma, J. M.;Kapur, V.",2005,,10.1016/j.virusres.2004.07.001,0
1451,Molecular epidemiologic survey of infectious bursal disease viruses in broiler farms raised under different vaccination programs,"Over a span of nearly 4 yr, 246 bursal tissue samples were collected from Brazilian commercial broiler flocks (Gallus gallus) throughout the country and imprinted to sample collection cards (Flinders Technology Associates (FTA) cards). A total of 75 infectious bursal disease virus (IBDV) strains was successfully detected from the FTA card imprints and were submitted for further identification and molecular characterization. Nucleotide and predicted amino acid sequences of the IBDV surface protein VP2 were used to identify strains of the virus and place them into phylogenetic groups. The amino acids across the hypervariable region of VP2 in this study varied, but around half of all positive samples were classified as vaccine virus. The IBD viruses fell into 3 categories: variant IBDV, classic IBDV (vaccine), and very virulent (vv) IBDV. The samples were collected according to the 3 different vaccination strategies used in broilers: vectored vaccine, antigen-antibody complex vaccine, and conventional live vaccine. The genetic profile and frequency of the strains recovered from the flocks were highly dependent on the vaccination program. This information helps us gain a better understanding of the current landscape of IBD in Brazil and provides additional scientific data to support selection of the most effective vaccination strategies, products, and practices to prevent disease.",gumboro;vaccination programs;poultry;epidemiology;HORIZONTAL TRANSMISSION;TURKEY HERPESVIRUS;CHICKENS;IBDV;INTERMEDIATE;PROTECTION;ANTIBODIES;EFFICACY;VACCINES,"Muniz, E. C.;Verdi, R.;Jackwood, D. J.;Kuchpel, D.;Resende, M. S.;Mattos, J. C. Q.;Cookson, K.",2018,Jun,,0
1452,Classical swine fever virus vs. Classical swine fever virus: The superinfection exclusion phenomenon in experimentally infected wild boar,"Two groups with three wild boars each were used: Group A (animals 1 to 3) served as the control, and Group B (animals 4 to 6) was postnatally persistently infected with the Cat01 strain of CSFV (primary virus). The animals, six weeks old and clinically healthy, were inoculated with the virulent strain Margarita (secondary virus). For exclusive detection of the Margarita strain, a specific qRT-PCR assay was designed, which proved not to have crossreactivity with the Cat01 strain. The wild boars persistently infected with CSFV were protected from superinfection by the virulent CSFV Margarita strain, as evidenced by the absence of clinical signs and the absence of Margarita RNA detection in serum, swabs and tissue samples. Additionally, in PBMCs, a well-known target for CSFV viral replication, only the primary infecting virus RNA (Cat01 strain) could be detected, even after the isolation in ST cells, demonstrating SIE at the tissue level in vivo. Furthermore, the data analysis of the Margarita qRT-PCR, by means of calculated ΔCt values, supported that PBMCs from persistently infected animals were substantially protected from superinfection after in vitro inoculation with the Margarita virus strain, while this virus was able to infect naive PBMCs efficiently. In parallel, IFN-α values were undetectable in the sera from animals in Group B after inoculation with the CSFV Margarita strain. Furthermore, these animals were unable to elicit adaptive humoral (no E2-specific or neutralising antibodies) or cellular immune responses (in terms of IFN-γ-producing cells) after inoculation with the second virus. Finally, a sequence analysis could not detect CSFV Margarita RNA in the samples tested from Group B. Our results suggested that the SIE phenomenon might be involved in the evolution and phylogeny of the virus, as well as in CSFV control by vaccination. To the best of our knowledge, this study was one of the first showing efficient suppression of superinfection in animals, especially in the absence of IFN-α, which might be associated with the lack of innate immune mechanisms.",alpha interferon;neutralizing antibody;virus RNA;adaptive immunity;animal cell;antibody titer;article;cellular immunity;Classical swine fever virus;controlled study;cross reaction;cytokine production;humoral immunity;in vitro study;in vivo study;innate immunity;male;nonhuman;phylogeny;RNA sequence;sequence analysis;strain identification;superinfection;virus interference;virus load;virus replication;virus virulence;European wild boar,"Muñoz-González, S.;Pérez-Simó, M.;Colom-Cadena, A.;Cabezón, O.;Bohórquez, J. A.;Rosell, R.;Pérez, L. J.;Marco, I.;Lavín, S.;Domingo, M.;Ganges, L.",2016,,10.1371/journal.pone.0149469,0
1453,Electron microscopical studies on 'nonsyncytia forming' bovine herpes viruses isolated in Tanzania,"A description is given of the morphology of 4 viruses recently isolated from bovines with widely differing clinical symptoms. The morphologic features of the isolates are characteristic of the herpes virus group, thus confirming the preliminary classification of the virus strains based on their biological and serological behavior. The findings also indicate that differential diagnosis of herpes viruses on morphologic criteria does not seem possible.",article;autopsy;bovine;electron microscopy;epiretinal membrane;Herpesviridae;histology;in vitro study;microorganism;virus;virus infection;virus isolation,"Munz, E.;Goebel, E.;Rweyemamu, M. M.",1974,,10.1016/0021-9975(74)90041-3,0
1454,Variations in the viral genome and biological properties of bovine leukemia virus wild-type strains,"Bovine leukemia virus (BLV) is the etiological agent of enzootic bovine leukosis (EBL), which causes enormous economic losses in the livestock industry worldwide. To reduce the economic loss caused by BLV infection, it is important to clarify the characters associated with BLV transmissibility and pathogenesis in cattle. In this study, we focused on viral characters and examined spontaneous mutations in the virus and viral properties by analyses of whole genome sequences and BLV molecular clones derived from cows with and without EBL. Genomic analysis indicated that all 28 strains harbored limited genetic variations but no deletion mutations that allowed classification into three groups (A, B, and C), except for one strain. Some nucleotide/amino acid substitutions were specific to a particular group. On the other hand, these genetic variations were not associated with the host bovine leukocyte antigen-DRB3 allele, which is known to be related to BLV pathogenesis. The viral replication activity in vitro was high, moderate, and low in groups A, B, and C, respectively. In addition, the proviral load, which is related to BLV transmissibility and pathogenesis, was high in cows infected with group A strains and low in those infected with group B/C strains. Therefore, these results suggest that limited genetic variations could affect viral properties relating to BLV transmissibility and pathogenesis.","Animals;Cattle;*Enzootic Bovine Leukosis/vi [Virology];*Genetic Variation;*Genome, Viral;Leukemia Virus, Bovine/cl [Classification];*Leukemia Virus, Bovine/ge [Genetics];Leukemia Virus, Bovine/ip [Isolation & Purification];Leukemia Virus, Bovine/ph [Physiology];Phylogeny;Virus Replication","Murakami, H.;Uchiyama, J.;Suzuki, C.;Nikaido, S.;Shibuya, K.;Sato, R.;Maeda, Y.;Tomioka, M.;Takeshima, S. N.;Kato, H.;Sakaguchi, M.;Sentsui, H.;Aida, Y.;Tsukamoto, K.",2018,07 15,,0
1455,Physicochemical and morphological relationships of some arthropod-borne viruses to bluetongue virus--a new taxonomic group. Electron microscopic studies,,"solvent;animal;Arbovirus;article;brain;cell culture;cell line;classification;drug effect;electron microscopy;growth, development and aging;hamster;kidney;microbiology;microtubule;morphogenesis;mouse;mouse strain;parasite vector;pathology;Reoviridae;RNA virus;sheep;sheep disease;virus inclusion;virus infection","Murphy, F. A.;Borden, E. C.;Shope, R. E.;Harrison, A.",1971,,,0
1456,Molecular and biophysical characterization of TT virus: Evidence for a new virus family infecting humans,"The recent isolation of a novel DNA virus from the serum of a Japanese patient (T.T.) has provided the latest possible candidate virus associated with cryptogenic hepatitis. In the present study, we report the complete nucleotide sequence of this virus (TTV) isolated from the serum of a West African. Based on PCR studies designed to amplify overlapping regions of the viral genome and sensitivity to digestion with mung bean nuclease, the vital genome is circular and negative stranded, and comprises 3,852 nt, which is 113 nt longer than the prototype isolate from Japan. Cesium chloride density gradient centrifugation demonstrated banding of the virus at 1.31-1.34 g/ml; filtration studies indicated that TTV had a particle size of 30-50 nm. These results suggest that the virus is similar to the Circoviridae, viruses known to infect plants and vertebrates (e.g, birds and swine); however, sequence similarity searches of available databases did not reveal identity between TTV and other viruses. Phylogenetic analyses of a 260-nt region from 151 globally distributed isolates demonstrated the existence of three major TTV genotypes. Several individuals at high risk for infection with parenterally transmitted viruses were infected with more than one genotype. There was no correlation between genotype and geographic origin. Finally, intravenous inoculation of TTV-positive human serum into chimpanzees demonstrated that TTV can be transmitted to primates; no biochemical or histological evidence for hepatitis was obtained. The distinct biophysical and molecular characteristics of TTV suggest that it is a member of a new family of viruses, which we have tentatively named the Circinoviridae.",circinoviridae;Circoviridae;conference paper;density gradient;DNA virus;genotype;Japan;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;priority journal;sequence analysis;Torque teno virus 1;virus characterization;virus transmission,"Mushahwar, I. K.;Erker, J. C.;Muerhoff, A. S.;Leary, T. P.;Simons, J. N.;Birkenmeyer, L. G.;Chalmers, M. L.;Pilot-Matias, T. J.;Dexai, S. M.",1999,,10.1073/pnas.96.6.3177,0
1457,Avian influenza virus wild bird surveillance in the azov and black sea regions of ukraine (2010-2011),"The Azov and Black Sea basins are part of the transcontinental wild bird migration routes from Northern Asia and Europe to the Mediterranean, Africa, and Southwest Asia. These regions constitute an area of transit, stops during migration, and nesting for many different bird species. From September 2010 to September 2011, a wild bird surveillance study was conducted in these regions to identify avian influenza viruses. Biological samples consisting of cloacal and tracheal swabs and fecal samples were collected from wild birds of different ecological groups, including waterfowl and sea-and land-based birds, in places of mass bird accumulations in Sivash Bay and the Utlyuksky and Molochniy estuaries. The sampling covered the following wild bird biological cycles: autumn migration, wintering, spring migration, nesting, and postnesting seasons. A total of 3634 samples were collected from 66 different species of birds. During the autumn migration, 19 hemagglutinating viruses were isolated, 14 of which were identified as low pathogenicity avian influenza (LPAI) virus subtypes H1N?, H3N8, H5N2, H7N?, H8N4, H10N7, and H11N8. From the wintering samples, 45 hemagglutinating viruses were isolated, 36 of which were identified as LPAI virus subtypes H1N1, H1N? H1N2, H4N?, H6N1, H7N3, H7N6, H7N7, H8N2, H9N2, H10N7, H10N4, H11N2, H12N2, and H15N7. Only three viruses were isolated during the spring migration, nesting, and postnesting seasons (serotypes H6, H13, and H16). The HA and NA genes were sequenced from the isolated H5 and N1 viruses, and the phylogenetic analysis revealed possible ecological connections between the Azov and Black Sea regions and Europe. The LPAI viruses were isolated mostly from mallard ducks, but also from shellducks, shovelers, teals, and white-fronted geese. The rest of the 14 hemagglutinating viruses isolated were identified as different serotypes of avian paramyxoviruses (APMV-1, APMV-4, APMV-6, and APMV-7). This information furthers our understanding of the ecology of avian influenza viruses in wild bird species.",animal;avian influenza;bird;Black Sea;classification;conference paper;genetics;health survey;Influenza A virus;phylogeny;Ukraine;virology;wild animal,"Muzyka, D.;Pantin-Jackwood, M.;Spackman, E.;Stegniy, B.;Rula, O.;Shutchenko, P.",2012,,10.1637/10157-040912-ResNote.1,0
1458,Prevalence and Molecular Characterization of the Hepatitis E Virus in Retail Pork Products Marketed in Canada,"Infection with the hepatitis E virus (HEV) is very common worldwide. HEV causes acute viral hepatitis with approximately 20 million cases per year. While HEV genotypes 1 and 2 cause large waterborne and foodborne outbreaks with a significant mortality in developing countries, genotypes 3 and 4 are more prevalent in developed countries with transmission being mostly zoonotic. In North America and Europe, HEV has been increasingly detected in swine, and exposure to pigs and pork products is considered to be the primary source of infection. Therefore we set out to investigate the prevalence of HEV in retail pork products available in Canada, by screening meal-size portions of pork pâtés, raw pork sausages, and raw pork livers. The presence of the HEV genomes was determined by RT-PCR and viral RNA was quantified by digital droplet PCR. Overall, HEV was detected in 47% of the sampled pork pâtés and 10.5% of the sampled raw pork livers, but not in the sampled pork sausages, and sequencing confirmed that all HEV strains belonged to genotype 3. Further phylogenetic analysis revealed that except for one isolate that clusters with subtype 3d, all isolates belong to subtype 3a. Amino acid variations between the isolates were also observed in the sequenced capsid region. In conclusion, the prevalence of HEV in pâtés and raw pork livers observed in this study is in agreement with the current HEV distribution in pork products reported in other developed countries.",amino acid;virus RNA;article;Canada;controlled study;droplet digital polymerase chain reaction;genotype;hepatitis E;market;nonhuman;nucleotide sequence;phylogeny;pork;prevalence;priority journal;reverse transcription polymerase chain reaction;Sanger sequencing;virus capsid;virus characterization;virus detection;virus genome;virus isolation;virus load;virus strain,"Mykytczuk, O.;Harlow, J.;Bidawid, S.;Corneau, N.;Nasheri, N.",2017,,10.1007/s12560-017-9281-9,0
1459,Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA),"Coronaviruses are of major importance for both animal and human health. With the emergence of novel coronaviruses such as SARS and MERS, the need for fast genome characteri-sation is ever so important. Further, in order to understand the influence of quasispecies of these viruses in relation to biology, techniques for deep-sequence and full-length viral genome analysis are needed. In the present study, we compared the efficiency of two sequence-independent approaches [sequence-independent single primer amplification (SISPA) and single primer isothermal amplification (SPIA, represented by the Ovation kit)] coupled with high-throughput sequencing to generate the full-length genome of bovine coronavirus (BCoV) from a nasal swab. Both methods achieved high genome coverage (100% for SPIA and 99% for SISPA), however, there was a clear difference in the percentage of reads that mapped to BCoV. While approximately 45% of the Ovation reads mapped to BCoV (sequence depth of 169–284 944), only 0.07% of the SISPA reads (sequence depth of 0–249) mapped to the reference genome. Although BCoV was the focus of the study we also identified a bovine rhinitis B virus (BRBV) in the data sets. The trend for this virus was similar to that observed for BCoV regarding Ovation vs. SISPA, but with fewer sequences mapping to BRBV due to a lower amount of this virus. In summary, the SPIA approach used in this study produced coverage of the entire BCoV (high copy number) and BRBV (low copy number) and a high sequence/ genome depth compared to SISPA. Although this is a limited study, the results indicate that the Ovation method could be a preferred approach for full genome sequencing if a low copy number of viral RNA is expected and if high sequence depth is desired.",article;Bovine coronavirus;bovine rhinitis B virus;controlled study;Erbovirus;gene amplification;gene dosage;gene mapping;high throughput sequencing;intermethod comparison;next generation sequencing;nonhuman;nose smear;sequence independent single primer amplification;single primer isothermal amplification;virus genome;virus identification;whole genome sequencing,"Myrmel, M.;Oma, V.;Khatri, M.;Hansen, H. H.;Stokstad, M.;Berg, M.;Blomström, A. L.",2017,,10.1371/journal.pone.0187780,0
1460,Phylogenetic analysis of bovine viral diarrhea viruses using five different genetic regions,"Phylogenetic analysis of the five different regions (5′ non-coding region (5′NCR), Npro, E2, NS3 and NS5B-3′NCR) of 48 Japanese and reported bovine viral diarrhea virus (BVDV) genomes was performed. Japanese BVDVs were segregated into BVDV1 subdivided into six subgroups and BVDV2. One isolate, So CP/75, isolated in 1975 and previously proposed as subgroup 1e according to its 5′NCR sequence, was quite unique and formed an independent lineage in the tree of any region. Another isolate, 190CP, obtained from an experimental mucosal disease case was classified as subgroup 1e, defined by Becher et al. in the 5′NCR, Npro and E2 regions, whereas it was classified as subgroup 1a in the NS5B-3′NCR region. The genomic sequences of the American isolates ILLC and ILLNC obtained from the GenBank database were assigned into subgroup 1b in the 5′NCR, N pro, E2 and NS5B-3′NCR regions, whereas they were assigned into subgroup 1a in the NS3 region, suggesting that recombination between the virus strains classified into different subgroups had occurred in an animal. These findings suggest that phylogenetic analysis of several genetic regions is useful for the further characterization of field BVDV isolates. © 2003 Elsevier B.V. All rights reserved.",article;Bovine viral diarrhea virus 1;cattle disease;gene sequence;nonhuman;nucleotide sequence;phylogeny;priority journal;unindexed sequence;virus genome;virus isolation;virus recombination;virus strain,"Nagai, M.;Hayashi, M.;Sugita, S.;Sakoda, Y.;Mori, M.;Murakami, T.;Ozawa, T.;Yamada, N.;Akashi, H.",2004,,10.1016/j.virusres.2003.10.006,0
1461,Genomic and serological diversity of bovine viral diarrhea virus in Japan,"Genomic properties of 62 field isolates of bovine viral diarrhea virus (BVDV) collected from 1974 to 1999 in Japan were investigated. The 5′ untranslated region (UTR) was amplified by reverse transcriptase-Polymerase chain reaction (RT-PCR) and the 244 to 247 base nucleotide sequences were determined. Serological properties were also characterized by the cross-Neutralization test using antisera against the representative strain of the classified genotype. Using phylogenetic tree analysis, BVDV 1 was subdivided into two major clusters, BVDV-1a (29 isolates) and BVDV-1b (27 isolates). In group 1a, 3 differed from the other viruses, and were classified in a branch assigned as 1a′. However, 4 isolates (So CP/75, 190 CP, 190 NCP and KS86-1-NCP) could not be assigned to group 1a or 1b. In comparison with the published sequence data, KS86-1-NCP, 190 CP and 190 NCP were similar to the Southern Africa isolates that have recently been proposed as BVDV 1c. The 5′UTR sequence of So CP/75 was unique among those of BVDV 1, suggesting that the isolate should be classified into a new genotype. Only 2 out of 62 isolates collected in 1989 and 1990 were iden-Tified as BVDV 2. The results of the cross-Neutralization test strongly supported these data, suggesting a close correlation between the 5′UTR sequence and the antigenicity of BVDV.",,"Nagai, M.;Ito, T.;Sugita, S.;Genno, A.;Takeuchi, K.;Ozawa, T.;Sakoda, Y.;Nishimori, T.;Takamura, K.;Akashi, H.",2001,,10.1007/s007050170139,0
1462,Identification and complete genome analysis of a novel bovine picornavirus in Japan,"We identified novel viruses in feces from cattle with diarrhea collected in 2009 in Hokkaido Prefecture, Japan, by using a metagenomics approach and determined the (near) complete sequences of the virus. Sequence analyses revealed that they had a standard picornavirus genome organization, i.e. 5' untranslated region (UTR) - L- P1 (VP4- VP3- VP2- VP1) - P2 (2A- 2B- 2C) - P3 (3A- 3B- 3C-3D) - 3'UTR- poly(A). They are closely related to other unclassified Chinese picornaviruses; bat picornaviruses group 1-3, feline picornavirus, and canine picornavirus, sharing 45.4-51.4% (P1), 38.0-44.9% (P2), and 49.6-53.3% (P3) amino acid identities, respectively. The phylogenetic analyses and detailed genome characterization showed that they, together with the unclassified Chinese picornaviruses, grouped as a cluster for the P1, 2C, 3CD and VP1 coding regions. These viruses had conserved features (e.g. predicted protein cleavage sites, presence of a leader protein, 2A, 2C, 3C, and 3D functional domains), suggesting they have a common ancestor. Reverse-transcription-PCR assays, using specific primers designed from the 5'UTR sequence of these viruses, showed that 23.0% (20/87) of fecal samples from cattle with diarrhea were positive, indicating the prevalence of these picornavirus in the Japanese cattle population in Hokkaido Prefecture. However, further studies are needed to investigate the pathogenic potential and etiological role of these viruses in cattle.",3' untranslated region;5' untranslated region;article;bat picornavirus;bovine picornavirus;canine picornavirus;feline picornavirus;genome analysis;Japan;nonhuman;phylogeny;Picornaviridae;priority journal;reverse transcription polymerase chain reaction;virus genome,"Nagai, M.;Omatsu, T.;Aoki, H.;Kaku, Y.;Belsham, G. J.;Haga, K.;Naoi, Y.;Sano, K.;Umetsu, M.;Shiokawa, M.;Tsuchiaka, S.;Furuya, T.;Okazaki, S.;Katayama, Y.;Oba, M.;Shirai, J.;Katayama, K.;Mizutani, T.",2015,,10.1016/j.virusres.2015.08.001,1
1463,Full genome analysis of bovine astrovirus from fecal samples of cattle in Japan: identification of possible interspecies transmission of bovine astrovirus,"A viral metagenomics approach was used to investigate fecal samples of Japanese calves with and without diarrhea. Of the different viral pathogens detected, read counts gave nearly complete astrovirus-related RNA sequences in 15 of the 146 fecal samples collected in three distinct areas (Hokkaido, Ishikawa, and Kagoshima Prefectures) between 2009 and 2015. Due to the lack of genetic information about bovine astroviruses (BoAstVs) in Japan, these sequences were analyzed in this study. Nine of the 15 Japanese BoAstVs were closely related to Chinese BoAstVs and clustered into a lineage (tentatively named lineage 1) in all phylogenetic trees. Three of 15 strains were phylogenetically separate from lineage 1, showing low sequence identities, and clustered instead with an American strain isolated from cattle with respiratory disease (tentatively named lineage 2). Interestingly, two of 15 strains clustered with lineage 1 in the open reading frame (ORF)1a and ORF1b regions, while they clustered with lineage 2 in the ORF2 region. Remarkably, one of 15 strains exhibited low amino acid sequence similarity to other BoAstVs and was clustered separately with porcine astrovirus type 5 in all trees, and ovine astrovirus in the ORF2 region, suggesting past interspecies transmission.",amino acid sequence;animal;astrovirus infection;bovine;cattle disease;classification;feces;female;genetics;isolation and purification;Japan;male;Mamastrovirus;molecular genetics;open reading frame;phylogeny;transmission;veterinary medicine;virology;virus genome,"Nagai, M.;Omatsu, T.;Aoki, H.;Otomaru, K.;Uto, T.;Koizumi, M.;Minami-Fukuda, F.;Takai, H.;Murakami, T.;Masuda, T.;Yamasato, H.;Shiokawa, M.;Tsuchiaka, S.;Naoi, Y.;Sano, K.;Okazaki, S.;Katayama, Y.;Oba, M.;Furuya, T.;Shirai, J.;Mizutani, T.",2015,,10.1007/s00705-015-2543-7,1
1464,"GiRaF: Robust, computational identification of influenza reassortments via graph mining","Reassortments in the influenza virus - a process where strains exchange genetic segments - have been implicated in two out of three pandemics of the 20th century as well as the 2009 H1N1 outbreak. While advances in sequencing have led to an explosion in the number of whole-genome sequences that are available, an understanding of the rate and distribution of reassortments and their role in viral evolution is still lacking. An important factor in this is the paucity of automated tools for confident identification of reassortments from sequence data due to the challenges of analyzing large, uncertain viral phylogenies. We describe here a novel computational method, called GiRaF (Graph-incompatibility-based Reassortment Finder), that robustly identifies reassortments in a fully automated fashion while accounting for uncertainties in the inferred phylogenies. The algorithms behind GiRaF search large collections of Markov chain Monte Carlo (MCMC)-sampled trees for groups of incompatible splits using a fast biclique enumeration algorithm coupled with several statistical tests to identify sets of taxa with differential phylogenetic placement. GiRaF correctly finds known reassortments in human, avian, and swine influenza populations, including the evolutionary events that led to the recent 'swine flu' outbreak. GiRaF also identifies several previously unreported reassortments via whole-genome studies to catalog events in H5N1 and swine influenza isolates. © The Author(s) 2010. Published by Oxford University Press.",article;avian influenza virus;software;controlled study;data mining;genetic algorithm;genetic reassortment;geographic distribution;human;influenza;Influenza A virus (H1N1);Influenza A virus (H3N2);Influenza A virus (H5N1);information processing;mathematical model;Monte Carlo method;nonhuman;phylogeny;priority journal;probability;statistical analysis;stem taxon;swine influenza;virus transmission;Graph incompatibility based Reassortment Finder,"Nagarajan, N.;Kingsford, C.",2011,,10.1093/nar/gkq1232,0
1465,"Novel Reassortant Highly Pathogenic Avian Influenza (H5N8) Virus in Zoos, India","Highly pathogenic avian influenza (H5N8) viruses were detected in waterfowl at 2 zoos in India in October 2016. Both viruses were different 7:1 reassortants of H5N8 viruses isolated in May 2016 from wild birds in the Russian Federation and China, suggesting virus spread during southward winter migration of birds.","Animals;*Animals, Zoo;Birds;India/ep [Epidemiology];*Influenza A Virus, H5N8 Subtype/ge [Genetics];Influenza in Birds/ep [Epidemiology];*Influenza in Birds/vi [Virology];Phylogeny;*Reassortant Viruses","Nagarajan, S.;Kumar, M.;Murugkar, H. V.;Tripathi, S.;Shukla, S.;Agarwal, S.;Dubey, G.;Nagi, R. S.;Singh, V. P.;Tosh, C.",2017,04,,0
1466,Genetic analysis of foot-and-mouth disease virus serotype A of Indian origin and detection of positive selection and recombination in leader protease- and capsid-coding regions,"The leader protease (Lpro) and capsid-coding sequences (P1) constitute approximately 3 kb of the foot-and-mouth disease virus (FMDV). We studied the phylogenetic relationship of 46 FMDV serotype A isolates of Indian origin collected during the period 1968-2005 and also eight vaccine strains using the neighbour-joining tree and Bayesian tree methods. The viruses were categorized under three major groups - Asian, Euro-South American and European. The Indian isolates formed a distinct genetic group among the Asian isolates. The Indian isolates were further classified into different genetic subgroups (<5% divergence). Post-1995 isolates were divided into two subgroups while a few isolates which originated in the year 2005 from Andhra Pradesh formed a separate group. These isolates were closely related to the isolates of the 1970s. The FMDV isolates seem to undergo reverse mutation or convergent evolution wherein sequences identical to the ancestors are present in the isolates in circulation. The eight vaccine strains included in the study were not related to each other and belonged to different genetic groups. Recombination was detected in the Lpro region in one isolate (A IND 20/82) and in the VP1 coding 1D region in another isolate (A RAJ 21/96). Positive selection was identified at aa positions 23 in the Lpro (P<0.05; 0.046*) and at aa 171 in the capsid protein VP1 (P<0.01; 0.003**). © 2009 Indian Academy of Sciences.",article;controlled study;Foot and mouth disease virus;genetic analysis;Indian;mutation;nonhuman;nucleotide sequence;serotype;statistical significance;virus capsid;virus strain,"Nagendrakumar, S. B.;Madhanmohan, M.;Rangarajan, P. N.;Srinivasan, V. A.",2009,,10.1007/s12038-009-0011-9,0
1467,Novel real-time PCR-based patho- and phylotyping of potentially zoonotic avian influenza a subtype H5 viruses at risk of incursion into Europe in 2017,"Since November 2016, Europe witnesses another wave of incursion of highly pathogenic avian influenza (HPAI) A(H5) viruses of the Asian origin goose/Guangdong (gs/GD) lineage. Infections with H5 viruses of clade 2.3.4.4b affect wild bird and poultry populations. H5 viruses of clades 2.2, 2.3.1.2c and 2.3.4.4a were detected previously in Europe in 2006, 2010 and 2014. Clades 2.2.1.2 and 2.3.2.1.c are endemic in Egypt and Western Africa, respectively and have caused human fatalities. Evidence exists of their cocirculation in the Middle East. Subtype H5 viruses of low pathogenicity (LPAI) are endemic in migratory wild bird populations. They potentially mutate into highly pathogenic phenotypes following transmission into poultry holdings. However, to date only the gs/GD H5 lineage had an impact on human health. Rapid and specific diagnosis marks the cornerstone for control and eradication of HPAI virus incursions. We present the development and validation of five real-time RT-PCR assays (RT-qPCR) that allow sequencing-independent pathotype and clade-specific distinction of major gs/GD HPAI H5 virus clades and of Eurasian LPAI viruses currently circulating. Together with an influenza A virus-generic RT-qPCR, the assays significantly speed up time-to-diagnosis and reduce reaction times in a OneHealth approach of curbing the spread of gs/GD HPAI viruses.",article;Avian infectious bronchitis virus;diagnostic accuracy;disease transmission;Europe;gene sequence;high throughput sequencing;highly pathogenic avian influenza;infection risk;limit of detection;migrant bird;nonhuman;pathogenicity;phenotype;reverse transcription polymerase chain reaction;sensitivity analysis;sequence analysis;virus isolation;virus virulence,"Naguib, M. M.;Graaf, A.;Fortin, A.;Luttermann, C.;Wernery, U.;Amarin, N.;Hussein, H. A.;Sultan, H.;Al Adhadh, B.;Hassan, M. K.;Beer, M.;Monne, I.;Harder, T. C.",2017,,10.2807/1560-7917.Es.2017.22.1.30435,0
1468,Full genome sequence analysis of a newly emerged QX-like infectious bronchitis virus from Sudan reveals distinct spots of recombination,"Infectious bronchitis virus (IBV) infection continues to cause economically important diseases in poultry while different geno- and serotypes continue to circulate globally. Two infectious bronchitis viruses (IBV) were isolated from chickens with respiratory disease in Sudan. Sequence analysis of the hypervariable regions of the S1 gene revealed a close relation to the QX-like genotype which has not been detected in Sudan before. Whole genome analysis of IBV/Ck/Sudan/AR251-15/2014 isolate by next generation sequencing revealed a genome size of 27,646 nucleotides harbouring 13 open reading frames: 5'-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3'. Highest nucleotide sequence identity of 93% for the whole genome was found with the Chinese IBV strain Ck/CH/LHLJ/140906, the Italian IBV isolate ITA/90254/2005 and the 4/91 vaccine strain. Phylogenetic analysis of the S1 gene revealed that the IBV/Ck/Sudan/AR251-15/2014 isolate clustered together with viruses of the GI-19 lineage. Recombination analysis gave evidence for distinct patterns of origin of RNA in the Sudanese isolate in multiple genes. Several sites of recombination were scattered throughout the genome suggesting that the Sudan-QX-like strain emerged as a unique recombinant from multiple recombination events of parental viruses from 4/91, H120 and ITA/90254/2005 genotypes. The Sudanese QX-like isolate is plausibly genetically different from IBV strains previously reported in Africa and elsewhere.","Animals;Chickens;Coronavirus Infections/ve [Veterinary];Coronavirus Infections/vi [Virology];*Genome, Viral/ge [Genetics];High-Throughput Nucleotide Sequencing;Infectious bronchitis virus/cl [Classification];*Infectious bronchitis virus/ge [Genetics];Phylogeny;RNA, Viral/an [Analysis];RNA, Viral/ge [Genetics];*Recombination, Genetic/ge [Genetics];Sequence Analysis, RNA;Sudan;0 (RNA, Viral)","Naguib, M. M.;Hoper, D.;Arafa, A. S.;Setta, A. M.;Abed, M.;Monne, I.;Beer, M.;Harder, T. C.",2016,12,,0
1469,Sequence analysis of porcine adenovirus serotype 5 fibre gene: Evidence for recombination,"The nucleic acid and deduced amino acid sequence of the fibre gene of the HNF-61 strain of porcine adenovirus serotype 5 (PAdV-5) was determined and compared to that of the HNF-70 strain of the same serotype (Nagy et al., J Gen Virol 82, 525-529, 2001) and also to adenovirus fibre genes from the genera Mastadenovirus and Atadenovirus. The putative HNF-61 and HNF-70 proteins were similar to each other, with 90% amino acid identity. Conserved amino acid sequences described for mastadenovirus fibre shafts were identified in the shaft regions of both PAdV-5 fibres, except for the so-called TLWT motif. The head regions of the PAdV-5 fibre did not resemble any of the known mastadenovirus fibre heads, but they showed characteristics of the fibre head protein sequences of viruses grouped in the proposed genus Atadenovirus (Benkö et al., Virus Taxonomy, Seventh Report of the International Committee on the Taxonomy of Viruses, Academic Press, New York, San Diego, 2000, pp. 227-238). The findings suggested recombination between viruses of different adenovirus genera.",hnf61 protein;hnf70 protein;unclassified drug;viral protein;Human adenovirus 5;amino acid sequence;article;Atadenovirus;gene sequence;genetic recombination;Mastadenovirus;nonhuman;nucleotide sequence;priority journal;protein motif;sequence analysis;serotyping;strain identification;taxonomy;virus gene,"Nagy, M.;Nagy;Tuboly, T.",2002,,10.1023/a:1014580802250,0
1470,Dynamic evolution of endogenous retrovirus-derived genes expressed in bovine conceptuses during the period of placentation,"In evolution of mammals, some of essential genes for placental development are known to be of retroviralorigin, as syncytin-1 derived from an envelope (env) gene of an endogenous retrovirus (ERV) aids in the cell fusion of placenta in humans. Although the placenta serves the same function in all placental mammals, env-derived genes responsible for trophoblast cell fusion and maternal immune tolerance differ among species and remain largely unidentified in the bovine species. To examine env-derived genes playing a role in the bovine placental development comprehensively, we determined the transcriptomic profiles of bovine conceptuses during three crucial windows of implantation periods using a high-throughput sequencer. The sequence reads were mapped into the bovine genome, in which ERV candidates were annotated using RetroTector© (7,624 and 1,542 for ERV-derived and env-derived genes, respectively). Themapped reads showed that approximately 18% (284 genes) of env-derived genes in the genome were expressed during placenta formation, and approximately 4% (63 genes) were detected for all days examined. We verified three env-derived genes that are expressed in trophoblast cells by polymerase chain reaction. Out of these three, the sequence of env-derived gene with the longest open reading frame (named BERV-P env) was found to show high expression levels in trophoblast cell lines and to be similar to those of syncytin-Car1 genes found in dogs and cats, despite their disparate origins. These results suggest that placentation depends on various retrovirus-derived genes that could have replaced endogenous predecessors during evolution. © 2013 The Author(s).","placenta protein;syncytin;virus envelope protein;animal;article;cat;bovine;dog;endogenous retrovirus;female;gene expression regulation;genetics;genome;growth, development and aging;human;molecular evolution;phylogeny;placenta;pregnancy;reproduction","Nakagawa, S.;Bai, H.;Sakurai, T.;Nakaya, Y.;Konno, T.;Miyazawa, T.;Gojobori, T.;Imakawa, K.",2013,,10.1093/gbe/evt007,0
1471,Identification of European-type hepatitis E virus subtype 3e isolates in Japanese wild boars: Molecular tracing of HEV from swine to wild boars,"Nucleotide sequences of hepatitis E virus (HEV) isolates infecting wild boars in Mie prefecture, which is located in the central region of Japan and is far from the most prevalent regions of HEV infection in Japan, were determined and characterised. Among 144 serum samples of wild boars captured in Mie prefecture, 7 were positive for HEV-RNA. The nucleotide sequence of nearly the entire genome was determined for 4 of the 7 positive samples. Phylogenetic tree analyses indicated that 6 samples were subtype 3e and 1 was subtype 3a among the 7 isolates. We identified the indigenization of subtype 3e isolates in Japanese wild boars. Furthermore, 5 subtype 3e isolates were closely related and were located in the peripheral branch of subtype 3e isolates from European countries in the phylogenetic tree. The structure indicated that the ancestor of the 5 subtype 3e isolates originated in Europe. The phylogenetic structure and coalescent analyses suggested that the subtype 3e isolates entered Japan from Europe by importation of large-race pigs around 1966. The results also indicated that several lineages of subtype 3e expanded to a wide area of Japan around 1992 and 1 of the lineages was indigenized in wild boars in Mie prefecture between 1992 and 2009. The appearance of a wild boar cluster in the peripheral branch in the phylogenetic lineage may indicate the direction of gene flow of HEV subtype 3e from swine to wild boars. Clarification of the transmission direction or route should be helpful to prevent a future endemic or epidemic of HEV infection. © 2013 Elsevier B.V..",virus RNA;article;controlled study;genome analysis;geographic origin;hepatitis E;Hepatitis E virus;Japan;last common ancestor;nonhuman;phylogenetic tree;priority journal;RNA sequence;pig;virus characterization;virus identification;virus isolation;virus transmission;virus typing;European wild boar,"Nakano, T.;Takahashi, K.;Arai, M.;Okano, H.;Kato, H.;Ayada, M.;Okamoto, H.;Mishiro, S.",2013,,10.1016/j.meegid.2013.06.004,0
1472,Dysfunction of bovine endogenous retrovirus K2 envelope glycoprotein is related to unsuccessful intracellular trafficking,"Endogenous retroviruses (ERVs) are the remnants of retroviral infection of ancestral germ cells. Mutations introduced into ERVs halt the production of infectious agents, but their effects on the function of retroviral proteins are not fully understood. Retroviral envelope glycoproteins (Envs) are utilized in membrane fusion during viral entry, and we recently identified intact coding sequences for bovine endogenous retrovirus K1 (BERV-K1) and BERV-K2 Envs. Amino acid sequences of BERV-K1 Env (also called Fematrin-1) and BERV-K2 Env are similar, and both viruses are classified in the genus Betaretrovirus. While Fematrin-1 plays an important role in cell-to-cell fusion in bovine placenta, the BERV-K2 envelope gene is marginally expressed in vivo, and its recombinant Env protein is defective in membrane fusion due to inefficient cleavage of surface (SU) and transmembrane subunits. Here, we conducted chimeric analyses of Fematrin-1 and BERV-K2 Envs and revealed that defective maturation of BERV-K2 Env contributed to failed intracellular trafficking. Fluorescence microscopy and flow cytometric analysis suggested that in contrast to Fematrin-1 Env, BERV-K2 Env could not be transported from the endoplasmic reticulum to the trans-Golgi network, where cellular proteases required for processing retroviral Envs are localized. We also identified that one of the responsive regions of this phenomenon resided within a 65-amino-acid region of BERV-K2 SU. This is the first report to identify that retroviral Env SU is involved in the regulation of intracellular trafficking, and it may help to elucidate the maturation process of Fematrin-1 and other related Envs. © 2014, American Society for Microbiology.",fematrin 1 protein;unclassified drug;virus glycoprotein;amino acid sequence;article;bovine endogenous retrovirus K2;cell migration;cell surface;cellular distribution;endogenous retrovirus;endoplasmic reticulum;envelope gene;flow cytometry;fluorescence microscopy;gene expression;in vivo study;nonhuman;priority journal;protein expression;sequence alignment;trans Golgi network;virogenesis;virus entry;virus envelope;virus gene,"Nakaya, Y.;Miyazawa, T.",2014,,10.1128/jvi.00288-14,0
1473,A metagenomic study of the rumen virome in domestic caprids,"This project sought to investigate the domestic caprid rumen virome by developing a robust viral DNA isolation and enrichment protocol (utilizing membrane filtration, ultra-centrifugation, overnight PEG treatment and nuclease treatment) and using RSD-PCR and high throughput sequencing (HTS) techniques. 3.53% of the reads obtained were analogous to those of viruses denoting Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, Microviridae, Poxviridae, Tectiviridae and Marseillevirus. Most of the sequenced reads from the rumen were similar to those of phages, which are critical in maintaining the rumen microbial populations under its carrying capacity. Though identified in the rumen, most of these viruses have been reported in other environments as well. Improvements in the viral DNA enrichment and isolation protocol are required to obtain data that are more representative of the rumen virome. The 102,130 unknown reads (92.31%) for the goat and 36,241 unknown reads (93.86%) for the sheep obtained may represent novel genomes that need further study.",animal;classification;domestic animal;genetics;goat;high throughput sequencing;isolation and purification;metagenomics;rumen;sheep;virology;virus,"Namonyo, S.;Wagacha, M.;Maina, S.;Wambua, L.;Agaba, M.",2018,,10.1007/s00705-018-4022-4,1
1474,Detection and Phylogenetic Analysis of the Hepatitis E Virus in a Canadian Swine Production Network,"Viral contamination along the production chain is a significant concern in both food safety and livestock health. Pigs have been reported to act as a reservoir for zoonotic viruses, sometimes emerging ones, and epidemiological studies have shown direct links between the consumption of uncooked pork offal and cases of hepatitis caused by the hepatitis E virus (HEV) genotype 3 in humans. The presence of HEV in swine herds has been reported, but its dissemination in pork production environments is still unknown. To investigate viral contamination sources in the swine industry, 452 environment and fecal samples, including samples from livestock transportation vehicles, were collected over a period of 11 months from ten farms and one slaughterhouse that together represent a single production network. Hepatitis E virus RNA was detected by nested RT-PCR in 32 samples from both inside and outside farm buildings, on trucks, and, mostly, from fomites collected in the slaughterhouse yard, such as on a utility vehicle. Phylogenetic analysis showed a wide diversity of HEV genotype 3 strains, similar to human and swine strains previously found. According to the results of this study, the movements of trucks and utility vehicles might play an important role in HEV dissemination on a slaughterhouse site and throughout an entire network.",DNA fragment;virus DNA;virus RNA;article;building;Canada;controlled study;fomite;Hepatitis E virus;motor vehicle;nonhuman;nucleotide sequence;phylogeny;pig farming;priority journal;slaughterhouse;viral contamination;viral genetics;virus detection,"Nantel-Fortier, N.;Letellier, A.;Lachapelle, V.;Fravalo, P.;L’Homme, Y.;Brassard, J.",2016,,10.1007/s12560-016-9252-6,0
1475,Genetic Predisposition To Acquire a Polybasic Cleavage Site for Highly Pathogenic Avian Influenza Virus Hemagglutinin,"Highly pathogenic avian influenza viruses with H5 and H7 hemagglutinin (HA) subtypes evolve from low-pathogenic precursors through the acquisition of multiple basic amino acid residues at the HA cleavage site. Although this mechanism has been observed to occur naturally only in these HA subtypes, little is known about the genetic basis for the acquisition of the polybasic HA cleavage site. Here we show that consecutive adenine residues and a stem-loop structure, which are frequently found in the viral RNA region encoding amino acids around the cleavage site of low-pathogenic H5 and H7 viruses isolated from waterfowl reservoirs, are important for nucleotide insertions into this RNA region. A reporter assay to detect nontemplated nucleotide insertions and deep-sequencing analysis of viral RNAs revealed that an increased number of adenine residues and enlarged stem-loop structure in the RNA region accelerated the multiple adenine and/or guanine insertions required to create codons for basic amino acids. Interestingly, nucleotide insertions associated with the HA cleavage site motif were not observed principally in the viral RNA of other subtypes tested (H1, H2, H3, and H4). Our findings suggest that the RNA editing-like activity is the key mechanism for nucleotide insertions, providing a clue as to why the acquisition of the polybasic HA cleavage site is restricted to the particular HA subtypes.<b>IMPORTANCE</b> Influenza A viruses are divided into subtypes based on the antigenicity of the viral surface glycoproteins hemagglutinin (HA) and neuraminidase. Of the 16 HA subtypes (H1 to -16) maintained in waterfowl reservoirs of influenza A viruses, H5 and H7 viruses often become highly pathogenic through the acquisition of multiple basic amino acid residues at the HA cleavage site. Although this mechanism has been known since the 1980s, the genetic basis for nucleotide insertions has remained unclear. This study shows the potential role of the viral RNA secondary structure for nucleotide insertions and demonstrates a key mechanism explaining why the acquisition of the polybasic HA cleavage site is restricted to particular HA subtypes in nature. Our findings will contribute to better understanding of the ecology of influenza A viruses and will also be useful for the development of genetically modified vaccines against H5 and H7 influenza A viruses with increased stability.","Adenine/ch [Chemistry];Animals;Chickens/vi [Virology];*Genetic Predisposition to Disease;Guanine/ch [Chemistry];Hemagglutinin Glycoproteins, Influenza Virus/ch [Chemistry];Hemagglutinin Glycoproteins, Influenza Virus/cl [Classification];*Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];High-Throughput Nucleotide Sequencing;Influenza A Virus, H5N1 Subtype/ch [Chemistry];*Influenza A Virus, H5N1 Subtype/ge [Genetics];*Influenza A Virus, H5N1 Subtype/py [Pathogenicity];Influenza in Birds;RNA, Viral/ch [Chemistry];*RNA, Viral/ge [Genetics];Virulence;0 (Hemagglutinin Glycoproteins, Influenza Virus);0 (RNA, Viral);0 (hemagglutinin, avian influenza A virus);5Z93L87A1R (Guanine);JAC85A2161 (Adenine)","Nao, N.;Yamagishi, J.;Miyamoto, H.;Igarashi, M.;Manzoor, R.;Ohnuma, A.;Tsuda, Y.;Furuyama, W.;Shigeno, A.;Kajihara, M.;Kishida, N.;Yoshida, R.;Takada, A.",2017,02 14,,0
1476,Characterization and phylogenetic analysis of a novel picornavirus from swine feces in Japan,"During an investigation of porcine fecal viruses using a metagenomics approach, a novel picornavirus was identified from the feces of a healthy two-month-old pig. This virus, named porcine picornavirus Japan (PPVJ), had a standard picornavirus genome organization, including the L protein region. The 5' untranslated region harbored a type II internal ribosomal entry site. This virus was most closely related to lesavirus 1 (amino acid sequence identity: 38.2 %) in P1, equine rhinitis A virus (25.8 %) in P2, and lesavirus 2 (40.9 %) in P3. According to the genus demarcations for the family Picornaviridae (less than 40 %, 40 %, and 50 % amino acid sequence identity in P1, P2, and P3, respectively), PPVJ represents a new genus in the family Picornaviridae. PPVJ was detected in 23.3 % of the fecal samples (from 58.3 % of the farms across a wide area) from pigs less than four months old, by reverse transcription PCR, using specific primers designed from the 3D sequence, followed by sequencing. The host range and pathogenic potential of this virus in animals is yet to be determined.",5' untranslated region;virus RNA;animal;chemistry;classification;conformation;feces;genetics;isolation and purification;Japan;phylogeny;Picornaviridae;pig;reverse transcription polymerase chain reaction;virology;virus genome,"Naoi, Y.;Kishimoto, M.;Masuda, T.;Ito, M.;Tsuchiaka, S.;Sano, K.;Yamasato, H.;Omatsu, T.;Aoki, H.;Furuya, T.;Katayama, Y.;Oba, M.;Okada, T.;Shirai, J.;Mizutani, T.;Nagai, M.",2016,,10.1007/s00705-016-2834-7,1
1477,Six-year surveillance of Newcastle disease virus in wild birds in north-eastern Spain (Catalonia),"Given that Newcastle disease (ND) is one of the major threats for the poultry industry, testing of Newcastle disease virus (NDV) has been carried out since 2010 in cases of mortality in wild birds (passive surveillance) in Catalonia. The objective is to provide an early warning system to prevent the infection of poultry. Since 2010, 35 episodes of mortality in wild birds were attributed to NDV infection. Throughout this period there was a progressive expansion of NDV to new areas, with an increase in the episodes of mortality, although it is not clear whether they were the result of the spread of the virus, or of the improvement of the surveillance. Phylogenetic analyses indicate that two distinct sublineages of NDV, 4a and 4b, were circulating in Catalonia. Both sublineages seem to be endemic in the wild bird population, affecting mainly Eurasian-collared doves, with a clear pattern in relation to its spatial distribution (coincident with the distribution of this species), and its temporal distribution (with the majority of cases between September and February). So far, endemicity in wild birds has not resulted in ND outbreaks in poultry. However, there are still many uncertainties about, for example, whether NDV may expand to new areas of Catalonia (with higher poultry density), or about the threat that the apparently more novel sublineage 4a may represent. Hence, efforts should be made so that measures to prevent infection of poultry farms (particularly in high-risk areas and periods) are encouraged, and surveillance is maintained.",animal;bird;bird disease;classification;Columbidae;epidemic;epidemiological monitoring;genetics;genotype;geography;isolation and purification;mortality;Newcastle disease;Newcastle disease virus;phylogeny;sequence analysis;Spain;veterinary medicine;virology,"Napp, S.;Alba, A.;Rocha, A. I.;Sánchez, A.;Rivas, R.;Majó, N.;Perarnau, M.;Massot, C.;Miguel, E. S.;Soler, M.;Busquets, N.",2017,,10.1080/03079457.2016.1206177,0
1478,Genotypic and epitope characteristics of group A porcine rotavirus strains circulating in Canada,"Surveillance of Rotavirus A (RVA) infections in North America swine populations are limited and not performed over a significant time period to properly assess the diversity of RVA strains in swine. The VP7 (G) and VP4 (P) genes of 32 Canadian RVA strains, circulating between 2009 and 2015 were sequenced, identifying the G3P[13], G5P[7], G9P[7], G9[13], and G9[19] genotype combinations. The Canadian RVA strains were compared to the RVA strains present in the swine ProSystems RCE rotavirus vaccine. The comparison revealed multiple amino acid differences in the G and P antigenic epitopes, regardless of the G and P genotypes but specifically in the Canadian G3, P[13] and P[19] genotypes. Our study further contributes to the characterization of RVA's evolution and disease mitigation among swine, which may optimize target vaccine design, thereby minimizing RVA disease in this economically important animal population.",epitope;protein VP4;protein VP7;Rotavirus vaccine;animal tissue;article;Canada;controlled study;drug design;genotype;infection control;molecular evolution;nonhuman;nucleotide sequence;phylogeny;porcine rotavirus;porcine rotavirus A;sequence analysis;strain difference;viral genetics;virus strain;virus transmission,"Naseer, O.;Jarvis, M. C.;Ciarlet, M.;Marthaler, D. G.",2017,,10.1016/j.virol.2017.03.008,0
1479,Long-term evolution of viruses: A Janus-faced balance,"The popular textbook image of viruses as noxious and selfish genetic parasites greatly underestimates the beneficial contributions of viruses to the biosphere. Given the crucial dependency of viruses to reproduce in an intracellular environment, viruses that engage in excessive killing (lysis) can drive their cellular hosts to extinction and will not survive. The lytic mode of virus propagation must, therefore, be tempered and balanced by non-lytic modes of virus latency and symbiosis. Here, we review recent bioinformatics and metagenomic studies to argue that viral endogenization and domestication may be more frequent mechanisms of virus persistence than lysis. We use a triangle diagram to explain the three major virus persistence strategies that explain the global scope of virus-cell interactions including lysis, latency and virus-cell symbiosis. This paradigm can help identify novel directions in virology research where scientists could artificially gain control over switching lytic and beneficial viral lifestyles.",beneficial viruses;persistence triangle;viral domestication;viral;endogenization;virus-host interactions;BACTERIOPHAGE-LAMBDA;BACTERIAL GENOMES;ARCHAEAL VIRUSES;MAJOR SOURCE;LIFE;POLYDNAVIRUSES;EUKARYOTES;PROPHAGES;ORIGIN;IMPACT,"Nasir, A.;Kim, K. M.;Caetano-Anolles, G.",2017,Aug,,0
1480,Biological and molecular characterization of chicken anaemia virus isolates of Indian origin,"In the present study, four chicken anaemia virus (CAV) isolates (CAV-A, -B, -E and -P) recovered from different geographical regions of India were characterized. CAV genome of 1766 bp nucleotide region containing the complete coding region of VP2 and VP3 proteins, and partial coding region of VP1 protein were sequenced. The nucleotide and deduced amino acid sequence of the Indian CAV isolates were aligned and compared with CAV isolates of European, Asian, American and Australian origin. Phylogenetic analysis of the Indian CAV isolates were also carried out based on the nucleotide and deduced amino acid sequences. The results indicated that Indian isolates were genetically evolved from different parts of the world. Indian isolate, CAV-A was found closely related to European Cux-1 strain, CAV-B and -P were closely related to Bangladesh BD-3 strain and CAV-E was closely related to Australian 704 strain. The pathogenicity of the four CAV isolates was studied in day-old specific pathogen free (SPF) chicks. Day-old SPF chicks (n = 50) were divided into five groups comprised of 10 chicks in each group. Group 1 was kept as control and groups 2-5 were infected with each CAV isolate separately. The chicks were infected at a dose rate of 1 ml cell culture fluid (104.5 TCID50/0.1 ml) per bird intramuscularly. The clinical signs, mortality and packed cell volume (PCV) and body weight gain were recorded on 5, 10 and 15 days post-infection. At 15th day, all the birds were sacrificed and various organs, viz., thymus, bone marrow, spleen, liver and bursa were examined for gross and microscopic changes. The pathogenicity study indicated that all the CAVs except CAV-B were able to produce clinical disease and immunosuppression in young chicks whereas the isolate CAV-B produced no clinical disease but only induced immunosuppression, which was revealed by microscopic examination of the lymphoid organs. The study showed valuable information on molecular epidemiological status of CAV isolates prevalent in India for the first time. © 2005 Elsevier B.V. All rights reserved.",protein VP1;protein VP2;protein VP3;unclassified drug;viral protein;amino acid sequence;animal cell;animal disease;animal experiment;animal tissue;article;Asia;Australia;chicken;Circoviridae;controlled study;Europe;genome analysis;geographic distribution;India;molecular evolution;newborn;nonhuman;nucleotide sequence;phylogeny;priority journal;sequence analysis;virus genome;virus infection;virus isolation;virus strain;Western Hemisphere,"Natesan, S.;Kataria, J. M.;Dhama, K.;Rahul, S.;Baradhwaj, N.",2006,,10.1016/j.virusres.2005.11.017,0
1481,Comparison of exosomes purified via ultracentrifugation (UC) and Total Exosome Isolation (TEI) reagent from the serum of Marek's disease virus (MDV)-vaccinated and tumor-bearing chickens,"Extracellular vesicles (EVs) is a collective term used to refer microparticles, exosomes, and apoptotic bodies produced by a variety of cells and released into interstitial spaces and bodily fluids. Serum exosomes can serve as invaluable biomarkers, containing m/miRNAs, lipids, and proteins, indicative of various conditions. There are currently limited studies on the characterization and mutual consensus of biomarker profiles of serum exosomes purified by different methods. Here we compared the advantages and disadvantages of two commonly used serum exosome purification procedures including ultracentrifugation (UC) and Total Exosome Isolation (TEI) reagent, by analyzing exosome size distribution, concentration, morphology and miRNA expression profiles. Serum was obtained from Marek's disease virus (MDV)-infected chickens that were either vaccinated against Marek's disease (MD), and thus protected, or unvaccinated and bearing MDV-induced tumors. Nanoparticle tracking analysis (NTA) and Transmission Electron Microscopy (TEM) were performed to evaluate particle size, concentration, and morphological integrity, respectively. Our results indicate that the size distribution of particles purified by either procedure is consistent with that of exosomes (30–150 nm). TEI reagent generated higher yields and co-isolated additional EV populations that are slightly larger (∼180 nm). Based on the miRNA expression profiles from a previous high throughput sequencing experiment of exosome small RNAs, we selected six cellular and four MDV1 miRNAs, to validate their expression in UC- and TEI-purified exosomes. miRNA expression profiles displayed relative correlation between the two procedures, but distinctive differences were observed in abundance with TEI-purified exosomes showing higher miRNA expression consistent with higher yield than those purified by UC. TEI-purified exosomes from vaccinated chickens exhibited greater expression of tumor suppressor miRNA, gga-mir-146b and least expression of oncomiR, gga-mir-21 compared to those obtained from tumor-bearing chickens. We propose that gga-mir-146 and -21 can serve as serum exosome biomarkers for vaccine-induced protection and MD tumors respectively.",Marek disease vaccine;microRNA;microRNA 146b;microRNA 21;reagent;total exosome isolation reagent;unclassified drug;analytic method;animal cell;animal experiment;animal model;article;cell population;cell size;cellular distribution;comparative study;concentration (parameter);controlled study;exosome;Gallid alphaherpesvirus 2;gene expression profiling;high throughput sequencing;Marek disease;morphology;nanoparticle tracking analysis;nonhuman;particle size;priority journal;quantitative analysis;reverse transcription polymerase chain reaction;transmission electron microscopy;ultracentrifugation;vaccination,"Nath Neerukonda, S.;Egan, N. A.;Patria, J.;Assakhi, I.;Tavlarides-Hontz, P.;Modla, S.;Muñoz, E. R.;Hudson, M. B.;Parcells, M. S.",2019,,10.1016/j.jviromet.2018.10.004,0
1482,Origins of the new influenza A(H1N1) virus: time to take action,"To gain insight into the possible origins of the 2009 outbreak of new influenza A(H1N1), we performed two independent analyses of genetic evolution of the new influenza A(H1N1) virus. Firstly, protein homology analyses of more than 400 sequences revealed that this virus most likely evolved from recent swine viruses. Secondly, phylogenetic analyses of 5,214 protein sequences of influenza A(H1N1) viruses (avian, swine and human) circulating in North America for the last two decades (from 1989 to 2009) indicated that the new influenza A(H1N1) virus possesses a distinctive evolutionary trait (genetic distinctness). This appears to be a particular characteristic in pig-human interspecies transmission of influenza A. Thus these analyses contribute to the evidence of the role of pig populations as ""mixing vessels"" for influenza A(H1N1) viruses.",article;epidemic;female;genetics;health survey;human;incidence;influenza;Influenza A virus (H1N1);male;methodology;North America;risk assessment;risk factor;statistics;virology,"Nava, G. M.;Attene-Ramos, M. S.;Ang, J. K.;Escorcia, M.",2009,,,0
1483,Genetic and antigenic analysis of type a foot-and-mouth disease viruses isolated in India during 1987-1996,"Twenty-three foot-and-mouth disease virus (FMDV) type A field isolates, recovered from different outbreaks during 1987-1996 in India, were subjected to antigenic and genetic analysis. The isolates showed a close antigenic relationship to the current vaccine strain (IND 17/77) in micro-neutralization test conducted using a vaccine strain (IND 17/77) antiserum and a peptide (aa 136-151 of VP1 protein of the A22/ Azerbaijan/65 strain) antiserum. However, the isolates revealed minor antigenic differences in their reactivity with three neutralizing monoclonal antibodies (MAbs) recognizing trypsin-sensitive conformation-independent epitopes of the vaccine virus strains. Phylogenetic relationship between the isolates was carried out employing a part of the ID gene (168 nucleotides at the 3′-end). Additional seven type A Indian field isolates reported earlier were included in the analysis. The percent similarity among the Indian isolates varied from 82.7% to 99.4% at nucleotide level, and from 83.9% to 100% at amino acid level. These observations clearly demonstrate genetic heterogeneity of the field isolates. The current vaccine strain IND 17/77 showed divergence of 9.7% at nucleotide level and 5.6% at amino acid level from the A22 Iraq 24/64 isolate. The field strains were divergent from the vaccine strain IND 17/77 by 5.6%-14.6% and 3.7%-13.7 % at nucleotide and amino acid level, respectively. In the phylogenetic tree, the isolates were distributed into 21 genetic groups. The clustering pattern of the isolates in the phylogenetic tree revealed no specific distribution pattern of the foot-and-mouth disease (FMD) outbreaks in relation to their geographical locations, caused by unrestricted animal movement and endemic nature of the disease.",monoclonal antibody;amino acid analysis;antigenicity;article;endemic disease;epidemic;foot and mouth disease;genetic analysis;geographic distribution;India;nonhuman;nucleotide sequence;phylogeny;sequence analysis;strain difference;virus isolation,"Nayak, B.;Pattnaik, B.;Tosh, C.;Sanyal, A.;Hemadri, D.;Patil, S. S.;Venkataramanan, R.",2001,,,0
1484,Detection of novel porcine bocaviruses in fecal samples of asymptomatic pigs in Cameroon,"Improvements and widespread use of nucleic acid amplification and sequencing methods have led to the recognition of new virus diversity in various domestic animals, including pigs. In this study we utilized either virus species specific or broadly reactive PCR assays to describe the occurrence and genetic diversity of selected DNA viruses belonging to families Adenoviridae, Circoviridae, Anelloviridae and Parvoviridae in Cameroonian pigs. Fecal specimens were collected during spring of 2011. No adenoviruses, circoviruses and anelloviruses were detected, however, high prevalence and remarkable genetic diversity within the identified parvoviruses and, particularly, within bocaviruses was observed. PPV4 was the most prevalent virus (20%), followed by PBoV3 (18%), PBoV4 (18%), PBoV5 plus 6V/7V (16%), and PBoV1 plus PBoV2 (6%). The frequency of mixed infections with various combinations of these virus species reached 20%. Genetic analysis of the identified viruses showed that the capsid gene of PBoV1 and PBoV2 strains shared up to 91% and 94%. nt sequence similarities to reference PBoV1 and PBoV2 strains, respectively. The identified PBoV3 and PBoV4 strains shared ≤95% and ≤98%. nt identities with reference PBoV3 and PBoV4 strains, respectively, along the NS gene, whereas the PBoV5 strains shared 86%. nt identities with Hungarian and 87%. nt identities with Chinese PBoV5 strains along the capsid gene. In addition, a single PBoV5-like strain shared ≤71%. nt sequence identity with other PBoV5 strains. This is the first study to report evidence of the circulation of bocaviruses in Africa and contributes to our understanding of the impact of globalization on the dispersal of new and emerging viruses. © 2013.",Anelloviridae;article;Bocavirus infection;capsid gene;Circoviridae;controlled study;feces analysis;genetic variability;mixed infection;nonhuman;nonstructural protein gene;nucleotide sequence;Parvoviridae;phylogeny;polymerase chain reaction;priority journal;sequence analysis;sequence homology;pig;viral genetics;virus classification;virus detection;virus gene;virus identification;virus strain,"Ndze, V. N.;Cadar, D.;Cságola, A.;Kisfali, P.;Kovács, E.;Farkas, S.;Ngu, A. F.;Esona, M. D.;Dán, T.;Tuboly, T.;Bányai, K.",2013,,10.1016/j.meegid.2013.03.006,0
1485,Avian Leukosis Virus Activation of an Antisense RNA Upstream of TERT in B-Cell Lymphomas,"UNLABELLED: Avian leukosis virus (ALV) induces tumors by integrating its proviral DNA into the chicken genome and altering the expression of nearby genes via strong promoter and enhancer elements. Viral integration sites that contribute to oncogenesis are selected in tumor cells. Deep-sequencing analysis of B-cell lymphoma DNA confirmed that the telomerase reverse transcriptase (TERT) gene promoter is a common ALV integration target. Twenty-six unique proviral integration sites were mapped between 46 and 3,552 nucleotides (nt) upstream of the TERT transcription start site, predominantly in the opposite transcriptional orientation to TERT Transcriptome-sequencing (RNA-seq) analysis of normal bursa revealed a transcribed region upstream of TERT in the opposite orientation, suggesting the TERT promoter is bidirectional. This transcript appears to be an uncharacterized antisense RNA. We have previously shown that TERT expression is upregulated in tumors with integrations in the TERT promoter region. We now report that the viral promoter drives the expression of a chimeric transcript containing viral sequences spliced to exons 4 through 7 of this antisense RNA. Clonal expansion of cells with ALV integrations driving overexpression of the TERT antisense RNA suggest it may have a role in tumorigenesis. IMPORTANCE: The data suggest that ALV integrations in the TERT promoter region drive the overexpression of a novel antisense RNA and contribute to the development of lymphomas.","Animals;*Avian Leukosis/ge [Genetics];*Avian Leukosis/vi [Virology];*Avian Leukosis Virus/ge [Genetics];Cell Transformation, Neoplastic/ge [Genetics];Chickens;High-Throughput Nucleotide Sequencing/mt [Methods];*Lymphoma, B-Cell/ge [Genetics];*Lymphoma, B-Cell/vi [Virology];Promoter Regions, Genetic/ge [Genetics];*RNA, Antisense/ge [Genetics];*Telomerase/ge [Genetics];Transcription Initiation Site/ph [Physiology];Transcriptome/ge [Genetics];Up-Regulation/ge [Genetics];Virus Integration/ge [Genetics];0 (RNA, Antisense)","Nehyba, J.;Malhotra, S.;Winans, S.;O'Hare, T. H.;Justice, J. t;Beemon, K.",2016,10 15,,0
1486,Molecular biology of bovine viral diarrhea virus,"Bovine viral diarrhea viruses (BVDV) are arguably the most important viral pathogen of ruminants worldwide and can cause severe economic loss. Clinical symptoms of the disease caused by BVDV range from subclinical to severe acute hemorrhagic syndrome, with the severity of disease being strain dependent. These viruses are classified as members of the Pestivirus genus of the Flaviviridae. BVDV are considered primarily a pathogen of cattle but can infect most ruminant species. The virus particle consists of a lipid bilayer membrane surrounding the encapsidated genomic RNA. Inserted in the outer membrane are two virus-encoded glycoproteins that contain the major antigenic determinants of the virus as well as receptor binding and cell fusion functions. A third glycoprotein is weakly associated with the virion, but also possesses unique features that play important roles in suppression of innate immunity. The viral proteins are encoded in a single, large open reading frame. The viral proteins are proteolytically cleaved from the polyprotein by different proteases. The structural proteins are processed by cellular signal peptidases while the processing of the nonstructural proteins is by the viral serine protease. The virus is assembled and matures in the endoplasmic reticulum and golgi bodies of the cell. The virus is released via exocytosis, where viral proteins are not exposed on the surface of the cell. © 2012.",genomic RNA;glycoprotein E1;glycoprotein E2;nonstructural protein 2;nonstructural protein 3;nonstructural protein 4A;nonstructural protein 4B;nonstructural protein 5A;nonstructural protein 5B;peptidase;serine;virus glycoprotein;viral protein;virus RNA;article;Bovine viral diarrhea virus 1;bovine viral diarrhea;cell fusion;endoplasmic reticulum;enzyme activity;exocytosis;genetic organization;genetic variability;Golgi complex;innate immunity;lipid membrane;molecular biology;nonhuman;open reading frame;priority journal;protein degradation;protein expression;protein function;protein processing;taxonomy;virion;virus assembly;virus particle;virus replication,"Neill, J. D.",2013,,10.1016/j.biologicals.2012.07.002,0
1487,Simultaneous rapid sequencing of multiple RNA virus genomes,"Comparing sequences of archived viruses collected over many years to the present allows the study of viral evolution and contributes to the design of new vaccines. However, the difficulty, time and expense of generating full-length sequences individually from each archived sample have hampered these studies. Next generation sequencing technologies have been utilized for analysis of clinical and environmental samples to identify viral pathogens that may be present. This has led to the discovery of many new, uncharacterized viruses from a number of viral families. Use of these sequencing technologies would be advantageous in examining viral evolution. In this study, a sequencing procedure was used to sequence simultaneously and rapidly multiple archived samples using a single standard protocol. This procedure utilized primers composed of 20 bases of known sequence with 8 random bases at the 3'-end that also served as an identifying barcode that allowed the differentiation each viral library following pooling and sequencing. This conferred sequence independence by random priming both first and second strand cDNA synthesis. Viral stocks were treated with a nuclease cocktail to reduce the presence of host nucleic acids. Viral RNA was extracted, followed by single tube random-primed double-stranded cDNA synthesis. The resultant cDNAs were amplified by primer-specific PCR, pooled, size fractionated and sequenced on the Ion Torrent PGM platform. The individual virus genomes were readily assembled by both de novo and template-assisted assembly methods. This procedure consistently resulted in near full length, if not full-length, genomic sequences and was used to sequence multiple bovine pestivirus and coronavirus isolates simultaneously.","*Genome, Viral;*High-Throughput Nucleotide Sequencing/mt [Methods];*RNA Viruses/ge [Genetics];*RNA, Viral/ge [Genetics];*Virology/mt [Methods];0 (RNA, Viral)","Neill, J. D.;Bayles, D. O.;Ridpath, J. F.",2014,Jun,,0
1488,Genetic relatedness of the caliciviruses: San Miguel sea lion and vesicular exanthema of swine viruses constitute a single genotype within the Caliciviridae,"The San Miguel sea lion viruses (SMSV) and vesicular exanthema of swine viruses (VESV) are related morphologically and antigenically, but little has been done to determine their genotypic relationship to each other and to other caliciviruses. To examine this relationship, reverse transcriptase PCRs were performed by using oligonucleotide primer sets designed to amplify portions of the 2C RNA helicase-like and RNA-dependent RNA polymerase regions with total cellular RNA purified from virus-infected cell cultures as a template. The 2C RNA helicase primers directed the amplification of this region from eight SMSV serotypes, five VESV serotypes, and four related viruses. The RNA polymerase primer sets amplified products from all these viruses except one. Phylogenetic comparison of the caliciviruses demonstrated that SMSV, VESV, and four related viruses are closely related while being distinct from feline calicivirus, the human caliciviruses (small, round- structured viruses), and rabbit hemorrhagic disease virus and that they should be classified as a single genotype within the Caliciviridae.",RNA polymerase;amino acid sequence;article;Caliciviridae;nonhuman;phylogeny;priority journal;reverse transcription polymerase chain reaction;san miguel sea lion virus;sequence analysis;swine disease,"Neill, J. D.;Meyer, R. F.;Seal, B. S.",1995,,,0
1489,Donor-derived infections and infectious risk in xenotransplantation and allotransplantation,"Post-transplantation infections are common in allograft recipients and should be expected in all immunocompromised hosts. Based on the need for immunosuppression in xenotransplantation, procedures developed to enhance safety in allotransplantation can be applied in future xenotransplantation clinical trials. Standardized approaches can be developed to guide the evaluation of common infectious syndromes in xenograft recipients. The opportunity created by screening of swine intended as xenograft donors has equal applicability to allotransplantation—notably broader screening strategies for allograft donors such as use of advanced sequencing modalities including broad-range molecular probes, microarrays, and high-throughput pyrosequencing. Considerations in management of allotransplant- and xenotransplant-associated infections are largely the same. Experience in xenotransplantation will continue to inform thinking regarding donor-derived infections in allotransplantation. We expect that experience in managing complex allotransplant recipients will similarly inform clinical trials in xenotransplantation.",allotransplantation;article;disease association;disease transmission;graft infection;graft recipient;high throughput sequencing;human;immune response;infection;infection risk;interspecies infection;microarray analysis;molecular probe;organ donor;patient safety;priority journal;pyrosequencing;risk assessment;screening test;species difference;tropism;xenotransplantation,"Nellore, A.;Fishman, J. A.",2018,,10.1111/xen.12423,0
1490,"Human-Origin Influenza A(H3N2) Reassortant Viruses in Swine, Southeast Mexico","The genetic diversity of influenza A viruses circulating in swine in Mexico complicates control efforts in animals and presents a threat to humans, as shown by influenza A(H1N1)pdm09 virus. To describe evolution of swine influenza A viruses in Mexico and evaluate strains for vaccine development, we sequenced the genomes of 59 viruses and performed antigenic cartography on strains from 5 regions. We found that genetic and antigenic diversity were particularly high in southeast Mexico because of repeated introductions of viruses from humans and swine in other regions in Mexico. We identified novel reassortant H3N2 viruses with genome segments derived from 2 different viruses that were independently introduced from humans into swine: pandemic H1N1 viruses and seasonal H3N2 viruses. The Mexico swine viruses are antigenically distinct from US swine lineages. Protection against these viruses is unlikely to be afforded by US virus vaccines and would require development of new vaccines specifically targeting these diverse strains.",,"Nelson, M. I.;Souza, C.;Trovao, N. S.;Diaz, A.;Mena, I.;Rovira, A.;Vincent, A. L.;Torremorell, M.;Marthaler, D.;Culhane, M. R.",2019,Apr 17,,0
1491,Evolutionary pathways of N2 neuraminidases of swine and human influenza A viruses: Origin of the neuraminidase genes of two reassortants (H1N2) isolated from pigs,"The complete nucleotide sequences of the neuraminidase (NA) genes of two reassortant (H1N2) and two H3N2 influenza A viruses isolated from pigs were determined and phylogenetic relationships between these and previously reported N2 NA genes were investigated. On the basis of pairwise nucleotide sequence identity, the NA genes of two reassortants, A/sw/Kanagawa/2/78 and A/sw/Ehime/1/80, were most closely related to those of human influenza A virus strains isolated in 1972 and the earliest available swine H3N2 influenza A viruses, respectively. Phylogenetic trees showed that the NA genes can be segregated into three groups, including lineages for (i) swine strains, (ii) the earliest human strain and (iii) recent human strains. The evolutionary tree for the 11 nucleotide and amino acid sequences suggested that the NAs of A/sw/HK/4/76 and A/sw/Kanagawa/2/78 belong to the lineage for recent human viruses. In contrast, the NA genes of the A/sw/HK/3/76 and H1N2 reassortant A/sw/Ehime/1/80 viruses were found to be of a swine lineage. The swine virus NA genes were further characterized by the cocirculation of two distinct lineages. Although the rates of synonymous (silent) substitutions for the swine and human viruses were nearly identical (0.00946 to 0.00884 per site per year), the rate of non-synonymous (amino acid changing) substitutions for swine virus NA genes was about 60% of that for the human virus.",sialidase;virus enzyme;animal tissue;article;evolution;Influenza A virus;nonhuman;nucleotide sequence;priority journal;pig;virus strain,"Nerome, K.;Kanegae, Y.;Yoshioka, Y.;Itamura, S.;Ishida, M.;Gojobori, T.;Oya, A.",1991,,,0
1492,"Approved and experimental countermeasures against pestiviral diseases: Bovine viral diarrhea, classical swine fever and border disease","The pestiviruses, bovine viral diarrhea virus (BVDV), classical swine fever (CSFV) and border disease virus, are important livestock pathogens in many countries, but current vaccines do not completely prevent the spread of infection. Control of pestiviral diseases is especially difficult due to the constant viremia and viral shedding of persistently infected (PI) animals, which must be identified and eliminated to prevent disease transmission. Existing vaccines are limited by the delay between vaccination and the onset of protection, the difficulty of differentiating serologically between vaccinated and naturally infected animals and the need for broad vaccine cross-protection against diverse virus strains. Antiviral therapy could potentially supplement vaccination by providing immediate protection in the case of an outbreak. Numerous compounds with in vitro antiviral activity against BVDV have been identified through its role as a surrogate for hepatitis C virus. Fewer drugs active against CSFV have been identified, but many compounds that are effective against BVDV will likely inhibit CSFV, given their similar genomic sequences. While in vitro research has been promising, the paucity of efficacy studies in animals has hindered the commercial development of effective antiviral drugs against the pestiviruses. In this article, we summarize the clinical syndromes and routes of transmission of BVD, CSF and border disease, discuss currently approved vaccines, review efforts to develop antiviral therapies for use in outbreak control and suggest promising directions for future research. © 2013 Elsevier B.V. All rights reserved.",1 deoxynojirimycin derivative;6 methylthioinosine;acridine derivative;adenine derivative;antibiotic g 418;artemisinin;azathioprine;benzimidazole derivative;cantharidin;carboline derivative;castanospermine 6 butyrate;cephalotaxine;coumarin derivative;deoxyuridine;imidazopyridine derivative;inactivated vaccine;live vaccine;mizoribine;mycophenolic acid;peginterferon;prostaglandin synthase inhibitor;pyrimidine derivative;pyrimidine nucleoside;quinoline derivative;ribavirin;subunit vaccine;thiazepine derivative;thiosemicarbazone derivative;unindexed drug;xanthohumol;antigen detection;antiviral activity;antiviral therapy;border disease;bovine viral diarrhea;classical swine fever;clinical feature;drug safety;epidemic;genetic variability;genotype;infection control;infection prevention;nonhuman;persistent infection;Pestivirus;priority journal;review;serology;single drug dose;vaccination;virion;virus classification;virus detection;virus genome;virus isolation;virus morphology;virus replication;virus transmission,"Newcomer, B. W.;Givens, M. D.",2013,,10.1016/j.antiviral.2013.07.015,0
1493,Characterisation of a rotavirus,"Acute gastroenteritis is one of the most common causes of illness in children, calves and piglets, and causes severe economic loss in domestic animals. Although some outbreaks of gastroenteritis are associated with bacterial pathogens, particularly Escherichia coli, no known pathogens had been isolated from a significant proportion of outbreaks until recently, when viruses with a distinctive morphology and antigenic similarity were found associated with diarrhoea in piglets, calves and children. These viruses are major pathogens and it has also been shown that viruses isolated from man are infectious for the pig. Initially, these viruses were described as reovirus like but subsequently the names rotavirus and duovirus were proposed. They are morphologically and antigenically distinct from both the reoviruses and orbiviruses, and also differ from them in some of their physicochemical properties. Studies of the structure of rotaviruses have been confined to the nucleic acid of the calf virus and the related virus of epizootic diarrhoea of infant mice (EDIM). Both viruses were shown to contain RNA, and it has been suggested that the calf virus RNA might be double stranded. The results of the experiments described here show that calf rotavirus possesses several of the features characteristic of the reo and blue tongue viruses and should be classified with them. Although the calf rotavirus has a smaller sedimentation coefficient and is morphologically distinct from the reo and blue tongue viruses, the segmented and double stranded nature of its RNA and the number and molecular weights of the RNA and polypeptides suggest that it should be regarded as a member of the reo and blue tongue virus group. Its precise relationship to the other members of the group, however, will require extensive cross hybridisation studies of the virus RNAs.",viral protein;virus RNA;classification;in vitro study;microorganism;theoretical study;virus characterization;virus classification,"Newman, J. F. E.;Brown, F.;Bridger, J. C.;Woode, G. N.",1975,,10.1038/258631a0,0
1494,"Oral papillomatosis caused by Enhydra lutris papillomavirus 1 (ElPV-1) in southern sea otters (Enhydra lutris nereis) in California, USA","The southern sea otter (Enhydra lutris nereis) is a threatened marine sentinel. During postmortem investigations of stranded sea otters from 2004 to 2013 in California, US, papillomas were detected in the oral cavity of at least seven otters via necropsy and histopathology. Next-generation sequencing of viral particles purified from a single papilloma revealed a novel papillomavirus, Enhydra lutris papillomavirus 1 (ElPV-1). The genome of ElPV-1 was obtained, representing the first fully sequenced viral genome from southern sea otters. Phylogenetic analysis of the entire L1 gene, as well as a concatenated protein identities plot of all papillomaviral genes revealed that ElPV-1 is a λ-papillomavirus, related to a raccoon papillomavirus (Procyon lotor papillomavirus type 1) and a canine oral papillomavirus. Immunohistochemical staining, using a cross-reactive bovine papillomavirus antibody, suggested that ElPV-1 is present in intranuclear inclusions and intracytoplasmic keratin granules. Virus-infected cells were scattered throughout the stratum granulosum and stratum spinosum of the gingival and buccal papillomas. Using ElPV-1-specific PCR, we confirmed viral DNA in oral papillomas from all seven stranded sea otters, with identical L1 sequences. This virus is associated with the development of oral papillomatosis in southern sea otters.",aging;animal;California;classification;genetics;immunohistochemistry;isolation and purification;metagenomics;mouth disease;otter;Papillomaviridae;papillomavirus infection;phylogeny;procedures;United States;veterinary medicine;virology,"Ng, T. F.;Miller, M. A.;Kondov, N. O.;Dodd, E. M.;Batac, F.;Manzer, M.;Ives, S.;Saliki, J. T.;Deng, X.;Delwart, E.",2015,,10.7589/2014-06-152,0
1495,Metagenomic identification of a novel anellovirus in Pacific harbor seal (Phoca vitulina richardsii) lung samples and its detection in samples from multiple years,"To investigate viral pathogens potentially involved in a mortality event of 21 Pacific harbor seals (Phoca vitulina richardsii) in California in 2000, viral metagenomics was performed directly on lung samples from five individuals. Metagenomics revealed a novel seal anellovirus (SealAV), which clusters phylogenetically with anelloviruses from California sea lions and domestic cats. Using specific PCR, SealAV was identified in lung tissue from two of five animals involved in the 2000 mortality event, as well as one of 20 harbor seal samples examined post-mortem in 2008. The identification of SealAV in multiple years demonstrates that this virus is persistent in the harbor seal population. SealAV is the second anellovirus reported in the lungs of pinnipeds, suggesting that anellovirus infections may be common amongst marine mammals and that more research is needed to understand the roles of these viruses in marine mammal health and disease.","Anelloviridae/cl [Classification];*Anelloviridae/ge [Genetics];*Anelloviridae/ip [Isolation & Purification];Animals;Animals, Domestic/vi [Virology];California;Cats/vi [Virology];*DNA Virus Infections/ve [Veterinary];DNA Virus Infections/vi [Virology];Genome, Viral;*Lung/vi [Virology];*Metagenomics;Molecular Sequence Data;*Phoca/vi [Virology];Phylogeny","Ng, T. F.;Wheeler, E.;Greig, D.;Waltzek, T. B.;Gulland, F.;Breitbart, M.",2011,Jun,,0
1496,A metagenomics and case-control study to identify viruses associated with bovine respiratory disease,"Bovine respiratory disease (BRD) is a common health problem for both dairy and beef cattle, resulting in significant economic loses. In order to identify viruses associated with BRD, we used a metagenomics approach to enrich and sequence viral nucleic acids in the nasal swabs of 50 young dairy cattle with symptoms of BRD. Following deep sequencing, de novo assembly, and translated protein sequence similarity searches, numerous known and previously uncharacterized viruses were identified. Bovine adenovirus 3, bovine adeno-associated virus, bovine influenza D virus, bovine parvovirus 2, bovine herpesvirus 6, bovine rhinitis A virus, and multiple genotypes of bovine rhinitis B virus were identified. The genomes of a previously uncharacterized astrovirus and picobirnaviruses were also partially or fully sequenced. Using real-time PCR, the rates of detection of the eight viruses that generated the most reads were compared for the nasal secretions of 50 animals with BRD versus 50 location-matched healthy control animals. Viruses were detected in 68% of BRD-affected animals versus 16% of healthy control animals. Thirtyeight percent of sick animals versus 8% of controls were infected with multiple respiratory viruses. Significantly associated with BRD were bovine adenovirus 3 (P<0.0001), bovine rhinitis A virus (P = 0.005), and the recently described bovine influenza D virus (P = 0.006), which were detected either alone or in combination in 62% of animals with BRD. A metagenomics and realtime PCR detection approach in carefully matched cases and controls can provide a rapid means to identify viruses associated with a complex disease, paving the way for further confirmatory tests and ultimately to effective intervention strategies.",nucleic acid;amino acid sequence;article;Astroviridae;Bovine adenovirus 3;bovine herpesvirus 6;bovine parvovirus 2;bovine rhinitis A virus;bovine rhinitis B virus;case control study;cattle disease;controlled study;dairy cattle;disease association;DNA virus;metagenomics;nonhuman;nose secretion;nucleotide sequence;Human parainfluenza virus 1;Picobirnavirus;priority journal;protein assembly;real time polymerase chain reaction;respiratory virus;RNA virus;sequence homology;virus detection;virus genome;virus identification;virus load,"Ng, T. F. F.;Kondov, N. O.;Deng, X.;Van Eenennaam, A.;Neibergs, H. L.;Delwart, E.",2015,,10.1128/jvi.00064-15,1
1497,Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics,"Viral metagenomics, consisting of viral particle purification and shotgun sequencing, is a powerful technique for discovering viruses associated with diseases with no definitive etiology, viruses that share limited homology with known viruses, or viruses that are not culturable. Here we used viral metagenomics to examine viruses associated with sea turtle fibropapillomatosis (FP), a debilitating neoplastic disease affecting sea turtles worldwide. By means of purifying and shotgun sequencing the viral community directly from the fibropapilloma of a Florida green sea turtle, a novel single-stranded DNA virus, sea turtle tornovirus 1 (STTV1), was discovered. The single-stranded, circular genome of S′l′l′Vl was approximately 1,800 nucleotides in length. S′l′l′Vl has only weak amino acid level identities (25%) to chicken anemia virus in short regions of its genome; hence, STTV1 may represent the first member of a novel virus family. A total of 35 healthy turtles and 27 turtles with FP were tested for STTV1 using PCR, and only 2 turtles severely afflicted with FP were positive. The affected turtles were systemically infected with S′l′l′Vl, since STTV1 was found in blood and all major organs. S′l′l′Vl exists as a quasispecies, with several genome variants identified in the fibropapilloma of each positive turtle, suggesting rapid evolution of this virus. The STTV1 variants were identical over the majority of their genomes but contained a hypervariable region with extensive divergence. This study demonstrates the potential of viral metagenomics for discovering novel viruses directly from animal tissue, which can enhance our understanding of viral evolution and diversity. Copyright © 2009, American Society for Microbiology.",single stranded DNA;animal cell;animal tissue;article;controlled study;DNA virus;fibropapilloma;metagenomics;nonhuman;nucleotide sequence;papilloma;polymerase chain reaction;priority journal;sea turtle tornovirus 1;turtle;virus particle,"Ng, T. F. F.;Manire, C.;Borrowman, K.;Langer, T.;Ehrhart, L.;Breitbart, M.",2009,,10.1128/jvi.01946-08,0
1498,Feline fecal virome reveals novel and prevalent enteric viruses,,,"Ng, T. F. F.;Mesquita, J. R.;Nascimento, M. S. J.",2014,,,0
1499,Novel anellovirus discovered from a mortality event of captive California sea lions,"A viral metagenomic study was performed to investigate potential viral pathogens associated with a mortality event of three captive California sea lions (Zalophus californianus). This study identified a novel California sea lion anellovirus (ZcAV), with 35% amino acid identity in the ORF1 region to feline anelloviruses. The double-stranded replicative form of ZcAV was detected in lung tissue, suggesting that ZcAV replicates in sea lion lungs. Specific PCR revealed the presence of ZcAV in the lung tissue of all three sea lions involved in the mortality event, but not in three other sea lions from the same zoo. In addition, ZcAV was detected at low frequency (11%) in the lungs of wild sea lions. The higher prevalence of ZcAV and presence of the double-stranded replicative form in the lungs of sea lions from the mortality event suggest that ZcAV was associated with the death of these animals.",SPECIES-SPECIFIC TTVS;CHICKEN ANEMIA VIRUS;TORQUE TENO VIRUS;VIRAL;METAGENOMICS;DNA VIRUS;POSTTRANSFUSION HEPATITIS;GENOMIC;CHARACTERIZATION;UNKNOWN ETIOLOGY;INFECTIONS;SEQUENCES,"Ng, T. F. F.;Suedmeyer, W. K.;Wheeler, E.;Gulland, F.;Breitbartt, M.",2009,May,,0
1500,"Development and evaluation of a non-ribosomal random PCR and next-generation sequencing based assay for detection and sequencing of hand, foot and mouth disease pathogens","BACKGROUND: Hand, foot and mouth disease (HFMD) has become a major public health problem across the Asia-Pacific region, and is commonly caused by enterovirus A71 (EV-A71) and coxsackievirus A6 (CV-A6), CV-A10 and CV-A16. Generating pathogen whole-genome sequences is essential for understanding their evolutionary biology. The frequent replacements among EV serotypes and a limited numbers of available whole-genome sequences hinder the development of overlapping PCRs for whole-genome sequencing. We developed and evaluated a non-ribosomal random PCR (rPCR) and next-generation sequencing based assay for sequence-independent whole-genome amplification and sequencing of HFMD pathogens. A total of 16 EV-A71/CV-A6/CV-A10/CV-A16 PCR positive rectal/throat swabs (Cp values: 20.9-33.3) were used for assay evaluation. RESULTS: Our assay evidently outperformed the conventional rPCR in terms of the total number of EV-A71 reads and the percentage of EV-A71 reads: 2.6 % (1275/50,000 reads) vs. 0.1 % (31/50,000) and 6 % (3008/50,000) vs. 0.9 % (433/50,000) for two samples with Cp values of 30 and 26, respectively. Additionally the assay could generate genome sequences with the percentages of coverage of 94-100 % of 4 different enterovirus serotypes in 73 % of the tested samples, representing the first whole-genome sequences of CV-A6/10/16 from Vietnam, and could assign correctly serotyping results in 100 % of 24 tested specimens. In all but three the obtained consensuses of two replicates from the same sample were 100 % identical, suggesting that our assay is highly reproducible. CONCLUSIONS: In conclusion, we have successfully developed a non-ribosomal rPCR and next-generation sequencing based assay for sensitive detection and direct whole-genome sequencing of HFMD pathogens from clinical samples.","Enterovirus A, Human/cl [Classification];Enterovirus A, Human/ge [Genetics];*Enterovirus A, Human/ip [Isolation & Purification];Genotype;Hand, Foot and Mouth Disease/di [Diagnosis];*Hand, Foot and Mouth Disease/vi [Virology];*High-Throughput Nucleotide Sequencing/mt [Methods];Humans;Phylogeny;*Polymerase Chain Reaction/mt [Methods];Serotyping","Nguyen, A. T.;Tran, T. T.;Hoang, V. M.;Nghiem, N. M.;Le, N. N.;Le, T. T.;Phan, Q. T.;Truong, K. H.;Le, N. N.;Ho, V. L.;Do, V. C.;Ha, T. M.;Nguyen, H. T.;Nguyen, C. V.;Thwaites, G.;van Doorn, H. R.;Le, T. V.",2016,07 07,,0
1501,Evolution of highly pathogenic avian influenza (H5N1) virus populations in Vietnam between 2007 and 2010,"We report on the genetic analysis of 213 highly pathogenic avian influenza (HPAI) H5N1 viruses isolated from poultry in Vietnam between 2007 and 2010. Phylogenetic analyses of the viral genomes revealed 38 distinct viral genotypes, 29 were novel and 9 were reported in Vietnam or neighboring countries in recent years. Viruses from only six genotypes persisted beyond one season or year. Thus, most reassortant viruses were transient, suggesting that such genotypes lacked significant fitness advantages. Viruses with clade 2.3.2.1 HA were re-introduced into Vietnam in 2009 and their prevalence rose steeply towards the end of 2010. Clade 2.3.4-like viruses (genotype V) were predominant in northern Vietnam and caused the majority of zoonotic infections, whereas clade 1.1 (genotype Z) viruses were only detected in the Mekong delta region, in southern Vietnam. Antigenic analysis of representative viruses from the four clades indicated substantial drift. © 2012.",antigenicity;article;cladistics;genetic drift;genotype;geographic distribution;Influenza A virus (H5N1);molecular evolution;nonhuman;phylogeny;prevalence;priority journal;Viet Nam;virus genome;zoonosis,"Nguyen, T.;Rivailler, P.;Davis, C. T.;Thi Hoa, D.;Balish, A.;Hoang Dang, N.;Jones, J.;Thi Vui, D.;Simpson, N.;Thu Huong, N.;Shu, B.;Loughlin, R.;Ferdinand, K.;Lindstrom, S. E.;York, I. A.;Klimov, A.;Donis, R. O.",2012,,10.1016/j.virol.2012.06.021,0
1502,Identification and genomic characterization of a novel porcine parvovirus (PPV6) in china,"Background: Parvoviruses are classified into two subfamilies based on their host range: the Parvovirinae, which infect vertebrates, and the Densovirinae, which mainly infect insects and other arthropods. In recent years, a number of novel parvoviruses belonging to the subfamily Parvovirinae have been identified from various animal species and humans, including human parvovirus 4 (PARV4), porcine hokovirus, ovine partetravirus, porcine parvovirus 4 (PPV4), and porcine parvovirus 5 (PPV5). Methods: Using sequence-independent single primer amplification (SISPA), a novel parvovirus within the subfamily Parvovirinae that was distinct from any known parvoviruses was identified and five full-length genome sequences were determined and analyzed. Results: A novel porcine parvovirus, provisionally named PPV6, was initially identified from aborted pig fetuses in China. Retrospective studies revealed the prevalence of PPV6 in aborted pig fetuses and piglets(50% and 75%, respectively) was apparently higher than that in finishing pigs and sows (15.6% and 3.8% respectively). Furthermore, the prevalence of PPV6 in finishing pig was similar in affected and unaffected farms (i.e. 16.7% vs. 13.6%-21.7%). This finding indicates that animal age, perhaps due to increased innate immune resistance, strongly influences the level of PPV6 viremia. Complete genome sequencing and multiple alignments have shown that the nearly full-length genome sequences were approximately 6,100 nucleotides in length and shared 20.5%-42.6% DNA sequence identity with other members of the Parvovirinae subfamily. Phylogenetic analysis showed that PPV6 was significantly distinct from other known parvoviruses and was most closely related to PPV4. Conclusion: Our findings and review of published parvovirus sequences suggested that a novel porcine parvovirus is currently circulating in China and might be classified into the novel genus Copiparvovirus within the subfamily Parvovirinae. However, the clinical manifestations of PPV6 are still unknown in that the prevalence of PPV6 was similar between healthy pigs and sick pigs in a retrospective epidemiological study. The identification of PPV6 within the subfamily Parvovirinae provides further insight into the viral and genetic diversity of parvoviruses.",age;animal tissue;article;China;comparative study;controlled study;DNA sequence;fetus;gene sequence;genetic analysis;genetic association;genetic variability;genome analysis;innate immunity;molecular phylogeny;nonhuman;nucleotide sequence;open reading frame;pig;piglet;polymerase chain reaction;Porcine parvovirus;Porcine parvovirus 4;Porcine parvovirus 5;Porcine parvovirus 6;prevalence;retrospective study;sequence alignment;sequence homology;virus classification;virus detection;virus genome;virus identification,"Ni, J.;Qiao, C.;Han, X.;Han, T.;Kang, W.;Zi, Z.;Cao, Z.;Zhai, X.;Cai, X.",2014,,10.1186/s12985-014-0203-2,0
1503,Hepatitis E virus,"Hepatitis E virus (HEV) is a non-enveloped positive-sense RNA virus, currently classified in a new family ""Hepeviridae genus hepevirus"" (single-stranded RNA viruses). The genome (7,2kb) contains three open reading frames (ORF) encoding for non structural (ORF1) and structural proteins (ORF2 & ORF3). HEV infection has been associated with developing countries as a major cause of epidemic acute hepatitis transmitted by faecal-oral route. But sporadic cases of hepatitis have been reported in Western countries, without a history of travel to endemic regions. Phylogenetic analysis of different geographical HEV identified four main genotypes: genotype I gathering Asian (I1) and African (I2) isolates, genotype II found in Mexico and Nigeria, genotype III discovered among US humans and US swine, and genotype IV in Taiwan. Additional genotypes were described in non HEV endemic areas (Greece, Italy, Argentina). Isolation of HEV in domestic animals supports an environmental reservoir of HEV. The current diagnosis of HEV infection includes molecular tools for the detection of the virus in stool or serum samples and serological tests for identification of anti-HEV Ig G and Ig M.",immunoglobulin G antibody;immunoglobulin M antibody;structural protein;Argentina;blood sampling;developing country;disease transmission;endemic disease;epidemic;feces;genotype;Greece;hepatitis E;Hepatitis E virus;Italy;Mexico;Nigeria;nonhuman;nucleotide sequence;open reading frame;phylogeny;review;RNA virus;Taiwan;travel;United States;virus detection;virus genome;virus isolation,"Nicand, E.;Grandadam, M.",2003,,,0
1504,Occurrence of Adenovirus Field Strains in Birds Infected with Marek's Disease Virus,"The strains of adenoviruses were isolated from 356 birds with clinical form of Marek's disease and coinfection with adenoviruses. A hexon gene fragment coding loop L1 of adenovirus strains was sequenced and obtained data were analysed with BLAST, Geneious 5.3, and MEGA5 software by comparison with nucleotide sequences of reference strains of fowl adenoviruses (FAdV-1-FadV-12), two turkey adenoviruses, and two goose adenovirus strains. On this basis, serotypes of adenovirus strains were determined. Sequences of all adenovirus strains isolated from birds infected with Marek's disease virus were classified into six serotypes representing four species. Mostly FAdV-7, FAdV2/11, and FAdV-8a serotypes were found.",chickens;Marek's disease;adenoviruses;phylogenetic analysis;INCLUSION-BODY HEPATITIS;EGG DROP SYNDROME;FOWL ADENOVIRUSES;AVIAN;ADENOVIRUSES;HYDROPERICARDIUM SYNDROME;PHYLOGENETIC ANALYSIS;GIZZARD;EROSIONS;BROILER-CHICKENS;HEXON GENE;PATHOGENICITY,"Niczyporuk, J. S.;Samorek-Salamonowicz, E.;Czekaj, H.",2012,,,0
1505,"Detection and phylogenetic analysis of Hepatitis E Viruses from mongooses in Okinawa, Japan","Hepatitis E virus (HEV) infection has previously been reported in wild mongooses on Okinawa Island; to date however, only one HEV RNA sequence has been identified in a mongoose. Hence, this study was performed to detect HEV RNA in 209 wild mongooses on Okinawa Island. Six (2.9%) samples tested positive for HEV RNA. Phylogenetic analysis revealed that 6 HEV RNAs belonged to genotype 3 and were classified into groups A and B. In group B, mongoose-derived HEV sequences were very similar to mongoose HEV previously detected on Okinawa Island, as well as to those of a pig. This investigation emphasized the possibility that the mongoose is a reservoir animal for HEV on Okinawa Island. © 2012 The Japanese Society of Veterinary Science.",virus RNA;animal;bile;chemistry;classification;disease carrier;genetics;Hepatitis E virus;isolation and purification;Japan;mongoose;note;phylogeny;reverse transcription polymerase chain reaction;virology,"Nidaira, M.;Takahashi, K.;Ogura, G.;Taira, K.;Okano, S.;Kudaka, J.;Itokazu, K.;Mishiro, S.;Nakamura, M.",2012,,10.1292/jvms.11-0520,0
1506,Genetic characterization of H5N1 influenza viruses isolated from chickens in Indonesia in 2010,"Since 2003, highly pathogenic H5N1 avian influenza viruses have caused outbreaks among poultry in Indonesia every year, producing the highest number of human victims worldwide. However, little is known about the H5N1 influenza viruses that have been circulating there in recent years. We therefore conducted surveillance studies and isolated eight H5N1 viruses from chickens. Phylogenic analysis of their hemagglutinin and neuraminidase genes revealed that all eight viruses belonged to clade 2.1.3.However, on the basis of nucleotide differences, these viruses could be divided into two groups. Other viruses genetically closely related to these two groups of viruses were all Indonesian isolates, suggesting that these new isolates have been evolving within Indonesia. Among these viruses, two distinct viruses circulated in the Kalimantan islands during the same season in 2010. Our data reveal the continued evolution of H5N1 viruses in Indonesia. © The Author(s) 2012.",Influenza virus hemagglutinin;virus sialidase;article;chicken;genetic analysis;hemagglutinin gene;Indonesia;Influenza A virus (H5N1);neuraminidase gene;nonhuman;nucleotide sequence;phylogeny;priority journal;sequence analysis;virus gene;virus isolation,"Nidom, C. A.;Yamada, S.;Nidom, R. V.;Rahmawati, K.;Alamudi, M. Y.;Kholik;Indrasari, S.;Hayati, R. S.;Iwatsuki Horimoto, K.;Kawaoka, Y.",2012,,10.1007/s11262-012-0722-0,0
1507,Near-complete genome sequencing of swine vesicular disease virus using the Roche GS FLX sequencing platform,"Swine vesicular disease virus (SVDV) is an enterovirus that is both genetically and antigenically closely related to human coxsackievirus B5 within the Picornaviridae family. SVDV is the causative agent of a highly contagious (though rarely fatal) vesicular disease in pigs. We report a rapid method that is suitable for sequencing the complete protein-encoding sequences of SVDV isolates in which the RNA is relatively intact. The approach couples a single PCR amplification reaction, using only a single PCR primer set to amplify the near-complete SVDV genome, with deep-sequencing using a small fraction of the capacity of a Roche GS FLX sequencing platform. Sequences were initially verified through one of two criteria; either a match between a de novo assembly and a reference mapping, or a match between all of five different reference mappings performed against a fixed set of starting reference genomes with significant genetic distances within the same species of viruses. All reference mappings used an iterative method to avoid bias. Further verification was achieved through phylogenetic analysis against published SVDV genomes and additional Enterovirus B sequences. This approach allows high confidence in the obtained consensus sequences, as well as provides sufficiently high and evenly dispersed sequence coverage to allow future studies of intra-host variation. © 2014 Nielsen et al.",article;biochemical equipment;consensus sequence;Enterovirus;gene mapping;gene sequence;genetic distance;high throughput sequencing;molecular phylogeny;nonhuman;nucleotide sequence;polymerase chain reaction;sequence analysis;swine vesicular disease virus;virus genome;GS FLX,"Nielsen, S. C. A.;Bruhn, C. A. W.;Samaniego, J. A.;Wadsworth, J.;Knowles, N. J.;Gilbert, M. T. P.",2014,,10.1371/journal.pone.0097180,0
1508,"Whole genome sequences of Japanese porcine species C rotaviruses reveal a high diversity of genotypes of individual genes and will contribute to a comprehensive, generally accepted classification system","Porcine rotavirus C (RVC) is distributed throughout the world and is thought to be a pathogenic agent of diarrhea in piglets. Although, the VP7, VP4, and VP6 gene sequences of Japanese porcine RVCs are currently available, there is no whole-genome sequence data of Japanese RVC. Furthermore, only one to three sequences are available for porcine RVC VP1-VP3 and NSP1-NSP3 genes. Therefore, we determined nearly full-length whole-genome sequences of nine Japanese porcine RVCs from seven piglets with diarrhea and two healthy pigs and compared them with published RVC sequences from a database. The VP7 genes of two Japanese RVCs from healthy pigs were highly divergent from other known RVC strains and were provisionally classified as G12 and G13 based on the 86% nucleotide identity cut-off value. Pairwise sequence identity calculations and phylogenetic analyses revealed that candidate novel genotypes of porcine Japanese RVC were identified in the NSP1, NSP2 and NSP3 encoding genes, respectively. Furthermore, VP3 of Japanese porcine RVCs was shown to be closely related to human RVCs, suggesting a gene reassortment event between porcine and human RVCs and past interspecies transmission. The present study demonstrated that porcine RVCs show greater genetic diversity among strains than human and bovine RVCs.","Animals;Antigens, Viral/ge [Genetics];Capsid Proteins/ge [Genetics];Diarrhea/ve [Veterinary];Diarrhea/vi [Virology];Feces/vi [Virology];*Genetic Variation;Genome, Viral;Genotype;High-Throughput Nucleotide Sequencing;Japan;Phylogeny;RNA-Binding Proteins/ge [Genetics];*Rotavirus/ge [Genetics];Rotavirus/ip [Isolation & Purification];Rotavirus/py [Pathogenicity];Rotavirus Infections/di [Diagnosis];*Rotavirus Infections/ve [Veterinary];Rotavirus Infections/vi [Virology];Swine;*Swine Diseases/vi [Virology];Viral Nonstructural Proteins/ge [Genetics];0 (Antigens, Viral);0 (Capsid Proteins);0 (NSP1 protein, Rotavirus);0 (NSP3 protein, Rotavirus);0 (RNA-Binding Proteins);0 (VP3 protein, Rotavirus);0 (VP7 protein, Rotavirus);0 (Viral Nonstructural Proteins);138414-65-0 (NS35 protein, rotavirus)","Niira, K.;Ito, M.;Masuda, T.;Saitou, T.;Abe, T.;Komoto, S.;Sato, M.;Yamasato, H.;Kishimoto, M.;Naoi, Y.;Sano, K.;Tuchiaka, S.;Okada, T.;Omatsu, T.;Furuya, T.;Aoki, H.;Katayama, Y.;Oba, M.;Shirai, J.;Taniguchi, K.;Mizutani, T.;Nagai, M.",2016,10,,1
1509,Different RNA splicing mechanisms contribute to diverse infective outcome of classical swine fever viruses of differing virulence: Insights from the deep sequencing data in swine umbilical vein endothelial cells,"Molecular mechanisms underlying RNA splicing regulation in response to viral infec- tion are poorly understood. Classical swine fever (CSF), one of the most economically important and highly contagious swine diseases worldwide, is caused by classical swine fever virus (CSFV). Here, we used high-throughput sequencing to obtain the digital gene expression (DGE) profile in swine umbilical vein endothelial cells (SUVEC) to identify different response genes for CSFV by using both Shimen and C strains. The numbers of clean tags obtained from the libraries of the control and both CSFV-infected libraries were 3,473,370, 3,498,355, and 3,327,493 respectively. In the comparison among the control, CSFV-C, and CSFV-Shimen groups, 644, 158, and 677 differentially expressed genes (DEGs) were confirmed in the three groups. Pathway enrichment analysis showed that many of these DEGs were enriched in spliceosome, ribosome, proteasome, ubiquitin-mediated proteolysis, cell cycle, focal adhesion, Wnt signalling pathway, etc., where the processes differ between CSFV strains of differing virulence. To further elucidate important mechanisms related to the differential infection by the CSFV Shimen andCstrains, we identified four possible profiles to assess the significantly expressed genes only by CSFV Shimen or CSFV C strain. GO analysis showed that infection with CSFV Shimen andCstrains disturbed `RNA splicing' of SUVEC, resulting in differential `gene expression' in SUVEC. Mammalian target of rapamycin (mTOR) was identified as a significant response regulator contributed to impact on SUVEC function for CSFV Shimen. This computational study suggests that CSFV of differing virulence could induce alterations in RNA splicing regulation in the host cell to change cell metabolism, resulting in acute haemorrhage and pathological damage or infectious tolerance.",mammalian target of rapamycin;transcriptome;animal cell;article;classical swine fever;Classical swine fever virus;controlled study;enzyme linked immunosorbent assay;expressed sequence tag;gene expression;gene ontology;gene sequence;high throughput sequencing;immune response gene;molecular genetics;molecular interaction;nonhuman;pig;polyacrylamide gel electrophoresis;protein content;protein determination;reverse transcription polymerase chain reaction;RNA splicing;umbilical vein endothelial cell;virus cell interaction;virus gene;virus infection;virus replication;virus virulence;Western blotting;Wnt signaling,"Ning, P.;Zhou, Y.;Liang, W.;Zhang, Y.",2016,,10.7717/peerj.2113,0
1510,Analysis of the entire genomes of fifteen torque teno midi virus variants classifiable into a third group of genus Anellovirus,"Recently, we identified a novel human virus with a circular DNA genome of 3.2 kb, tentatively designated as torque teno midi virus (TTMDV), with a genomic organization resembling those of torque teno virus (TTV) of 3.8-3.9 kb and torque teno mini virus (TTMV) of 2.8-2.9 kb. To investigate the extent of genomic variability of TTMDV genomes, the full-length sequence was determined for 15 TTMDV isolates obtained from viremic individuals in Japan. The 15 TTMDV isolates comprised 3175-3230 bases and shared 67.0-90.3% identities with each other, and were only 68.4-73.0% identical to the 3 reported TTMDV isolates over the entire genome. TTMDV possessed a genomic organization with four open reading frames (ORF1-ORF4) with characteristic sequence motifs and stem and loop structures with high GC content, similar to TTV and TTMV. The total of 18 TTMDV genomes differed by up to 60.7% from each other in the amino acid sequence of ORF1 (658-677 amino acids), but segregated phylogenetically into the same cluster, which was distantly related to the TTVs and TTMVs. These results indicate that TTMDV with a circular DNA genome of 3.2 kb, has an extremely high degree of genomic variability, and is classifiable into a third group in the genus Anellovirus.",CHICKEN ANEMIA VIRUS;MOLECULAR EVOLUTIONARY ANALYSIS;FEATHER DISEASE;VIRUS;SPECIES-SPECIFIC TTVS;FRENCH BLOOD-DONORS;NUCLEOTIDE-SEQUENCE;NONHUMAN-PRIMATES;HEPATITIS-C;MINI VIRUS;DNA VIRUS,"Ninomiya, M.;Takahashi, M.;Shimosegawa, T.;Okamoto, H.",2007,Oct,,0
1511,Monoclonal antibodies to the HN glycoprotein of Newcastle disease virus. Biological characterization and use for strain comparisons,"We have isolated nine hybridomas secreting monoclonal antibodies directed against the HN glycoprotein of D26 strain of Newcastle disease virus (NDV) and classified them into three groups by their biological reactivities. The group I antibodies from six clones had high hemagglutination inhibition (HI) and neutralization titers, and exhibited neuraminidase inhibition (NI) activity with substrates, both bovine fetuin and N-acetyl neuraminlactose, although the levels of maximum inhibition were greater with the former substrate. The group II antibodies from two clones also had high HI activity but showed a strongly substrate-dependent NI, with efficient inhibition against fetuin and a total lack of inhibition against neuraminlactose. These antibodies had neutralization capacity but the titers were much lower than those of group I antibodies. One clone (group III) secreted antibody which exhibited HI and NI with either substrate but no detectable neutralization activity. Frequency of isolation of antigenic variants and competitive binding assays have shown that group I and group II antibodies may recognize distinct regions not overlapping each other whereas antibodies placed within each of the two groups are to the respective same overlapping regions. The site of group III seemed to be close to or overlap the group I determinant but distinct from group II region. Using the isolated monoclonal antibodies we compared seven heterologous strains by HI and neutralization tests as well as by enzyme-linked immunosorbent assay. The results indicated that the regions recognized by group I antibodies would be conserved among the strains whereas those by the other two antibody groups might undergo considerable changes.",monoclonal antibody;virus glycoprotein;enzyme immunoassay;Newcastle disease virus;nonhuman,"Nishikawa, K.;Isomura, S.;Suzuki, S.",1983,,,0
1512,Production of monoclonal antibodies against classical swine fever virus and their use for antigenic characterization of Japanese isolates,"Twenty monoclonal antibodies (MAbs) were produced against the virulent ALD or vaccinal GPE- strains of classical swine fever (CSF) virus. The MAbs were divided into 7 groups on the basis of the difference in the reaction spectrum to various CSF and bovine viral diarrhea-mucosal disease (BVD-MD) viruses. The panel of the MAbs could classify 20 CSF viruses into 6 types, and could discriminate between not only CSF and BVD-MD viruses but also the vaccinal GPE- strain and the field isolates of CSF virus. The results indicated that the MAbs were useful for diagnosis and investigation of CSF viruses.",monoclonal antibody;animal;antibody specificity;article;Bagg albino mouse;Bovine viral diarrhea virus 1;bovine;cattle disease;differential diagnosis;immunology;isolation and purification;Japan;mouse;Pestivirus;pig;swine disease,"Nishimori, T.;Yamada, S.;Shimizu, M.",1996,,,0
1513,Identification and full-genome characterization of novel circoviruses in masked palm civets (Paguma larvata),"The family Circoviridae comprises a large group of small, circular, single-stranded DNA viruses and is classified into two genera: Circovirus and Cyclovirus. They have marked genetic diversity and a broad host range. In this study, three novel circovirus genomes were identified from wild-caught masked palm civets (Paguma larvata) in Japan and classified as a new species within the genus Circovirus based on the demarcation criteria of the International Committee on the Taxonomy of Viruses. Of note, the presence of two predicted introns at the 5'-terminus of the rep gene was suggested in the Paguma larvata circovirus genomes.",Circoviridae;ssDNA viruses;Paguma larvata;Rep gene;Intron;Rolling;circle amplification (RCA);FEATHER-DISEASE-VIRUS;TYPE-3;SEQUENCE;PCV3;BEAK;PIGS;DNA,"Nishizawa, T.;Sugimoto, Y.;Takeda, T.;Kodera, Y.;Hatano, Y.;Takahashi, M.;Okamoto, H.",2018,Oct,,0
1514,Relationship of Theiler's murine encephalomyelitis viruses to the cardiovirus genus of picornaviruses,"Sequence analysis of VP1 in the DA strain of Theiler's murine encephalomyelitis viruses (TMEV) showed that 13 of the first 23 N-terminal amino acids were identical to those in the corresponding protein of encephalomyocarditis virus. There was little similarity to the corresponding VP1 sequences of poliovirus types 1, 2 and 3, coxsackievirus B3, human rhinoviruses 2 and 14, human hepatitis A virus or foot-and-mouth disease virus. These results, as well as serological relationships detected by immunoblotting, suggest that the TMEV are more closely related to the cardioviruses than to the enteroviruses with which they are presently classified. This newly recognized relationship suggests potential for recombinant infectious cDNA studies between TMEV and cardioviruses.",viral protein;virus RNA;classification;Encephalomyocarditis virus;gene sequence;heredity;nonhuman;priority journal;virus classification,"Nitayaphan, S.;Omilianowski, D.;Toth, M. M.",1986,,,0
1515,"Epidemiological investigation of H9 avian influenza virus, Newcastle disease virus, Tembusu virus, goose parvovirus and goose circovirus infection of geese in China","To deepen the knowledge about epidemic prevalence in the goose breeding field, a triplex PCR assay was established, and 478 samples were collected from scaled goose farms in 11 provinces in China. The results of this epidemiological investigation showed that incidence rates of H9 avian influenza and goose circovirus were the highest among five infectious diseases that were evaluated. In addition, the triplex PCR assay established remarkable sensitivity, rapidity and versatility compared to other diagnostic methods. Dual infection comprised a large proportion of the co-infections in the field, of which the combinations of H9/Tembusu, H9/goose circovirus and goose circovirus/Tembusu co-infected cases were more common. Epidemics were more severe in winter and spring. Additionally, significant differences in the prevalence of these infectious diseases were observed in association with different age groups. In addition, phylogenetic analysis, determined by the neighbour-joining method, was carried out to investigate the evolution of these viruses during the study period. For the most part, virus strains isolated during the study were consistent with most goose-origin strains isolated from the Chinese mainland over the past few years. However, mutations were observed between isolated H9 avian influenza virus strains and sequences available from GenBank, which should draw much attention.",Animals;China/ep [Epidemiology];Circoviridae Infections/ep [Epidemiology];*Circoviridae Infections/ve [Veterinary];Circoviridae Infections/vi [Virology];Circovirus/ge [Genetics];Circovirus/ip [Isolation & Purification];Flavivirus/ge [Genetics];Flavivirus/ip [Isolation & Purification];Flavivirus Infections/ep [Epidemiology];*Flavivirus Infections/ve [Veterinary];Flavivirus Infections/vi [Virology];*Geese/vi [Virology];Influenza A virus/ge [Genetics];Influenza A virus/ip [Isolation & Purification];*Influenza in Birds/ep [Epidemiology];Influenza in Birds/vi [Virology];Multiplex Polymerase Chain Reaction/ve [Veterinary];Newcastle disease virus/ge [Genetics];Newcastle disease virus/ip [Isolation & Purification];Parvoviridae Infections/ep [Epidemiology];*Parvoviridae Infections/ve [Veterinary];Parvoviridae Infections/vi [Virology];Parvovirinae/ge [Genetics];Parvovirinae/ip [Isolation & Purification];Phylogeny,"Niu, X.;Wang, H.;Wei, L.;Zhang, M.;Yang, J.;Chen, H.;Tang, Y.;Diao, Y.",2018,Apr,,0
1516,Metapneumoviruses in birds and humans,"Avian pneumovirus (APV, Turkey rhinotracheitis virus) and Human metapneumovirus (hMPV) are pathogens of birds and humans, respectively, that are associated with upper respiratory tract infections. Based on their different genomic organization and low level of nucleotide (nt) and amino acid (aa) identity with paramyxoviruses in the genus Pneumovirus, APV and hMPV have been classified into a new genus referred to as Metapneumovirus. First isolated in 1970s, APV strains have since been isolated in Europe, Africa, middle east, and United States (US) and classified in four subgroups, APV/A, APV/B, APV/C, and APV/D based on nt and predicted aa sequence identity. Although it was first isolated in 2001, serological evidence indicates that hMPV may have been present in human population from as early as the 1950s. There is only one subgroup of hMPV so far, whose nt and aa sequence identity indicates that it is more closely related to APV/C than to APV/A, APV/B, or APV/D. © 2002 Elsevier Science B.V. All rights reserved.",amino acid;nucleotide;bird;genome analysis;human;Metapneumovirus;nonhuman;pathogenesis;Pneumovirinae;priority journal;review;rhinotracheitis;sequence analysis;turkey (bird);upper respiratory tract infection;virus classification;virus isolation,"Njenga, M. K.;Lwamba, H. M.;Seal, B. S.",2003,,10.1016/s0168-1702(02)00256-3,0
1517,"Isolation of Fukuoka virus, a member of the Kern Canyon serogroup viruses of the family Rhabdoviridae, from cattle","Four virus strains with identical antigenic properties were isolated from blood samples of 4 sentinel calves having a fever and leukopenea in cultures of HmLu-1 cells derived from baby hamster lung. The virus was identified as Fukuoka virus, classified as a member of the Kern Canyon serogroup viruses of the family Rhabdoviridae, on the basis of its antigenic properties.",antibody titer;article;blood sampling;bovine;cell culture;cytopathogenic effect;nonhuman;Rhabdoviridae;serology;virus isolation;virus neutralization,"Noda, M.;Inaba, Y.;Banjo, M.;Kubo, M.",1992,,,0
1518,Pestivirus infection in cattle dairy farms: E2 glycoprotein ELISA reveals the presence of bovine viral diarrhea virus type 2 in northwestern Italy,"Background: Bovine viral diarrhea virus (BVDV) types 1 and 2 are members of the Pestivirus genus of the Flaviviridae family. This genus also includes the HoBi-like virus, tentatively classified as BVDV type 3. BVDV-1 is widely distributed in Italy despite the extensive use of BVDV-1-based vaccines, while BVDV-2 and HoBi-like Pestivirus have been detected occasionally. Monitoring the occurrence of sporadic or atypical pestiviruses is a useful approach to evaluate the need for additional vaccine strains that can be used in BVDV control programs. Results: In this study we developed a multiwell antibody ELISA based on the recombinant E2 protein of the three bovine pestiviruses. We evaluated the assay's applicability for surveillance purposes using pooled milk samples, each prepared from a maximum of 35 lactating cows and collected from 176 dairy herds. As expected, the majority of the pooled samples reacted to a greater extent against the BVDV-1 E2 antigen. All three milk pools from a single farm reacted to the BVDV-2 antigen, however. Further analysis using spot tests, antigen detection, and sequence analysis of the 5'-UTR region confirmed the presence of five persistently infected calves carrying a BVDV-2a strain. Conclusions: This study highlights for the first time that sporadic circulation of BVDV-2 can be predicted by immunoenzymatic methods in the absence of specific vaccination.",ExCell293;glycoprotein E2;propiolactone;amino acid sequence;animal cell;animal experiment;antigen detection;article;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;controlled study;dairy cattle;disease surveillance;enzyme linked immunosorbent assay;experimental infection;female;immunization;Italy;MDBK cell line;molecular cloning;nonhuman;Pestivirus infection;sequence alignment;sequence analysis;sheep;transient transfection;virus neutralization,"Nogarol, C.;Decaro, N.;Bertolotti, L.;Colitti, B.;Iotti, B.;Petrini, S.;Lucente, M. S.;Elia, G.;Perona, G.;Profiti, M.;Buonavoglia, C.;Rosati, S.",2017,,10.1186/s12917-017-1305-z,0
1519,Genetic analysis of a bovine viral diarrhea virus 2 isolate from Slovakia,"The identification and genetic characterization of bovine viral diarrhea virus (BVDV) isolate 17237 detected in western Slovakia is described. The analysis of 5′-untranslated region (5′-UTR), autoprotease (N pro) gene, and structural genes (C, Erns, E1, E2) was carried out. The percentage of nucleotide and deduced amino acid identity in analyzed genes implied that the isolate was closely related to the bovine viral diarrhea virus 2 (BVDV-2). Furthermore, the phylogenetic analysis revealed that this isolate fall into BVDV-2b subtype that is sporadic in Europe. The cleavage sites between viral proteins were similar to the ones of a reference strain of BVDV-2.",amino acid derivative;viral protein;5' untranslated region;article;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;cow;gene structure;genetic analysis;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;sequence analysis;Slovakia;structural gene;virus identification;virus isolation;virus strain,"Nováčková, M.;Jacková, A.;Kolesárová, M.;Vilček, Š",2008,,,0
1520,Rotavirus-associated diarrhoea in foals in Greece,"Severe outbreaks of diarrhoeic syndrome occurred in young foals at the same stud farm during two consecutive breeding periods namely spring 2006 and 2007. Rotavirus-like particles were detected by electron microscopy in the faeces of the affected foals and group A rotavirus infection was confirmed by Reverse-Transcription (RT)-PCR with selected sets of rotavirus-specific primers. Sequence analysis of the genes encoding the outer capsid rotavirus proteins VP7 and VP4 enabled classification of the viruses as G3AP[12] and revealed that the viruses were highly similar to recently reported equine rotavirus strains circulating in Europe. All Greek equine rotavirus isolates were genetically identical, suggesting persistence of the same viral strain in the stud farm, over the two consecutive foaling periods. © 2010 Elsevier B.V.",capsid protein;viral protein;animal experiment;article;breeding;diarrhea;electron microscopy;epidemic;Europe;farm animal;feces analysis;female;gene sequence;Greece;nonhuman;nucleotide sequence;reverse transcription polymerase chain reaction;Rotavirus;viral genetics;virus classification;virus strain,"Ntafis, V.;Fragkiadaki, E.;Xylouri, E.;Omirou, A.;Lavazza, A.;Martella, V.",2010,,10.1016/j.vetmic.2010.01.020,0
1521,Differential expression of porcine microRNAs in African swine fever virus infected pigs: A proof-of-concept study,"Background: African swine fever (ASF) is a re-expanding devastating viral disease currently threatening the pig industry worldwide. MicroRNAs are a class of 17-25 nucleotide non- coding RNAs that have been shown to have critical functions in a wide variety of biological processes, such as cell differentiation, cell cycle regulation, carcinogenesis, apoptosis, regulation of immunity as well as in viral infections by cleavage or translational repression of mRNAs. Nevertheless, there is no information about miRNA expression in an ASFV infection. Methods: In this proof-of-concept study, we have analyzed miRNAs expressed in spleen and submandibular lymph node of experimentally infected pigs with a virulent (E75) or its derived attenuated (E75CV1) ASFV strain, as well as, at different times post-infection with the virulent strain, by high throughput sequencing of small RNA libraries. Results: Spleen presented a more differential expression pattern than lymph nodes in an ASFV infection. Of the most abundant miRNAs, 12 were differentially expressed in both tissues at two different times in infected animals with the virulent strain. Of these, miR-451, miR-145-5p, miR-181a and miR-122 presented up-regulation at late times post-infection while miR-92a, miR-23a, miR-92b-3p, miR-126-5p, miR-126-3p, miR-30d, miR-23b and miR-92c showed down-regulation. Of the 8 differentially expressed miRNAs identified at the same time post-infection in infected animals with the virulent strain compared with animals infected with its attenuated strain, miR-126-5p, miR-92c, miR-92a, miR-30e-5p and miR-500a-5p presented up-regulation whereas miR-125b, miR-451 and miR-125a were down-regulated. All these miRNAs have been shown to be associated with cellular genes involved in pathways related to the immune response, virus-host interactions as well as with several viral genes. Conclusion: The study of miRNA expression will contribute to a better understanding of African swine fever virus pathogenesis, essential in the development of any disease control strategy.",microRNA;microRNA 122;microRNA 125a;microRNA 125b;microRNA 126 3p;microRNA 126 5p;microRNA 145 5p;microRNA 181a;microRNA 23a;microRNA 23b;microRNA 30d;microRNA 30e 5p;microRNA 451;microRNA 500a 5p;microRNA 92a;microRNA 92b 3p;microRNA 92c;unclassified drug;African swine fever;African swine fever virus;animal experiment;animal tissue;article;controlled study;down regulation;gene expression;immune response;in vivo study;Landrace pig;nonhuman;spleen;submandibular lymph node;upregulation;virus cell interaction;virus gene;virus strain;virus virulence,"Núñez-Hernández, F.;Pérez, L. J.;Muñoz, M.;Vera, G.;Accensi, F.;Sánchez, A.;Rodríguez, F.;Núñez, J. I.",2017,,10.1186/s12985-017-0864-8,0
1522,Identification of microRNAs in PCV2 subclinically infected pigs by high throughput sequencing,"Porcine circovirus type 2 (PCV2) is the essential etiological infectious agent of PCV2-systemic disease and has been associated with other swine diseases, all of them collectively known as porcine circovirus diseases. MicroRNAs (miRNAs) are a new class of small non-coding RNAs that regulate gene expression post-transcriptionally. miRNAs play an increasing role in many biological processes. The study of miRNA-mediated host-pathogen interactions has emerged in the last decade due to the important role that miRNAs play in antiviral defense. The objective of this study was to identify the miRNA expression pattern in PCV2 subclinically infected and non-infected pigs. For this purpose an experimental PCV2 infection was carried out and small-RNA libraries were constructed from tonsil and mediastinal lymph node (MLN) of infected and non-infected pigs. High throughput sequencing determined differences in miRNA expression in MLN between infected and non-infected while, in tonsil, a very conserved pattern was observed. In MLN, miRNA 126-3p, miRNA 126-5p, let-7d-3p, mir-129a and mir-let-7b-3p were up-regulated whereas mir-193a-5p, mir-574-5p and mir-34a down-regulated. Prediction of functional analysis showed that these miRNAs can be involved in pathways related to immune system and in processes related to the pathogenesis of PCV2, although functional assays are needed to support these predictions. This is the first study on miRNA gene expression in pigs infected with PCV2 using a high throughput sequencing approach in which several host miRNAs were differentially expressed in response to PCV2 infection.",microRNA;animal;Circoviridae infection;Circovirus;genetics;high throughput sequencing;isolation and purification;metabolism;pig;swine disease;veterinary medicine;virology,"Núñez-Hernández, F.;Pérez, L. J.;Muñoz, M.;Vera, G.;Tomás, A.;Egea, R.;Córdoba, S.;Segalés, J.;Sánchez, A.;Núñez, J. I.",2015,,10.1186/s13567-014-0141-4,0
1523,African swine fever virus does not express viral microRNAs in experimentally infected pigs,"Background: African swine fever virus (ASFV) is the etiological agent of African swine fever (ASF), a re-expanding devastating and highly lethal hemorrhagic viral disease. microRNAs (miRNAs) are a new class of small non-coding RNAs that regulate gene expression post-transcriptionally. The discovery of virus specific miRNAs has increased both in number and importance in the past few years. We have recently described the differential expression of several porcine miRNAs during in vivo infection with attenuated and virulent ASFV strains. Here, we have extended these studies trying to identify the presence of viral miRNAs encoded by ASFV in an in vivo infection in pigs. Results: Sixteen small RNA libraries were analyzed from spleen and submandibular lymph nodes obtained from eight pigs, seven infected with either the virulent E75 ASFV strain or its attenuated counterpart E75CV1, or from pigs surviving E75CV1-infection and challenged with BA71 (heterologous challenge) and one non infected as negative control. Samples were recovered at different times post-infection. Libraries were analyzed by next-generation sequencing. Some viral miRNA candidates were initially identified, which did not correspond to porcine miRNAs. Further structural analyses were carried out in order to confirm if they met the conformational requirements to be considered a viral miRNA. Conclusions: The analysis of sixteen small RNA libraries prepared from two different tissues obtained from pigs experimentally infected with E75, E75CV1 or with E75CV1 plus BA71, revealed the presence of six potential miRNA sequences but none of them met the requirements to be considered as viral miRNAs. Thus, we can conclude that ASFV does not express miRNAs in vivo, at least under the experimental conditions described here.",microRNA;African swine fever;African swine fever virus;animal experiment;animal tissue;article;computer model;controlled study;gene dosage;gene expression;gene sequence;high throughput sequencing;male;nonhuman;pig;real time polymerase chain reaction;RNA extraction;RNA library;RNA structure;virus genome;virus replication,"Núñez-Hernández, F.;Vera, G.;Sánchez, A.;Rodríguez, F.;Núñez, J. I.",2018,,10.1186/s12917-018-1601-2,0
1524,PRODUCTION OF THE NUCLEOCAPSID PROTEIN OF A SWINE,,,"Nviine, Coli;Ongs, T. I. N.",2002,,,0
1525,Discovery of genome of an immunodeficiencyassociated virus-like virus from pig feces in Japan,,,"Oba, M.;Katayama, Y.;Tsuchiaka, S.",2018,,,1
1526,"Metagenomic identification and sequence analysis of a Teschovirus A-related virus in porcine feces in Japan, 2014–2016","Porcine Teschoviruses (PTVs) are associated with polioencephalomyelitis and various diseases, including reproductive and gastrointestinal disorders, of pigs and wild boars, and are also detected in the feces of healthy pigs. The genus Teschovirus contains a single species Teschovirus A that currently includes 13 serotypes. In the present study, we identified novel PTVs that are distantly related to Teschovirus A and were found in fecal samples of pigs with or without diarrhea in Japan. Phylogenetic analysis of amino acid (aa) sequences of the complete coding region revealed that these newly identified viruses did not cluster with any strains of PTVs or other strains within the picornavirus supergroup 1, suggesting that the viruses may not belong to Teschovirus A or any genus of the family Picornaviridae. These novel PTVs share a type IV internal ribosomal entry site and conserved characteristic motifs in the coding region, yet exhibit 62.2–79.0%, 86.6–92.8%, 77.1–81.0%, and 84.3–86.7% aa identities to PTV strains in P1, 2C, 3C, and 3D regions, respectively. In contrast, PTV 1–13 strains of the Teschovirus A share 76.5–92.1%, 88.1–99.7%, 93.2–100%, and 95.8–100% aa identities in the P1, 2C, 3C, and 3D, respectively, within the species. These data imply that the newly identified viruses belong to teschoviruses, and may represent a novel species in the genus Teschovirus.",amino acid sequence;article;diarrhea;feces analysis;gene structure;genetic code;internal ribosome entry site;Japan;metagenomics;nonhuman;phylogeny;Picornaviridae;pig;priority journal;protein motif;sequence analysis;Teschovirus;virus identification;virus strain,"Oba, M.;Naoi, Y.;Ito, M.;Masuda, T.;Katayama, Y.;Sakaguchi, S.;Omatsu, T.;Furuya, T.;Yamasato, H.;Sunaga, F.;Makino, S.;Mizutani, T.;Nagai, M.",2018,,10.1016/j.meegid.2018.10.004,1
1527,A new comprehensive method for detection of livestock-related pathogenic viruses using a target enrichment system,"We tested usefulness of a target enrichment system SureSelect, a comprehensive viral nucleic acid detection method, for rapid identification of viral pathogens in feces samples of cattle, pigs and goats. This system enriches nucleic acids of target viruses in clinical/field samples by using a library of biotinylated RNAs with sequences complementary to the target viruses. The enriched nucleic acids are amplified by PCR and subjected to next generation sequencing to identify the target viruses. In many samples, SureSelect target enrichment method increased efficiencies for detection of the viruses listed in the biotinylated RNA library. Furthermore, this method enabled us to determine nearly full-length genome sequence of porcine parainfluenza virus 1 and greatly increased Breadth, a value indicating the ratio of the mapping consensus length in the reference genome, in pig samples. Our data showed usefulness of SureSelect target enrichment system for comprehensive analysis of genomic information of various viruses in field samples.","Animals;Cattle;Chromosome Mapping/mt [Methods];*Chromosome Mapping/ve [Veterinary];*Cytopathogenic Effect, Viral/ge [Genetics];*Genome, Viral/ge [Genetics];High-Throughput Nucleotide Sequencing/mt [Methods];*High-Throughput Nucleotide Sequencing/ve [Veterinary];*Livestock/vi [Virology];Swine;*Viruses/ge [Genetics];*Viruses/ip [Isolation & Purification];Viruses/py [Pathogenicity]","Oba, M.;Tsuchiaka, S.;Omatsu, T.;Katayama, Y.;Otomaru, K.;Hirata, T.;Aoki, H.;Murata, Y.;Makino, S.;Nagai, M.;Mizutani, T.",2018,01 08,,0
1528,COMPLETE GENOMIC SEQUENCE OF VIRULENT PIGEON PARAMYXOVIRUS IN LAUGHING DOVES (STREPTOPELIA SENEGALENSIS) IN KENYA,"Following mass deaths of Laughing Doves (Streptopelia senegalensis) in different localities throughout Kenya, internal organs obtained during necropsy of two moribund birds were sampled and analyzed by next generation sequencing. We isolated the virulent strain of pigeon paramyxovirus type-1 (PPMV-1), PPMV1/Laughing Dove/Kenya/Isiolo/B2/2012, which had a characteristic fusion gene motif (110)GGRRQKRF(117). We obtained a partial full genome of 15,114 nucleotides. The phylogenetic relationship based on the fusion gene and genomic sequence grouped our isolate as class II genotype VI, a group of viruses commonly isolated from wild birds but potentially lethal to Chickens ( Gallus gallus domesticus ). The fusion gene isolate clustered with PPMV-I strains from pigeons (Columbidae) in Nigeria. The complete genome showed a basal and highly divergent lineage to American, European, and Asian strains, indicating a divergent evolutionary pathway. The isolated strain is highly virulent and apparently species-specific to Laughing Doves in Kenya. Risk of transmission of such a strain to poultry is potentially high whereas the cyclic epizootic in doves is a threat to conservation of wild Columbidae in Kenya.",animal;chicken;Columbidae;genetics;genomics;high throughput sequencing;Kenya;Newcastle disease;Newcastle disease virus;phylogeny;virology,"Obanda, V.;Michuki, G.;Jowers, M. J.;Rumberia, C.;Mutinda, M.;Lwande, O. W.;Wangoru, K.;Kasiiti-Orengo, J.;Yongo, M.;Angelone-Alasaad, S.",2016,,10.7589/2015-07-199,0
1529,Cross-hybridization and relationships of various papillomavirus DNAs at different degrees of stringency,"Cloned DNAs of 21 different papillomaviruses which naturally infect mammals and one bird papillomavirus were compared for relative homology by Southern blot hybridization. Blots were carried out under low (T(m)-40°), medium (T(m)-33°), and high (T(m)-22°) stringency conditions. At higher stringency, human papillomaviruses cross-hybridized with each other reflecting species-specific similarities. Bovine papillomavirus types 1, 2, 5, European elk papillomavirus, and deer papillomavirus also cross-hybridized at higher stringencies probably reflecting the association of these viruses with fibroblast-prolific lesions. The hybridization data presented here may be useful in future classification attempts. They are also useful as a guide in the selection of papillomavirus DNA probes for analysis of extracts from warts and tumors.",genetic engineering;hybridization;nonhuman;Papillomaviridae;priority journal;virus classification,"O'Banion, M. K.;Sundberg, J. P.;Reszka, A. A.;Reichmann, M. E.",1987,,,0
1530,Molecular evolution of the human enteroviruses: Correlation of serotype with VP1 sequence and application to picornavirus classification,"Sixty-six human enterovirus serotypes have been identified by serum neutralization, but the molecular determinants of the serotypes are unknown. Since the picornavirus VP1 protein contains a number of neutralization domains, we hypothesized that the VP1 sequence should correspond with neutralization (serotype) and, hence, with phylogenetic lineage. To test this hypothesis and to analyze the phylogenetic relationships among the human enteroviruses, we determined the complete VP1 sequences of the prototype strains of 47 human enterovirus serotypes and 10 antigenic variants. Our sequences, together with those available from GenBank, comprise a database of complete VP1 sequences for all 66 human enterovirus serotypes plus additional strains of seven serotypes. Phylogenetic trees constructed from complete VP1 sequences produced the same four major clusters as published trees based on partial VP2 sequences; in contrast to the VP2 trees, however, in the VP1 trees strains of the same serotype were always monophyletic. In pairwise comparisons of complete VP1 sequences, enteroviruses of the same serotype were clearly distinguished from those of heterologous serotypes, and the limits of intraserotypic divergence appeared to be about 25% nucleotide sequence difference or 12% amino acid sequence difference. Pairwise comparisons suggested that coxsackie A11 and A15 viruses should be classified as strains of the same serotype, as should coxsackie A13 and A18 viruses. Pairwise identity scores also distinguished between enteroviruses of different clusters and enteroviruses from picornaviruses of different genera. The data suggest that VP1 sequence comparisons may be valuable in enterovirus typing and in picornavirus taxonomy by assisting in the genus assignment of unclassified picornaviruses.",COMPLETE NUCLEOTIDE-SEQUENCE;VACCINE-RELATED POLIOVIRUSES;VESICULAR;DISEASE VIRUS;COMMON COLD VIRUS;BIOLOGICAL PROPERTIES;BOVINE;ENTEROVIRUS;TREE TOPOLOGIES;RNA PROBES;GENOME;IDENTIFICATION,"Oberste, M. S.;Maher, K.;Kilpatrick, D. R.;Pallansch, M. A.",1999,Mar,,0
1531,Genomic evidence that simian virus 2 and six other simian picornaviruses represent a new genus in Picornaviridae,"Analysis of the VP1 capsid protein coding region of simian virus (SV) 2, SV16, SV18, SV42, SV44, SV45, and SV49 demonstrates that they are clearly distinct from members of the Enterovirus genus and from members of other existing picornavirus genera. To further characterize this group of viruses and to clarify their classification within the Picornaviridae, we have determined the complete genomic sequence of SV2 (8126 nucleotides). The genome was typical of members of Picornaviridae, encoding a single open reading frame. The putative polyprotein contained typical picornavirus protease cleavage sites, yielding mature proteins homologous to each of the known picornavirus proteins. SV2 contained an amino-terminal extension of the reading frame, which was analogous to the leader protein of members of the Aphthovirus, Cardiovirus, Erbovirus, Kobuvirus, and Teschovirus genera, but there was no significant amino acid homology with any of these known leader proteins. The 2A protein also aligned poorly with the 2A proteins of other picornaviruses. The deduced amino acid sequences of the SV2 structural and nonstructural proteins were related to but phylogenetically distinct from those of enteroviruses and human rhinoviruses. The major distinguishing features of SV2 were the presence of a type 2 internal ribosome entry site in the 5′-NTR, a putative leader protein encoded upstream of the structural proteins, and an unusually large 2A protein. On the basis of the molecular analysis, we propose that SV2, SV16, SV18, SV42, SV44, SV45, SV49, and porcine enterovirus 8 be classified as members of a new genus in Picornaviridae and that SV2 (strain 2383) be designated as the type strain. © 2003 Elsevier Inc. All rights reserved.",amino acid;polyprotein;signal peptide;structural protein;virus enzyme;viral protein;5' untranslated region;amino acid sequence;amino terminal sequence;Aphthovirus;article;Cardiovirus;controlled study;Enterovirus;enzyme degradation;gene deletion;gene sequence;genetic variability;genomics;genus;internal ribosome entry site;molecular phylogeny;nonhuman;nucleotide sequence;open reading frame;Picornaviridae;priority journal;Rhinovirus;sequence homology;simian virus;upregulation;virus classification;virus genome;virus strain,"Oberste, M. S.;Maher, K.;Pallansch, M. A.",2003,,10.1016/s0042-6822(03)00420-3,0
1532,Genetic typing of bovine viral diarrhoea virus in cattle on Irish farms,"The aim was to carry out a phylogenetic study of bovine viral diarrhoea viruses (BVDV) circulating in Irish cattle herds from 2011 to 2014. Three hundred and twenty five viruses from 267 herds were subtyped by nucleotide sequence analysis of the 5′UTR and/or the Npro regions. All viruses investigated in this study belonged to species BVDV-1 with BVDV-1a as the prominent subtype (97%). Subtypes BVDV-1b, BVDV-1d and BVDV-1e were also identified for the first time in Ireland. Pairwise alignments of 225 viruses with complete sequences for the 5′UTR and the Npro regions were performed to determine a low conflict threshold for virus strain demarcation. One hundred and seventy seven unique virus strains were identified. The study revealed significant levels of herd specific clustering of strains but no geographical or temporal clustering. Similar virus strains were identified in different counties, provinces and years indicating the potential to investigate the epidemiology of the disease by combining sequence analysis with animal movement data.",5' untranslated region;amplicon;article;bovine;Bovine viral diarrhea virus 1;controlled study;genetic procedures;genetic typing;geographic distribution;Ireland;Irish (citizen);nonhuman;nucleotide sequence;Pestivirus;phylogenetic tree;sequence analysis;virus classification;virus identification,"O'Brien, E.;Garvey, M.;Walsh, C.;Arkins, S.;Cullinane, A.",2017,,10.1016/j.rvsc.2016.10.017,0
1533,High throughput genomic sequencing of bioaerosols in broiler chicken production facilities,"Chronic inhalation exposure to agricultural dust promotes the development of chronic respiratory diseases among poultry workers. Poultry dust is composed of dander, chicken feed, litter bedding and microbes. However, the microbial composition and abundance has not been fully elucidated. Genomic DNA was extracted from settled dust and personal inhalable dust collected while performing litter sampling or mortality collection tasks. DNA libraries were sequenced using a paired-end sequencing-by-synthesis approach on an Illumina HiSeq 2500. Sequencing data showed that poultry dust is predominantly composed of bacteria (64-67%) with a small quantity of avian, human and feed DNA (< 2% of total reads). Staphylococcus sp. AL1, Salinicoccus carnicancri and Lactobacillus crispatus were the most abundant bacterial species in personal exposure samples of inhalable dust. Settled dust had a moderate relative abundance of these species as well as Staphylococcus lentus and Lactobacillus salivarius. There was a statistical difference between the microbial composition of aerosolized and settled dust. Unlike settled dust composition, aerosolized dust composition had little variance between samples. These data provide an extensive analysis of the microbial composition and relative abundance in personal inhalable poultry dust and settled poultry dust.","*Aerosols;*Air Microbiology;*Animal Husbandry;Animals;Archaea/cl [Classification];Archaea/ge [Genetics];Bacteria/cl [Classification];Bacteria/ge [Genetics];*Biota;Chickens;*Computational Biology/mt [Methods];Dust;Fungi/cl [Classification];Fungi/ge [Genetics];*High-Throughput Nucleotide Sequencing/mt [Methods];Humans;Sequence Analysis, DNA;Soil Microbiology;Viruses/cl [Classification];Viruses/ge [Genetics];0 (Aerosols);0 (Dust)","O'Brien, K. M.;Chimenti, M. S.;Farnell, M.;Tabler, T.;Bair, T.;Bray, J. L.;Nonnenmann, M. W.",2016,11,,0
1534,Molecular detection and characterization of bovine viral diarrhea virus in Mongolian cattle and yaks,"Bovine viral diarrhea virus (BVDV) is classified into two species, namely, Bovine viral diarrhea virus 1 and Bovine viral diarrhea virus 2, and affects cattle worldwide, resulting in significant economic loss. The prevalence of BVDV-1 and BVDV-2 infections and its genotypes in Mongolian animals has not been studied. In this study, we surveyed BVDV infection in dairy cattle and yaks from Bornuur and Bulgan counties by RT-PCR, and the average infection rate in the sampling sites was 15.8 % and 20.0 %, respectively. In addition, molecular features of the 5'-UTR region of the BVDV genome in Mongolian cattle and yaks were identified as belonging to the subtypes BVDV-1a and BVDV-2a, respectively. Determining the prevalence, geographical distribution, and molecular diversity of BVDV-1 and BVDV-2 in various host species in Mongolia is important for further studies and process control programs.",animal;bovine;bovine viral diarrhea;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;classification;female;genetics;genotype;isolation and purification;male;Mongolia;phylogeny;virology,"Ochirkhuu, N.;Konnai, S.;Odbileg, R.;Odzaya, B.;Gansukh, S.;Murata, S.;Ohashi, K.",2016,,10.1007/s00705-016-2890-z,0
1535,Characterization and Distribution of a Potyvirus Associated with Passion Fruit Woodiness Disease in Uganda,"This article describes the incidence and etiology of a viral disease of passion fruit in Uganda. Symptoms, including those characteristic of passion fruit woodiness disease (PWD), were observed on 32% of plants in producing areas. Electron microscopic observations of infected tissues revealed flexuous filaments of ca. 780 nm. Enzymelinked immunosorbent assays indicated a serological relationship with Cowpea aphid-borne mosaic virus (CABMV) and Passion fruit ringspot virus (PFRSV). In host range studies, only species in the families Solanaceae and Chenopodiaceae were susceptible, and neither Vigna unguiculata nor Phaseolus vulgaris became infected. Coat protein (CP) gene sequences of eight isolates exhibited features typical of potyviruses and were highly similar (88 to 100% identity). However, the sequences had limited sequence identity with CP genes of two of the three potyviruses reported to cause PWD: East Asian Passiflora virus and Passion fruit woodiness virus (PWV). Deduced amino acid sequences for the CP of isolates from Uganda had highest identity with Bean common mosaic necrosis virus (BCMNV) (72 to 79%, with evolutionary divergence values between 0.17 and 0.19) and CABMV (73 to 76%, with divergence values between 0.21 and 0.25). Based on these results and in accordance with International Committee for Taxonomy of Viruses criteria for species demarcation in the family Potyviridae, we conclude that a previously unreported virus causes viral diseases on passion fruit in Uganda. The name ""Ugandan Passiflora virus"" is proposed for this virus.",,"Ochwo-Ssemakula, M.;Sengooba, T.;Hakiza, J. J.;Adipala, E.;Edema, R.;Redinbaugh, M. G.;Aritua, V.;Winter, S.",2012,May,,0
1536,"Bovine viral diarrhea virus genomic associations in mucosal disease, enteritis and generalized dermatitis outbreaks in Argentina","The objective of the present work is the description outbreaks caused by bovine viral diarrhea virus (BVDV) in commercial beef cattle ranches in Argentina. Genetic affiliation and their association with the clinical manifestation were carried out with five BVDV isolates from an outbreak of mucosal disease (MD) (Outbreak #1), acute enteritis (Outbreaks #2 and #3) and generalized dermatitis (Outbreaks #4 and #5). Upon genetic analysis CP BVDV isolate of Outbreak #1 clustered to closely to BVDV Oregon (Genotype 1). BVDV isolates from the outbreaks of generalized dermatitis (Outbreaks #4 and #5) were located close to BVDV Osloss within Genotype 1. The identification by immunohistochemistry of BVDV in exudative dermatitis indicates the epithelial cell tropism of the virus. Phylogenic characterization of BVDV from Outbreaks #2 and #3 locate them as BVDV-2. 5′UTR sequence of these viruses revealed a homology of 88 and 90% to BVDV-890 (Genotype 2) and a 77 and 75% to BVDV-SD1 (Genotype 1), respectively. The association of BVDV-2 with severe disease indicates the presence of highly virulent strains. Data from natural outbreaks where BVDV-1 and BVDV-2 were isolated revealed that pathology overlaps and not clearly allows the differentiation between genotypes based on gross or microscopic lesions. Thus, for a definitive diagnosis, further virology and molecular studies are necessary. Additionally, the results of this work focused on the origin and consequences of genetic variations of BVDV with regard to pathogenesis and suggest the association between genotype and a defined clinical syndrome. © 2003 Elsevier B.V. All rights reserved.",Argentina;article;beef cattle;Bovine viral diarrhea virus 1;cattle disease;dermatitis;differentiation;disease association;enteritis;epithelium cell;genetic analysis;genetic variability;genome;genotype;immunohistochemistry;microscopy;nonhuman;pathogenesis;phylogeny;plant growth;virology;virus characterization;virus isolation;virus virulence,"Odeón, A. C.;Risatti, G.;Kaiser, G. G.;Leunda, M. R.;Odriozola, E.;Campero, C. M.;Donis, R. O.",2003,,10.1016/s0378-1135(03)00210-4,0
1537,"African Swine Fever Virus Georgia 2007 with a Deletion of Virulence-Associated Gene 9GL (B119L), when Administered at Low Doses, Leads to Virus Attenuation in Swine and Induces an Effective Protection against Homologous Challenge","UNLABELLED: African swine fever virus (ASFV) is the etiological agent of an often lethal disease of domestic pigs. Disease control strategies have been hampered by the unavailability of vaccines against ASFV. Since its introduction in the Republic of Georgia, a highly virulent virus, ASFV Georgia 2007 (ASFV-G), has caused an epizootic that spread rapidly into Eastern European countries. Currently no vaccines are available or under development to control ASFV-G. In the past, genetically modified ASFVs harboring deletions of virulence-associated genes have proven attenuated in swine, inducing protective immunity against challenge with homologous parental viruses. Deletion of the gene 9GL (open reading frame [ORF] B119L) in highly virulent ASFV Malawi-Lil-20/1 produced an attenuated phenotype even when administered to pigs at 10(6) 50% hemadsorption doses (HAD50). Here we report the construction of a genetically modified ASFV-G strain (ASFV-G-DELTA9GLv) harboring a deletion of the 9GL (B119L) gene. Like Malawi-Lil-20/1-DELTA9GL, ASFV-G-DELTA9GL showed limited replication in primary swine macrophages. However, intramuscular inoculation of swine with 10(4) HAD50 of ASFV-G-DELTA9GL produced a virulent phenotype that, unlike Malawi-Lil-20/1-DELTA9GL, induced a lethal disease in swine like parental ASFV-G. Interestingly, lower doses (10(2) to 10(3) HAD50) of ASFV-G-DELTA9GL did not induce a virulent phenotype in swine and when challenged protected pigs against disease. A dose of 10(2) HAD50 of ASFV-G-DELTA9GLv conferred partial protection when pigs were challenged at either 21 or 28 days postinfection (dpi). An ASFV-G-DELTA9GL HAD50 of 10(3) conferred partial and complete protection at 21 and 28 dpi, respectively. The information provided here adds to our recent report on the first attempts toward experimental vaccines against ASFV-G. IMPORTANCE: The main problem for controlling ASF is the lack of vaccines. Studies on ASFV virulence lead to the production of genetically modified attenuated viruses that induce protection in pigs but only against homologous virus challenges. Here we produced a recombinant ASFV lacking virulence-associated gene 9GL in an attempt to produce a vaccine against virulent ASFV-G, a highly virulent virus isolate detected in the Caucasus region in 2007 and now spreading though the Caucasus region and Eastern Europe. Deletion of 9GL, unlike with other ASFV isolates, did not attenuate completely ASFV-G. However, when delivered once at low dosages, recombinant ASFV-G-DELTA9GL induces protection in swine against parental ASFV-G. The protection against ASFV-G is highly effective after 28 days postvaccination, whereas at 21 days postvaccination, animals survived the lethal challenge but showed signs of ASF. Here we report the design and development of an experimental vaccine that induces protection against virulent ASFV-G.","*African Swine Fever/pc [Prevention & Control];*African Swine Fever Virus/ge [Genetics];*African Swine Fever Virus/im [Immunology];Animals;Base Sequence;DNA Primers/ge [Genetics];Gene Deletion;Genetic Engineering/mt [Methods];High-Throughput Nucleotide Sequencing;Molecular Sequence Data;Mutation, Missense/ge [Genetics];Polymerase Chain Reaction;Swine;*Viral Proteins/ge [Genetics];Viral Vaccines/ge [Genetics];*Viral Vaccines/pd [Pharmacology];*Virulence Factors/ge [Genetics];0 (9GL protein, African swine fever virus);0 (DNA Primers);0 (Viral Proteins);0 (Viral Vaccines);0 (Virulence Factors)","O'Donnell, V.;Holinka, L. G.;Krug, P. W.;Gladue, D. P.;Carlson, J.;Sanford, B.;Alfano, M.;Kramer, E.;Lu, Z.;Arzt, J.;Reese, B.;Carrillo, C.;Risatti, G. R.;Borca, M. V.",2015,Aug,,0
1538,Isolation and characterization of orf viruses from korean black goats,Five cases of orf virus infection in Korean black goats were diagnosed in our laboratory between 2010 and 2011. One orf virus (ORF/2011) was isolated from an ovine testis cell line (OA3.Ts) for use as a vaccine candidate. Sequences of the major envelope protein and orf virus interferon resistance genes were determined and compared with published reference sequences. Phylogenetic analyses revealed that orf viruses from Korean black goats were most closely related to an isolate (ORF/09/Korea) from dairy goats in Korea. This result indicates that the orf viruses might have been introduced from dairy goats into the Korean black goat population. © 2013 The Korean Society of Veterinary Science.,animal;animal disease;article;contagious ecthyma;DNA sequence;genetics;goat;goat disease;isolation;isolation and purification;metabolism;molecular genetics;phylogeny;polymerase chain reaction;Poxviridae;sequence homology;South Korea;virology,"Oem, J. K.;Chung, J. Y.;Kim, Y. J.;Lee, K. K.;Kim, S. H.;Jung, B. Y.;Hyun, B. H.",2013,,10.4142/jvs.2013.14.2.227,0
1539,Complete genome sequences of three rabies viruses isolated from rabid raccoon dogs and a cow in Korea,,,"Oem, J. K.;Kim, S. H.;Kim, Y. H.;Lee, M. H.;Lee, K. K.",2013,,,0
1540,"Reemergence of rabies in the southern Han river region, Korea","Recently, 11 cases of animal rabies were reported in the southern region (Suwon and Hwaseong cities) of Gyeonggi Province, South Korea. The cases were temporally separated into two cases in dogs (Canis lupus familiaris) in spring 2012 and nine cases in domestic animals and wildlife in winter 2012-13. All carcasses were submitted for histopathologic examination and viral antigen identification. Sequences of the glycoprotein, nucleoprotein, and glycoprotein-large polymerase protein intergenic noncoding loci of the 11 strains were determined and compared with published reference sequences. All rabies strains were closely related to the Gangwon strains isolated in 2008-09, suggesting that the rabies virus strains isolated in Gyeonggi were introduced from Gangwon Province.",animal;bovine;cat;cat disease;cattle disease;communicable disease;dog;dog disease;rabies;raccoon dog;South Korea;veterinary medicine;virology;wild animal,"Oem, J. K.;Kim, S. H.;Kim, Y. H.;Lee, M. H.;Lee, K. K.",2014,,10.7589/2013-07-177,0
1541,Bovine papular stomatitis virus (BPSV) infections in Korean native cattle,"An outbreak of a disease with parapox-like symptoms was reported in South Korea in April 2012. Three of 45 Korean native cattle, age 20-24 months, were affected. Parapoxviruses were detected and identified by electron microscopy and polymerase chain reaction (PCR). To determine the genetic characteristics of the Korean strains, the sequence of the major envelope protein (B2L) was determined and compared with published reference sequences. Phylogenetic analysis revealed that the parapoxvirus strains were closely related to not only isolates from Japan, but also isolates from Germany, Sudan and the United states. This is the first report on an outbreak and the molecular characterization of BPSV in Korea. © 2013 The Japanese Society of Veterinary Science.",primer DNA;virus envelope protein;amino acid sequence;animal;animal disease;bovine;cattle disease;cluster analysis;DNA sequence;epidemic;genetics;molecular genetics;note;nucleotide sequence;Parapoxvirus;phylogeny;polymerase chain reaction;poxvirus infection;South Korea;transmission electron microscopy;ultrastructure;virology,"Oem, J. K.;Lee, E. Y.;Lee, K. K.;Kim, S. H.;Lee, M. H.;Hyun, B. H.",2013,,10.1292/jvms.12-0312,0
1542,Novel Kobuvirus species identified from black goat with diarrhea,,,"Oem, J. K.;Lee, M. H.;Lee, K. K.;An, D. J.",2014,,,0
1543,Foot-and-mouth disease in Asiatic black bears (Ursus thibetanus),"Foot-and-mouth disease (FMD) is a highly contagious, debilitating, and globally significant viral disease typically affecting cloven-hoofed hosts. The diagnosis of FMD in bears in Vietnam is described. The current study describes a confirmed case of FMD in a bear species, and the clinical signs compatible with FMD in a Malayan sun bear. Thirteen Asiatic black bears (Ursus thibetanus) and 1 Malayan sun bear (Helarctos malayanus) were apparently affected. In August 2011, an adult bear became lethargic, and developed footpad vesicles. Over 15 days, 14 out of 17 bears developed similar signs; the remaining 3 co-housed bears and another 57 resident bears did not. All affected bears developed vesicles on all footpads, and most were lethargic for 24-48 hr. Nasal and oral lesions were noted in 6 and 3 cases, respectively. Within 1 month, all looked normal. Foot-and-mouth disease virus (FMDV) was detected by reverse transcription polymerase chain reaction, classified as serotype O, and isolated by virus isolation techniques. Phylogenetic analysis demonstrated clustering of 3 bear isolates, in a branch distinct from other FMDV type O isolates. The outbreak likely occurred due to indirect contact with livestock, and was facilitated by the high density of captive bears. It showed that Asiatic black bears are capable of contracting FMDV and developing clinical disease, and that the virus spreads easily between bears in close contact.",animal;bear;epidemic;Foot and mouth disease virus;foot and mouth disease;genetics;isolation and purification;Phyllachorales;phylogeny;Viet Nam;virology,"Officer, K.;Lan, N. T.;Wicker, L.;Hoa, N. T.;Weegenaar, A.;Robinson, J.;Ryoji, Y.;Loukopoulos, P.",2014,,10.1177/1040638714547256,0
1544,Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment,"MutS proteins are ubiquitous in cellular organisms and have important roles in DNA mismatch repair or recombination. In the virus world, the amoeba-infecting Mimivirus, as well as the recently sequenced Cafeteria roenbergensis virus are known to encode a MutS related to the homologs found in octocorals and epsilon-proteobacteria. To explore the presence of MutS proteins in other viral genomes, we performed a genomic survey of four giant viruses ('giruses') (Pyramimonas orientalis virus (PoV), Phaeocystis pouchetii virus (PpV), Chrysochromulina ericina virus (CeV) and Heterocapsa circularisquama DNA virus (HcDNAV)) that infect unicellular marine algae. Our analysis revealed the presence of a close homolog of Mimivirus MutS in all the analyzed giruses. These viral homologs possess a specific domain structure, including a C-terminal HNH-endonuclease domain, defining the new MutS7 subfamily. We confirmed the presence of conserved mismatch recognition residues in all members of the MutS7 subfamily, suggesting their role in DNA mismatch repair rather than DNA recombination. PoV and PpV were found to contain an additional type of MutS, which we propose to call MutS8. The MutS8 proteins in PoV and PpV were found to be closely related to homologs from ` Candidatus Amoebophilus asiaticus', an obligate intracellular amoeba-symbiont belonging to the Bacteroidetes. Furthermore, our analysis revealed that MutS7 and MutS8 are abundant in marine microbial metagenomes and that a vast majority of these environmental sequences are likely of girus origin. Giruses thus seem to represent a major source of the underexplored diversity of the MutS family in the microbial world. The ISME Journal (2011) 5, 1143-1151; doi:10.1038/ismej.2010.210; published online 20 January 2011 Subject Category: evolutionary genetics",mimivirus;girus;virus;DNA repair;MutS;SWINE-FEVER VIRUS;GIANT VIRUSES;PHYLOGENETIC ANALYSIS;MITOCHONDRIAL;GENOME;SYMBIOTIC BACTERIA;GENE;MIMIVIRUS;EVOLUTION;SEQUENCE;HOMOLOG,"Ogata, H.;Ray, J.;Toyoda, K.;Sandaa, R. A.;Nagasaki, K.;Bratbak, G.;Claverie, J. M.",2011,Jul,,0
1545,Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus,"Heterocapsa circularisquama DNA virus (HcDNAV; previously designated as HcV) is a giant virus (girus) with a ∼356-kbp double-stranded DNA (dsDNA) genome. HcDNAV lytically infects the bivalve-killing marine dinoflagellate H. circularisquama, and currently represents the sole DNA virus isolated from dinoflagellates, one of the most abundant protists in marine ecosystems. Its morphological features, genome type, and host range previously suggested that HcDNAV might be a member of the family Phycodnaviridae of Nucleo-Cytoplasmic Large DNA Viruses (NCLDVs), though no supporting sequence data was available. NCLDVs currently include two families found in aquatic environments (Phycodnaviridae, Mimiviridae), one mostly infecting terrestrial animals (Poxviridae), another isolated from fish, amphibians and insects (Iridoviridae), and the last one (Asfarviridae) exclusively represented by the animal pathogen African swine fever virus (ASFV), the agent of a fatal hemorrhagic disease in domestic swine. In this study, we determined the complete sequence of the type B DNA polymerase (PolB) gene of HcDNAV. The viral PolB was transcribed at least from 6 h post inoculation (hpi), suggesting its crucial function for viral replication. Most unexpectedly, the HcDNAV PolB sequence was found to be closely related to the PolB sequence of ASFV. In addition, the amino acid sequence of HcDNAV PolB showed a rare amino acid substitution within a motif containing highly conserved motif: YSDTDS was found in HcDNAV PolB instead of YGDTDS in most dsDNA viruses. Together with the previous observation of ASFV-like sequences in the Sorcerer II Global Ocean Sampling metagenomic datasets, our results further reinforce the ideas that the terrestrial ASFV has its evolutionary origin in marine environments. © 2009 Ogata et al; licensee BioMed Central Ltd.",DNA directed DNA polymerase beta;double stranded DNA;African swine fever virus;amino acid sequence;amino acid substitution;article;dinoflagellate;gene function;gene sequence;genetic transcription;Heterocapsa circularisquama DNA virus;inoculation;marine environment;metagenomics;nonhuman;nucleotide sequence;Phycodnaviridae;terrestrial species;virus replication,"Ogata, H.;Toyoda, K.;Tomaru, Y.;Nakayama, N.;Shirai, Y.;Claverie, J. M.;Nagasaki, K.",2009,,10.1186/1743-422x-6-178,0
1546,Complete genome and phylogenetic position of bovine papillomavirus type 7,"Six bovine papillomavirus (BPV) types and 16 putative BPV types have been reported previously. Here, the complete genome sequence of BAPV6, a novel putative BPV type isolated from cattle in Japan, was determined by using multiple-primed rolling-circle amplification. The genome consisted of 7412 bp (G+C content of 46 mol%) that encoded five early (El, E2, E4, E6 and E7) and two late (L1 and L2) genes, but did not encode the E5 gene. The E6 protein contained a non-consensus CxxC(x)33CxxC and a consensus CxxC(x)29CxxC zinc-binding domain, and the E7 protein lacked the LxCxE motif. The nucleotide sequence of the L1 open reading frame (ORF) was related most closely (57-58 %) to the L1 ORF of member(s) of the genera Betapapillomavirus, Gammapapillomavirus and Pipapillomavirus. Phylogenetic analysis based on the complete L1 ORF suggests that BAPV6 should be classified in a novel genus in the family Papillomaviridae as BPV-7. © 2007 SGM.",glycoprotein E1;protein E2;protein E4;protein E5;protein E6;protein l1;protein l2;unclassified drug;virus DNA;viral protein;article;Betapapilloma virus;binding site;bovine;controlled study;DNA content;DNA virus;Gammapapilloma virus;gene amplification;genetic code;Japan;new genus;nonhuman;nucleotide sequence;open reading frame;Papillomaviridae;Papilloma virus 6;Papilloma virus 7;phylogeny;Pipapillomavirus;priority journal;protein motif;taxonomic rank;virus classification;virus genome;virus isolation,"Ogawa, T.;Tomita, Y.;Okada, M.;Shirasawa, H.",2007,,10.1099/vir.0.82794-0,0
1547,The human gut virome: a multifaceted majority,,,"Ogilvie, L. A.;Jones, B. V.",2015,,,0
1548,The human gut virome: form and function,,,"Ogilvie, L. A.;Jones, B. V.",2017,,,0
1549,Isolation of maedi/visna virus from a sheep in Japan,"Maedi/visna (MV) is a lentiviral disease of sheep caused by the maedi/visna virus (MVV). Although MV is prevalent in many countries, it had not been reported in Japan. In 2011, however, three sheep in northern Japan were reported to be seropositive against the MVV antigen, indicating a persistent MVV infection. In the present study, we isolated MVV from one sheep to confirm MVV infection and conducted genomic classification of the virus. The co-culture of leukocytes from a seropositive sheep with fetal goat lung cells resulted in the formation of syncytial cells and the amplification of a long terminal repeat sequence of MVV by polymerase chain reaction. The isolate was confirmed as being MVV, rather than the caprine arthritis-encephalitis virus based on phylogenetic analysis of the gag gene sequence. Although the sheep was asymptomatic, nonpurulent meningitis and demyelination were found in the spinal cord. These were considered to be early lesions associated with pathogenic MVV infection. Therefore, the present study demonstrated that MVV is distributed in Japan. © 2014 The Japanese Society of Veterinary Science.",primer DNA;animal;animal disease;article;biological model;classification;cluster analysis;DNA sequence;genetics;isolation and purification;Japan;Lentivirus infection;long terminal repeat;molecular genetics;nucleotide sequence;phylogeny;polymerase chain reaction;prevalence;sequence alignment;sheep;sheep disease;structural gene;virology;Visna virus,"Oguma, K.;Tanaka, C.;Harasawa, R.;Kimura, A.;Sasaki, J.;Goryo, M.;Sentsui, H.",2014,,10.1292/jvms.13-0269,0
1550,Evidence of an antigenic shift among Palyam serogroup orbiviruses,"The Japanese isolates of Palyam serogroup viruses isolated from 1985 to 2001 were investigated for the genome sequence of segments 2 and 7 and were phylogenetically analyzed in comparison with Australian and African isolates of the same serogroup. The nucleotide sequences of segment 7 were highly conserved within Japanese isolates (95.1 to 100%) and between Japanese and Taiwanese isolates (96.0 to 100%), whereas the identities between Japanese and Taiwanese isolates and Australian and African isolates were fairly conserved (84.2 to 92.0%). Phylogenetic analysis based on segment 7 revealed three clusters according to geographical origin. As a result of the nucleotide sequence analysis of segment 2, which encodes a serotype-specific antigen, Japanese isolates were classified into two groups by genome length and nucleotide identities. Four of the nine Japanese isolates were categorized into the same group as prototype strain K-47 of the Chuzan virus, and the remaining isolates were categorized into the same group as the D'Aguilar virus and Nyabira virus. Phylogenetic analysis based on segment 2 revealed two clusters, the cluster containing Chuzan virus and the cluster containing the D'Aguilar and Nyabira viruses. To examine the antigenic relationship among viruses categorized in different clusters, we conducted a cross-neutralization test. KSB-29/E/01, isolated in 2001 in Japan, was neutralized by antiserum not only to strain B8112 of D'Aguilar virus but also to Chuzan virus. These results indicated that genetically and antigenically unique characteristics of KSB-29/E/01 were attributed to genetic reassortment of segment 2 between Chuzan virus and D'Aguilar virus.","Animals;*Antigenic Variation;Antigens, Viral/ge [Genetics];Antigens, Viral/im [Immunology];*Antigens, Viral;Cattle;Cattle Diseases/vi [Virology];Culex/vi [Virology];Japan;Molecular Sequence Data;Neutralization Tests;Palyam Virus/cl [Classification];Palyam Virus/ge [Genetics];*Palyam Virus/im [Immunology];Phylogeny;*Recombination, Genetic;Reoviridae Infections/ve [Veterinary];Reoviridae Infections/vi [Virology];Sequence Analysis, DNA;Serotyping;0 (Antigens, Viral)","Ohashi, S.;Matsumori, Y.;Yanase, T.;Yamakawa, M.;Kato, T.;Tsuda, T.",2004,Oct,,0
1551,Sequence analysis of an Asian isolate of minute virus of canines (canine parvovirus type 1),"Minute virus of canines (MVC), also known as canine parvovirus (CPV) type 1, is an autonomous parvovirus that infects domestic dogs worldwide and responsible for clinical problems of neonates and pregnant bitches. It was preliminary described that MVC is antigenically as well as genetically different from CPV type 2 that emerged later. However, much of MVC is still obscure since only a limited number of MVC isolates have been available for the study. MVC infections of Japanese and Korean dogs were epidemiologically studied in the previous study, and several MVC isolates could be cultivated in vitro. In the present study an almost full-length nucleotide sequence of a Korean MVC strain HM-6 genome was obtained and comparatively analyzed with those of the American MVC strain GA3 characterized recently. Genome structure of the HM-6 strain was similar to the GA3 strain showing 96.4% identity at the nucleotide sequence. Each of the deduced amino acid sequences of NS1, NP-1, and VP1/2 showed homology of 96.5%, 92.5%, and 97.5% between the HM-6 and GA3 strains. When compared with other parvovirus species, the HM-6 strain was most closely related to bovine parvovirus (BPV) as described for the GA3 strain. These results suggest that MVC together with BPV can possibly be classified into a new clade in the Parvovirinae subfamily. © 2004 Kluwer Academic Publishers.",amino acid sequence;article;comparative study;correlation analysis;genome analysis;nonhuman;nucleotide sequence;Parvoviridae;phylogeny;priority journal;sequence analysis;virus infection;virus strain,"Ohshima, T.;Kishi, M.;Mochizuki, M.",2004,,10.1007/s11262-004-7430-3,0
1552,First isolation and genetic characterization of pseudocowpox virus from cattle in Japan,"Background: Pseudocowpox virus (PCPV) infects cattle worldwide with zoonotic potential but has not been isolated in Japan. Thus, the epidemiological status of PCPV infection in cattle is undetermined. Results: In May 2016, a cattle in a farm in Yamaguchi Prefecture showed white vesicles and hyperemia in the mucosa under the tongue surface, but not on the teats and coronary cushions. A parapoxvirus was isolated from the oral lesion swab and was genetically characterized based on the full-length sequence of B2L gene encoding viral envelope. Phylogenetic analysis showed that the isolated virus was classified into PCPV. Conclusion: This case indicates its potential spread in Japan. This is the first report of isolation of PCPV in Japan.",animal tissue;article;B2L gene;bovine;controlled study;female;gene sequence;genetic trait;hyperemia;Japan;mouth lesion;nonhuman;oral biopsy;phylogeny;poxvirus infection;Pseudocowpox virus;salivation disorder;virus envelope;virus gene;virus isolation,"Ohtani, A.;Yokoyama, A.;Narushige, H.;Inoshima, Y.",2017,,10.1186/s12985-017-0840-3,0
1553,Genetic characterization and classification of human and animal sapoviruses,"Sapoviruses (SaVs) are enteric caliciviruses that have been detected in multiple mammalian species, including humans, pigs, mink, dogs, sea lions, chimpanzees, and rats. They show a high level of diversity. A SaV genome commonly encodes seven nonstructural proteins (NSs), including the RNA polymerase protein NS7, and two structural proteins (VP1 and VP2). We classified human and animal SaVs into 15 genogroups (G) based on available VP1 sequences, including three newly characterized genomes from this study. We sequenced the full length genomes of one new genogroup V (GV), one GVII and one GVIII porcine SaV using long range RT-PCR including newly designed forward primers located in the conserved motifs of the putative NS3, and also 5′ RACE methods. We also determined the 5′- and 3′-ends of sea lion GV SaV and canine GXIII SaV. Although the complete genomic sequences of GIX-GXII, and GXV SaVs are unavailable, common features of SaV genomes include: 1) ""GTG"" at the 5′-end of the genome, and a short (9-14 nt) 5′-untranslated region; and 2) the first five amino acids (M [A/V] S [K/R] P) of the putative NS1 and the five amino acids (FEMEG) surrounding the putative cleavage site between NS7 and VP1 were conserved among the chimpanzee, two of five genogroups of pig (GV and GVIII), sea lion, canine, and human SaVs. In contrast, these two amino acid motifs were clearly different in three genogroups of porcine (GIII, GVI and GVII), and bat SaVs. Our results suggest that several animal SaVs have genetic similarities to human SaVs. However, the ability of SaVs to be transmitted between humans and animals is uncertain.",nonstructural protein 3;nonstructural protein 7;protein VP1;protein VP2;unclassified drug;viral protein;5' rapid amplification of cDNA end;5' untranslated region;amino acid sequence;article;bat;controlled study;dog;gene amplification;genetic similarity;genetic variability;genotype;human;nonhuman;nucleotide sequence;Otariidae;phylogeny;pig;protein cleavage;protein motif;reverse transcription polymerase chain reaction;Sapovirus;sequence alignment;sequence analysis;viral genetics;virus classification;virus genome;virus transmission;zoonosis,"Oka, T.;Lu, Z.;Phan, T.;Delwart, E. L.;Saif, L. J.;Wang, Q.",2016,,10.1371/journal.pone.0156373,0
1554,Bovine rotavirus G and P types and sequence analysis of the VP7 gene of two G8 bovine rotaviruses from JPN,"A total of 1481 fecal specimens were collected from diarrheic calves under 1 month of age on 29 dairy and beef farms in 11 prefectures in Japan during the period from 1987 to 2000. Those calves and their dams were not vaccinated against rotavirus. One hundred and forty-two bovine rotaviruses were isolated on MA-104 cell cultures and detected by latex agglutination test. They were classified into 18 G6P[1] (11.2%), 53 G6P[5] (37.3%), 15 G6P[11] (10.6%), 12 G10P[5] (8.5%), 42 G10P[11] (29.6%) and 1 G8P[11] (0.7%) by reverse transcription-polymerase chain reaction. One serotype G8 virus was untypable for the P genotype suggesting a new type of bovine origin. The least common G8 serotype viruses were isolated from the samples of farms from Niigata and Tokushima prefectures. The VP7 gene sequences of the two isolates exhibited a high degree of homology as well as previously reported G8 viruses with 93.3-98.8% identity of deduced amino acids. A phylogenetic analysis of the VP7 gene of the two G8 viruses and 13 previously reported G8 viruses by the neighbor-joining method indicated that the two newly isolated G8 rotaviruses had a common origin and they were assigned to a new disparate cluster. © 2002 Elsevier Science B.V. All rights reserved.",amino acid;agglutination test;amino acid sequence;animal cell;article;bovine;cell culture;controlled study;feces analysis;gene sequence;nonhuman;phylogeny;reverse transcription polymerase chain reaction;Rotavirus;sequence analysis;sequence homology;serotype;virus characterization;virus isolation;virus typing,"Okada, N.;Matsumoto, Y.",2002,,10.1016/s0378-1135(01)00445-x,0
1555,Isolation and characterization of a novel type of rotavirus species A in sugar gliders (Petaurus breviceps),"To estimate the risk of interspecies transmission of rotavirus species A (RVA) from exotic pets to other mammalian species, the prevalence of RVA in sugar gliders (Petaurus breviceps) was investigated. RVAs were detected in 10 of 44 sugar gliders by reverse transcription (RT)-seminested PCR. These viruses were classified as G27P[3] and G27P[36] genotypes, with G27 and P[36] being new genotypes as assigned by the Rotavirus Classification Working Group. To characterize sugar glider RVA in detail, one strain, RVA/SugarGlider-tc/JPN/SG385/2012/ G27P[36] (SG385-tc), was isolated. All of the genes of the strain were classified as new genotypes (G27-P[36]-I19-R10-C10-M9-A20-N11-T13-E17-H12). The enterotoxin domain in NSP4, which is important for the induction of diarrhoea, was conserved between SG385-tc and previously reported mammalian strains, suggesting the potential of sugar glider RVA to cause diarrhoea in mammalian species. In fact, seven out of nine suckling mice inoculated orally with 3.9 x 10(4) f.f.u. of strain SG385-tc had diarrhoea and the 50 % diarrhoea-inducing dose (DD50) of strain SG385-tc in suckling mice was 1.2 x 10(4) f.f.u. Our findings suggest that sugar glider RVA is infective to and possibly pathogenic in other mammalian species.",GROUP-A ROTAVIRUS;AGE-DEPENDENT DIARRHEA;SUCKLING MOUSE MODEL;MOLECULAR CHARACTERIZATION;AVIAN ROTAVIRUS;NONSTRUCTURAL GLYCOPROTEIN;GENOTYPE CONSTELLATION;ELECTRON-MICROSCOPY;PORCINE ROTAVIRUS;SCIURUS-VULGARIS,"Okadera, K.;Abe, M.;Ito, N.;Mitake, H.;Okada, K.;Nakagawa, K.;Une, Y.;Tsunemitsu, H.;Sugiyama, M.",2016,May,,0
1556,"The genetic and antigenic diversity of avian influenza viruses isolated from domestic ducks, muscovy ducks, and chickens in northern and southern Vietnam, 2010-2012","To estimate the prevalence of avian influenza virus infection in Vietnam, surveillance was conducted in domestic and wild birds from households, live-bird markets, slaughtering sites, and bird sanctuaries in Vietnam between October 2010 and October 2012. Of the 4,550 samples collected, 226 influenza A virus isolates were obtained from domestic ducks, muscovy ducks, and chickens. Of these, 25 and 22 H5N1 highly pathogenic avian influenza viruses (HPAIVs) were isolated from apparently healthy domestic ducks in live-bird markets and slaughtering sites in northern and southern Vietnam, respectively. The HA genes of H5 viruses isolated from birds in northern Vietnam phylogenetically belonged to the genetic clade 2.3.2.1 and those in southern Vietnam belonged to the genetic clade 1.1. In addition, 39 H3, 12 H4, 1 H5, 93 H6, 2 H7, 18 H9, 3 H10, and 11 H11 viruses were isolated. Phylogenetic and antigenic analyses of the H6 and H9 viruses revealed that they were closely related to the isolates obtained from domestic poultry in China. Phylogenetic analyses of internal gene segments of these isolates revealed that these viruses were circulating in both domestic and wild birds in Asia and reassortment events had occurred frequently. Therefore, it will be important to continue the surveillance and strict controls over the movement and trade of poultry and poultry products in order to eradicate H5N1 HPAIV from Asia. © 2013 Springer Science+Business Media New York.",animal experiment;antigenic variation;article;avian influenza;avian influenza virus;chicken;domestic animal;duck;genetic reassortment;genetic variability;Influenza A virus (H5N1);molecular phylogeny;nonhuman;priority journal;Viet Nam;virus gene;virus isolation;virus mutation;virus strain,"Okamatsu, M.;Nishi, T.;Nomura, N.;Yamamoto, N.;Sakoda, Y.;Sakurai, K.;Chu, H. D.;Thanh, L. P.;Van Nguyen, L.;Van Hoang, N.;Tien, T. N.;Yoshida, R.;Takada, A.;Kida, H.",2013,,10.1007/s11262-013-0954-7,0
1557,"Characterization of Highly Pathogenic Avian Influenza Virus A(H5N6), Japan, November 2016","Highly pathogenic avian influenza viruses (HPAIVs) A(H5N6) were concurrently introduced into several distant regions of Japan in November 2016. These viruses were classified into the genetic clade 2.3.4.4c and were genetically closely related to H5N6 HPAIVs recently isolated in South Korea and China. In addition, these HPAIVs showed further antigenic drift.",Animals;Birds;*Influenza A virus/ge [Genetics];*Influenza A virus/py [Pathogenicity];Influenza in Birds/ep [Epidemiology];Influenza in Birds/mo [Mortality];*Influenza in Birds/vi [Virology];Japan;Phylogeny,"Okamatsu, M.;Ozawa, M.;Soda, K.;Takakuwa, H.;Haga, A.;Hiono, T.;Matsuu, A.;Uchida, Y.;Iwata, R.;Matsuno, K.;Kuwahara, M.;Yabuta, T.;Usui, T.;Ito, H.;Onuma, M.;Sakoda, Y.;Saito, T.;Otsuki, K.;Ito, T.;Kida, H.",2017,04,,0
1558,Genetic variability and evolution of hepatitis E virus,"Hepatitis E virus (HEV) is the sole member of the genus Hepevirus in the family Hepeviridae. HEV is transmitted primarily by the fecal-oral route, and water-borne epidemics are characteristic of hepatitis E in many developing countries in Asia, Africa and Latin America where sanitation conditions are suboptimal. Accumulating lines of evidence indicate that HEV-associated hepatitis also occurs domestically among individuals in industrialized countries, that there are animal reservoirs of HEV such as domestic pigs and wild boars, and that hepatitis E is a zoonosis. Based on the extensive genomic variability among HEV isolates, HEV sequences have been classified into four genotypes: genotype 1 consists of epidemic strains in developing countries in Asia and Africa; genotype 2 has been described in Mexico and several African countries; genotype 3 HEV is widely distributed and has been isolated from sporadic cases of acute hepatitis E and/or domestic pigs in many countries in the world, except for countries in Africa; and genotype 4 contains strains isolated from humans and/or domestic pigs exclusively in Asian countries. This paper reviews current knowledge on the genomic variability, geographic distribution and zoonotic aspects of HEV as well as the clinical significance of genotype and evolution of HEV. © 2007 Elsevier B.V. All rights reserved.",clinical feature;epidemic;gene cluster;genetic variability;genotype;geographic distribution;hepatitis E;Hepatitis E virus;human;molecular evolution;nonhuman;nucleotide sequence;open reading frame;priority journal;review;sanitation;sequence analysis;unindexed sequence;zoonosis,"Okamoto, H.",2007,,10.1016/j.virusres.2007.02.002,0
1559,Features of hepatitis E virus infection in Japan,"Hepatitis E virus (HEV) is a major cause of acute hepatitis in many developing countries. HEV is transmitted principally by the fecal-oral route, and water-borne epidemics are characteristic of hepatitis E. Recently, there is growing consensus that HEV-associated hepatitis also occurs among individuals in industrialized nations who had no history of travel to endemic areas. Zoonotic spread of HEV has been suggested as human and swine HEV strains are closely related genetically and experimental cross-species infection of swine HEV to a chimpanzee and that of human HEV to swine have been demonstrated. This review describes the clinical, epidemiological and virological characteristics of domestic HEV infection in Japan, the genetic relatedness of Japanese human and swine HEV strains, and possible modes of HEV transmission, emphasizing that HEV should be considered in the diagnosis of acute or fulminant hepatitis of non-A, non-B, non-C etiology, even in patients who have not traveled abroad.",acute hepatitis;chimpanzee;developing country;endemic disease;genotype;hepatitis E;Hepatitis E virus;hepatitis non A non B non C;human;industrialization;Japan;laboratory test;nonhuman;nucleotide sequence;phylogeny;review;pig;unindexed sequence;virus strain;virus transmission;zoonosis,"Okamoto, H.;Takahashi, M.;Nishizawa, T.",2003,,,0
1560,"Characterization of sporadic acute hepatitis E and comparison of hepatitis E virus genomes in acute hepatitis patients and pig liver sold as food in Mie, Japan","Aim: To characterize hepatitis E in Mie prefecture and to investigate whether raw pig liver sold as food in Mie is contaminated with hepatitis E virus (HEV) strains similar to those recovered from patients. Methods: Seventeen patients with sporadic acute hepatitis E treated from 2004 to 2012 were studied. A total of 243 packages of raw pig liver from regional grocery stores were tested for the presence of HEV RNA. The partial genomic sequences of human and swine HEV isolates were determined and subjected to the phylogenetic analyses. Results: The HEV isolates recovered from the 17 patients segregated into genotype 3 (n=15) and genotype 4 (n=2), and 15 genotype 3 isolates further segregated into 3e (n=11) and 3b (n=4). Pig liver specimens from 12 (4.9%) of the 243 packages had detectable HEV RNA. All 12 swine HEV isolates were grouped into genotype 3 (3a or 3b). Although no 3e strains were isolated from pig liver specimens, two 3b swine strains were 99.5-100% identical to two HEV strains recovered from hepatitis patients, within 412-nt partial sequences. Conclusion: The 3e HEV was prevalent among hepatitis E patients. HEV RNA was detected in approximately 5% of pig liver sold as food. The presence of identical HEV strains between hepatitis patients and pig liver indicated that pigs play an important role as reservoirs for HEV in humans in Mie. Further studies are needed to clarify the source of 3e HEV in the animal and environmental reservoirs.",virus RNA;acute hepatitis E;adult;aged;animal tissue;article;clinical article;controlled study;female;food contamination;gene sequence;hepatitis E;Hepatitis E virus;Hepatitis E virus genotype 3;Hepatitis E virus genotype 3a;Hepatitis E virus genotype 3b;Hepatitis E virus genotype 3e;Hepatitis E virus genotype 4;human;Japan;male;middle aged;nonhuman;phylogeny;pig;raw meat;viral contamination;virus genome;virus strain,"Okano, H.;Takahashi, M.;Isono, Y.;Tanaka, H.;Nakano, T.;Oya, Y.;Sugimoto, K.;Ito, K.;Ohmori, S.;Maegawa, T.;Kobayashi, M.;Nagashima, S.;Nishizawa, T.;Okamoto, H.",2014,,10.1111/hepr.12216,0
1561,Application of antisense molecules to poultry production,"Antisense molecules, which are single strand nucleic acids complementary to a specific mRNA, target and bind with the mRNA, interfering with and preventing the translation of mRNA encoding a specific protein. Recently, in order to prevent antisense molecules from nucleases, phosphorothioate antisense oligodeoxynucleotides, which were originally developed as nuclease-resistant alternatives to phosphodiesters oligomers, and protein nucleic acids have been used. The delivery system for antisense molecules is basically equal to DNA delivery system. Traditionally, DNA delivery systems have been classified as viral vcctor-mediated systems and nonviral vector-mediated systems. As the importance of current methodology is attributable to the limitation of viral vector-mediated delivery, nonviral vector-mediated systems, especially synthetic DNA delivery systems, have become increasingly desirable. For stimulating appetite of poultry, the possibility to apply antisense protein nucleic acids against leptin MRNA was discussed. Antisense phosphorothioate oligodeoxynucleotide against insulin-like growth factor-binding protein-2 mRNA successfully suppressed its hepatic gene expression in the chicken. Protein synthesis of chicken embryo myoblasts was decreased by administration of antisense phosphorothioate oligodeoxynucleotide against myostatin mRNA, which suggests the decrease in protein degradation by antisense administration.",antisense;phosphorothioate oligodeoxynucleotide;protein nucleic acid;insulin-like growth factor binding protein;myostatin;leptin;GROWTH-FACTOR-I;FACTOR-BINDING PROTEINS;PEPTIDE NUCLEIC-ACIDS;MEAT-TYPE CHICKENS;OBESE GENE;IGF-I;PLASMA-CONCENTRATIONS;BROILER-CHICKENS;DOMESTIC-FOWL;DNA,"Okumura, J.;Kita, K.",2001,Dec,,0
1562,Distribution of gene segments of the pandemic A(H1N1) 2009 virus lineage in pig populations,"Swine influenza viruses (SIVs) are important not only for pig farming, but also for public health. In fact, pandemic A(H1N1) 2009 viruses [A(H1N1)pdm09] were derived from SIVs. Therefore, timely characterization of locally circulating SIVs is necessary for understanding the global status of SIVs. To genetically characterize SIVs circulating in Japanese pig populations, we isolated 24 SIVs of three subtypes (17 H1N1, four H1N2 and three H3N2 strains) from 14 pig farms in Japan from 2013 to 2016. Genetic analyses revealed that the haemagglutinin (HA) and neuraminidase (NA) genes of the 17 H1N1 and the HA gene of one H1N2, A/swine/Aichi/02/2016 (H1N2), SIVs belonged to the A(H1N1)pdm09 lineage. More importantly, all of the remaining six gene segments (i.e., PB1, PB1, PA, NP, M and NS) of the 24 SIVs, regardless of the HA and NA subtype, were also classified as belonging to the A(H1N1)pdm09 lineage. These results indicate that gene segments of A(H1N1)pdm09 lineage are widely distributed in SIVs circulating in Japanese pig populations In addition, the NA gene of A/swine/Aichi/02/2016 (H1N2) shared less than 88.5% nucleotide identity with that of the closest relative A/swine/Miyagi/5/2003 (H1N2), which was isolated in Japan in 2003. These results indicate the sustained circulation of classical H1N2-derived SIVs with remarkable diversity in the NA genes in Japanese pig populations. These findings highlight the necessity of both intensive biosecurity systems and active SIV surveillance in pig populations worldwide for both animal and public health.",hemagglutinin;sialidase;2009 H1N1 influenza;animal cell;animal tissue;article;Classical swine fever virus;coughing;disease surveillance;gene segment;genetic analysis;genetic parameters;genetic variability;haemagglutinin gene;hemagglutination;Influenza A virus (H1N1);Influenza A virus (H1N2);Influenza A virus (H3N2);lung parenchyma;matrix protein gene;MDCK cell line;neuraminidase gene;non structural protein gene;nonhuman;nose smear;nucleoprotein gene;nucleotide sequence;pandemic A (H1N1)pdm09;phylogenetic tree;pig;polymerase acid protein gene;polymerase basic protein 1 gene;real time polymerase chain reaction;reverse transcription polymerase chain reaction;RNA extraction;sequence analysis;smear;swine influenza virus;tracheal swab;virus classification;virus gene;virus isolation;virus lineage,"Okuya, K.;Matsuu, A.;Kawabata, T.;Koike, F.;Ito, M.;Furuya, T.;Taneno, A.;Akimoto, S.;Deguchi, E.;Ozawa, M.",2018,,10.1111/tbed.12887,0
1563,Molecular characterization of canine kobuvirus in wild carnivores and the domestic dog in Africa,"Knowledge of Kobuvirus (Family Picornaviridae) infection in carnivores is limited and has not been described in domestic or wild carnivores in Africa. To fill this gap in knowledge we used RT-PCR to screen fresh feces from several African carnivores. We detected kobuvirus RNA in samples from domestic dog, golden jackal, side-striped jackal and spotted hyena. Using next generation sequencing we obtained one complete Kobuvirus genome sequence from each of these species. Our phylogenetic analyses revealed canine kobuvirus (CaKV) infection in all four species and placed CaKVs from Africa together and separately from CaKVs from elsewhere. Wild carnivore strains were more closely related to each other than to those from domestic dogs. We found that the secondary structure model of the IRES was similar to the Aichivirus-like IRES subclass and was conserved among African strains. We describe the first CaKVs from Africa and extend the known host range of CaKV.","Africa;Animals;Animals, Domestic;Animals, Wild;*Carnivora;Cluster Analysis;*Dog Diseases/vi [Virology];Dogs;Feces/vi [Virology];*Genetic Variation;Genome, Viral;High-Throughput Nucleotide Sequencing;*Kobuvirus/cl [Classification];*Kobuvirus/ge [Genetics];Kobuvirus/ip [Isolation & Purification];Molecular Sequence Data;Phylogeny;*Picornaviridae Infections/ve [Veterinary];Picornaviridae Infections/vi [Virology];RNA, Viral/ge [Genetics];Reverse Transcriptase Polymerase Chain Reaction;0 (RNA, Viral)","Olarte-Castillo, X. A.;Heeger, F.;Mazzoni, C. J.;Greenwood, A. D.;Fyumagwa, R.;Moehlman, P. D.;Hofer, H.;East, M. L.",2015,Mar,,0
1564,Characterization of infectious laryngotracheitis virus isolates from the US by polymerase chain reaction and restriction fragment length polymorphism of multiple genome regions,"Infectious laryngotracheitis (ILT) is an acute viral respiratory disease, primarily of chickens. Economic losses attributable to ILT affect many poultry-producing areas throughout the United States (US) and the world. Despite efforts to control the disease by vaccination, prolonged epidemics of ILT remain a threat to the poultry industry. Earlier epidemiological and molecular evidence indicated that outbreaks in the US are caused by vaccine-related strains. In this study, polymerase chain reaction and restriction fragment polymorphism (PCR-RFLP) of four genome regions was utilized to characterize 25 isolates from commercial poultry and backyard flocks from the US. Combinations of PCR-RFLP patterns classified the ILT virus isolates into nine groups. Backyard flock isolates were categorized in three separate groups. The ILT virus US Department of Agriculture (USDA) reference strain and the tissue culture origin (TCO) vaccine strain were categorized into two separate groups. Twenty-two isolates from commercial poultry were categorized into four groups: one group, of six isolates, showed patterns identical to the chicken embryo origin (CEO) vaccines; a second group, of nine isolates, differed in only one pattern from the CEO vaccines; a third group, of two isolates, differed in only one pattern from the TCO vaccine; a fourth group, of five isolates, differed in six and nine patterns from the CEO and TCO vaccines, respectively. Results obtained from this study clearly demonstrated that most of the commercial poultry isolates (17 of 22 isolates) were closely related to the vaccine strains. However, isolates different to the vaccine strains were also identified in commercial poultry. © 2007 Houghton Trust Ltd.",animal;animal disease;article;chicken;genetics;herpes virus infection;isolation and purification;phylogeny;polymerase chain reaction;restriction fragment length polymorphism;United States;Varicella zoster virus;virology;virus genome,"Oldoni, I.;García, M.",2007,,10.1080/03079450701216654,0
1565,Epidemiological survey in single-species flocks from Poland reveals expanded genetic and antigenic diversity of small ruminant lentiviruses,"Small ruminant lentivirus (SRLV) infections are widespread in Poland and circulation of subtypes A1, A12, A13, B1 and B2 was detected. The present work aimed at extending previous study based on the analysis of a larger number of animals from single-species flocks. Animals were selected for genetic analysis based on serological reactivity towards a range of recombinant antigens derived from Gag and Env viral proteins. Phylogenetic analysis revealed the existence of subtypes B2 and A12 in both goats and sheep and subtypes A1 and B1 in goats only. In addition, two novel subtypes, A16 and A17, were found in goats. Co-infections with strains belonging to different subtypes within A and B groups were detected in 1 sheep and 4 goats originating from four flocks. Although the reactivity of serum samples towards the recombinant antigens confirmed immunological relatedness between Gag epitopes of different subtypes and the cross-reactive nature of Gag antibodies, eleven serum samples failed to react with antigens representing all subtypes detected up-to-date in Poland, highlighting the limitations of the serological diagnosis. These data showed the complex nature of SRLV subtypes circulating in sheep and goats in Poland and the need for improving SRLV-related diagnostic capacity.",epitope;Gag antibody;Gag protein;recombinant antigen;unclassified drug;virus antibody;virus envelope protein;antigen detection;antigenicity;article;cross reaction;envelope gene;epidemiological data;expanded antigenic diversity;expanded genetic variability;gag gene;gene sequence;genetic analysis;genetic distance;genetic epidemiology;genetic variability;goat;herd;immunoreactivity;Lentivirus infection;mixed infection;nonhuman;nucleotide sequence;Ovine/caprine lentivirus;phylogenetic tree;Poland;sequence analysis;serodiagnosis;sheep;single species flock;strain difference;strain identification;taxonomic rank;virus gene;virus identification;virus strain,"Olech, M.;Valas, S.;Kuźmak, J.",2018,,10.1371/journal.pone.0193892,0
1566,Porcine B-cells recognize epitopes that are conserved between the structural proteins of American- and European-type porcine reproductive and respiratory syndrome virus,"By selecting phage display libraries with immune sera from experimentally infected pigs, porcine B-cell epitopes in the open reading frame (ORF) 2, 3, 5 and 6 proteins of European-type porcine reproductive and respiratory syndrome virus (PRRSV) were identified. The sequences of all the epitopes were well conserved in European-type PRRSV and even between European- and American-type PRRSV. Accordingly, sera from pigs infected with American-type PRRSV cross-reacted with the European-type epitopes. Thus, this study showed, for the first time, the presence of highly conserved epitopes in the matrix protein and envelope glycoproteins of PRRSV. ORF5 and 6 epitopes localized to protein parts that are predicted to be hidden in PRRSV virions. In contrast, ORF2 and 3 epitopes localized to putative protein ectodomains. Due to the interesting localization, the sequence surrounding the ORF2 and 3 epitopes was subjected to closer scrutiny. A heptad motif, VSRRIYQ, which is present in a single copy in ORF2 and 3 proteins, was identified; this arrangement is completely conserved in all European-type PRRSV sequences available. The VSRRIYQ repeat motif colocalized closely with one of the ORF2 epitopes and secondary structure modelling showed that this segment of the ORF2 protein could form an amphipathic helix. Intriguingly, a mutation associated with virulence/attenuation of an American vaccine strain of PRRSV also localized to this ORF2 protein segment and affected the hydrophobic face of the predicted amphipathic helix. Further work is needed to determine whether these findings delineate a functional domain in the PRRSV ORF2 protein.",antiserum;envelope protein;epitope;matrix protein;peptide derivative;structural protein;unclassified drug;valinylserylarginylarginylisoleucyltyrosylglutamine;virus glycoprotein;viral protein;virus vaccine;antigen recognition;article;B lymphocyte;controlled study;cross reaction;genetic conservation;hydrophobicity;nonhuman;nucleotide sequence;open reading frame;phage display;prediction;priority journal;protein domain;protein localization;protein motif;protein secondary structure;Reproductive syndrome virus;Respiratory syndrome virus;sequence analysis;pig;swine disease;virion;virus attenuation;virus classification;virus mutation;virus strain;virus virulence,"Oleksiewicz, M. B.;Bøtner, A.;Normann, P.",2002,,,0
1567,Determination of the sequence of the complete open reading frame and the 5′NTR of the Paderborn isolate of classical swine fever virus,"The classical swine fever (CSF) epidemic in the Netherlands in 1997-1998 lasted 14 months, during which 429 infected and 1300 at risk herds were culled, at an estimated economical cost of 2 billion US dollars. Despite the overwhelming scale of the epizootic, the CSF virus (CSFV) strain causing the outbreak has remained largely uncharacterized. The Dutch epizootic is epidemiologically linked to a small CSF outbreak in 1997, in Paderborn in Germany. E2 and partial 5′NTR sequencing has shown that the index Paderborn isolate, and several Dutch isolates taken during the 1997-1998 epizootic, are virtually identical, confirming that the Paderborn isolate triggered the Dutch outbreak, and furthermore showing that this single isolate was stable throughout the whole Dutch outbreak (the above reviewed in [C. Terpstra, A. J. de Smit, Veterinary Microbiol. 77 (2000) 3-15]). We determined the nucleotide sequence of the 5′NTR (by 5′RACE) and the complete open reading frame of the Paderborn isolate (GenBank AY072924). Our sequence was identical to previously published partial 5′NTR and E2 sequences for the index Paderborn 1997 and Dutch 1997 (Venhorst) isolates, confirming the identity of the virus we sequenced. Phylogenetic analysis based on the complete open reading frame showed that Paderborn is genetically very different from common European laboratory reference strains. Neutralization studies showed that Paderborn is also antigenically very different from common laboratory strains such as Alfort 187. Paderborn is the only recent European CSFV field isolate for which a complete sequence is available, and given Paderborns genetic and antigenic uniqueness, the Paderborn sequence may have practical use for diagnostic and vaccine antigen development. © 2002 Elsevier Science B.V. All rights reserved.",neutralizing antibody;5' untranslated region;analytic method;antigenic variation;article;assay;controlled study;diagnostic value;genetic variability;Germany;nonhuman;nucleotide sequence;open reading frame;Pestivirus;phylogeny;sequence analysis;sequence homology;standard;swine disease;vaccine production;virus identification;virus strain,"Oleksiewicz, M. B.;Rasmussen, T. B.;Normann, P.;Uttenthal, Å",2003,,10.1016/s0378-1135(02)00424-8,0
1568,Screening for viral extraneous agents in live-attenuated avian vaccines by using a microbial microarray and sequencing,"The absence of extraneous agents (EA) in the raw material used for production and in finished products is one of the principal safety elements related to all medicinal products of biological origin, such as live-attenuated vaccines. The aim of this study was to investigate the applicability of the Lawrence Livermore Microbial detection array version 2 (LLMDAv2) combined with whole genome amplification and sequencing for screening for viral EAs in live-attenuated vaccines and specific pathogen-free (SPF) eggs. We detected positive microarray signals for avian endogenous retrovirus EAV-HP and several viruses belonging to the Alpharetrovirus genus in all analyzed vaccines and SPF eggs. We used a microarray probe mapping approach to evaluate the presence of intact retroviral genomes, which in addition to PCR analysis revealed that several of the positive microarray signals were most likely due to cross hybridization with the EAV-HPDELTApol and ALV-E ev1, ev3 and ev6 loci sequences originating from the chicken genome. Sequencing of the vaccines on a MiSeq instrument verified the microarray findings and showed similar cross hybridization. Our results suggest that genomic microarrays and sequencing of avian attenuated vaccines may be applied in tests for EA.","Animals;Chick Embryo;Chickens;Drug Contamination/pc [Prevention & Control];Endogenous Retroviruses/ge [Genetics];*Endogenous Retroviruses/im [Immunology];*High-Throughput Nucleotide Sequencing/mt [Methods];*Oligonucleotide Array Sequence Analysis/mt [Methods];Specific Pathogen-Free Organisms;*Vaccines, Attenuated/im [Immunology];*Viral Vaccines/im [Immunology];0 (Vaccines, Attenuated);0 (Viral Vaccines)","Olesen, M. L.;Jorgensen, L. L.;Blixenkrone-Moller, M.;Sandberg, E.;Frandsen, P. L.;Ostergaard, E.;Baekdahl, E. R.;Fridholm, H.;Fomsgaard, A.;Rosenstierne, M. W.",2018,Jan,,0
1569,Genetic variability of HEV isolates: Inconsistencies of current classification,"Many HEV and HEV-like sequences have been reported during the last years, including isolates which may represent a number of potential new genera, new genotypes or new subtypes within the family Hepeviridae. Using the most common classification system, difficulties in the establishment of subtypes have been reported. Moreover the relevance of subtype classification for epidemiology can be questioned. In this study we have performed phylogenetic analyses based on whole capsid gene and complete HEV genomic sequences in order to evaluate the current classification of HEV at genotype and subtype levels. The results of our analyses modify the current taxonomy of genotype 3 and refine the established system for typing of HEV. In addition we suggest a classification for hepeviruses recently isolated from bats, ferrets, rats and wild boar. © 2013 Elsevier B.V.",article;gene sequence;genetic variability;genomics;genotype;Hepatitis E virus;human;nonhuman;nucleotide sequence;phylogeny;virus isolation,"Oliveira-Filho, E. F.;König, M.;Thiel, H. J.",2013,,10.1016/j.vetmic.2013.01.026,0
1570,"Virologic and serologic surveillance for human, swine and avian influenza virus infections among pigs in the north-central United States","Influenza virus infection in pigs is both an animal health problem and a public health concern. As such, surveillance and characterization of influenza viruses in swine is important to the veterinary community and should be a part of human pandemic preparedness planning. Studies in 1976/1977 and 1988/1989 demonstrated that pigs in the U.S. were commonly infected with classical swine H1N1 viruses, whereas human H3 and avian influenza virus infections were very rare. In contrast, human H3 and avian H1 viruses have been isolated frequently from pigs in Europe and Asia over the last two decades. From September 1997 through August 1998, we isolated 26 influenza viruses from pigs in the north central United States at the point of slaughter. All 26 isolates were H1N1 viruses, and phylogenetic analyses of the hemagglutinin and nucleoprotein genes from 11 representative viruses demonstrated that these were classical swine H1 viruses. However, monoclonal antibody analyses revealed antigenic heterogeneity among the HA proteins of the 26 viruses. Serologically, 27.7% of 2,375 pigs tested had hemagglutination-inhibiting antibodies against classical swine H1 influenza virus. Of particular significance, however, the rates of seropositivity to avian H1 (7.6%) and human H3 (8.0%) viruses were substantially higher than in previous studies.",amino acid sequence;animal;animal disease;article;epidemiology;human;influenza;Influenza A virus;isolation and purification;molecular genetics;pig;swine disease;United States;virology,"Olsen, C. W.;Carey, S.;Hinshaw, L.;Karasin, A. I.",2000,,,0
1571,Characterization of a swine-like reassortant H1N2 influenza virus isolated from a wild duck in the United States,"An H1N2 influenza virus (A/Duck/North Carolina/91347/01) (Dk/NC) was isolated from a wild duck in the United States in 2001. Genetic analyses showed that this duck virus has the same human/classical swine/avian reassortant genotype as the H1N2 viruses that have been isolated from pigs and turkeys in the US since 1999. Phylogenetic analyses of each gene segment further confirmed that the Dk/NC virus is closely related to the domestic animal H1N2 isolates. In particular, Dk/NC is most closely related to a swine H1N2 virus also isolated in North Carolina. These two viruses and a phylogenetically-defined subset of additional swine H1N2 viruses share a common mutation in the Sb antigenic site on the hemagglutinin protein. The recovery of Dk/NC from a wild bird raises concerns for further widespread distribution of these H1N2 viruses via waterfowl migration. © 2003 Elsevier Science B.V. All rights reserved.",hemagglutinin;mutant protein;virus antigen;viral protein;article;controlled study;domestic animal;duck;fowl;genetic analysis;genetic reassortment;genotype;Influenza A virus;nonhuman;nucleotide sequence;phylogeny;priority journal;species comparison;pig;turkey (bird);United States;virus gene;virus isolation;virus mutation;virus typing,"Olsen, C. W.;Karasin, A.;Erickson, G.",2003,,10.1016/s0168-1702(03)00073-x,0
1572,Genetic changes in pigeon paramyxovirus type-1 induced by serial passages in chickens and microscopic lesions caused by the virus in various avian hosts,"Introduction: Genotype VI of avian avulavirus 1 (AAvV-1) has pigeons and doves as its reservoir and is often termed pigeon paramyxovirus type-1 (PPMV-1). The pathogenesis of PPMV-1 infections in poultry is largely obscure. It is known that PPMV-1 requires a series of passages in chickens before it becomes adapted to gallinaceous poultry. Material and Methods: Changes in the genome of PPMV-1 were analysed after serial passages in specific pathogen free (SPF) chickens, using high-throughput sequencing. Additionally, histopathological lesions induced by PPMV-1 in experimentally inoculated pigeons, chickens, and turkeys were evaluated. Results: Following six passages of PPMV-1 in chickens, 10 nonsynonymous substitutions were found including one (in the NP protein) which dominated the genetic pool of viral quasispecies. Histopathological changes induced by the post-passage PPMV-1 strain were more prominent than changes wrought by the pre-passaged PPMV-1 strain and the lesions were most intense in pigeons followed by chickens and turkeys. Conclusion: PPMV-1 is highly adapted to pigeons and passaging through chickens results in the acquisition of novel amino acids in the polymerase complex, which may alter the pathogenic potential of the virus.",animal cell;animal experiment;animal tissue;article;Columbidae;genome;germfree chicken;high throughput sequencing;histopathology;nonhuman;Paramyxoviridae;quasispecies;turkey (bird);virus culture;amino acid,"Olszewska-Tomczyk, M.;Dolka, I.;Świȩtoń, E.;Śmietanka, K.",2018,,10.2478/jvetres-2018-0059,0
1573,Occurrence and Phylogenetic Studies of Chicken Anemia Virus from Polish Broiler Flocks,"Chicken anemia virus (CAV) is a widespread chicken pathogen of significant economic importance. In 2013, broiler chicken flocks in Poland were examined for the presence of CAV, and phylogenetic relatedness between the strains was established. Ten cloacal swabs from each of 106 broiler flocks (birds aged 3-6 wk) were collected in different regions of the country and tested with the use of real-time PCR (all samples) and conventional PCR (those samples positive in real-time PCR) assays. The presence of CAV was detected in 16 of the flocks tested. Phylogenetic analysis clearly confirmed the existence of genetic diversity within the group of circulating CAV strains and their distinctiveness from vaccine strains used in Poland.","capsid protein;VP1 protein, Chicken anemia virus;animal;chicken;chicken anemia virus;Circoviridae infection;cloaca;DNA sequence;genetic variation;genetics;metabolism;phylogeny;physiology;Poland;bird disease;prevalence;real time polymerase chain reaction;veterinary medicine;virology","Olszewska-Tomczyk, M.;Świętoń, E.;Minta, Z.;Śmietanka, K.",2016,,10.1637/11277-091415-ResNote.1,0
1574,Applying phylogenetic analysis to viral livestock diseases: Moving beyond molecular typing,"Changes in livestock production systems in recent years have altered the presentation of many diseases resulting in the need for more sophisticated control measures. At the same time, new molecular assays have been developed to support the diagnosis of animal viral disease. Nucleotide sequences generated by these diagnostic techniques can be used in phylogenetic analysis to infer phenotypes by sequence homology and to perform molecular epidemiology studies. In this review, some key elements of phylogenetic analysis are highlighted, such as the selection of the appropriate neutral phylogenetic marker, the proper phylogenetic method and different techniques to test the reliability of the resulting tree. Examples are given of current and future applications of phylogenetic reconstructions in viral livestock diseases. © 2009 Elsevier Ltd. All rights reserved.",virus vaccine;amino acid sequence;animal disease;antigenic variation;Avian infectious bronchitis virus;Circoviridae;epidemic;gene sequence;genetic analysis;genetic reassortment;genetic selection;genotype;human;infectious bursal disease virus;intermethod comparison;livestock;molecular epidemiology;molecular typing;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;postweaning multisystemic wasting syndrome;reliability;review;species differentiation;vaccination;virus identification;virus infection;virus virulence;zoonosis,"Olvera, A.;Busquets, N.;Cortey, M.;Deus, N. d;Ganges, L.;Núñez, J. I.;Peralta, B.;Toskano, J.;Dolz, R.",2010,,10.1016/j.tvjl.2009.02.015,0
1575,Detection of enterovirus genome sequence from diarrheal feces of goat,"Goat diarrheal feces were subjected to metagenome analysis by the next-generation sequencing. Nucleotide sequences with homology to enteroviruses were obtained. Primers for RT-PCR were designed based on the nucleotide sequence of these sequences at the 5′-untranslated region, and we determined 563 bp nucleotide sequences that showed homology to bovine-like and ovine enteroviruses (77-87%). We named the virus detected in this study goat enterovirus G1 (GEV-G1). In the phylogenetic analysis, GEV-G1 belonged to a cluster containing ovine enteroviruses. To our knowledge, this is the first report on nucleotide sequences of an enterovirus infecting Japanese goats. © Springer Science+Business Media 2014.",5' untranslated region;article;bovine;diarrhea;Enterovirus;feces analysis;genome analysis;goat;goat enterovirus G1;nonhuman;nucleotide sequence;phylogenetic tree;priority journal;sequence analysis;sequence homology;sheep;virus genome,"Omatsu, T.;Tsuchiaka, S.;Hirata, T.;Shiroma, Y.;Okazaki, S.;Katayama, Y.;Oba, M.;Nishiura, N.;Sassa, Y.;Furuya, T.;Nagai, M.;Ochiai, H.;Tamaki, S.;Mizutani, T.",2014,,10.1007/s11262-014-1057-9,1
1576,Influenza A Virus: Phylogeny of Neuraminidase Primers and Amplification of Polymerase Basic Protein 2 and Neuraminidase Genes,,,"Omega, M.;Lai, R.;Hein, H.",2010,,,0
1577,Massively parallel sequencing: a new tool in virus discovery and vaccine safety,"The introduction of new sequencing technologies is revolutionizing virus discovery and providing a new means to demonstrate the safety of vaccines. Since these methods do not depend on prior assumptions of the types of viruses that may be present, they have detected viruses missed by other methods like degenerate or, family specific, PCRs. We have used massively parallel sequencing (MP-Seq) to detect new viruses in bovine serum and in the faeces of animals. When applied to sequencing the transcriptome, MP-Seq can reveal latent or silent infections. While the sequencing technology is impressive, it is bioinformatics that is the key to its successful application.",biological product;virus vaccine;animal;article;biology;bovine;drug contamination;feces;genetics;high throughput sequencing;isolation and purification;product safety;serum;standard;virology;virus,"Onions, D.",2011,,,0
1578,Ensuring the safety of vaccine cell substrates by massively parallel sequencing of the transcriptome,"Massively parallel, deep, sequencing of the transcriptome coupled with algorithmic analysis to identify adventitious agents (MP-SeqTM) is an important adjunct in ensuring the safety of cells used in vaccine production. Such cells may harbour novel viruses whose sequences are unknown or latent viruses that are only expressed following stress to the cells. MP-Seq is an unbiased and comprehensive method to identify such viruses and other adventitious agents without prior knowledge of the nature of those agents. Here we demonstrate its utility as part of an integrated approach to identify and characterise potential contaminants within commonly used virus and vaccine production cell lines. Through this analysis, in combination with more traditional approaches, we have excluded the presence of porcine circoviruses in the ATCC Vero cell bank (CCL-81), however, we found that a full length betaretrovirus related to SRV can be expressed in these cells, a factor that may be of importance in the production of certain vaccines. Similarly, insect cells are proving to be valuable for the production of virus like particles and sub-unit vaccines, but they can harbour a range of latent viruses. We show that following MP-Seq of the Trichoplusia ni (High Five cell line) transcriptome we were able to detect a contaminating, latent nodavirus and identify an expressed errantivirus genome. Collectively, these studies have reinforced the role of MP-Seq as an integral tool for the identification of contaminating agents in vaccine cell substrates.","Animals;Betaretrovirus/ip [Isolation & Purification];Cell Culture Techniques/st [Standards];Cell Line;Cercopithecus aethiops;*Drug Contamination/pc [Prevention & Control];*High-Throughput Nucleotide Sequencing/mt [Methods];Lepidoptera;Nodaviridae/ip [Isolation & Purification];*Technology, Pharmaceutical/st [Standards];*Transcriptome;*Vaccines/bi [Biosynthesis];0 (Vaccines)","Onions, D.;Cote, C.;Love, B.;Toms, B.;Koduri, S.;Armstrong, A.;Chang, A.;Kolman, J.",2011,Sep 22,,0
1579,"Uncovering vector, parasite, blood meal and microbiome patterns from mixed-DNA specimens of the Chagas disease vector Triatoma dimidiata","Chagas disease, considered a neglected disease by the World Health Organization, is caused by the protozoan parasite Trypanosoma cruzi, and transmitted by >140 triatomine species across the Americas. In Central America, the main vector is Triatoma dimidiata, an opportunistic blood meal feeder inhabiting both domestic and sylvatic ecotopes. Given the diversity of interacting biological agents involved in the epidemiology of Chagas disease, having simultaneous information on the dynamics of the parasite, vector, the gut microbiome of the vector, and the blood meal source would facilitate identifying key biotic factors associated with the risk of T. cruzi transmission. In this study, we developed a RADseq-based analysis pipeline to study mixed-species DNA extracted from T. dimidiata abdomens. To evaluate the efficacy of the method across spatial scales, we used a nested spatial sampling design that spanned from individual villages within Guatemala to major biogeographic regions of Central America. Information from each biotic source was distinguished with bioinformatics tools and used to evaluate the prevalence of T. cruzi infection and predominant Discrete Typing Units (DTUs) in the region, the population genetic structure of T. dimidiata, gut microbial diversity, and the blood meal history. An average of 3.25 million reads per specimen were obtained, with approximately 1% assigned to the parasite, 20% to the vector, 11% to bacteria, and 4% to putative blood meals. Using a total of 6,405 T. cruzi SNPs, we detected nine infected vectors harboring two distinct DTUs: TcI and a second unidentified strain, possibly TcIV. Vector specimens were sufficiently variable for population genomic analyses, with a total of 25,710 T. dimidiata SNPs across all samples that were sufficient to detect geographic genetic structure at both local and regional scales. We observed a diverse microbiotic community, with significantly higher bacterial species richness in infected T. dimidiata abdomens than those that were not infected. Unifrac analysis suggests a common assemblage of bacteria associated with infection, which co-occurs with the typical gut microbial community derived from the local environment. We identified vertebrate blood meals from five T. dimidiata abdomens, including chicken, dog, duck and human; however, additional detection methods would be necessary to confidently identify blood meal sources from most specimens. Overall, our study shows this method is effective for simultaneously generating genetic data on vectors and their associated parasites, along with ecological information on feeding patterns and microbial interactions that may be followed up with complementary approaches such as PCR-based parasite detection, 18S eukaryotic and 16S bacterial barcoding.","Animals;Archaea/ge [Genetics];Archaea/ip [Isolation & Purification];Bacteria/ge [Genetics];Bacteria/ip [Isolation & Purification];Central America;Cluster Analysis;Computational Biology;*DNA/ge [Genetics];*DNA/ip [Isolation & Purification];*Feeding Behavior;Fungi/ge [Genetics];Fungi/ip [Isolation & Purification];*Gastrointestinal Microbiome;High-Throughput Nucleotide Sequencing;Humans;Nematoda/ge [Genetics];Nematoda/ip [Isolation & Purification];Phylogeny;Sequence Analysis, DNA;*Triatoma/ge [Genetics];Triatoma/mi [Microbiology];Triatoma/ps [Parasitology];Triatoma/ph [Physiology];Trypanosoma cruzi/ge [Genetics];*Trypanosoma cruzi/ip [Isolation & Purification];Viruses/ge [Genetics];Viruses/ip [Isolation & Purification];9007-49-2 (DNA)","Orantes, L. C.;Monroy, C.;Dorn, P. L.;Stevens, L.;Rizzo, D. M.;Morrissey, L.;Hanley, J. P.;Rodas, A. G.;Richards, B.;Wallin, K. F.;Helms Cahan, S.",2018,10,,0
1580,Host-independent evolution and a genetic classification of the hepadnavirus family based on nucleotide sequences,"An analysis of molecular phylogeny was undertaken to examine whether the evolution of the hepadnavirus family is host-dependent. Using the nucleotide sequences of 18 strains, we constructed phylogenetic trees. The trees obtained show that all 12 strains of hepatitis B virus can be classified into four subgroups that are not compatible with conventional subtypes. We estimated the rate of synonymous (silent) substitution for hepatitis B virus to be 4.57 x 10-5 per site per year. Applying this rate to the phylogenetic tree, we estimated that duck hepatitis B virus diverged from a common ancestor about 30,000 years ago at the earliest, that woodchuck hepatitis virus and ground squirrel hepatitis virus diverged about 10,000 years ago, and that hepatitis B virus diverged within the last 3000 years. Because these divergence times of the viruses are much more recent than those of the host species, it suggests that the hepadnavirus family evolved independently of host-species divergence.",DNA sequence;DNA virus;evolution;Hepatitis B virus;nonhuman;priority journal,"Orito, E.;Mizokami, M.;Ina, Y.;Moriyama, E. N.;Kameshima, N.;Yamamoto, M.;Gojobori, T.",1989,,,0
1581,Degenerate primers for PCR amplification and sequencing of the avian influenza A neuraminidase gene,"This study describes the design of degenerate primers and their use for synthesis of full-length avian influenza A neuramindase (NA). Each reaction was performed using either two forward primers and one reverse primer, or one forward primer and one reverse primer. Both primer combinations had comparable amplification efficiencies for all NA subtypes (1-9). A total of 115 virus strains, including both field isolates and reference strains, were amplified successfully using these degenerate primer sets. Of the sequences amplified, 108 strains (93.9%) resulted in near full-length NA cDNAs after two readings with one forward primer and one reverse primer. Of the remaining sequences, five strains (4.3%) yielded reads with enough information for subtype categorization by BLAST although they were of insufficient quality for assembly. One strain (0.9%) yielded different subtypes from both sequence reads whereas the other one (0.9%) was not possible to assemble and subtype. This successful demonstration of these degenerate primers for the amplification and sequencing of all avian NA subtypes suggests that these primers could be employed in the avian influenza surveillance program as well as studies of antiviral resistance, virus ecology or viral phylogeny.","Animals;Base Sequence;DNA Primers;DNA, Complementary;Ducks/vi [Virology];Influenza A virus/cl [Classification];*Influenza A virus/ge [Genetics];Influenza A virus/ip [Isolation & Purification];*Influenza in Birds/vi [Virology];*Neuraminidase/ge [Genetics];Phylogeny;Polymerase Chain Reaction;*RNA, Viral/ge [Genetics];Sequence Analysis, RNA;0 (DNA Primers);0 (DNA, Complementary);0 (RNA, Viral)","Orozovic, G.;Latorre-Margalef, N.;Wahlgren, J.;Muradrasoli, S.;Olsen, B.",2010,Dec,,0
1582,In vitro surrogate models to aid in the development of antivirals for the containment of foot-and-mouth disease outbreaks,"Foot-and-mouth disease virus (FMDV) is a highly pathogenic member of the genus Aphthovirus (family Picornaviridae) that is only to be manipulated in high-containment facilities, thus complicating research on and discovery of antiviral strategies against the virus. Bovine rhinitis B virus (BRBV) and equine rhinitis A virus (ERAV), phylogenetically most closely related to FMDV, were explored as surrogates for FMDV in antiviral studies. Although no efficient cell culture system has been reported so far for BRBV, we demonstrate that infection of primary bovine kidney cells resulted in an extensive but rather poorly-reproducible induction of cytopathic effect (CPE). Madin-Darby bovine kidney cells on the other hand supported viral replication in the absence of CPE. Antiviral tests were developed for ERAV in Vero A cells employing a viral RNA-reduction assay and CPE-reduction assay; the latter having a Z' factor of 0.83. ±. 0.07. The BRBV and ERAV models were next used to assess the anti-aphthovirus activity of two broad-spectrum antiviral agents 2'- C-methylcytidine (2CMC) and ribavirin, as well as of the enterovirus-specific inhibitor enviroxime. The effects of the three compounds in the CPE-reduction (ERAV) and viral RNA-reduction assays (BRBV and ERAV) were comparable. Akin to 2CMC, compound A, a recently-discovered non-nucleoside pan-serotype FMDV inhibitor, also inhibited the replication of both BRBV and ERAV, whereas enviroxime was devoid of activity. The BRBV and ERAV surrogate models reported here can be manipulated in BSL-2 laboratories and may facilitate studies to unravel the mechanism of action of novel FMDV inhibitors. © 2014 Elsevier B.V.",2' methylcytidine;antivirus agent;enviroxime;ribavirin;animal cell;antiviral therapy;article;Bovine rhinitis B virus;controlled study;epidemic;equine rhinitis A virus;foot and mouth disease;Foot and mouth disease virus;in vitro study;kidney cell;nonhuman;priority journal;RNA virus;virus replication,"Osiceanu, A. M.;Murao, L. E.;Kollanur, D.;Swinnen, J.;De Vleeschauwer, A. R.;Lefebvre, D. J.;De Clercq, K.;Neyts, J.;Goris, N.",2014,,,0
1583,"The spread of highly pathogenic avian influenza (subtype H5N1) clades in Bangladesh, 2010 and 2011","Since the global spread of highly pathogenic avian influenza H5N1 during 2005-2006, control programs have been successfully implemented in most affected countries. HPAI H5N1 was first reported in Bangladesh in 2007, and since then 546 outbreaks have been reported to the OIE. The disease has apparently become endemic in Bangladesh. Spatio-temporal information on 177 outbreaks of HPAI H5N1 occurring between February 2010 and April 2011 in Bangladesh, and 37 of these outbreaks in which isolated H5N1 viruses were phylogenetically characterized to clade, were analyzed.Three clades were identified, 2.2 (21 cases), 2.3.4 (2 cases) and 2.3.2.1 (14 cases). Clade 2.2 was identified throughout the time period and was widely distributed in a southeast-northwest orientation. Clade 2.3.2.1 appeared later and was generally confined to central Bangladesh in a north-south orientation. Based on a direction test, clade 2.2 viruses spread in a southeast-to-northwest direction, whereas clade 2.3.2.1 spread west-to-east. The magnitude of spread of clade 2.3.2.1 was greater relative to clade 2.2 (angular concentration 0.2765 versus 0.1860). In both cases, the first outbreak(s) were identified as early outliers, but in addition, early outbreaks (one each) of clade 2.2 were also identified in central Bangladesh and in northwest Bangladesh, a considerable distance apart.The spread of highly pathogenic avian influenza H5N1 in Bangladesh is characterized by reported long-distance translocation events. This poses a challenge to disease control efforts. Increased enforcement of biosecurity and stronger control of movements between affected farms and susceptible farms, and better surveillance and reporting, is needed. Although the movement of poultry and equipment appears to be a more likely explanation for the patterns identified, the relative contribution of trade and the market chain versus wild birds in spreading the disease needs further investigation. © 2014 Elsevier B.V.",animal;animal disease;animal husbandry;article;avian influenza;Bangladesh;bird disease;chicken;Clades;classification;disease transmission;duck;epidemic;genetics;highly pathogenic avian influenza;Influenza A virus (H5N1);phylogeny;physiology;spatial analysis;traffic and transport;virology,"Osmani, M. G.;Ward, M. P.;Giasuddin, M.;Islam, M. R.;Kalam, A.",2014,,10.1016/j.prevetmed.2014.01.010,0
1584,Some viral zoonoses transmitted by pets (author's transl) Dutch,"Besides dogs and cats, various other animals are more or less popular as pets in the Netherlands. It is importance to the veterinary practitioner to know which diseases may be transmitted to man by these animals. Of the viral zoonoses. rabies constitutes a menace to man, in which dogs and, to a less extent, cats supply a link between man and free-living wild animals. Another viral zoonosis in which interest was centered in recent years, is lymphocytic choriomeningitis (LCM) caused by a virus which often is latent in mice but which may also be detected in young hamsters. A human disease caused by a pathogenic agent which should not be classified with the viruses, is chlamydiosis (psittacosis, ornithosis), which disease is usually transmitted to man by psittacine birds or pigeons. Of the above disease, the pathogenic agents, the clinical pictures in man and animals, the mode of transmission and possible preventive and therapeutic measures are discussed. Finally, the risk of transmission of viral zoonoses by less current ""pets"" is stressed.","Animals;*Animals, Domestic;Birds;Cats;Chlamydia Infections/tm [Transmission];Cricetinae;*Disease Vectors;Dogs;Foxes;Humans;Lymphocytic Choriomeningitis/tm [Transmission];Mice;Rabies/tm [Transmission];*Zoonoses","Osterhaus, A. D.",1977,Jan 01,,0
1585,Epidemiology and molecular characterization of chicken anaemia virus from commercial and native chickens in Taiwan,"Chicken infectious anaemia (CIA) is a disease with a highly economic impact in the poultry industry. The infected chickens are characterized by aplastic anaemia and extreme immunosuppression, followed by the increased susceptibility to secondary infectious pathogens and suboptimal immune responses for vaccination. Commercially available CIA vaccines are routinely used in the breeders in Taiwan to protect their progeny with maternal-derived antibodies. However, CIA cases still occur in the field and little is known about the genetic characteristics of Taiwanese chicken anaemia viruses (CAVs). In this study, CAV DNA was detected in 72 of 137 flocks collected during 2010–2015. Among the PCR-positive samples, the coding regions of 51 CAVs were sequenced. Phylogenetic analysis of the VP1 gene revealed that, although most of Taiwanese CAVs belonged to genotypes II and III, some isolates were clustered into a novel genotype (genotype IV). Moreover, a Taiwanese isolate in this novel genotype IV appeared to be derived from a recombination event between genotypes II and III viruses. Five Taiwanese CAV isolates were highly similar to the vaccine strains, 26P4 or Del-Ros. Taken together, these results indicate that the sequences of CAVs in Taiwan are variable, and inter-genotypic recombination had occurred between viruses of different genotypes. Moreover, vaccine-like strains might induce clinical signs of CIA in chickens. Our findings could be useful for understanding the evolution of CAVs and development of a better control strategy for CIA.",QIAamp DNA Mini Kit;protein VP2;amino acid sequence;amino acid substitution;animal experiment;aplastic anemia;article;chicken;chicken anemia virus;chicken anemia virus infection;clinical feature;controlled study;DNA isolation;gene mutation;gene sequence;genotype;molecular diagnosis;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;polymerase chain reaction;sequence alignment;sequence analysis;Taiwan;virus infection;virus isolation;virus recombination,"Ou, S. C.;Lin, H. L.;Liu, P. C.;Huang, H. J.;Lee, M. S.;Lien, Y. Y.;Tsai, Y. L.",2018,,10.1111/tbed.12886,0
1586,"Phylogenetic variations of highly pathogenic H5N6 avian influenza viruses isolated from wild birds in the Izumi plain, Japan, during the 2016–17 winter season","During the 2016–2017 winter season, we isolated 33 highly pathogenic avian influenza viruses (HPAIVs) of H5N6 subtype and three low pathogenic avian influenza viruses (LPAIVs) from debilitated or dead wild birds, duck faeces, and environmental water samples collected in the Izumi plain, an overwintering site for migratory birds in Japan. Genetic analyses of the H5N6 HPAIV isolates revealed previously unreported phylogenetic variations in the PB2, PB1, PA, and NS gene segments and allowed us to propose two novel genotypes for the contemporary H5N6 HPAIVs. In addition, analysis of the four gene segments identified close phylogenetic relationships between our three LPAIV isolates and the contemporary H5N6 HPAIV isolates. Our results implied the co-circulation and co-evolution of HPAIVs and LPAIVs within the same wild bird populations, thereby highlighting the importance of avian influenza surveillance targeting not only for HPAIVs but also for LPAIVs.",article;coevolution;highly pathogenic avian influenza virus;human;Japan;low pathogenic avian influenza virus;nonhuman;winter,"Ozawa, M.;Matsuu, A.;Khalil, A. M.;Nishi, N.;Tokorozaki, K.;Masatani, T.;Horie, M.;Okuya, K.;Ueno, K.;Kuwahara, M.;Toda, S.",2018,,10.1111/tbed.13087,0
1587,"Theiler's virus genome is closely related to that of encephalomyocarditis virus, the prototype cardiovirus","Theiler's virus causes a persistent demyelinating infection of the mouse central nervous system. Our study of the molecular mechanism of persistence led us to sequence 1925 nucleotides located at the 3' end of the viral genome. We observed extensive homologies between this region and the corresponding region of encephalomyocarditis virus, the prototype cardiovirus, and only some homologies with the 3' ends of foot-and-mouth disease virus, rhinovirus, and poliovirus genomes.",complementary DNA;radioisotope;classification;Encephalomyocarditis virus;gene sequence;genetic engineering;heredity;Theiler's murine encephalomyelitis virus;nonhuman;priority journal;virus classification,"Ozden, S.;Tangy, F.;Chamorro, M.;Brahic, M.",1986,,,0
1588,Genetic and epidemiological insights into the emergence of peste des petits ruminants virus (PPRV) across Asia and Africa,"Small ruminants are important components in the livelihood of millions of households in many parts of the world. The spread of the highly contagious peste des petits ruminants (PPR) disease, which is caused by an RNA virus, PPRV, across Asia and Africa remains a major concern. The present study explored the evolutionary and epidemiological dynamics of PPRV through the analyses of partial N-gene and F-gene sequences of the virus. All the four previously described PPRV lineages (I-IV) diverged from their common ancestor during the late-19(th) to early-20(th) century. Among the four lineages, PPRV-IV showed pronounced genetic structuring across the region; however, haplotype sharing among the geographic regions, together with the presence of multiple genetic clusters within a country, indicates the possibility of frequent mobility of the diseased individuals across the region. The gradual decline in the effective number of infections suggests a limited genetic variation, which could be attributed to the effective vaccination that has been practiced since 1990s. However, the movement of infected animals across the region likely contributes to the spread of PPRV-IV. No evidence of positive selection was identified from this study.",virus antibody;viral protein;virus vaccine;Africa;animal;Asia;Bayes theorem;blood;classification;genetics;genotype;high throughput sequencing;immunology;isolation and purification;molecular typing;pathogenicity;peste des petits ruminants;Peste-des-petits-ruminants virus;phylogeny;ruminant;transmission;vaccination;virology,"Padhi, A.;Ma, L.",2014,,10.1038/srep07040,0
1589,Time-dependent selection pressure on two arthropod-borne RNA viruses in the same serogroup,"Understanding the genetic basis of viral adaptation to taxonomically diverse groups of host species inhabiting different eco-climatic zones is crucial for the discovery of factors underpinning the successful establishment of these infectious pathogens in new hosts/environments. To gain insights into the dynamics of nonsynonymous (dN) and synonymous substitutions (dS) and the ratio between the two (ω = dN/. dS), we analyzed the complete nucleotide coding sequence data of the M segment, which encodes glycoproteins of two negative-sense RNA viruses, Akabane virus (AKV) and Schmallenberg virus (SBV) that belong to the same serogroup. While AKV is relatively older and has been circulating in ruminant populations since 1970s, SBV was first reported in 2011. The ω was estimated to be 1.67 and 0.09 for SBV and AKV, respectively, and the estimated mutation rate of SBV is at least 25 times higher than that of AKV. Given the different evolutionary stages of the two viruses, most of the slightly deleterious mutations were likely purged out or kept in low frequency in the AKV genome, whereas positive selection together with the accumulation of slightly deleterious mutations might contribute to such an inflated mutation rate of SBV. The evolutionary distance (d) is nonlinearly and negatively correlated with ω, but is positively correlated with dN and dS. Collectively, the different patterns in ω, dN, dS, and d between AKV and SBV identified in this study provide empirical evidence for a time-dependent selection pressure.",virus glycoprotein;Akabane virus;arthropod;article;evolutionary rate;genetic distance;genetic selection;mutation rate;nonhuman;phylogeny;priority journal;RNA virus;Schmallenberg virus;serotype;virus genome;virus strain,"Padhi, A.;Ma, L.",2015,,10.1016/j.meegid.2015.03.019,0
1590,Detection and characterization of a novel genotype of porcine astrovirus 4 from nasal swabs from pigs with acute respiratory disease,"Metagenomic sequencing of three nasal swabs collected from 10- to 21-day-old pigs exhibiting unexplained acute respiratory disease from two different commercial production facilities in Oklahoma identified a novel genotype of porcine astrovirus 4 (PAstV-4). The genomes had only ~75 % nucleotide sequence identity to previously characterized PAstV-4 isolates, while the capsid-encoding ORF2 had only ~53 % amino acid sequence identity to reference strains. A TaqMan assay targeting the novel ORF2 gene found 21 % and 19 % incidence in nasal and fecal swabs, respectively, submitted for unrelated diagnostic testing. PAstV-4 RNA levels were significantly higher (P = 0.04) in nasal swabs, suggesting a possible atypical respiratory tropism.",viral protein;acute disease;animal;Astroviridae;astrovirus infection;gene expression regulation;genetics;genotype;isolation and purification;metabolism;phylogeny;pig;respiratory tract disease;swine disease;veterinary medicine;virology,"Padmanabhan, A.;Hause, B. M.",2016,,10.1007/s00705-016-2937-1,1
1591,"Serological and molecular investigation of the prevalence of Aujeszky's disease in feral swine (Sus scrofa) in the subregions of the Pantanal wetland, Brazil","The feral swine (FS) originated from the domestic pig and is present throughout the Brazilian wetland plain (the Pantanal). Aujeszky's disease (AD) was first serologically confirmed in the state of Mato Grosso do Sul (MS) in 2001; however, there was no viral confirmation. The aim of this study was to investigate antibodies against-SuHV-1 in the sera of feral swine in the studied areas, detect SuHV-1 through PCR and classify the viral genome. Among the 218 animals sampled, 186 were analyzed by ELISA, resulting in 88 (47.3%) reactive samples. In the serum neutralization test (SN), 57/179 (31.8%) samples presented antibodies against the AD virus (SuHV-1). By nested PCR, 104 DNA samples were extracted for analysis and confirmed with amplification of a fragment of glycoprotein B (gB) in five samples. The SuHV-1 was detected in 12 samples by using primers for glycoprotein E (gE) and viral genome was classified as Type I by ul44 partial sequencing. The amplification of SuHV-1 glycoprotein fragments in the fetuses of seropositive sows indicate that the vertical transmission contribute to maintain SuHV-1 in a free-living feral swine population. The origin of AD in the feral swine populations of the Pantanal is unknown, however, the determination of viral latency, the vertical transmission of the antigen by the amplification of SuHV-1 glycoprotein fragments in the fetuses of seropositive sows and genome typing contribute to the elucidation of the epidemiology of this disease in the wetlands of MS, Brazil. © 2013 Elsevier B.V.",DNA;glycoprotein B;glycoprotein E;adult;article;Brazil;controlled study;DNA determination;DNA extraction;female;fetus;gene amplification;latent period;male;nonhuman;prevalence;pseudorabies;Pseudorabies virus;serodiagnosis;serology;pig;vertical transmission;virus genome;wetland,"Paes, R. D. C. D. S.;Fonseca, A. A.;Monteiro, L. A. R. C.;Jardim, G. C.;Piovezan, U.;Herrera, H. M.;Mauro, R. A.;Vieira-da-Motta, O.",2013,,10.1016/j.vetmic.2013.03.028,0
1592,Heart and skeletal muscle inflammation of farmed salmon is associated with infection with a novel reovirus,"Atlantic salmon (Salmo salar L.) mariculture has been associated with epidemics of infectious diseases that threaten not only local production, but also wild fish coming into close proximity to marine pens and fish escaping from them. Heart and skeletal muscle inflammation (HSMI) is a frequently fatal disease of farmed Atlantic salmon. First recognized in one farm in Norway in 1999[1], HSMI was subsequently implicated in outbreaks in other farms in Norway and the United Kingdom[2]. Although pathology and disease transmission studies indicated an infectious basis, efforts to identify an agent were unsuccessful. Here we provide evidence that HSMI is associated with infection with piscine reovirus (PRV). PRV is a novel reovirus identified by unbiased high throughput DNA sequencing and a bioinformatics program focused on nucleotide frequency as well as sequence alignment and motif analyses. Formal implication of PRV in HSMI will require isolation in cell culture and fulfillment of Koch's postulates, or prevention or modification of disease through use of specific drugs or vaccines. Nonetheless, as our data indicate that a causal relationship is plausible, measures must be taken to control PRV not only because it threatens domestic salmon production but also due to the potential for transmission to wild salmon populations. © 2010 Palacios et al.",animal tissue;article;Salmo salar;controlled study;disease association;DNA sequence;farm animal;heart and skeletal muscle inflammation;myositis;nonhuman;nucleotide sequence;phylogeny;Piscine reovirus;pyrosequencing;Reoviridae;reovirus infection;sequence alignment;sequence analysis;virus detection;virus virulence,"Palacios, G.;Lovoll, M.;Tengs, T.;Hornig, M.;Hutchison, S.;Hui, J.;Kongtorp, R. T.;Savji, N.;Bussetti, A. V.;Solovyov, A.;Kristoffersen, A. B.;Celone, C.;Street, C.;Trifonov, V.;Hirschberg, D. L.;Rabadan, R.;Egholm, M.;Rimstad, E.;Lipkin, W. I.",2010,,10.1371/journal.pone.0011487,0
1593,High prevalence of Turkey parvovirus in Turkey flocks from hungary experiencing enteric disease syndromes,"Samples collected in 2008 and 2009, from 49 turkey flocks of 6 to 43 days in age and presenting clinical signs of enteric disease and high mortality, were tested by polymerase chain reaction and reverse transcriptionpolymerase chain reaction for the presence of viruses currently associated with enteric disease (ED) syndromes: astrovirus, reovirus, rotavirus, coronavirus, adenovirus, and parvovirus. Turkey astroviruses were found in 83.67% of the cases and turkey astrovirus 2 (TAst-2) in 26.53%. The investigations directly demonstrated the high prevalence of turkey parvovirus (TuPV) in 23 flocks (46.9%) experiencing signs of ED, making this pathogen the second most identified after astroviruses. Phylogenetic analysis on a 527 base pair-long region from the NS1 gene revealed two main clusters, a chicken parvovirus (ChPV) and a TuPV group, but also the presence of a divergent branch of tentatively named ""TuPV-like ChPV"" strains. The 23 Hungarian TuPV strains were separately positioned in two groups from the American origin sequences in the TuPV cluster. An AvaII-based restriction fragment length polymorphism assay has also been developed for the quick differentiation of TuPV, ChPV, and divergent TuPV-like ChPV strains. As most detected enteric viruses have been directly demonstrated in healthy turkey flocks as well, the epidemiology of this disease complex remains unclear, suggesting that a certain combination of pathogens, environmental factors, or both are necessary for the development of clinical signs. © American Association of Avian Pathologists.",Adenoviridae;adenovirus infection;animal;animal disease;article;bird disease;classification;genetic variability;genetics;Hungary;isolation and purification;Parvoviridae;parvovirus infection;phylogeny;prevalence;RNA virus;RNA virus infection;turkey (bird),"Palade, E. A.;Demeter, Z.;Hornyák, A.;Nemes, C.;Kisary, J.;Rusvai, M.",2011,,10.1637/9688-021711-ResNote.1,0
1594,Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso,"Cowpea, (Vigna unguiculata L. (Walp)) is an annual tropical grain legume. Often referred to as ""poor man's meat"", cowpea is one of the most important subsistence legumes cultivated in West Africa due to the high protein content of its seeds. However, African cowpea production can be seriously constrained by viral diseases that reduce yields. While twelve cowpea- infecting viruses have been reported from Africa, only three of these have so-far been reported from Burkina Faso. Here we use a virion-associated nucleic acids (VANA)-based metagenomics method to screen for the presence of cowpea viruses from plants collected from the three agro-climatic zones of Burkina Faso. Besides the three cowpea-infecting virus species which have previously been reported from Burkina Faso (Cowpea aphid borne mosaic virus [Family Potyviridae], the Blackeye cowpea mosaic virus - a strain of Bean common mosaic virus - [Family Potyviridae] and Cowpea mottle virus [Family Tombusviridae]) five additional viruses were identified: Southern cowpea mosaic virus (Sobemovirus genus), two previously uncharacterised polerovirus-like species (Family Luteoviridae), a previously uncharacterised tombusvirus-like species (Family Tombusviridae) and a previously uncharacterised mycotymovirus-like species (Family Tymoviridae). Overall, potyviruses were the most prevalent cowpea viruses (detected in 65.5% of samples) and the Southern Sudan zone of Burkina Faso was found to harbour the greatest degrees of viral diversity and viral prevalence. Partial genome sequences of the two novel polerovirus-like and tombusvirus-like species were determined and RT-PCR primers were designed for use in Burkina Faso to routinely detect all of these cowpea-associated viruses.",article;Bean common mosaic virus;Blackeye cowpea mosaic virus;Burkina Faso;cowpea;Cowpea aphid borne mosaic virus;Cowpea mosaic virus;Cowpea mottle virus;gene sequence;geographic distribution;Luteoviridae;metagenomics;mycotymovirus;new species;nonhuman;Polerovirus;Potyviridae;Potyvirus;prevalence;reverse transcription polymerase chain reaction;Southern cowpea mosaic virus;species diversity;Tombusviridae;Tombusvirus;Tymoviridae;viral plant disease;virion;virus detection;virus genome;virus identification;virus strain,"Palanga, E.;Filloux, D.;Martin, D. P.;Fernandez, E.;Gargani, D.;Ferdinand, R.;Zabré, J.;Bouda, Z.;Neya, J. B.;Sawadogo, M.;Traore, O.;Peterschmitt, M.;Roumagnac, P.",2016,,10.1371/journal.pone.0165188,0
1595,A novel porcine circovirus distantly related to known circoviruses is associated with porcine dermatitis and nephropathy syndrome and reproductive failure,"Porcine circovirus-associated disease (PCVAD) is clinically manifested by postweaning multisystemic wasting syndrome (PMWS), respiratory and enteric disease, reproductive failure, and porcine dermatitis and nephropathy syndrome (PDNS). Porcine circovirus 2 (PCV2) is an essential component of PCVAD, although an etiologic role in PDNS is not well established. Here, a novel circovirus, designated porcine circovirus 3 (PCV3), was identified in sows that died acutely with PDNS-like clinical signs. The capsid and replicase proteins of PCV3 are only 37% and 55% identical to PCV2 and bat circoviruses, respectively. Aborted fetuses from sows with PDNS contained high levels of PCV3 (7.57 × 107 genome copies/ml), and no other viruses were detected by PCR and metagenomic sequencing. Immunohistochemistry (IHC) analysis of sow tissue samples identified PCV3 antigen in skin, kidney, lung, and lymph node samples localized in typical PDNS lesions, including necrotizing vasculitis, glomerulonephritis, granulomatous lymphadenitis, and bronchointerstitial pneumonia. Further study of archived PDNS tissue samples that were negative for PCV2 by IHC analysis identified 45 of 48 that were PCV3 positive by quantitative PCR (qPCR), with 60% of a subset also testing positive for PCV3 by IHC analysis. Analysis by qPCR of 271 porcine respiratory disease diagnostic submission samples identified 34 PCV3-positive cases (12.5%), and enzyme-linked immunosorbent assay detection of anti-PCV3 capsid antibodies in serum samples found that 46 (55%) of 83 samples tested were positive. These results suggest that PCV3 commonly circulates within U.S. swine and may play an etiologic role in reproductive failure and PDNS. Because of the high economic impact of PCV2, this novel circovirus warrants further studies to elucidate its significance and role in PCVAD.",animal cell;animal experiment;animal model;animal tissue;article;bronchointerstitial pneumonia;Circovirus;controlled study;enzyme linked immunosorbent assay;fetus;glomerulonephritis;immunohistochemistry;interstitial pneumonia;kidney;kidney disease;lung;lymph node;lymphadenitis;mouse;necrotizing arteritis;nonhuman;polymerase chain reaction;Porcine circovirus 2;Porcine circovirus 3;porcine dermatitis and nephropathy syndrome;porcine reproductive and respiratory syndrome;Porcine reproductive and respiratory syndrome virus;priority journal;retrospective study;skin;viral skin disease;virus pathogenesis,"Palinski, R.;Piñeyro, P.;Shang, P.;Yuan, F.;Guo, R.;Fang, Y.;Byers, E.;Hause, B. M.",2017,,10.1128/jvi.01879-16,1
1596,"Discovery of a novel Parvovirinae virus, porcine parvovirus 7, by metagenomic sequencing of porcine rectal swabs","Parvoviruses are a diverse group of viruses containing some of the smallest known species that are capable of infecting a wide range of animals. Metagenomic sequencing of pooled rectal swabs from adult pigs identified a 4103-bp contig consisting of two major open reading frames encoding proteins of 672 and 469 amino acids (aa) in length. BLASTP analysis of the 672-aa protein found 42.4 % identity to fruit bat (Eidolon helvum) parvovirus 2 (EhPV2) and 37.9 % to turkey parvovirus (TuPV) TP1-2012/HUN NS1 proteins. The 469-aa protein had no significant similarity to known proteins. Genetic and phylogenetic analyses suggest that PPV7, EhPV2, and TuPV represent a novel genus in the family Parvoviridae. Quantitative PCR screening of 182 porcine diagnostic samples found a total of 16 positives (8.6 %). Together, these data suggest that PPV7 is a highly divergent novel parvovirus prevalent within the US swine.",amino acid;nonstructural protein 1;viral protein;adult;animal tissue;article;bat;DNA virus;gene sequence;genus;metagenomics;nonhuman;nucleotide sequence;open reading frame;Parvovirus 2;Parvovirus TP1 2012 HUN;phylogeny;pig;polymerase chain reaction;Porcine parvovirus;priority journal;protein analysis;quantitative analysis;rectal swab;sequence homology;smear;turkey (bird);viral genetics;virus identification,"Palinski, R. M.;Mitra, N.;Hause, B. M.",2016,,10.1007/s11262-016-1322-1,1
1597,Molecular cloning and sequence analysis of the duck enteritis virus UL5 gene,"Duck enteritis virus (DEV) is a herpesvirus that causes an acute, contagious, and fatal disease. In the present article, the DEV UL5 gene was cloned and sequenced from a vaccine virus. According to the consensus sequence of herpesvirus UL5 and UL3 gene degenerate oligonucleotide primers were designed and were used in the polymerase chain reaction (PCR) to amplify DNA products with 4577 bp in size. DNA sequence analysis revealed a 2568 bp open reading frame (ORF) encoding a 855 amino acid polypeptide homologous to herpesvirus UL5 proteins. The DEV UL5 gene has a base composition of 769 adenine (29.95%), 556 cytosine (21.65%), 533 guanine (20.76%) and 710 thymine (27.65%). Sequence comparison revealed that the nucleotide sequence of the DEV UL5 gene was highly similar to other alphaherpesviruses. Phylogenetic tree analysis showed that the fifteen herpesviruses viruses analyzed fell into four large groups, and the duck enteritis virus itself branched and was most closely related to meleagrid herpesvirus 1, gallid herpesvirus 2 and gallid herpesvirus 3 subtrees. © 2008 Elsevier B.V. All rights reserved.",article;controlled study;Coronavirinae;duck;gene amplification;gene sequence;genetic analysis;Herpesviridae;molecular cloning;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;priority journal;ul3 gene;ul5 gene;virus gene,"Pan, H.;Cao, R.;Liu, L.;Niu, M.;Zhou, B.;Chen, P.;Hu, J.",2008,,10.1016/j.virusres.2008.05.003,0
1598,Molecular characterization of the duck enteritis virus UL4 gene,"Duck enteritis virus (DEV) is a herpesvirus that causes an acute, contagious and fatal disease. In the present article, the DEV UL4 gene was cloned and sequenced from a vaccine virus. A degenerate oligonucleotide primer for the consensus site of herpesvirus UL3 gene and a specific primer located in UL5 were used in the polymerase chain reaction (PCR) to amplify a DNA product 2 086 bp in size. DNA sequence analysis revealed that a 714 bp open reading frame (ORF) of DEV encoding a 237 amino acid polypeptide is homologous to the family of herpesvirus UL4 proteins and therefore has been characterized as a DEV UL4 gene. Alignment of the DEV UL4 protein sequence with those of other alphaherpesviruses showed that 10 amino acid residues are completely conserved. Phylogenetic tree analysis showed that the seventeen alphaherpesviruses viruses analyzed were classified into four large groups, and the duck enteritis virus branched separately, closely related to the Mardiviruses group comprising Gallid herpesvirus 2 (GaHV-2), Gallid herpesvirus 3 (GaHV-3) and Meleagrid herpesvirus 1 (MeHV-1). The present study showed that the evolutionary relationship of the UL4 protein could be used for classification of alphaherpesviruses. © Wuhan Institute of Virology, CAS and Springer-Verlag GmbH 2009.",amino acid;primer DNA;protein UL4;protein UL5;unclassified drug;viral protein;article;consensus sequence;DNA sequence;duck enteritis virus;gene amplification;genetic conservation;Herpesviridae;Mardivirus;molecular cloning;nonhuman;nucleotide sequence;open reading frame;phylogeny;polymerase chain reaction;sequence analysis;sequence homology;taxonomy;virus gene;virus strain,"Pan, H. Q.;Wang, N.;Liu, L.;Liu, L.;Hu, J. C.;Chen, P. Y.;Wang, S. J.;Cao, R. B.",2009,,10.1007/s12250-009-3002-y,0
1599,Genetic diversity and phylogenetic analysis of glycoprotein GP85 of ALV-J isolates from Mainland China between 1999 and 2010: Coexistence of two extremely different subgroups in layers,"Avian leukosis virus subgroup J (ALV-J), first isolated in 1989, preferentially infects meat-type birds. However, layer flocks in China have experienced outbreaks of this virus since 2008. To understand the genetic diversity of ALV-J in Chinese layers, we compared and analyzed the GP85 gene sequences of 106 ALV-J isolates that were isolated between 1999 and 2010 in Mainland China. The GP85 gene sequences of 41 layer isolates collected from 9 provinces of China between 2008 and 2010 belonged to two separate, highly diverse subgroups and were differentiated from meat-type chicken isolates. When compared to all meat-type isolates from China, Subgroup 1 exclusively contained current layer isolates and seemed to be dominant; all the isolates in this subgroup exhibited gene diversity, and many unique amino acid mutations were present. In contrast, the viruses in Subgroup 2 were perfectly conserved and shared high identity with the prototype meat-type chicken ALV-J strain HPRS-103. The two subgroups contained only two concurrent mutations at the same position. Moreover, most of the isolates in Subgroup 1 had two additional glycosylation sites (at positions 101 and 191) when compared with those in Subgroup 2. Our study provides evidence for the coexistence of two extremely different ALV-J subgroups in Chinese layers from 2008 to 2010, supporting the need for vaccine development and purification measures to prevent ALV-J infection in layers in China. © 2011.",amino acid;glycoprotein;glycoprotein 85;unclassified drug;article;Avian leukosis virus;China;drug development;gene mutation;gene sequence;genetic variability;glycosylation;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;protein folding;viral genetics;virus classification;virus detection;virus isolation;virus strain,"Pan, W.;Gao, Y.;Qin, L.;Ni, W.;Liu, Z.;Yun, B.;Wang, Y.;Qi, X.;Gao, H.;Wang, X.",2012,,10.1016/j.vetmic.2011.10.019,0
1600,Modulation of host miRNAs transcriptome in lung and spleen of peste des petits ruminants virus infected sheep and goats,"Peste des petits ruminants (PPR) is one of the highly contagious viral disease, characterized by fever, sore mouth, conjunctivitis, gastroenteritis, and pneumonia, primarily affecting sheep and goats. Reports suggested variable host response in goats and sheep and this host response vis-a-vis the expression of microRNAs (miRNAs) has not been investigated. Here, miRNAs were sequenced and proteomics data were generated to identify the role of differentially expressed miRNA (DEmiRNA) in PPR virus (PPRV) infected lung and spleen tissues of sheep and goats. In lungs, 67 and 37 DEmiRNAs have been identified in goats and sheep, respectively. Similarly, in spleen, 50 and 56 DEmiRNAs were identified in goats and sheep, respectively. A total of 20 and 11 miRNAs were found to be common differentially expressed in both the species in PPRV infected spleen and lung, respectively. Six DEmiRNAs-miR-21-3p, miR-1246, miR-27a-5p, miR-760-3p, miR-320a, and miR-363 were selected based on their role in viral infections, apoptosis, and fold change. The target prediction analysis of these six selected DEmiRNAs from the proteome data generated, revealed involvement of more number of genes in lung and spleen of goats than in sheep. On gene ontology analysis of host target genes these DEmiRNAs were found to regulate several immune response signaling pathways. It was observed that the pathways viz. T cell receptor signaling, Rap1 signaling, Toll-like receptor signaling, and B cell receptor signaling governed by DEmiRNAs were more perturbed in goats than in sheep. The data suggests that PPRV-induced miR-21-3p, miR-320a, and miR-363 might act cooperatively to enhance viral pathogenesis in the lung and spleen of sheep by downregulating several immune response genes. The study gives an important insight into the molecular pathogenesis of PPR by identifying that the PPRV-Izatnagar/94 isolate elicits a strong host response in goats than in sheep.",B lymphocyte receptor;microRNA;microRNA 21;mitogen activated protein kinase 7;proteome;T lymphocyte receptor;toll like receptor;animal experiment;animal model;article;controlled study;DNA transcription;down regulation;enzyme linked immunosorbent assay;gene expression;gene ontology;goat disease;high throughput sequencing;host pathogen interaction;immune response gene;lung disease;lung infection;modulation;molecular pathology;nonhuman;Peste-des-petits-ruminants virus;real time polymerase chain reaction;reverse transcription polymerase chain reaction;sheep disease;spleen;transcriptomics;upregulation;virus infection;virus neutralization,"Pandey, A.;Sahu, A. R.;Wani, S. A.;Saxena, S.;Kanchan, S.;Sah, V.;Rajak, K. K.;Khanduri, A.;Sahoo, A. P.;Tiwari, A. K.;Mishra, B.;Muthuchelvan, D.;Mishra, B. P.;Singh, R. K.;Gandham, R. K.",2017,,10.3389/fmicb.2017.01146,0
1601,Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types,"Background: Salmonella enterica serovar Typhimurium (or simply Typhimurium) is the most common serovar in both human infections and farm animals in Australia and many other countries. Typhimurium is a broad host range serovar but has also evolved into host-adapted variants (i.e. isolated from a particular host such as pigeons). Six Typhimurium strains of different phage types (defined by patterns of susceptibility to lysis by a set of bacteriophages) were analysed using Illumina high-throughput genome sequencing. Results: Variations between strains were mainly due to single nucleotide polymorphisms (SNPs) with an average of 611 SNPs per strain, ranging from 391 SNPs to 922 SNPs. There were seven insertions/deletions (indels) involving whole or partial gene deletions, four inactivation events due to IS200 insertion and 15 pseudogenes due to early termination. Four of these inactivated or deleted genes may be virulence related. Nine prophage or prophage remnants were identified in the six strains. Gifsy-1, Gifsy-2 and the sopE2 and sspH2 phage remnants were present in all six genomes while Fels-1, Fels-2, ST64B, ST104 and CP4-57 were variably present. Four strains carried the 90-kb plasmid pSLT which contains several known virulence genes. However, two strains were found to lack the plasmid. In addition, one strain had a novel plasmid similar to Typhi strain CT18 plasmid pHCM2.Conclusion: The genome data suggest that variations between strains were mainly due to accumulation of SNPs, some of which resulted in gene inactivation. Unique genetic elements that were common between host-adapted phage types were not found. This study advanced our understanding on the evolution and adaptation of Typhimurium at genomic level. © 2013 Pang et al.; licensee BioMed Central Ltd.",article;bacterial gene;bacterial genome;bacterial virulence;bacteriophage typing;evolutionary adaptation;gene deletion;gene identification;gene inactivation;gene insertion;genetic analysis;genetic variability;high throughput sequencing;nonhuman;nucleotide sequence;plasmid;prophage;pseudogene;Salmonella enterica serovar Typhimurium;serotype;single nucleotide polymorphism;strain difference,"Pang, S.;Octavia, S.;Feng, L.;Liu, B.;Reeves, P. R.;Lan, R.;Wang, L.",2013,,10.1186/1471-2164-14-718,0
1602,"Detection of a mammalian-like astrovirus in bird, European roller (Coracias garrulus)","Astroviruses are small, non-enveloped viruses with positive sense, single-stranded RNA genomes. The family Astroviridae contains two genera, Mamastrovirus and Avastrovirus, which - based upon our current knowledge - infect mammals and birds, respectively. However, recent seroprevalence study indicated that people with contact to turkeys can develop serological responses to the turkey astrovirus and minks might have been infected with the avastrovirus. These data suggest that the ""host species/astrovirus genus"" association should be permeable; however, mamastrovirus infection has not been reported from avian species, yet. In this study, a novel astrovirus was identified by viral metagenomics and RT-PCR methods in 2 (11%) out of 19 faecal samples collected from a wild, carnivorous bird species, European rollers (. Coracias garrulus) from two breeding territories in Hungary. The complete genome sequence of astrovirus Er/SZAL6/HUN/2011 (KP663426) was 7025. nt-long and had some unique genomic features including an unusually long spacer between the subgenomic RNA promoter and the ORF2 initiation codon. Using the BLASTp Er/SZAL6/HUN/2011 had the highest aa identities 35%, 61% and 34% to MAstV 32 (JF713710, host: porcine), to MAstV 23 (JF729316, host: rabbit) and to unclassified porcine astrovirus (JX684071) in ORF1a, ORF1b and ORF2, respectively. The same proteins of Er/SZAL6/HUN/2011 had 25%, 66% and 33% aa identities to the corresponding proteins of murine astrovirus (JX544743) as the closest strain. The sequence- and phylogenetic analysis indicated that Er/SZAL6/HUN/2011 represents the first member of a novel mamastrovirus species. Data suggest that both mammals and birds could have been exposed to mamastroviruses and avastroviruses providing opportunities for cross-species infection and viral adaptation with cross-class astroviruses especially in carnivorous animals. Further investigation is needed to determine the origin, natural host species spectrum, distribution and spread of Er/SZAL6/HUN/2011 among vertebrates.",article;Astroviridae;bird;Coracias garrulus;feces analysis;gene sequence;Hungary;Mamastrovirus;Mamastrovirus Er/SZAL6/HUN/2011;metagenomics;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;promoter region;reverse transcription polymerase chain reaction;virus detection;virus strain,"Pankovics, P.;Boros, A.;Kiss, T.;Delwart, E.;Reuter, G.",2015,,10.1016/j.meegid.2015.06.020,0
1603,First detection of nebovirus (Caliciviridae) in faecal sample of diarrhoeic calf in Hungary,"Neboviruses are the most recent members of family Calicivirdae, in genus Nebovirus, which can be etiological agents of diarrhoea and enteric diseases of calves (Bos taurus). The genus has two prototypes: the Newbury-1 (Bo/Newbury1/1976/ UK, DQ013304) and the Nebraska (BEC/NB/80/US, AY082891) viruses. Based on the viral capsid protein (VP1), neboviruses are classified into 4 phylogenetic lineages (lineage 1-4). The authors aims were the detection, genetic characterization and phylogenetic classification of neboviruses from 1-1 faecal samples collected from diarrhoeic calves living in two different cattle farms in Hungary. After the routine diagnostic bacteriological and virological investigation the detection and complete genome determination of nebovirus were done by molecular biological methods (454-pyrosequencing, RT-PCR, 5'/3' RACE RT-PCR and direct chain terminated sequencing). Using pyrosequencing method the contigs of nebovirus sequences were aligned from one of the faecal samples and the complete viral genome was expanded with the help of additional 4 RT-PCR reactions. The genome of strain Bo/M3641/2011/HUN (JX018212) nebovirus - 5'UTR (74nt)/ORF1 (6630nt)/ORF2 (677nt)/3'UTR(67nt) - was 7453nt in length and it has a close to 95% nucleotide match with strain Bo/BEC/Penrith140/2000/UK virus. Strain Bo/M3641/2011/HUN virus can phylogenetically be classified into lineage 1; Newbury-1-like phylogenetic group. In this study, the authors report the first detection, characterization and phylogenetic analysis of nebovirus in Hungary, being supposedly pathogenic agents, have already been present in Hungarian cattle herds and may contribute to calves' diarrheic diseases of unknown origin.",BOVINE ENTERIC CALICIVIRUSES;NEWBURY AGENT;VIRUSES;GENUS;RECOMBINATION;NOROVIRUSES;CHILDREN;CALVES,"Pankovics, P.;Boros, A.;Nemes, C.;Delwart, E.;Reuter, G.",2013,Jan,,0
1604,Molecular characterization of a novel picobirnavirus in a chicken,"Picobirnaviruses (PBVs) are bisegmented viruses with a wide geographical and host species distribution. The number of novel PBV sequences has been increasing with the help of the viral metagenomics. A novel picobirnavirus strain, pbv/CHK/M3841/HUN/2011, was identified by viral metagenomics; the complete segment 1 (MH327933) and 2 (MH327934) sequences were obtained by RT-PCR from a cloacal sample of a diseased broiler breeder pullet in Hungary. Although the conserved nucleotide (e.g., ribosome binding site) and amino acid motifs (e.g., ExxRxNxxxE, S-domain of the viral capsid and motifs in the RNA-dependent RNA polymerase) were identifiable in the chicken picobirnavirus genome, the putative segment 1 showed low (< 30%) amino acid sequence identity to the corresponding proteins of marmot and dromedary PBVs, while segment 2 showed higher (< 70%) amino acid sequence identity to a wolf PBV protein sequence. This is the first full-genome picobirnavirus sequence from a broiler breeder chicken, but the pathogenicity of this virus is still questionable.",animal;bird disease;chicken;classification;DNA sequence;genetics;isolation and purification;open reading frame;phylogeny;Picobirnavirus;RNA virus infection;veterinary medicine;virology;virus genome,"Pankovics, P.;Boros, Á;Nemes, C.;Kapusinszky, B.;Delwart, E.;Reuter, G.",2018,,10.1007/s00705-018-4012-6,1
1605,A novel passerivirus (family Picornaviridae) in an outbreak of enteritis with high mortality in estrildid finches (Uraeginthus sp.),"An enteric outbreak with high mortality (34/52, 65.4%) was recorded in 2014 in home-reared estrildid finches (Estrildidae) in Hungary. A novel passerivirus was identified in a diseased violet-eared waxbill using viral metagenomics and confirmed by RT-(q)PCR. The complete genome of finch picornavirus strain waxbill/DB01/HUN/2014 (MF977321) showed the highest amino acid sequence identity of 38.9%, 61.6%, 69.6% in P1cap, 2Chel and 3CproDpol, respectively, to passerivirus A1 (GU182406). A high viral load (6.58 × 1010 genomic copies/ml) was measured in a cloacal specimen and in the tissues (spinal cord, lung, and the intestines) of two additional affected finches. In addition to intestinal symptoms (diarrhoea), the presence of extra-intestinal virus suggests a generalized infection in this fatal disease, for which the passerivirus might be a causative agent.",amino acid sequence;animal;bird disease;classification;epidemic;finch;gastroenteritis;genetics;Hungary;inverted repeat;isolation and purification;mortality;nucleotide sequence;pathogenicity;phylogeny;Picornaviridae;picornavirus infection;sequence alignment;sequence homology;survival analysis;veterinary medicine;virology;virus genome,"Pankovics, P.;Boros, Á;Phan, T. G.;Delwart, E.;Reuter, G.",2018,,10.1007/s00705-017-3699-0,0
1606,Enteric viruses detected by molecular methods in commercial chicken and turkey flocks in the United States between 2005 and 2006,"Intestinal samples collected from 43 commercial broiler and 33 commercial turkey flocks from all regions of the United States during 2005 and 2006 were examined for the presence of astrovirus, rotavirus, reovirus, and coronavirus by reverse transcription-polymerase chain reaction (PCR), and for the presence of groups 1 and 2 adenovirus by PCR. Phylogenetic analysis was performed to further characterize the viruses and to evaluate species association and geographic patterns. Astroviruses were identified in samples from 86% of the chicken flocks and from 100% of the turkey flocks. Both chicken astrovirus and avian nephritis virus (ANV) were identified in chicken samples, and often both viruses were detected in the same flock. Turkey astrovirus type-2 and turkey astrovirus type-1 were found in 100% and 15.4% of the turkey flocks, respectively. In addition, 12.5% of turkey flocks were positive for ANV. Rotaviruses were present in 46.5% of the chicken flocks tested and in 69.7% of the turkey flocks tested. Based upon the rotavirus NSP4 gene sequence, the chicken and turkey origin rotaviruses assorted in a species-specific manner. The turkey origin rotaviruses also assorted based upon geographical location. Reoviruses were identified in 62.8% and 45.5% of chicken and turkey flocks, respectively. Based on the reovirus S4 gene segment, the chicken and turkey origin viruses assorted separately, and they were distinct from all previously reported avian reoviruses. Coronaviruses were detected in the intestinal contents of chickens, but not turkeys. Adenoviruses were not detected in any chicken or turkeys flocks. Of the 76 total chicken and turkey flocks tested, only three chicken flocks were negative for all viruses targeted by this study. Most flocks were positive for two or more of the viruses, and overall no clear pattern of virus geographic distribution was evident. This study provides updated enteric virus prevalence data for the United States using molecular methods, and it reinforces that enteric viruses are widespread in poultry throughout the United States, although the clinical importance of most of these viruses remains unclear.",primer DNA;virus DNA;animal;animal disease;article;Astroviridae;Avian orthoreovirus;bird disease;chicken;classification;Coronavirinae;genetics;isolation and purification;methodology;molecular genetics;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;Rotavirus;turkey (bird);United States;virology,"Pantin-Jackwood, M. J.;Day, J. M.;Jackwood, M. W.;Spackman, E.",2008,,10.1637/8174-111507-Reg.1,0
1607,Periodic monitoring of commercial turkeys for enteric viruses indicates continuous presence of astrovirus and rotavirus on the farms,"A longitudinal survey to detect enteric viruses in intestinal contents collected from turkeys in eight commercial operations and one research facility was performed using molecular detection methods. Intestinal contents were collected from turkeys prior to placement, with each flock resampled at 2, 4, 6, 8, 10, and 12 wk of age. The samples were screened for astrovirus, rotavirus, reovirus, and turkey coronavirus (TCoV) by a reverse transcriptase and polymerase chain reaction (RT-PCR), and for groups 1 and 2 adenovirus by PCR. Rotavirus was the only virus detected prior to placement (7 of 16 samples examined). All of the commercial flocks were positive for rotavirus and astrovirus from 2 until 6 wk of age, and most were intermittently positive until 12 wk of age, when the birds were processed. Of the 96 samples collected from birds on the farms, 89.5% were positive for astrovirus, and 67.7% were positive for rotavirus. All flocks were negative for TCoV, reovirus, and group 1 adenovirus at all time points, and positive for group 2 adenovirus (hemorrhagic enteritis virus) at 6 wk of age. All the flocks monitored were considered healthy or normal by field personnel. Turkeys placed on research facilities that had been empty for months and thoroughly cleaned had higher body weights and lower feed conversion rates at 5 wk of age when compared to turkeys placed on commercial farms. Intestinal samples collected at 1, 2, and 3 wk of age from these turkeys were free of enteric viruses. This report demonstrates that astroviruses and rotaviruses may be present within a turkey flock through the life of the flock. Comparison of infected birds with one group of turkeys that were negative for enteric viruses by the methods used here suggests that astrovirus and/or rotavirus may affect production. The full impact on flock performance needs to be further determined.",aging;animal;article;Astroviridae;Aviadenovirus;bird disease;Coronavirinae;female;genetics;isolation and purification;phylogeny;Reoviridae;Rotavirus;stomach juice;turkey (bird);virology,"Pantin-Jackwood, M. J.;Spackman, E.;Day, J. M.;Rives, D.",2007,,10.1637/0005-2086(2007)51[674:Pmoctf]2.0.Co;2,0
1608,Molecular characterization and typing of chicken and turkey astroviruses circulating in the United States: Implications for diagnostics,"Avian astroviruses were detected by reverse transcriptase and polymerase chain reaction in intestinal contents collected from commercial chickens and turkeys from throughout the United States from 2003 through 2005. Astroviruses were detected in birds from both healthy and poorly performing flocks with or without enteric disease. Phylogenetic analysis was performed with sequence data from the polymerase (ORF-1b) genes of 41 turkey-origin astroviruses and 23 chicken-origin astroviruses. All currently available avian astrovirus sequence data and selected mammalian astrovirus sequence data were included in the analysis. Four groups of avian astroviruses were observed by phylogenetic analysis: turkey astrovirus type 1 (TAstV-1)-like viruses, turkey astrovirus type 2 (TAstV-2)-like viruses, both detected in turkeys; avian nephritis virus (ANV)-like viruses, detected in both chickens and turkeys; and a novel group of chicken-origin astroviruses (CAstV). Among these four groups, amino acid identity was between 50.1% and 73.8%, and was a maximum of 49.4% for all avian isolates when compared with the mammalian astroviruses. There were multiple phylogenetic subgroups within the TAstV-2, ANV, and CAstV groups based on 9% nucleotide sequence divergence. Phylogenetic analysis revealed no clear assortment by geographic region or isolation date. Furthermore, no correlation was observed between the detection of a particular astrovirus and the presence of enteric disease or poor performance. Based on these data, a revision of the present taxonomic classification for avian astroviruses within the genus Avastrovirus is warranted.",animal;animal disease;article;Astroviridae;bird disease;chicken;genetic variability;genetics;isolation and purification;phylogeny;stomach juice;turkey (bird);United States;virology;virus infection,"Pantin-Jackwood, M. J.;Spackman, E.;Woolcock, P. R.",2006,,10.1637/7512-020606r.1,0
1609,Two oncogenes in avian carcinoma virus MH2: myc and mht,"The 5.2-kilobase (kb) RNA genome of avian carcinoma virus MH2 has the genetic structure 5' - delta gag (0.2 kb)-mht (1.2 kb)-myc (1.4 kb)-c(0.4 kb)-poly (A) (0.2 kb)-3'. delta gag is a partial retroviral core protein, mht and myc are cell-derived MH2-specific sequences, and c is the 3'-terminal retroviral vector sequence. the following results were obtained from the complete nucleotide sequences of the mht and myc genes in MH2. (i) delta gag-mht forms a hybrid gene with a contiguous reading frame of 2682 nucleotides that terminates with a stop codon near the 3' end of the mht gene. The 3' 969 nucleotides of mht up to the stop codon are 80% sequence related to the onc-specific raf sequence of murine sarcoma virus 3611 (MSV 3611) (94% homologous at the deduced amino acid level). (ii) The myc coding region in MH2 is preceded by 181 nucleotides derived from the intron immediately upstream from the second exon of the chicken cellular proto-myc gene, followed by an RNA splice acceptor site shared with the proto-myc gene, followed by an RNA splice acceptor site shared with the proto-myc, beyond which it is colinear up to a 3'-termination codon and 40 noncoding nucleotides with the myc sequences of avian retrovirus MC29 and chicken proto-myc. Thus, myc forms, together with a 5' retroviral exon, a second MH2-specific gene. It is concluded that MH2 contains two genes with oncogenic potential, the delta gag-mht gene, which is closely related to the delta gag-raf transforming gene of MSV 3611, and the myc gene, which is related to the transforming gene of MC29. Furthermore, it may be concluded that the cellular proto-onc genes, which on sequence transduction become viral onc genes, are a small group because among the 19 known onc sequences, 5 are shared by different taxonomic groups of viruses of which the mht/raf homology is the closest so far.",animal;article;chicken;chromosome map;codon;comparative study;genetics;human;molecular cloning;nucleotide sequence;oncogene;Retroviridae;species difference,"Papas, T. S.;Kan, N. C.;Watson, D. K.;Flordellis, C.;Lautenberger, J. A.;Psallidopoulos, M. C.;Rovigatti, U. G.;Samuel, K. P.;Ascione, R.;Duesberg, P. H.",1985,,,0
1610,Classification and characterization of a laboratory chicken rotavirus strain carrying G7P[35] neutralization antigens on the genotype 4 backbone gene configuration,"The laboratory rotavirus strain, BRS/115, has been used for more than two decades to monitor rotaviruses in specific pathogen free flocks of laying hens. However, the virus strain has not been characterized in detail. Therefore we aimed at the description of molecular features of BRS115 by using random primed reverse transcription-PCR of the genomic RNA followed by massive parallel sequencing using the semiconductor sequencing technology. Over 64,000 trimmed reads mapped to reference sequences obtained from GenBank. The strain classified into the species Rotavirus A and genotyped G7-P[35]-I4-R4-C4-M4-A16-N4-T4-E11-H4 according to guidelines of the Rotavirus Classification Working Group. Phylogenetic analysis identified shared features with chicken, turkey and pigeon origin rotaviruses. This study demonstrates the robustness of next generation sequencing in the characterization of reference virus materials used in specialized laboratories.",antigen;genomic RNA;neutralization antigen;unclassified drug;article;chicken;controlled study;gene mapping;gene sequence;genotype;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;Rotavirus;Rotavirus A;virus classification;virus strain,"Papp, H.;Marton, S.;Farkas, S. L.;Jakab, F.;Martella, V.;Malik, Y. S.;Palya, V.;Bányai, K.",2014,,10.1016/j.biologicals.2014.08.004,0
1611,Phylogenetic tracking of current porcine epidemic diarrhea virus (PEDV) strains in the Philippines,"To trace the possible route of introduction of porcine epidemic diarrhea virus (PEDV), the phylogenetic relationships of PEDV strains in the regions of epidemicity in the Philippines to PEDV strains that are endemic in other countries were investigated. Partial nucleotide sequences of the S1 spike gene was determined from the PEDV-positive samples and compared with S1 sequences from other countries. Phylogenetic analysis indicated that PEDV strains in the Philippines segregate into two groups. Members of group 1 are related to strains from the USA, Taiwan, Japan and Canada, while those in group 2 are related to strains from China and Vietnam.",animal;Coronavirus infection;genetics;Philippines;phylogeny;pig;Porcine epidemic diarrhea virus;season;swine disease;veterinary medicine;virology,"Paraguison-Alili, R.;Domingo, C. Y.",2016,,10.1007/s00705-016-2938-0,0
1612,Ten years (2004-2014) of influenza surveillance in Northern Italy,"As the regional influenza reference centre operating within the Italian network InfluNet, here we report data on virological and epidemiological surveillance of influenza, as well as on the vaccination coverage rates achieved in Lombardy (Northern Italy) over 10 consecutive winter seasons (2004-2014). Over the past 10 years, influenza vaccine coverage declined both in the general population (from 15.7% in 2004-2005 to 11.7% in 2013-2014) and in the vaccine-target population of individuals ≥65-y-of-age (from 65.3% in 2004-2005 to 48.6% in 2013-2014) and is far below the minimum planned threshold level (75%). The highest influenza-like illness (ILI) rates were recorded during the 2004-2005 and 2009-2010 epidemics (peak incidence: 12.04‰ and 13.28‰, respectively). Both seasons were characterised by the introduction of novel viral strains: A/Fujian/411/2002(H3N2) (a drifted hemagglutinin variant) and A/California/7/2009(H1N1) pandemic virus (a swine origin quadruple reassortant), respectively. Because the antigenic match between vaccine and circulating strains was good in both of these seasons, a relevant proportion of cases may have been prevented by vaccination. A different situation was observed during the 2011-2012 season, when ILI morbidity rates in individuals ≥65-y-of-age were 1.5-6-fold higher than those registered during the other epidemics under review. The higher morbidity resulted from the circulation during the 2011-2012 season of an A/Victoria/361/2011(H3N2)-like variant that presented a reduced genetic match with the A(H3N2) strain included in the 2011-2012 vaccine composition. The continuous surveillance of the characteristics of circulating viruses is an essential tool for monitoring their matching with seasonal vaccine strains. Strategies to increase coverage rates are warranted.",diseases;epidemic;epidemiology;genetic reassortment;influenza;influenza vaccination;Influenza virus;Italy;monitoring;morbidity;pandemic;phylogeny;population;season;pig;vaccination;virus;virus strain;winter;hemagglutinin;influenza vaccine;vaccine,"Pariani, E.;Amendola, A.;Piatti, A.;Anselmi, G.;Ranghiero, A.;Bubba, L.;Rosa, A. M.;Pellegrinelli, L.;Binda, S.;Coppola, L.;Gramegna, M.;Zanetti, A.",2015,,10.4161/hv.35863,0
1613,Molecular detection and genetic characterization of kobuviruses in fecal samples collected from diarrheic cattle in Korea,,,"Park, S. J.;Kim, H. K.;Song, D. S.;Moon, H. J.",2011,,,0
1614,Full genome analysis of a novel adenovirus from the South Polar skua (Catharacta maccormicki) in Antarctica,"Adenoviruses have been identified in humans and a wide range of vertebrate animals, but not previously from the polar region. Here, we report the entire 26,340-bp genome of a novel adenovirus, detected by PCR, in tissues of six of nine South Polar skuas (Catharacta maccormicki), collected in Lake King Sejong, King George Island, Antarctica, from 2007 to 2009. The DNA polymerase, penton base, hexon and fiber genes of the South Polar skua adenovirus (SPSAdV) exhibited 68.3%, 75.4%, 74.9% and 48.0% nucleotide sequence similarity with their counterparts in turkey hemorrhagic enteritis virus. Phylogenetic analysis based on the entire genome revealed that SPSAdV belonged to the genus Siadenovirus, family Adenoviridae. This is the first evidence of a novel adenovirus, SPSAdV, from a large polar seabird (family Stercorariidae) in Antarctica.","*Adenoviridae Infections/ve [Veterinary];Adenoviridae Infections/vi [Virology];Animals;Antarctic Regions;*Aviadenovirus/ge [Genetics];Aviadenovirus/ip [Isolation & Purification];Base Sequence;*Bird Diseases/vi [Virology];Capsid Proteins/ge [Genetics];*Charadriiformes/vi [Virology];DNA-Directed DNA Polymerase/ge [Genetics];*Genome, Viral;Phylogeny;Sequence Analysis, DNA;Siadenovirus/cl [Classification];*Siadenovirus/ge [Genetics];Siadenovirus/ip [Isolation & Purification];0 (Capsid Proteins);0 (hexon capsid protein, Adenovirus);0 (penton protein, adenovirus)","Park, Y. M.;Kim, J. H.;Gu, S. H.;Lee, S. Y.;Lee, M. G.;Kang, Y. K.;Kang, S. H.;Kim, H. J.;Song, J. W.",2012,Jan 05,,0
1615,Focus: Microbiome: An Ecological Framework of the Human Virome Provides Classification of Current Knowledge and Identifies Areas of Forthcoming …,,,"Parker, M. T.",2016,,,0
1616,"Characterisation of Wongorr virus, an Australian orbivirus","Sequence analyses of VP3 gene segments of Wongorr virus isolates from the Northern Territory of Australia were compared with the cognate gene segments from Picola and Paroo River viruses. Previous serological investigations had demonstrated some relationships between these viruses, however VP3 gene sequence and phylogenetic analyses placed these viruses within the same serogroup which was distinct from other described orbivirus serogroups. A polymerase chain reaction (PCR) was developed for the detection of this serogroup and used to identify and determine partial sequence data for other isolates of the virus. Wongorr virus and the other tick and mosquito-borne orbiviruses (Kemerovo and Corriparta), were more closely related than the Culicoides transmitted orbiviruses, such as bluetongue (BTV) and African horse sickness virus (AHSV) which were shown to be on a separate branch of the orbivirus phylogenetic tree.",animal cell;article;Australia;bovine;controlled study;mosquito;nonhuman;Orbivirus;phylogeny;polymerase chain reaction;priority journal;RNA sequence;virus characterization;virus purification,"Parkes, H.;Gould, A. R.",1996,,10.1016/0168-1702(96)01344-5,0
1617,Rumen virome: an assessment of viral communities and their functions in the rumen of an Indian buffalo,"Viruses play a key role in compensating bacterial population in any ecosystem of the planet. Rumen, a highly diverse ecosystem, is still under-explored for viral communities and their metabolic capabilities. We carried out shotgun sequencing of enriched viral particles from rumen fluid collected from an Indian buffalo. The study revealed that well-assembled contigs of Newbler and Velvet got majority of assignments to virus domain that further revealed Caudovirales as a major order. A majority of the Firmicutes bacteriophages were found in the study, which also confirm the presence of conserved domains such as peptidases against Firmicutes phages.",Bacteriophage;contigs;gene prediction;peptidase;virome;METAGENOMIC DATA;BACTERIOPHAGES;VIRUS;MICROBIOME;DISCOVERY;QUALITY;CATTLE,"Parmar, N. R.;Jakhesara, S. J.;Mohapatra, A.;Joshi, C. G.",2016,Sep,,0
1618,Development of cDNA probes for typing group A bovine rotaviruses on the basis of VP4 specificity,"Dot and Northern (RNA) blot hybridization assays were developed for the P typing of group A bovine rotaviruses (BRV) by using cDNA probes prepared from gene segment 4. The probes were prepared by polymerase chain reaction amplification of hyperdivergent regions (nucleotides 211 to 686) of BRV strain UK, IND, NCDV, and Cr VP4 cDNA by using specific oligonucleotide primers. The probes were P type specific (VP4) and exhibited little or no cross-reactivity with double-stranded RNA from heterologous rotavirus P types. Our studies indicate that at least three P types, as defined by polymerase chain reaction-derived VP4 gene probes from the UK, NCDV, and Cr strains, exist among the seven BRV isolates tested.",complementary DNA;bovine;controlled study;cross reaction;DNA probe;dot hybridization;gene structure;nonhuman;Northern blotting;note;polymerase chain reaction;priority journal;Rotavirus;serotype;viral genetics;virus classification,"Parwani, A. V.;Rosen, B. I.;McCrae, M. A.;Saif, L. J.",1992,,,0
1619,Complete genome sequence analysis of chicken astrovirus isolate from India,"Objective: Chicken astroviruses have been known to cause severe disease in chickens leading to increased mortality and “white chicks” condition. Here we aim to characterize the causative agent of visceral gout suspected for astrovirus infection in broiler breeder chickens. Methods: Total RNA isolated from allantoic fluid of SPF embryo passaged with infected chicken sample was sequenced by whole genome shotgun sequencing using ion-torrent PGM platform. The sequence was analysed for the presence of coding and non-coding features, its similarity with reported isolates and epitope analysis of capsid structural protein. Results: The consensus length of 7513 bp genome sequence of Indian isolate of chicken astrovirus was obtained after assembly of 14,121 high quality reads. The genome was comprised of 13 bp 5′-UTR, three open reading frames (ORFs) including ORF1a encoding serine protease, ORF1b encoding RNA dependent RNA polymerase (RdRp) and ORF2 encoding capsid protein, and 298 bp of 3′-UTR which harboured two corona virus stem loop II like “s2m” motifs and a poly A stretch of 19 nucleotides. The genetic analysis of CAstV/INDIA/ANAND/2016 suggested highest sequence similarity of 86.94% with the chicken astrovirus isolate CAstV/GA2011 followed by 84.76% with CAstV/4175 and 74.48%% with CAstV/Poland/G059/2014 isolates. The capsid structural protein of CAstV/INDIA/ANAND/2016 showed 84.67% similarity with chicken astrovirus isolate CAstV/GA2011, 81.06% with CAstV/4175 and 41.18% with CAstV/Poland/G059/2014 isolates. However, the capsid protein sequence showed high degree of sequence identity at nucleotide level (98.64-99.32%) and at amino acids level (97.74–98.69%) with reported sequences of Indian isolates suggesting their common origin and limited sequence divergence. The epitope analysis by SVMTriP identified two unique epitopes in our isolate, seven shared epitopes among Indian isolates and two shared epitopes among all isolates except Poland isolate which carried all distinct epitopes.",capsid protein;epitope;open reading frame 1a encoding serine protease;open reading frame 1b encoding RNA dependent RNA polymerase;open reading frame 2 encoding capsid protein;RNA directed RNA polymerase;serine proteinase;unclassified drug;amino acid sequence;amnion fluid;animal cell;animal tissue;article;astrovirus infection;Avastrovirus;broiler;chicken astrovirus;embryo;epitope mapping;Gallus gallus;gene sequence;genetic code;genetic similarity;genome analysis;gout;India;nonhuman;nucleotide sequence;open reading frame;pathogenesis;phylogeny;protein structure;ribosomal frameshifting;RNA isolation;sequence analysis;visceral gout;whole genome sequencing,"Patel, A. K.;Pandit, R. J.;Thakkar, J. R.;Hinsu, A. T.;Pandey, V. C.;Pal, J. K.;Prajapati, K. S.;Jakhesara, S. J.;Joshi, C. G.",2017,,10.1007/s11259-016-9673-6,0
1620,Metagenomic of clinically diseased and healthy broiler affected with respiratory disease complex,"In recent past, the respiratory infection has emerged as a great challenge to the poultry farmers. Various pathogens including Avian pneumovirus (APV), Avian influenza virus (AIV), Infectious bronchitis virus (IBV) and Newcastle disease virus (NDV), Avibacterium paragallinarum, Ornithobacterium rhinotracheale (ORT), Mycoplasma synoviae (MS), Mycoplasma gallisepticum (MG) and Avian pathogenic Escherichia coli (APEC) are involved in the respiratory disease complex in birds [1], [2] (Bradbury, 1984; Roussan et al., 2008). Hence, respiratory disease complex is the most serious disease affecting to poultry and causes heavy economic losses in the poultry industry worldwide [3] (Murthy et al., 2008). In recent years, metagenomics is powerful analyzing tool for detection of pathogens directly from clinical samples without any prior knowledge of the organism in a given sample [4], [5] (Schuster, 2008; Pereira et al., 2010). High throughput Next-Generation-Sequencing technology was used for sequencing the isolated genomic DNA. These data provides an insight about taxonomic and functional status of microorganisms responsible for causing respiratory infection in broiler. The data of these metagenome are available in the BioSample Submission Portal as Bioproject PRJNA339659 and SRA accession number SRR5997823, SRR5992854, SRR6037376, SRR6024702, SRR6012248 and SRR6008913.",,"Patel, J. G.;Patel, B. J.;Patel, S. S.;Raval, S. H.;Parmar, R. S.;Joshi, D. V.;Chauhan, H. C.;Chandel, B. S.;Patel, B. K.",2018,Aug,,0
1621,"Equine herpesviruses 1 (EHV-1) and 4 (EHV-4) - Epidemiology, disease and immunoprophylaxis: A brief review","This review concentrates on the epidemiology, latency and pathogenesis of, and the approaches taken to control infection of horses by equine herpesvirus types 1 (EHV-1) and 4 (EHV-4). Although both viruses may cause febrile rhinopneumonitis, EHV-1 is the main cause of abortions, paresis and neonatal foal deaths. The lesion central to these three conditions is necrotising vasculitis and thrombosis resulting from lytic infection of endothelial cells lining blood capillaries. The initiation of infection in these lesions is likely to be by reactivated EHV-1 from latently infected leukocytes. However, host factors responsible for reactivation remain poorly understood. While vaccine development against these important viruses of equines involving classical and modern approaches has been ongoing for over five decades, progress, compared to other alpha herpesviruses of veterinary importance affecting cattle and pigs, has been slow. However recent data with a live temperature sensitive EHV-1 vaccine show promise. © 2004 Elsevier Ltd. All rights reserved.",adjuvant;antiserum;carbomer;corticosteroid;cyclophosphamide;double e ft ehv;duvaxyn ehv 1 4;equi guard;equi vac ehv 1 4;equiffa;equigard flu;fluvac ehv 4 1;herpes vaccine;inactivated vaccine;live vaccine;pnemabort k +1b;prestige ii;prestige v;Prodigy;resequin;resequin plus;rhino flu;rhinomune;subunit vaccine;unclassified drug;bovine;cytolysis;endothelium cell;epidemiological data;Equid herpesvirus 1;herpes virus infection;horse disease;immunoprophylaxis;infection control;leukocyte;necrotizing arteritis;newborn mortality;nonhuman;paresis;prestige;respiratory tract infection;review;rhinitis;septic abortion;pig;thrombosis;veterinary abortion;veterinary medicine;virus carrier;virus classification;virus latency;virus pathogenesis;virus pneumonia;virus reactivation;virus transmission,"Patel, J. R.;Heldens, J.",2005,,10.1016/j.tvjl.2004.04.018,0
1622,Phylogenetic analysis of NS5B gene of classical swine fever virus isolates indicates plausible Chinese origin of Indian subgroup 2.2 viruses,"Twenty-three CSFV isolates recovered from field outbreaks in various parts of India during 2006-2009 were used for genetic analysis in the NS5B region (409 nts). Seventeen of these were studied earlier [16] in the 50UTR region. Phylogenetic analysis indicated the continued dominance of subgroup 1.1 strains in the country. Detailed analysis of a subgroup 2.2 virus indicated the plausible Chinese origin of this subgroup in India and provided indirect evidence of routes of CSFV movement within South East Asia region. © Springer Science+Business Media, LLC 2011.",nonstructural protein 5B;virus RNA;5' untranslated region;article;Chinese;classical swine fever;gene activity;gene function;genetic analysis;geographic distribution;Indian;nonhuman;NS5B gene;nucleotide sequence;Pestivirus;phylogeny;priority journal;RNA extraction;RNA sequence;virus gene;virus isolation;virus strain,"Patil, S. S.;Hemadri, D.;Veeresh, H.;Sreekala, K.;Gajendragad, M. R.;Prabhudas, K.",2012,,10.1007/s11262-011-0572-1,0
1623,"A proposed division of the pestivirus genus using monoclonal antibodies, supported by cross-neutralisation assays and genetic sequencing","Sixty-six pestiviruses from ruminant and porcine hosts were analysed with a panel of 76 monoclonal antibodies raised against 9 different viruses. Reactivity was used to construct epitope similarity maps for all of the viruses. Four principal virus subgroups were demonstrated. One subgroup equated to classical swine fever virus (CSFV) and included most porcine pestiviruses but none from ruminants. A second subgroup contained mainly viruses of bovine origin, including reference bovine viral diarrhoea viruses (BVDV) such as NADL; however viruses from pigs and sheep were also represented. A third subgroup represented by reference strains of border disease virus (BDV) comprised mainly ovine isolates, but also viruses from pigs. The fourth and most recently defined subgroup contained no reference strains of CSFV, BVDV or BDV, but included atypical viruses from cattle, sheep and pigs. The subgrouping scheme was supported by genetic comparisons between representative viruses from the 4 subgroups and by virus neutralisation with polyclonal sera.",monoclonal antibody;article;bioassay;genetics;nonhuman;Pestivirus;virus classification,"Paton, D. J.;Sands, J. J.;Lowings, J. P.;Smith, J. E.;Ibata, G.;Edwards, S.",1995,,,0
1624,"Options for control of foot-and-mouth disease: Knowledge, capability and policy","Foot-and-mouth disease can be controlled by zoo-sanitary measures and vaccination but this is difficult owing to the existence of multiple serotypes of the causative virus, multiple host species including wildlife and extreme contagiousness. Although intolerable to modern high-production livestock systems, the disease is not usually fatal and often not a priority for control in many developing countries, which remain reservoirs for viral dissemination. Phylogenetic analysis of the viruses circulating worldwide reveals seven principal reservoirs, each requiring a tailored regional control strategy. Considerable trade benefits accrue to countries that eradicate the disease but as well as requiring regional cooperation, achieving and maintaining this status using current tools takes a great deal of time, money and effort. Therefore, a progressive approach is needed that can provide interim benefits along the pathway to final eradication. Research is needed to understand and predict the patterns of viral persistence and emergence and to improve vaccine selection. Better diagnostic methods and especially better vaccines could significantly improve control in both the free and the affected parts of the world. In particular, vaccines with improved thermostability and a longer duration of immunity would facilitate control and make it less reliant on advanced veterinary infrastructures. © 2009 The Royal Society.","virus vaccine;animal;animal disease;developing country;disease carrier;domestic animal;foot and mouth disease;Foot and mouth disease virus;growth, development and aging;immunology;review;virology","Paton, D. J.;Sumption, K. J.;Charleston, B.",2009,,10.1098/rstb.2009.0100,0
1625,Genetic heterogeneity of Indian field isolates of foot-and-mouth disease virus serotype O as revealed by partial sequencing of 1D gene,"The sequence of 165 nucleotides at the 3' end of the 1D gene, determined from RT-PCR amplified cDNA fragments, of 25 type O strains isolated from different parts/regions of India during 1987-1995 and the vaccine strain (R2/75) currently in use in India were subjected to phylogenetic analysis. One isolate from the neighbouring country Nepal was also included in the study. The virus/ field strains showed high degree of genetic heterogeneity among themselves with % divergence in nucleotide sequence ranging from 1.2 to 19.4%. The Indian strains were much away (13.3-20.6%) from the exotic type O strains of O1BFS, O1K, and O1Campos. The type O strains analyzed were classified into three genotypes basing on level of divergence observed in nucleotide sequence. The type O vaccine virus (R2/75) was >7% divergent (7.3-15.2%) from the field strains which revealed significant (>5%) genetic heterogeneity between the two. The phylogenetic analysis identified three distinct lineages, viz., (i) lineage 1 represented by the exotic strains, (ii) lineage 2 represented by 25 of the field strains which clustered into seven subgroups/sublines (2a-2g), and (iii) lineage 3 represented by a unique field isolate which shared the branching/origin with the vaccine strain. The lineage 2 which comprised of 25 of the 26 type O field strains analyzed, was placed almost at equidistance from the lineages 1 and 3 in the phylogenetic tree. The vaccine strain was closer to the viruses in lineage 2. Though there was no specific distribution pattern of sequences in different geographical regions of India, the viruses/ sequences in subgroup 2f appeared to be restricted to the southern states. Comparison of deduced amino acid sequence in the immunodominant regions 133-160 and 200-208 of the 1D gene product (VP1) showed that the two viruses in lineage 3 had unique amino acid residues at the positions 138 (D), 139 (G), 144 (I), and 158 (A) compared to rest of the strains including the exotic ones. Comparison of amino acid residues at critical positions 144, 148, 149, 151, 153, 154, and 208 revealed similarity between the type O strains analyzed. The virus strains showed variation (V/L/I) at position 144. One field strain showed replacement from Q149→E and another from P208→L. Thus, the study revealed that the type O FMD virus populations circulating in India and causing disease outbreaks are genetically much heterogeneous but related at the immunodominant region of VP1 polypeptide, and there are more than one genetically distinct virus populations in almost every region of the country which is possible due to unrestricted animal movement in the country. The involvement of vaccine virus in disease outbreaks was ruled out as the field strains (excluding the one in lineage 3) were phylogenetically distinct from it. Copyright (C) 1998 Elsevier Science B.V.",article;Foot and mouth disease virus;gene sequence;genetic heterogeneity;nonhuman;nucleotide sequence;phylogeny;priority journal;virus strain,"Pattnaik, B.;Venkataramanan, R.;Tosh, C.;Sanyal, A.;Hemadri, D.;Samuel, A. R.;Knowles, N. J.;Kitching, R. P.",1998,,10.1016/s0168-1702(98)00044-6,0
1626,Isolation of a bovine rotavirus with a 'super-short' RNA electrophoretic pattern from a calf with diarrhea,"A rotavirus with a 'super-short' RNA electropherotype was isolated from a calf with diarrhea and was designated VMRI strain. Segments 10 and 11 of this rotavirus migrated more slowly than did those of bovine rotavirus strains NCDV, B641, and B223. The electrophoretic pattern of the VMRI strain was similar to that reported for rotaviruses with super-short RNA electropherotypes from humans and rabbits. Northern (RNA) blot hybridization indicated that gene 11 of the VMRI strain was altered and migrated between gene segments 9 and 10. The subgroup of the VMRI strain was shown to be subgroup I. The VMRI strain of bovine rotavirus was neutralized by antisera containing polyclonal antibodies to rotavirus serotype 6 (bovine rotavirus serotype I) strains NCDV and B641 and by ascitic fluid containing monoclonal antibodies directed to VP7 of serotype 6 rotavirus. The VMRI strain was not neutralized by either polyclonal or monoclonal antibodies to strain B223 (bovine rotavirus serotype II). Collective data on the neutralization of the VMRI strain with monoclonal antibodies and polyclonal antibodies suggest that this virus is a member of the NCDV group (serotype 6) of rotaviruses (bovine rotavirus serotype I).",monoclonal antibody;radioisotope;bovine;cell culture;classification;diarrhea;hybridization;immunoblotting;nonhuman;polyacrylamide gel electrophoresis;priority journal;RNA analysis;Rotavirus;virus classification;virus gene;virus isolation;virus neutralization,"Paul, P. S.;Lyoo, Y. S.;Woode, G. N.;Zheng, S.;Greenberg, H. B.;Matsui, S.;Schwartz, K. J.;Hill, H. T.",1988,,,0
1627,Characterization of the full-length genomic sequences of vesicular stomatitis Cocal and Alagoas viruses,"In Brazil and Argentina, vesicular stomatitis (VS) is caused by distinct viral strains serologically related to the classical vesicular stomatitis virus Indiana (VSIV), namely VS Indiana-2 (VSIV-2) and VS Indiana-3 (VSIV-3). Here we describe the full-length genomic sequences and organization of the prototype strains of VSIV-2 Cocal virus (COCV) and VSIV-3 Alagoas virus (VSAV). These viruses showed similar genomic organizations to VSIV field isolates except that the non-structural C'/C proteins, markedly conserved throughout the vesiculoviruses, were absent in VSAV. Phylogenetic analyses consistently grouped COCV, VSAV and VSIV in a monophyletic group distinct from VSNJV, supporting the classification of these viruses within the Indiana serogroup.","Animals;Animals, Domestic/vi [Virology];Argentina;Base Sequence;Brazil;Gene Order;*Genome, Viral;Molecular Sequence Data;Phylogeny;*RNA, Viral/ge [Genetics];Sequence Alignment;Sequence Analysis, DNA;Vesicular Stomatitis/vi [Virology];*Vesiculovirus/ge [Genetics];Viral Proteins/ge [Genetics];0 (RNA, Viral);0 (Viral Proteins)","Pauszek, S. J.;Allende, R.;Rodriguez, L. L.",2008,,,0
1628,Genetic and antigenic relationships of vesicular stomatitis viruses from South America,"Vesicular stomatitis (VS) viruses have been classified into two serotypes: New Jersey (VSNJV) and Indiana (VSIV). Here, we have characterized field isolates causing vesicular stomatitis in Brazil and Argentina over a 35-year span. Cluster analysis based on either serological relatedness, as inferred from virus neutralization and complement fixation assays, or nucleotide sequences of two separate genes (phosphoprotein or glycoprotein) grouped the field isolates into two distinct monophyletic groups within the Indiana serogroup. One group included seven viruses from Brazil and Argentina that were serologically classified as Indiana-2 and Cocal virus (COCV). The other group contained three viruses from Brazil that were serologically classified as Indiana-3 and the prototype of this group, Alagoas virus (VSAV). Interestingly, two vesiculoviruses that were isolated from insects but do not cause disease in animals, one from Brazil (Maraba virus; MARAV) and the other from Colombia (CoAr 171638), grouped into two separate genetic lineages within the Indiana serotype. Our data provide support for the classification of viruses causing clinical VS in livestock in Brazil and Argentina into two distinct groups: Indiana-2 (VSIV-2) and Indiana-3 (VSIV-3). We suggest using nomenclature for these viruses that includes the serotype, year and place of occurrence, and affected host. This nomenclature is consistent with that currently utilized to describe field isolates of VSNJV or VSIV in scientific literature. © 2011 Springer-Verlag (outside the USA).",virus antigen;animal;animal disease;article;bovine;cattle disease;classification;genetics;horse;horse disease;immunology;insect;isolation and purification;molecular genetics;nucleotide sequence;phylogeny;rhabdovirus infection;serodiagnosis;South America;Vesiculovirus;virology,"Pauszek, S. J.;del Barrera, J. C.;Goldberg, T.;Allende, R.;Rodriguez, L. L.",2011,,10.1007/s00705-011-1081-1,0
1629,Zoonotic hepatitis E: animal reservoirs and emerging risks,"Hepatitis E virus (HEV) is responsible for enterically-transmitted acute hepatitis in humans with two distinct epidemiological patterns. In endemic regions, large waterborne epidemics with thousands of people affected have been observed, and, in contrast, in non-endemic regions, sporadic cases have been described. Although contaminated water has been well documented as the source of infection in endemic regions, the modes of transmission in non-endemic regions are much less known. HEV is a single-strand, positive-sense RNA virus which is classified in the Hepeviridae family with at least four known main genotypes (1-4) of mammalian HEV and one avian HEV. HEV is unique among the known hepatitis viruses, in which it has an animal reservoir. In contrast to humans, swine and other mammalian animal species infected by HEV generally remain asymptomatic, whereas chickens infected by avian HEV may develop a disease known as Hepatitis-Splenomegaly syndrome. HEV genotypes 1 and 2 are found exclusively in humans while genotypes 3 and 4 are found both in humans and other mammals. Several lines of evidence indicate that, in some cases involving HEV genotypes 3 and 4, animal to human transmissions occur. Furthermore, individuals with direct contact with animals are at higher risk of HEV infection. Cross-species infections with HEV genotypes 3 and 4 have been demonstrated experimentally. However, not all sources of human infections have been identified thus far and in many cases, the origin of HEV infection in humans remains unknown. © INRA, EDP Sciences, 2010.",animal;animal disease;communicable disease;disease carrier;disease transmission;hepatitis E;human;review;risk factor;virology;zoonosis,"Pavio, N.;Meng, X. J.;Renou, C.",2010,,,0
1630,A novel subgroup of exogenous avian leukosis virus in chickens,"An avian leukosis virus with a wide host range belonging to a new subgroup for chickens was isolated from meat-type chicken lines. The virus, of which HPRS-103 strain is the prototype, was of low oncogenicity in chickens but appeared to behave like an exogenous leukosis virus. Neutralizing antibodies to the virus were found in three of five meat-type chicken lines, but not in seven layer lines. The virus and its Rous sarcoma virus pseudotype did not replicate in, or transform, mammalian cells.",virus antibody;animal cell;article;Avian leukosis virus;chicken;nonhuman;pathogenicity;priority journal;virus classification;virus isolation,"Payne, L. N.;Brown, S. R.;Bumstead, N.;Howes, K.;Frazier, J. A.;Thouless, M. E.",1991,,,0
1631,"Host range of Rous sarcoma virus pseudotype RSV(HPRS-103) in 12 avian species: Support for a new avian retrovirus envelope subgroup, designated J","The host ranges of the Rous sarcoma virus (RSV) pseudotype RSV(HPRS-103) of a novel avian leukosis virus (ALV), strain HPRS-103, and representative RSV pseudotypes of subgroups A to F, have been determined in embryo fibroblasts from 12 avian species. Domestic fowl, red jungle fowl, Sonnerat's jungle fowl and turkey were susceptible to infection by RSV(HPRS-103); ring-necked pheasant, Japanese green pheasant, golden pheasant, Japanese quail, guinea-fowl, Peking duck, Muscovy duck and goose were resistant. The host range pattern of RSV(HPRS-103) differs from those of viruses of subgroups A to G and I, and provides support for placing the HPRS-103 strain of ALV in a new envelope subgroup, designated J.",animal cell;article;Avian leukosis virus;chicken;duck;embryo;fibroblast;fowl;goose;host;nonhuman;priority journal;quail;Retroviridae;Rous sarcoma virus;turkey (bird);virus cell interaction;virus classification;virus infectivity;virus typing,"Payne, L. N.;Howes, K.;Gillespie, A. M.;Smith, L. M.",1992,,,0
1632,Limited evidence of trans-hemispheric movement of avian influenza viruses among contemporary North American shorebird isolates,"Migratory routes of gulls, terns, and shorebirds (Charadriiformes) are known to cross hemispheric boundaries and intersect with outbreak areas of highly pathogenic avian influenza (HPAI). Prior assessments of low pathogenic avian influenza (LPAI) among species of this taxonomic order found some evidence for trans-hemispheric movement of virus genes. To specifically clarify the role of shorebird species in the trans-hemispheric movement of influenza viruses, assess the temporal variation of Eurasian lineages observed previously among North American shorebirds, and evaluate the necessity for continued sampling of these birds for HPAI in North America, we conducted a phylogenetic analysis of >700 contemporary sequences isolated between 2000 and 2008. Evidence for trans-hemispheric reassortment among North American shorebird LPAI gene segments was lower (0.88%) than previous assessments and occurred only among eastern North American isolates. Furthermore, half of the reassortment events occurred in just two isolates. Unique phylogenetic placement of these samples suggests secondary infection and or involvement of other migratory species, such as gulls. Eurasian lineages observed in North American shorebirds before 2000 were not detected among contemporary samples, suggesting temporal variation of LPAI lineages.",Animal Migration;Animals;*Charadriiformes/vi [Virology];Influenza A virus/cl [Classification];Influenza A virus/ge [Genetics];*Influenza A virus/ip [Isolation & Purification];Influenza in Birds/ep [Epidemiology];*Influenza in Birds/tm [Transmission];*Influenza in Birds/vi [Virology];Molecular Sequence Data;North America/ep [Epidemiology];Phylogeny;Viral Proteins/ge [Genetics];0 (Viral Proteins),"Pearce, J. M.;Ramey, A. M.;Ip, H. S.;Gill, R. E., Jr.",2010,Mar,,0
1633,Viral recombination blurs taxonomic lines: Examination of single-stranded DNA viruses in a wastewater treatment plant,"Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a broad range of hosts. To examine this complex collection of viruses, full-length genomes of circular ssDNA viruses were isolated from a wastewater treatment facility using a combination of sucrose-gradient size selection and rolling-circle amplification and sequenced on an Illumina MiSeq. Single-stranded DNA viruses are among the least understood groups of microbial pathogens due to genomic biases and culturing difficulties, particularly compared to the larger, more often studied dsDNA viruses. However, the group contains several notable well-studied examples, including agricultural pathogens which infect both livestock and crops (Circoviridae and Geminiviridae), and model organisms for genetics and evolution studies (Microviridae). Examination of the collected viral DNA provided evidence for 83 unique genotypic groupings, which were genetically dissimilar to known viral types and exhibited broad diversity within the community. Furthermore, although these genomes express similarities to known viral families, such as Circoviridae, Geminiviridae, and Microviridae, many are so divergent that they may represent new taxonomic groups. This study demonstrated the efficacy of the protocol for separating bacteria and large viruses from the sought after ssDNA viruses and the ability to use this protocol to obtain an in-depth analysis of the diversity within this group.",article;Circoviridae;controlled study;Geminiviridae;gene amplification;gene expression;gene library;gene mapping;genetic polymorphism;microbial diversity;Microviridae;nonhuman;sequence alignment;single-stranded DNA virus;taxonomic rank;virus genome;virus identification;virus isolation;virus recombination;waste water treatment plant,"Pearson, V. M.;Caudle, S. B.;Rokyta, D. R.",2016,,10.7717/peerj.2585,0
1634,First finding of genetic and antigenic diversity in 1b-BVDV isolates from Argentina,"Infection with Bovine Viral Diarrhea Viruses (BVDV) in cattle results in a wide range of clinical manifestations, ranging from mild respiratory disease to fetal death and mucosal disease, depending on the virulence of the virus and the immune and reproductive status of the host. In this study 30 Argentinean BVDV isolates were characterized by phylogenetic analysis. The isolates were genotyped based on comparison of the 5' untranslated region (5' UTR) and the E2 gene. In both phylogenetic trees, 76% of the viruses were assigned to BVDV 1b, whereas BVDV 1a, 2a and 2b were also found. Eight of the BVDV 1b isolates were further characterized by cross-neutralization tests using guinea pig antisera and sera from bovines vaccinated with two different commercial vaccines. The results demonstrated the presence of a marked antigenic diversity among Argentinean BVDV isolates and suggest the need to incorporate BVDV 1b isolates in diagnostic strategies. © 2013 Elsevier Ltd.",glycoprotein E2;5' untranslated region;adult;animal cell;animal tissue;antigenic variation;Argentina;article;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 1a;Bovine viral diarrhea virus 1b;Bovine viral diarrhea virus 2a;Bovine viral diarrhea virus 2b;bovine;controlled study;E2 gene;fetus;genetic variability;genotype;guinea pig;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;unindexed sequence;virus isolation;virus neutralization,"Pecora, A.;Malacari, D. A.;Ridpath, J. F.;Perez Aguirreburualde, M. S.;Combessies, G.;Odeón, A. C.;Romera, S. A.;Golemba, M. D.;Wigdorovitz, A.",2014,,10.1016/j.rvsc.2013.11.004,0
1635,Neuraminidase-inhibition assay for the identification of influenza A virus neuraminidase subtype or neuraminidase antibody specificity,"The neuraminidase-inhibition (NI) assay is a laboratory procedure for the identification of the neuraminidase (NA) glycoprotein subtype in influenza viruses or the NA subtype specificity of antibodies to influenza virus. A serological procedure for subtyping the NA glycoprotein is critical for the identification and classification of avian influenza (AI) viruses. The macro-procedure was first described in 1961 by D. Aminoff et al. [2] and was later modified to a microtiter plate procedure (micro-NI) by Van Deusen et al. [4]. The micro-NI procedure reduces the quantity of reagents required, permits the antigenic classification of many isolates simultaneously, and eliminates the spectrophotometric interpretation of results. Although the macro-NI has been shown to be more sensitive than the micro-NI, the micro-NI test is very suitable for testing sera for the presence of NA antibodies and has proven to be a practical and rapid method for virus classification. This chapter will provide an overview of the USDA-validated micro-NI procedure for the identification of subtype-specific NA in AIV and antibodies.","Animals;*Antibody Specificity/im [Immunology];Birds;*Influenza A virus/en [Enzymology];Influenza A virus/im [Immunology];Influenza in Birds/vi [Virology];Models, Biological;Neuraminidase/im [Immunology];*Neuraminidase/me [Metabolism]","Pedersen, J. C.",2008,,,0
1636,Phylogenetic Relationships among Virulent Newcastle Disease Virus Isolates from the 2002-2003 Outbreak in California and Other Recent Outbreaks in North America,"Isolates from the 2002-2003 virulent Newcastle disease virus (v-NDV) outbreak in southern California, Nevada, Arizona, and Texas in the United States were compared to each other along with recent v-NDV isolates from Mexico and Central America and reference avian paramyxovirus type 1 strains. Nucleotide sequencing and phylogenetic analyses were conducted on a 1,195-base genomic segment composing the 3′ region of the matrix (M) protein gene and a 5′ portion of the fusion (F) protein gene including the M-F intergenic region. This encompasses coding sequences for the nuclear localization signal of the M protein and the F protein cleavage activation site. A dibasic amino acid motif was present at the predicted F protein cleavage activation site in all v-NDVs, including the California 2002-2003, Arizona, Nevada, Texas, Mexico, and Central America isolates. Phylogenetic analyses demonstrated that the California 2002-2003, Arizona, Nevada, and Texas viruses were most closely related to isolates from Mexico and Central America. An isolate from Texas obtained during 2003 appeared to represent a separate introduction of v-NDV into the United States, as this virus was even more closely related to the Mexico 2000 isolates than the California, Arizona, and Nevada viruses. The close phylogenetic relationship between the recent 2002-2003 U.S. v-NDV isolates and those viruses from countries geographically close to the United States warrants continued surveillance of commercial and non-commercial poultry for early detection of highly virulent NDV.",fusion protein;matrix protein;spacer DNA;article;bird disease;controlled study;epidemic;geographic distribution;Newcastle disease virus;nonhuman;North America;nuclear localization signal;nucleotide sequence;Paramyxoviridae;phylogeny;priority journal;protein degradation;protein motif;sequence analysis;United States;virus detection;virus genome;virus isolation;virus virulence,"Pedersen, J. C.;Senne, D. A.;Woolcock, P. R.;Kinde, H.;King, D. J.;Wise, M. G.;Panigrahy, B.;Seal, B. S.",2004,,10.1128/jcm.42.5.2329-2334.2004,0
1637,"Emerging and reemerging enterovirus diseases: From poliomyelitis to hand, foot and mouth disease","Several picornaviruses (Picornaviridae) are currently attracting interest without the need of being ""emergent"". The Parechovirus genus, validated 40 years after the discovery of the first two members (""echoviruses 22 and 23"") includes neurotropic viruses whose molecular diagnosis demonstrated the involvement in infant meningitis and newborn sepsis, in particular type 3. Improvements in multiplex molecular diagnosis of respiratory infections - thanks to the Influenza AH1N1pdm2009 pandemy - showed that rhinoviruses may be involved in severe forms. The risk of the re-emergence of poliomyelitis in Europe, after an 11-year period of elimination, is a serious threat, owing to the circulation of the wild-type poliovirus in the Middle East and Africa because of conflicts, population displacements and poverty. The current widespread epidemics of hand-foot-mouth disease and/or meningitis infections due to enterovirus 71, with fatal encephalitis and cardio-pulmonary failure, are clear evidence of its emergence in South-East Asia. Although uncommon in Europe and less frequently incriminated than coxsackieviruses A6 and A10 in hand-foot-mouth disease, EV71 represents a real risk for the future. Extensive genotyping of the enteroviruses by the Enterovirus Surveillance Network should ward off these two potential risks of emergence/reemergence.",Africa;Enterovirus;coxsackie virus a10;Coxsackie virus A6;disease re-emergence;echo virus 22;Echo virus 23;encephalitis;Enterovirus A71;epidemic;Europe;genotype;hand foot and mouth disease;human;infant disease;infection risk;lung insufficiency;meningitis;Middle East;molecular diagnosis;newborn sepsis;nonhuman;poliomyelitis;Poliomyelitis virus;poverty;review;Rhinovirus;Southeast Asia;viral clearance;viral respiratory tract infection;wild type,"Peigue-Lafeuille, H.;Mirand, A.;Archimbaud, C.;Bailly, J. L.;Henquell, C.",2014,,10.1684/vir.2014.0563,0
1638,"Cocirculation of avian H9N2 and contemporary ""human"" H3N2 influenza A viruses in pigs in southeastern China: Potential for genetic reassortment?","Pigs are permissive to both human and avian influenza viruses and have been proposed to be an intermediate host for the genesis of pandemic influenza viruses through reassortment or adaptation of avian viruses. Prospective virological surveillance carried out between March 1998 and June 2000 in Hong Kong, Special Administrative Region, People's Republic of China, on pigs imported from southeastern China, provides the first evidence of interspecies transmission of avian H9N2 viruses to pigs and documents their cocirculation with contemporary human H3N2 (A/Sydney/5/97-like, Sydney97-like) viruses. All gene segments of the porcine H9N2 viruses were closely related to viruses similar to chicken/Beijing/1/94 (H9N2), duck/Hong Kong/Y280/97 (H9N2), and the descendants of the latter virus lineage. Phylogenetic analysis suggested that repeated interspecies transmission events had occurred from the avian host to pigs. The Sydney97-like (H3N2) viruses isolated from pigs were related closely to contemporary human H3N2 viruses in all gene segments and had not undergone genetic reassortment. Cocirculation of avian H9N2 and human H3N2 viruses in pigs provides an opportunity for genetic reassortment leading to the emergence of viruses with pandemic potential.",article;chicken;China;gene rearrangement;Influenza A virus;nonhuman;nucleotide sequence;phylogeny;priority journal;pig;virus isolation;virus transmission,"Peiris, J. S. M.;Guan, Y.;Markwell, D.;Ghose, P.;Webster, R. G.;Shortridge, K. F.",2001,,10.1128/jvi.75.20.9679-9686.2001,0
1639,The origin of novel avian influenza a (H7N9) and mutation dynamics for its human-to-human transmissible capacity,"In February 2013, H7N9 (A/H7N9/2013-China), a novel avian influenza virus, broke out in eastern China and caused human death. It is a global priority to discover its origin and the point in time at which it will become transmittable between humans. We present here an interdisciplinary method to track the origin of H7N9 virus in China and to establish an evolutionary dynamics model for its human-to-human transmission via mutations. After comparing influenza viruses from China since 1983, we established an A/H7N9/2013-China virus evolutionary phylogenetic tree and found that the human instances of virus infection were of avian origin and clustered into an independent line. Comparing hemagglutinin (HA) and neuraminidase (NA) gene sequences of A/H7N9/2013-China viruses with all human-to-human, avian, and swine influenza viruses in China in the past 30 years, we found that A/H7N9/2013-China viruses originated from Baer's Pochard H7N1 virus of Hu Nan Province 2010 (HA gene, EPI: 370846, similarity with H7N9 is 95.5%) and duck influenza viruses of Nanchang city 2000 (NA gene, EPI: 387555, similarity with H7N9 is 97%) through genetic re-assortment. HA and NA gene sequence comparison indicated that A/H7N9/2013-China virus was not similar to human-to-human transmittable influenza viruses. To simulate the evolution dynamics required for human-to-human transmission mutations of H7N9 virus, we employed the Markov model. The result of this calculation indicated that the virus would acquire properties for human-to-human transmission in 11.3 years (95% confidence interval (CI): 11.2-11.3, HA gene). © 2014 Peng et al.",Influenza virus hemagglutinin;virus sialidase;amino acid sequence;article;evolution;gene mutation;gene sequence;hemagglutinin gene;Influenza A virus (H7N9);neuraminidase gene;nonhuman;phylogenetic tree;virus transmission,"Peng, J.;Yang, H.;Jiang, H.;Lin, Y. X.;Lu, C. D.;Xu, Y. W.;Zeng, J.",2014,,10.1371/journal.pone.0093094,0
1640,"Analysis of the entire genomes of thirteen TT virus variants classifiable into the fourth and fifth genetic groups, isolated from viremic infants","TT virus (TTV) DNA in serum samples obtained from 24 TTV-infected infants was amplified by polymerase chain reaction (PCR) with inverse primers derived from the untranslated region. The amplified PCR products were molecularly cloned; six clones each were analyzed. Seventy-six (53%) of the 144 TTV clones were classified into group 4 (YONBAN isolates), and 22 (15%) into a novel genetic group (group 5). The TTV clones in group 4 were classified into 9 types, and those in group 5 into 4 types. The entire nucleotide sequence of one representative clone each from the 13 types were determined; they comprised 3570-3770 nucleotides, and had poor homology to TTVs of groups 1-3 (TA278, PMV and SANBAN isolates). A phylogenetic tree based on the entire nucleotide sequence of open reading frame 1 confirmed the presence of five distinct clusters separated by a bootstrap value of 100%. Analysis of 13 TTV variants demonstrated preservation of the genomic organization and transcription profile in all TTV groups. TTV group 4 was detected in 54% or 72% of 7-to-12-month-old infants in Japan and China, respectively, which is comparable with that among adults in the respective country, indicating early and frequent acquisition of this TTV group in infancy.",ENTIRE NUCLEOTIDE-SEQUENCES;CHICKEN ANEMIA VIRUS;POSTTRANSFUSION;HEPATITIS;DIFFERENT GENOTYPES;UNKNOWN ETIOLOGY;MESSENGER-RNA;DNA;GENOME;MINI VIRUS;INFECTION;HETEROGENEITY,"Peng, Y. H.;Nishizawa, T.;Takahashi, M.;Ishikawa, T.;Yoshikawa, A.;Okamoto, H.",2002,,,0
1641,Maedi-visna virus infection in sheep: a review,"The maedi-visna virus (MVV) is classified as a lentivirus of the retroviridae family. The genome of MVV includes three genes: gag, which encodes for group-specific antigens; pol, which encodes for reverse transcriptase, integrase, RNAse H, protease and dUTPase and env, the gene encoding for the surface glycoprotein responsible for receptor binding and entry of the virus into its host cell. In addition, analogous to other lentiviruses, the genome contains genes for regulatory proteins, i.e. vif, rev and tat. The coding regions of the genome are flanked by long terminal repeats (LTR) which play a crucial role in the replication of the viral genome and provide binding sites for cellular transcription factors. The organs targeted by MVV are, in descending order of importance, the lungs, mammary glands, joints and the brain. In these organs, the virus replicates in mature macrophages and induces slowly progressing inflammatory lesions containing B and T lymphocytes. The clinical signs of MVV infection, i.e. dyspnea, loss of weight, mastitis and arthritis, are related to the location of these lesions. Infection with MVV induces the formation of antibodies which can be detected by agar gel immunodiffusion, ELISA and the serum neutralization assay. As neither antiviral treatment nor vaccination is available, diagnostic tests are the backbone of most of the schemes implemented to prevent the spread of MVV. However, since current serological assays are still lacking in sensitivity and specificity, molecular biological methods are being developed permitting the detection of virus in peripheral blood, milk and tissue samples. Future research will have to focus on both the development of new diagnostic tests and a better understanding of the pathogenesis of MVV infection.",virus antibody;virus DNA;viral protein;virus RNA;animal;blood;disease transmission;genetic variability;genetics;immunology;physiology;review;sheep;sheep disease;virology;virus genome;Visna virus,"Pépin, M.;Vitu, C.;Russo, P.;Mornex, J. F.;Peterhans, E.",1998,,,0
1642,Identification and molecular characterization of Orf virus in Argentina,"Orf virus (ORFV) is the etiological agent of contagious ecthyma (CE), a pustular dermatitis of sheep and goats. Outbreaks of ORFV have been observed in all geographical regions of the world, including Argentina. The origin and identity of Argentinian ORFVs are unknown, and no comparative or phylogenetic studies of these viruses have been performed. In this study, we described the sequencing and analysis of five ORFV molecular markers: a partial B2L gene (ORF011), VIR (ORF020), an envelope mature protein (ORF109), vIL10 (ORF127), and GIF (ORF117) from two particular Argentinian outbreaks of CE.",Argentina;article;controlled study;gene sequence;genetic identification;genetic marker;nonhuman;nucleotide sequence;Orf virus;ORF011 gene;ORF020 gene;ORF109 gene;ORF117 gene;ORF127 gene;phylogeny;priority journal;unindexed sequence;virus gene,"Peralta, A.;Robles, C.;Martínez, A.;Alvarez, L.;Valera, A.;Calamante, G.;König, G. A.",2015,,10.1007/s11262-015-1189-6,0
1643,Avian influenza virus isolated in wild waterfowl in Argentina: Evidence of a potentially unique phylogenetic lineage in South America,"Avian influenza (AI) viruses have been sporadically isolated in South America. The most recent reports are from an outbreak in commercial poultry in Chile in 2002 and its putative ancestor from a wild bird in Bolivia in 2001. Extensive surveillance in wild birds was carried out in Argentina during 2006-2007. Using RRT-PCR, 12 AI positive detections were made from cloacal swabs. One of those positive samples yielded an AI virus isolated from a wild kelp gull (Larus dominicanus) captured in the South Atlantic coastline of Argentina. Further characterization by nucleotide sequencing reveals that it belongs to the H13N9 subtype. Phylogenetic analysis of the 8 viral genes suggests that the 6 internal genes are related to the isolates from Chile and Bolivia. The analysis also indicates that a cluster of phylogenetically related AI viruses from South America may have evolved independently, with minimal gene exchange, from influenza viruses in other latitudes. The data produced from our investigations are valuable contributions to the study of AI viruses in South America. © 2008 Elsevier Inc. All rights reserved.",Argentina;article;controlled study;fowl;genetic analysis;Influenza virus;nonhuman;nucleotide sequence;phylogeny;priority journal;reverse transcription polymerase chain reaction;South America;virus isolation,"Pereda, A. J.;Uhart, M.;Perez, A. A.;Zaccagnini, M. E.;La Sala, L.;Decarre, J.;Goijman, A.;Solari, L.;Suarez, R.;Craig, M. I.;Vagnozzi, A.;Rimondi, A.;König, G.;Terrera, M. V.;Kaloghlian, A.;Song, H.;Sorrell, E. M.;Perez, D. R.",2008,,10.1016/j.virol.2008.06.010,0
1644,Isolation and complete genomic characterization of pandemic H1N1/2009 influenza viruses from Cuban swine herds,"The emergence of the pandemic H1N1/2009 influenza virus poses a potential global threat for human and animal health. In this study, we carried out pandemic H1N1/2009 influenza virus surveillance in swine herds in Cuba intending to determine whether the virus was circulating among pig populations. As a result we describe, for the first time, the detection of pandemic H1N1/2009 influenza virus in swine herds in Cuba. In addition, phylogenetic analysis and molecular characterization of three viral isolates were performed. Phylogenetic relationships confirmed that all of the eight genes of the three isolates were derived from the pandemic H1N1/2009 virus. The Cuban isolates, formed an independent cluster within the pandemic H1N1/2009 influenza strains. Different molecular markers, previously described in pandemic H1N1/2009 influenza viruses, related with adaptive evolution, viral evasion from the host-immune response, virulence and dissemination were also present in Cuban pandemic H1N1/2009 isolates. © 2012 Elsevier Ltd.",oseltamivir;2009 H1N1 influenza;amino acid sequence;amino acid substitution;animal experiment;antiviral resistance;article;biosurveillance;cluster analysis;controlled study;Cuba;evolutionary adaptation;gene expression;gene identification;gene sequence;genome analysis;genomics;HA gene;herd;immune evasion;Influenza A virus (H1N1);M gene;mutational analysis;NA gene;nonhuman;NP gene;NS gene;nucleotide sequence;PA gene;PB1 gene;PB2 gene;phylogeny;population genetics;swine disease;virus cell interaction;virus detection;virus gene;virus genome;virus identification;virus isolation;virus transmission;virus virulence,"Pérez, L. J.;Perera, C. L.;Vega, A.;Frías, M. T.;Rouseaux, D.;Ganges, L.;Nuñez, J. I.;Díaz de Arce, H.",2013,,10.1016/j.rvsc.2012.11.018,0
1645,Hepatitis E: An emerging disease,"Currently, the infection with the hepatitis E virus represents the most frequent cause for acute hepatitis and jaundice in the world. According to WHO estimations, around two billion people, representing one third of the world's population, live in endemic areas for HEV and, therefore, are at risk of infection. In developed countries, the circulation of the virus in both human and animal (swine, boar, deer) sewage has been confirmed; however, the incidence rate is low compared to that of developing countries where outbreaks of acute hepatitis transmitted via the fecal-oral route are originated, more frequently in the flooding season or after natural disasters, combined with deficient sanitary conditions.There are currently 4 known genotypes of HEV. Genotypes 1 and 2 are isolated in all human epidemic outbreaks in developing countries, while genotypes 3 and 4 are isolated not only in humans but also in animals, in both developing and industrialized countries. These data support genotypes 3 and 4 having zoonotic nature. The diagnosis of this disease is based in the detection of anti-HEV IgG and IgM in blood serum using enzyme-linked immunosorbent methods. However, the method that best confirms the diagnosis is the RT-PCR, which detects HEV RNA in blood serum and also provides the genotype. The clinical course is generally that of an acute hepatitis which in some cases may require hospitalization and that, in transplant patients or HIV infected individuals can become a chronic hepatitis. Furthermore, the virus constitutes an important risk for pregnant women. The hepatitis E can present a wide range of symptoms, from a subclinical case to chronic liver disease with extrahepatic manifestations. For this reason, the diagnostic is challenging if no differential diagnosis is included. There is no specific antiviral drug for hepatitis E, but satisfactory results have been observed in some patients treated with pegylated interferon alfa2a and/or ribavirin.This revision is an update of all the molecular, epidemiological, clinic and preventive knowledge on this emergent disease up to date.",hepatitis E vaccine;immunoglobulin G antibody;immunoglobulin M antibody;peginterferon alpha2a;ribavirin;virus RNA;acute hepatitis;antibody blood level;chronic hepatitis;chronic liver disease;clinical feature;comorbidity;developed country;developing country;differential diagnosis;disease course;environmental sanitation;enzyme linked immunosorbent assay;epidemic;flooding;gene isolation;genotype;hepatitis E;Hepatitis E virus;hospitalization;human;immune deficiency;incidence;industrialization;infection risk;jaundice;molecular biology;natural disaster;nonhuman;pathogenesis;phylogeny;pregnant woman;reverse transcription polymerase chain reaction;review;risk assessment;virus classification;virus genome;virus replication;virus transmission;virus typing;World Health Organization;zoonosis,"Pérez-Gracia, M. T.;Suay, B.;Mateos-Lindemann, M. L.",2014,,10.1016/j.meegid.2014.01.002,0
1646,Y155H amino acid substitution in influenza A(H1N1) pdm09 viruses does not confer a phenotype of reduced susceptibility to neuraminidase inhibitors,"The Y155H amino acid substitution in the neuraminidase gene (NA) has previously been associated with highly reduced inhibition by neuraminidase inhibitors in the seasonal H1N1 influenza A virus which circulated in humans before the 2009 pandemic. During the 2012/13 epidemic season in Spain, two A(H1N1) pdm09 viruses bearing the specific Y155H substitution in the NA were detected and isolated from two patients diagnosed with severe respiratory syndrome and pneumonia requiring admission to the intensive care unit. Contrary to what was observed in the seasonal A(H1N1) viruses, neither of the Y155H A(H1N1) pdm09 viruses described here showed a phenotype of reduced inhibition by NAIs as determined by the neuraminidase enzyme inhibition assay (MUNANA). High-throughput sequencing of the NA of both Y155H viruses showed that they were composed to > 99% of H155 variants. We believe that this report can contribute to a better understanding of the biological significance of amino acid substitutions in the neuraminidase protein with regard to susceptibility of influenza viruses to neuraminidase inhibitors. This is of critical importance for optimal management of influenza disease patients.",OSELTAMIVIR-RESISTANT 2009;PANDEMIC H1N1 2009;DRUG SUSCEPTIBILITY;NORTH-CAROLINA;SWINE-ORIGIN;A VIRUS;TRANSMISSION;ZANAMIVIR;CHILDREN;CLUSTER,"Perez-Sautu, U.;Pozo, F.;Cuesta, I.;Monzon, S.;Calderon, A.;Gonzalez, M.;Molinero, M.;Lopez-Miragaya, I.;Rey, S.;Canizares, A.;Rodriguez, G.;Gonzalez-Velasco, C.;Lackenby, A.;Casas, I.",2014,Jul,,0
1647,Molecular characterization of the glycoprotein genes of H5N1 influenza A viruses isolated in Israel and the Gaza Strip during 2006 outbreaks,"Highly pathogenic H5N1 avian influenza A viruses (AIV) have caused outbreaks among domestic poultry and wild aquatic birds in many Asian, European, and African countries since 1997. In March 2006 an avian H5N1 influenza A virus was isolated from poultry in Israel. In the present study we molecularly characterized the hemagglutinin (HA) and neuraminidase (NA) genes of eleven H5N1 viruses isolated from domestic poultry in Israel and Gaza in March-April 2006. Phylogenetic analysis of the HA and NA genes showed that the Israeli and Gazian viruses were closely related to viruses isolated in Egypt in 2006. © 2007 Springer Science+Business Media, LLC.",glycoprotein;hemagglutinin;sialidase;article;domestic animal;genetic trait;Influenza A virus (H5N1);Israel;nonhuman;nucleotide sequence;phylogeny;poultry;priority journal;virus isolation,"Perk, S.;Banet-Noach, C.;Golender, N.;Simanov, L.;Rozenblut, E.;Nagar, S.;Pokamunski, S.;Pirak, M.;Tendler, Y.;García, M.;Panshin, A.",2007,,10.1007/s11262-007-0120-1,0
1648,"Phylogenetic analysis of hemagglutinin, neuraminidase, and nucleoprotein genes of H9N2 avian influenza viruses isolated in Israel during the 2000-2005 epizootic","The first two isolates of H9N2 influenza virus in Israel were collected from turkey and chicken hosts in May 2000. The actual epizootic of the H9N2 virus started in December 2001, after a 1.5-year period of silence, and still continues. A total of more than 500 isolations from turkeys and chickens were registered during the outbreaks. The present study has revealed some genetic peculiarities among the local isolates, namely: all the isolates belong to the same G1-like phylogenetic lineage, within which they form a single group, which, in turn, is divided into three subgroups in the cases of the HA and NP genes, and two subgroups in the case of the NA gene. The results present a basis for suggesting the existence of two parallel evolutionary trends originating from the same local ""prototype"" isolate. © 2007 Elsevier Ltd. All rights reserved.",Influenza virus hemagglutinin;virus nucleoprotein;virus sialidase;article;chicken;controlled study;Influenza A virus (H9N2);Israel;molecular evolution;molecular phylogeny;nonhuman;nucleotide sequence;turkey (bird);viral genetics;virus gene;virus isolation,"Perk, S.;Golender, N.;Banet-Noach, C.;Shihmanter, E.;Pokamunsky, S.;Pirak, M.;Tendler, Y.;Lipkind, M.;Panshin, A.",2009,,10.1016/j.cimid.2007.06.008,0
1649,Henipavirus receptor usage and tropism,"Nipah (NiV) and Hendra (HeV) viruses are the deadliest human pathogens within the Paramyxoviridae family, which include human and animal pathogens of global biomedical importance. NiV and HeV infections cause respiratory and encephalitic illness with high mortality rates in humans. Henipaviruses (HNV) are the only Paramyxoviruses classified as biosafety level 4 (BSL4) pathogens due to their extreme pathogenicity, potential for bioterrorism, and lack of licensed vaccines and therapeutics. HNV use ephrin-B2 and ephrin-B3, highly conserved proteins, as viral entry receptors. This likely accounts for their unusually broad species tropism, and also provides opportunities to study how receptor usage, cellular tropism, and end-organ pathology relates to the pathobiology of HNV infections. The clinical and pathologic manifestations of NiV and HeV virus infections are reviewed in the chapters by Wong et al. and Geisbert et al. in this issue. Here, we will review the biology of the HNV receptors, and how receptor usage relates to HNV cell tropism in vitro and in vivo. © 2012 Springer-Verlag Berlin Heidelberg.",ephrin B2;ephrin B3;virus receptor;biological warfare;clinical feature;Hendra virus;Hendra virus infection;Henipavirus;Henipavirus infection;human;in vitro study;in vivo study;molecular biology;mortality;Nipah virus;Nipah virus infection;nonhuman;Paramyxoviridae;priority journal;protein expression;protein localization;regulatory mechanism;review;symptom;viral respiratory tract infection;viral tropism;virus attachment;virus cell interaction;virus classification;virus encephalitis;virus entry;virus particle;virus virulence,"Pernet, O.;Wang, Y. E.;Lee, B.",2012,,10.1007/82-2012-222,0
1650,Biological and phylogenetic characterization of virulent Newcastle disease virus circulating in Mexico,"In 2002-2003, velogenic Newcastle Disease Virus outbreaks, closely related to the Mexican isolates, were confirmed in the United States (U.S.) in southern California, Arizona, Nevada, and Texas. In this report, virulent NDVs isolated in Mexico between 1998 and 2006 were subjected to biologic characterization, using standard pathogenicity tests, and to phylogenetic analysis. Chicken embryo mean death time (MDT) test results ranged from 39.7 to 61.5 hours, and intracerebral pathogenicity index (ICPI) values were between 1.59 and 1.94, compared to a possible maximum value of 2.0. These isolates showed a dibasic amino acid motif at the fusion protein cleavage site sequence required for host systemic replication. Phylogenetic analysis indicated that the Mexican virulent NDVs belong to the class II, genotype V viruses and can be clearly divided in two groups as follows: isolates from 1998 to 2001 with close epidemiologic relationship with the latest U.S. NDV outbreaks, and phylogenetically distinct viruses, isolated from 2004 to 2006, which showed higher virulence. The assessment of the evolution of viruses from Mexico and other neighboring countries will aid in the U.S surveillance efforts for early detection of highly virulent NDV.",primer DNA;virus fusion protein;animal;article;biological model;chick embryo;chicken;comparative study;DNA sequence;genetics;Mexico;molecular genetics;Newcastle disease virus;nucleotide sequence;pathogenicity;phylogeny;reverse transcription polymerase chain reaction;statistical model;virology;virulence,"Perozo, F.;Merino, R.;Afonso, C. L.;Villegas, P.;Calderon, N.",2008,,10.1637/8276-022908-Reg.1,0
1651,The antigen-specific cell-mediated immune response in mice is suppressed by infection with pathogenic lyssaviruses,"Responsiveness of T cells (RTC) was studied in BALB/c mice intramuscularly infected with various lyssaviruses. After infection by this peripheral route, two types of viruses could be classified according to their effects: 1) pathogenic viruses, including fixed rabies Pasteur virus (serogenotype 1) and wild viruses belonging to serogenotype 1 (from a rabid fox in France and from a cow infected by a vampire bat in Brazil) or to serogenotype 5 (European bat lyssavirus 1); and 2) non-pathogenic viruses, including Mokola virus (serogenotype 3). RTC was tested by analysing in vitro the capacity of splenic T cells from infected BALB/c mice to produce cytokines after antigenic (purified lyssavirus antigens) or polyclonal stimulation (concanavalin A). Cytokine production was followed by assaying the biological activity of interteukin-2 and by testing for interleukin-2, interleukin-4 and interferon-γ (IL2, IL4 and IFNγ) messenger RNAs (mRNA) by transcription into complementary DNA and amplification by the polymerase chain reaction. The initial biologically active IL2 and cytokine mRNA production was observed in mice infected with pathogenic or non-pathogenic lyssaviruses. Only mice with symptoms (infected with pathogenic viruses) lost the capacity to produce cytokines in vitro after antigen-specific stimulation. No such loss was observed after polyclonal stimulation. In mice peripherally infected with non-pathogenic viruses, no loss was observed after stimulation with lyssavirus antigens. Thus, infection with pathogenic lyssaviruses by the peripheral route induces in BALB/c mice a loss of T-cell responsiveness after antigen activation, but not after polyclonal activation.",concanavalin A;cytokine;interleukin 2;messenger RNA;animal experiment;article;cellular immunity;controlled study;female;in vitro study;mouse;nonhuman;polymerase chain reaction;priority journal;rabies;Rabies virus;T lymphocyte;T lymphocyte activation,"Perrin, P.;Tino De Franco, M.;Jallet, C.;Fouque, F.;Morgeaux, S.;Tordo, N.;Colle, J. H.",1996,,10.1016/0923-2516(96)82287-4,0
1652,Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses,"G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter. Folding of HIV-1 LTR G4s inhibits viral transcription; stabilization by G4 ligands intensifies this effect. Cellular proteins modulate viral transcription by inducing/unfolding LTR G4s. We here expanded our investigation on the presence of LTR G4s to all lentiviruses. G4s in the 5'-LTR U3 region were completely conserved in primate lentiviruses. A G4 was also present in a cattle-infecting lentivirus. All other non-primate lentiviruses displayed hints of less stable G4s. In primate lentiviruses, the possibility to fold into G4s was highly conserved among strains. LTR G4 sequences were very similar among phylogenetically related primate viruses, while they increasingly differed in viruses that diverged early from a common ancestor. A strong correlation between primate lentivirus LTR G4s and Sp1/NFκB binding sites was found. All LTR G4s folded: their complexity was assessed by polymerase stop assay. Our data support a role of the lentiviruses 5'-LTR G4 region as control centre of viral transcription, where folding/unfolding of G4s and multiple recruitment of factors based on both sequence and structure may take place.",guanine quadruplex;protein binding;transcription factor Sp1;animal;binding site;classification;conserved sequence;genetics;human;Human immunodeficiency virus 1;Lentivirus;long terminal repeat;metabolism;nucleotide sequence;phylogeny;position weight matrix;promoter region,"Perrone, R.;Lavezzo, E.;Palù, G.;Richter, S. N.",2017,,10.1038/s41598-017-02291-1,0
1653,Comparison and contrast of genes and biological pathways responding to Marek's disease virus infection using allele-specific expression and differential expression in broiler and layer chickens,"Background: Marek's disease (MD) is a commercially important neoplastic disease of chickens caused by the Marek's disease virus (MDV), a naturally occurring oncogenic alphaherpesvirus. Enhancing MD genetic resistance is desirable to augment current vaccines and other MD control measures. High throughput sequencing was used to profile splenic transcriptomes from individual F1 progeny infected with MDV at 4 days of age from both outbred broilers (meat-type) and inbred layer (egg-type) chicken lines that differed in MD genetic resistance. The resulting information was used to identify SNPs, genes, and biological pathways exhibiting allele-specific expression (ASE) in response to MDV infection in each type of chicken. In addition, we compared and contrasted the results of pathway analyses (ASE and differential expression (DE)) between chicken types to help inform on the biological response to MDV infection. Results: With 7 individuals per line and treatment group providing high power, we identified 6,132 single nucleotide polymorphisms (SNPs) in 4,768 genes and 4,528 SNPs in 3,718 genes in broilers and layers, respectively, that exhibited ASE in response to MDV infection. Furthermore, 548 and 434 genes in broilers and layers, respectively, were found to show DE following MDV infection. Comparing the datasets, only 72 SNPs and 850 genes for ASE and 20 genes for DE were common between the two bird types. Although the chicken types used in this study were genetically different, at the pathway level, both TLR receptor and JAK/STAT signaling pathways were enriched as well as exhibiting a high proportion of ASE genes, especially at the beginning of both above mentioned regulatory pathways. Conclusions: RNA sequencing with adequate biological replicates is a powerful approach to identify high confidence SNPs, genes, and pathways that are associated with transcriptional response to MDV infection. In addition, the SNPs exhibiting ASE in response to MDV infection provide a strong foundation for determining the extent to which variation in expression influences MD incidence plus yield genetic markers for genomic selection. However, given the paucity of overlap among ASE SNP sets (broilers vs. layers), it is likely that separate screens need to be incorporated for each population. Finally, comparison of gene lists obtained between these two diverse chicken types indicate the TLR and JAK/STAT signaling are conserved when responding to MDV infection and may be altered by selection of genes exhibiting ASE found at the start of each pathway. © 2013 Perumbakkam et al.; licensee BioMed Central Ltd.",Janus kinase;STAT protein;toll like receptor;allele;animal experiment;animal tissue;article;avian genetics;broiler;chicken;comparative study;controlled study;gene expression;gene identification;genetic analysis;genetic association;genetic marker;Marek disease;nonhuman;RNA sequence;signal transduction;single nucleotide polymorphism;species comparison;transcription regulation,"Perumbakkam, S.;Muir, W. M.;Black-Pyrkosz, A.;Okimoto, R.;Cheng, H. H.",2013,,10.1186/1471-2164-14-64,0
1654,Foot-and-mouth disease outbreaks due to an exotic virus serotype A lineage (A/AFRICA/G-IV) in Algeria in 2017,"This study describes the genetic characterization of serotype A viruses collected during outbreaks of foot-and-mouth disease (FMD) that occurred in Algeria in 2017. These are the first reports of clinical cases due to this serotype in the country since 1977. One complete genomic sequence (comprising 8,119 nucleotides) and three additional near-complete genomic sequences were generated. Phylogenetic analyses demonstrated that these viruses were classified within the A/AFRICA/G-IV lineage, most closely related to viruses circulating in Nigeria between 2009 and 2015. These unexpected results motivate further studies to define the precise pathways by which this viral lineage has been introduced into North Africa in order to understand risks of future disease incursions into the region.",DNA directed DNA polymerase beta;5' untranslated region;Algeria;animal experiment;animal model;antigen detection;article;cell culture;cell lineage;codon;controlled study;enzyme linked immunosorbent assay;epithelium cell;evolutionary adaptation;foot and mouth disease;gene amplification;gene replication;genetic analysis;geographic distribution;incubation temperature;maximum likelihood method;neighbor joining method;nonhuman;phylogenetic tree construction method;phylogeny;real time polymerase chain reaction;reliability;reverse transcription polymerase chain reaction;RNA extraction;sequence alignment;sequence analysis;serotype;serotyping;virus characterization;virus isolation,"Pezzoni, G.;Bregoli, A.;Grazioli, S.;Barbieri, I.;Madani, H.;Omani, A.;Sadaoui, H.;Bouayed, N.;Wadsworth, J.;Bachanek-Bankowska, K.;Knowles, N. J.;King, D. P.;Brocchi, E.",2019,,10.1111/tbed.13017,0
1655,Natural reservoirs for homologs of hepatitis C virus,"Hepatitis C virus is considered a major public health problem, infecting 2%-3% of the human population. Hepatitis C virus infection causes acute and chronic liver disease, including chronic hepatitis, cirrhosis and hepatocellular carcinoma. In fact, hepatitis C virus infection is the most frequent indication for liver transplantation and a vaccine is not available. Hepatitis C virus displays a narrow host species tropism, naturally infecting only humans, although chimpanzees are also susceptible to experimental infection. To date, there is no evidence for an animal reservoir of viruses closely related to hepatitis C virus which may have crossed the species barrier to cause disease in humans and resulted in the current pandemic. In fact, due to this restricted host range, a robust immunocompetent small animal model is still lacking, hampering mechanistic analysis of virus pathogenesis, immune control and prophylactic vaccine development. Recently, several studies discovered new viruses related to hepatitis C virus, belonging to the hepaci- and pegivirus genera, in small wild mammals (rodents and bats) and domesticated animals which live in close contact with humans (dogs and horses). Genetic and biological characterization of these newly discovered hepatitis C virus-like viruses infecting different mammals will contribute to our understanding of the origins of hepatitis C virus in humans and enhance our ability to study pathogenesis and immune responses using tractable animal models. In this review article, we start with an introduction on the genetic diversity of hepatitis C virus and then focus on the newly discovered viruses closely related to hepatitis C virus. Finally, we discuss possible theories about the origin of this important viral human pathogen. © 2014 SSCC. All rights reserved.",bat;bat Hepatitis C virus;canine Hepatitis C virus;Cercopithecidae;chimpanzee;dog;domestic animal;equine pegivirus;Flavivirus;genetic variability;gnereza Hepatitis C virus;hepatitis C;Hepatitis C virus;Hepatitis C virus subtype 1a;Hepatitis G virus;Pegivirus A;Pegivirus B;Hepatitis GB virus D;hepatitis virus;horse;host pathogen interaction;host range;human;immune response;natural host;non primate Hepatitis C virus;nonhuman;nucleotide sequence;priority journal;review;rodent;rodent pegivirus;viral tropism;virus classification;virus pathogenesis;virus replication,"Pfaender, S.;Brown, R. J. P.;Pietschmann, T.;Steinmann, E.",2014,,10.1038/emi.2014.19,0
1656,A novel astrovirus associated with encephalitis and ganglionitis in domestic sheep,"In June 2013, a 4-year-old Welsh Mountain ewe and in March 2014 a 10-day-old lamb of the same breed and the same flock presented progressive neurological signs including depressed sensorium, tremor, and unusual behaviour. Neuropathological examination of the brain and spinal cord detected non-suppurative polioencephalomyelitis and dorsal root ganglionitis, characteristic of a neurotropic viral agent in both sheep. Metagenomic analysis of different tissue samples from both animals identified a novel Ovine Astrovirus (OvAstV). The presence of viral genome in the central nervous system was confirmed by RT-qPCR. Although the cases presented nine months apart, the identified OvAstV shared nearly identical sequences, differing in only three nucleotide positions across the complete genome. Phylogenetic analysis revealed a close relation of OvAstV to neurotropic bovine astroviruses and an enteric OvAstV. In conclusion, these are the first reported cases of astrovirus infection in domestic sheep that were associated with encephalitis and ganglionitis.",animal;astrovirus infection;brain;female;genetics;Mamastrovirus;metagenomics;pathology;phylogeny;sheep;sheep disease;veterinary medicine;virology;virus encephalitis;virus genome,"Pfaff, F.;Schlottau, K.;Scholes, S.;Courtenay, A.;Hoffmann, B.;Höper, D.;Beer, M.",2017,,10.1111/tbed.12623,1
1657,"Porcine bocavirus infection associated with encephalomyelitis in a pig, Germany",,animal tissue;autopsy;blood brain barrier;Bocaparvovirus;Bocavirus infection;Classical swine fever virus;controlled study;coughing;diarrhea;encephalitis;encephalitis virus;encephalomyelitis;Enterovirus;female;fluorescence in situ hybridization;fluorescence microscopy;Germany;growth retardation;Human bocavirus;interstitial pneumonia;letter;metagenomics;Mycoplasma hyorhinis;next generation sequencing;nonhuman;panencephalitis;Parvoviridae;pathogenesis;phylogeny;piglet;polymerase chain reaction;Pseudorabies virus;Teschovirus,"Pfankuche, V. M.;Bodewes, R.;Hahn, K.;Puff, C.;Beineke, A.;Habierski, A.;Osterhaus, A. D. M. E.;Baumgärtner, W.",2016,,10.3201/eid2207.152049,1
1658,The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin,"Viral metagenomics of feces collected from 58 Peruvian children with unexplained diarrhea revealed several small circular ssDNA genomes. Two genomes related to sequences previously reported in feces from chimpanzees and other mammals and recently named smacoviruses were characterized and then detected by PCR in 1.7 % (1/58) and 19 % (11/58) of diarrheal samples, respectively. Another three genomes from a distinct small circular ssDNA viral group provisionally called pecoviruses encoded Cap and Rep proteins with <35 % identity to those in related genomes reported in human, seal, porcine and dromedary feces. Pecovirus DNA was detected in 15.5 % (9/58), 5.9 % (3/51) and 3 % (3/100) of fecal samples from unexplained diarrhea in Peru, Nicaragua and Chile, respectively. Feces containing these ssDNA genomes also contained known human enteric viral pathogens. The cellular origins of these circular ssDNA viruses, whether human cells, ingested plants, animals or fungal foods, or residents of the gut microbiome, are currently unknown.",circular DNA;virus DNA;Chile;diarrhea;feces;genetics;human;Nicaragua;Peru;phylogeny;virology;virus infection;virus genome,"Phan, T. G.;da Costa, A. C.;Del Valle Mendoza, J.;Bucardo-Rivera, F.;Nordgren, J.;O'Ryan, M.;Deng, X.;Delwart, E.",2016,,10.1007/s00705-016-2756-4,0
1659,A new gyrovirus in human feces,"A novel gyrovirus genome found in the feces of an adult with diarrhea is described. The genome shows the three expected main ORFs encoding a structural protein (VP1), nonstructural protein (VP2), and Apoptin protein (VP3), which shared identities of 41, 42, and 38 % with those of the most closely related gyrovirus proteins, respectively. Given the high divergence in its genome, this gyrovirus may be considered the prototype for a new viral species (GyV9) in the Gyrovirus genus. Because the closest relatives of this gyrovirus infect chicken, a possible dietary origin for the presence of this virus in human feces is discussed.",apoptin;structural protein;structural protein VP2;structural protein VP3;unclassified drug;virus DNA;article;chicken;diarrhea;feces;feces analysis;gene sequence;genetic code;Gyrovirus;human;metagenomics;nonhuman;nucleotide sequence;open reading frame;phylogeny;polymerase chain reaction;priority journal;virus genome,"Phan, T. G.;da Costa, A. C.;Zhang, W.;Pothier, P.;Ambert-Balay, K.;Deng, X.;Delwart, E.",2015,,10.1007/s11262-015-1210-0,0
1660,Detection of a novel circovirus PCV3 in pigs with cardiac and multi-systemic inflammation,"Background: Porcine circovirus 2 causes different clinical syndromes resulting in a significant economic loss in the pork industry. Three pigs with unexplained cardiac and multi-organ inflammation that tested negative for PCV2 and other known porcine pathogens were further analyzed. Methods: Histology was used to identify microscopic lesions in multiple tissues. Metagenomics was used to detect viral sequences in tissue homogenates. In situ hybridization was used to detect viral RNA expression in cardiac tissue. Results: In all three cases we characterized the genome of a new circovirus we called PCV3 with a replicase and capsid proteins showing 55 and 35 % identities to the genetically-closest proteins from a bat-feces associated circovirus and were even more distant to those of porcine circovirus 1 and 2. Common microscopic lesions included non-suppurative myocarditis and/or cardiac arteriolitis. Viral mRNA was detected intralesionally in cardiac cells. Deep sequencing in tissues also revealed the presence of porcine astrovirus 4 in all three animals as well as rotavirus A, porcine cytomegalovirus and porcine hemagglutinating encephalomyelitis virus in individual cases. Conclusion: The pathogenicity and molecular epidemiology of this new circovirus, alone or in the context of co-infections, warrants further investigations.",capsid protein;messenger RNA;virus RNA;animal tissue;anorexia;article;bronchiolitis;cardiac muscle cell;Circovirus;Cytomegalovirus;encephalomyelitis;gene expression;genetic analysis;Haemophilus parasuis;in situ hybridization;interstitial pneumonia;lung alveolitis;metagenomics;Mycoplasma hyorhinis;myocarditis;necrotizing arteritis;nonhuman;phylogenetic tree;Porcine circovirus 1;Porcine circovirus 2;Porcine circovirus 3;RNA sequence;Rotavirus A;sequence analysis;Streptococcus suis;synovitis;virus detection;virus genome;virus hemagglutination;weaning;body weight loss,"Phan, T. G.;Giannitti, F.;Rossow, S.;Marthaler, D.;Knutson, T.;Li, L.;Deng, X.;Resende, T.;Vannucci, F.;Delwart, E.",2016,,10.1186/s12985-016-0642-z,1
1661,Sesavirus: prototype of a new parvovirus genus in feces of a sea lion,"We describe the nearly complete genome of a highly divergent parvovirus, we tentatively name Sesavirus, from the feces of a California sea lion pup (Zalophus californianus) suffering from malnutrition and pneumonia. The 5,049-base-long genome contained two major ORFs encoding a 553-aa nonstructural protein and a 965-aa structural protein which shared closest amino acid identities of 25 and 28 %, respectively, with members of the copiparvovirus genus known to infect pigs and cows. Given the low degree of similarity, Sesavirus might be considered as prototype for a new genus with a proposed name of Marinoparvovirus in the subfamily Parvovirinae.",nonstructural protein 1;viral protein;amino acid analysis;article;feces analysis;genetic similarity;Marinoparvovirus;metagenomics;new genus;nonhuman;open reading frame;Parvoviridae;priority journal;protein analysis;protein structure;Pinnipedia;Sesavirus;taxonomic rank,"Phan, T. G.;Gulland, F.;Simeone, C.;Deng, X.;Delwart, E.",2015,,10.1007/s11262-014-1123-3,0
1662,The Fecal Viral Flora of Wild Rodents,"The frequent interactions of rodents with humans make them a common source of zoonotic infections. To obtain an initial unbiased measure of the viral diversity in the enteric tract of wild rodents we sequenced partially purified, randomly amplified viral RNA and DNA in the feces of 105 wild rodents (mouse, vole, and rat) collected in California and Virginia. We identified in decreasing frequency sequences related to the mammalian viruses families Circoviridae, Picobirnaviridae, Picornaviridae, Astroviridae, Parvoviridae, Papillomaviridae, Adenoviridae, and Coronaviridae. Seventeen small circular DNA genomes containing one or two replicase genes distantly related to the Circoviridae representing several potentially new viral families were characterized. In the Picornaviridae family two new candidate genera as well as a close genetic relative of the human pathogen Aichi virus were characterized. Fragments of the first mouse sapelovirus and picobirnaviruses were identified and the first murine astrovirus genome was characterized. A mouse papillomavirus genome and fragments of a novel adenovirus and adenovirus-associated virus were also sequenced. The next largest fraction of the rodent fecal virome was related to insect viruses of the Densoviridae, Iridoviridae, Polydnaviridae, Dicistroviriade, Bromoviridae, and Virgaviridae families followed by plant virus-related sequences in the Nanoviridae, Geminiviridae, Phycodnaviridae, Secoviridae, Partitiviridae, Tymoviridae, Alphaflexiviridae, and Tombusviridae families reflecting the largely insect and plant rodent diet. Phylogenetic analyses of full and partial viral genomes therefore revealed many previously unreported viral species, genera, and families. The close genetic similarities noted between some rodent and human viruses might reflect past zoonoses. This study increases our understanding of the viral diversity in wild rodents and highlights the large number of still uncharacterized viruses in mammals.",TICK-BORNE ENCEPHALITIS;HANTAVIRUS PULMONARY SYNDROME;SIN-NOMBRE-VIRUS;PORCINE-CIRCOVIRUS TYPE-1;HIV-INFECTED PATIENTS;PICORNA-LIKE VIRUSES;MOLECULAR CHARACTERIZATION;METAGENOMIC ANALYSIS;PUBLIC-HEALTH;PUUMALA VIRUS,"Phan, T. G.;Kapusinszky, B.;Wang, C. L.;Rose, R. K.;Lipton, H. L.;Delwart, E. L.",2011,Sep,,0
1663,A third gyrovirus species in human faeces,"Until 2011 the genus Gyrovirus in the family Circoviridae consisted of a single virus (Chicken anemia virus or CAV) causing a common immunosuppressive disease in chickens when a second gyrovirus (HGyV) was reported on the skin of 4% of healthy humans. HGyV is very closely related to a recently described chicken gyrovirus, AGV2, suggesting that they belong to the same viral species. During a viral metagenomic analysis of 100 human faeces from children with diarrhoea in Chile we identified multiple known human pathogens (adenoviruses, enteroviruses, astroviruses, sapoviruses, noroviruses, parechoviruses and rotaviruses) and a novel gyrovirus species we named GyV3 sharing <63% similarity with other gyrovirus proteins with evidence of recombination with CAV in its UTR. Gyroviridae consensus PCR revealed a high prevalence of CAV DNA in diarrhoea and normal faeces from Chilean children and faeces of USA cats and dogs, which may reflect consumption of CAV-infected/vaccinated chickens. Whether GyV3 can infect humans and/or chickens requires further studies. © 2012 SGM.",apoptin;protein VP1;protein VP2;protein VP3;single stranded DNA;virus DNA;viral protein;Adenoviridae;article;Astroviridae;Chile;diarrhea;Enterovirus;feces analysis;Gyrovirus;human;metagenomics;nonhuman;Norovirus;Parechovirus;polymerase chain reaction;priority journal;Rotavirus;Sapovirus;untranslated region,"Phan, T. G.;Li, L.;O'Ryan, M. G.;Cortes, H.;Mamani, N.;Bonkoungou, I. J. O.;Wang, C.;Leutenegger, C. M.;Delwart, E.",2012,,10.1099/vir.0.041731-0,0
1664,New astrovirus in human feces from Burkina Faso,"Background: A significant fraction of cases of diarrhea, a leading cause of childhood mortality worldwide, remain unexplained. Objectives: To identify viruses in unexplained cases of diarrhea using an unbiased metagenomics approach. Study design: Viral nucleic acids were enriched from the feces from 48 cases of unexplained diarrhea from Burkina Faso, sequenced, and compared against all known viral genomes. Results: The full genome of a highly divergent astrovirus was sequenced in a sample co-infected with parechovirus 1. RT-PCR identified a single astrovirus infection in these 48 patients indicating a low prevalence. Human astrovirus-BF34 was most closely related to mamastrovirus species 8 and 9 also found in human with which it shared 62%, 74%, and 57% amino acid identities over its protease, RNA dependent RNA polymerase and capsid proteins, respectively. Conclusions: Burkina Faso astrovirus is proposed as prototype for a novel species in the genus Mamastrovirus, here tentatively called Mamastrovirus 20, representing the fifth human astrovirus species. © 2014 Elsevier B.V.",capsid protein;RNA directed RNA polymerase;abdominal pain;acute gastroenteritis;amino acid sequence;article;Astroviridae;astrovirus infection;Burkina Faso;child;clinical article;diarrhea;DNA base composition;dog;feces analysis;fever;GenBank;health maintenance organization;human;liquid feces;metagenomics;mixed infection;nonhuman;nucleotide sequence;open reading frame;Parechovirus;phylogenetic tree;phylogeny;priority journal;protein database;reverse transcription polymerase chain reaction;start codon;pig;virus capsid;virus detection;virus particle;vomiting,"Phan, T. G.;Nordgren, J.;Ouermi, D.;Simpore, J.;Nitiema, L. W.;Deng, X.;Delwart, E.",2014,,10.1016/j.jcv.2014.03.024,0
1665,Acute Diarrhea in West African Children: Diverse Enteric Viruses and a Novel Parvovirus Genus,"Parvoviruses cause a variety of mild to severe symptoms or asymptomatic infections in humans and animals. During a viral metagenomic analysis of feces from children with acute diarrhea in Burkina Faso, we identified in decreasing prevalence nucleic acids from anelloviruses, dependoviruses, sapoviruses, enteroviruses, bocaviruses, noroviruses, adenoviruses, parechoviruses, rotaviruses, cosavirus, astroviruses, and hepatitis B virus. Sequences from a highly divergent parvovirus, provisionally called bufavirus, were also detected whose NS1 and VP1 proteins showed <39% and <31% identities to those of previously known parvoviruses. Four percent of the fecal samples were PCR positive for this new parvovirus, including a related bufavirus species showing only 72% identity in VP1. The high degree of genetic divergence of these related genomes from those of other parvoviruses indicates the presence of a proposed new Parvoviridae genus containing at least two species. Studies of the tropism and pathogenicity of these novel parvoviruses will be facilitated by the availability of their genome sequences.",HUMAN BOCAVIRUS;BOVINE PARVOVIRUS;MOLECULAR-CLONING;HYDROPS-FETALIS;STOOL SAMPLES;DNA VIRUSES;INFECTION;IDENTIFICATION;PORCINE;PARV4,"Phan, T. G.;Vo, N. P.;Bonkoungou, I. J. O.;Kapoor, A.;Barro, N.;O'Ryan, M.;Kapusinszky, B.;Wang, C. L.;Delwart, E.",2012,Oct,,0
1666,The Viruses of Wild Pigeon Droppings,"Birds are frequent sources of emerging human infectious diseases. Viral particles were enriched from the feces of 51 wild urban pigeons (Columba livia) from Hong Kong and Hungary, their nucleic acids randomly amplified and then sequenced. We identified sequences from known and novel species from the viral families Circoviridae, Parvoviridae, Picornaviridae, Reoviridae, Adenovirus, Astroviridae, and Caliciviridae (listed in decreasing number of reads), as well as plant and insect viruses likely originating from consumed food. The near full genome of a new species of a proposed parvovirus genus provisionally called Aviparvovirus contained an unusually long middle ORF showing weak similarity to an ORF of unknown function from a fowl adenovirus. Picornaviruses found in both Asia and Europe that are distantly related to the turkey megrivirus and contained a highly divergent 2A1 region were named mesiviruses. All eleven segments of a novel rotavirus subgroup related to a chicken rotavirus in group G were sequenced and phylogenetically analyzed. This study provides an initial assessment of the enteric virome in the droppings of pigeons, a feral urban species with frequent human contact. © 2013 Phan et al.",Adenoviridae;article;Asia;Astroviridae;Aviparvovirus;Caliciviridae;Circoviridae;Columba livia;Europe;feces microflora;food intake;Hong Kong;Hungary;insect virus;megrivirus;mesivirus;microbial community;nonhuman;nucleic acid amplification;nucleotide sequence;open reading frame;Parvoviridae;phylogeny;Picornaviridae;plant virus;Reoviridae;Rotavirus;sequence homology;virus genome;virus identification;virus particle;virus shedding,"Phan, T. G.;Vo, N. P.;Boros, Á;Pankovics, P.;Reuter, G.;Li, O. T. W.;Wang, C.;Deng, X.;Poon, L. L. M.;Delwart, E.",2013,,10.1371/journal.pone.0072787,0
1667,Nucleotide sequence analysis of a novel circovirus of canaries and its relationship to other members of the genus Circovirus of the family Circoviridae,"The circular, single-stranded DNA genome of a novel circovirus of canaries, tentatively named canary circovirus (CaCV), was cloned and sequenced. Sequence analysis indicated that the genome was 1952 nucleotides (nt) in size and had the potential to encode three viral proteins, including the putative capsid and replication-associated (Rep) proteins. The CaCV genome shared greatest sequence similarity (58.3% nt identity) with the newly characterized columbid circovirus (CoCV) and was more distantly related to the two porcine circovirus strains, PCV1 and PCV2, beak and feather disease virus (BFDV) and a recently isolated goose circovirus (GCV) isolate (46.8-50.9% nt identity). In common with other members of the Circovirus genus, several nt structures and amino acid motifs thought to be implicated in virus replication were identified on the putative viral strand. Phylogenetic analysis of both the capsid and Rep protein-coding regions provided further evidence that CaCV is more closely related to CoCV and BFDV and more distantly related to GCV, PCV1 and PCV2.",capsid protein;circular DNA;helicase;single stranded DNA;virus DNA;viral protein;amino acid sequence;article;Beak and feather disease virus;Serinus;Circoviridae;columbid circovirus;controlled study;gene structure;genetic code;goose circovirus;molecular cloning;nonhuman;nucleotide sequence;phylogeny;priority journal;protein motif;sequence analysis;sequence homology;pig;virus genome;virus isolation;virus replication;virus strain,"Phenix, K. V.;Weston, J. H.;Ypelaar, I.;Lavazza, A.;Smyth, J. A.;Todd, D.;Wilcox, G. E.;Raidal, S. R.",2001,,,0
1668,Wild bird's-eye view of influenza virus A(H1N1) phylogenetic evolution,"Wild bird fecal samples collected and characterized by the USDA as part of a national surveillance effort were sequenced to study the genetic relatedness of avian, swine, and human H1 and N1 subtypes. Our results find that the 2009 H1N1 human outbreak is closely related to swine virus, but falls into different clades in the H1 and N1 trees. Further, there is evidence of multiple viral genetic exchanges between birds and swine. Ongoing research across host species contributes to an understanding of the circulation of influenza viruses.",animal;article;avian influenza;bird;classification;genetics;government;human;influenza;Influenza A virus (H1N1);molecular evolution;orthomyxovirus infection;phylogeny;swine disease;United States;virology;zoonosis,"Piaggio, A. J.;Clark, L.;Franklin, A. B.;Kolokotronis, S. O.",2009,,10.1007/s10393-009-0270-9,0
1669,Full genome sequence-based comparative study of wild-type and vaccine strains of infectious laryngotracheitis virus from Italy,"Infectious laryngotracheitis (ILT) is an acute and highly contagious respiratory disease of chickens caused by an alphaherpesvirus, infectious laryngotracheitis virus (ILTV). Recently, full genome sequences of wild-type and vaccine strains have been determined worldwide, but none was from Europe. The aim of this study was to determine and analyse the complete genome sequences of five ILTV strains. Sequences were also compared to reveal the similarity of strains across time and to discriminate between wild-type and vaccine strains. Genomes of three ILTV field isolates from outbreaks occurred in Italy in 1980,2007 and 2011, and two commercial chicken embryo origin (CEO) vaccines were sequenced using the 454 Life Sciences technology. The comparison with the Serva genome showed that 35 open reading frames (ORFs) differed across the five genomes. Overall, 54 single nucleotide polymorphisms (SNPs) and 27 amino acid differences in 19 ORFs and two insertions in the UL52 and ORFC genes were identified. Similarity among the field strains and between the field and the vaccine strains ranged from 99.96% to 99.99%. Phylogenetic analysis revealed a close relationship among them, as well. This study generated data on genomic variation among Italian ILTV strains revealing that, even though the genetic variability of the genome is well conserved across time and between wild-type and vaccine strains, some mutations may help in differentiating among them and maybe involved in ILTV virulence/attenuation. The results of this study can contribute to the understanding of the molecular bases of ILTV pathogenicity and provide genetic markers to differentiate between wild-type and vaccine strains.",virus vaccine;article;comparative study;controlled study;gene insertion;gene sequence;genetic association;genetic marker;genetic variability;high throughput sequencing;Infectious laryngotracheitis virus;Italy;nonhuman;nucleotide sequence;open reading frame;phylogeny;sequence alignment;sequence analysis;single nucleotide polymorphism;viral tropism;virus attenuation;virus infectivity;virus isolation;virus strain;virus virulence;nobilis laringovac;poulvac ilt,"Piccirillo, A.;Lavezzo, E.;Niero, G.;Moreno, A.;Massi, P.;Franchin, E.;Toppo, S.;Salata, C.;Palù, G.",2016,,10.1371/journal.pone.0149529,0
1670,Evidence for presumable feline origin of sporadic G6P[9] rotaviruses in humans,"Species A rotaviruses are highly diverse and impose a substantial burden to human and animal health. Interspecies transmission between livestock, domestic animals and humans is commonly observed, but spread of animal-like rotaviruses within the human population is limited. During the continued monitoring of rotavirus strains in Germany, an unusual G6P[9] rotavirus strain was detected in feces of a child. The complete rotavirus coding sequences revealed a unique G6-P[9]-I2-R2-C2-M2-A3-N2-T3-E2-H3 genotype constellation. The virus was phylogenetically related to feline G3P[9] strains and other human G6P[9] rotaviruses of presumable zoonotic origin. Analysis of primer binding sites of G6 specific genotyping revealed further evidence of a G6P[9] feline reservoir. Moreover, substantial deficits of conventional semi-nested PCR genotyping approaches in detecting contemporary G6P[9] were revealed. Rotavirus strain GER29-14 most likely resulted from a direct or recent interspecies transmission from a cat to human. Further studies could assess nucleic acid sequences and genotype constellations of feline rotavirus to confirm the likely feline origin of sporadic human G6P[9] strains.",article;binding site;cat;G6P rotavirus;genotype;Germany;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;priority journal;Rotavirus;virus carrier;virus detection;virus strain;virus transmission;zoonosis,"Pietsch, C.;Liebert, U. G.",2018,,10.1016/j.meegid.2018.05.030,0
1671,Low-pathogenic avian influenza virus A/turkey/ Ontario/6213/1966 (H5N1) is the progenitor of highly pathogenic A/turkey/Ontario/7732/1966 (H5N9),"The first confirmed outbreak of highly pathogenic avian influenza (HPAI) virus infections in North America was caused by A/turkey/Ontario/7732/1966 (H5N9); however, the phylogeny of this virus is largely unknown. This study performed genomic sequence analysis of 11 avian influenza isolates from 1956 to 1979 for comparison with A/turkey/Ontario/7732/1966 (H5N9). Phylogenetic and genetic analyses included these viruses in combination with all known fullgenome sequences of avian viruses isolated before 1981. It was shown that a low-pathogenic avian influenza virus, A/turkey/Ontario/6213/1966 (H5N1), that had been isolated 3 months previously, was the closest known genetic relative with six genome segments of common lineage encoding the polymerase subunits PB2, PB1 and PA, nucleoprotein (NP), haemagglutinin (HA) and non-structural (NS) proteins. The lineages of these genome segments included reassortment with other North American turkey viruses that were all rooted in North American wild waterfowl with the HA gene originating from the H5N2 serotype. The phylogenies demonstrated adaptation from North American wild birds to turkeys with the possible involvement of domestic waterfowl. The turkey isolate, A/turkey/Wisconsin/1968 (H5N9), was the second most closely related poultry isolate to A/turkey/Ontario/7732/1966 (H5N9), possessing five common lineage genome segments (PB2, PB1, PA, HA and neuraminidase). The A/turkey/Ontario/6213/1966 (H5N1) virus was more virulent than A/turkey/Wisconsin/68 (H5N9) for chicken embryos and mice, indicating a greater biological similarity to A/turkey/Ontario/7732/1966 (H5N9). Thus, A/turkey/ Ontario/6213/1966 (H5N1) was identified as the closest known ancestral relative of HPAI A/ turkey/Ontario/7732/1966 (H5N9), which will serve as a useful reference virus for characterizing the early genetic and biological properties associated with the emergence of pathogenic avian influenza strains. © 2012 SGM.",hemagglutinin;nucleoprotein;animal experiment;article;waterfowl;embryo;female;gene sequence;Influenza A virus;Influenza A virus (H5N1);Influenza virus A H5N9;mouse;nonhuman;phylogeny;priority journal;sequence alignment;serotype;virus genome;virus isolation;virus strain;virus virulence,"Ping, J.;Selman, M.;Tyler, S.;Forbes, N.;Keleta, L.;Brown, E. G.",2012,,10.1099/vir.0.042895-0,0
1672,Evaluation of a droplet digital polymerase chain reaction format for DNA copy number quantification,"Droplet digital polymerase chain reaction (ddPCR) is a new technology that was recently commercialized to enable the precise quantification of target nucleic acids in a sample. ddPCR measures absolute quantities by counting nucleic acid molecules encapsulated in discrete, volumetrically defined, water-in-oil droplet partitions. This novel ddPCR format offers a simple workflow capable of generating highly stable partitioning of DNA molecules. In this study, we assessed key performance parameters of the ddPCR system. A linear ddPCR response to DNA concentration was obtained from 0.16% through to 99.6% saturation in a 20,000 droplet assay corresponding to more than 4 orders of magnitude of target DNA copy number per ddPCR. Analysis of simplex and duplex assays targeting two distinct loci in the Lambda DNA genome using the ddPCR platform agreed, within their expanded uncertainties, with values obtained using a lower density microfluidic chamber based digital PCR (cdPCR). A relative expanded uncertainty under 5% was achieved for copy number concentration using ddPCR. This level of uncertainty is much lower than values typically observed for quantification of specific DNA target sequences using currently commercially available real-time and digital cdPCR technologies. © 2011 American Chemical Society.",DNA;article;Enterobacteria phage lambda;copy number variation;evaluation study;genetics;genome;high throughput sequencing;polymerase chain reaction,"Pinheiro, L. B.;Coleman, V. A.;Hindson, C. M.;Herrmann, J.;Hindson, B. J.;Bhat, S.;Emslie, K. R.",2012,,10.1021/ac202578x,0
1673,Development of generic Taqman PCR and RT-PCR assays for the detection of DNA and mRNA of β-actin-encoding sequences in a wide range of animal species,"As a member of the European Virus Archive (EVA) consortium, our laboratory is developing and maintaining a large collection of viruses. This collection implies the use of a panel of cell lines originating from various animal species.In order to make easier the handling of such a large panel of cell lines, wide spectrum real-time PCR and RT-PCR assays were developed to allow the detection and the quantification of DNA and mRNA of β-actin, one of the most commonly used eukaryotic housekeeping genes. By using two degenerated primers and a unique probe, these two assays were shown to detect nucleic acids of a panel of vertebrate and invertebrate cell lines commonly used in animal virology. This panel included human, monkey, rodent, dog, pig, fish, batrachian, mosquito and tick cell lines. Additionally, the two assays amplified successfully β-actin-encoding sequences of sandflies. Sensitivity evaluation performed on synthetic DNA and RNA sequences showed that the two assays were very sensitive and suitable for accurate quantification.The two assays constitute together a convenient method suitable for multiple purposes. They can be used for instance to estimate the amount of contaminating cellular genetic material prior to sequence-independent amplification of viral genomes achieved before high-throughput sequencing, to evaluate the efficiency of DNase and/or RNase treatments performed on cellular extract and to check nucleic acid extraction by using β-actin-encoding sequences as endogenous control. This assay will constitute a precious tool for virologists working with multiple cell lines or animal models. © 2014 Elsevier B.V.",beta actin;DNA;messenger RNA;accuracy;animal cell;article;cell line;controlled study;DNA determination;DNA sequence;dog;fish;Haplorhini;human;human cell;mosquito;nonhuman;nucleotide sequence;priority journal;process development;Psychodidae;quantitative analysis;real time polymerase chain reaction;reverse transcription polymerase chain reaction;RNA analysis;RNA sequence;rodent;sensitivity analysis;pig;tick,"Piorkowski, G.;Baronti, C.;de Lamballerie, X.;de Fabritus, L.;Bichaud, L.;Pastorino, B. A.;Bessaud, M.",2014,,10.1016/j.jviromet.2014.02.026,0
1674,Transmission of a pestivirus infection in a population of Pyrenean chamois,"Outbreaks of a previously unrecorded disease have recently affected Pyrenean chamois (Rupicapra pyrenaica pyrenaica) populations across the mountain range. A pestivirus was hypothesized to be the cause of this emerging disease and this type of virus can cross the species barrier and be transmitted to or from wildlife. Using an epidemiological survey conducted from 1995 to 2004 at Orlu, France, we characterized the virus and analyzed its transmission. A phylogenetic analysis of viral sequences and virus neutralization tests showed that the virus belonged to the newly described border disease virus-4 group. The increase of seroprevalence with age indicated that infection can occur at any age and resulted in lifelong immunity. Overall, 70.3% of 323 samples were positive for anti-p80 antibodies and 10.2% of 167 samples showed viremia, as demonstrated by either positive ELISA antigen test or RT-PCR. Infection has thus been widespread in this population since 1995, whereas no mass mortality or clinical signs have been observed. Incidence and seroprevalence varied seasonally and according to number of individuals aged less than 2 years old in the population, so viral transmission was dependent on host population age structure. We propose that the virus is now endemic in this population and is likely detrimental for reproduction and juveniles. Further investigation is needed to estimate the impact of pestivirus on host population dynamics and the risk of cross-transmission to farm animals. © 2006 Elsevier B.V. All rights reserved.",age distribution;animal tissue;article;controlled study;enzyme linked immunosorbent assay;female;France;gene sequence;immunity;male;mortality;nonhuman;nucleotide sequence;Pestivirus;phylogeny;reverse transcription polymerase chain reaction;seasonal variation;seroprevalence;viremia;virus infection;virus neutralization;virus transmission,"Pioz, M.;Loison, A.;Gibert, P.;Dubray, D.;Menaut, P.;Le Tallec, B.;Artois, M.;Gilot-Fromont, E.",2007,,10.1016/j.vetmic.2006.09.001,0
1675,Influenza A Viruses Detected in Swine in Southern Germany after the H1N1 Pandemic in 2009,"Infections with influenza A viruses (IAV) are highly prevalent in swine populations, and stable cocirculation of at least three lineages has been well documented in European swine – till 2009. However, since the emergence of the human pandemic pdmH1N1 virus in 2009, which has been (re)introduced into individual swine herds worldwide, the situation has been changing. These variations in the respective IAV pools within pig populations are of major interest, and the zoonotic potential of putative emerging viruses needs to be evaluated. As data on recent IAV in swine from southern Germany were relatively sparse, the purpose of this study was to determine the major IAV subtypes actually present in this region. To this aim, from 2010 to 2013, 1417 nasal swabs or lung tissue samples from pigs with respiratory disease were screened for IAV genomes. Overall, in 130 holdings IAV genomes were detected by real-time RT-PCR targeting the matrix protein gene. For further analyses, several PCR protocols were adapted to quickly subtype between H1, pdmH1, H3, N1 and N2 sequences. Taken together, cocirculation of the three stable European lineages of IAV was confirmed for Bavaria. H1N1 sequences were identified in 59, whereas H1N2 genomes were only diagnosed in 14, and H3N2 in 9 of the holdings analysed. However, pdmH1 in combination with N1 was detected in 2010, 2012 and 2013 confirming a presence, albeit in low prevalence, likewise pdmH1N2 reassortant viruses. Interestingly, individual cases of coinfections with more than one subtype were diagnosed. Partial genome sequences were determined and phylogenetic analyses performed. Clearly other than in the human population classically circulating IAV have not been displaced by pdmH1N1 in Bavarian swine. However, some interesting viruses were detected. Further surveillance of these viruses in the Bavarian pig population will be of major importance, to monitor future developments.",matrix protein;animal tissue;article;gene sequence;genetic reassortment;Germany;influenza A (H1N1);Influenza A virus (H1N1);Influenza A virus (H1N2);Influenza A virus (H3N2);lung parenchyma;nonhuman;nose smear;nucleotide sequence;pandemic;phylogeny;pig;priority journal;reverse transcription polymerase chain reaction;swine influenza;virus detection;virus genome,"Pippig, J.;Ritzmann, M.;Büttner, M.;Neubauer-Juric, A.",2016,,10.1111/zph.12264,0
1676,Principles of classification illustrated by the problem of virus classification,,,"Pirie, N. W.",1962,,,0
1677,High turnover drives prolonged persistence of influenza in managed pig herds,"Pigs have long been hypothesized to play a central role in the emergence of novel human influenza A virus (IAV) strains, by serving as mixing vessels for mammalian and avian variants. However, the key issue of viral persistence in swine populations at different scales is ill understood. We address this gap using epidemiological models calibrated against seroprevalence data from Dutch finishing pigs to estimate the 'critical herd size' (CHS) for IAV persistence. We then examine the viral phylogenetic evidence for persistence by comparing human and swine IAV. Models suggest a CHS of approximately 3000 pigs above which influenza was likely to persist, i.e. orders of magnitude lower than persistence thresholds for IAV and other acute viruses in humans. At national and regional scales, we found much stronger empirical signatures of prolonged persistence of IAV in swine compared with human populations. These striking levels of persistence in small populations are driven by the high recruitment rate of susceptible piglets, and have significant implications for management of swine and for overall patterns of genetic diversity of IAV.",aging;animal experiment;article;controlled study;genetic variability;herd;human;influenza A;mathematical model;nonhuman;phylogeny;seroprevalence;stochastic model;turnover rate,"Pitzer, V. E.;Aguas, R.;Riley, S.;Loeffen, W. L. A.;Wood, J. L. N.;Grenfell, B. T.",2016,,10.1098/rsif.2016.0138,0
1678,"Bioaerosol sampling for airborne respiratory viruses in an experimental medicine pig handling facility, Singapore",,,"Poh, M. K.;Ma, M.;Nguyen, T. T.;Su, Y. C. F.",2017,,,0
1679,Viral shedders in a herd vaccinated against infection with bovine viral diarrhoea virus (BVDV) without prior testing for the presence of persistently infected animals,"Introduction: Bovine viral diarrhoea (BVD), caused by the bovine viral diarrhoea virus (BVDV), is one of the most important diseases of cattle worldwide. The purpose of the study was to determine the BVDV infection status in a dairy herd vaccinated against BVD. Before vaccination started in 2008, there had been no prior identification or the removal of the possible source of infection (persistently infected animals). It was expected that vaccination itself would enable the elimination of viral shedders on a long term basis. Material and Methods: Serological screening for antibodies against BVDV with determination for antibodies titres, BVDV antigen, and the presence of the viral genome with phylogenetic analysis of positive samples in the herd were performed, despite the lack of any clinical problems indicating possible presence of BVDV infection. Results: 19 individuals persistently infected with BVDV were identified among calves and heifers but not in adult cattle. All virus shedders were antibody negative and the genotype of isolated virus was BVDV-lb, indicating a single source of infection. The vaccine used in the herd was composed of BVDV-Ia strain. In each of the tested cowsheds, antibody titres against BVDV- lb were higher than against BVDV-la (median values). Conclusion: Despite a long-lasting vaccination programme and relatively high sequence homology of vaccinal and field strains of BVDV (83.6%), it was not possible to avoid transplacental infections of foetuses and the birth of persistently infected calves from vaccinated heifers although the protection against clinical disease was accomplished.",cattle;bovine viral diarrhoea virus;persistent infection;inactivated;vaccine;cross protection;PHYLOGENETIC ANALYSIS;CATTLE;POLAND;PROTECTION;DIVERSITY;DISEASE;CALVES;1D,"Polak, M. P.;Antos, A.;Rola, J.;Zmudzinski, J. F.",2016,Dec,,0
1680,Risk factors and molecular characterization of acute sporadic symptomatic hepatitis E virus infection in Thailand,"Objective: To report clinical outcomes and viral genotypes of acute symptomatic hepatitis E virus (HEV) infection in Thailand. Methods: Forty patients with acute symptomatic HEV infection were recruited during 2009-2013. Clinical, demographic and laboratory data were collected. Diagnosis was accomplished by detection of anti-HEV IgM and/or HEV RNA in the serum or stool. HEV genotypes were classified by direct sequencing of RT-PCR products and phylogenetic analysis. Results: The high risk group, comprising immune-compromised, liver cirrhosis and very elderly (>80 years) patients (17 cases), had higher levels of serum alkaline phosphatase at presentation compared with the low risk group. Two fatal cases resulted from acute hepatitis E in the high risk group. Initial clinical presentation did not show statistically significant differences. In six cases (6/40), the virus could be detected in serum or stool by RT-PCR and sequencing. Upon molecular characterization, the viruses were classified as HEV genotype 3f and were in the same cluster as Thai swine HEV. Conclusions: Our data showed that acute HEV infection has various clinical presentations and outcomes. Higher levels of serum alkaline phosphatase were observed in high risk patients. All isolated viruses were identified as HEV genotype 3f possibly originating from swine. © 2014 Hainan Medical College.",adult;age;aged;alkaline phosphatase blood level;article;cause of death;clinical article;controlled study;environmental exposure;female;gene sequence;genotyping technique;hepatitis E;Hepatitis E virus;hepatitis e virus genotype 3f;high risk population;human;infection risk;liver cirrhosis;male;mortality;multiple organ failure;nucleotide sequence;phylogenetic tree;phylogeny;pork;priority journal;risk factor;Thailand;very elderly;viral genetics,"Poovorawan, K.;Jitmitrapab, S.;Treeprasertsuk, S.;Thongmee, T.;Theamboonlers, A.;Tangkijvanich, P.;Komolmit, P.;Poovorawan, Y.",2014,,10.1016/s1995-7645(14)60121-8,0
1681,Describing the silent human virome with an emphasis on giant viruses,,,"Popgeorgiev, N.;Temmam, S.;Raoult, D.;Desnues, C.",2013,,,0
1682,Molecular detection of hepatitis E virus in wild boar population in eastern Romania,"In industrialized countries, Hepatitis E is a recognized zoonosis, with wild boar and swine representing the main reservoirs for zoonotic genotype HEV-3 in Europe. Data related to HEV infection in wild boar population in Romania are restricted to serological surveys. Therefore, our main goal was to determine the HEV prevalence in wild boar population and to characterize HEV strains circulating in Romania. Using TaqMan real-time RT-PCR assay, we analyzed the presence of RNA HEV in 45 liver samples and five spleen samples collected from 50 wild boars. Samples were collected during the 2013–2015 hunting seasons. Nine samples of 50 were tested positive for HEV RNA, resulting an overall prevalence of 18%. Phylogenetic analysis revealed that the isolates clustered in different HEV-3 monophyletic groups, depending on the sampling county. This is the first study signalling, based on molecular analysis, the presence of HEV in wild boar population from Romania. Also, in this study, we report the detection of HEV in splenic tissue from wild boar.",virus RNA;animal tissue;article;European wild boar;gene sequence;Hepatitis E virus;liver;molecular diagnosis;nonhuman;nucleotide sequence;phylogeny;prevalence;real time polymerase chain reaction;reverse transcription polymerase chain reaction;RNA extraction;Romania;sequence alignment;sequence analysis;sequence homology;spleen tissue;virus load,"Porea, D.;Anita, A.;Demange, A.;Raileanu, C.;Oslobanu, L.;Anita, D.;Savuta, G.;Pavio, N.",2018,,10.1111/tbed.12736,0
1683,The basis of arbovirus classification,"The biologically defined set of arboviruses contains well over 300 separate viruses which have been subdivided into some 40 serological groups on the basis of antigenic cross reactivity. More than three quarters of all arboviruses can now be placed into one of the following five major taxonomic genera based upon the fundamental properties of the virion: alphavirus, flavivirus, orbivirus, rhabdovirus, bunyavirus. There are 20 alphaviruses, representing serological Group A, and 57 flaviviruses in serological Group B; these two genera fall into the family Togaviridae. The 40 orbiviruses, in the family Reoviridae, include some 8 serological groups, and the 8 rhabdoviruses, in the family Rhabdoviridae include another 3 groups. About 160 bunyaviruses, family Bunyaviridae, are divisible into 20 serological groups, 10 of which show intra group cross reactions in the Bunyamwera supergroup. One arbovirus contains DNA, namely African swine fever virus; this is classified as an Iridovirus, or icosahedral cytoplasmic deoxyvirus. Nodamura virus, which has been classified as a picornavirus, must be reclassified on the evidence that it possesses a divided genome. A number of arboviruses remain unclassified in taxonomic terms. The absence of arbovirus representatives in several major genera, such as the adenoviruses and the myxoviruses is of interest.",Arbovirus;arthropod;classification;microorganism;virus classification,"Porterfield, J. S.",1975,,,0
1684,Systemic virus distribution and host responses in brain and intestine of chickens infected with low pathogenic or high pathogenic avian influenza virus,"Background: Avian influenza virus (AIV) is classified into two pathotypes, low pathogenic (LP) and high pathogenic (HP), based on virulence in chickens.Differences in pathogenicity between HPAIV and LPAIV might eventually be related to specific characteristics of strains, tissue tropism and host responses. Methods: To study differences in disease development between HPAIV and LPAIV, we examined the first appearance and eventual load of viral RNA in multiple organs as well as host responses in brain and intestine of chickens infected with two closely related H7N1 HPAIV or LPAIV strains. Results: Both H7N1 HPAIV and LPAIV spread systemically in chickens after a combined intranasal/intratracheal inoculation. In brain, large differences in viral RNA load and host gene expression were found between H7N1 HPAIV and LPAIV infected chickens. Chicken embryo brain cell culture studies revealed that both HPAIV and LPAIV could infect cultivated embryonic brain cells, but in accordance with the absence of the necessary proteases, replication of LPAIV was limited. Furthermore, TUNEL assay indicated apoptosis in brain of HPAIV infected chickens only. In intestine, where endoproteases that cleave HA of LPAIV are available, we found minimal differences in the amount of viral RNA and a large overlap in the transcriptional responses between HPAIV and LPAIV infected chickens. Interestingly, brain and ileum differed clearly in the cellular pathways that were regulated upon an AI infection. Conclusions: Although both H7N1 HPAIV and LPAIV RNA was detected in a broad range of tissues beyond the respiratory and gastrointestinal tract, our observations indicate that differences in pathogenicity and mortality between HPAIV and LPAIV could originate from differences in virus replication and the resulting host responses in vital organs like the brain.",RNA;virus RNA;proteinase;chicken;brain;intestine;immune response;avian influenza virus;virus;pathogenicity;brain cell;TUNEL assay;tissues;inoculation;gene expression;embryo;tropism;virulence;cell culture;apoptosis;ileum;infection;gastrointestinal tract;mortality;virus replication;disease course,"Post, J.;Burt, D. W.;Cornelissen, J. B. W. J.;Broks, V.;van Zoelen, D.;Peeters, B.;Rebel, J. M. J.",2012,,10.1186/1743-422x-9-61,0
1685,Classical swine fever virus isolates from Cuba form a new subgenotype 1.4,"Identification and classification of classical swine fever virus (CSFV) on the basis of nucleotide sequencing and phylogenetic analysis have become an important tool to study the epidemiology and to control CSF disease. According to phylogenetic analyses of short sequences from the 5'nontranslated region (150nt) and the E2 (190nt), most CSFV isolates from South and Central America have been assorted to the subgenotypes 1.1 and 1.3, while CSFV isolates from Cuba have been allocated to subgenotype 1.2. Here we demonstrate that determination and comparison of full-length E2 sequences as well as of the sequences encoding for Npro, C, Erns, E1 and E2 (3361nt) do not support segregation of Cuban CSFV isolates to subgenotype 1.2. In fact, our analysis revealed that the Cuban isolates are more divergent from other so far known CSFV subgenotype 1 isolates and form a novel separate subgenotype that is proposed to be designated subgenotype 1.4. © 2012 Elsevier B.V.",5' untranslated region;article;classical swine fever;controlled study;Cuba;genetic code;genotype;nonhuman;nucleotide sequence;Pestivirus;phylogeny;South and Central America;virus classification;virus identification;virus isolation,"Postel, A.;Schmeiser, S.;Perera, C. L.;Rodríguez, L. J. P.;Frias-Lepoureau, M. T.;Becher, P.",2013,,10.1016/j.vetmic.2012.07.045,0
1686,Virome definition in cerebrospinal fluid of patients with neurological complications after hematopoietic stem cell transplantation,,,"Pou, C.;Barrientos-Somarribas, M.;Marin-Juan, S.",2018,,,0
1687,Cowpea mosaic virus: effects on host cell processes,"SUMMARY Taxonomy: Cowpea mosaic virus (CPMV) is the type member of the Comoviridae and bears a strong resemblance to animal picornaviruses, both in gene organization and in the amino acid sequence of replication proteins. Little systematic work has been done to compare isolates of the virus from different parts of the world. Physical properties: Purified preparations of virus contain three centrifugal components; empty protein shells without RNA (T) and two nucleoprotein components (M and B), containing 24% and 34% RNA, respectively. The icosahedral particles have with a diameter of 28 nm, consist of 60 copies of two coat proteins, and are heat stable. Hosts: CPMV causes one of the most commonly reported virus diseases of cowpea (Vigna unguiculata), in which it produces chlorotic spots with diffuse borders in inoculated primary leaves. Trifoliate leaves develop a bright yellow or light green mosaic of increasing severity in younger leaves. The host range is rather limited, and few hosts are known outside the Leguminosae. The virus is transmitted by various beetles with biting mouthparts. Reported in Africa, the Philippines and Iran. Is apparently absent from North and South America. Useful website: http://mmtsb.scripps.edu/viper/1cpmv.html (structure); http://image.fs.uidaho.edu/vide/descr254.htm (general information).",,"Pouwels, J.;Carette, J. E.;Van Lent, J.;Wellink, J.",2002,Nov 01,,0
1688,Development of epitope-blocking ELISA for universal detection of antibodies to human H5N1 influenza viruses,Background: Human infections with highly pathogenic H5N1 avian influenza viruses have generally been confirmed by molecular amplification or culture-based methods. Serologic surveillance has potential advantages which have not been realized because rapid and specific serologic tests to detect H5N1 infection are not widely available. Methodology/Principal Findings: Here we describe an epitope-blocking ELISA to detect specific antibodies to H5N1 viruses in human or animal sera. The assay relies on a novel monoclonal antibody (5F8) that binds to an epitope comprising amino acid residues 274-281 (CNTKCQTP) in the HA1 region of H5 hemagglutinin. Database search analysis of publicly available sequences revealed that this epitope is conserved in 100% of the 163 H5N1 viruses isolated from humans. The sensitivity and specificity of the epitope-blocking ELISA for H5N1 were evaluated using chicken antisera to multiple virus clades and other influenza subtypes as well as serum samples from individuals naturally infected with H5N1 or seasonal influenza viruses. The epitope-blocking ELISA results were compared to those of hemagglutinin inhibition (HI) and microneutralization assays. Antibodies to H5N1 were readily detected in immunized animals or convalescent human sera by the epitope-blocking ELISA whereas specimens with antibodies to other influenza subtypes yielded negative results. The assay showed higher sensitivity and specificity as compared to HI and microneutralization. Conclusions/Significance: The epitope-blocking ELISA based on a unique 5F8 mAb provided highly sensitive and 100% specific detection of antibodies to H5N1 influenza viruses in human sera.,amino acid;epitope;Influenza virus hemagglutinin;monoclonal antibody;amino acid sequence;animal cell;animal experiment;antibody detection;antigen binding;article;chicken;clinical article;controlled study;enzyme linked immunosorbent assay;hemagglutination inhibition test;human;influenza;Influenza A virus (H5N1);intermethod comparison;mouse;nonhuman;sensitivity and specificity;virus classification;virus isolation;virus neutralization,"Prabakaran, M.;Ho, H. T.;Prabhu, N.;Velumani, S.;Szyporta, M.;He, F.;Chan, K. P.;Chen, L. M.;Matsuoka, Y.;Donis, R. O.;Kwang, J.",2009,,10.1371/journal.pone.0004566,0
1689,New hepatitis B virus of cranes that has an unexpected broad host range,"All hepadnaviruses known so far have a very limited host range, restricted to their natural hosts and a few closely related species. This is thought to be due mainly to sequence divergence in the large envelope protein and species-specific differences in host components essential for virus propagation. Here we report an infection of cranes with a novel hepadnavirus, designated CHBV, that has an unexpectedly broad host range and is only distantly evolutionarily related to avihepadnaviruses of related hosts. Direct DNA sequencing of amplified CHBV DNA as well a sequencing of cloned viral genomes revealed that CHBV is most closely related to, although distinct from, Ross' goose hepatitis B virus (RGHBV) and slightly less closely related to duck hepatitis B virus (DHBV). Phylogenetically, cranes are very distant from geese and ducks and are most closely related to herons and storks. Naturally occurring hepadnaviruses in the last two species are highly divergent in sequence from RGHBV and DHBV and do not infect ducks or do so only marginally. In contrast, CHBV from crane sera and recombinant CHBV produced from LMH cells infected primary duck hepatocytes almost as efficiently as DHBV did. This is the first report of a rather broad host range of an avihepadnavirus. Our data imply either usage of similar or identical entry pathways and receptors by DHBV and CHBV, unusual host and virus adaptation mechanisms, or divergent evolution of the host genomes and cellular components required for virus propagation.",animal cell;article;controlled study;DNA sequence;gene amplification;Hepatitis B virus;host range;liver cell;molecular cloning;molecular evolution;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;priority journal;sequence analysis;species difference,"Prassolov, A.;Hohenberg, H.;Kalinina, T.;Schneider, C.;Cova, L.;Krone, O.;Frölich, K.;Will, H.;Sirma, H.",2003,,10.1128/jvi.77.3.1964-1976.2003,0
1690,Genomic characterization of pestiviruses isolated from lambs and kids in southern Italy,"A nested polymerase chain reaction was used to identify 13 pestivirus strains isolated from small ruminants in several mixed (sheep and goats) flocks of Southern Italy, and for classification as bovine viral diarrhoea virus (BVDV) type 1, BVDV type 2, and Border disease virus (BDV) genotypes. Of the nine ovine isolates, two were characterized as BVDV type 1, and seven as BVDV type 2. The four pestiviruses isolated from kids belong to BVDV type 1. None of the pestivirus strains tested could be classified as 'true' BDV (genotype 3). Although BVDV type 2 has been described in Europe rarely, the characterization of BD/90-1M strain as BVDV type 2, isolated in Italy in 1990, demonstrates that this genotype has been circulating in Italy since the 1990s. © 2001 Elsevier Science B.V.",article;cattle disease;controlled study;genome;genotype;goat;Italy;lamb;nonhuman;Pestivirus;polymerase chain reaction;priority journal;sheep disease;strain difference;virus characterization;virus isolation,"Pratelli, A.;Martella, V.;Cirone, F.;Buonavoglia, D.;Elia, G.;Tempesta, M.;Buonavoglia, C.",2001,,10.1016/s0166-0934(01)00277-4,0
1691,Isolation and comparative study 'in vitro' of five strains of contagious ecthyma of sheep,"Five samples of scabs from sheep bred in various countries, clinically affected with contagious ecthyma, yielded infectious agents causing a cytopathic effect on primary cultures of lamb kidney cells. The 5 infectious agents 'in vitro' showed similar properties of stability in the presence of various physical and chemical agents. These properties relate viruses of the pox viruses group and identify them as ecthyma viruses. The study of the 5 agents by serum neutralization made it possible to express their respective characters of relationship and dominance quantitatively. Applying to these characters the serologic definition of strains, types and subtypes proposed for Foot and Mouth Disease viruses, it appears that 4 of the agents can be classified within the same antigenic subtype while the 5th is very close to the other 4 since it can be classified at the limit as a different subtype. The 5 agents are serologically very close to each other but their different properties regarding dominance could be of interest in the choice of one as a vaccine.",cytology;electron microscopy;histology;methodology;microorganism;sheep;sheeppox;theoretical study;virus classification;virus isolation,"Precausta, P.;Stellmann, C.",1973,,,0
1692,Host Response to Probiotics Determined by Nutritional Status of Rotavirus-infected Neonatal Mice,"Objectives: Beneficial microbes and probiotics are promising agents for the prevention and treatment of enteric and diarrheal diseases in children; however, little is known about their in vivo mechanisms of action. We used a neonatal mouse model of rotavirus diarrhea to gain insight into how probiotics ameliorate acute gastroenteritis. Methods: Rotavirus-infected mice were treated with I of 2 strains of human-derived Lactobacillus reuteri. We assessed intestinal microbiome composition with 16S metagenomic sequencing, enterocyte migration and proliferation with 5-bromo-2'-deoxyuridine, and antibody and cytokine concentrations with multiplex analyses of intestinal explant cultures. Results: Probiotics reduced diarrhea duration, improved intestinal histopathology, and enhanced intestinal microbiome richness and phylogenetic diversity. The magnitude of reduction of diarrhea by probiotics was strain specific and influenced by nutritional status. L reuteri DSM 17938 reduced diarrhea duration by 0, 1, and 2 days in underweight, normal weight, and overweight pups, respectively. The magnitude of reduction of diarrhea duration correlated with increased enterocyte proliferation and migration. Strain ATCC PTA 6475 reduced diarrhea duration by 1 day in all of the mice without increasing enterocyte proliferation. Both probiotic strains decreased concentrations of proinflammatory cytokines, including macrophage inflammatory protein-I alpha a and interleukin-I beta, in all of the animals, and increased rotavirus-specific antibodies in all but the underweight animals. Body weight also influenced the host response to rotavirus, in terms of diarrhea duration, enterocyte turnover, and antibody production. Conclusions: These data suggest that probiotic enhancement of enterocyte proliferation, villus repopulation, and virus-specific antibodies may contribute to diarrhea resolution, and that nutritional status influences the host response to both beneficial microbes and pathogens.",epithelial cells;gastroenteritis;immunity;metagenome;mucosal;probiotics;PLACEBO-CONTROLLED TRIALS;NF-KAPPA-B;LACTOBACILLUS-REUTERI;ACUTE;DIARRHEA;GNOTOBIOTIC PIGS;GENE-EXPRESSION;DENDRITIC CELLS;DOUBLE-BLIND;MALNUTRITION;COLONIZATION,"Preidis, G. A.;Saulnier, D. M.;Blutt, S. E.;Mistretta, T. A.;Riehle, K. P.;Major, A. M.;Venable, S. F.;Barrish, J. P.;Finegold, M. J.;Petrosino, J. F.;Guerrant, R. L.;Conner, M. E.;Versalovic, J.",2012,Sep,,0
1693,Full-length genome of a novel genotype 3 hepatitis E virus strain obtained from domestic pigs in Japan,"Hepatitis E virus (HEV) causes acute or chronic hepatitis in humans and can be transmitted via the fecal-oral route. Pigs are one of the main reservoirs for this infection. Sixty pigs, 4–5 months of age, on a swine herd in Japan had detectable anti-HEV IgG antibodies, and five (8.3%) of them had ongoing infection of genotype 3 HEV. Five HEV strains obtained from the viremic pigs shared 98.8–100% nucleotide identity, and one representative strain (swHE1606845), whose entire genomic sequence was determined in this study, differed by 14.1–19.6% from the reported HEV strains of subtypes 3a–3k and by 14.7–19.1% from other genotype 3 HEV strains whose subtypes have not yet been assigned. swHE1606845 showed a higher nucleotide p-distance value of ≥0.143 with the genotype 3 HEV strains of subtypes 3a–3k and ≥0.152 with other genotype 3 strains of unassigned subtypes. A SimPlot analysis revealed a lack of recombination events. These results indicate that swHE1606845 is a candidate member of a novel subtype of genotype 3. Further efforts to identify the swHE1606845-like novel strain are warranted to clarify the origin of this strain and to determine the complete nucleotide sequences of two additional swHE1606845-like strains for assigning a new subtype.",immunoglobulin G antibody;antibody detection;article;domestic pig;gene amplification;genotype;Hepatitis E virus;Japan;nonhuman;nucleotide sequence;phylogeny;priority journal;sequence analysis;virus genome;virus strain;virus typing,"Primadharsini, P. P.;Miyake, M.;Kunita, S.;Nishizawa, T.;Takahashi, M.;Nagashima, S.;Tanggis;Ohnishi, H.;Kobayashi, T.;Nishiyama, T.;Jirintai, S.;Okamoto, H.",2017,,10.1016/j.virusres.2017.08.003,0
1694,"Virus taxonomy at the XIth International Congress of Virology, Sydney, Australia, 1999",,"Animals;Birds/vi [Virology];Chickens/vi [Virology];*Circoviridae/ge [Genetics];Horses/vi [Virology];*Picornaviridae/cl [Classification];*Plant Viruses/cl [Classification];Societies, Scientific;Swine/vi [Virology]","Pringle, C. R.",1999,,,0
1695,Diagnosis of EDS-76 infection by filter paper strip method,"Egg drop syndrome - 7E5 (EDS - 76) virus is classified under group III of the genus Avisadenovirus in the family Adenoviridae. The virus is not closely related to other avian adenoviruses whereas it is closely related to bovine and ovine adenoviruses. The disease caused by EDS-76 virus is one of the major problems causing huge economic losses in poultry industry. Haemagglutination inhibition (HI) test is accepted as a rapid, reliable and economic diagnostic test for this disease. Nobuto (1967) and Brugh and Beard (1980) reported that blood can be absorbed and dried on filter paper strips without impairing the antibody activity. Hence, the present study was undertaken to evaluate the suitability of whole blood dried on filter paper strips for quantitative assay of HI antibodies to EDS-76 virus.",,"Priya, P. M.;Nair, G. K.;Mini, M.;Jayaprakash, V.",2007,Jun,,0
1696,Analysis of the S1 gene of the avian infectious bronchitis virus (IBV) reveals changes in the IBV genetic groups circulating in southern Thailand,"The new variants of the avian infectious bronchitis virus (IBV) produce a range of symptoms and cause global economic losses to the poultry industry. We investigated the S1 glycoprotein of 24 recent IBV isolates from chickens and demonstrated that two predominant genetic groups were circulating in southern Thailand between 2008 and 2013. Seven IBV variants, isolated from 2008 to 2009, were clustered in the Thailand THA001 group I while 15 IBV variants, isolated from 2009 to 2013, were classified into the QX-like group II. Moreover, a single isolate from a broiler was categorized into the Massachusetts-type, and an isolate from a layer belonged to the 4/91 type virus. Interestingly, both the IBV groups I and II were isolated from native chickens (62.5%) and caused a range of symptoms. Our results indicate that the QX-like viruses were predominant after 2009, replacing the THA001 type viruses. Furthermore, native chickens may contribute to the epidemiology of IB.",amino acid;envelope protein;genomic RNA;glycoprotein;membrane protein;S1 glycoprotein;single stranded RNA;structural protein;unclassified drug;amino acid sequence;article;Avian infectious bronchitis virus;broiler;controlled study;Gammacoronavirus;gene;genetic analysis;genetic variability;molecular cloning;nonhuman;S1 gene;Thailand;virus isolation,"Promkuntod, N.;Thongmee, S.;Yoidam, S.",2015,,10.1016/j.rvsc.2015.05.002,0
1697,Wild bird migration across the Qinghai-Tibetan Plateau: A transmission route for highly pathogenic H5N1,"Background: Qinghai Lake in central China has been at the center of debate on whether wild birds play a role in circulation of highly pathogenic avian influenza virus H5N1. In 2005, an unprecedented epizootic at Qinghai Lake killed more than 6000 migratory birds including over 3000 bar-headed geese (Anser indicus). H5N1 subsequently spread to Europe and Africa, and in following years has re-emerged in wild birds along the Central Asia flyway several times. Methodology/Principal Findings: To better understand the potential involvement of wild birds in the spread of H5N1, we studied the movements of bar-headed geese marked with GPS satellite transmitters at Qinghai Lake in relation to virus outbreaks and disease risk factors. We discovered a previously undocumented migratory pathway between Qinghai Lake and the Lhasa Valley of Tibet where 93% of the 29 marked geese overwintered. From 2003-2009, sixteen outbreaks in poultry or wild birds were confirmed on the Qinghai-Tibet Plateau, and the majority were located within the migratory pathway of the geese. Spatial and temporal concordance between goose movements and three potential H5N1 virus sources (poultry farms, a captive bar-headed goose facility, and H5N1 outbreak locations) indicated ample opportunities existed for virus spillover and infection of migratory geese on the wintering grounds. Their potential as a vector of H5N1 was supported by rapid migration movements of some geese and genetic relatedness of H5N1 virus isolated from geese in Tibet and Qinghai Lake. Conclusions/Significance: This is the first study to compare phylogenetics of the virus with spatial ecology of its host, and the combined results suggest that wild birds play a role in the spread of H5N1 in this region. However, the strength of the evidence would be improved with additional sequences from both poultry and wild birds on the Qinghai-Tibet Plateau where H5N1 has a clear stronghold.",article;China;controlled study;ecology;epidemic;epizootiology;geographic distribution;global positioning system;goose;Influenza A virus (H5N1);migratory species;nonhuman;phylogeny;telemetry;virology;virus transmission;wetland,"Prosser, D. J.;Cui, P.;Takekawa, J. Y.;Tang, M.;Hou, Y.;Collins, B. M.;Yan, B.;Hill, N. J.;Li, T.;Li, Y.;Lei, F.;Guo, S.;Xing, Z.;He, Y.;Zhou, Y.;Douglas, D. C.;Perry, W. M.;Newman, S. H.",2011,,10.1371/journal.pone.0017622,0
1698,ICTV virus taxonomy profile: Hepeviridae,"The family Hepeviridae includes enterically transmitted small non-enveloped positive-sense RNA viruses. It includes the genera Piscihepevirus, whose members infect fish, and Orthohepevirus, whose members infect mammals and birds. Members of the genus Orthohepevirus include hepatitis E virus, which is responsible for self-limiting acute hepatitis in humans and several mammalian species; the infection may become chronic in immunocompromised individuals. Extrahepatic manifestations of Guillain–Barré syndrome, neuralgic amyotrophy, glomerulonephritis and pancreatitis have been described in humans. Avian hepatitis E virus causes hepatitis–splenomegaly syndrome in chickens. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Hepeviridae, which is available at www.ictv.global/report/hepeviridae.",acute hepatitis;article;bird;brachial plexus neuropathy;chicken;cutthroat trout;fish;genome analysis;glomerulonephritis;Guillain Barre syndrome;hepatitis E;Hepatitis E virus;Hepeviridae;host range;human;nonhuman;pancreatitis;priority journal;RNA translation;species;splenomegaly;taxonomy;virion;virus genome;virus replication,"Purdy, M. A.;Harrison, T. J.;Jameel, S.;Meng, X. J.;Okamoto, H.;Van Der Poel, W. H. M.;Smith, D. B.",2017,,10.1099/jgv.0.000940,0
1699,Characterization of Marek’s disease virus and phylogenetic analyses of meq gene from an outbreak in poultry in Meghalaya of Northeast India,"The aim of the present study was to characterize the virus from the lesions and histopathology of organs associated with mortality in Kuroiler (dual purpose variety of poultry developed and marketed by Keggfarms Pvt. Ltd, India) birds suspected of Marek’s disease. Among 1047 birds from two farms of different location with 5.5 and 34% mortality, two types of lesion were observed in post mortem examination; tumors in vital organs—liver, spleen, kidney, lung and ovaries and generalized small nodular tumour in the abdominal cavity. Molecular characterization based on detection of ICP4 gene showed the presence of Marek’s disease virus (MDV) from tissues and cell culture adapted isolates in Madin Darby Canine Kidney cell lines. Histopathological examination revealed multinucleated immature lymphoid cells infiltration in the organs. Phylogenetic analysis of the isolates based on meq gene showed the isolates belongs to cluster I genotype of MDV. This is for the first time the MDV virus is characterized from an outbreak in the poultry flock in farmer’s field affecting production in Meghalaya state of North east India.",abdominal cavity;animal cell;animal tissue;article;cell culture;epidemic;Gallid alphaherpesvirus 2;genotype;histopathology;icp4 gene;kidney;liver;lung;Marek disease;MDCK cell line;Meghalaya;meq gene;nonhuman;ovary;phylogeny;polymerase chain reaction;poultry;spleen;tissue culture;tumor virus;virulence;virus gene,"Puro, K. U.;Bhattacharjee, U.;Baruah, S.;Sen, A.;Das, S.;Ghatak, S.;Doley, S.;Sanjukta, R.;Shakuntala, I.",2018,,10.1007/s13337-018-0448-2,0
1700,"Genotype characterization of Newcastle disease virus isolated from commercial chicken flocks in West Java, Indonesia","Newcastle disease (ND) is a worldwide very contagious poultry disease, caused by Newcastle disease virus (NDV). Despite the vaccination, ND outbreaks in Indonesia's commercial chicken flocks have been reported regularly. Our study aimed to determine the genotype of isolates and genetic relatedness with other Indonesia's NDVs published on the GenBank. Four NDV isolates were obtained from vaccinated flocks in 2011, 2014, 2015 in West Java, Indonesia. Two NDVs belong to virulent strain and the other two belong to avirulent strain. Phylogenetic analyses of F gene revealed that NDV/Ck/BGR/11 and NDV/Ck/GS/14 belong to genotype VII sub-genotype (h) and (i); whilst NDV/Ck/CJR/15 and NDV/Ck/BGR/15 belong to genotype II. The virulent NDVs were clustered in the same genotype and closely related to earlier Indonesia's NDVs isolated in 2007, 2009 and 2010. Result of current study showed that recent NDVs of sub-genotype VIIh and VIIi circulating in commercial chicken farm in West Java, Indonesia have high similarity with NDVs isolated during 2007 and 2010 in Indonesia. Our findings may be valuable for future studies to develop improved control and diagnostic strategies of ND.",amino acid substitution;animal experiment;article;chicken;gene amplification;gene mutation;gene sequence;genotype;Indonesia;Newcastle disease;Newcastle disease virus;nonhuman;phylogeny;reverse transcription polymerase chain reaction;RNA isolation;sequence alignment;virus isolation;virus strain,"Putri, D. D.;Handharyani, E.;Soejoedono, R. D.;Setiyono, A.;Mayasari, N. L. P. I.;Poetri, O. N.",2018,,10.29261/pakvetj/2018.041,0
1701,The ecology and age structure of a highly pathogenic avian influenza virus outbreak in wild mute swans,"The first UK epizootic of highly pathogenic (HP) H5N1 influenza in wild birds occurred in 2008, in a population of mute swans that had been the subject of ornithological study for decades. Here we use an innovative combination of ornithological, phylogenetic and immunological approaches to investigate the ecology and age structure of HP H5N1 in nature. We screened samples from swans and waterbirds using PCR and sequenced HP H5N1-positive samples. The outbreak's origin was investigated by linking bird count data with a molecular clock analysis of sampled virus sequences. We used ringing records to reconstruct the age-structure of outbreak mortality, and we estimated the age distribution of prior exposure to avian influenza. Outbreak mortality was low and all HP H5N1-positive mute swans in the affected population were <3 years old. Only the youngest age classes contained an appreciable number of individuals with no detectable antibody responses to viral nucleoprotein. Phylogenetic analysis indicated that the outbreak strain circulated locally for ~1 month before detection and arrived when the immigration rate of migrant waterbirds was highest. Our data are consistent with the hypothesis that HP H5N1 epizootics in wild swans exhibit limited mortality due to immune protection arising from previous exposure. Our study population may represent a valuable resource for investigating the natural ecology and epidemiology of avian influenza.","Age Distribution;Animals;*Animals, Wild/vi [Virology];Anseriformes/vi [Virology];Antibodies, Viral/bl [Blood];*Disease Outbreaks/ve [Veterinary];Hemagglutinins, Viral/ge [Genetics];*Influenza A Virus, H5N1 Subtype/cl [Classification];*Influenza A Virus, H5N1 Subtype/ge [Genetics];*Influenza in Birds/ep [Epidemiology];Influenza in Birds/im [Immunology];Influenza in Birds/mo [Mortality];Influenza in Birds/vi [Virology];Molecular Sequence Data;Phylogeny;Time Factors;United Kingdom/ep [Epidemiology];0 (Antibodies, Viral);0 (Hemagglutinins, Viral)","Pybus, O. G.;Perrins, C. M.;Choudhury, B.;Manvell, R. J.;Nunez, A.;Schulenburg, B.;Sheldon, B. C.;Brown, I. H.",2012,Dec,,0
1702,Molecular characterization of highly pathogenic H5N1 avian influenza a viruses isolated from raccoon dogs in China,"Background: The highly pathogenic avian influenza H5N1 virus can infect a variety of animals and continually poses a threat to animal and human health. While many genotypes of H5N1 virus can be found in chicken, few are associated with the infection of mammals. Characterization of the genotypes of viral strains in animal populations is important to understand the distribution of different viral strains in various hosts. This also facilitates the surveillance and detection of possible emergence of highly pathogenic strains of specific genotypes from unknown hosts or hosts that have not been previously reported to carry these genotypes. Methodology/Principal Findings: Two H5N1 isolates were obtained from lung samples of two raccoon dogs that had died from respiratory disease in China. Pathogenicity experiments showed that the isolates were highly pathogenic to chicken. To characterize the genotypes of these viruses, their genomic sequences were determined and analyzed. The genetic contents of these isolates are virtually identical and they may come from the same progenitor virus. Phylogenetic analysis indicated that the isolates were genetically closely related to genotype V H5N1 virus, which was first isolated in China in 2003, and were distinct from the dominant virus genotypes (e.g. genotype Z) of recent years. The isolates also contain a multibasic amino acid motif at their HA cleavage sites and have an E residue at position 627 of the PB2 protein similar to the previously-identified avian viruses. Conclusions/Significance: This is the first report that genotype V H5N1 virus is found to be associated with a mammalian host. Our results strongly suggest that genotype V H5N1 virus has the ability to cross species barriers to infect mammalian animals. These findings further highlight the risk that avian influenza H5N1 virus poses to mammals and humans, which may be infected by specific genotypes that are not known to infect these hosts. © 2009 Qi et al.",guanine nucleotide binding protein;Influenza virus hemagglutinin;protein m;protein NP;protein PB1;protein PB2;stimulatory guanine nucleotide binding protein;unclassified drug;viral protein;article;controlled study;gene sequence;genetic similarity;genotype;host;Influenza A virus (H5N1);nonhuman;pathogenicity;phylogeny;protein degradation;protein motif;raccoon dog;virus identification;virus isolation;virus strain;virus virulence,"Qi, X.;Li, X.;Rider, P.;Fan, W.;Gu, H.;Xu, L.;Yang, Y.;Lu, S.;Wang, H.;Liu, F.",2009,,10.1371/journal.pone.0004682,0
1703,Genetic characterization of H1N1 swine influenza A viruses isolated in eastern China,"Three influenza H1N1 viruses were isolated in 2005 from pigs with respiratory disease on a farm in eastern China. The three isolates were characterized to determine their probable origin. Each of the eight genes of the isolates was most closely related to the corresponding gene from the classical swine H1N1 virus. Also, phylogenetic analysis further confirmed that each of the eight genes of the isolates was closely related to the classical swine H1N1 viruses, especially those isolated in China. The HA1 proteins of the three isolates were identical to that of A/Swine/Guangdong/1/01, a virus isolated in 2001 in China, even though three nucleotide differences were observed. These results further support the concept that swine can serve as a reservoir of genetically stable influenza viruses. © 2009 Springer Science+Business Media, LLC.",article;China;genetic stability;Influenza A virus (H1N1);nonhuman;nucleotide sequence;phylogeny;priority journal;respiratory tract disease;pig;viral genetics;virus isolation,"Qi, X.;Pang, B.;Lu, C. P.",2009,,10.1007/s11262-009-0375-9,0
1704,MicroRNA expression profiling of goat peripheral blood mononuclear cells in response to peste des petits ruminants virus infection,"Peste des petits ruminants virus (PPRV) belongs to the genus Morbillivirus that causes an acute and highly contagious disease in goats and sheep. Virus infection can trigger the change in the cellular microRNA (miRNA) expression profile, which play important post-transcriptional regulatory roles in gene expression and can greatly influence viral replication and pathogenesis. Here, we employed deep sequencing technology to determine cellular miRNA expression profile in goat peripheral blood mononuclear cells (PBMC) infected with Nigeria 75/1 vaccine virus, a widely used vaccine strain for mass vaccination programs against Peste des petits ruminants. Expression analysis demonstrated that PPRV infection can elicit 316 significantly differentially expressed (DE) miRNA including 103 known and 213 novel miRNA candidates in infected PBMC at 24 hours post-infection (hpi) as compared with a mock control. Target prediction and functional analysis of these DEmiRNA revealed significant enrichment for several signaling pathways including TLR signaling pathways, PI3K-Akt, endocytosis, viral carcinogenesis, and JAK-STAT signaling pathways. This study provides a valuable basis for further investigation of the roles of miRNA in PPRV replication and pathogenesis.","Animals;China;Gene Expression Profiling/ve [Veterinary];*Gene Expression Regulation;*Goat Diseases/ge [Genetics];Goat Diseases/vi [Virology];Goats;High-Throughput Nucleotide Sequencing/ve [Veterinary];*Leukocytes, Mononuclear/me [Metabolism];*MicroRNAs/ge [Genetics];MicroRNAs/me [Metabolism];*Peste-des-Petits-Ruminants/ge [Genetics];Peste-des-Petits-Ruminants/vi [Virology];*Peste-des-petits-ruminants virus/ph [Physiology];0 (MicroRNAs)","Qi, X.;Wang, T.;Xue, Q.;Li, Z.;Yang, B.;Wang, J.",2018,07 16,,0
1705,Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis,"The West Nile virus (WNV) is an emerging infection of biodefense concern and there are no available treatments or vaccines. Here we used a high-throughput method based on a novel gene expression analysis, RNA-Seq, to give a global picture of differential gene expression by primary human macrophages of 10 healthy donors infected in vitro with WNV. From a total of 28 million reads per sample, we identified 1,514 transcripts that were differentially expressed after infection. Both predicted and novel gene changes were detected, as were gene isoforms, and while many of the genes were expressed by all donors, some were unique. Knock-down of genes not previously known to be associated with WNV resistance identified their critical role in control of viral infection. Our study distinguishes both common gene pathways as well as novel cellular responses. Such analyses will be valuable for translational studies of susceptible and resistant individuals-and for targeting therapeutics-in multiple biological settings. © 2013 by the authors; licensee MDPI, Basel, Switzerland.",article;controlled study;gene cluster;gene expression;gene identification;gene silencing;genetic transcription;high throughput sequencing;human;human cell;in vitro study;infection resistance;macrophage;RNA interference;RNA sequence;sequence analysis;viral genetics;West Nile fever,"Qian, F.;Chung, L.;Zheng, W.;Bruno, V.;Alexander, R. P.;Wang, Z.;Wang, X.;Kurscheid, S.;Zhao, H.;Fikrig, E.;Gerstein, M.;Snyder, M.;Montgomery, R. R.",2013,,10.3390/v5071664,0
1706,Molecular characterization of glycoprotein genes and phylogenetic analysis of two swine paramyxoviruses isolated from United States,"Two swine paramyxoviruses (SPMV)-(81-19252 (Texas-81) and 92-7783 (ISU-92)-were isolated from encephalitic pigs in the United States in 1981 and 1992. Antigenic, morphologic, and biological characteristics of these two viruses were essentially similar to members of the family Paramyxoviridae. Antigenic analysis by indirect fluorescent antibody, immunoblot, and one-way cross-neutralization tests placed these viruses along with bovine parainfluenza 3 (BPIV3) viruses. Purified virions were 50-300 nm in size and morphologically indistinguishable from other paramyxoviruses. These two viruses hemagglutinated red blood cells and had neuraminidase activity. The gene junctions of fusion (F) and hemagglutinin (HN) glycoprotein genes of these viruses contained highly conserved transcription start and stop signal sequences and trinucleotide intergenic regions similar to other Paramyxoviridae. The F gene of ISU-92 was longer than Texas-81 due to insertion of a 24-nucleotide ""U""-rich 3 untranslated region. Structure-based sequence alignment of glycoproteins of these two SPMVs indicated that they are essentially similar in structure and function to parainfluenzaviruses. The Texas-81 strain was closely related to BPIV3 Shipping Fever (SF) strain at nucleotide and amino acid level, while the ISU-92 strain was more closely related to BPIV3 910N strain. The envelope glycoproteins of ISU-92 had only ~92 and ~96% identity at nucleotide and amino acid levels with BPIV3-SF strain, respectively. The high sequence identities to BPIV3 indicated cross-species infection in pigs. Phylogenetic analyses based on both F protein and HN protein suggested the classification of these viruses into the subfamily Paramyxovirinae, genus Respirovirus, and genotype A of BPIV3. © 2009 Springer Science+Business Media, LLC.",hemagglutinin;spacer DNA;virus envelope protein;virus glycoprotein;virus sialidase;3' untranslated region;animal cell;antigenicity;article;controlled study;cross infection;enzyme activity;erythrocyte;fluorescent antibody technique;fusion gene;gene insertion;hemagglutination;immunoblotting;molecular genetics;nonhuman;nucleotide sequence;Human parainfluenza virus 3;Paramyxoviridae;phylogeny;pneumonic pasteurellosis;priority journal;protein function;protein structure;serodiagnosis;pig;trinucleotide repeat;United States;virion;virus encephalitis;virus isolation;virus morphology;virus transcription,"Qiao, D.;Janke, B. H.;Elankumaran, S.",2009,,10.1007/s11262-009-0353-2,0
1707,"Viral communities associated with porcine respiratory disease complex in intensive commercial farms in Sichuan province, China","Porcine respiratory disease complex (PRDC), a common piglet disease, causes substantive economic losses in pig farming. To investigate the viral diversity associated with PRDC, the viral communities in serum and nasal swabs from 26 PRDC-affected piglets were investigated using metagenomics. By deep sequencing and de novo assembly, 17 viruses were identified in two pooled libraries (16 viruses from serum, nine from nasal swabs). Porcine circovirus (PCV)-2, porcine reproductive and respiratory syndrome virus (PRRSV) and pseudorabies virus, all commonly associated with PRDC, were identified in the two pooled samples by metagenomics, but most viruses comprised small linear and circular DNAs (e.g. parvoviruses, bocaviruses and circoviruses). PCR was used to compare the detection rates of each virus in the serum samples from 36 PRDC-affected piglets versus 38 location-matched clinically healthy controls. The average virus category per sample was 6.81 for the PRDC-affected piglets and 4.09 for the controls. Single or co-infections with PCV-2 or PRRSV had very high detection rates in the PRDC-affected piglets. Interestingly, porcine parvovirus (PPV)-2, PPV-3, PPV-6 and torque teno sus virus 1a were significantly associated with PRDC. These results illustrate the complexity of viral communities in the PRDC-affected piglets and highlight the candidate viruses associated with it.",,"Qin, S.;Ruan, W.;Yue, H.;Tang, C.;Zhou, K.;Zhang, B.",2018,Sep 06,,1
1708,Full genome sequence of the first bluetongue virus serotype 21 (BTV-21) isolated from China: evidence for genetic reassortment between BTV-21 and bluetongue virus serotype 16 (BTV-16),"Bluetongue (BT) is one of the most important insect-borne, non-contagious viral diseases of ruminants and can cause severe disease and death in sheep. Its pathogen, bluetongue virus (BTV) has a double-stranded RNA genome consisting of 10 segments that provides an opportunity for field and vaccine strains of different serotypes to reassort whilst simultaneously infecting the same animal. For the first time, we report the full-length genome sequence of a BTV strain of serotype 21 (5149E) isolated from sentinel cattle in Guangxi Province in China in 2015. Sequence analysis suggested that the isolate 5149E had undergone a reassortment incident and acquired seg-6 from an isolate of BTV-16 which originated from Japan. This study aims to provide more understanding as to the origin and epidemiology of BTV.",virus RNA;animal;bluetongue;Bluetongue orbivirus;bovine;China;genetic reassortment;genetics;high throughput sequencing;phylogeny;serotype;sheep;virology;virus genome,"Qin, S.;Yang, H.;Zhang, Y.;Li, Z.;Lin, J.;Gao, L.;Liao, D.;Cao, Y.;Ren, P.;Li, H.;Wu, J.",2018,,10.1007/s00705-018-3718-9,0
1709,A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors,"Although segmented and unsegmented RNA viruses are commonplace, the evolutionary links between these two very different forms of genome organization are unclear. We report the discovery and characterization of a tick-borne virus-Jingmen tick virus (JMTV)-that reveals an unexpected connection between segmented and unsegmented RNA viruses. The JMTV genome comprises four segments, two of which are related to the nonstructural protein genes of the genus Flavivirus (family Flaviviridae), whereas the remaining segments are unique to this virus, have no known homologs, and contain a number of features indicative of structural protein genes. Remarkably, homology searching revealed that sequences related to JMTV were present in the cDNA library from Toxocara canis (dog roundworm; Nematoda), and that shared strong sequence and structural resemblances. Epidemiological studies showed that JMTV is distributed in tick populations across China, especially Rhipicephalus and Haemaphysalis spp., and experiences frequent host-switching and genomic reassortment. To our knowledge, JMTV is the first example of a segmented RNA virus with a genome derived in part from unsegmented viral ancestors.",contig;methyltransferase;nonstructural protein 1;nonstructural protein 2;nonstructural protein 2B;nonstructural protein 3;nonstructural protein 5;polyadenylic acid;protein VP1;protein VP2;protein VP3;RNA directed RNA polymerase;serine proteinase;signal peptidase;unclassified drug;viral protein;3' untranslated region;5' untranslated region;amino acid sequence;amino acid substitution;animal cell;animal cell culture;animal experiment;animal model;Anopheles;armigeres;article;Bos (genus);China;controlled study;Culex;cytopathogenic effect;DNA library;endoplasmic reticulum;Flavivirus;gene sequence;genetic reassortment;genetic similarity;genetic variability;genome analysis;Haemaphysalis;Haemaphysalis campanulata;Haemaphysalis flava;Haemaphysalis hystricis;Haemaphysalis longicornis;Hepatitis C virus;high throughput sequencing;immunofluorescence test;in vitro study;inoculation;Ixodes granulatus;Ixodide sinensis;Jingmen tick virus;mammal cell;monophyly;mosquito;mouse;newborn;nonhuman;parasite prevalence;Pestivirus;phylogenetic tree;priority journal;protein database;protein glycosylation;reverse transcription polymerase chain reaction;Rhipicephalus;Rhipicephalus (Boophilus) microplus;Rhipicephalus sanguineus;RNA virus;tick;Tick borne flavivirus;Toxocara canis;virion;virus characterization;virus genome;virus isolation;virus particle;virus purification;virus replication,"Qin, X. C.;Shi, M.;Tian, J. H.;Lin, X. D.;Gao, D. Y.;He, J. R.;Wang, J. B.;Li, C. X.;Kang, Y. J.;Yu, B.;Zhou, D. J.;Xu, J.;Plyusnin, A.;Holmes, E. C.;Zhang, Y. Z.",2014,,10.1073/pnas.1324194111,0
1710,Subtyping animal influenza virus with general multiplex RT-PCR and Liquichip high throughput (GMPLex),"This study developed a multiplex RT-PCR integrated with luminex technology to rapidly subtype simultaneously multiple influenza viruses. Primers and probes were designed to amplify NS and M genes of influenza A viruses HA gene of H1, H3, H5, H7, H9 subtypes, and NA gene of the N1 and N2 subtypes. Universal super primers were introduced to establish a multiplex RT-PCR (GM RT-PCR). It included three stages of RT-PCR amplification, and then the RT-PCR products were further tested by LiquiChip probe, combined to give an influenza virus (IV) rapid high throughput subtyping test, designated as GMPLex. The IV GMPLex rapid high throughput subtyping test presents the following features: high throughput, able to determine the subtypes of 9 target genes in H1, H3, H5, H7, H9, N1, and N2 subtypes of the influenza A virus at one time; rapid, completing the influenza subtyping within 6 hours; high specificity, ensured the specificity of the different subtypes by using two nested degenerate primers and one probe, no cross reaction occurring between the subtypes, no non-specific reactions with other pathogens and high sensitivity. When used separately to detect the product of single GM RT-PCR for single H5 or N1 gene, the GMPLex test showed a sensitivity of 10-5(= 280ELD50) forboth tests and the Luminex qualitative ratio results were 3.08 and 3.12, respectively. When used to detect the product of GM RT-PCR for H5N1 strain at the same time, both showed a sensitivity of 10-4(=2800 ELD50). The GMPLex rapid high throughput subtyping test can satisfy the needs of influenza rapid testing.","Animals;Birds;DNA Primers/ge [Genetics];High-Throughput Nucleotide Sequencing/is [Instrumentation];*High-Throughput Nucleotide Sequencing/mt [Methods];Influenza A virus/cl [Classification];Influenza A virus/ge [Genetics];*Influenza A virus/ip [Isolation & Purification];Influenza in Birds/di [Diagnosis];*Influenza in Birds/vi [Virology];*Multiplex Polymerase Chain Reaction/mt [Methods];RNA, Viral/ge [Genetics];Real-Time Polymerase Chain Reaction/mt [Methods];0 (DNA Primers);0 (RNA, Viral)","Qin, Z. F.;Sun, J.;Lu, T. K.;Zeng, S. L.;Hua, Q. Y.;Ling, Q. Y.;Chen, S. K.;Lv, J. Q.;Zhang, C. H.;Cheng, B.;Ruan, Z. X.;Bi, Y. Z.;Giambrone, J. J.;Wu, H. Z.",2012,Apr,,0
1711,"Comprehensive transcriptome analysis reveals competing endogenous RNA networks during avian leukosis virus, subgroup J-induced tumorigenesis in chickens","Avian leukosis virus subgroup J (ALV-J) is an avian oncogenic retrovirus that induces myeloid tumors and hemangiomas in chickens and causes severe economic losses with commercial layer chickens and meat-type chickens. High-throughput sequencing followed by quantitative real-time polymerase chain reaction and bioinformatics analyses were performed to advance the understanding of regulatory networks associated with differentially expressed non-coding RNAs and mRNAs that facilitate ALV-J infection. We examined the expression of mRNAs, long non-coding RNAs (lncRNAs), and miRNAs in the spleens of 20-week-old chickens infected with ALV-J and uninfected chickens. We found that 1723 mRNAs, 7,883 lncRNAs and 13 miRNAs in the spleen were differentially expressed between the uninfected and infected groups (P < 0.05). Transcriptome analysis showed that, compared to mRNA, chicken lncRNAs shared relatively fewer exon numbers and shorter transcripts. Through competing endogenous RNA and co-expression network analyses, we identified several tumor-associated or immune-related genes and lncRNAs. Along transcripts whose expression levels significantly decreased in both ALV-J infected spleen and tumor tissues, BCL11B showed the greatest change. These results suggest that BCL11B may be mechanistically involved in tumorigenesis in chicken and neoplastic diseases, may be related to immune response, and potentially be novel biomarker for ALV-J infection. Our results provide new insight into the pathology of ALV-J infection and high-quality transcriptome resource for in-depth study of epigenetic influences on disease resistance and immune system.",long untranslated RNA;messenger RNA;microRNA;transcriptome;adult;animal experiment;animal model;animal tissue;article;Avian leukosis virus;Avian leukosis virus subgroup J;BCL11B gene;bioinformatics;chicken;controlled study;exon;female;gene;gene expression;gene expression level;gene regulatory network;genetic association;high throughput sequencing;infant;malignant neoplasm;nonhuman;quantitative analysis;real time polymerase chain reaction;RNA transcription;spleen;transcriptomics;virus carcinogenesis,"Qiu, L.;Chang, G.;Li, Z.;Bi, Y.;Liu, X.;Chen, G.",2018,,10.3389/fphys.2018.00996,0
1712,Discovery of novel long non-coding RNAs induced by subgroup J avian leukosis virus infection in chicken,"Avian leukosis virus subgroup J (ALV-J) is an avian oncogenic retrovirus that has led to severe economic losses in the poultry industry in China in recent decades. Here, using high throughput transcriptome sequencing of HD11 and CEF cells infected with ALV-J, a set of 4804 novel long non-coding transcripts and numerous differentially expressed long non-coding RNAs (lncRNAs) were identified. We also found that they share relatively shorter transcripts and fewer exon numbers compared to mRNA. Correlation analysis suggested that many lncRNAs may activate gene expression in an enhancer-like manner other than through transcriptional regulation. Expression level analyses in vivo showed that three lncRNAs (NONGGAT001975.2, NONGGAT005832.2 and NONGGAT009792.2) may be associated with immune response regulation and could function as novel biomarkers for ALV-J infection. Our findings provides new insight into the pathological process of ALV-J infection and should serve as a high-quality resource for further research on epigenetic influences on disease-resistance breeding as well as immune system and genomic studies.",long untranslated RNA;messenger RNA;animal cell;article;avian leukosis;Avian leukosis virus;Avian leukosis virus subgroup J;chicken;chicken embryo fibroblast;controlled study;enhancer region;epigenetics;exon;fibroblast cell line;gene expression;gene induction;genetic association;genomics;LSCC-HD11 cell line;high throughput sequencing;immune system;immunoregulation;macrophage cell line;nonhuman;pathophysiology;poultry farming;priority journal;real time polymerase chain reaction;RNA analysis;transcription regulation;transcriptomics;virus cell interaction,"Qiu, L.;Li, Z.;Chang, G.;Bi, Y.;Liu, X.;Xu, L.;Zhang, Y.;Zhao, W.;Xu, Q.;Chen, G.",2017,,10.1016/j.dci.2017.06.015,0
1713,Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods,"Virome (viral megagenomics) detection using next generation sequencing has been widely applied in virology, but its methods remain complicated and need optimization. In this study, we detected the viromes of RNA viruses of one mock sample, one pooled duck feces sample and one pooled mink feces sample on the Personal Genome Machine platform using the sequencing libraries prepared by three methods. The sequencing primers were added through random hybridization and ligation to fragmented viral RNA using a RNA-Seq kit in method 1, through random reverse transcription (RT) and polymerase chain reaction (PCR) in method 2 which was developed in our laboratory, and through hybridization and ligation to fragmented amplicons of random RT-PCR using a single primer in method 3. Although the results of these three samples (nine libraries) all showed that more classified viral families and genera were identified using methods 2 and 3 than using method 1, and more classified viral families and genera were identified using method 2 than using method 3, most of the differences were of no statistical significance. Moreover, 11 mammalian viral genera in minks were possibly identified for the first time through this study.",virus RNA;article;controlled study;duck;feces analysis;hybridization;Neovison vison;next generation sequencing;nonhuman;priority journal;reverse transcription polymerase chain reaction;RNA virus,"Qiu, Y.;Chen, J. M.;Wang, T.;Hou, G. Y.;Zhuang, Q. Y.;Wu, R.;Wang, K. C.",2017,,10.1016/j.virusres.2017.05.003,1
1714,Evolutionary genomics of the pandemic 2009 H1N1 influenza viruses (pH1N 1v),"Background: A new strain of human H1N1 influenza A viruses was broken out in the April 2009 and caused worldwide pandemic emergency. The present study is trying to estimate a temporal reassortment history of 2009 H1N1 viruses by phylogenetic analysis based on a total 394 sequences of H1N1viruses isolated from swine, human and avian. Results: Phylogenetic trees of eight gene segments showed that viruses sampled from human formed a well-supported clade, whereas swine and avian lineages were intermixed together. A new divergence swine sublineage containing gene segments of 2009 H1N1 viruses was characterized, which were closely related with swine viruses collected from USA and South Korea during 2004 to 2007 in six segments (PB2, PB1, PA, HA, NP and NS), and to swine viruses isolated from Thailand during 2004 to 2005 in NA and M. Substitution rates were varied drastically among eight segments and the average substitution rate was generally higher in 2009 H1N1 than in swine and human viruses (F 2,23= 5.972, P < 0.01). Similarly, higher d N/dSsubstitution ratios were identified in 2009 H1N1 than in swine and human viruses except M2 gene (F2, 25= 3.779, P < 0.05). The ages of 2009 H1N1 viruses were estimated around 0.1 to 0.5 year, while their common ancestors with closest related swine viruses existed between 9.3 and 17.37 years ago. Conclusion: Our results implied that at least four reassortments or transmissions probably occurred before 2009 H1N1 viruses. Initial reassortment arose in 1976 and avian-like Eurasian swine viruses emerged. The second transmission happened in Asia and North America between 1988 and 1992, and mostly influenced six segments (PB2, PB1, PA, HA, NP and NS). The third reassortment occurred between North American swine and avian viruses during 1998 to 2000, which involved PB2 and PA segments. Recent reassortments occurred among avian-to-swine reassortant, Eurasian and classical swine viruses during 2004 to 2005. South Korea, Thailand and USA, were identified as locations where reassortments most likely happened. The co-circulation of multiple swine sublineages and special lifestyle in Asia might have facilitated mixing of diverse influenza viruses, leading to generate a novel virus strain. © 2011 Qu et al; licensee BioMed Central Ltd.",nonstructural protein 1;nonstructural protein 2;protein HA;protein m1;protein M2;protein PA;protein PB1;protein PB2;unclassified drug;viral protein;article;cladistics;controlled study;fowl;gene sequence;genetic variability;genome analysis;human;Influenza A virus (H1N1);molecular evolution;nonhuman;pandemic influenza;phylogeny;sequence analysis;South Korea;substitution line;pig;Thailand;United States;virus gene;virus genome;virus isolation,"Qu, Y.;Zhang, R.;Cui, P.;Song, G.;Duan, Z.;Lei, F.",2011,,10.1186/1743-422x-8-250,0
1715,The complex microbiota of raw milk,"Here, we review what is known about the microorganisms present in raw milk, including milk from cows, sheep, goats and humans. Milk, due to its high nutritional content, can support a rich microbiota. These microorganisms enter milk from a variety of sources and, once in milk, can play a number of roles, such as facilitating dairy fermentations (e.g. Lactococcus, Lactobacillus, Streptococcus, Propionibacterium and fungal populations), causing spoilage (e.g. Pseudomonas, Clostridium, Bacillus and other spore-forming or thermoduric microorganisms), promoting health (e.g. lactobacilli and bifidobacteria) or causing disease (e.g. Listeria, Salmonella, Escherichia coli, Campylobacter and mycotoxin-producing fungi). There is also concern that the presence of antibiotic residues in milk leads to the development of resistance, particularly among pathogenic bacteria. Here, we comprehensively review these topics, while comparing the approaches, both culture-dependent and culture-independent, which can be taken to investigate the microbial composition of milk. © 2013 Federation of European Microbiological Societies.",antibiotic agent;beta lactoglobulin;casein;iron;mycotoxin;Arthrobacter;Bacillus;bacteriophage;breast milk;Brevibacterium;buffalo;Campylobacter;Clostridium;Corynebacterium;cryopreservation;denaturing gradient gel electrophoresis;DNA binding;DNA sequence;Enterococcus;Escherichia coli;fermentation;food contamination;goat;Gram negative bacterium;high throughput sequencing;human;Lactobacillus;Lactococcus;Leuconostoc;microbial community;microbial population dynamics;microflora;milk;milk allergy;nonhuman;pasteurization;pathogen load;Propionibacterium;Pseudomonas;review;sheep;Staphylococcus;Streptococcus,"Quigley, L.;O'Sullivan, O.;Stanton, C.;Beresford, T. P.;Ross, R. P.;Fitzgerald, G. F.;Cotter, P. D.",2013,,10.1111/1574-6976.12030,0
1716,A direct high-throughput in Cell-ELISA for measuring infectivity of cytopathic and non-cytopathic bovine viral diarrhoea virus strains applied to the assessment of antiviral activity,"Low-cost high-throughput methods applicable to any virus strain are required for screening antiviral compounds against multiple field strains. Colorimetric cell-viability assays are used for this purpose as long as the viruses are cytopathic (CP) in cell culture. However, bovine viral diarrhoea virus (BVDV) strains circulating in the field are mostly non-cytopathic (NCP). An In Cell-ELISA aimed to measure viral infectivity by detecting a conserved protein produced during viral replication (non-structural protein 3, “NS3”) was developed. The ELISA is performed without harvesting the cells, directly on the 96-wells culture plate. NS3 In Cell-ELISA was tested for its ability to assess BVDV-specific antiviral activity of recombinant bovine type I and III IFNs. Results correlated to those measured by qRT-PCR and virus titration. NS3 In Cell-ELISA was also efficient in estimating the IC50 of two compounds with different antiviral activity. Estimation of the 50% inhibition dose of each IFN using six BVDV strains of different biotype and genotype showed that CP strains were more susceptible to both IFNs than NCP, while type 2 NCP viruses were more sensitive to IFN-I. The In Cell-ELISA format using a detector antibody against a conserved non-structural protein can be potentially applied to accurately measure infectivity of any viral strain.",interferon;interferon type III;nonstructural protein 3;unclassified drug;animal cell;article;Bovine viral diarrhea virus 1;cell culture;cell viability;controlled study;enzyme linked immunosorbent assay;genotype;high throughput sequencing;IC50;nonhuman;priority journal;quantitative analysis;reverse transcription polymerase chain reaction;virus infectivity;virus replication;virus strain,"Quintana, M. E.;Barone, L.;Forlenza, M. B.;Trotta, M. V.;Turco, C.;Mansilla, F. C.;Cardoso, N. P.;Capozzo, A. V.",2018,,10.1016/j.jviromet.2018.07.010,0
1717,Genome Dynamics and Molecular Infection Epidemiology of Multidrug-Resistant Helicobacter pullorum Isolates Obtained from Broiler and Free-Range Chickens in India,"Some life-threatening, foodborne, and zoonotic infections are transmitted through poultry birds. Inappropriate and indiscriminate use of antimicrobials in the livestock industry has led to an increased prevalence of multidrug-resistant bacteria with epidemic potential. Here, we present a functional molecular epidemiological analysis entailing the phenotypic and whole-genome sequence-based characterization of 11 H. pullorum isolates from broiler and free-range chickens sampled from retail wet markets in Hyderabad City, India. Antimicrobial susceptibility tests revealed all of the isolates to be resistant to multiple antibiotic classes such as fluoroquinolones, cephalosporins, sulfonamides, and macrolides. The isolates were also found to be extended-spectrum β-lactamase producers and were even resistant to clavulanic acid. Whole-genome sequencing and comparative genomic analysis of these isolates revealed the presence of five or six well-characterized antimicrobial resistance genes, including those encoding a resistance-nodulation-division efflux pump(s). Phylogenetic analysis combined with pan-genome analysis revealed a remarkable degree of genetic diversity among the isolates from free-range chickens; in contrast, a high degree of genetic similarity was observed among broiler chicken isolates. Comparative genomic analysis of all publicly available H. pullorum genomes, including our isolates (n = 16), together with the genomes of 17 other Helicobacter species, revealed a high number (8,560) of H. pullorum-specific protein-encoding genes, with an average of 535 such genes per isolate. In silico virulence screening identified 182 important virulence genes and also revealed high strain-specific gene content in isolates from free-range chickens (average, 34) compared to broiler chicken isolates. A significant prevalence of prophages (ranging from 1 to 9) and a significant presence of genomic islands (0 to 4) were observed in free-range and broiler chicken isolates. Taken together, these observations provide significant baseline data for functional molecular infection epidemiology of nonpyloric Helicobacter species such as H. pullorum by unraveling their evolution in chickens and their possible zoonotic transmission to humans. IMPORTANCE: Globally, the poultry industry is expanding with an ever-growing consumer base for chicken meat. Given this, food-associated transmission of multidrug-resistant bacteria represents an important health care issue. Our study involves a critical baseline approach directed at genome sequence-based epidemiology and transmission dynamics of H. pullorum, a poultry pathogen having established zoonotic potential. We believe our studies would facilitate the development of surveillance systems that ensure the safety of food for humans and guide public health policies related to the use of antibiotics in animal feed in countries such as India. We sequenced 11 new genomes of H. pullorum as a part of this study. These genomes would provide much value in addition to the ongoing comparative genomic studies of helicobacters.",antiinfective agent;bacterial DNA;beta lactamase;cephalosporin derivative;quinolone derivative;animal;bacterial genome;biosynthesis;chicken;drug effect;food control;genetics;genomic island;Helicobacter;Helicobacter infection;high throughput sequencing;human;India;isolation and purification;microbial sensitivity test;microbiology;molecular epidemiology;multidrug resistance;phylogeny;bird disease;prophage;veterinary medicine,"Qumar, S.;Majid, M.;Kumar, N.;Tiwari, S. K.;Semmler, T.;Devi, S.;Baddam, R.;Hussain, A.;Shaik, S.;Ahmed, N.",2017,,,0
1718,Identification of bovine papilloma virus 10 in teat warts of cattle by DNase-SISPA,"Papilloma viruses are detected and identified by PCR with consensus primers designed from human papilloma virus sequences. These and other primers could not detect papilloma virus in bovine teat wart samples despite repeated attempts. DNase-SISPA, a metagenomic method for identifying viruses, could identify bovine papilloma virus type 10 in bovine teat warts. The sequence comparison between consensus primers and bovine papilloma virus type 10 sequences revealed many differences between consensus primers and BPV-10 sequences. We suggest, DNase-SISPA may be used as an alternate method for papilloma virus diagnosis, in cases where PCR fails to identify papilloma viruses. © 2010 Elsevier B.V.",deoxyribonuclease;article;bovine;cow;metagenomics;nipple;nonhuman;nucleotide sequence;Papillomaviridae;polymerase chain reaction;sequence analysis;virus identification,"Rai, G. K.;Saxena, M.;Singh, V.;Somvanshi, R.;Sharma, B.",2011,,10.1016/j.vetmic.2010.07.015,0
1719,Review of psittacine beak and feather disease and its effect on Australian endangered species,"BACKGROUND: Since it was first described in the early 1980s, psittacine beak and feather disease (PBFD) has become recognised as the dominant viral pathogen of psittacine birds in Australia. Our aim was to evaluate and review the effect of PBFD and its position as a key threatening process to Australian psittacine bird species. We review the origin/evolutionary pathways and potential threat of PBFD to endangered psittacine bird populations and captive-breeding flocks. CONCLUSIONS: The most recent beak and feather disease virus (BFDV) phylogenetic analyses indicate that all endangered Australian psittacine bird species are susceptible to, and equally likely to be infected by, BFDV genotypes from a range of host psittacine species. Management of the disease in captive-breeding programs has relied on testing and culling, which has proven costly. The risk of PBFD should be considered very carefully by management teams contemplating the establishment of captive-breeding flocks for endangered species. Alternative disease prevention tools, including vaccination, which are increasingly being used in wildlife health, should be considered more seriously for managing and preventing PBFD in captive flocks of critically endangered species.",animal;Australia;bird disease;Circoviridae infection;Circovirus;endangered species;genetics;genotype;psittacine;veterinary medicine;virology,"Raidal, S. R.;Sarker, S.;Peters, A.",2015,,10.1111/avj.12388,0
1720,Functional characterization of a new holin-like antibacterial protein coding gene tmp1 from goat skin surface metagenome,"We have identified a holin-like gene from a goat skin surface metagenome. The ORF designated tmp1 coding for 34 amino acids shared sequence similarity with putative holin-like toxin genes. To analyze the antibacterial activity of tmp1 encoded protein, this ORF was cloned and expressed in Escherichia coli BL21(DE3). The expressed gene product Tmp1 exhibited antibacterial activity against Gram-positive bacteria but not to Gram-negative bacteria. A single transmembrane domain (TMD) was identified within Tmp1 and deletion analysis of the N-terminal region and TMD indicated TMD to be responsible for antibacterial activity. The TMD-dependent antibacterial activity was validated using a synthetic peptide with the amino acid sequence of TMD. Besides antibacterial activity, Tmp1 also complemented the function of holin in a lysis-defective bacteriophage lambda. To broaden the spectrum of antibacterial activity, a mutant library of tmp1 was generated by random mutagenesis. Four mutants with amino acid substitutions at the N-terminus of Tmp1 exhibited increased antibacterial activity against Gram-positive and Gram-negative bacteria and were not hemolytic. An improved activity of these mutant proteins is attributed to their increased hydrophobicity. © 2011 Springer-Verlag.",bacterial protein;tmp1 protein;unclassified drug;amino acid sequence;amino acid substitution;amino terminal sequence;antibacterial activity;article;bacteriolysis;Enterobacteria phage lambda;controlled study;drug specificity;Escherichia coli;gene deletion;gene expression;gene identification;gene sequence;genotype;goat;Gram negative bacterium;Gram positive bacterium;hemolysis;hydrophobicity;metagenome;molecular cloning;nonhuman;nucleotide sequence;open reading frame;phenotype;protein analysis;protein domain;protein function;protein synthesis;randomized controlled trial;sequence homology;site directed mutagenesis;skin surface;zymography,"Rajesh, T.;Anthony, T.;Saranya, S.;Pushpam, P. L.;Gunasekaran, P.",2011,,10.1007/s00253-010-2907-6,0
1721,Sequence analysis of infectious bursal disease virus isolates from India: Phylogenetic relationships,"Prevalence of infectious bursal disease (IBD) among chickens in different parts of Tamil Nadu, India, has been studied by collection of bursal samples from suspected flocks and by performing reverse transcription-polymerase chain reaction (RT-PCR) for amplification of a specific product of 474 bp from the variable region of the VP2 gene. Among 53 bursal samples examined by RT-PCR, 40 showed a positive reaction. The amplified products were subjected to nucleotide sequencing and the obtained sequences were compared with those of IBD virus (IBDV) vaccine strain Georgia, the classical virulent strain 52/70 and the very virulent Japanese OKYM strain. Nucleotide homology data indicated that all the Tamil Nadu isolates showed homology ranging from 91 to 99.6% among themselves. When compared with the very virulent Japanese OKYM strain, four isolates grouped with that strain. Majority of the isolates clustered with the very the virulent OKYM strain as evident from phylogenetic analysis performed using the MEGA program. Comparison of the deduced amino acid sequences of IBDV isolates with those of the vaccine strain Georgia, the classical virulent strain 52/70 and the very virulent strain OKYM also revealed the presence of conserved serine-rich heptapeptide sequence in most of the isolates. Results of this study indicate that majority of the IBDV isolates are very virulent, which is evident from heavy mortality that has been reported in few flocks of poultry in spite of regular vaccination.",amino acid sequence;animal tissue;article;chicken;gene;India;infectious bursal disease virus;nonhuman;nucleotide sequence;phylogeny;poultry;prevalence;reverse transcription polymerase chain reaction;sampling;sequence analysis;strain difference;vaccination;virus genome;virus infection;virus isolation;VP2 gene,"Ramadass, P.;Thiagarajan, V.;Parthiban, M.;Senthil Kumar, T. M. A.;Latha, D.;Anbalagan, S.;Krishnakumar, M.;Nachimuthu, K.",2003,,,0
1722,Differentiation of bovine herpesvirus1 subtypes based on UL0.5 gene sequencing,"Infectious bovine rhinotracheitis/infectious pustular vulvovaginitis is one of the high economic importance diseases of cattle and caused by bovine herpesvirus1 (BoHV1). Based on the restriction endonuclease fingerprinting of viral DNA, the BoHV1 can be divided into three subtypes viz., BoHV1.1, 1.2a, and 1.2b. Since this method requires a pure viral DNA, it is time-consuming and labour intense. In the current study, the UL0.5 gene based PCR sequencing has been used for the subtyping of BoHV1. Out of five isolates, four had BoHV1-like signatures and one isolate had BoHV1.2-like signatures. Further, these viruses phylogenetically clustered under the respective subtypes. These results indicate that the UL 0.5 gene based PCR sequencing could be used as an alternate method of subtyping of BoHV1.",article;Bovine herpesvirus 1;gene sequence;nonhuman;phylogeny;polymerase chain reaction;virus gene;virus isolation,"Ramakrishnan, M. A.;Pundkar, C. Y.;Fayaz, A.;ChandraSekar, S.;Mageswary, R.;Ashokkumar, D.;Bano, R.;Muthuchelvan, D.;Nandi, S.;Gupta, V. K.",2018,,10.1007/s13337-018-0422-z,0
1723,Molecular Signature of High Yield (Growth) Influenza A Virus Reassortants Prepared as Candidate Vaccine Seeds,"Background:Human influenza virus isolates generally grow poorly in embryonated chicken eggs. Hence, gene reassortment of influenza A wild type (wt) viruses is performed with a highly egg adapted donor virus, A/Puerto Rico/8/1934 (PR8), to provide the high yield reassortant (HYR) viral 'seeds' for vaccine production. HYR must contain the hemagglutinin (HA) and neuraminidase (NA) genes of wt virus and one to six 'internal' genes from PR8. Most studies of influenza wt and HYRs have focused on the HA gene. The main objective of this study is the identification of the molecular signature in all eight gene segments of influenza A HYR candidate vaccine seeds associated with high growth in ovo.Methodology:The genomes of 14 wt parental viruses, 23 HYRs (5 H1N1; 2, 1976 H1N1-SOIV; 2, 2009 H1N1pdm; 2 H2N2 and 12 H3N2) and PR8 were sequenced using the high-throughput sequencing pipeline with big dye terminator chemistry.Results:Silent and coding mutations were found in all internal genes derived from PR8 with the exception of the M gene. The M gene derived from PR8 was invariant in all 23 HYRs underlining the critical role of PR8 M in high yield phenotype. None of the wt virus derived internal genes had any silent change(s) except the PB1 gene in X-157. The highest number of recurrent silent and coding mutations was found in NS. With respect to the surface antigens, the majority of HYRs had coding mutations in HA; only 2 HYRs had coding mutations in NA.Significance:In the era of application of reverse genetics to alter influenza A virus genomes, the mutations identified in the HYR gene segments associated with high growth in ovo may be of great practical benefit to modify PR8 and/or wt virus gene sequences for improved growth of vaccine 'seed' viruses. © 2013 Ramanunninair et al.",article;gene;gene identification;gene mutation;gene sequence;genetic reassortment;HA gene;high throughput sequencing;HYR gene;Influenza A virus;Influenza A virus (H1N1);Influenza A virus (H2N2);Influenza A virus (H3N2);M gene;NA gene;nonhuman;NS gene;nucleotide sequence;PB1 gene;phenotype;PR8 gene;virogenesis;virus genome;wild type,"Ramanunninair, M.;Le, J.;Onodera, S.;Fulvini, A. A.;Pokorny, B. A.;Silverman, J.;Devis, R.;Arroyo, J. M.;He, Y.;Boyne, A.;Bera, J.;Halpin, R.;Hine, E.;Spiro, D. J.;Bucher, D.",2013,,10.1371/journal.pone.0065955,0
1724,Genetic diversity and mutation of avian paramyxovirus serotype 1 (Newcastle disease virus) in wild birds and evidence for intercontinental spread,"Avian paramyxovirus serotype 1 (APMV-1), or Newcastle disease virus, is the causative agent of Newcastle disease, one of the most economically important diseases for poultry production worldwide and a cause of periodic epizootics in wild birds in North America. In this study, we examined the genetic diversity of APMV-1 isolated from migratory birds sampled in Alaska, Japan, and Russia and assessed the evidence for intercontinental virus spread using phylogenetic methods. Additionally, we predicted viral virulence using deduced amino acid residues for the fusion protein cleavage site and estimated mutation rates for the fusion gene of class I and class II migratory bird isolates. All 73 isolates sequenced as part of this study were most closely related to virus genotypes previously reported for wild birds; however, five class II genotype I isolates formed a monophyletic clade exhibiting previously unreported genetic diversity, which met criteria for the designation of a new sub-genotype. Phylogenetic analysis of wild-bird isolates provided evidence for intercontinental virus spread, specifically viral lineages of APMV-1 class II genotype I sub-genotypes Ib and Ic. This result supports migratory bird movement as a possible mechanism for the redistribution of APMV-1. None of the predicted deduced amino acid motifs for the fusion protein cleavage site of APMV-1 strains isolated from migratory birds in Alaska, Japan, and Russia were consistent with those of previously identified virulent viruses. These data therefore provide no support for these strains contributing to the emergence of avian pathogens. The estimated mutation rates for fusion genes of class I and class II wild-bird isolates were faster than those reported previously for non-virulent APMV-1 strains. Collectively, these findings provide new insight into the diversity, spread, and evolution of APMV-1 in wild birds.",virulence factor;virus fusion protein;virus RNA;amino acid substitution;animal;bird;classification;cluster analysis;DNA sequence;genetic variability;genetics;genotype;isolation and purification;Japan;molecular epidemiology;molecular genetics;mutation;mutation rate;Newcastle disease;Newcastle disease virus;phylogeny;Russian Federation;sequence homology;United States;virology,"Ramey, A. M.;Reeves, A. B.;Ogawa, H.;Ip, H. S.;Imai, K.;Bui, V. N.;Yamaguchi, E.;Silko, N. Y.;Afonso, C. L.",2013,,10.1007/s00705-013-1761-0,0
1725,Evidence for common ancestry among viruses isolated from wild birds in Beringia and highly pathogenic intercontinental reassortant H5N1 and H5N2 influenza A viruses,"Highly pathogenic clade 2.3.4.4 H5N8, H5N2, and H5N1 influenza A viruses were first detected in wild, captive, and domestic birds in North America in November-December 2014. In this study, we used wild waterbird samples collected in Alaska prior to the initial detection of clade 2.3.4.4 H5 influenza A viruses in North America to assess the evidence for: (1) dispersal of highly pathogenic influenza A viruses from East Asia to North America by migratory birds via Alaska and (2) ancestral origins of clade 2.3.4.4 H5 reassortant viruses in Beringia. Although we did not detect highly pathogenic influenza A viruses in our sample collection from western Alaska, we did identify viruses that contained gene segments sharing recent common ancestry with intercontinental reassortant H5N2 and H5N1 viruses.","Alaska;Animals;Animals, Wild;Birds/vi [Virology];Far East;Genes, Viral;*Influenza A Virus, H5N1 Subtype/ge [Genetics];Influenza A Virus, H5N1 Subtype/ip [Isolation & Purification];Influenza A Virus, H5N1 Subtype/py [Pathogenicity];*Influenza A Virus, H5N2 Subtype/ge [Genetics];Influenza A Virus, H5N2 Subtype/ip [Isolation & Purification];Influenza A Virus, H5N2 Subtype/py [Pathogenicity];*Influenza in Birds/vi [Virology];North America;Phylogeny;RNA, Viral;*Reassortant Viruses;0 (RNA, Viral)","Ramey, A. M.;Reeves, A. B.;TeSlaa, J. L.;Nashold, S.;Donnelly, T.;Bahl, J.;Hall, J. S.",2016,06,,0
1726,Fecal virome composition of migratory wild duck species,"The fecal virome comprises a complex diversity of eukaryotic viruses, phages and viruses that infect the host. However, little is known about the intestinal community of viruses that is present in wild waterfowl, and the structure of this community in wild ducks has not yet been studied. The fecal virome compositions of six species of wild dabbling ducks and one species of wild diving duck were thus analyzed. Fecal samples were collected directly from the rectums of 60 ducks donated by hunters. DNA and RNA virus particles were purified and sequenced using the MiSeq Illumina platform. The reads obtained from the sequencing were analyzed and compared with sequences in the GenBank database. Viral-related sequences from the Herpesviridae, Alloherpesviridae, Adenoviridae, Retroviridae and Myoviridae viral families showed the highest overall abundances in the samples. The virome analysis identified viruses that had not been found in wild duck feces and revealed distinct virome profiles between different species and between samples of the same species. This study increases our understanding of viruses in wild ducks as possible viral reservoirs and provides a basis for further studying and monitoring the transmission of viruses from wild animals to humans and disease outbreaks in domestic animals.",genetic analyzer;virus DNA;virus RNA;Adenoviridae;Alloherpesviridae;Anas acuta;Anas discors;animal tissue;article;DNA virus;duck;feces;Herpesviridae;Mareca americana;Mareca strepera;Myoviridae;nonhuman;Oxyura jamaicensis;rectum;Retroviridae;RNA virus;Spatula clypeata;Spatula cyanoptera;species composition;virus detection;virus particle;wetland,"Ramírez-Martínez, L. A.;Loza-Rubio, E.;Mosqueda, J.;González-Garay, M. L.;García-Espinosa, G.",2018,,10.1371/journal.pone.0206970,0
1727,Nucleotide sequence of the gene encoding the viral polymerase of avian pneumovirus,"We report here the nucleotide sequence of the L gene of avian pneumovirus (APV). This is the second pneumovirus L gene and the second avian paramyxovirus L gene, following that of Newcastle disease virus, to be sequenced. The APV L gene is 6099 nucleotides long and encodes a single large ORF of 2004 amino acids. This makes the APV L protein the smallest to be described for any nonsegmented, negative-strand RNA virus. The protein contains six linear non-contiguous domains, a putative ATP-binding site and four polymerase motifs previously described for the L proteins of negative-strand RNA viruses. Phylogenetic analysis of domain III of 14 different L proteins suggests the pneumoviruses to be as distant in evolutionary terms from the other members of the Paramyxoviridae as are the Filoviridae.",TURKEY RHINOTRACHEITIS VIRUS;RESPIRATORY SYNCYTIAL VIRUS;L-PROTEIN;RNA;ANTIBODIES;CHICKENS,"Randhawa, J. S.;Wilson, S. D.;Tolley, K. P.;Cavanagh, D.;Pringle, C. R.;Easton, A. J.",1996,Dec,,0
1728,Adventitious agent risk assessment case study: Evaluation of RotaTeq® for the presence of porcine circovirus,"In June of 2010, results of metagenomic and panmicrobial microarray analysis of a number of commercially available vaccine products were published, identifying the unexpected presence of porcine circovirus (PCV) in of one of the vaccine products tested. This testing did not detect any sequences of contaminating viruses in RotaTeq® (rotavirus vaccine, live, oral, pentavalent, RV5, Merck & Co., Inc., Whitehouse Station, NJ). To confirm this finding, Merck developed and applied a number of polymerase chain reaction-based analytical methods and a test algorithm to systematically demonstrate the absence of infectious PCV in RotaTeq®. This paper will describe the methodology and rationale developed to thoroughly assess key starting materials, product intermediates, and final product to demonstrate the absence of infectious PCV, and the continued quality of this product. This approach could be applied to assess the validity of other adventitious agent risks encountered in biological processes and products. ©PDA, Inc. 2011.",deoxyribonuclease;DNA fragment;monoclonal antibody;rota teq;Rotavirus vaccine;trypsin;unclassified drug;cell assay;Circovirus;conference paper;DNA replication;DNA sequence;enzyme linked immunosorbent assay;gene amplification;genome;immunofluorescence;in vitro study;limit of detection;nonhuman;polymerase chain reaction;quantitative analysis,"Ranucci, C. S.;Tagmyer, T.;Duncan, P.",2011,,10.5731/pdajpst.2011.00827,0
1729,Deep sequencing as a method of typing bluetongue virus isolates,"Bluetongue (BT) is an economically important endemic disease of livestock in tropics and subtropics. In addition, its recent spread to temperate regions like North America and Northern Europe is of serious concern. Rapid serotyping and characterization of BT virus (BTV) is an essential step in the identification of origin of the virus and for controlling the disease. Serotyping of BTV is typically performed by serum neutralization, and of late by nucleotide sequencing. This report describes the near complete genome sequencing and typing of two isolates of BTV using Illumina next generation sequencing platform. Two of the BTV RNAs were multiplexed with ten other unknown samples. Viral RNA was isolated and fragmented, reverse transcribed, the cDNA ends were repaired and ligated with a multiplex oligo. The genome library was amplified using primers complementary to the ligated oligo and subjected to single and paired end sequencing. The raw reads were assembled using a de novo method and reference-based assembly was performed based on the contig data. Near complete sequences of all segments of BTV were obtained with more than 20x coverage, and single read sequencing method was sufficient to identify the genotype and serotype of the virus. The two viruses used in this study were typed as BTV-1 and BTV-9E.",Animals;Bluetongue/ep [Epidemiology];*Bluetongue/vi [Virology];*Bluetongue virus/cl [Classification];*Bluetongue virus/ge [Genetics];Bluetongue virus/ip [Isolation & Purification];Genotype;*High-Throughput Nucleotide Sequencing/mt [Methods];Molecular Epidemiology/mt [Methods];Serotyping/mt [Methods];*Virology/mt [Methods],"Rao, P. P.;Reddy, Y. N.;Ganesh, K.;Nair, S. G.;Niranjan, V.;Hegde, N. R.",2013,Nov,,0
1730,Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; Use of NGS to analyse genomic and sub-genomic RNAs,"Porcine epidemic diarrhoea virus, strain CV777, was initially characterized in 1978 as the causative agent of a disease first identified in the UK in 1971. This coronavirus has been widely distributed among laboratories and has been passaged both within pigs and in cell culture. To determine the variability between different stocks of the PEDV strain CV777, sequencing of the full-length genome (ca. 28kb) has been performed in 6 different laboratories, using different protocols. Not surprisingly, each of the different full genome sequences were distinct from each other and from the reference sequence (Accession number AF353511) but they are >99% identical. Unique and shared differences between sequences were identified. The coding region for the surface-exposed spike protein showed the highest proportion of variability including both point mutations and small deletions. The predicted expression of the ORF3 gene product was more dramatically affected in three different variants of this virus through either loss of the initiation codon or gain of a premature termination codon. The genome of one isolate had a substantially rearranged 5'-terminal sequence. This rearrangement was validated through the analysis of sub-genomic mRNAs from infected cells. It is clearly important to know the features of the specific sample of CV777 being used for experimental studies.","Animals;Base Sequence;*Coronavirus Infections/vi [Virology];Evolution, Molecular;Genome, Viral;*High-Throughput Nucleotide Sequencing/mt [Methods];Open Reading Frames;Phylogeny;Point Mutation;*Porcine epidemic diarrhea virus/ge [Genetics];Porcine epidemic diarrhea virus/ip [Isolation & Purification];RNA, Viral/ch [Chemistry];RNA, Viral/ge [Genetics];*Sequence Analysis, RNA/mt [Methods];Sequence Deletion;Swine;*Swine Diseases/vi [Virology];0 (RNA, Viral)","Rasmussen, T. B.;Boniotti, M. B.;Papetti, A.;Grasland, B.;Frossard, J. P.;Dastjerdi, A.;Hulst, M.;Hanke, D.;Pohlmann, A.;Blome, S.;van der Poel, W. H. M.;Steinbach, F.;Blanchard, Y.;Lavazza, A.;Botner, A.;Belsham, G. J.",2018,,,0
1731,Detection of three porcine vesicular viruses using multiplex real-time primer-probe energy transfer,"Rapid identification of the etiologic agent in infected animals is important for the control of an outbreak of vesicular disease in livestock. We have in the present study developed a multiplex real-time reverse transcription-PCR, based on primer-probe energy transfer (PriProET), for simultaneous detection and differentiation of three Office International des Epizooties (OIE) classified vesicular viruses: foot-and-mouth disease virus, vesicular stomatitis virus and swine vesicular disease, causing clinically indistinguishable vesicular diseases in swine. The multiplex assay consists of extraction of total RNA from clinical samples; reverse transcription to cDNA using random primers and one-tube real-time amplification of cDNA using multiplex PriProET with specific fluorescent-labelled primers and probes for detection of the three viruses from the vesicular disease complex. The probes are labelled with unique reporter fluorophores, which during amplification are excited by donor fluorophores incorporated in the 5′ end of specific amplicons by primer extension. The sensitivity of the multiplex assay was approximately 100 TCID50, which is 10-fold lower compared to the individual PriProET assays for the three vesicular viruses. © 2006 Elsevier B.V. All rights reserved.",RNA;amplicon;animal cell;article;DNA transcription;energy transfer;fluorescence;Foot and mouth disease virus;gene amplification;methodology;nonhuman;nucleotide sequence;priority journal;reverse transcription polymerase chain reaction;RNA extraction;pig;Vesiculovirus;virus detection,"Rasmussen, T. B.;Uttenthal, A.;Agüero, M.",2006,,10.1016/j.jviromet.2006.01.002,0
1732,Use of Genomic Tools to Improve Cattle Health in the Context of Infectious Diseases Review,"Although infectious diseases impose a heavy economic burden on the cattle industry, the etiology of many disorders that affect livestock is not fully elucidated, and effective countermeasures are often lacking. The main tools available until now have been vaccines, antibiotics and antiparasitic drugs. Although these have been very successful in some cases, the appearance of parasite and microbial resistance to these treatments is a cause of concern. Next-generation sequencing provides important opportunities to tackle problems associated with pathogenic illnesses. This review describes the rapid gains achieved to track disease progression, identify the pathogens involved, and map pathogen interactions with the host. Use of novel genomic tools subsequently aids in treatment development, as well as successful creation of breeding programs aimed toward less susceptible livestock. These may be important tools for mitigating the long term effects of combating infection and helping reduce the reliance on antibiotic treatment.",,"Raszek, M. M.;Guan le, L.;Plastow, G. S.",2016,,,0
1733,Use of genomic tools to improve cattle health in the context of infectious diseases,"Although infectious diseases impose a heavy economic burden on the cattle industry, the etiology of many disorders that affect livestock is not fully elucidated, and effective countermeasures are often lacking. The main tools available until now have been vaccines, antibiotics and antiparasitic drugs. Although these have been very successful in some cases, the appearance of parasite and microbial resistance to these treatments is a cause of concern. Next-generation sequencing provides important opportunities to tackle problems associated with pathogenic illnesses. This review describes the rapid gains achieved to track disease progression, identify the pathogens involved, and map pathogen interactions with the host. Use of novel genomic tools subsequently aids in treatment development, as well as successful creation of breeding programs aimed toward less susceptible livestock. These may be important tools for mitigating the long term effects of combating infection and helping reduce the reliance on antibiotic treatment.",anthelmintic agent;carrier proteins and binding proteins;interferon;interleukin 1;vaccine;animal health;antibiotic resistance;breeding;disease course;DNA modification;gene expression;gene mutation;genetic engineering;genomics;host pathogen interaction;infection;mastitis;microbiome;microorganism detection;molecular genetics;next generation sequencing;nonhuman;review;single nucleotide polymorphism,"Raszek, M. M.;Guan, L. L.;Plastow, G. S.",2016,,10.3389/fgene.2016.00030,0
1734,Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus,"BACKGROUND: Across the world, ticks act as vectors of human and animal pathogens. Ticks rely on bacterial endosymbionts, which often share close and complex evolutionary links with tick-borne pathogens. As the prevalence, diversity and virulence potential of tick-borne agents remain poorly understood, there is a pressing need for microbial surveillance of ticks as potential disease vectors. METHODOLOGY/PRINCIPAL FINDINGS: We developed a two-stage protocol that includes 16S-amplicon screening of pooled samples of hard ticks collected from dogs, sheep and camels in Palestine, followed by shotgun metagenomics on individual ticks to detect and characterise tick-borne pathogens and endosymbionts. Two ticks isolated from sheep yielded an abundance of reads from the genus Rickettsia, which were assembled into draft genomes. One of the resulting genomes was highly similar to Rickettsia massiliae strain MTU5. Analysis of signature genes showed that the other represents the first genome sequence of the potential pathogen Candidatus Rickettsia barbariae. Ticks from a dog and a sheep yielded draft genome sequences of Coxiella strains. A sheep tick yielded sequences from the sheep pathogen Anaplasma ovis, while Hyalomma ticks from camels yielded sequences belonging to Francisella-like endosymbionts. From the metagenome of a dog tick from Jericho, we generated a genome sequence of a canine parvovirus. SIGNIFICANCE: Here, we have shown how a cost-effective two-stage protocol can be used to detect and characterise tick-borne pathogens and endosymbionts. In recovering genome sequences from an unexpected pathogen (canine parvovirus) and a previously unsequenced pathogen (Candidatus Rickettsia barbariae), we demonstrate the open-ended nature of metagenomics. We also provide evidence that ticks can carry canine parvovirus, raising the possibility that ticks might contribute to the spread of this troublesome virus.",amplicon;Anaplasma ovis;animal experiment;animal tissue;article;camel;Canine parvovirus;Coxiella;dog;endosymbiont;Francisella;genus;Hyalomma;infectious agent;metagenome;metagenomics;nonhuman;Palestine;Rickettsia massiliae;sheep,"Ravi, A.;Ereqat, S.;Al-Jawabreh, A.;Abdeen, Z.;Abu Shamma, O.;Hall, H.;Pallen, M. J.;Nasereddin, A.",2019,,10.1371/journal.pntd.0006805,0
1735,Network inference from multimodal data: A review of approaches from infectious disease transmission,"Networks inference problems are commonly found in multiple biomedical subfields such as genomics, metagenomics, neuroscience, and epidemiology. Networks are useful for representing a wide range of complex interactions ranging from those between molecular biomarkers, neurons, and microbial communities, to those found in human or animal populations. Recent technological advances have resulted in an increasing amount of healthcare data in multiple modalities, increasing the preponderance of network inference problems. Multi-domain data can now be used to improve the robustness and reliability of recovered networks from unimodal data. For infectious diseases in particular, there is a body of knowledge that has been focused on combining multiple pieces of linked information. Combining or analyzing disparate modalities in concert has demonstrated greater insight into disease transmission than could be obtained from any single modality in isolation. This has been particularly helpful in understanding incidence and transmission at early stages of infections that have pandemic potential. Novel pieces of linked information in the form of spatial, temporal, and other covariates including high-throughput sequence data, clinical visits, social network information, pharmaceutical prescriptions, and clinical symptoms (reported as free-text data) also encourage further investigation of these methods. The purpose of this review is to provide an in-depth analysis of multimodal infectious disease transmission network inference methods with a specific focus on Bayesian inference. We focus on analytical Bayesian inference-based methods as this enables recovering multiple parameters simultaneously, for example, not just the disease transmission network, but also parameters of epidemic dynamics. Our review studies their assumptions, key inference parameters and limitations, and ultimately provides insights about improving future network inference methods in multiple applications.",Bayes theorem;decision tree;disease model;disease transmission;epidemic;epidemiological data;foot and mouth disease;genomics;human;influenza;molecular clock;molecular epidemiology;Monte Carlo method;mutation rate;network inference;network learning;phylogenetic tree;priority journal;review;severe acute respiratory syndrome;social network;virus transmission,"Ray, B.;Ghedin, E.;Chunara, R.",2016,,10.1016/j.jbi.2016.09.004,0
1736,Finding a needle in the virus metagenome haystack - micro-metagenome analysis captures a snapshot of the diversity of a bacteriophage armoire,"Viruses are ubiquitous in the oceans and critical components of marine microbial communities, regulating nutrient transfer to higher trophic levels or to the dissolved organic pool through lysis of host cells. Hydrothermal vent systems are oases of biological activity in the deep oceans, for which knowledge of biodiversity and its impact on global ocean biogeochemical cycling is still in its infancy. In order to gain biological insight into viral communities present in hydrothermal vent systems, we developed a method based on deep-sequencing of pulsed field gel electrophoretic bands representing key viral fractions present in seawater within and surrounding a hydrothermal plume derived from Loki's Castle vent field at the Arctic Mid-Ocean Ridge. The reduction in virus community complexity afforded by this novel approach enabled the near-complete reconstruction of a lambda-like phage genome from the virus fraction of the plume. Phylogenetic examination of distinct gene regions in this lambdoid phage genome unveiled diversity at loci encoding superinfection exclusion- and integrase-like proteins. This suggests the importance of fine-tuning lyosgenic conversion as a viral survival strategy, and provides insights into the nature of host-virus and virus-virus interactions, within hydrothermal plumes. By reducing the complexity of the viral community through targeted sequencing of prominent dsDNA viral fractions, this method has selectively mimicked virus dominance approaching that hitherto achieved only through culturing, thus enabling bioinformatic analysis to locate a lambdoid viral ""needle"" within the greater viral community ""haystack"". Such targeted analyses have great potential for accelerating the extraction of biological knowledge from diverse and poorly understood environmental viral communities. © 2012 Ray et al.",double stranded DNA;sea water;article;Enterobacteria phage lambda;biodiversity;biogeochemical cycling;bioinformatics;biological activity;controlled study;cytolysis;genome;host cell;hydrothermal vent;marine environment;microbial community;microbiome;microgenome;nonhuman;nucleotide sequence;nutrient;phylogeny;plume;pulsed field gel electrophoresis;sea;virus;virus cell interaction;virus genome;virus identification;virus micro metagenome;virus survival,"Ray, J.;Dondrup, M.;Modha, S.;Steen, I. H.;Sandaa, R. A.;Clokie, M.",2012,,10.1371/journal.pone.0034238,0
1737,Porcine sapelovirus among diarrhoeic piglets in India,"Porcine sapelovirus (PSV) A belongs to the genus Sapelovirus, family Picornaviridae. PSV infections in pigs have been reported from European countries, United States, Japan, China, Korea and Brazil. The virus has been isolated/detected from faeces of healthy pigs as well as those affected with diarrhoea, respiratory signs, encephalitis, skin lesions and fertility disorders. This study was planned to investigate whether PSV is prevalent among pigs in India and to characterize PSV encountered in the study population. The study revealed that five of 70 (7.14%) faecal samples were found positive for PSV using RT-PCR. Three viruses were successfully isolated from faecal samples using IB-RS-2 cell line. Complete genome sequencing and analysis of one Indian PSV isolate revealed highest homology (88%) with V13 strain from England. Phylogenetic analysis of the complete polyprotein nucleotide sequences of 14 strains of PSV classified the viruses into four distinct clades. This first report from India adds to our knowledge on genetic diversity of PSV detected so far among pigs in different countries. A large-scale surveillance of the virus is required to understand its genomic diversity and economic impact.",animal cell;animal experiment;animal tissue;cell line;cladistics;England;genetic variability;India;nonhuman;nucleotide sequence;phylogeny;piglet;reverse transcription polymerase chain reaction;virus isolation;whole genome sequencing;polyprotein,"Ray, P. K.;Desingu, P. A.;Kumari, S.;John, J. K.;Sethi, M.;Sharma, G. K.;Pattnaik, B.;Singh, R. K.;Saikumar, G.",2018,,10.1111/tbed.12628,0
1738,Genetic variety of influenza A virus in the populations of wild birds in the south of Western Siberia,"Influenza A virus variants belonging to H3 and H4 subtypes were isolated from wild ducks inhabiting in the south of Western Siberia. Phylogenetic analysis of hemagglutinin (HA) gene of these viruses has revealed that H3 isolates are closely related to those isolated from the bird inhabiting in West Europe (A/Teal/Germany/wv01r/01, A/ Duck/Ukraine/1/63) and China (A/Aquatic bird/Hong Kong/399/99); and those isolated from the birds inhabiting in Germany (A/Garganey/Germany/wv157k/01, A/Teal/Germany/wv153k/01). Thus, closely related influenza A virus variants circulate in the populations of the wild birds inhabiting in greatly spaced regions of Eurasia. © KOJIJlEKTHB ABTOPOB, 2005.",Influenza virus hemagglutinin;animal;article;bird;genetic variability;genetics;Influenza A virus;isolation and purification;phylogeny;rat;Russian Federation;virology,"Razumova Yu, V.;Shchelkanov, M. Yu;Durymanova, A. A.;Zolotykh, S. I.;Ternovoi, V. A.;Slavsky, A. A.;Yurlov, A. K.;Beklemishev, A. B.;Shestopalov, A. M.;Lvov, D. K.",2005,,,0
1739,Comparison between Transcriptome Sequencing and 16S Metagenomics for Detection of Bacterial Pathogens in Wildlife,"Background Rodents are major reservoirs of pathogens responsible for numerous zoonotic diseases in humans and livestock. Assessing their microbial diversity at both the individual and population level is crucial for monitoring endemic infections and revealing microbial association patterns within reservoirs. Recently, NGS approaches have been employed to characterize microbial communities of different ecosystems. Yet, their relative efficacy has not been assessed. Here, we compared two NGS approaches, RNA-Sequencing (RNA-Seq) and 16S-metagenomics, assessing their ability to survey neglected zoonotic bacteria in rodent populations. Methodology/Principal Findings We first extracted nucleic acids from the spleens of 190 voles collected in France. RNA extracts were pooled, randomly retro-transcribed, then RNA-Seq was performed using HiSeq. Assembled bacterial sequences were assigned to the closest taxon registered in GenBank. DNA extracts were analyzed via a 16S-metagenomics approach using two sequencers: the 454 GS-FLX and the MiSeq. The V4 region of the gene coding for 16S rRNA was amplified for each sample using barcoded universal primers. Amplicons were multiplexed and processed on the distinct sequencers. The resulting datasets were de-multiplexed, and each read was processed through a pipeline to be taxonomically classified using the Ribosomal Database Project. Altogether, 45 pathogenic bacterial genera were detected. The bacteria identified by RNA-Seq were comparable to those detected by 16S-metagenomics approach processed with MiSeq (16S-MiSeq). In contrast, 21 of these pathogens went unnoticed when the 16S-metagenomics approach was processed via 454-pyrosequencing (16S-454). In addition, the 16S-metagenomics approaches revealed a high level of coinfection in bank voles. Conclusions/Significance We concluded that RNA-Seq and 16S-MiSeq are equally sensitive in detecting bacteria. Although only the 16S-MiSeq method enabled identification of bacteria in each individual reservoir, with subsequent derivation of bacterial prevalence in host populations, and generation of intra-reservoir patterns of bacterial interactions. Lastly, the number of bacterial reads obtained with the 16S-MiSeq could be a good proxy for bacterial prevalence.",RNA GENE DATABASE;INFECTIOUS-DISEASES;SCRUB TYPHUS;RODENTS;MICROBIOME;FRANCE;RISK;LEPTOSPIRA;VIRUSES;EUROPE,"Razzauti, M.;Galan, M.;Bernard, M.;Maman, S.;Klopp, C.;Charbonnel, N.;Vayssier-Taussat, M.;Eloit, M.;Cosson, J. F.",2015,Aug,,0
1740,Insights into resistome and stress responses genes in Bubalus bubalis rumen through metagenomic analysis,"Buffalo rumen microbiota experience variety of diets and represents a huge reservoir of mobilome, resistome and stress responses. However, knowledge of metagenomic responses to such conditions is still rudimentary. We analyzed the metagenomes of buffalo rumen in the liquid and solid phase of the rumen biomaterial from river buffalo adapted to varying proportion of concentrate to green or dry roughages, using high-throughput sequencing to know the occurrence of antibiotics resistance genes, genetic exchange between bacterial population and environmental reservoirs. A total of 3914.94 MB data were generated from all three treatments group. The data were analysed with Metagenome rapid annotation system tools. At phyla level, Bacteroidetes were dominant in all the treatments followed by Firmicutes. Genes coding for functional responses to stress (oxidative stress and heat shock proteins) and resistome genes (resistance to antibiotics and toxic compounds, phages, transposable elements and pathogenicity islands) were prevalent in similar proportion in liquid and solid fraction of rumen metagenomes. The fluoroquinolone resistance, MDR efflux pumps and Methicillin resistance genes were broadly distributed across 11, 9, and 14 bacterial classes, respectively. Bacteria responsible for phages replication and prophages and phage packaging and rlt-like streptococcal phage genes were mostly assigned to phyla Bacteroides, Firmicutes and proteaobacteria. Also, more reads matching the sigma B genes were identified in the buffalo rumen. This study underscores the presence of diverse mechanisms of adaptation to different diet, antibiotics and other stresses in buffalo rumen, reflecting the proportional representation of major bacterial groups.",article;bacterial gene;bacteriophage;Bacteroides;controlled study;Firmicutes;gene identification;genome analysis;metagenomics;molecular phylogeny;nonhuman;pathogenicity island;Proteobacteria;antibiotic resistome;ruminant stomach;stress gene;transposon;water buffalo,"Reddy, B.;Singh, K. M.;Patel, A. K.;Antony, A.;Panchasara, H. J.;Joshi, C. G.",2014,,10.1007/s11033-014-3521-y,0
1741,Molecular characterization of Indian rabies virus isolates by partial sequencing of nucleoprotein (N) and phosphoprotein (P) genes,"Rabies is endemic and an important zoonosis in India. There are very few reports available on molecular epidemiology of rabies virus of Indian origin. In this study to know the dynamics of rabies virus, a total of 41 rabies positive brain samples from dogs, cats, domestic animals, wildlife, and humans from 11 states were subjected to RT-PCR amplification of N gene between nucleotide N521-N1262 (742 bp) and P gene between nucleotide P239-P750 (512 bp). The N gene could be amplified from 30, while P gene from 41 samples, using specific sets of primers. The N gene-based phylogenetic analysis indicated that all Indian virus isolates are genetically closely related with a single cluster under arctic/arctic-like viruses. However, two distinct clusters were realized in P gene-based phylogeny viz., Rabies virus isolates of Punjab and Rabies virus isolates of remaining parts of India (other than Punjab). All the Indian rabies virus isolates were closely related to geography (>95% homology), but not to host species. © 2011 Springer Science+Business Media, LLC.",nucleoprotein;phosphoprotein;virus RNA;article;controlled study;gene cluster;gene sequence;geographic origin;India;molecular dynamics;molecular epidemiology;molecular genetics;n gene;nonhuman;nucleotide sequence;P gene;phylogeny;priority journal;rabies;Rabies virus;virus gene;virus strain,"Reddy, G. B. M.;Singh, R.;Singh, R. P.;Singh, K. P.;Gupta, P. K.;Desai, A.;Shankar, S. K.;Ramakrishnan, M. A.;Verma, R.",2011,,10.1007/s11262-011-0601-0,0
1742,Genetic Characterization of the Belgian Nephropathogenic Infectious Bronchitis Virus (NIBV) Reference Strain B1648,"The virulent nephropathogenic infectious bronchitis virus (NIBV) strain B1648 was first isolated in 1984, in Flanders, Belgium. Despite intensive vaccination, B1648 and its variants are still circulating in Europe and North Africa. Here, the full-length genome of this Belgian NIBV reference strain was determined by next generation sequencing (NGS) to understand its evolutionary relationship with other IBV strains, and to identify possible genetic factors that may be associated with the nephropathogenicity. Thirteen open reading frames (ORFs) were predicted in the B1648 strain (51UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-31UTR). ORFs 4b, 4c and 6b, which have been rarely reported in literature, were present in B1648 and most of the other IBV complete genomes. According to phylogenetic analysis of the full-length genome, replicase transcriptase complex, spike protein, partial S1 gene and M protein, B1648 strain clustered with the non-Massachusetts type strains NGA/A116E7/2006, UKr 27-11, QX-like ITA/90254/2005, QX-like CK/SWE/0658946/10, TN20/00, RF-27/99, RF/06/2007 and SLO/266/05. Based on the partial S1 fragment, B1648 clustered with the strains TN20/00, RF-27/99, RF/06/2007 and SLO/266/05 and, further designated as B1648 genotype. The full-length genome of B1648 shared the highest sequence homology with UKr 27-11, Gray, JMK, and NGA/A116E7/2006 (91.2% to 91.6%) and was least related with the reference Beaudette and Massachusetts strains (89.7%). Nucleotide and amino acid sequence analyses indicated that B1648 strain may have played an important role in the evolution of IBV in Europe and North Africa. Further, the nephropathogenicity determinants might be located on the 1a, spike, M and accessory proteins (3a, 3b, 4b, 4c, 5a, 5b and 6b). Overall, strain B1648 is distinct from all the strains reported so far in Europe and other parts of the world.","Animals;Belgium;Chickens;Cluster Analysis;Coronavirus Infections/ve [Veterinary];Evolution, Molecular;Genetic Variation;*Genome, Viral;High-Throughput Nucleotide Sequencing;*Infectious bronchitis virus/cl [Classification];*Infectious bronchitis virus/ge [Genetics];Infectious bronchitis virus/ip [Isolation & Purification];Molecular Sequence Data;Open Reading Frames;Phylogeny;Poultry Diseases/vi [Virology];*RNA, Viral/ge [Genetics];Sequence Analysis, DNA;Sequence Homology;0 (RNA, Viral)","Reddy, V. R.;Theuns, S.;Roukaerts, I. D.;Zeller, M.;Matthijnssens, J.;Nauwynck, H. J.",2015,Aug 07,,0
1743,Avian influenza in swine: a threat for the human population?,,,"Reeth, K. Van",2006,,,0
1744,Tracking the antigenic evolution of foot-and-mouth disease virus,"Quantifying and predicting the antigenic characteristics of a virus is something of a holy grail for infectious disease research because of its central importance to the emergence of new strains, the severity of outbreaks, and vaccine selection. However, these characteristics are defined by a complex interplay of viral and host factors so that phylogenetic measures of viral similarity are often poorly correlated to antigenic relationships. Here, we generate antigenic phylogenies that track the phenotypic evolution of two serotypes of footand-mouth disease virus by combining host serology and viral sequence data to identify sites that are critical to their antigenic evolution. For serotype SAT1, we validate our antigenic phylogeny against monoclonal antibody escape mutants, which match all of the predicted antigenic sites. For serotype O, we validate it against known sites where available, and otherwise directly evaluate the impact on antigenic phenotype of substitutions in predicted sites using reverse genetics and serology. We also highlight a critical and poorly understood problem for vaccine selection by revealing qualitative differences between assays that are often used interchangeably to determine antigenic match between field viruses and vaccine strains. Our approach provides a tool to identify naturally occurring antigenic substitutions, allowing us to track the genetic diversification and associated antigenic evolution of the virus. Despite the hugely important role vaccines have played in enhancing human and animal health, vaccinology remains a conspicuously empirical science. This study advances the field by providing guidance for tuning vaccine strains via site-directed mutagenesis through this high-resolution tracking of antigenic evolution of the virus between rare major shifts in phenotype.",animal cell;antigenicity;article;controlled study;evolution;Foot and mouth disease virus;genetic variability;immune response;mutant;nonhuman;nucleotide sequence;phenotype;phylogeny;qualitative analysis;reverse genetics;serology;serotype;site directed mutagenesis;virus strain,"Reeve, R.;Borley, D. W.;Maree, F. F.;Upadhyaya, S.;Lukhwareni, A.;Esterhuysen, J. J.;Harvey, W. T.;Blignaut, B.;Fry, E. E.;Parida, S.;Paton, D. J.;Mahapatra, M.",2016,,10.1371/journal.pone.0159360,0
1745,Identification and characterization of a potyvirus isolated from siratro plants,"The present work describes the identification and characterization of a potyvirus isolated from siratro (Macroptilium atropurpureum Urb.) in the north-west region of the State of Sdo Paulo, Brazil. The virus was transmitted by mechanical inoculation. Its host range was restricted mainly to members of the Fabaceae. A cDNA fragment of about 930 bp was amplified by RT/PCR, cloned and sequenced. The fragment, which included the coat protein gene, had amino acid identity percentages between 88 and 98% with isolates of Bean common mosaic virus (BCMV). Phylogenetic analysis grouped the. siratro potyvirus and BCMV isolates in 99% of the replicates, including Azuki mosaic virus, Dendrobium mosaic virus, Blackeye cowpea mosaic virus and Peanut stripe virus, which have been classified as BCMV strains. This is the first citation on the presence of BCMV in siratro plants in Brazil.",macroptilium atropurpureum;plant virus;RT/PCR;sequencing;Brazil,"Regatier, L. J.;Gaspar, J. O.;Belintani, P.;Yuki, V. A.",2008,Apr,,0
1746,Beak and feather disease viruses circulating in Cape parrots (Poicepahlus robustus) in South Africa,"Captive and wild psittacines are vulnerable to the highly contagious psittacine beak and feather disease. The causative agent, beak and feather disease virus (BFDV), was recently detected in the largest remaining population of endangered Cape parrots (Poicepahlus robustus), which are endemic to South Africa. Full-length genomes were isolated and sequenced from 26 blood samples collected from wild and captive Cape parrots to determine possible origins of infection. All sequences had characteristic BFDV sequence motifs and were similar in length to those described in the literature. However, BFDV coat protein (CP) sequences from this study did not contain a previously identified bipartite nuclear localisation signal (NLS) within residues 39-56, which indicates that an alternate NLS is involved in shuttling the CP into the nucleus. Sequences from the wild population shared a high degree of similarity, irrespective of year or location, suggesting that the disease outbreak occurred close to the time when the samples were collected. Phylogenetic analysis of full-length genomes showed that the captive Cape parrot sequences cluster with those isolated from captive-bred budgerigars in KwaZulu-Natal Province, South Africa. Exposure to captive-bred Cape parrots from a breeding facility in KwaZulu-Natal is suggested as a possible source for the virus infection. Phylogenetic analysis of BFDV isolates from wild and captive Cape parrots indicated two separate infection events in different populations, which highlights the potential risk of introducing new strains of the virus into the wild population. The present study represents the first systematic investigation of BFDV virus diversity in the southern-most population of Cape parrots.",animal;bird disease;Circoviridae infection;Circovirus;classification;genetics;isolation and purification;parrot;phylogeny;South Africa;veterinary medicine;virology;wild animal,"Regnard, G. L.;Boyes, R. S.;Martin, R. O.;Hitzeroth, I. I.;Rybicki, E. P.",2015,,10.1007/s00705-014-2226-9,0
1747,Detection of non-notifiable H4N6 avian influenza virus in poultry in Great Britain,"A 12-month pilot project for notifiable avian disease (NAD) exclusion testing in chicken and turkey flocks in Great Britain (GB) offered, in partnership with industry, opportunities to carry out differential diagnosis in flocks where NAD was not suspected, and to identify undetected or undiagnosed infections. In May 2014, clinical samples received from a broiler breeder chicken premises that had been experiencing health and production problems for approximately one week tested positive by avian influenza (AI) real-time reverse transcription polymerase chain reaction (RRT-PCR). Following immediate escalation to an official, statutory investigation to rule out the presence of notifiable AI virus (AIV; H5 or H7 subtypes), a non-notifiable H4N6 low pathogenicity (LP) AIV was detected through virus isolation in embryonated specific pathogen free (SPF) fowls' eggs, neuraminidase inhibition test, cleavage site sequencing and AIV subtype H4-specific serology. Premises movement restrictions were lifted, and no further disease control measures were implemented as per the United Kingdom (UK) legislation. Phylogenetic analysis of the haemagglutinin and neuraminidase genes of the virus revealed closest relationships to viruses from Mallard ducks in Sweden during 2007 and 2009. In June 2014, clinical suspicion of NAD was reported in a flock of free-range laying chickens elsewhere in GB, due to increasing daily mortality and reduced egg production over a five-day period. An H4N6 LPAIV with an intravenous pathogenicity index of 0.50 was isolated. This virus was genetically highly similar, but not identical, to the virus detected during May 2014. Full viral genome analyses showed characteristics of a strain that had not recently transferred from wild birds, implying spread within the poultry sector had occurred. A stalk deletion in the neuraminidase gene sequence indicated an adaptation of the virus to poultry. Furthermore, there was unexpected evidence of systemic spread of the virus on post-mortem. No other cases were reported. Infection with LPAIVs often result in variable clinical presentation in poultry, making detection of disease more difficult.","Animals;Animals, Wild/vi [Virology];Chickens/vi [Virology];Diagnosis, Differential;Disease Outbreaks/pc [Prevention & Control];Disease Outbreaks/ve [Veterinary];Epidemiological Monitoring;Hemagglutinins/ge [Genetics];High-Throughput Nucleotide Sequencing;*Influenza A virus/ge [Genetics];Influenza A virus/gd [Growth & Development];*Influenza A virus/ip [Isolation & Purification];Influenza A virus/py [Pathogenicity];*Influenza in Birds/ep [Epidemiology];Influenza in Birds/vi [Virology];Neuraminidase/ge [Genetics];Phylogeny;Pilot Projects;Poultry/vi [Virology];*Poultry Diseases/di [Diagnosis];*Poultry Diseases/ep [Epidemiology];Poultry Diseases/vi [Virology];Real-Time Polymerase Chain Reaction;Turkeys/vi [Virology];0 (Hemagglutinins)","Reid, S. M.;Brookes, S. M.;Nunez, A.;Banks, J.;Parker, C. D.;Ceeraz, V.;Russell, C.;Seekings, A.;Thomas, S. S.;Puranik, A.;Brown, I. H.",2018,Oct,,0
1748,Full genome of influenza A (H7N9) virus derived by direct sequencing without culture,An epidemic caused by influenza A (H7N9) virus was recently reported in China. Deep sequencing revealed the full genome of the virus obtained directly from a patient's sputum without virus culture. The full genome showed substantial sequence heterogeneity and large differences compared with that from embryonated chicken eggs.,nucleocapsid protein;virus hemagglutinin;virus sialidase;adult;amino acid sequence;article;chicken;female;genetic heterogeneity;high throughput sequencing;human;Influenza A virus;Influenza A virus (H7N9);nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;point mutation;real time polymerase chain reaction;reverse transcription polymerase chain reaction;sequence alignment;sequence homology;virus genome;virus transmission;virus virulence,"Ren, X.;Yang, F.;Hu, Y.;Zhang, T.;Liu, L.;Dong, J.;Sun, L.;Zhu, Y.;Xiao, Y.;Li, L.;Yang, J.;Wang, J.;Jin, Q.",2013,,10.3201/eid1911.130664,0
1749,"Faustovirus, an asfarvirus-related new lineage of giant viruses infecting amoebae","Giant viruses are protist-associated viruses belonging to the proposed order Megavirales; almost all have been isolated from Acanthamoeba spp. Their isolation in humans suggests that they are part of the human virome. Using a high-throughput strategy to isolate new giant viruses from their original protozoan hosts, we obtained eight isolates of a new giant viral lineage from Vermamoeba vermiformis, the most common free-living protist found in human environments. This new lineage was proposed to be the faustovirus lineage. The prototype member, faustovirus E12, forms icosahedral virions of ≈ 200 nm that are devoid of fibrils and that encapsidate a 466-kbp genome encoding 451 predicted proteins. Of these, 164 are found in the virion. Phylogenetic analysis of the core viral genes showed that faustovirus is distantly related to the mammalian pathogen African swine fever virus, but it encodes ≈ 3 times more mosaic gene complements. About two-thirds of these genes do not show significant similarity to genes encoding any known proteins. These findings show that expanding the panel of protists to discover new giant viruses is a fruitful strategy. IMPORTANCE By using Vermamoeba, a protist living in humans and their environment, we isolated eight strains of a new giant virus that we named faustovirus. The genomes of these strains were sequenced, and their sequences showed that faustoviruses are related to but different from the vertebrate pathogen African swine fever virus (ASFV), which belongs to the family Asfarviridae. Moreover, the faustovirus gene repertoire is ≈ 3 times larger than that of ASFV and comprises approximately two-thirds ORFans (open reading frames [ORFs] with no detectable homology to other ORFs in a database).",African swine fever virus;Amoeba (genus);article;Asfarviridae;controlled study;Faustovirus;Faustovirus E12;genetic complementation;genome analysis;nonhuman;phylogeny;priority journal;Vermamoeba vermiformis;virion;virus gene;virus genome;virus isolation,"Reteno, D. G.;Benamar, S.;Khalil, J. B.;Andreani, J.;Armstrong, N.;Klose, T.;Rossmann, M.;Colson, P.;Raoult, D.;La Scola, B.",2015,,10.1128/jvi.00115-15,0
1750,Analysis of hepatitis C virus/classical swine fever virus chimeric 5′NTRs: Sequences within the hepatitis C virus IRES are required for viral RNA replication,"Hepatitis C virus (HCV) is classified in the genus Hepacivirus of the family Flaviviridae, whose members have a single-stranded RNA genome of positive polarity, which encodes a single polyprotein. Within this family, HCV is closely related to viruses of the genus Pestivirus, which includes classical swine fever virus (CSFV). Translation of the hepaci- and pestiviral polyprotein is initiated by internal entry of ribosomes, promoted by the 5′NTR. The secondary and tertiary RNA structures of the HCV and pestivirus 5′NTRs are well conserved, despite the fact that their sequences differ significantly from one another. By analogy with other positive-stranded RNA viruses, the 5′NTR of HCV is likely to contain cis-acting determinants for replication as well as the determinants for translation. Studies on both signals could be complicated, as these signals might overlap. In this study, this problem was addressed by constructing chimeric HCV/CSFV 5′NTRs. A two-step analysis of these 5′NTRs was performed: (a) in a translation assay, which provided the possibility to study translation independently of the possible effects on replication; and (b) in a replication assay, in which were studied only the chimeric 5′NTRs for which IRES-dependent translation was demonstrated. An overlap was observed between HCV RNA elements involved in these processes. Exchange of domain II had a minor effect on the translation efficiency of the chimeric 5′NTRs, while replication of subgenomic replicons with these chimeric 5′NTRs was abolished. Exchange of domain III subdomains severely decreased translation activity, while replication was maintained.",polyprotein;virus RNA;5' untranslated region;article;assay;chimera;controlled study;Flavivirus;gene sequence;Hepatitis C virus;human;human cell;internal ribosome entry site;nonhuman;nucleotide sequence;Pestivirus;priority journal;protein localization;replicon;RNA replication;RNA sequence;RNA structure;RNA translation;signal transduction;virus classification;virus genome;virus replication,"Reusken, C. B. E.;Dalebout, T. J.;Eerligh, P.;Bredenbeek, P. J.;Spaan, W. J. M.",2003,,10.1099/vir.0.19063-0,0
1751,"Divergent hepatitis E virus in birds of prey, common kestrel (Falco tinnunculus) and red-footed falcon (F. vespertinus), Hungary","Hepatitis E virus (HEV), family Hepeviridae, has raised considerable public health concerns because of its zoonotic potential; however, the animal to animal transmissions and the natural chain of hepevirus infections in wildlife are less known. Using random amplification and next generation sequencing technology a novel HEV in birds of prey was serendipitously identified in Hungary. HEV RNA was detected in total of 2 (18%) of the 11 and 1 (14%) of the 7 faecal samples from common kestrels and red-footed falcons, respectively. High faecal viral load (2.03x10(8) genomic copies/ml) measured by qPCR. The complete genome of strain kestrel/MR22/2014/HUN (KU670940) HEV is 7033-nt long including a 35-nt 5'end and a 63-nt 3'end (excluding the poly(A)-tail). Sequence analyses indicated that the ORF1 (4920nt/639 aa), ORF2 (1989nt/662 aa) and ORF3 (360nt/119aa) proteins of kestrel/MR22/2014/HUN shared the highest identity (58.1%, 66.8% and 28.5%) to the corresponding proteins of ferret, rat and human genotype 4 Orthohepeviruses, respectively. Interestingly, the ORF3 protein is potentially initiated with leucine (L) using an alternate, non-AUG (UUG) start codon. This study reports the identification and complete genome characterization of a novel Orthohepevirus species related to mammalian HEVs in birds of prey. It is important to recognize all potential hosts, reservoirs and spreaders in nature and to reconstruct the phylogenetic history of hepeviruses.","Amino Acid Sequence;Animals;*Bird Diseases/ep [Epidemiology];Bird Diseases/tm [Transmission];Bird Diseases/vi [Virology];*Falconiformes/vi [Virology];Feces/vi [Virology];Ferrets/vi [Virology];*Genome, Viral;Genotype;*Hepatitis E/ep [Epidemiology];Hepatitis E/tm [Transmission];Hepatitis E/vi [Virology];Hepatitis E virus/cl [Classification];*Hepatitis E virus/ge [Genetics];Hepatitis E virus/ip [Isolation & Purification];High-Throughput Nucleotide Sequencing;Humans;Hungary/ep [Epidemiology];Open Reading Frames;*Phylogeny;Predatory Behavior/ph [Physiology];Rats;Sequence Analysis, DNA;Viral Proteins;0 (Viral Proteins)","Reuter, G.;Boros, A.;Matics, R.;Kapusinszky, B.;Delwart, E.;Pankovics, P.",2016,09,,0
1752,"A novel avian-like hepatitis E virus in wild aquatic bird, little egret (Egretta garzetta), in Hungary","Hepatitis E virus (HEV), family Hepeviridae, has public health concerns because of its zoonotic potential; however, the host species spectrum, animal to animal transmissions, the natural chain of hepevirus infections and the genetic diversity of HEV in wildlife especially in birds are less known. Using random amplification and next generation sequencing technology a genetically divergent avian HEV was serendipitously identified in wild bird in Hungary. HEV RNA was detected with high faecal viral load (1.33 × 108 genomic copies/ml) measured by real-time PCR in faecal sample from a little egret (Egretta garzetta). The complete genome of HEV strain little egret/kocsag02/2014/HUN (KX589065) is 6660-nt long including a 18-nt 5′ end and a 103-nt 3′ end (excluding the poly(A)-tail). Sequence analyses indicated that the ORF1 (4554nt/1517aa), ORF2 (1728nt/593aa) and ORF3 (339nt/112aa) encoded proteins of little egret/kocsag02/2014/HUN shared the highest identity (62.8%, 71% and 61.5%) to the corresponding proteins of genotype 1 avian (chicken) HEV in species Orthohepevirus B, respectively. This study reports the identification and complete genome characterization of a novel orthohepevirus distantly related to avian (chicken) HEVs at the first time in wild bird. It is important to recognize all potential hosts, reservoirs and spreaders in nature and to reconstruct the phylogenetic history of hepeviruses. Birds could be an important reservoir of HEV generally and could be infected with genetically highly divergent strains of HEV.",virus RNA;aquatic species;article;bird;controlled study;Egretta garzetta;feces culture;gene amplification;genetic variability;genome analysis;genome size;genotype;Hepatitis E virus;Hungary;metagenomics;next generation sequencing;nonhuman;open reading frame;Orthohepevirus B;phylogeny;priority journal;real time polymerase chain reaction;sequence analysis;virus characterization;virus genome;virus identification;virus load;wild species,"Reuter, G.;Boros, Á;Mátics, R.;Kapusinszky, B.;Delwart, E.;Pankovics, P.",2016,,10.1016/j.meegid.2016.10.026,0
1753,Kobuviruses - a comprehensive review,"Kobuviruses are members of the large and growing family Picornaviridae. Until now, two official, Aichi virus and Bovine kobuvirus, and one candidate kobuvirus species, 'porcine kobuvirus', have been identified in human, cattle and swine, respectively. In addition, kobu-like viruses were detected very recently in the bat. Aichi virus could be one of the causative agents of gastroenteritis in humans, and kobuviruses probably also cause diarrhoea in cattle and swine. Although Aichi virus has been detected relatively infrequently (0-3%) in human diarrhoea, high seroprevalence, up to 80-95% at the age of 30-40, was found indicating the general nature of infection in different human populations. In the previous years, much new information has accumulated relating to kobuviruses and their host species. This review summarises the current knowledge on kobuviruses including taxonomy, biology and viral characteristics, and covers all aspects of infection including epidemiology, clinical picture, host species diversity, laboratory diagnosis and it gives a summary about possible future perspectives. © 2011 John Wiley & Sons, Ltd.",genomic RNA;virus antigen;virus RNA;5' untranslated region;acute gastroenteritis;antigen detection;blood sampling;cow;diarrhea;enzyme immunoassay;genetic variability;host;human;incidence;Kobuvirus;Kobuvirus infection;laboratory diagnosis;laboratory test;molecular biology;nonhuman;nucleotide sequence;oyster;Picornaviridae;picornavirus infection;reverse transcription polymerase chain reaction;review;seroepidemiology;seroprevalence;species diversity;pig;symptom;taxonomy;viral genetics;virus detection;virus genome;virus isolation;virus replication;virus strain;virus transmission,"Reuter, G.;Boros, A.;Pankovics, P.",2011,,10.1002/rmv.677,0
1754,Molecular detection of hepatitis E virus in non-imported hepatitis case--identification of a potential new human hepatitis E virus lineage in Hungary Hungarian,"INTRODUCTION: Hepatitis E virus (HEV) one of the most common cause of hepatitis in endemic areas. However recently demonstrated that human infection may occur in developed countries without any travel history and that swine may act as a reservoir. AIMS: The objective of this study was to identified hepatitis E virus by molecular methods in patient with acute non-A-C hepatitis infection with no recent travel history in Hungary and to determine the viral genetic relationship to known HEV strains. MATERIALS: Laboratory diagnosis of hepatitis E virus infection was performed in patient sera by HEV IgM and IgG ELISA, IgM and IgG immunoblot and reverse transcription polymerase chain reaction using primers for partial viral capsid region. RESULTS: Patient with acute hepatitis with unknown origin was treated in Hospital of Szeged in June 2004. The acute patient's sera was positive by HEV IgM and IgG confirmed by immunoblot. Viral genome was successfully amplified in sera by RT-PCR. By sequence- and phylogenetic analysis the virus, designated Hungary-1, showed 95% nucleotide identity to genotype 3 hepatitis E viruses related to highest identity to swine HEV strain (Sp354-1-02) and having 90% nucleic acid identity to human strain (Greece2). DISCUSSION: Hepatitis E virus infection is present in Hungary without travelling to known endemic regions. The first identified HEV in Hungary, which is represent a new human genetic lineage, support the possibility of the endemic infections caused by genotype 3 strains in developed countries and that swine may act as reservoir of human HEV.","DNA, Viral/an [Analysis];Enzyme-Linked Immunosorbent Assay;*Hepatitis E virus/cl [Classification];*Hepatitis E virus/ip [Isolation & Purification];Humans;Hungary;Immunoblotting;RNA, Viral/ip [Isolation & Purification];Reverse Transcriptase Polymerase Chain Reaction;Sequence Analysis, DNA;0 (DNA, Viral);0 (RNA, Viral)","Reuter, G.;Fodor, D.;Katai, A.;Szucs, G.",2005,Nov 20,,0
1755,Astrovirus in wild boars (Sus scrofa) in Hungary,"The family Astroviridae consists of two genera, Avastrovirus and Mamastrovirus whose members are associated with gastroenteritis in avian and mammalian hosts, respectively. In this study, we report the first detection of astrovirus from fecal specimens of wild boars (Sus scrofa) using viral metagenomics and complete genome sequencing. The wild boar astrovirus (WBAstV-1/2011/HUN, JQ340310) genome is 6707 nucleotide long and had 76%, 95% and 56% amino acid (aa) identity in the ORF1a (852aa), ORF1b (522aa) and ORF2 (845aa) regions, respectively, to porcine astrovirus 4 (PAstV-4, JF713713), the closest match. This study indicates that wild boar could be a reservoir for astroviruses. © 2012 Springer-Verlag.",animal;animal disease;article;Astroviridae;astrovirus infection;classification;feces;genetics;Hungary;isolation and purification;molecular genetics;nucleotide sequence;open reading frame;phylogeny;pig;swine disease;virology;virus genome,"Reuter, G.;Nemes, C.;Boros, Á;Kapusinszky, B.;Delwart, E.;Pankovics, P.",2012,,10.1007/s00705-012-1272-4,0
1756,Porcine kobuvirus in wild boars (Sus scrofa),"Fecal samples (N = 10) from 6- to 8-week-old wild boar piglets (Sus scrofa), collected from an animal park in Hungary in April 2011, were analyzed using viral metagenomics and complete genome sequencing. Kobuvirus (genus Kobuvirus, family Picornaviridae) was detected in all (100 %) specimens, with the closest nucleotide (89 %) and amino acid (94 %) sequence identity of the strain wild boar/WB1-HUN/2011/HUN (JX177612) to the prototype porcine kobuvirus S-1-HUN (EU787450). This study suggests that genetically highly similar (practically the same geno-/serotype) porcine kobuvirus circulate in wild boars, the wildlife counterparts of domestic pigs. Wild boars could be an important host and reservoir for kobuvirus. © 2012 Springer-Verlag.",animal;animal disease;article;classification;genetics;isolation and purification;Kobuvirus;molecular genetics;nucleotide sequence;phylogeny;picornavirus infection;pig;swine disease;virology,"Reuter, G.;Nemes, C.;Boros, Á;Kapusinszky, B.;Delwart, E.;Pankovics, P.",2013,,10.1007/s00705-012-1456-y,0
1757,Nonsuppurative (Aseptic) Meningoencephalomyelitis Associated with Neurovirulent Astrovirus Infections in Humans and Animals Review,"Astroviruses are thought to be enteric pathogens. Since 2010, a certain group of astroviruses has increasingly been recognized, using up-to-date random amplification and high-throughput next-generation sequencing (NGS) methods, as potential neurovirulent (Ni) pathogens of severe central nervous system (CNS) infections, causing encephalitis, meningoencephalitis, and meningoencephalomyelitis. To date, neurovirulent astrovirus cases or epidemics have been reported for humans and domesticated mammals, including mink, bovines, ovines, and swine. This comprehensive review summarizes the virology, epidemiology, pathology, diagnosis, therapy, and future perspective related to neurovirulent astroviruses in humans and mammals, based on a total of 30 relevant articles available in PubMed (searched by use of the terms ""astrovirus/encephalitis"" and ""astrovirus/meningitis"" on 2 March 2018). A paradigm shift should be considered based on the increasing knowledge of the causality-effect association between neurotropic astroviruses and CNS infection, and attention should be drawn to the role of astroviruses in unknown CNS diseases.",,"Reuter, G.;Pankovics, P.;Boros, A.",2018,10,,0
1758,Nonsuppurative (Aseptic) Meningoencephalomyelitis Associated with Neurovirulent Astrovirus Infections in Humans and Animals,"SUMMARYAstroviruses are thought to be enteric pathogens. Since 2010, a certain group of astroviruses has increasingly been recognized, using up-to-date random amplification and high-throughput next-generation sequencing (NGS) methods, as potential neurovirulent (Ni) pathogens of severe central nervous system (CNS) infections, causing encephalitis, meningoencephalitis, and meningoencephalomyelitis. To date, neurovirulent astrovirus cases or epidemics have been reported for humans and domesticated mammals, including mink, bovines, ovines, and swine. This comprehensive review summarizes the virology, epidemiology, pathology, diagnosis, therapy, and future perspective related to neurovirulent astroviruses in humans and mammals, based on a total of 30 relevant articles available in PubMed (searched by use of the terms ""astrovirus/encephalitis"" and ""astrovirus/meningitis"" on 2 March 2018). A paradigm shift should be considered based on the increasing knowledge of the causality-effect association between neurotropic astroviruses and CNS infection, and attention should be drawn to the role of astroviruses in unknown CNS diseases.",astrovirus infection;attention;causality;diagnosis;encephalitis;human;mammal;Medline;meningitis;nonhuman;review;systematic review;virology,"Reuter, G.;Pankovics, P.;Boros, Á",2018,,10.1128/cmr.00040-18,0
1759,Identification of a novel astrovirus in domestic sheep in Hungary,"The family Astroviridae consists of two genera, Avastrovirus and Mamastrovirus, whose members are associated with gastroenteritis in avian and mammalian hosts, respectively. We serendipitously identified a novel ovine astrovirus in a fecal specimen from a domestic sheep (Ovis aries) in Hungary by viral metagenomic analysis. Sequencing of the fragment indicated that it was an ORF1b/ORF2/3′UTR sequence, and it has been submitted to the GenBank database as ovine astrovirus type 2 (OAstV-2/Hungary/2009) with accession number JN592482. The unique sequence characteristics and the phylogenetic position of OAstV-2 suggest that genetically divergent lineages of astroviruses exist in sheep. © 2011 Springer-Verlag.",animal;animal disease;article;Astroviridae;astrovirus infection;classification;domestic animal;feces;genetics;Hungary;isolation and purification;molecular genetics;nucleotide sequence;phylogeny;sheep;sheep disease;virology,"Reuter, G.;Pankovics, P.;Delwart, E.;Boros, Á",2012,,10.1007/s00705-011-1151-4,1
1760,Genetic variability of immunomodulatory genes in ectromelia virus isolates detected by denaturing high-performance liquid chromatography,"The genetic variability of nine genes in 12 isolates and strains of ectromelia virus, which causes a smallpox-like disease (mousepox) in mice, was determined and allows for classification of ectromelia viruses. The low genetic variability suggests that evolutionary pressure maintains the activity of immunomodulatory genes in natural poxvirus infections.",NECROSIS-FACTOR RECEPTOR;A-TYPE INCLUSION;VACCINIA VIRUS;SPECIES-SPECIFICITY;MUTATION DETECTION;IMMUNE EVASION;MOUSEPOX VIRUS;HOST RESPONSE;CD30 HOMOLOG;COWPOX,"Ribas, G.;Rivera, J.;Saraiva, M.;Campbell, R. D.;Alcami, A.",2003,Sep,,0
1761,Kobuvirus (Aichivirus B) infection in Brazilian cattle herds,,,"Ribeiro, J.;Lorenzetti, E.;Alfieri, A. F.;Alfieri, A. A.",2014,,,0
1762,First demonstration of the circulation of a pneumovirus in French pigs by detection of anti-swine orthopneumovirus nucleoprotein antibodies,,,"Richard, C. A.;Hervet, C.;Ménard, D.",2018,,,0
1763,Further studies of the physical and metabolic properties of foot and mouth disease virus temperature sensitive mutants,"Three temperature sensitive (ts) mutants of foot and mouth disease virus were classified as ribonucleic acid negative and as belonging to the same complementation group when measured by virus yields and [3H]uridine incorporation in paired, mixed infections at the nonpermissive temperature (38.5 C). Mutants ts 22, the only mutant able to produce plaques at 38.5 C, was more sensitive to acid than were the parental wild type or other mutant viruses. Diethylaminoethyl dextran did not enhance the plaque forming ability of the mutant viruses at 38.5 C. All of the viruses inhibited host cell protein synthesis at both permissive (33 C) and nonpermissive (38.5 C) temperatures.",Foot and mouth disease virus;in vitro study;microorganism;temperature sensitive mutant;theoretical study,"Richmond, J. Y.;Polatnick, J.",1976,,,0
1764,Borna disease virus: a mystery as an emerging zoonotic pathogen,"For Central European veterinarians, Borna disease (BD) has been known for a long time as a sporadically occurring, progressive viral polioencephalomyelitis predominantly affecting horses and sheep and-as discovered in the last decade-an increasing number of domestic and zoo animals. The aetiological agent, the Borna disease virus (BDV), a negative-sense, single-stranded RNA virus classified in the new virus family Bornaviridae within the order Mononegavirales, can induce severe clinical signs typically of a viral encephalitis with striking behavioural disturbances. After an incubation period lasting a few weeks to several months, BDV-infection causes locomotor and sensory dysfunctions followed by paralysis and death. Natural infections seem to be subclinical in most cases. BD received world-wide attention when it was reported that sera and/or cerebrospinal fluids from neuro-psychiatric patients can contain BDV-specific antibodies. Since infected animals produce BDV-specific antibodies only after virus replication, it was assumed that the broad spectrum of BDV-susceptible species also includes man. However, reports describing the presence of other BDV-markers, i.e. BDV-RNA or BDV-antigen, in peripheral blood leukocytes or brain tissue of neuro-psychiatric patients are highly controversial and, therefore, the role of BDV in human neuro-psychiatric disorders is questionable. (c) 2001 Harcourt Publishers Ltd.",animal;Borna disease;Borna disease virus;disease transmission;health;human;review;virology;zoonosis,"Richt, J. A.;Rott, R.",2001,,,0
1765,Segregation of bovine viral diarrhea virus into genotypes,"Isolates of bovine viral diarrhea virus (BVDV) were segregated into two groups based on comparison of sequences from the 5' untranslated region (UTR) of the viral genome. Phylogenic analysis suggested that these groups, termed BVDV I and BVDV II, are as different from each other as reference BVDV (BVDV-NADL, BVDV-SD-1, BVDV-Osloss) are from hog cholera virus. Polymerase chain reaction (PCR) tests, based on the 5' untranslated region and the genomic region coding for the p125 polypeptide, were designed to differentiate between BVDV I and BVDV II. Using these tests, 76 of 140 isolates of BVDV were identified as BVDV II. Antigenic and pathologic differences were noted between BVDV I and BVDV II viruses. Among BVDV I were viruses commonly used in vaccine production, diagnostic tests, and research. BVDV II was isolated predominantly from fetal bovine sera, persistently infected carves born to dams vaccinated against BVDV, and cattle that had died from an acute form of BVDV termed hemorrhagic syndrome.",antigenicity;article;Bovine viral diarrhea virus 1;controlled study;genotype;nonhuman;phylogeny;priority journal;virus genome,"Ridpath, J. F.;Bolin, S. R.;Dubovi, E. J.",1994,,10.1006/viro.1994.1620,0
1766,Change in predominance of Bovine viral diarrhea virus subgenotypes among samples submitted to a diagnostic laboratory over a 20-year time span,"Although the causative agent of bovine viral diarrhea was initially categorized as 1 species, phylogenetic analysis revealed that these viruses belong to 2 different species, Bovine viral diarrhea virus 1 (BVDV-1) and BVDV-2, with 2-11 subgenotypes within each species. Distribution of species and subgenotypes has been shown to vary with geographic region. Whether distribution shifts over time is not known. Surveys conducted between 1994 and 2008 reported 3 subgenotypes circulating among cattle in the United States: BVDV-1a, BVDV-1b, and BVDV-2a. The average percent prevalence of BVDV-1a, BVDV-1b, and BVDV-2a strains reported in surveys before 2001 were 21%, 43%, and 36%, respectively. Surveys conducted on viruses isolated after 2001 reported decreasing percentages of BVDV-1a and BVDV-2a strains, with BVDV-1b strains accounting for 75-100% of samples. Comparison of these surveys is confounded by differences in geographic location, collection methods, and sample type used in the survey. The purpose of the present study was to determine whether the prevalence of BVDV subgenotypes shifted in samples collected from the same geographic region and by the same laboratory over time. BVDV strains isolated in years 1988, 1998, and 2008, at the Texas Veterinary Medical Diagnostic Laboratory, Amarillo, Texas, were genotyped, and the prevalence of BVDV-1a, BVDV-1b, and BVDV-2a strains were determined. Typing, on the basis of phylogenetic analysis, was done on 148 samples. The strongest trend detected among these samples was a pronounced decrease in the number of BVDV-1a strains over time.",virus DNA;animal;animal disease;antigenic variation;article;Bovine viral diarrhea virus 1;bovine viral diarrhea;bovine;chemistry;genetics;phylogeny;polymerase chain reaction;retrospective study;United States;virology,"Ridpath, J. F.;Lovell, G.;Neill, J. D.;Hairgrove, T. B.;Velayudhan, B.;Mock, R.",2011,,,0
1767,Isolation and characterization of a novel cervid adenovirus from white-tailed deer (Odocoileus virginianus) fawns in a captive herd,"A novel adenovirus, CeAdV1, was isolated from buffy coat and nasal swab samples collected from two captive white-tailed deer (Odocoileus virginianus) fawns. The isolation was an incidental finding in the course of screening animals for use in a research study on an unrelated pathogen. In the screening process, virus isolation was performed on both nasal swabs and buffy coat samples and cytopathic effect was observed. Electron microscopy revealed viral particles with the shape and morphology of an adenovirus. Next generation sequencing followed by phylogenetic analysis classified this virus to the Mastadenovirus genus. Its sequence was genetically distinct from all other recognized species in this genus, with only 76% sequence identity to its closest genetic match, bovine adenovirus 3 (BAdV3). The virus could be propagated in bovine derived cells but grew to a higher titer in cervid derived cells. Inoculation of white-tailed deer fawns with the isolated virus resulted in pyrexia, depletion of thymus tissue and mild respiratory disease. Comparative serology performed using convalescent sera revealed distinct antigenic differences between the novel cervid adenovirus and BAdV3. A retrospective serological survey of the captive deer herd indicated that this virus had been circulating in the herd for at least 14 years with no report of clinical disease. A survey of serum collected from free ranging mule deer residing in Nevada revealed high serum titers against this novel adenovirus.",Adenoviridae;animal cell;animal tissue;article;Bovine adenovirus 3;cervid adenovirus;controlled study;convalescence;electron microscopy;fawn;fever;freeze thawing;herd;in vivo study;Mastadenovirus;mule deer;next generation sequencing;nonhuman;nose smear;phylogeny;primary cell culture;priority journal;rectal temperature;retrospective study;thymus tissue;virus characterization;virus classification;virus isolation;virus particle;white tailed deer,"Ridpath, J. F.;Neill, J. D.;Palmer, M. V.;Bauermann, F. V.;Falkenberg, S. M.;Wolff, P. L.",2017,,10.1016/j.virusres.2017.06.020,0
1768,Stability of the parainfluenza virus 5 genome revealed by deep sequencing of strains isolated from different hosts and following passage in cell culture,"UNLABELLED: The strain diversity of a rubulavirus, parainfluenza virus 5 (PIV5), was investigated by comparing 11 newly determined and 6 previously published genome sequences. These sequences represent 15 PIV5 strains, of which 6 were isolated from humans, 1 was from monkeys, 2 were from pigs, and 6 were from dogs. Strain diversity is remarkably low, regardless of host, year of isolation, or geographical origin; a total of 7.8% of nucleotides are variable, and the average pairwise difference between strains is 2.1%. Variation is distributed unevenly across the PIV5 genome, but no convincing evidence of selection for antibody-mediated evasion in hemagglutinin-neuraminidase was found. The finding that some canine and porcine, but not primate, strains are mutated in the SH gene, and do not produce SH, raised the possibility that dogs (or pigs) may not be the natural host of PIV5. The genetic stability of PIV5 was also demonstrated during serial passage of one strain (W3) in Vero cells at a high multiplicity of infection, under conditions of competition with large proportions of defective interfering genomes. A similar observation was made for a strain W3 mutant (PIV5VDELTAC) lacking V gene function, in which the dominant changes were related to pseudoreversion in this gene. The mutations detected in PIV5VDELTAC during pseudoreversion, and also those characterizing the SH gene in canine and porcine strains, predominantly involved U-to-C transitions. This suggests an important role for biased hypermutation via an adenosine deaminase, RNA-specific (ADAR)-like activity. IMPORTANCE: Here we report the sequence variation of 16 different isolates of parainfluenza virus 5 (PIV5) that were isolated from a number of species, including humans, monkeys, dogs, and pigs, over 4 decades. Surprisingly, strain diversity was remarkably low, regardless of host, year of isolation, or geographical origin. Variation was distributed unevenly across the PIV5 genome, but no convincing evidence of immune or host selection was found. This overall genome stability of PIV5 was also observed when the virus was grown in the laboratory, and the genome stayed remarkably constant even during the selection of virus mutants. Some of the canine isolates had lost their ability to encode one of the viral proteins, termed SH, suggesting that although PIV5 commonly infects dogs, dogs may not be the natural host for PIV5.",Animals;*Genetic Variation;*Genomic Instability;*High-Throughput Nucleotide Sequencing;Humans;Molecular Sequence Data;*Parainfluenza Virus 5/ge [Genetics];*Parainfluenza Virus 5/ip [Isolation & Purification];Parainfluenza Virus 5/ph [Physiology];*Rubulavirus Infections/ve [Veterinary];*Rubulavirus Infections/vi [Virology];Serial Passage;Virus Cultivation,"Rima, B. K.;Gatherer, D.;Young, D. F.;Norsted, H.;Randall, R. E.;Davison, A. J.",2014,Apr,,0
1769,New Minto virus: A new rhabdovirus from ticks in Alaska,"Three strains of a virus were isolated from Haemaphysalis leporis-palustris (Packard) ticks removed from snowshoe hares (Lepus americanus Erxleben) in east central Alaska. We suggest that the virus be named New Minto for the location in which the ticks were collected. Prototype New Minto virus is sensitive to the action of sodium deoxycholate and kills suckling mice by the intracerebral but not intraperitoneal route; weaned mice do not die after intracerebral, intraperitoneal, or subcutaneous inoculation. The virus produces plaque in serially propagated Vero but not in primary Pekin duck embryo cells. By complement-fixation and neutralization tests New Minto is related to Sawgrass virus, a hitherto ungrouped virus from Florida. The establishment of a Sawgrass group is suggested. In addition, Sawgrass virus was found by electron microscopy to belong to the Family Rhabdoviridae.",arthropod;classification;Rhabdoviridae;virus classification;virus isolation,"Ritter, D. G.;Calisher, C. H.;Muth, D. J.",1978,,,0
1770,Multiple hosts and Influenza A viruses genetic mixing,"Influenza A viruses have a segmented, negative-stranded RNA genome. These viruses are classified according to the antigenic properties of the two glycoproteins, expressed on the surface of the virus particles, the hemagglutinin (HA or H) and the neuraminidase (NA or N). To date, 17 H and 10N have been described and 116 HxNy combinations or subtypes reported. Except for the H17N10 subtype recently identified in bats, all identified subtypes have been identified in wild aquatic birds. These birds are considered to be the natural reservoir of influenzaAviruses, from which some subtypes can be transmitted to other bird and mammal species, including humans. Interspecies transmissions seem to occur regularly, and can occasionally lead to the adaptation and stable establishment of a new viral lineage in a given species. This review recalls the genetic diversity of avian, swine and human influenza viruses and focuses on lesserknown influenza A viruses, identified in horses, dogs and very recently in bats. It discusses the genetic mixing that may result from interspecies transmission, and the associated risks of epizootics, zoonosis and pandemics.",avian influenza;avian influenza virus;bat;dog;equine influenza;genetic variability;host;Influenza virus;Influenza A virus;nonhuman;pandemic;review;swine influenza;swine influenza virus;virus;virus transmission;zoonosis,"Rivailler, P.;Moisy, D.;Naffakh, N.",2013,,10.1684/vir.2013.0540,0
1771,Detection of cattle infected with bovine viral diarrhea virus using nucleic acid hybridization,"A ribonucleic acid (RNA) hybridization assay to identify cattle infected by bovine viral diarrhea virus (BVDV) is described. The RNA probe was derived from the coding region at the 3' end of the genome of the NADL strain of BVDV. Total RNA from infected cell cultures or peripheral blood leukocytes from suspect animals was extracted and applied to nylon membranes with a slot blot apparatus. Peripheral blood leukocytes were tested concurrently for BVDV by virus isolation. The results of hybridization and virus isolation were in agreement for 92% of the cases. When compared with virus isolation, hybridization had a sensitivity of detection of 59.5% and a specificity of 95%. Cross-reactivity to RNA extracts of border disease virus-infected cells was noted. No cross-reactivity was detected to other common bovine viruses (bovine herpesvirus-1, bovine respiratory syncytial virus, parainfluenza-3 virus, and bluetongue virus), to viruses classified in related families (equine arteritis virus and Venezuelan equine encephalitis virus), or to viruses having similar genomic organization (dengue virus type 2 and Japanese encephalitis virus).",virus RNA;animal;article;Bovine viral diarrhea virus 1;bovine;cattle disease;genetics;isolation and purification;nucleic acid hybridization;prediction and forecasting;RNA probe;species difference,"Roberts, K. L.;Collins, J. K.;Carman, J.;Blair, C. D.",1991,,,0
1772,First Report of Apple mosaic virus in Alaska,"Apple mosaic virus (ApMV; family Bromoviridae, genus Ilarvirus) is one of the oldest and most economically important viruses of apples (Malus x domestica Borkh.) (1,3). Yield losses may vary from negligible to as much as 50%, depending on the affected cultivar. Although ApMV is found worldwide and occurs naturally in more than 65 plant species (1), it has not been reported to occur in Alaska. In July 2011, noticeably bright yellow mosaic leaves were observed on apple 'Valentine' and its rootstalk 'Ranetka' from an apple orchard in Wasilla, AK. Leaves were collected and assayed by reverse transcription (RT)-PCR using ApMV-specific primers (2) and total RNA extracted with buffer modifications to RNeasy Plant Mini Kit (Qiagen, Valencia, CA). Briefly, 50 mg of leaf tissue was ground in liquid nitrogen and 450 mul of SE buffer (0.14 M NaCl, 2 mM KCl, 2 mM KH<sub>2</sub>PO<sub>4</sub>, 8 mM Na<sub>2</sub>HPO<sub>4</sub>.2H<sub>2</sub>O [pH 7.4], 0.05% vol/vol Tween-20, 2% wt/vol polyvinylpyrrolidone 40, 0.2% wt/vol ovalbumin, 0.5% wt/vol bovine serum albumin, and 0.05% wt/vol sodium azide) was added, and after vigorous vortexing, 80 mul of the mixture was added to 400 mul of RLT buffer supplied by the kit and then processed as directed by the manufacturer (4). Direct sequencing of the predicted ~260-bp PCR product resulted in 97 to 98% nucleotide identities to ApMV accessions in GenBank when analyzed by BLAST. To determine the distribution and incidence of infection in the Wasilla orchard, all 118 apple trees (99 cultivars) were then sampled and assayed serologically by double-antibody sandwich-ELISA with ApMV antiserum according to the manufacturer's protocol (Agdia, Inc., Elkhart, IN). Apple 'Geneva Early' and the same 'Valentine' tree and its rootstock tested positive for ApMV by ELISA and RT-PCR. Strong diagnostic ApMV symptoms were not apparent on the infected 'Geneva Early', which is typical for most commercially grown apples. No leaves were available on the 'Ranetka' rootstock of ApMV-infected 'Geneva Early' for virus indexing. An additional 21 apple trees with no symptoms from an orchard in Talkeetna, AK tested negative to ApMV by ELISA. Limited natural spread of ApMV to other plants may be by pollen and seed transmission. The most prevalent mode of transmission is from ApMV-infected rootstock and grafts. It is important to obtain new propagation plant material from certified virus tested nurseries and to avoid grafting plant material containing ApMV. To my knowledge, this is the first report of ApMV in Alaska. References: (1) R. W. Fulton. No. 83. CMI/AAB Descriptions of Plant Viruses. 1972. (2) W. Menzel et al. J. Virol.",,"Robertson, N. L.",2012,Mar,,0
1773,Genomics and outbreak investigation: From sequence to consequence,"Outbreaks of infection can be devastating for individuals and societies. In this review, we examine the applications of new high-throughput sequencing approaches to the identification and characterization of outbreaks, focusing on the application of whole-genome sequencing (WGS) to outbreaks of bacterial infection. We describe traditional epidemiological analysis and show how WGS can be informative at multiple steps in outbreak investigation, as evidenced by many recent studies. We conclude that high-throughput sequencing approaches can make a significant contribution to the investigation of outbreaks of bacterial infection and that the integration of WGS with epidemiological investigation, diagnostic assays and antimicrobial susceptibility testing will precipitate radical changes in clinical microbiology and infectious disease epidemiology in the near future. However, several challenges remain before WGS can be routinely used in outbreak investigation and clinical practice. © 2013 BioMed Central Ltd.",anthrax;bacterial infection;Bordetella pertussis;bovine tuberculosis;cholera;clinical practice;gene sequence;genomics;hepatitis B;high throughput sequencing;human;influenza;Influenza H7N9;legionnaire disease;measles;nonhuman;priority journal;review,"Robinson, E. R.;Walker, T. M.;Pallen, M. J.",2013,,10.1186/gm440,0
1774,"Recent progress in henipavirus research: Molecular biology, genetic diversity, animal models","Nipah and Hendra virus are members of a newly identified genus of emerging paramyxoviruses, the henipaviruses. Both viruses have the ability to cause severe pulmonary infection and severe acute encephalitis. Following their discovery in the 1990s, outbreaks caused by these zoonotic paramyxoviruses have been associated with high public health and especially economic threat potential. Currently, only geographic groupings in Asia and Australia have been described for the henipaviruses. However, while few viral isolates are available and more detailed characterization is necessary, there has been recent evidence that divergent henipaviruses might be present on the African continent. This review endeavours to capture recent advances in the field of henipavirus research, with a focus on genome structure and replication mechanisms, reservoir hosts, genetic diversity, pathogenesis and animal models. © 2012 Elsevier B.V..",glycoprotein;fusion protein;matrix protein;nucleocapsid protein;phosphoprotein;virulence factor;antigenic variation;bat;diagnostic procedure;epidemic;experimental cat;experimental guinea pig;Mustela putorius furo;genetic variability;geographic distribution;hamster;Henipavirus;Henipavirus infection;horse;host;human;molecular biology;Nipah virus;Nipah virus infection;nonhuman;pathogenesis;primate;priority journal;review;structure analysis;pig;virion;virus classification;virus entry;virus genome;virus replication;virus transmission,"Rockx, B.;Winegar, R.;Freiberg, A. N.",2012,,10.1016/j.antiviral.2012.05.008,0
1775,Bovine leukemia virus can be classified into seven genotypes: Evidence for the existence of two novel clades,"Previous studies have classified the env sequences of bovine leukemia virus (BLV) provirus from different locations worldwide into between two and four genetic groupings. These different studies gave unique names to the identified groups and no study has yet integrated all the available sequences. Thus, we hypothesized that many of the different groups previously identified actually correspond to a limited group of genotypes that are unevenly distributed worldwide. To examine this hypothesis, we sequenced the env gene from 28 BLV field strains and compared these sequences to 46 env sequences that represent all the genetic groupings already identified. By using phylogenetic analyses, we recovered six clades, or genotypes, that we have called genotypes 1, 2, 3, 4, 5 and 6. Genotypes 1-5 have counterparts among the sequence groupings identified previously. One env sequence did not cluster with any of the others and was highly divergent when compared with the six genotypes identified here. Thus, an extra genotype, which we named 7, may exist. Similarity comparisons were highly congruent with phylogenetic analyses. Furthermore, our analyses confirmed the existence of geographical clusters. © 2009 SGM.",virus envelope protein;article;Bovine leukemia virus;cladistics;controlled study;gene cluster;gene sequence;genetic variability;genotype;nonhuman;nucleotide sequence;phylogeny;priority journal;sequence homology;strain difference;virus classification;virus gene;virus identification;virus strain;virus typing,"Rodriguez, S. M.;Golemba, M. D.;Campos, R. H.;Trono, K.;Jones, L. R.",2009,,10.1099/vir.0.011791-0,0
1776,Ultrastructural findings in lymph nodes from pigs suffering from naturally occurring postweaning multisystemic wasting syndrome,"The aims of this study were to evaluate ultrastructural lesions in lymph nodes from postweaning multisystemic wasting syndrome (PMWS)-affected pigs and to correlate these alterations with detection of viral-like particles (VLPs). Samples of lymph nodes were taken from 4 PMWS-affected pigs and 2 healthy animals and processed by transmission electron microscopy. Significant ultrastructural alterations were only noted in PMWS-affected pigs, mainly in histiocytes and rarely in other cell types. Histiocytes showed severe swelling and proliferation of mitochondria, and proliferation and dilation of rough endoplasmic reticulum and Golgi complex. Infected histiocytes contained large numbers of intracytoplasmic inclusion (ICI) bodies with VLPs; some histiocytes also had intranuclear inclusions (INIs). Small inclusions were surrounded by double membrane, with a granular appearance or containing paracrystalline arrays; icosahedral VLPs were 8-17 nm in diameter. Large ICIs were double-membrane bounded or not and contained VLPs usually forming paracrystalline arrays. ICIs were often found next to mitochondria with severe swelling, and also inside them. INIs were not surrounded by membranes and contained virions of 10-13 nm diameter. Lymphocyte depletion was a striking finding of lymph nodes from PMWS-affected pigs. The inclusion bodies containing VLPs referred to in the present study should be classified as viral factories, suggesting that viral replication is probably a frequent event in macrophages, in which mitochondria might play a role.",animal;animal disease;article;electron microscopy;histiocyte;in situ hybridization;lymph node;pathology;pig;swine disease;ultrastructure;virion;virus inclusion;wasting syndrome,"Rodriguez-Cariño, C.;Segalés, J.",2009,,,0
1777,Characterisation of p20 gene sequences from a border disease-like pestivirus isolated from pigs,"A pestivirus, isolated from pigs with haemorrhagic lesions, was antigenically more similar to border disease (BD) virus than to either hog cholera (HC) or bovine viral diarrhoea (BVD) viruses. After reverse transcription the genome at the 5' end, along with the same region from a BD isolate from sheep, was amplified by the polymerase chain reaction and cloned. The region of the p20 gene was sequenced and compared with published data for BVD and HC viruses. A number of motifs were conserved in the amino acid sequences of all the viruses. The pig isolate had a greater degree of homology in this region with the BD isolate (87%) than with BVD (73%) or HC (74%) viruses. This further confirms the BD-like nature of the virus.",amino acid sequence;animal model;conference paper;controlled study;nonhuman;nucleotide sequence;Pestivirus;protein analysis;pig;veterinary medicine;virus characterization;virus classification,"Roehe, P. M.;Woodward, M. J.;Edwards, S.",1992,,10.1016/0378-1135(92)90051-t,0
1778,Natural case of bovine herpesvirus 1 meningoencephalitis in an adult cow,,restriction endonuclease;animal cell;animal tissue;article;Bovine herpesvirus 1;brain stem;cow;differential diagnosis;histopathology;meningoencephalitis;nonhuman;transmission electron microscopy;virus classification,"Roels, S.;Charlier, G.;Letellier, C.;Meyer, G.;Schynts, F.;Kerkhofs, P.;Thiry, E.;Vanopdenbosch, E.",2000,,,0
1779,Characterization of five unclassified orthobunyaviruses (Bunyaviridae) from Africa and the Americas,"The Bunyaviridae family is made up of a diverse range of viruses, some of which cause disease and are a cause for concern in human and veterinary health. Here, we report the genomic and antigenic characterization of five previously uncharacterized bunyaviruses. Based on their ultrastructure, antigenic relationships and phylogenomic relationships, the five viruses are classified as members of the Orthobunyavirus genus. Three are viruses in the California encephalitis virus serogroup and are related to Trivittatus virus; the two others are most similar to the Mermet virus in the Simbu serogroup, and to the Tataguine virus, which is not currently assigned to a serogroup. Each of these five viruses was pathogenic to newborn mice, indicating their potential to cause illness in humans and other animals.",*Aedes/vi [Virology];Africa;Americas;Animals;*Bird Diseases/vi [Virology];Bunyaviridae/cl [Classification];Bunyaviridae/ge [Genetics];*Bunyaviridae/ip [Isolation & Purification];Bunyaviridae/ul [Ultrastructure];*Bunyaviridae Infections/ve [Veterinary];Bunyaviridae Infections/vi [Virology];Mice;Passeriformes/vi [Virology];Phylogeny,"Rogers, M. B.;Gulino, K. M.;Tesh, R. B.;Cui, L.;Fitch, A.;Unnasch, T. R.;Popov, V. L.;Travassos da Rosa, A. P. A.;Guzman, H.;Carrera, J. P.;Vasilakis, N.;Ghedin, E.",2017,Sep,,0
1780,Re-Emergence of a Novel H5N1 Avian Influenza Virus Variant Subclade 2.2.1.1 in Egypt During 2014,"Large-scale surveillance is crucial for understanding the evolution and the emergence of avian influenza viruses (AIVs) in endemic areas. Circulation of highly pathogenic avian influenza (HPAI) subtype H5N1 is continuously causing significant economic losses to the Egyptian poultry industry and is a threat to public health. In this report, a HPAI H5N1 strain (A/chicken/Egypt/Fadllah-7/2014) was detected from a vaccinated flock showing clinical signs of infection. Genetic characterization of the isolate indicated a high level of nucleotide identity (95–98%) with variant and classical groups of H5N1. Moreover, multiple-nucleotide and amino acid alignments revealed several prominent and characteristic substitutions in the surface glycoprotein, which may have biological relevance to the pathobiology of the virus. Phylogenetic analysis demonstrated that the reported isolate closely relates to H5N1 AIVs subclade 2.2.1.1 in spite of no reports of this subclade since 2011 from AI reported cases in Egyptian avian species. In conclusion, our results highlight the re-emergence of a novel H5N1 AIV variant subclade 2.2.1.1 that could escape immunity induced by vaccines. This discovery illustrates the importance of continuous monitoring of poultry in this country for controlling AIV including identifying sources of vaccine seed viruses.",avian influenza vaccine;Newcastle disease vaccine;article;avian influenza (H5N1);avian influenza;chick;clinical feature;controlled study;disease re-emergence;disease surveillance;Egypt;embryo;gene sequence;hemagglutination inhibition test;hemagglutination test;Newcastle disease virus;nonhuman;phylogeny;real time polymerase chain reaction;RNA extraction;vaccination;virus detection;virus isolation;virus virulence;vectormune,"Rohaim, M. A.;El-Naggar, R. F.;Hamoud, M. M.;Nasr, S. A.;Ismael, E.;Laban, S. E.;Ahmed, H. A.;Munir, M.",2017,,10.1111/tbed.12472,0
1781,Do hemagglutinin genes of highly pathogenic avian influenza viruses constitute unique phylogenetic lineages?,"Avian influenza A viruses of the H5 and H7 subtypes periodically cause severe outbreaks of disease in poultry. The question we wished to address in this study is whether these highly pathogenic strains constitute unique lineages or whether they and related nonpathogenic viruses are derived from common ancestors in the wild bird reservoir. We therefore compared the nucleotide and amino acid sequences of the hemagglutinin (HA) genes of 15 H5 and 26 H7 influenza A viruses isolated over 91 years from a variety of host species in Eurasia, Africa, Australia, and North America Phylogenetic analysis indicated that the HA genes of H5 and H7 viruses that cause severe disease in domestic birds do not form unique lineages but share common ancestors with nonpathogenic H5 and H7 viruses. These findings predict that highly pathogenic avian H5 and H7 influenza A viruses will continue to emerge from wild bird reservoirs. Another important question is whether H7 influenza viruses found in mammalian species are derived from avian strains. We included eight equine influenza viruses and one seal isolate in the phylogenetic analysis of H7 HA genes. We could show that the HA genes of both, the equine and the seal viruses, shared ancestors with avian H7 HA genes. This indicates that currently circulating H7 viruses with an avian HA gene may have the potential to adapt to mammalian species and to cause an influenza outbreak in the new host.",hemagglutinin;amino acid sequence;article;epidemic;Fowl plague virus;host cell;nonhuman;phylogeny;poultry;priority journal;species difference;strain difference;virus gene;virus infectivity;virus isolation,"Rohm, C.;Horimoto, T.;Kawaoka, Y.;Suss, J.;Webster, R. G.",1995,,10.1006/viro.1995.1301,0
1782,454-pyrosequencing: A molecular battiscope for freshwater viral ecology,"Viruses, the most abundant biological entities on the planet, are capable of infecting organisms from all three branches of life, although the majority infect bacteria where the greatest degree of cellular diversity lies. However, the characterization and assessment of viral diversity in natural environments is only beginning to become a possibility. Through the development of a novel technique for the harvest of viral DNA and the application of 454 pyrosequencing, a snapshot of the diversity of the DNA viruses harvested from a standing pond on a cattle farm has been obtained. A high abundance of viral genotypes (785) were present within the virome. The absolute numbers of lambdoid and Shiga toxin (Stx) encoding phages detected suggested that the depth of sequencing had enabled recovery of only ca. 8% of the total virus population, numbers that agreed within less than an order of magnitude with predictions made by rarefaction analysis. The most abundant viral genotypes in the pond were bacteriophages (93.7%). The predominant viral genotypes infecting higher life forms found in association with the farm were pathogens that cause disease in cattle and humans, e.g. members of the Herpesviridae. The techniques and analysis described here provide a fresh approach to the monitoring of viral populations in the aquatic environment, with the potential to become integral to the development of risk analysis tools for monitoring the dissemination of viral agents of animal, plant and human diseases. © 2010 by the authors; licensee MDPI, Basel, Switzerland.",double stranded DNA;RNA 16S;RNA 18S;Shiga toxin;small subunit ribosomal RNA;virus DNA;amino acid sequence;article;bacteriophage;bioinformatics;chemotaxis;DNA extraction;DNA virus;freshwater environment;gene amplification;genotype;metagenome;metagenomics;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;pyrosequencing;sequence homology;taxonomy;viral gene delivery system;virus virulence,"Rooks, D. J.;Smith, D. L.;McDonald, J. E.;Woodward, M. J.;McCarthy, A. J.;Allison, H. E.",2010,,10.3390/genes1020210,0
1783,"Studies of genetic relationships between bovine, caprine, cervine, and rangiferine alphaherpesviruses and improved molecular methods for virus detection and identification","The glycoprotein B (gB) and D (gD) genes from five ruminant alphaherpesviruses, bovine herpesvirus 1 (BHV-1), bovine herpesvirus 5 (BHV- 5), caprine herpesvirus 1 (CapHV-1), cervine herpesvirus 1, and rangiferine herpesvirus 1, were partially sequenced. The nucleotide sequence alignments revealed a highly conserved gB gene, with homologies ranging between 87.2 and 99.6%, and a more variable gD gene, with homologies ranging between 71.3 and 98.9%. The phylogenetic analysis of the gB and gD nucleotide and deduced amino acid sequences revealed that BHV-5 is the most closely related virus to the BHV-1 subtype 1 and BHV-1 subtype 2 cluster and that CapHV-1 is the most distantly related virus. The phylogenetic data showed a close relationship of all the studied viruses with suid herpesvirus 1. On the basis of sequence data for the gB gene, a nested PCR combined with restriction enzyme analysis (REA) of the PCR products was developed for the simultaneous detection and identification of the viruses that were studied. Nested primers from highly conserved sequence stretches were selected in order to amplify a region of 294 bp in all five viruses, and a subsequent REA of the PCR products allowed specific identification. A mimic molecule that served as an internal standard of the amplification efficiency was constructed. The practical diagnostic applicability of the assay was evaluated with clinical samples consisting of semen and organ specimens from experimentally infected animals.",glycoprotein B;glycoprotein D;unclassified drug;virus DNA;virus glycoprotein;animal experiment;animal model;article;Bovine herpesvirus 1;Bovine herpesvirus 5;caprine herpesvirus 1;bovine;cervine herpesvirus 1;controlled study;diagnostic value;DNA determination;gene sequence;Herpesviridae;herpes virus infection;male;nonhuman;nucleotide sequence;phylogeny;priority journal;rangiferine herpesvirus 1;semen analysis;sequence homology;Pseudorabies virus;virus characterization;virus detection;virus gene,"Ros, C.;Belák, S.",1999,,,0
1784,Revisiting the taxonomy of the family Circoviridae: establishment of the genus Cyclovirus and removal of the genus Gyrovirus,"The family Circoviridae contains viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, including the smallest known autonomously replicating, capsid-encoding animal pathogens. Members of this family are known to cause fatal diseases in birds and pigs and have been historically classified in one of two genera: Circovirus, which contains avian and porcine pathogens, and Gyrovirus, which includes a single species (Chicken anemia virus). However, over the course of the past six years, viral metagenomic approaches as well as degenerate PCR detection in unconventional hosts and environmental samples have elucidated a broader host range, including fish, a diversity of mammals, and invertebrates, for members of the family Circoviridae. Notably, these methods have uncovered a distinct group of viruses that are closely related to members of the genus Circovirus and comprise a new genus, Cyclovirus. The discovery of new viruses and a re-evaluation of genomic features that characterize members of the Circoviridae prompted a revision of the classification criteria used for this family of animal viruses. Here we provide details on an updated Circoviridae taxonomy ratified by the International Committee on the Taxonomy of Viruses in 2016, which establishes the genus Cyclovirus and reassigns the genus Gyrovirus to the family Anelloviridae, a separate lineage of animal viruses that also contains circular ssDNA genomes. In addition, we provide a new species demarcation threshold of 80% genome-wide pairwise identity for members of the family Circoviridae, based on pairwise identity distribution analysis, and list guidelines to distinguish between members of this family and other eukaryotic viruses with circular, ssDNA genomes.",virus DNA;animal;Circoviridae infection;classification;genetics;Gyrovirus;nucleotide sequence;veterinary medicine;virology;virus genome,"Rosario, K.;Breitbart, M.;Harrach, B.;Segalés, J.;Delwart, E.;Biagini, P.;Varsani, A.",2017,,10.1007/s00705-017-3247-y,0
1785,RNA viral metagenome of whiteflies leads to the discovery and characterization of a whitefly-transmitted Carlavirus in North America,"Whiteflies from the Bemisia tabaci species complex have the ability to transmit a large number of plant viruses and are some of the most detrimental pests in agriculture. Although whiteflies are known to transmit both DNA and RNA viruses, most of the diversity has been recorded for the former, specifically for the Begomovirus genus. This study investigated the total diversity of DNA and RNA viruses found in whiteflies collected from a single site in Florida to evaluate if there are additional, previously undetected viral types within the B. tabaci vector. Metagenomic analysis of viral DNA extracted from the whiteflies only resulted in the detection of begomoviruses. In contrast, whiteflies contained sequences similar to RNA viruses from divergent groups, with a diversity that extends beyond currently described viruses. The metagenomic analysis of whiteflies also led to the first report of a whitefly-transmitted RNA virus similar to Cowpea mild mottle virus (CpMMV Florida) (genus Carlavirus) in North America. Further investigation resulted in the detection of CpMMV Florida in native and cultivated plants growing near the original field site of whitefly collection and determination of its experimental host range. Analysis of complete CpMMV Florida genomes recovered from whiteflies and plants suggests that the current classification criteria for carlaviruses need to be reevaluated. Overall, metagenomic analysis supports that DNA plant viruses carried by B. tabaci are dominated by begomoviruses, whereas significantly less is known about RNA viruses present in this damaging insect vector. © 2014 Rosario et al.",article;Begomovirus;Bromovirus;Bunyaviridae;Carlavirus;Cowpea mild mottle virus;disease carrier;DNA extraction;gene sequence;genetic variability;host range;metagenome;metagenomics;nonhuman;North America;nucleotide sequence;open reading frame;phylogeny;protein motif;sequence alignment;sweet potato whitefly;virus detection;virus genome;virus isolation;virus transmission;whitefly,"Rosario, K.;Capobianco, H.;Ng, T. F. F.;Breitbart, M.;Polston, J. E.",2014,,10.1371/journal.pone.0086748,0
1786,Diverse circovirus-like genome architectures revealed by environmental metagenomics,"Single-stranded DNA (ssDNA) viruses with circular genomes are the smallest viruses known to infect eukaryotes. The present study identified 10 novel genomes similar to ssDNA circovinuses through data-mining of public viral metagenomes. The metagenomic libraries included samples from reclaimed water and three different marine environments (Chesapeake Bay, British Columbia coastal waters and Sargasso Sea). All the genomes have similarities to the replication (Rep) protein of circoviruses; however, only half have genomic features consistent with known circoviruses. Some of the genomes exhibit a mixture of genomic features associated with different families of ssDNA viruses (i.e. circoviruses, geminiviruses and parvoviruses). Unique genome architectures and phylogenetic analysis of the Rep protein suggest that these viruses belong to novel genera and/or families. Investigating the complex community of ssDNA viruses in the environment can lead to the discovery of divergent species and help elucidate evolutionary links between ssDNA viruses.",ROLLING-CIRCLE AMPLIFICATION;NONESSENTIAL TRANSCRIPTION UNITS;FEATHER;DISEASE VIRUS;STRANDED-DNA VIRUSES;MAIZE STREAK VIRUS;PORCINE-CIRCOVIRUS;PROTEIN-SYNTHESIS;CAPSID PROTEIN;IN-VITRO;RECOMBINATION,"Rosario, K.;Duffy, S.;Breitbart, M.",2009,Oct,,0
1787,Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates,"Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including economically valuable agricultural crops and livestock. Although circular Rep-encoding ssDNA (CRESS DNA) viruses are a widespread group for which our knowledge is rapidly expanding, biased sampling toward vertebrates and land plants has limited our understanding of their diversity and evolution. Here, we screened terrestrial arthropods for CRESS DNA viruses and report the identification of 44 viral genomes and replicons associated with specimens representing all three major terrestrial arthropod lineages, namely Euchelicerata (spiders), Hexapoda (insects), and Myriapoda (millipedes). We identified virus genomes belonging to three established CRESS DNA viral families (Circoviridae, Genomoviridae, and Smacoviridae); however, over half of the arthropod-associated viral genomes are only distantly related to currently classified CRESS DNA viral sequences. Although members of viral and satellite families known to infect plants (Geminiviridae, Nanoviridae, Alphasatellitidae) were not identified in this study, these plant-infecting CRESS DNA viruses and replicons are transmitted by hemipterans. Therefore, members from six out of the seven established CRESS DNA viral families circulate among arthropods. Furthermore, a phylogenetic analysis of Reps, including endogenous viral sequences, reported to date from a wide array of organisms revealed that most of the known CRESS DNA viral diversity circulates among invertebrates. Our results highlight the vast and unexplored diversity of CRESS DNA viruses among invertebrates and parallel findings from RNA viral discovery efforts in undersampled taxa.",article;Circoviridae;Geminiviridae;Hemiptera;millipede;Nanoviridae;nonhuman;phylogeny;replicon;spider;virus genome,"Rosario, K.;Mettel, K. A.;Benner, B. E.;Johnson, R.;Scott, C.;Yusseff-Vanegas, S. Z.;Baker, C. C. M.;Cassill, D. L.;Storer, C.;Varsani, A.;Breitbart, M.",2018,,10.7717/peerj.5761,0
1788,Challenges of the Unknown: Clinical Application of Microbial Metagenomics,"Availability of fast, high throughput and low cost whole genome sequencing holds great promise within public health microbiology, with applications ranging from outbreak detection and tracking transmission events to understanding the role played by microbial communities in health and disease. Within clinical metagenomics, identifying microorganisms from a complex and host enriched background remains a central computational challenge. As proof of principle, we sequenced two metagenomic samples, a known viral mixture of 25 human pathogens and an unknown complex biological model using benchtop technology. The datasets were then analysed using a bioinformatic pipeline developed around recent fast classification methods. A targeted approach was able to detect 20 of the viruses against a background of host contamination from multiple sources and bacterial contamination. An alternative untargeted identification method was highly correlated with these classifications, and over 1,600 species were identified when applied to the complex biological model, including several species captured at over 50% genome coverage. In summary, this study demonstrates the great potential of applying metagenomics within the clinical laboratory setting and that this can be achieved using infrastructure available to nondedicated sequencing centres.",article;bacterium contamination;bioinformatics;biological model;gene sequence;metagenomics;microbial community;microbial genetics;microbial identification;nonhuman;pig;priority journal,"Rose, G.;Wooldridge, D. J.;Anscombe, C.;Mee, E. T.;Misra, R. V.;Gharbia, S.",2015,,10.1155/2015/292950,0
1789,Distribution of genotypes of porcine reproductive and respiratory syndrome virus in Ontario During 2004-2007 and the association between genotype and clinical signs of disease,"Restriction fragment length polymorphism (RFLP) was first proposed to classify porcine reproductive and respiratory syndrome virus (PRRSV) in 1998. The primary objective of this study was to identify associations between different PRRSV RFLP types in swine herds in southern Ontario and clinical signs of disease in those herds. Herds included in the study submitted samples to the Animal Health Laboratory at the University of Guelph between September 2004 and August 2007. Each farm owner was surveyed to describe the clinical disease in the herd and the RFLP pattern of an isolate of PRRSV was obtained from a diagnostic sample. The most frequent isolates were RFLP types 1-4 (25.1%), 252 (14.7%), 134 (12%), and 1-2 (7.7%). The distribution of RFLP types in this study was found to be different from a previous investigation in Ontario. Those RFLP types most associated with clinical disease in the farrowing phase of production were 1-4, 1-2, and 134. The only virus type to be significantly associated with disease in the finisher phase was RFLP type 262. During the study period RFLP type 184 emerged in the population in November 2005.",Arterivirus;article;Canada;clinical feature;genetic analysis;genetic association;genotype;herd;nonhuman;pig farming;restriction fragment length polymorphism;reverse transcription polymerase chain reaction;pig;virus classification;virus isolation,"Rosendal, T.;Dewey, C.;Young, B.;Carman, S.;Ge, L.;Poljak, Z.",2010,,,0
1790,Deep sequencing reveals abundant noncanonical retroviral microRNAs in B-cell leukemia/lymphoma,"Viral tumor models have significantly contributed to our understanding of oncogenic mechanisms. How transforming delta-retroviruses induce malignancy, however, remains poorly understood, especially as viral mRNA/protein are tightly silenced in tumors. Here, using deep sequencing of broad windows of small RNA sizes in the bovine leukemia virus ovine model of leukemia/lymphoma, we provide in vivo evidence of the production of noncanonical RNA polymerase III (Pol III)-transcribed viral microRNAs in leukemic B cells in the complete absence of Pol II 5′-LTR-driven transcriptional activity. Processed from a cluster of five independent self-sufficient transcriptional units located in a proviral region dispensable for in vivo infectivity, bovine leukemia virus microRNAs represent ~40% of all microRNAs in both experimental and natural malignancy. They are subject to strong purifying selection and associate with Argonautes, consistent with a critical function in silencing of important cellular and/or viral targets. Bovine leukemia virus microRNAs are strongly expressed in preleukemic and malignant cells in which structural and regulatory gene expression is repressed, suggesting a key role in tumor onset and progression. Understanding how Pol III-dependent microRNAs subvert cellular and viral pathways will contribute to deciphering the intricate perturbations that underlie malignant transformation.",argonaute protein;DNA directed RNA polymerase III;microRNA;untranslated RNA;virus RNA;article;B cell leukemia;B cell lymphoma;B lymphocyte;Bovine leukemia virus;cancer cell;carcinogenesis;CD4+ T lymphocyte;gene silencing;high throughput sequencing;Human T-lymphotropic virus 1;in vivo study;nonhuman;primary tumor;priority journal;protein expression;purifying selection;regulator gene;RNA sequence;tumor growth,"Rosewick, N.;Momont, M.;Durkin, K.;Takeda, H.;Caiment, F.;Cleuter, Y.;Vernin, C.;Mortreux, F.;Wattel, E.;Burny, A.;Georges, M.;Van Den Broeke, A.",2013,,10.1073/pnas.1213842110,0
1791,Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle,"Background: The bovine rumen hosts a diverse and complex community of Eukarya, Bacteria, Archea and viruses (including bacteriophage). The rumen viral population (the rumen virome) has received little attention compared to the rumen microbial population (the rumen microbiome). We used massively parallel sequencing of virus like particles to investigate the diversity of the rumen virome in thirteen lactating Australian Holstein dairy cattle all housed in the same location, 12 of which were sampled on the same day. Results: Fourteen putative viral sequence fragments over 30Kbp in length were assembled and annotated. Many of the putative genes in the assembled contigs showed no homology to previously annotated genes, highlighting the large amount of work still required to fully annotate the functions encoded in viral genomes. The abundance of the contig sequences varied widely between animals, even though the cattle were of the same age, stage of lactation and fed the same diets. Additionally the twelve animals which were co-habited shared a number of their dominant viral contigs. We compared the functional characteristics of our bovine viromes with that of other viromes, as well as rumen microbiomes. At the functional level, we found strong similarities between all of the viral samples, which were highly distinct from the rumen microbiome samples. Conclusions: Our findings suggest a large amount of between animal variation in the bovine rumen virome and that co-habiting animals may have more similar viromes than non co-habited animals. We report the deepest sequencing to date of the rumen virome. This work highlights the enormous amount of novelty and variation present in the rumen virome.",contig;metagenomics;ruminant stomach;bacteriophage;dairy cattle;microbiome;population;gene;diet;lactation;bovine;virus genome;virus;bacterium;eukaryote;virus like agent;community,"Ross, E. M.;Petrovski, S.;Moate, P. J.;Hayes, B. J.",2013,,10.1186/1471-2180-13-242,0
1792,Identification and complete genome sequencing of paramyxoviruses in mallard ducks (Anas platyrhynchos) using random access amplification and next generation sequencing technologies,"BACKGROUND: During a wildlife screening program for avian influenza A viruses (AIV) and avian paramyxoviruses (APMV) in Belgium, we isolated two hemagglutinating agents from pools of cloacal swabs of wild mallards (Anas platyrhynchos) caught in a single sampling site at two different times. AIV and APMV1 were excluded using hemagglutination inhibition (HI) testing and specific real-time RT-PCR tests. METHODS: To refine the virological identification of APMV2-10 realized by HI subtyping tests and in lack of validated molecular tests for APMV2-10, random access amplification was used in combination with next generation sequencing for the sequence independent identification of the viruses and the determination of their genomes. RESULTS: Three different APMVs were identified. From one pooled sample, the complete genome sequence (15054 nucleotides) of an APMV4 was assembled from the random sequences. From the second pooled sample, the nearly complete genome sequence of an APMV6 (genome size of 16236 nucleotides) was determined, as well as a partial sequence for an APMV4. This APMV4 was closely related but not identical to the APMV4 isolated from the first sample. Although a cross-reactivity with other APMV subtypes did not allow formal identification, the HI subtyping revealed APMV4 and APMV6 in the respective pooled samples but failed to identify the co-infecting APMV4 in the APMV6 infected pool. CONCLUSIONS: These data further contribute to the knowledge about the genetic diversity within the serotypes APMV4 and 6, and confirm the limited sensitivity of the HI subtyping test. Moreover, this study demonstrates the value of a random access nucleic acid amplification method in combination with massive parallel sequencing. Using only a moderate and economical sequencing effort, the characterization and full genome sequencing of APMVs can be obtained, including the identification of viruses in mixed infections.","Animals;Avulavirus/cl [Classification];*Avulavirus/ge [Genetics];*Avulavirus/ip [Isolation & Purification];*Avulavirus Infections/ve [Veterinary];Avulavirus Infections/vi [Virology];Belgium;*Ducks/vi [Virology];*Genetic Variation;*Genome, Viral;Genotype;High-Throughput Nucleotide Sequencing;Molecular Sequence Data;*RNA, Viral/ge [Genetics];Serotyping;0 (RNA, Viral)","Rosseel, T.;Lambrecht, B.;Vandenbussche, F.;van den Berg, T.;Van Borm, S.",2011,Oct 06,,0
1793,False-positive results in metagenomic virus discovery: A strong case for follow-up diagnosis,"A viral metagenomic approach using virion enrichment, random amplification and next-generation sequencing was used to investigate an undiagnosed cluster of dairy cattle presenting with high persistent fever, unresponsive to anti-microbial and anti-inflammatory treatment, diarrhoea and redness of nose and teat. Serum and whole blood samples were taken in the predicted hyperviraemic state of an animal that a few days later presented with these clinical signs. Bioinformatics analysis of the resulting data from the DNA virus identification workflow (a total of 32 757 sequences with average read length 335 bases) initially demonstrated the presence of parvovirus-like sequences in the tested blood sample. Thorough follow-up using specific real-time RT-PCR assays targeting the detected sequence fragments confirmed the presence of these sequences in the original sample as well as in a sample of an additional animal, but a contamination with an identical genetic signature in negative extraction controls was demonstrated. Further investigation using an alternative extraction method identified a contamination of the originally used Qiagen extraction columns with parvovirus-like nucleic acids or virus particles. Although we did not find any relevant virus that could be associated with the disease, these observations clearly illustrate the importance of using a proper control strategy and follow-up diagnostic tests in any viral metagenomic study. © 2014 Blackwell Verlag GmbH.",virus DNA;virus RNA;animal;animal disease;article;bovine;cattle disease;classification;contamination;female;genetics;isolation and purification;laboratory diagnosis;metagenomics;methodology;next generation sequencing;Parvoviridae;parvovirus infection;real time polymerase chain reaction;reverse transcription polymerase chain reaction;viral metagenomics;virology;virus,"Rosseel, T.;Pardon, B.;De Clercq, K.;Ozhelvaci, O.;Van Borm, S.",2014,,10.1111/tbed.12251,0
1794,DNase SISPA-next generation sequencing confirms Schmallenberg virus in Belgian field samples and identifies genetic variation in Europe,"In 2011, a novel Orthobunyavirus was identified in cattle and sheep in Germany and The Netherlands. This virus was named Schmallenberg virus (SBV). Later, presence of the virus was confirmed using real time RT-PCR in cases of congenital malformations of bovines and ovines in several European countries, including Belgium. In the absence of specific sequencing protocols for this novel virus we confirmed its presence in RT-qPCR positive field samples using DNase SISPA-next generation sequencing (NGS), a virus discovery method based on random amplification and next generation sequencing. An in vitro transcribed RNA was used to construct a standard curve allowing the quantification of viral RNA in the field samples. Two field samples of aborted lambs containing 7.66 and 7.64 log(10) RNA copies per micro L total RNA allowed unambiguous identification of SBV. One sample yielded 192 SBV reads covering about 81% of the L segment, 56% of the M segment and 13% of the S segment. The other sample resulted in 8 reads distributed over the L and M segments. Three weak positive field samples (one from an aborted calf, two from aborted lambs) containing virus quantities equivalent to 4.27-4.89 log(10) RNA copies per micro L did not allow identification using DNase SISPA-NGS. This partial sequence information was compared to the whole genome sequence of SBV isolated from bovines in Germany, identifying several sequence differences. The applied viral discovery method allowed the confirmation of SBV in RT-qPCR positive brain samples. However, the failure to confirm SBV in weak PCR-positive samples illustrates the importance of the selection of properly targeted and fresh field samples in any virus discovery method. The partial sequences derived from the field samples showed several differences compared to the sequences from bovines in Germany, indicating sequence divergence within the epidemic.","Belgium;*DNA Primers/ge [Genetics];*Deoxyribonucleases/me [Metabolism];*Genetic Variation;*High-Throughput Nucleotide Sequencing/mt [Methods];Molecular Sequence Data;*Nucleic Acid Amplification Techniques;*Orthobunyavirus/ge [Genetics];RNA, Viral/ge [Genetics];*Sequence Analysis, RNA/mt [Methods];0 (DNA Primers);0 (RNA, Viral)","Rosseel, T.;Scheuch, M.;Hoper, D.;De Regge, N.;Caij, A. B.;Vandenbussche, F.;Van Borm, S.",2012,,,1
1795,Markers for ongoing or previous hepatitis E virus infection are as common in wild ungulates as in humans in Sweden,"Hepatitis E virus (HEV) is a human pathogen with zoonotic spread, infecting both domestic and wild animals. About 17% of the Swedish population is immune to HEV, but few cases are reported annually, indicating that most infections are subclinical. However, clinical hepatitis E may also be overlooked. For identified cases, the source of infection is mostly unknown. In order to identify whether HEV may be spread from wild game, the prevalence of markers for past and/or ongoing infection was investigated in sera and stool samples collected from 260 hunted Swedish wild ungulates. HEV markers were found in 43 (17%) of the animals. The most commonly infected animal was moose (Alces alces) with 19 out of 69 animals (28%) showing HEV markers, followed by wild boar (Sus scrofa) with 21 out of 139 animals (15%), roe deer (Capreolus capreolus) with 2 out of 30 animals, red deer (Cervus elaphus) with 1 out of 15 animals, and fallow deer (Dama dama) 0 out of 7 animals. Partial open reading frame 1 (ORF1) of the viral genomes from the animals were sequenced and compared with those from 14 endemic human cases. Phylogenetic analysis revealed that three humans were infected with HEV strains similar to those from wild boar. These results indicate that wild animals may be a source of transmission to humans and could be an unrecognized public health concern.",animal experiment;article;disease transmission;European wild boar;gene amplification;gene sequence;hepatitis E;Hepatitis E virus;moose;nonhuman;open reading frame;phylogeny;prevalence;real time polymerase chain reaction;reverse transcription polymerase chain reaction;roe deer;Sweden;virus detection,"Roth, A.;Lin, J.;Magnius, L.;Karlsson, M.;Belák, S.;Widén, F.;Norder, H.",2016,,10.3390/v8090259,0
1796,A new influenza A virus infection in turkeys. VII. Comparative immunology,"Four influenza A strains isolated from turkeys in Ontario as well as strain Chicken/Scotland/59 were found to immunize turkeys against the lethal disease caused by virus Turkey/Ontario 7732/66 (V7732). These viruses form the avian influenza A serotype 5 (AA5). Immunoprotection against V7732 was not obtained with influenza viruses of other serotypes. Immunoprotective relationships among AA5 viruses were not always demonstrable in hemagglutination-inhibition (HI) and serum-neutralization (SN) tests, especially with turkey and mammalian antisera; better correlation between immunoprotection and these in vitro tests was seen with chicken antisera. The implications of these findings relative to virus classification, serodiagnosis and vaccination are discussed.",Animals;Antigen-Antibody Reactions;Antigens/an [Analysis];Chickens;Cross Reactions;Guinea Pigs;Hemagglutination Inhibition Tests;Immune Sera;Neutralization Tests;Orthomyxoviridae/cl [Classification];*Orthomyxoviridae/im [Immunology];Orthomyxoviridae/ip [Isolation & Purification];Orthomyxoviridae Infections/im [Immunology];*Orthomyxoviridae Infections/ve [Veterinary];*Poultry Diseases/im [Immunology];Rabbits;Rats;Serotyping;*Turkeys;0 (Antigens);0 (Immune Sera),"Rouse, B. T.;Lang, G.;Narayan, O.",1971,Jan,,0
1797,"Investigation of foot-and mouth disease outbreak in a pig farm at Kollam district of Kerala, India","The present paper describes the investigation of foot-and-mouth disease (FMD) outbreak in a private pig farm at Kotty in Kollam district of Kerala during October 2013. During the clinical phase, severe vesicular lesions on snout and skin around the coronary bands were observed in pigs. A total of 48 serum samples and 12 clinical samples (ruptured snout epithelia) were collected. All serum samples were subjected to indirect 3AB nonstructural protein (NSP) ELISA and liquid phase blocking (LPB) ELISA. In 3AB NSP ELISA, all serum samples were found positive for NSP antibodies indicating infection. In LPB ELISA, 42 of 48 (87.5%) pigs were found to have protective log10 antibody titre of ≥1.8 against FMD virus serotypes O, A and Asia 1. All the clinical materials were found positive for serotype O in antigen detection ELISA as well as in multiplex reverse transcription-polymerase chain reaction (mRT-PCR). In VP1 region-based phylogenetic analysis, the serotype O isolates causing the outbreak were found to conglomerate within Ind2001 lineage. Pigs infected with FMD may pose rigorous threat to other susceptible domestic livestock as they exhale enormous quantity of virus. As a consequence, they should be included under prophylactic vaccination and surveillance programmes ongoing in the country.",nonstructural protein 3;agar gel electrophoresis;animal lameness;antibody titer;antigen detection;article;controlled study;disease surveillance;enzyme linked immunosorbent assay;farm animal;fever;foot and mouth disease;Foot and mouth disease virus;high throughput sequencing;India;liquid liquid extraction;livestock;multiplex polymerase chain reaction;nonhuman;nucleotide sequence;pain;phylogenetic tree;phylogeny;pig;ruminant;serotype;vaccination;vesicular rash;virus detection;virus transmission,"Rout, M.;Subramaniam, S.;Mohapatra, J. K.;Dash, B. B.;Pattnaik, B.",2018,,10.18805/ijar.B-3071,0
1798,Discovery of a new avian bornavirus genotype in estrildid finches (Estrildidae) in Germany,"Avian bornaviruses (ABV) are known to be the causative agent of proventricular dilatation disease (PDD) in parrots and their relatives (Psittaciformes). A broad range of ABV genotypes has been detected not only in psittacine birds, but also in other avian species including canary birds (Serinus canaria forma domestica) and Bengalese finches (Lonchura striata f. dom.), which are both members of the order songbirds (Passeriformes). During this study 286 samples collected from captive and wild birds of various passerine species in different parts of Germany were screened for the presence of ABV. Interestingly, only three ABV-positive samples were identified by RT-PCR. They originated from one yellow-winged pytilia (Pytilia hypogrammica) and two black-rumped waxbills (Estrilda troglodytes) from a flock of captive estrildid finches in Saxony. The ABV isolates detected here were only distantly related to ABV isolates found in passerine species in Germany and Japan and form a new genotype tentatively called ABV-EF (for ""estrildid finches"").","Animals;Animals, Wild;Base Sequence;*Bird Diseases/vi [Virology];*Bornaviridae/ge [Genetics];Bornaviridae/gd [Growth & Development];*Bornaviridae/ip [Isolation & Purification];*Finches/vi [Virology];Genotype;Germany;Molecular Sequence Data;Mononegavirales Infections/ve [Veterinary];*Mononegavirales Infections/vi [Virology];Phylogeny;Reverse Transcriptase Polymerase Chain Reaction","Rubbenstroth, D.;Schmidt, V.;Rinder, M.;Legler, M.;Corman, V. M.;Staeheli, P.",2014,Jan 31,,0
1799,Phylogenetic characterization of Newcastle disease virus isolated in the mainland of China during 2001-2009,"Twenty Newcastle disease virus (NDV) isolates from infected chicken flocks during 2001 to 2009 in China were biologically and genetically characterized. All the 20 NDVs were categorized into velogenic (n = 17) and lentogenic (n = 3) viruses, respectively, according to the mean death time (MDT) of chicken embryos. Velogenic viruses carry the motif 112R-R-Q-K-R/F117 (n = 14) or 112G-R-Q-G-R/L117 (n = 3) at the F0 cleavage site, while all the lentogenic virus had a sequence motif of 112G-R-Q-G-R/L117 (n = 3) at the same site. Phylogenetic analysis revealed that at least three distinct genotypes (genotypes I, II and VII) existed in chicken flocks in China and VIId of genotype VII were mainly responsible for the present ND panzootic. Two natural recombinants (XD/Shandong/08 and QG/Hebei/07) were supposed and identified by the SimPlot program, and their two parental-like strains might be from the NDV vaccine lineage and VIId velogenic lineage respectively. The results indicate that recombination play a role in NDV evolution and the live vaccines have capacity to boost NDV evolution by homologous recombination with circulating virus. © 2009 Elsevier B.V. All rights reserved.",live vaccine;amino acid sequence;article;bird disease;chicken;China;gene amplification;genotype;herd;Newcastle disease virus;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;sequence alignment;sequence analysis;sequence homology;unindexed sequence;virus isolation;virus recombination;virus strain,"Rui, Z.;Juan, P.;Jingliang, S.;Jixun, Z.;Xiaoting, W.;Shouping, Z.;Xiaojiao, L.;Guozhong, Z.",2010,,10.1016/j.vetmic.2009.09.020,0
1800,The potential for respiratory droplet-transmissible A/H5N1 influenza virus to evolve in a mammalian host,"Avian A/H5N1 influenza viruses pose a pandemic threat. As few as five amino acid substitutions, or four with reassortment, might be sufficient for mammal-to-mammal transmission through respiratory droplets. From surveillance data, we found that two of these substitutions are common in A/H5N1 viruses, and thus, some viruses might require only three additional substitutions to become transmissible via respiratory droplets between mammals. We used a mathematical model of within-host virus evolution to study factors that could increase and decrease the probability of the remaining substitutions evolving after the virus has infected a mammalian host. These factors, combined with the presence of some of these substitutions in circulating strains, make a virus evolving in nature a potentially serious threat. These results highlight critical areas in which more data are needed for assessing, and potentially averting, this threat.","Adaptation, Physiological;Air Microbiology;Amino Acid Substitution;Animals;Birds;*Evolution, Molecular;Genetic Fitness;Glycosylation;*Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];Hemagglutinin Glycoproteins, Influenza Virus/me [Metabolism];High-Throughput Nucleotide Sequencing;Humans;*Influenza A Virus, H5N1 Subtype/ge [Genetics];*Influenza A Virus, H5N1 Subtype/py [Pathogenicity];Influenza in Birds/vi [Virology];Influenza, Human/im [Immunology];Influenza, Human/tm [Transmission];*Influenza, Human/vi [Virology];Mammals;Models, Biological;Mutation;Orthomyxoviridae Infections/tm [Transmission];*Orthomyxoviridae Infections/vi [Virology];Probability;*RNA Replicase/ge [Genetics];Receptors, Virus/me [Metabolism];*Respiratory System/vi [Virology];Selection, Genetic;Sialic Acids/me [Metabolism];*Viral Proteins/ge [Genetics];0 (Hemagglutinin Glycoproteins, Influenza Virus);0 (PB2 protein, Influenzavirus A);0 (Receptors, Virus);0 (Sialic Acids);0 (Viral Proteins);0 (hemagglutinin, avian influenza A virus)","Russell, C. A.;Fonville, J. M.;Brown, A. E.;Burke, D. F.;Smith, D. L.;James, S. L.;Herfst, S.;van Boheemen, S.;Linster, M.;Schrauwen, E. J.;Katzelnick, L.;Mosterin, A.;Kuiken, T.;Maher, E.;Neumann, G.;Osterhaus, A. D.;Kawaoka, Y.;Fouchier, R. A.;Smith, D. J.",2012,Jun 22,,0
1801,H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets,"A pandemic-capable influenza virus requires a hemagglutinin (HA) surface glycoprotein that is immunologically unseen by most people and is capable of supporting replication and transmission in humans. HA stabilization has been linked to 2009 pH1N1 pandemic potential in humans and H5N1 airborne transmissibility in the ferret model. Swine have served as an intermediate host for zoonotic influenza viruses, yet the evolutionary pressure exerted by this host on HA stability was unknown. For over 70 contemporary swine H1 and H3 isolates, we measured HA activation pH to range from pH 5.1 to 5.9 for H1 viruses and pH 5.3 to 5.8 for H3 viruses. Thus, contemporary swine isolates vary widely in HA stability, having values favored by both avian (pH >5.5) and human and ferret (pH <=5.5) species. Using an early 2009 pandemic H1N1 (pH1N1) virus backbone, we generated three viruses differing by one HA residue that only altered HA stability: WT (pH 5.5), HA1-Y17H (pH 6.0), and HA2-R106K (pH 5.3). All three replicated in pigs and transmitted from pig-to-pig and pig-to-ferret. WT and R106 viruses maintained HA genotype and phenotype after transmission. Y17H (pH 6.0) acquired HA mutations that stabilized the HA protein to pH 5.8 after transmission to pigs and 5.5 after transmission to ferrets. Overall, we found swine support a broad range of HA activation pH for contact transmission and many recent swine H1N1 and H3N2 isolates have stabilized (human-like) HA proteins. This constitutes a heightened pandemic risk and underscores the importance of ongoing surveillance and control efforts for swine viruses.","Animals;Ferrets/vi [Virology];HEK293 Cells;*Hemagglutinin Glycoproteins, Influenza Virus/me [Metabolism];High-Throughput Nucleotide Sequencing;Humans;Immunohistochemistry;*Influenza A Virus, H1N1 Subtype/me [Metabolism];*Orthomyxoviridae Infections/tm [Transmission];Protein Stability;Real-Time Polymerase Chain Reaction;Swine/vi [Virology];0 (H1N1 virus hemagglutinin);0 (Hemagglutinin Glycoproteins, Influenza Virus)","Russier, M.;Yang, G.;Marinova-Petkova, A.;Vogel, P.;Kaplan, B. S.;Webby, R. J.;Russell, C. J.",2017,03,,0
1802,"Discovery of an expanded set of avian leukosis subroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline","Transposable elements (TEs), such as endogenous retroviruses (ERVs), are common in the genomes of vertebrates. ERVs result from retroviral infections of germ-line cells, and once integrated into host DNA they become part of the host's heritable genetic material. ERVs have been ascribed positive effects on host physiology such as the generation of novel, adaptive genetic variation and resistance to infection, as well as negative effects as agents of tumorigenesis and disease. The avian leukosis virus subgroup E family (ALVE) of endogenous viruses of chickens has been used as a model system for studying the effects of ERVs on host physiology, and approximately 30 distinct ALVE proviruses have been described in the Gallus gallus genome. In this report we describe the development of a software tool, which we call Vermillion, and the use of this tool in combination with targeted next-generation sequencing (NGS) to increase the number of known proviruses belonging to the ALVE family of ERVs in the chicken genome by 4-fold, including expanding the number of known ALVE elements on chromosome 1 (Gga1) from the current 9 to a total of 40. Although we focused on the discovery of ALVE elements in chickens, with appropriate selection of target sequences Vermillion can be used to develop profiles of other families of ERVs and TEs in chickens as well as in species other than the chicken.",animal;avian leukosis;Avian leukosis virus;bird disease;chicken;genetics;high throughput sequencing;physiology;provirus;software;veterinary medicine;virology,"Rutherford, K.;Meehan, C. J.;Langille, M. G.;Tyack, S. G.;McKay, J. C.;McLean, N. L.;Benkel, K.;Beiko, R. G.;Benkel, B.",2016,,10.3382/ps/pew194,0
1803,Identification and classification of bovine leukemia virus isolates in Russia and ukraine based on the pol viral gene polymorphism,"Bovine leukemia virus (BLV) is a widespread specific pathogen of cattle. Analysis of the pol viral gene polymorphism has been used to characterize the polymorphism of BLV isolates at stock-breeding farms in Russia and Ukraine. The fragments of the pol gene corresponding to the reverse transcriptase and integrase 494 and 233 bp in size, respectively, have been used for analysis. Phylogenetic analysis has revealed several variants of BLV clustered with a high bootstrap support in Russia and Ukraine. A new classification of BLV variants is suggested. Comparison of phylograms based on the polymorphism of the nucleotide sequences of the integrase and reverse transcriptase domains did not show topological conflicts. Therefore, recombination between BLV variants has not been found. © 2012 Pleiades Publishing, Ltd.",integrase;Pol protein;RNA directed DNA polymerase;amino acid substitution;article;Bovine leukemia virus;controlled study;DNA polymorphism;gene mapping;gene sequence;genetic recombination;genetic variability;nonhuman;nucleotide sequence;phylogeny;priority journal;Russian Federation;sequence analysis;structural gene;Ukraine;virus classification;virus gene;virus genome;virus identification;virus recombination,"Ruzina, M. N.;Andrianov, B. V.;Shaikhaev, G. O.;Sulimova, G. E.",2012,,10.1134/s1022795412060117,0
1804,Serological differentiation of foot-and-mouth disease virus strains in relation to selection of suitable vaccine viruses,"Serological differentiations for the purpose of selecting suitable vaccine strains or for advice on vaccine usage attempt to predict whether a given vaccine/antigen is likely to induce antibody that will be protective against prevailing field strains. The purpose of such differentiations is not identical with virus classification. It is proposed, therefore, that the most appropriate measure of this relationship (r) is given by: r = activity of serum against heterologous (Field) strain/activity of serum against homologous (Vaccine) strain. A comparison of the complement fixation test with virus neutralization test systems - i.e. metabolic inhibition (colour), plaque reduction, a two-dimensional microneutralization cytopathic end point (microneut.) and neutralization kinetics - showed that the two test systems did not always give identical results. Experience has also shown that there is a good correlation in cattle between the serum neutralizing titre and protection to challenge both in homologous and heterologous systems. It is possible to demonstrate a dose response relationship between vaccine antigen dose and serum neutralizing titre. It is suggested, therefore, that the preferred test for strain comparison for the purpose of vaccine usage should be one based on the virus neutralization system. In carrying out comparison of two virus strains they must be assumed to be identical until they have been shown to be probably different. For each test system, therefore, it is necessary to know the intrinsic test error so that the least difference between two test values that is statistically significant can be recognised. An analysis of the discriminating power of the various test systems used in our laboratory is presented. Experience has shown that methods of handling and storage of vaccine viruses may result in significant changes in the bio-physical characteristics of the virus, e.g. virulence, plaque morphology, behaviour in sucrose density gradient, even in antigenic shift and immunogenicity. It is suggested, therefore, that as far as possible, reference antisera for comparison of strains for judgement on vaccine usage should be prepared from those strains that are in current use in vaccine production.",inactivated virus vaccine;bovine;Foot and mouth disease virus;prevention;vaccination,"Rweyemamu, M. M.;Pay, T. W. F.;Parker, M. J.",1977,,,0
1805,Universal oligonucleotide microarray for sub-typing of Influenza A virus,"A universal microchip was developed for genotyping Influenza A viruses. It contains two sets of oligonucleotide probes allowing viruses to be classified by the subtypes of hemagglutinin (H1-H13, H15, H16) and neuraminidase (N1-N9). Additional sets of probes are used to detect H1N1 swine influenza viruses. Selection of probes was done in two steps. Initially, amino acid sequences specific to each subtype were identified, and then the most specific and representative oligonucleotide probes were selected. Overall, between 19 and 24 probes were used to identify each subtype of hemagglutinin (HA) and neuraminidase (NA). Genotyping included preparation of fluorescently labeled PCR amplicons of influenza virus cDNA and their hybridization to microarrays of specific oligonucleotide probes. Out of 40 samples tested, 36 unambiguously identified HA and NA subtypes of Influenza A virus.",complementary DNA;Influenza virus hemagglutinin;virus DNA;virus sialidase;amino acid sequence;amplicon;article;controlled study;DNA microarray;fluorescence analysis;genotype;Influenza A virus;Influenza A virus (H1N1);microchip analysis;nonhuman;nucleotide sequence;oligonucleotide probe;polymerase chain reaction;virus classification,"Ryabinin, V. A.;Kostina, E. V.;Maksakova, G. A.;Neverov, A. A.;Chumakov, K. M.;Sinyakov, A. N.",2011,,10.1371/journal.pone.0017529,0
1806,Invertebrate RNA virus diversity from a taxonomic point of view,"Invertebrates are hosts to diverse RNA viruses that have all possible types of encapsidated genomes (positive, negative and ambisense single stranded RNA genomes, or a double stranded RNA genome). These viruses also differ markedly in virion morphology and genome structure. Invertebrate RNA viruses are present in three out of four currently recognized orders of RNA viruses: Mononegavirales, Nidovirales, and Picornavirales, and 10 out of 37 RNA virus families that have yet to be assigned to an order. This mini-review describes general properties of the taxonomic groups, which include invertebrate RNA viruses on the basis of their current classification by the International Committee on Taxonomy of Viruses (ICTV). (C) 2016 Elsevier Inc. All rights reserved.",Taxonomy;RNA viruses;Invertebrates;Pathogens;Review;PICORNA-LIKE VIRUS;PENAEUS-MONODON PRAWNS;GILL-ASSOCIATED NIDOVIRUS;BOVINE EPHEMERAL FEVER;IMPORTED FIRE ANT;GENOME SEQUENCE;SOLENOPSIS-INVICTA;BLUETONGUE VIRUS;EVOLUTION;INSECT,"Ryabov, E. V.",2017,Jul,,0
1807,"Rabies of canid biotype in wild dog (Lycaon pictus) and spotted hyaena (Crocuta crocuta) in Madikwe Game Reserve, South Africa in 2014-2015: Diagnosis, possible origins and implications for control","Both domestic and wild carnivore species are commonly diagnosed with rabies virus (RABV) infection in South Africa. Although the majority of confirmed rabies cases in wild carnivore species are reported from the yellow mongoose (Cynictis penicillata), the rest are from other wild carnivores including the highly endangered wild dog (Lycaon pictus). Lyssavirus infection was confirmed in two wild dogs and a spotted hyaena (Crocuta crocuta) in the Madikwe Game Reserve, North West province in South Africa, in 2014 and 2015, using a direct fluorescent antibody test and immunohistochemistry. There had been no new wild dog introductions to the Madikwe Game Reserve for many years and the wild dogs were last vaccinated against rabies approximately 11 years prior to the incident. The first euthanised wild dog was the last surviving of a break-away pack of 6, and the second was the last of a larger pack of 18, the rest of which died with no carcasses being found or carcasses too decomposed for sampling. Subsequent antigenic typing of the lyssaviruses indicated that they were canid RABVs. The RABVs originating from 22 wild carnivore species, 7 dogs, and a caprine, mostly from the North West province, were genetically characterised by targeting a partial region of the nucleoprotein gene. The nucleotide sequence analyses of these viruses and two previously characterised RABVs confirmed that the outbreak viruses were also canid rabies, phylogenetically clustering with virus isolates originating from black-backed jackals recovered between 2012 and 2015 from the North West province, and domestic dogs from neighbouring communal areas. The source(s) of the mortalities and possible reservoir host(s) for the virus could only be speculated upon from data on specific predator numbers, movements and behaviour, kills, park management and the changing environmental ecology, which were monitored closely in Madikwe over several years. The most likely rabies sources were from boundary fence contacts between wild carnivores within the park, with domestic dogs or cats and/or naturally occurring wild carnivores outside the park. The associated risk of zoonotic infection and threat to important and endangered predators may be mitigated through regional rabies control primarily in domestic dogs and cats, as well as by preventative vaccination of at-risk park employees and their pets. The importance of ongoing prophylactic rabies protection by regular vaccination of highly endangered wildlife carnivores and the submission of carcasses for rabies diagnosis of any wild or domestic animals behaving uncharacteristically or found dead is emphasised.",virus antigen;adult;animal tissue;axon;brain tissue;Canidae;carcass;Crocuta crocuta;dendrite;direct fluorescent antibody technique;dog;epidemic;gene sequence;immunohistochemistry;Lycaon pictus;Lyssavirus;nonhuman;nucleotide sequence;perikaryon;phylogeny;rabies;review;sequence analysis,"Sabeta, C. T.;Janse Van Rensburg, D. D.;Phahladira, B.;Mohale, D.;Harrison-White, R. F.;Esterhuyzen, C.;Williams, J. H.",2018,,10.4102/jsava.v89i0.1517,0
1808,Characterization of a novel VIIl sub-genotype of Newcastle disease virus circulating in Iran,"Newcastle disease is an economically important and highly contagious disease affecting wild and domestic avian species. Despite extensive vaccination efforts within the poultry industry, Newcastle disease virus (NDV) outbreaks causing significant economic losses still occur. Rural chickens may act as a potential reservoir of NDVs for commercial poultry due to poor biosecurity and inadequate vaccination. The aim of this study was to investigate the phylogenetic relationship and molecular characterization of eight NDVs isolated from backyard poultry in Iran during 2011–2013. The complete coding sequence of fusion (F) and haemagglutinin-neuraminidase (HN) genes of eight NDVs were determined and compared with other published NDVs. Based on inter-population distances and phylogenetic topology between available NDV categories, Iranian isolates formed a novel VIIl sub-genotype distinct from previous groups designated in genotype VII. Furthermore, both F and HN genes of the Iranian isolates shared high nucleotide sequence similarity with viruses isolated in China. All viruses analysed contained a polybasic cleavage site motif (111G/RRRQKR↓F117), indicating that all isolates could be categorized as a virulent pathotype. No mutation was observed in the neutralizing epitopes of the F protein. Analysis of amino acids associated with neutralizing antigenic sites within the HN protein revealed that all isolates exhibited a unique amino acid (Q) at position 347. These results emphasize the need for strengthening the biosecurity measures implemented on village flocks and practicing a mandatory vaccination programme for local poultry. Moreover, continuous monitoring of NDVs in different species of birds can help to gain more knowledge about the evolution of this virus and prevent future panzootics.",nucleocapsid protein;amino acid analysis;article;fusion gene;gene sequence;haemagglutinin neuraminidase gene;Iran;Newcastle disease virus;Newcastle disease virus subgenotype VIIb;Newcastle disease virus subgenotype VIId;Newcastle disease virus subgenotype VIIe;Newcastle disease virus subgenotype VIIf;Newcastle disease virus subgenotype VIIg;Newcastle disease virus subgenotype VIIh;Newcastle disease virus subgenotype VIIi;Newcastle disease virus subgenotype VIIj;Newcastle disease virus subgenotype VIIk;Newcastle disease virus subgenotype VIIl;nonhuman;nucleotide sequence;phylogeny;virus gene;virus isolation,"Sabouri, F.;Vasfi Marandi, M.;Bashashati, M.",2018,,10.1080/03079457.2017.1376735,0
1809,Simultaneous identification of DNA and RNA viruses present in pig faeces using process-controlled deep sequencing,"BACKGROUND: Animal faeces comprise a community of many different microorganisms including bacteria and viruses. Only scarce information is available about the diversity of viruses present in the faeces of pigs. Here we describe a protocol, which was optimized for the purification of the total fraction of viral particles from pig faeces. The genomes of the purified DNA and RNA viruses were simultaneously amplified by PCR and subjected to deep sequencing followed by bioinformatic analyses. The efficiency of the method was monitored using a process control consisting of three bacteriophages (T4, M13 and MS2) with different morphology and genome types. Defined amounts of the bacteriophages were added to the sample and their abundance was assessed by quantitative PCR during the preparation procedure. RESULTS: The procedure was applied to a pooled faecal sample of five pigs. From this sample, 69,613 sequence reads were generated. All of the added bacteriophages were identified by sequence analysis of the reads. In total, 7.7% of the reads showed significant sequence identities with published viral sequences. They mainly originated from bacteriophages (73.9%) and mammalian viruses (23.9%); 0.8% of the sequences showed identities to plant viruses. The most abundant detected porcine viruses were kobuvirus, rotavirus C, astrovirus, enterovirus B, sapovirus and picobirnavirus. In addition, sequences with identities to the chimpanzee stool-associated circular ssDNA virus were identified. Whole genome analysis indicates that this virus, tentatively designated as pig stool-associated circular ssDNA virus (PigSCV), represents a novel pig virus. CONCLUSION: The established protocol enables the simultaneous detection of DNA and RNA viruses in pig faeces including the identification of so far unknown viruses. It may be applied in studies investigating aetiology, epidemiology and ecology of diseases. The implemented process control serves as quality control, ensures comparability of the method and may be used for further method optimization.",Animals;Base Sequence;*DNA Viruses/ge [Genetics];*Feces/vi [Virology];*High-Throughput Nucleotide Sequencing/mt [Methods];Molecular Sequence Data;*RNA Viruses/ge [Genetics];Swine,"Sachsenroder, J.;Twardziok, S.;Hammerl, J. A.;Janczyk, P.;Wrede, P.;Hertwig, S.;Johne, R.",2012,,,0
1810,"The general composition of the faecal virome of pigs depends on age, but not on feeding with a probiotic bacterium","Background: The pig faecal virome, which comprises the community of viruses present in pig faeces, is complex and consists of pig viruses, bacteriophages, transiently passaged plant viruses and other minor virus species. Only little is known about factors influencing its general composition. Here, the effect of the probiotic bacterium Enterococcus faecium (E. faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. Results: From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. In average, 14% of the reads showed significant sequence identities to known viruses. The percentage of detected mammalian virus sequences was highest (55-77%) in the samples of the youngest piglets and lowest (8-10%) in the samples of the sows. In contrast, the percentage of bacteriophage sequences increased from 22-44% in the youngest piglets to approximately 90% in the sows. The dominating mammalian viruses differed remarkably among 12 day-old piglets (kobuvirus), 54 day-old piglets (boca-, dependo- and pig stool-associated small circular DNA virus [PigSCV]) and the sows (PigSCV, circovirus and ""circovirus-like"" viruses CB-A and RW-A). In addition, the Shannon index, which reflects the diversity of sequences present in a sample, was generally higher for the sows as compared to the piglets. No consistent differences in the virome composition could be identified between the viromes of the probiotic bacterium-treated group and the control group. Conclusion: The analysis indicates that the pig faecal virome shows a high variability and that its general composition is mainly dependent on the age of the pigs. Changes caused by feeding with the probiotic bacterium E. faecium could not be demonstrated using the applied metagenomics method. © 2014 Sachsenröder et al.",circular DNA;virus DNA;virus RNA;animal experiment;article;bacteriophage;Circovirus;controlled study;Enterococcus faecium;feces analysis;feeding;Kobuvirus;metagenomics;nonhuman;piglet;sow (swine);pig;virus genome;virus particle,"Sachsenröder, J.;Twardziok, S. O.;Scheuch, M.;Johne, R.",2014,,10.1371/journal.pone.0088888,1
1811,Virome of US bovine calf serum,"Using viral metagenomics we analyzed four bovine serum pools assembled from 715 calves in the United States. Two parvoviruses, bovine parvovirus 2 (BPV2) and a previously uncharacterized parvovirus designated as bosavirus (BosaV), were detected in 3 and 4 pools respectively and their complete coding sequences generated. Based on NS1 protein identity, bosavirus qualifies as a member of a new species in the copiparvovirus genus. Also detected were low number of reads matching ungulate tetraparvovirus 2, bovine hepacivirus, and several papillomaviruses. This study further characterizes the diversity of viruses in calf serum with the potential to infect fetuses and through fetal bovine serum contaminate cell cultures.",nonstructural protein 1;animal cell;animal cell culture;article;bosavirus;bovine hepacivirus;bovine parvovirus 2;calf (bovine);controlled study;copiparvovirus;fetus blood;gene sequence;intrauterine infection;metagenomics;microbial diversity;nonhuman;Papillomaviridae;Parvoviridae;parvovirus infection;serum;ungulate tetraparvovirus 2;United States;viral contamination;viral genetics;virus detection;virus gene;virus strain,"Sadeghi, M.;Kapusinszky, B.;Yugo, D. M.;Phan, T. G.;Deng, X.;Kanevsky, I.;Opriessnig, T.;Woolums, A. R.;Hurley, D. J.;Meng, X. J.;Delwart, E.",2017,,10.1016/j.biologicals.2016.12.009,1
1812,Detection of Porcine Bocavirus From a Child With Acute Respiratory Tract Infection,"Porcine bocavirus is a recently discovered virus classified within the Bocavirus genus. We present a case of upper respiratory tract infection associated with porcine bocavirus in a 3-year-old child who was in close contact with hogs in northeastern Iran. To the best of our knowledge, this is the first report on the human porcine bocavirus infection.",animal experiment;animal model;article;Bocavirus infection;female;Iran;male;nonhuman;pig;upper respiratory tract infection,"Safamanesh, S.;Azimian, A.;Shakeri, A.;Ghazvini, K.;Jamehdar, S. A.;Khosrojerdi, M.;Youssefi, M.",2018,,10.1097/inf.0000000000002003,0
1813,No viral association found in a set of differentiated vulvar intraepithelial neoplasia cases by human papillomavirus and pan-viral microarray testing,"Vulvar Intraepithelial Neoplasia (VIN) is the precursor lesion of Vulvar Squamous Cell Carcinoma (VSCC), and the differentiated type (dVIN) is more frequently observed in relation to VSCC. In contrast to usual-type VIN (uVIN), which is related to infection by human papillomavirus (HPV), a germline mutation in the p53 gene is thought to be associated with ∼90% of dVIN cases. To date, no infectious agent has been identified in association with dVIN, and studies investigating this possibility have been hindered by the difficulty in accurately diagnosing dVIN from small biopsies. Here, we used immunostaining for p16<sup>ink4a</sup>, a biomarker for HPV infection, to study 14 uVIN high-grade VIN and 14 dVIN cases, and to select 10 dVIN cases to broadly screen for all known viruses using a pan-viral microarray platform (ViroChip). All of the uVIN tissue samples, including 8 warty and 6 basaloid cases, showed positivity with the p16<sup>ink4a</sup> immunostain. The staining pattern was full-thickness for all except two cases in which positive staining was localized in the lower 1/3 of the epidermis. In contrast, immunostaining for p16<sup>ink4a</sup> was negative in all dVIN cases. ViroChip analysis of 10 pure dVIN samples confirmed the absence of human papillomavirus subtypes or any other virus with the exception of a single sample that showed a weak microarray signature to a porcine herpesvirus. Follow-up PCR testing of the sample was negative for herpesvirus, and in-depth metagenomic next-generation sequencing revealed only sequences corresponding to non-pathogenic viral flora and bacterial contamination. In this study, we demonstrated lack of a virus association in 10 dVIN cases. Alternative pathways for carcinogenesis such as the p53 mutation should be considered for investigation of potential treatment options in dVIN.",protein p16;protein p53;adult;aged;article;bacterium contamination;cancer classification;cancer grading;carcinogenesis;controlled study;diagnostic accuracy;female;gene mutation;germline mutation;human;human tissue;immunohistochemistry;male;metagenomics;microarray analysis;middle aged;next generation sequencing;papillomavirus infection;polymerase chain reaction;vulva carcinoma;Wart virus,"Saglam, O.;Samayoa, E.;Somasekar, S.;Naccache, S.;Iwasaki, A.;Chiu, C. Y.",2015,,10.1371/journal.pone.0125292,0
1814,Antigenic subtyping and epitopes' competition analysis of porcine circovirus type 2 using monoclonal antibodies,"Porcine circovirus type 2 (PCV2) strains have been classified into two major genotypes (PCV2a and PCV2b) and 8 genetic clusters: PCV2b-1A to PCV2b-1C and PCV2a-2A to PCV2a-2E. To date, no studies have been performed to antigenically subtype PCV2 strains enclosing eight PCV2 clusters. The present study aimed to antigenically subtype PCV2 and perform epitopes' competition analysis using monoclonal antibodies (mAbs). Fourteen PCV2 strains representative for eight clusters were tested with 20 mAbs (fifteen of them were generated against PCV2a strain Stoon-1010 and 5 of them against PCV2b strain 1147) in immunoperoxidase monolayer assays. Four mAbs reacted to all 14 PCV2 strains and one mAb reacted with all strains except for a PCV2a-2C strain. One mAb reacted with all PCV2a strains, except for a PCV2a-2C strain and one mAb reacted with all PCV2b strains, except for a PCV2b-1C strain. Nine mAbs reacted with the strains of PCV2b-1A/1B, PCV2a-2A and PCV2a-2E. Three mAbs only reacted with the strains of PCV2a-2A and PCV2a-2E. One mAb reacted specifically with the strains of PCV2b-1A/1B. This suggests that discrete antigenic differences exist between different PCV2 genetic clusters and that these clusters can be discriminated by the use of a panel of universal and cluster-specific mAbs. Six mAbs were selected for cross-competition analysis by a competitive ELISA using PCV2 strain Stoon-1010. Six overlapping epitopes were identified on the PCV2 capsid protein. The universal mAbs recognized larger epitopes than the cluster-specific mAbs. These findings are helpful in the development of diagnostic tests and new generation vaccines against PCV2. © 2011 Elsevier B.V.",epitope;monoclonal antibody;virus antigen;analysis;article;assay;Circovirus;enzyme linked immunosorbent assay;gene cluster;nonhuman;nucleotide sequence;Porcine circovirus 2;virus classification;virus strain,"Saha, D.;Huang, L.;Bussalleu, E.;Lefebvre, D. J.;Fort, M.;Van Doorsselaere, J.;Nauwynck, H. J.",2012,,10.1016/j.vetmic.2011.11.030,0
1815,"Comparison of the characteristics of avian reoviruses isolated from the digestive and respiratory tract, with viruses isolated from the synovia","Two week old gnotobiotic chicks were inoculated in the foot pad with viruses isolated from synovia and synovial membrane: WVU 1464-29H, WVU 1675, WVU 2937, WVU 2986, and WVU 71-212; from digestive tract: reoviruses 24, 25, and 59; or from respiratory tract: reovirus Fahey Crawley (FC). All viruses induced swelling of the foot pad and inflammatory changes of synovial membrane. Serum from virus infected chicks had a common agar gel precipitin (AGP) line. On the basis of the plaque reduction test in primary chicken kidney (PCK) cells, the viruses were classified into 4 major serotypes. All viruses produced cytopathic effects (CPE) in primary chicken tissue cultures. Other than reovirus FC and WVU 1464-29H, all viruses produced CPE in the Vero cell line.",avian virus;cell culture;chicken;cytopathogenic effect;etiology;foot pad;gastrointestinal tract;histology;in vitro study;microorganism;Reoviridae;respiratory system;serotype;synovial fluid;synovium;theoretical study;virus;virus characterization;virus infection;virus inhibition;virus plaque,"Sahu, S. P.;Olson, N. O.",1975,,,0
1816,Sequence analysis of in vivo defective interfering-like RNA of influenza A H1N1 pandemic virus,"Influenza virus defective interfering (DI) particles are naturally occurring noninfectious virions typically generated during in vitro serial passages in cell culture of the virus at a high multiplicity of infection. DI particles are recognized for the role they play in inhibiting viral replication and for the impact they have on the production of infectious virions. To date, influenza virus DI particles have been reported primarily as a phenomenon of cell culture and in experimentally infected embryonated chicken eggs. They have also been isolated from a respiratory infection of chickens. Using a sequencing approach, we characterize several subgenomic viral RNAs from human nasopharyngeal specimens infected with the influenza A(H1N1)pdm09 virus. The distribution of these in vivo-derived DI-like RNAs was similar to that of in vitro DIs, with the majority of the defective RNAs generated from the PB2 (segment 1) of the polymerase complex, followed by PB1 and PA. The lengths of the in vivo-derived DI-like segments also are similar to those of known in vitro DIs, and the in vivo-derived DI-like segments share internal deletions of the same segments. The presence of identical DI-like RNAs in patients linked by direct contact is compatible with transmission between them. The functional role of DI-like RNAs in natural infections remains to be established.","Base Sequence;Cloning, Molecular;Computational Biology;*Defective Viruses/ge [Genetics];High-Throughput Nucleotide Sequencing;Humans;*Influenza A Virus, H1N1 Subtype/ge [Genetics];Molecular Sequence Data;*RNA, Viral/ge [Genetics];Sequence Alignment;Sequence Analysis, DNA;0 (RNA, Viral)","Saira, K.;Lin, X.;DePasse, J. V.;Halpin, R.;Twaddle, A.;Stockwell, T.;Angus, B.;Cozzi-Lepri, A.;Delfino, M.;Dugan, V.;Dwyer, D. E.;Freiberg, M.;Horban, A.;Losso, M.;Lynfield, R.;Wentworth, D. N.;Holmes, E. C.;Davey, R.;Wentworth, D. E.;Ghedin, E.;Group, I. F. S.;Group, I. F. S.",2013,Jul,,0
1817,Characterization of a human H9N2 influenza virus isolated in Hong Kong,"Two H9N2 viruses were isolated, for the first time, from humans in Hong Kong in 1999. Isolation of influenza viruses with a novel subtype of the hemagglutinin (HA) drew attention of health care authorities worldwide from the view of pandemic preparedness. Sequence analysis of the HA genes reveals that HA of A/Hong Kong/1073/99 (H9N2) is most closely related to that of A/quail/HK/G1/97 (H9N2) that contains the internal genes similar to those of Hong Kong/97 (H5N1) viruses. Phylogenetic and antigenic analyses demonstrated the diversity among H9 HA. A/Hong Kong/1073/99 was shown to cause a respiratory infection in Syrian hamsters, suggesting that the virus can replicate efficiently in mammalian hosts. We developed a whole virion test vaccine with a formalin-inactivated egg-grown HK1073. Intraperitoneal administration of the vaccine twice to hamsters conferred a complete protection against challenge infection by the MDCK cell-grown homologous virus. Receptor specificity of HK1073 appeared different from that of other avian influenza viruses of H9 subtype which recognize preferentially α-2,3 linked sialic acid. Hemagglutination of HK1073 with guinea pig erythrocytes was inhibited by both α-2,3 and α-2,6 linked sialic acid containing polymers. These data suggested that HK1073 had acquired a broader host range, including humans. Together with data so far available, the present study suggested that isolation of the H9 influenza viruses from humans requires precaution against the emergence of a novel human influenza. © 2001 Elsevier Science Ltd. All rights reserved.",formaldehyde;hemagglutinin;influenza vaccine;polymer;sialic acid;animal model;antigenicity;article;biodiversity;cell growth;controlled study;diagnostic test;erythrocyte;female;guinea pig;health care;hemagglutination;Hong Kong;human;infection prevention;influenza;influenza vaccination;Influenza virus;male;mammal;nonhuman;phylogeny;priority journal;sequence analysis;Syrian hamster;virion;virus characterization;virus isolation;virus replication,"Saito, T.;Lim, W.;Suzuki, T.;Suzuki, Y.;Kida, H.;Nishimura, S. I.;Tashiro, M.",2001,,10.1016/s0264-410x(01)00279-1,0
1818,DNA Virome: Sequencing and Data Analysis of Viral Metagenome of Poultry Suffering from Respiratory Diseases,,,"Sajnani, M. R.;Sudarsanam, D.",2018,,,0
1819,Viral Metagenomics of chickens with respiratory infection using MG-RAST,,,"Sajnani, M. R.;Sudarsanam, D.",2018,,,0
1820,Metagenomic data of DNA viruses of poultry affected with respiratory tract infection,"The incidence and severity of respiratory diseases in commercial broiler chicken flocks have increased recently in India because of intensification of the broiler industry. Viral population are predominant in respiratory tract infections and they pose continuous economic burden to poultry industry by causing severe economic losses through decreased productivity [1], [2]. To understand viral metagenome of poultry associated with respiratory infections, we performed DNA virome sequencing and data analysis of broilers from 8 districts of Gujarat State in India. We report high quality sequencing reads and highly abundant DNA viral population present in the infected broiler birds. The raw sequencing data used to perform metagenomic analysis is available in the Sequence Read Archive (SRA) under the BioProject No. PRJNA322592 and Accession No. MAUZ00000000, MAVA00000000, MAVB00000000, MAVC00000000, MAVD00000000, MAVE00000000, MAVF00000000, MAVG00000000 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA322592).",,"Sajnani, M. R.;Sudarsanam, D.;Pandit, R. J.;Oza, T.;Hinsu, A. T.;Jakhesara, S. J.;Solosanc, S.;Joshi, C. G.;Bhatt, V. D.",2018,Feb,,1
1821,Isolation and characterization of a novel Rhabdovirus from a wild boar (Sus scrofa) in Japan,"A novel rhabdovirus was isolated from the serum of a healthy Japanese wild boar (Sus scrofa leucomystax) and identified using the rapid determination system for viral nucleic acid sequences (RDV), next-generation sequencing, and electron microscopy. The virus was tentatively named wild boar rhabdovirus 1 (WBRV1). Phylogenetic analysis of the entire genome sequence indicated that WBRV1 is closely related to Tupaia rhabdovirus (TRV), which was isolated from cultured cells of hepatocellular carcinoma tissue of tree shrew. TRV has not been assigned to any genus of Rhabdoviridae till date. Analysis of the L gene indicated that WBRV1 belongs to the genus Vesiculovirus. These observations suggest that both TRV and WBRV1 belong to a new genus of Rhabdoviridae. Next-generation genome sequencing of WBRV1 revealed 5 open reading frames of 1329, 765, 627, 1629, and 6336 bases in length. The WBRV1 gene sequences are similar to those of other rhabdoviruses. Epizootiological analysis of a population of wild boars in Wakayama prefecture in Japan indicated that 6.5% were positive for the WBRV1 gene and 52% were positive for WBRV1-neutralizing antibodies. Furthermore, such viral neutralizing antibodies were found in domestic pigs in another prefecture. WBRV1 was inoculated intranasally and intraperitoneally into SCID and BALB/c mice and viral RNA was detected in SCID mice, suggesting that WBRV1 can replicate in immunocompromised mice. These results indicate this novel virus is endemic in wild animals and livestock in Japan.","Animals;Base Sequence;DNA, Viral/ch [Chemistry];DNA, Viral/ge [Genetics];*Genome, Viral/ge [Genetics];High-Throughput Nucleotide Sequencing/ve [Veterinary];Japan/ep [Epidemiology];Mice;Mice, Inbred BALB C;Mice, SCID;Molecular Sequence Data;Open Reading Frames/ge [Genetics];Phylogeny;*Rhabdoviridae/cl [Classification];Rhabdoviridae/ge [Genetics];Rhabdoviridae/ip [Isolation & Purification];Rhabdoviridae Infections/ep [Epidemiology];*Rhabdoviridae Infections/ve [Veterinary];Rhabdoviridae Infections/vi [Virology];Sequence Analysis, DNA/ve [Veterinary];Sus scrofa;Swine;Swine Diseases/ep [Epidemiology];*Swine Diseases/vi [Virology];0 (DNA, Viral)","Sakai, K.;Hagiwara, K.;Omatsu, T.;Hamasaki, C.;Kuwata, R.;Shimoda, H.;Suzuki, K.;Endoh, D.;Nagata, N.;Nagai, M.;Katayama, Y.;Oba, M.;Kurane, I.;Saijo, M.;Morikawa, S.;Mizutani, T.;Maeda, K.",2015,Sep 30,,0
1822,Bunyaviruses are common in male and female Ixodes scapularis ticks in central Pennsylvania,"The blacklegged tick Ixodes scapularis is widely distributed in the United States and transmits multiple pathogens to humans, wildlife and domestic animals. Recently, several novel viruses in the family Bunyaviridae (South Bay virus (SBV) and Blacklegged tick phlebovirus (BTPV)) were identified infecting female I. scapularis ticks collected in New York State. We used metagenomic sequencing to investigate the distribution of viruses infecting male and female I. scapularis ticks collected in Centre County, Pennsylvania. We identified both SBV and BTPV in both male and female ticks from all collection locations. The role of male I. scapularis in pathogen epidemiology has been overlooked because they rarely bite and are not considered important pathogen vectors. However, males may act as reservoirs for pathogens that can then be transmitted to females during mating. Our data highlight the importance of examining all potential avenues of pathogen maintenance and transmission throughout the vector-pathogen life cycle in order to understand the epidemiology of tick-borne pathogens.",adult;animal experiment;animal model;article;bioinformatics;bunyavirus infection;centrifugation;controlled study;female;Ixodes scapularis;life cycle;male;maximum likelihood method;nonhuman;nucleotide sequence;Pennsylvania;phylogenetic tree;polymerase chain reaction;sequence analysis;validation process,"Sakamoto, J. M.;Ng, T. F. F.;Suzuki, Y.;Tsujimoto, H.;Deng, X.;Delwart, E.;Rasgon, J. L.",2016,,10.7717/peerj.2324,0
1823,Genetic heterogeneity of porcine and ruminant pestiviruses mainly isolated in Japan,"The genetic variability of porcine and ruminant pestiviruses was studied by comparative nucleotide sequence analysis of 73 isolates (42 porcine and 31 ruminant), including 65 Japanese isolates (35 porcine and 30 ruminant). The 5'-untranslated region (UTR) amplified by reverse transcriptase-polymerase chain reaction (RT-PCR) was determined by direct sequencing and phylogenetic analysis was performed from the nucleotide sequence data. Most porcine isolates were divided into two major subgroups, classical swine fever virus (CSFV) subgroup 1 (CSFV-1, represented by Brecia strain) and subgroup 2 (CSFV-2, represented by Alfort strain). However, the Japanese Kanagawa/74, Okinawa/86, Okinawa/86-2 and Thai CBR/93 strains were the most distinct variants and these were assigned to another new disparate subgroup, CSFV-3 (represented by p97 strain). Most ruminant isolates were classified as the bovine viral diarrhoea virus (BVDV) genotype-I (BVDV-I) and subdivided into two subgroups, BVDV-Ia (represented by the NADL strain) and Ib (represented by the Osloss strain). Two bovine isolates (MS-1 and SY-89) and a contaminating strain (V/FLL) from an ovine cell line were classified as BVDV genotype-II (BVDV-II) on genetic characteristics. These data suggested that the detection and phylogenetic analysis of 5'-UTRs are useful for the rapid characterization of field isolates.",article;bacterium isolation;disease classification;genetic heterogeneity;genetic variability;Japan;nucleotide sequence;Pestivirus;phylogeny;reverse transcription polymerase chain reaction,"Sakoda, Y.;Ozawa, S. I.;Damrongwatanapokin, S.;Sato, M.;Ishikawa, K.;Fukusho, A.",1999,,10.1016/s0378-1135(98)00284-3,0
1824,"Virus RNA Load in Patients with Tick-Borne Encephalitis, Slovenia","We determined levels of tick-borne encephalitis (TBE) virus (TBEV) RNA in serum samples obtained from 80 patients during the initial phase of TBE in Slovenia. For most samples, levels were within the range of 3-6 log(10) copies RNA/mL. Levels were higher in female patients than in male patients, but we found no association between virus load and several laboratory and clinical parameters, including severity of TBE. However, a weak humoral immune response was associated with a more severe disease course, suggesting that inefficient clearance of virus results in a more serious illness. To determine whether a certain genetic lineage of TBEV had a higher virulence potential, we obtained 56 partial envelope protein gene sequences by directly sequencing reverse transcription PCR products from clinical samples of patients. This method provided a large set of patient-derived TBEV sequences. We observed no association between phylogenetic clades and virus load or disease severity.",WEST-NILE-VIRUS;RAW GOAT MILK;RT-PCR ASSAY;CENTRAL-EUROPE;STRAINS;EPIDEMIOLOGY;PATHOGENESIS;REPLICATION;CONSUMPTION;LITHUANIA,"Saksida, A.;Jakopin, N.;Jelovsek, M.;Knap, N.;Fajs, L.;Lusa, L.;Lotric-Furlan, S.;Bogovic, P.;Arnez, M.;Strle, F.;Avsic-Zupanc, T.",2018,Jul,,0
1825,Alternative growth promoters Modulate broiler gut microbiome and enhance body weight gain,"Antibiotic growth promoters (AGPs) are frequently used to enhance weight-gain in poultry production. However, there has been increasing concern over the impact of AGP on the emergence of antibiotic resistance in zoonotic bacterial pathogens in the microbial community of the poultry gut. In this study, we adopted mass-spectrophotometric, phylogenetic, and shotgun-metagenomic approaches to evaluate bioactive phenolic extracts (BPE) from blueberry (Vaccinium corymbosum) and blackberry (Rubus fruticosus) pomaces as AGP alternatives in broilers. We conducted two trials with 100 Cobb-500 broiler chicks (in each trial) in four equal groups that were provided water with no supplementation, supplemented with AGP (tylosin, neomycin sulfate, bacitracin, erythromycin, and oxytetracycline), or supplemented with 0.1 g Gallic acid equivalent (GAE)/L or 1.0 g GAE/L (during the last 72 h before euthanasia) of BPE for 6 weeks. When compared with the control group (water only), the chickens supplemented with AGP and 0.1 g GAE/L of BPE gained 9.5 and 5.8% more body weight, respectively. The microbiomes of both the AGP- and BPE-treated chickens had higher Firmicutes to Bacteroidetes ratios. AGP supplementation appeared to be associated with higher relative abundance of bacteriophages and unique cecal resistomes compared with BPE supplementation or control. Functional characterization of cecal microbiomes revealed significant animal-to-animal variation in the relative abundance of genes involved in energy and carbohydrate metabolism. These findings established a baseline upon which mechanisms of plant-based performance enhancers in regulation of animal growth can be investigated. In addition, the data will aid in designing alternate strategies to improve animal growth performance and consequently production.",bacitracin;erythromycin;gallic acid;growth promotor;neomycin;oxytetracycline;phenol;tylosin;animal experiment;animal model;antibiotic resistance;article;bacteriophage;blackberry;blueberry;broiler;carbohydrate metabolism;controlled study;energy metabolism;high performance liquid chromatography;intestine flora;liquid chromatography-mass spectrometry;metagenomics;nonhuman;phylogeny;body weight gain,"Salaheen, S.;Kim, S. W.;Haley, B. J.;Van Kessel, J. A. S.;Biswas, D.",2017,,10.3389/fmicb.2017.02088,0
1826,Biological and molecular diagnosis of seedborne viruses in cowpea germplasm of geographically diverse sub-Saharan origins,"A total of 983 cowpea accessions obtained from the University of California, Riverside (UCR) Cowpea Repository were analysed for seedborne viruses. A majority of the accessions originated from 11 countries representing different agroclimatic zones in sub-Saharan Africa, and included landraces, local cultivars and breeding lines. Following the initial grow-out tests, 69 cowpea accessions, mostly with symptoms of virus infection, were selected for further evaluation using a combination of host range, reverse transcription-polymerase chain reaction (RT-PCR) and sequence analyses. The analyses revealed that samples from 46 (67%) accessions harboured one or more known seedborne viruses of cowpea. These included seed samples of accessions originating from Botswana (13 accessions), Ghana (6), Nigeria (6), Mali (1), Kenya (5), Cameroon (7), Niger (4), Cote d'lvoire (1), Benin (1), India (1) and China (1). Viruses were identified by RT-PCR analysis of total RNAs extracted from suspected virus-infected samples using virus species-specific primers, as well as the cloning and sequencing of RT-PCR products amplified using virus genus-and family-specific degenerate oligonucleotide primers. The viruses identified included Cowpea aphid-borne mosaic virus (CABMV), Cucumber mosaic virus (CMV) and Southern bean mosaic virus (SBMV). Phylogenetic analysis of the deduced coat protein (CP) amino acid sequences of selected CMV isolates recovered from five agroclimatically distinct locations confirmed their affiliations as new members of CMV subgroup IB. This is the first time that seedborne viruses of cowpea accessions in a major collection (UCR) have been identified using RT-PCR and sequencing approaches.",biosecurity;Cucumovirus;genetic diversity;Potyviridae;RT-PCR;Vigna;unguiculata;CUCUMBER-MOSAIC-VIRUS;UNGUICULATA L WALP;MILD MOTTLE VIRUS;VIGNA-UNGUICULATA;PLANT-VIRUS;RT-PCR;PHYLOGENETIC ANALYSIS;NATURAL;OCCURRENCE;GERM PLASM;IDENTIFICATION,"Salem, N. M.;Ehlers, J. D.;Roberts, P. A.;Ng, J. C. K.",2010,Aug,,0
1827,Identification and characterization of lumpy skin disease virus isolated from cattle in the Republic of North Ossetia-Alania in 2015,"The first notifications of the unknown disease of cattle appeared in September–October 2015 in North Caucasus region of Russia (Republic of North Ossetia-Alania). The clinical signs included watery discharge from eyes, apathy, loss of appetite, salivation, lameness and nodular skin lesions. Capripoxvirus genome was detected by real-time PCR in the tissue samples of sick animals. The aetiological agent was isolated in the primary cell cultures of lamb testis and goat testis, as well as in the continuous MDBK cell culture. Further sequencing of the GPCR gene and phylogenetic analysis showed the close genetic relationship of isolated capripoxvirus with a group of lumpy skin disease virus. Koch's postulates were fulfilled by the experimental infection of four calves with a suspension of tissue samples from sick animals.",alpha tocopherol;amphotericin B;ascorbic acid;colecalciferol;gentamicin;oleandomycin;oxytetracycline;retinol;tetracycline;virus DNA;animal tissue;article;Capripoxvirus;cell culture;disease transmission;fever;gene;gene sequence;GPCR gene;ID50 (median infectious dose);Lumpy skin disease virus;molecular phylogeny;nonhuman;nucleotide sequence;phylogeny;real time polymerase chain reaction;skin biopsy;skin defect;testis cell;vaccination;virus characterization;virus genome;virus identification;virus isolation;virus strain,"Salnikov, N.;Usadov, T.;Kolcov, A.;Zhivoderov, S.;Morgunov, Y.;Gerasimov, V.;Gogin, A.;Titov, I.;Yurkov, S.;Malogolovkin, A.;Kolbasov, D.;Lunitsyn, A.",2018,,10.1111/tbed.12818,0
1828,Sequence of a Complete Chicken BG Haplotype Shows Dynamic Expansion and Contraction of Two Gene Lineages with Particular Expression Patterns,"Many genes important in immunity are found as multigene families. The butyrophilin genes are members of the B7 family, playing diverse roles in co-regulation and perhaps in antigen presentation. In humans, a fixed number of butyrophilin genes are found in and around the major histocompatibility complex (MHC), and show striking association with particular autoimmune diseases. In chickens, BG genes encode homologues with somewhat different domain organisation. Only a few BG genes have been characterised, one involved in actin-myosin interaction in the intestinal brush border, and another implicated in resistance to viral diseases. We characterise all BG genes in B12 chickens, finding a multigene family organised as tandem repeats in the BG region outside the MHC, a single gene in the MHC (the BF-BL region), and another single gene on a different chromosome. There is a precise cell and tissue expression for each gene, but overall there are two kinds, those expressed by haemopoietic cells and those expressed in tissues (presumably non-haemopoietic cells), correlating with two different kinds of promoters and 5′ untranslated regions (5′UTR). However, the multigene family in the BG region contains many hybrid genes, suggesting recombination and/or deletion as major evolutionary forces. We identify BG genes in the chicken whole genome shotgun sequence, as well as by comparison to other haplotypes by fibre fluorescence in situ hybridisation, confirming dynamic expansion and contraction within the BG region. Thus, the BG genes in chickens are undergoing much more rapid evolution compared to their homologues in mammals, for reasons yet to be understood. © 2014 Salomonsen et al.",5' untranslated region;actin myosin interaction;animal cell;animal tissue;article;Bg gene;chicken;chromosome 16;chromosome 2;female;fluorescence in situ hybridization;gene cluster;gene deletion;gene expression;gene sequence;genetic code;genetic line;haplotype;hematopoietic cell;molecular evolution;molecular phylogeny;nonhuman;nucleotide sequence;promoter region;regulator gene;sequence analysis;unindexed sequence,"Salomonsen, J.;Chattaway, J. A.;Chan, A. C. Y.;Parker, A.;Huguet, S.;Marston, D. A.;Rogers, S. L.;Wu, Z.;Smith, A. L.;Staines, K.;Butter, C.;Riegert, P.;Vainio, O.;Nielsen, L.;Kaspers, B.;Griffin, D. K.;Yang, F.;Zoorob, R.;Guillemot, F.;Auffray, C.;Beck, S.;Skjødt, K.;Kaufman, J.",2014,,10.1371/journal.pgen.1004417,0
1829,Molecular characterization and phylogenetic study of velogenic Newcastle disease virus isolates in Iran,"The pathogenicity and genetic characterizations of six Newcastle disease virus (NDV) isolates obtained from chicken farms in six different regions in Iran were carried out using conventional and molecular techniques. Based on the pathogenicity indices (MDT, ICPI, and IVPI), all of these isolates were found to be velogenic (highly virulent) strains. A sequence analysis of the full-length mRNA encoding the fusion glycoprotein precursor (F0) of the NDV's fusion proteins F1 and F2 in these six isolates showed the presence of point mutations in form of nucleic acid substitutions at positions 82(C→T), 83(T→C), 736(A→G), and 1,633(G→A). However, the nucleic acid residues at positions 330-347 of the precursor F0 gene, corresponding to the cleavage site of the F0 protein, were found to have remained conserved among the six NDV isolates. A phylogenetic comparison between the six Iranian isolates and the NDVs whose F0 gene sequences were previously deposited in GenBank Database showed that all of the newly characterized Iranian NDV isolates belonged to genotype VII. © 2013 Springer Science+Business Media New York.",alanine;cysteine;F1 virus protein;F2 virus protein;glycine;fusion protein;messenger RNA;threonine;unclassified drug;virus glycoprotein;article;chicken;controlled study;gene sequence;genetic analysis;genotype;Iran;molecular phylogeny;Newcastle disease virus;nonhuman;nucleotide sequence;point mutation;priority journal;protein cleavage;RNA sequence;sequence analysis;virus characterization;virus strain;virus transmission;virus virulence,"Samadi, S.;Kianizadeh, M.;Najafi, M. F.;Nasab, S. D. M.;Davatgar, A. M. H.;Royaee, A.;Pilvar, P.",2014,,10.1007/s11262-013-1015-y,0
1830,Phylogenetic analysis of the lumpy skin disease viruses in northwest of Iran,"Lumpy skin disease (LSD) is a devastating viral disease of cattle which has recently spread from Africa into the countries of the Middle East. The aim of the present study was to investigate the relationships among lumpy skin disease viruses (LSDV) isolated from different regions of Iran and the origin and spread of these viruses. In this study, a total of 234 blood samples from clinically affected animals from four provinces in the northwest of Iran were screened for LSDV using polymerase chain reaction (PCR). From 80 positive samples for LSDV detected by PCR, the partial P32 gene (759 bp) of 12 isolates were sequenced and phylogenetically analyzed. LSD viruses were grouped in three subclusters with an overall 97.1-100% nucleotide identity. LSDVs isolated from Gilan showed lowest nucleotide identity with the other LSDVs. Four isolates of LSDV including KO-1, EA-1, EA-3, and WA-3 showed 100% similarity with each other and also with the Neethling strain. Phylogenetic analysis indicated that the identified LSDVs were closely related to each other and had high-sequence homology with other LSDV isolates from Africa. It was concluded that LSD outbreak probably occurred in the northwest of Iran by LSDVs entering the country from Iraq and P32 nucleotide sequence information obtained in the present study is a valuable resource in understanding the genetic nature and molecular epidemiology of local LSDV isolates which can be used for future vaccine development based on the circulating strains in the region.",virus DNA;animal;bovine;cattle disease;cluster analysis;epidemic;genetics;genotype;Iran;lumpy skin disease;Lumpy skin disease virus;nucleotide sequence;phylogeny;polymerase chain reaction;sequence homology;veterinary medicine;virology,"Sameea Yousefi, P.;Dalir-Naghadeh, B.;Mardani, K.;Jalilzadeh-Amin, G.",2018,,10.1007/s11250-018-1634-3,0
1831,A Four-Biomarker Blood Signature Discriminates Systemic Inflammation Due to Viral Infection Versus Other Etiologies,"The innate immune system of humans and other mammals responds to pathogen-associated molecular patterns (PAMPs) that are conserved across broad classes of infectious agents such as bacteria and viruses. We hypothesized that a blood-based transcriptional signature could be discovered indicating a host systemic response to viral infection. Previous work identified host transcriptional signatures to individual viruses including influenza, respiratory syncytial virus and dengue, but the generality of these signatures across all viral infection types has not been established. Based on 44 publicly available datasets and two clinical studies of our own design, we discovered and validated a four-gene expression signature in whole blood, indicative of a general host systemic response to many types of viral infection. The signature's genes are: Interferon Stimulated Gene 15 (ISG15), Interleukin 16 (IL16), 2',5'-Oligoadenylate Synthetase Like (OASL), and Adhesion G Protein Coupled Receptor E5 (ADGRE5). In each of 13 validation datasets encompassing human, macaque, chimpanzee, pig, mouse, rat and all seven Baltimore virus classification groups, the signature provides statistically significant (p < 0.05) discrimination between viral and non-viral conditions. The signature may have clinical utility for differentiating host systemic inflammation (SI) due to viral versus bacterial or non-infectious causes.",biological marker;transcriptome;adolescent;blood;case control study;child;factual database;female;gene expression profiling;genetics;host pathogen interaction;human;immunology;infant;inflammation;male;preschool child;reproducibility;virology;virus infection,"Sampson, D. L.;Fox, B. A.;Yager, T. D.;Bhide, S.;Cermelli, S.;McHugh, L. C.;Seldon, T. A.;Brandon, R. A.;Sullivan, E.;Zimmerman, J. J.;Noursadeghi, M.;Brandon, R. B.",2017,,10.1038/s41598-017-02325-8,0
1832,Complete genome sequence of Avian Paramyxovirus (APMV) serotype 5 completes the analysis of nine APMV serotypes and reveals the longest APMV genome,"Background: Avian paramyxoviruses (APMV) consist of nine known serotypes. The genomes of representatives of all APMV serotypes except APMV type 5 have recently been fully sequenced. Here, we report the complete genome sequence of the APMV-5 prototype strain budgerigar/Kunitachi/74. Methodology/Principal Findings: APMV-5 Kunitachi virus is unusual in that it lacks a virion hemagglutinin and does not grow in the allantoic cavity of embryonated chicken eggs. However, the virus grew in the amniotic cavity of embryonated chicken eggs and in twelve different established cell lines and two primary cell cultures. The genome is 17,262 nucleotides (nt) long, which is the longest among members of genus Avulavirus, and encodes six non-overlapping genes in the order of 3′N-P/V/W-M-F-HN-L-5′ with intergenic regions of 4-57 nt. The genome length follows the 'rule of six' and contains a 55-nt leader sequence at the 3′end and a 552 nt trailer sequence at the 5′ end. The phosphoprotein (P) gene contains a conserved RNA editing site and is predicted to encode P, V, and W proteins. The cleavage site of the F protein (G-K-R-K-K-R ↓ F) conforms to the cleavage site motif of the ubiquitous cellular protease furin. Consistent with this, exogenous protease was not required for virus replication in vitro. However, the intracerebral pathogenicity index of APMV-5 strain Kunitachi in one-day-old chicks was found to be zero, indicating that the virus is avirulent for chickens despite the presence of a polybasic F cleavage site. Conclusions/Significance: Phylogenetic analysis of the sequences of the APVM-5 genome and proteins versus those of the other APMV serotypes showed that APMV-5 is more closely related to APMV-6 than to the other APMVs. Furthermore, these comparisons provided evidence of extensive genome-wide divergence that supports the classification of the APMVs into nine separate serotypes. The structure of the F cleavage site does not appear to be a reliable indicator of virulence among APMV serotypes 2-9. The availability of sequence information for all known APMV serotypes will facilitate studies in epidemiology and vaccinology.",hemagglutinin;phosphoprotein;animal cell;article;Avulavirus;cell culture;chicken;controlled study;gene sequence;genetic analysis;nonhuman;pathogenicity;phylogeny;RNA cleavage;RNA editing;serotype;type strain;vaccination;virion;virus classification;virus gene;virus replication;virus virulence,"Samuel, A. S.;Paldurai, A.;Kumar, S.;Collins, P. L.;Samal, S. K.",2010,,10.1371/journal.pone.0009269,0
1833,Climate change influences on the global potential distribution of bluetongue virus,"The geographic distribution of arboviruses has received considerable attention after several dramatic emergence events around the world. Bluetongue virus (BTV) is classified among category ""A"" diseases notifiable to the World Organization of Animal Health (OIE), and is transmitted among ruminants by biting midges of the genus Culicoides. Here, we developed a comprehensive occurrence data set to map the current distribution, estimate the ecological niche, and explore the future potential distribution of BTV globally using ecological niche modeling and based on diverse future climate scenarios from general circulation models (GCMs) for four representative concentration pathways (RCPs). The broad ecological niche and potential geographic distribution of BTV under present-day conditions reflected the disease's current distribution across the world in tropical, subtropical, and temperate regions. All model predictions were significantly better than random expectations. As a further evaluation of model robustness, we compared our model predictions to 331 independent records from most recent outbreaks from the Food and Agriculture Organization Emergency Prevention System for Transboundary Animal and Plant Pests and Diseases Information System (EMPRES-i); all were successfully anticipated by the BTV model. Finally, we tested ecological niche similarity among possible vectors and BTV, and could not reject hypotheses of niche similarity. Under future-climate conditions, the potential distribution of BTV was predicted to broaden, especially in central Africa, United States, and western Russia.",article;Bluetongue orbivirus;Central Africa;climate change;ecological niche;geographic distribution;nonhuman;prediction;Russian Federation;subtropical climate;temperate climate;tropic climate;United States,"Samy, A. M.;Peterson, A. T.",2016,,10.1371/journal.pone.0150489,0
1834,Antigenic homology among coronaviruses related to transmissible gastroenteritis virus,"The antigenic homology of 26 coronavirus isolates, of which 22 were antigenically related to transmissible gastroenteritis virus (TGEV), was determined with 42 monoclonal antibodies. Type, group, and interspecies specific epitopes were defined. Two groups specific MAbs distinguished the enteric (TGEV) isolates from the respiratory variants. An antigenic subsite involved in neutralization was conserved in porcine, feline, and canine coronavirus. The classification of the human coronavirus 229E in a taxonomic cluster distinct from TGEV group is suggested.",monoclonal antibody;radioisotope;virus antigen;article;Coronavirinae;gastroenteritis virus;nonhuman;priority journal;radioimmunoassay;virus characterization;virus classification,"Sanchez, C. M.;Jimenez, G.;Laviada, M. D.;Correa, I.;Sune, C.;Bullido, M.;Gebauer, F.;Smerdou, C.;Callebaut, P.;Escribano, J. M.;Enjuanes, L.",1990,,10.1016/0042-6822(90)90094-8,0
1835,Analyzing swine sera for functional antibody titers against influenza a neuraminidase proteins using an enzyme-linked lectin assay (ELLA),"Neuraminidase (NA) is an envelope glycoprotein of influenza viruses, including swine-lineage influenza A viruses. NA possesses sialidase activity, which is functionally important at multiple points in viral replication, counter-balancing the sialic acid receptor binding activity of the hemagglutinin (HA), the other major envelope glycoprotein. The NA proteins of influenza A viruses have been classified into nine serological subtypes, and they undergo antigenic drift variation similar to that of HA. Antibodies to NA are analyzed much less often than antibodies to HA. The conventional assay for NA inhibition (NI) antibody titration, established decades ago, is widely considered unwieldy and inefficient for routine use. In recent years, a few new formats have been developed which still measure inhibition of NA enzymatic function, but more efficiently and with less chemical waste produced. Described here is the enzyme-linked lectin assay (ELLA), which is performed in 96-well plates and analyzed on a spectrophotometric plate reader. An important factor in adoption of the ELLA technique for animal studies, such as swine, is the choice of NA antigen, which may be purified protein or whole virus containing an antigenically irrelevant HA protein. This NI assay, in conjunction with the hemagglutination inhibiting (HI) antibody assay, offers a practical way to characterize viral isolates more fully and to quantify antibodies induced by infection or vaccination.",antibody;antigen;hemagglutinin;reagent;sialidase;viral protein;antibody titer;article;assay;controlled study;enzyme activity;enzyme linked lectin assay;hemagglutination;immunoassay;influenza A;Influenza A virus;microplate reader;nonhuman;pig;priority journal;serum;spectrophotometry;titrimetry,"Sandbulte, M. R.;Eichelberger, M. C.",2014,,10.1007/978-1-4939-0758-8_28,0
1836,Identification of further diversity among posaviruses,"Recently, there have been reports of new members of posavirus-like viruses in the order Picornavirales. In this study, using a metagenomics approach, 11 posavirus-like sequences (>7,000 nucleotides) were detected in 155 porcine fecal samples. Phylogenetic analysis revealed that the newly identified virus sequences, together with other posavirus-like viruses, form distinct clusters within the order Picornavirales, composed of eight genogroups and unassigned sequences based on amino acid sequences of the helicase and RNA-dependent RNA polymerase regions, with <40 % and <50 % sequence identity, respectively. We propose further classifications of highly diverse posavirus populations based on newly identified sequences from Japanese pig feces.",RNA directed RNA polymerase;RNA helicase;animal;classification;cluster analysis;DNA sequence;feces;genetic variation;genetics;isolation and purification;metagenomics;phylogeny;pig;RNA virus;sequence homology;virology,"Sano, K.;Naoi, Y.;Kishimoto, M.;Masuda, T.;Tanabe, H.;Ito, M.;Niira, K.;Haga, K.;Asano, K.;Tsuchiaka, S.;Omatsu, T.;Furuya, T.;Katayama, Y.;Oba, M.;Ouchi, Y.;Yamasato, H.;Ishida, M.;Shirai, J.;Katayama, K.;Mizutani, T.;Nagai, M.",2016,,,1
1837,Detection and characterization of atypical capripoxviruses among small ruminants in India,"Recent developments in molecular biology shed light on cross-species transmission of SPPV and GTPV. The present study was planned to characterize the capripoxviruses which were circulating in the field condition among sheep and goats using RPO30 gene-based viral lineage (SPPV/GTPV) differentiating PCR and sequencing of RPO30 and GPCR genes from clinical samples. Out of 58 scabs (35 sheep and 23 goats) screened, 27 sheep and 18 goat scabs were found positive for capripox virus infections. With the exception of one sheep and one goat scabs, all the positive samples yielded amplicon size according to host origin, i.e. SPPV in sheep and GTPV in goats. In the above two exceptional cases, goat scab and sheep scab yielded amplicon size as that of SPPV and GTPV, respectively. Further, sequencing and phylogenetic analyses of complete ORFs of RPO30 and GPCR genes from six sheep and three goat scabs revealed that with the exception of above two samples, all had host-specific signatures and clustered according to their host origin. In case of cross-species infecting samples, sheep scab possessed GTPV-like signatures and goat scab possessed SPPV-like signatures. Our study identifies the circulation of cross-infecting SPPV and GTPV in the field and warrants the development of single-strain vaccine which can protect the animals from both sheeppox and goatpox diseases.",G protein coupled receptor;genomic DNA;RNA polymerase;amplicon;article;Capripoxvirus;controlled study;gene amplification;gene cluster;genome size;goat;goatpox;GPCR gene;host range;India;molecular cloning;molecular epidemiology;nonhuman;open reading frame;phylogeny;polymerase chain reaction;poxvirus infection;priority journal;RPO30 gene;ruminant;sequence analysis;sheep;sheeppox;species comparison;virus characterization;virus detection;virus gene,"Santhamani, R.;Venkatesan, G.;Minhas, S. K.;Shivachandra, S. B.;Muthuchelvan, D.;Pandey, A. B.;Ramakrishnan, M. A.",2015,,10.1007/s11262-015-1206-9,0
1838,The human urine virome in association with urinary tract infections,,,"Santiago-Rodriguez, T. M.;Ly, M.;Bonilla, N.",2015,,,0
1839,"Genetic characterization of small ruminant lentiviruses circulating in naturally infected sheep and goats in Ontario, Canada","Maedi-visna virus (MVV) and caprine arthritis encephalitis virus (CAEV) are related members of a group of small ruminant lentiviruses (SRLVs) that infect sheep and goats. SRLVs are endemic in many countries, including Canada. However, very little is known about the genetic characteristics of Canadian SRLVs, particularly in the province of Ontario. Given the importance of surveillance and eradication programs for the control of SRLVs, it is imperative that the diagnostic tests used to identify infected animals are sensitive to local strains of SRLVs. The aim of this work was to characterize SRLV strains circulating in Ontario and to evaluate the variability of the immunodominant regions of the Gag protein. In this study, the nearly complete gag sequence of 164 SRLVs, from 130 naturally infected sheep and 32 naturally infected goats from Ontario, was sequenced. Animals belonged to distantly located single and mixed species (sheep and goats) farms. Ovine lentiviruses from the same farm tended to cluster more closely together than did caprine lentiviruses from the same farm. Sequence analysis revealed a higher degree of heterogeneity among the caprine lentivirus sequences with an average inter-farm pairwise DNA distance of 10% and only 5% in the ovine lentivirus group. Interestingly, amplification of SRLVs from ELISA positive sheep was successful in 81% of cases, whereas amplification of SRLV proviral DNA was only possible in 55% of the ELISA positive goat samples; suggesting that a significant portion of caprine lentiviruses circulating in Ontario possess heterogeneity at the primer binding sites used in this study. Sequences of sheep and goat SRLVs from Ontario were assembled into phylogenetic trees with other known SRLVs and were found to belong to sequence groups A2 and B1, respectively, as defined by Shah et al. (2004a). A novel caprine lentivirus with a pairwise genetic difference of 15.6-25.4% relative to other group B subtypes was identified. Thus we suggest the designation of a novel subtype, B4, within the caprine lentivirus-like cluster. Lastly, we demonstrate evidence of recombination between ovine lentiviruses. These results emphasize the broad genetic diversity of SRLV strains circulating in the province of Ontario and show that the gag region is suitable for phylogenetic studies and may be applied to monitor SRLV eradication programs. © 2013 Elsevier B.V.",Gag protein;virus DNA;amino acid sequence;article;binding site;Canada;Caprine arthritis encephalitis virus;disease transmission;gene amplification;gene sequence;genetic recombination;genotype;goat disease;nonhuman;nucleotide sequence;phylogenetic tree;priority journal;viral genetics;virus capsid;virus characterization;virus strain,"Santry, L. A.;de Jong, J.;Gold, A. C.;Walsh, S. R.;Menzies, P. I.;Wootton, S. K.",2013,,10.1016/j.virusres.2013.03.019,0
1840,Genomic characterization of two novel pathogenic avipoxviruses isolated from pacific shearwaters (Ardenna spp.),"BACKGROUND: Over the past 20 years, many marine seabird populations have been gradually declining and the factors driving this ongoing deterioration are not always well understood. Avipoxvirus infections have been found in a wide range of bird species worldwide, however, very little is known about the disease ecology of avian poxviruses in seabirds. Here we present two novel avipoxviruses from pacific shearwaters (Ardenna spp), one from a Flesh-footed Shearwater (A. carneipes) (SWPV-1) and the other from a Wedge-tailed Shearwater (A. pacificus) (SWPV-2). RESULTS: Epidermal pox lesions, liver, and blood samples were examined from A. carneipes and A. pacificus of breeding colonies in eastern Australia. After histopathological confirmation of the disease, PCR screening was conducted for avipoxvirus, circovirus, reticuloendotheliosis virus, and fungal agents. Two samples that were PCR positive for poxvirus were further assessed by next generation sequencing, which yielded complete Shearwaterpox virus (SWPV) genomes from A. pacificus and A. carneipes, both showing the highest degree of similarity with Canarypox virus (98% and 67%, respectively). The novel SWPV-1 complete genome from A. carneipes is missing 43 genes compared to CNPV and contains 4 predicted genes which are not found in any other poxvirus, whilst, SWPV-2 complete genome was deemed to be missing 18 genes compared to CNPV and a further 15 genes significantly fragmented as to probably cause them to be non-functional. CONCLUSION: These are the first avipoxvirus complete genome sequences that infect marine seabirds. In the comparison of SWPV-1 and -2 to existing avipoxvirus sequences, our results indicate that the SWPV complete genome from A. carneipes (SWPV-1) described here is not closely related to any other avipoxvirus genome isolated from avian or other natural host species, and that it likely should be considered a separate species.","Animals;Aquatic Organisms/vi [Virology];Australia;*Avipoxvirus/ge [Genetics];Avipoxvirus/ip [Isolation & Purification];Avipoxvirus/py [Pathogenicity];*Bird Diseases/vi [Virology];Birds/cl [Classification];Birds/vi [Virology];*Genome, Viral;High-Throughput Nucleotide Sequencing/mt [Methods];Phylogeny;*Poxviridae Infections/di [Diagnosis];Poxviridae Infections/vi [Virology];Sequence Analysis, DNA/mt [Methods]","Sarker, S.;Das, S.;Lavers, J. L.;Hutton, I.;Helbig, K.;Imbery, J.;Upton, C.;Raidal, S. R.",2017,04 13,,0
1841,"Genetic variations of the Hemagglutinin gene of Pandemic Influenza A (H1N1) viruses in Assam, India during 2016","Since its emergence in 2009, Influenza A/H1N1pdm09 virus has evolved continuously. Marked genetic variations have occurred in the HAl domain of the hemagglutinin gene causing the emergence of new variants. The present study genetically characterized the hemagglutinin (HA) gene of Influenza A/H1N1pdm09 strains from Assam circulating in 2016 that caused a mild outbreak without any reported mortality. Sequence analysis of the HA gene of 20 positive Assam/H1N1pdm09 strains revealed 3 mutations (K180Q, 5202T, S220T) at the antigenic sites along with several other reported mutations which are in close proximity to the antigenic sites and therefore might affect the viral antigenicity. Phylogenetically, the Assam/H1N1pdm09 strains clustered into genogroup 6B. These genetic variations highlight the importance of continuous surveillance and characterization of Influenza A/H1N1pdm09 virus activity to track the genetic makeup and diversification that may affect the behavior of the virus.",Influenza A virus;Swine flu H1N1;Hemagglutinin;Genetic variation;Assam,"Sarmah, K.;Borkakoty, B.;Sarma, K.;Hazarika, R.;Das, P. K.;Jakharia, A.;Das, M.;Biswas, D.",2018,Sep,,0
1842,Multi-reassortant G3P[3] group a rotavirus in a horseshoe bat in Zambia,"Group A rotavirus is a major cause of diarrhoea in humans, especially in young children. Bats also harbour group A rotaviruses, but the genetic backgrounds of bat rotavirus strains are usually distinct from those of human rotavirus strains. We identified a new strain of group A rotavirus in the intestinal contents of a horseshoe bat in Zambia. Whole genome sequencing revealed that the identified virus, named RVA/Bat-wt/ZMB/LUS12-14/2012/G3P[3], possessed the genotype constellation G3-P[3]-I3-R2-C2-M3-A9-N2-T3-E2-H3. Several genome segments of LUS12-14 were highly similar to those of group A rotaviruses identified from humans, cows and antelopes, indicating interspecies transmission of rotaviruses between bats and other mammals with possible multiple genomic reassortment events.",article;bat;gene sequence;genetic reassortment;genotype;horseshoe bat;nonhuman;nucleotide sequence;priority journal;Rotavirus A;virus genome;virus identification;virus strain;virus transmission;Zambia,"Sasaki, M.;Orba, Y.;Sasaki, S.;Gonzalez, G.;Ishii, A.;Hang’Ombe, B. M.;Mweene, A. S.;Ito, K.;Sawa, H.",2016,,10.1099/jgv.0.000591,0
1843,Metagenomic analysis of the shrew enteric virome reveals novel viruses related to human stool-associated viruses,,,"Sasaki, M.;Orba, Y.;Ueno, K.;Ishii, A.",2015,,,0
1844,How to Classify Inuenza A Viruses and Understand Their Severity,"As an application of the chaos degree introduced in the framework of information adaptive dynamics, we study the classification of the Influenza A viruses. What evolutional processes determine the severity and the ability for transmission among human of influenza A viruses? We performed phylogenetic classifications of influenza A viruses that were sampled between 1918 and 2009 by using a measure called entropic chaos degree, that was developed through the study of chaos in information dynamics. The phylogenetic analysis of the internal protein (PB2, PB1, PA, NS, M1, M2, NS1, and NS2) indicated that Influenza A viruses adapting to human and transmitting among human were clearly distinguished from swine lineage and avian lineage. Furthermore, the HA, NA, and internal proteins of the influenza strain that caused a pandemic or a severe epidemic with high mortality were phylogenetically different from those from previous pandemic and severe epidemic strains. We have come to the conclusion that the internal protein has a significant impact on the ability for transmission among human. Based of this study, we are convinced that entropic chaos degree is very useful as a measure of understanding the classification and severity of an isolated strain of influenza A virus.",INFLUENZA-A VIRUS;PANDEMIC INFLUENZA;CHAOS DEGREE;EPIDEMIC;BIRDS,"Sato, K.;Tanabe, T.;Ohya, M.",2010,Sep,,0
1845,Antiviral activities of xanthates,"Strategies in the development of antivirals have been directed to development of substances to interact preferentially with virus-encoded enzymes e.g., polymerases and reverse transcriptase. Xanthates, antiviral/antitumor with different mode of action, interact selectively with cell proteins which regulate cell growth by phosphorylation pathways mediated by protein kinase C. Such regulatory processes appear to be indispensible for growth of various taxonomically unrelated viruses. Xanthate structures in position R1 were substituted with aliphatic cyclic and non-cyclic residues, and in position R2 with alkali metal. The antiviral effect of such substitutions was evaluated in plaque reduction assays using herpes virus as a quick reliable test system. The criteria of cytotoxicity was based on the ability of logarithmically growing cell cultures to undergo active mitotic divisions. Position R1 should be occupied with a lipophilic substituent which, should be structurally constrained as mono-, bi- and tricyclic residues. The specific antiviral activity of the xanthate compound D609 as expressed by its IC50 compares well with that of other herpes inhibitors e.g., phosphonoformic acid (10 uM) or phosphonoacetic acid (20 uM). Unlike the herpes virus which code for its own DNA polymerase, the DNA tumor virus 'SV40' depends on cellular DNA polymerase for its DNA replication. There was a selective antiviral effect of xanthate in the absence of cytotoxicity of bovine papilloma virus (BPV-1) transformed cells. The inhibition of viral gene functions by xanthate in the absence of deleterious effects on indispensible cellular functions shows the high selectivity of the antiviral effect. Depending on the multiplicity of coxsackie B4 virus, there was direct correlation of the amount of viral proteins synthesized despite the presence of D609. In the case of vesicular stomatitis virus (VSV), xanthate did not curtail the synthesis of primary transcripts which, being endowed with positive strand polarity, serve as messengers. The antiviral effect of xanthate occurs only under acidic pH otherwise the antiviral/antitum or effects decline. As HIV-1 replicates only in appropriate lymphoma cells displaying properties of transformed cells, a careful calibration of D609/monocarbonic acid concentration had to precede antiviral therapy. Such treatment inhibits the shedding of infectious HIV from chronically virus producing lymphoma cultures. This is the only compound to prevent the shedding of HIV infections from carrier cultures. D609 acts antagonistically to the effect of tumor promoting compound TPA (12-O-tetradecanoylphorbol-13-acetate). The effects of D609 is not directed to pkc itself. Phospholipase C seems to be the main target. Diacylglycerol, the product of phospholipase C activity, is lacking in D609 treated cells. D609 interacts in a very specific mechanism with the sequence of growth signal transduction. Transacting mechanisms may lack biological activity since xanthate blocks pkC-activity responsible for appropriate phosphorylation of these parameters. Bolus injections of D609 in conjunction with monocarbonic acid exert therapeutic effects on tumor xenotransplants in athymic mice when D609/undecanoic or dodecanoic acid were administered. This compound can be applied at very high concentrations via the intraveneous route.",antivirus agent;diacylglycerol;protein kinase;tricyclo[4.3.0.1]decan 9 yl xanthogenate;xanthic acid derivative;human;Human immunodeficiency virus infection;intravenous drug administration;review;structure activity relation;d609,"Sauer, G.;Amtmann, E.;Mellert, W.",1989,,,0
1846,A member of a new Picornaviridae genus is shed in pig feces,"During a study of the fecal microbiomes from two healthy piglets using high-throughput sequencing (HTS), we identified a viral genome containing an open reading frame encoding a predicted polyprotein of 2,133 amino acids. This novel viral genome displayed the typical organization of picornaviruses, containing three structural proteins (VP0, VP3, and VP1), followed by seven nonstructural proteins (2A, 2B, 2C, 3A, 3B, 3Cpro , and 3Dpol). Given its particular relationship with Parechovirus, we propose to name it ""Pasivirus"" for Parecho sister clade virus, with ""Swine pasivirus 1"" (SPaV1) as the type species. Fecal samples collected at an industrial farm from healthy sows and piglets from the same herd (25 and 75, respectively) with ages ranging from 4 to 28 weeks were analyzed for the presence of SPaV1 by one-step reverse transcription (RT)-PCR targeting a 3D region of 151 bp. SPaV1 was detected in fecal samples from 51/75 healthy piglets (68% of the animals) and in none of the 25 fecal samples from healthy sows, indicating that SPaV1 circulates through enteric infection of healthy piglets. We propose that SPaV1 represents the first member of a novel Picornaviridae genus related to parechoviruses. © 2012, American Society for Microbiology.",article;feces analysis;female;genetic variability;high throughput sequencing;molecular phylogeny;new genus;nonhuman;nucleotide sequence;open reading frame;Picornaviridae;priority journal;reverse transcription polymerase chain reaction;pig;Swine pasivirus 1;unindexed sequence;virus genome;virus identification,"Sauvage, V.;Ar Gouilh, M.;Cheval, J.;Muth, E.;Pariente, K.;Burguiere, A.;Caro, V.;Manuguerra, J. C.;Eloit, M.",2012,,10.1128/jvi.00046-12,0
1847,"Identification of the first human gyrovirus, a virus related to chicken anemia virus",,,"Sauvage, V.;Cheval, J.;Foulongne, V.;Gouilh, M. A.",2011,,,0
1848,"Novel putative Bluetongue virus in healthy goats from Sardinia, Italy","In recent years, novel Bluetongue virus (BTV) serotypes have been isolated and/or sequenced by researchers within the field. During Bluetongue surveillance activities, we identified a putative novel BTV serotype in healthy goats from Sardinia, Italy. RNAs purified from blood and serum samples were positive for BTV by a generic real time RT-PCR and c-ELISA, respectively, whereas genotyping and serotyping were unsuccessful. By NGS, the whole genome sequence was obtained from two blood samples (BTV-X ITL2015 strains 34200 and 33531). Overall, Seg 2 of BTV-X ITL2015 shows the highest identity (75.3-75.5% nt/77.4-78.1% aa) with recently isolated BTV-27s from Corsica and with the last discovered BTV XJ1407 from China (75.9% nt /78.2% aa), whereas it is less related with BTV-25 from Switzerland (73.0% nt/75.0% aa) and BTV-26 from Kuwait (62.0% nt/60.5% aa). A specific RT-qPCR targeting Seg 2 of BTV-X ITL2015 was assessed in this study. Considering the Seg 2/VP2 identity of BTV-X ITL2015 with BTV-25, 26, 27s and BTV XJ1407 and that serum of BTV-X ITL2015 infected goats failed to neutralize all tested extant serotypes, we propose the existence of a novel BTV serotype circulating in goats in Sardinia. Isolation was so far unsuccessful thus hampering proper antigenic characterization.","Amino Acid Sequence;Animals;Asymptomatic Diseases;*Bluetongue/ep [Epidemiology];Bluetongue/im [Immunology];Bluetongue/vi [Virology];Bluetongue virus/cl [Classification];*Bluetongue virus/ge [Genetics];Bluetongue virus/im [Immunology];Enzyme-Linked Immunosorbent Assay;Epidemiological Monitoring;*Genome, Viral;Goats;High-Throughput Nucleotide Sequencing;Immune Sera/ch [Chemistry];Italy/ep [Epidemiology];*Phylogeny;*RNA, Viral/ge [Genetics];Reverse Transcriptase Polymerase Chain Reaction;Serogroup;0 (Immune Sera);0 (RNA, Viral)","Savini, G.;Puggioni, G.;Meloni, G.;Marcacci, M.;Di Domenico, M.;Rocchigiani, A. M.;Spedicato, M.;Oggiano, A.;Manunta, D.;Teodori, L.;Leone, A.;Portanti, O.;Cito, F.;Conte, A.;Orsini, M.;Camma, C.;Calistri, P.;Giovannini, A.;Lorusso, A.",2017,07,,0
1849,"Morphological, chemical, and antigenic organization of mammalian C type viruses","New features in the architecture of mammalian type C viruses, in particular knoblike surface projections and hexagonally arranged subunits on the core shell could be demonstrated by electron microscopy, taking advantage of newly developed preparation techniques. As examples, murine leukemia viruses (MuLVs) and newly isolated porcine and bovine C virus are presented. The major proteins of a MuLV were isolated and partially characterized in chemical terms and with respect to their serological and other biological activities such as interfering and hemagglutinating (HA) capacity. Most of the characterized proteins could be localized in particular substructures of the virion either by selective removal or isolation of electron microscopically identifiable constituents. The information obtained allowed the design of a more detailed model of mammalian C viruses. Special attention was devoted to the further characterization of interspecies antigens of mammalian C viruses. Different antigenic determinants were revealed. Their distribution allows further subgrouping of mammalian C viruses.",virus antigen;viral protein;in vitro study;leukemia virus;mouse;murine leukemia;Orthoretrovirinae;theoretical study;virus;virus characterization;virus classification;virus hemagglutination;virus interference,"Schaefer, W.;Demsey, A.;Frank, H.",1975,,,0
1850,Origin of the pandemic 1957 H2 influenza A virus and the persistence of its possible progenitors in the avian reservoir,"H2N2 influenza A viruses caused the Asian pandemic of 1957 and then disappeared from the human population 10 years later. To assess the potential for similar outbreaks in the future, we determined the antigenicity of H2 hemagglutinins (HAs) from representative human and avian H2 viruses and then analyzed the nucleotide and amino acid sequences to determine their evolutionary characteristics in different hosts. The results of longitudinal virus surveillance studies were also examined to estimate the prevalence of avian H2 isolates among samples collected from wild ducks and domestic poultry. Reactivity patterns obtained with a large panel of monoclonal antibodies indicated antigenic drift in the HA of human H2 influenza viruses, beginning in 1962. Amino acid changes were clustered in two regions of HA1 that correspond to antigenic sites A and D of the H3 HA. By contrast, the antigenic profiles of the majority of avian H2 HAs were remarkably conserved through 1991, resembling the prototype Japan 57 (H2N2) strain. Amino acid changes were distributed throughout HA1, indicating that antibodies do not play a major role in the selection of avian H2 viruses. Phylogenetic analysis revealed two geographic site-specific lineages of avian H2 HAs: North American and Eurasian. Evidence is presented to support interregion transmission of gull H2 viruses. The human H2 HAs that circulated in 1957-1968 form a separate phylogenetic lineage, most closely related to the Eurasian avian H2 HAs. There was an increased prevalence of H2 influenza viruses among wild ducks in 1988 in North America, preceding the appearance of H2N2 viruses in domestic fowl. As the prevalence of avian H2N2 influenza viruses increased on turkey farms and in live bird markets in New York City and elsewhere, greater numbers of these viruses have come into direct contact with susceptible humans. We conclude that antigenically conserved counterparts of the human Asian pandemic strain of 1957 continue to circulate in the avian reservoir and are coming into closer proximity to susceptible human populations.",article;chicken;controlled study;duck;epidemic;guinea pig;Influenza A virus;nonhuman;priority journal;virus carrier;virus replication,"Schafer, J. R.;Kawaoka, Y.;Bean, W. J.;Suss, J.;Senne, D.;Webster, R. G.",1993,,10.1006/viro.1993.1319,0
1851,Caliciviridae,"The caliciviruses, as a proposed family Caliciviridae, have a distinct virion morphology with cup-shaped depressions on a spherical capsid surface. The viruses have single-stranded RNA, which has a molecular weight about 2.6 x 106 and is infectious. The RNA is covalently linked to a small protein. A single major polypeptide is found in the capsid. A sub-genomic RNA, molecular weight about 1 x 106, coding for the capsid polypeptide is found in infected cells. Caliciviruses infecting swine, pinnipeds and cats have been characterized. Viruses which are morphologically identical to the known caliciviruses have been identified in human feces; these viruses have been shown to be associated with gastroenteritis, but they have not yet been propagated in the laboratory.",classification;electron microscopy;short survey;virus classification;virus morphology,"Schaffer, F. L.;Bachrach, H. L.;Brown, F.",1980,,,0
1852,Single major polypeptide of a calicivirus: characterization by polyacrylamide gel electrophoresis and stabilization of virions by cross linking with dimethyl suberimidate,"A calicivirus, San Miguel sea lion virus serotype 4, isolate 15FT, externally labeled with 125I, was shown by gel electrophoresis to possess a single major polypeptide. The polypeptide migrated anomalously upon electrophoresis in two sodium dodecyl sulfate (SDS) systems: more slowly than bovine serum albumin in a continuous phosphate buffered system and more rapidly than bovine serum albumin in a discontinuous system. Estimated molecular weights in the two systems were approximately 71,000 and 64,000, respectively. There was no clear evidence for a minor virion polypeptide. Treatment of purified San Miguel sea lion virions with dimethyl suberimidate, a cross linking reagent, preserved virion integrity during long term storage at 4°C. Oligomeric species of the polypeptide were observed upon electrophoresis of products from cross linked virions. Based upon a preferred polypeptide molecular weight estimate of 71,000 and distribution of oligomeric species, a calicivirion model with 120 monomeric protein units is proposed as an alternative to a 180 unit model.",viral protein;Caliciviridae;virus classification;virus isolation,"Schaffer, F. L.;Soergel, M. E.",1976,,,0
1853,Surveying the global virome: identification and characterization of HCV-related animal hepaciviruses,,,"Scheel, T. K. H.;Simmonds, P.;Kapoor, A.",2015,,,0
1854,Genome sequence of bubaline alphaherpesvirus 1 (BuHV1) isolated in Australia in 1972,"Bubaline alphaherpesvirus 1 (BuHV1) is a member of the family Herpesviridae, subfamily Alphaherpesvirinae, genus Varicellovirus. To date, no full genome sequence of BuHV has been published. Here, we report the complete genome sequence of bubaline alphaherpesvirus 1 (BuHV1) strain b6 (BuHV1-b6), isolated from a water buffalo (Bubalus bubalis) in 1972 in Australia. The virus was multiplied in MDBK cells, and the DNA was extracted and subjected to high-throughput sequencing. The reads were aligned and combined into a single genome sequence, with bovine alphaherpesvirus 5 (BoHV5) strain SV507/99 (accession number NC005261) as a reference. The BuHV1-b6 genome is a linear double-stranded DNA molecule, 137,452 bp long, with a GC content of 76.8%. The genome consists of two unique sequences: a long, or UL, sequence (103,818 bp) and a short, or US, sequence (9,586 bp), with the latter being flanked by inverted IR and TR elements of 12,024 bp each. The arrangement is typical of herpesvirus genomes of the D-type. The overall sequence has a 92.2% similarity at the nucleotide level to the reference BoHV5 strain. Our report provides a significant landmark in the history of herpesviruses, represented by the genome sequence of this 44-year-old virus isolate.",virus DNA;animal;Australia;bovine;buffalo;cell line;classification;DNA sequence;dog;genetics;high throughput sequencing;isolation and purification;MDCK cell line;nucleotide sequence;Varicellovirus;virology;virus genome,"Scheffer, C. M.;Varela, A. P.;Cibulski, S. P.;Schmidt, C.;Campos, F. S.;Paim, W. P.;Dos Santos, R. N.;Teixeira, T. F.;Loiko, M. R.;Tochetto, C.;Dos Santos, H. F.;de Lima, D. A.;Cerva, C.;Mayer, F. Q.;Petzhold, S. A.;Franco, A. C.;George, T. S.;Spilki, F. R.;Roehe, P. M.",2017,,10.1007/s00705-016-3218-8,0
1855,Comparisons of Venezuelan encephalitis virus strains by hemagglutination-inhibition tests with chicken antibodies,"Twenty strains of Venezuelan encephalitis (VE) virus inoculated intravenously in large doses into roosters produced hemagglutination-inhibition (HI) antibodies detectable in plasmas within 7 to 10 days. No signs of illness occurred, and there was no evidence of viral growth in tissues since blood concentrations of infectious virus steadily decreased after inoculation. HI antibodies in early plasmas were specific for VE virus and did not cross-react significantly with two other North American alphaviruses, eastern and western encephalitis viruses. VE virus strains could be distinguished by virus-dilution, short-incubation HI, but not by plasma-dilution neutralization tests, by using early rooster antibodies. The distinctions by HI test were similar with some strains to, but different with other strains from, those described by Young and Johnson with the spiny rat antisera used to establish their subtype classifications of VE virus. Nevertheless, results of HI tests with rooster antibodies correlated with equine virulence, as did results with spiny rat antibodies, and distinguished the new strains of virus that appeared in Middle America during the VE outbreak of 1969 from preexisting strains.",hemagglutination inhibiting antibody;virus antibody;Alphavirus;chicken;in vitro study;microorganism;theoretical study;Venezuelan equine encephalitis virus,"Scherer, W. F.;Pancake, B. A.",1977,,,0
1856,"Prevalence of porcine Noroviruses, molecular characterization of emerging porcine sapoviruses from finisher swine in the United States, and unified classification scheme for sapoviruses","Noroviruses (NoVs) and sapoviruses (SaVs) are important human pathogens. Although the involvement of porcine NoVs in disease in pigs is unclear, they are genetically and antigenically closely related to human NoVs. Human NoV-like strains have been detected in pigs, raising public health concerns of potential interspecies transmission. Porcine SaVs are highly diverse and emerging in swine populations. Recently, at least three new genogroups of porcine SaVs have been proposed. In this study, we tested 413 pooled fecal samples collected from apparently healthy finisher pigs in North Carolina swine farms during 2009. Reverse transcription (RT)-PCR coupled hybridization assays were performed to detect known porcine NoVs. The overall prevalence of porcine NoVs determined was 18.9% based on this method. Samples were then tested by RT-PCR targeting the 5= end of the capsid region for genogroup II (GII) NoVs, a group which includes human NoVs, followed by sequence analysis. All NoVs identified belonged to typical porcine NoV genotypes, and no human NoV-like strains were detected in specimens from these pigs. Porcine NoV-negative samples (n = 335) were subsequently screened using universal calicivirus primers, and 17 SaV strains were confirmed by sequencing. Based on the partial RNA-dependent RNA polymerase (RdRp) region, they clustered with GIII, GVII, and GVIII and with currently unclassified SaVs. According to analysis of the complete capsid sequences, 7 representative strains clustered with GVII, GVIII, and GIX? SaVs. We tentatively classified SaVs into 14 genogroups based on the complete capsid protein VP1. In summary, porcine NoVs and highly divergent SaVs were present in North Carolina finisher pigs. © 2013, American Society for Microbiology.",RNA directed RNA polymerase;3' untranslated region;article;calicivirus infection;controlled study;feces analysis;gene cluster;gene sequence;genotype;hybridization;molecular epidemiology;nonhuman;Norovirus;norovirus infection;nucleotide sequence;open reading frame;priority journal;reverse transcription polymerase chain reaction;Sapovirus;sequence analysis;species diversity;pig;unindexed sequence;United States;virus capsid;virus classification;virus detection;virus genome;virus identification;virus strain;virus transmission,"Scheuer, K. A.;Oka, T.;Hoet, A. E.;Gebreyes, W. A.;Molla, B. Z.;Saif, L. J.;Wang, Q.",2013,,10.1128/jcm.00865-13,0
1857,Molecular characterization and module composition of P22-related Salmonella phage genomes,"Genomes of newly isolated Salmonella phages were analysed by comparison of their EcoRI restriction patterns and by hybridization. Characteristic hybridization probes from reference phages P22, ES18 and E. coli phage λ were chosen. Four probes selected from the lysis region examined the dispersal of the lambdoid lysis genes. Other probes characterized were the replication genes and part of the structural genes. The complex immunity region was investigated by means of hybridization as well as biological tests. The results showed the relationship of the isolated phages to the P22 branch of the lambdoid phages and revealed their modular genome organization consisting of different proportions of P22-related sequences. DNA restriction patterns of phages released from Salmonella strains sampled in limited geographical areas were significantly less heterogeneous than those of phages released from the worldwide sampled SARA collection. The use of prophage restriction patterns as a tool for the typing of Salmonellae to support the epidemiologic classification of pathogenic strains is discussed. Copyright (C) 1999 Elsevier Science B.V.",bacteriophage;Enterobacteria phage lambda;conference paper;controlled study;cytolysis;epidemiology;gene sequence;genetic analysis;geographic distribution;hybridization;molecular genetics;nonhuman;priority journal;restriction mapping;Salmonella;Salmonella enterica serovar Typhimurium;structural gene;virus classification;virus genome,"Schicklmaier, P.;Wieland, T.;Schmieger, H.",1999,,10.1016/s0168-1656(99)00120-0,0
1858,Genomic features of the human bocaviruses,"The human bocavirus (HBoV) was initially discovered in 2005 as the second pathogenic member of the parvovirus family, next to the human parvovirus B19. HBoV has since been shown to be extremely common worldwide and to cause a systemic infection in small children often resulting in respiratory disease. Three more, presumably enteric, human bocaviruses (HBoV2-4) have been identified in stool samples. Parvoviruses are assumed to replicate via their genomic terminal hairpin-like structures in a so-called 'rolling-hairpin model'. These terminal sequences have recently been partially identified in head-to-tail HBoV-PCR amplicons from clinical samples, and are most likely hybrid relics of HBoV's predecessors, namely bovine parvovirus 1 on the left-hand side and minute virus of canines on the right, shown for the first time in this article. Thereby, the replication model postulated for HBoV remains questionable as the occurrence of head-to-tail sequences is not a typical feature of the rolling-hairpin replication model. However, such episomes can also be persistent storage forms of the genome.",transcriptome;virus DNA;amplicon;Bocaparvovirus;DNA replication;feces analysis;gene sequence;gene structure;genetic variability;nonhuman;nucleotide sequence;open reading frame;Parvoviridae;persistent virus infection;polymerase chain reaction;priority journal;review;viral respiratory tract infection;virus classification;virus gene;virus replication,"Schildgen, O.;Qiu, J.;Sderlund-Venermo, M.",2012,,10.2217/fvl.11.136,0
1859,"First identification of porcine parvovirus 6 in North America by viral metagenomic sequencing of serum from pigs infected with porcine reproductive and respiratory syndrome virus Other viruses (e.g. pox, papilloma, parvo, reoviridae)","Background: Currently, eight species in four genera of parvovirus have been described that infect swine. These include ungulate protoparvovirus 1 (classical porcine parvovirus, PPV), ungulate tetraparvovirus 2 (PPV3), ungulate tetraparvovirus 3 (which includes PPV2, porcine hokovirus, porcine partetravirus and porcine PARV4), ungulate copiparvovirus 2 (which includes PPV4 and PPV5), ungulate bocaparvovirus 2 (which includes porcine bocavirus 1, 2 and 6), ungulate bocaparvovirus 3 (porcine bocavirus 5), ungulate bocaparvovirus 4 (porcine bocavirus 7) and ungulate bocaparvovirus 5 (porcine bocavirus 3, 4-1 and 4-2). PPV6, the most recently described porcine parvovirus, was first identified in China in late 2014 in aborted pig fetuses. Prevalence of PPV6 in China was found to be similar in finishing age pigs from farms with and without evidence of swine reproductive failure. Methods: Porcine parvovirus 6 (PPV6) was detected by sequence-independent single primer amplification (SISPA) and confirmed by overlapping and real-time PCR in the serum of porcine reproductive and respiratory virus (PRRSv) positive samples. Results: Seven nearly complete genomes of PPV6 were identified in PRRSv genotype 2 positive serum samples submitted to state veterinary diagnostic laboratories in 2014. Further testing using overlapping and real-time PCR determined PPV6 to be present in 13.2 % of the serums tested. Additionally, PPV6 was present in samples from all of the geographic locations sampled encompassing nine states in the United States and one state in Mexico. The presence of PPV6 in serum indicates that the PPV6 infection is disseminated and not localized to a specific tissue type. Alignments of the near full length genomes, NS1, and capsid genes identified one of the five PPV6 isolates from China (98.6-99.5 % identity with the North American strains) to be the North American strains nearest relative. Conclusions: These results are the first to report the presence of PPV6 in North America and demonstrate that the virus is found in multiple geographic areas in the United States and in Mexico. The overall prevalence of PPV6 in PRRSv viremic animals is relatively low. Further, all of the PPV6 genomes found in North America are most closely related to a PPV6 strain first identified in 2014 in healthy pigs from the Tianjin province of China.",animal experiment;animal model;article;controlled study;genotype;metagenomics;Mexico;nonhuman;nucleotide sequence;pig;Porcine parvovirus;Porcine parvovirus 6;Porcine reproductive and respiratory syndrome virus;United States;virus capsid;virus genome;virus identification;virus strain,"Schirtzinger, E. E.;Suddith, A. W.;Hause, B. M.;Hesse, R. A.",2015,,10.1186/s12985-015-0401-6,1
1860,Detection of a Novel Bovine Astrovirus in a Cow with Encephalitis,"Encephalitis can be caused by several infectious agents, including bacteria, fungi, parasites and viruses. In many cases, the causative agent cannot be identified, because the pathogens are unknown or detection methods are not routinely available. In our case, a 15-month-old cow developed central nervous disorders and died within 6 days after the onset of clinical signs. The histopathology revealed an acute encephalitis, predominantly in the brain stem, and a ganglionitis of the trigeminal ganglion with massive neuronal necroses in both the brain and the ganglion. However, a relevant panel of bacterial and viral infections of cattle could be routinely excluded. Therefore, a brain sample from the cow was analysed using a metagenomics approach with next-generation sequencing. A novel bovine astrovirus (BoAstV-BH89/14) could be identified using the analysis pipeline RIEMS, and the finding could be confirmed with a specific BoAstV RT-qPCR. The genome of the bovine astrovirus (BoAstV), belonging to the family Astroviridae in the genus Mamastrovirus, has a length of 6478 bp. Sequence identities between 71% to a sheep astrovirus and 69% to two recently described bovine astroviruses from the USA and Switzerland were ascertained. The latter were also connected to encephalitis cases in cattle. Like these, the new virus described here was detected in different brain sections using the specific BoAstV RT-qPCR and fluorescent in situ hybridization. In conclusion, while astroviruses so far were mainly found in relation to gastroenteritis in animals and humans, recently detected astrovirus infections were also related to encephalitis.",animal;astrovirus infection;bovine;case report;cattle disease;classification;DNA sequence;encephalitis;fatality;female;genetics;Germany;isolation and purification;Mamastrovirus;phylogeny;veterinary medicine;virology;virus genome,"Schlottau, K.;Schulze, C.;Bilk, S.;Hanke, D.;Höper, D.;Beer, M.;Hoffmann, B.",2016,,10.1111/tbed.12493,1
1861,Presence of two different bovine hepacivirus clusters in Germany,"During the last years, genetic information of hepaciviruses (family Flaviviridae), whose type species is the human hepatitis C virus, was detected in a wide range of primates and non-primate vertebrates. Here, samples collected from 263 German cattle kept in 22 different holdings were analysed for the presence of hepacivirus N (syn. bovine hepacivirus; BovHepV). One hundred eighty-six cattle that suffered from unspecific clinical signs such as fever and a reduced milk yield as well as 77 apparently healthy animals were included. A total of 39 cattle (14.8%) tested positive for BovHepV by real-time RT-PCR, but a correlation between clinical signs and virus infection could not be found. From 31 of the virus-positive samples, sequences of the NS3 coding region were generated and from two samples, viral sequences of the complete coding region were produced and compared to further European and African BovHepV sequences. Based on the NS3 genomic region, two distinct German BovHepV clusters were identified which differed between each other up to 20% at the nucleotide level, the diversity within the individual clusters reached up to 10%. Based on the full-length sequences, the newly detected virus variants group together with further German and African viruses in a sister relationship to other hepaciviruses from primates and further mammalians, but form distinct clusters within the BovHepV branch. In conclusion, highly diverse hepaciviruses were detected in German cattle further expanding the known phylogenetic diversity of the genus Hepacivirus.",hepacivirin;nucleotide;animal experiment;article;Bluetongue orbivirus;Bovine viral diarrhea virus 1;fever;Flaviviridae;Foot and mouth disease virus;gene sequence;genetic code;genetic variability;genome;Hepacivirus;metagenomics;microbial diversity;milk yield;multiplex polymerase chain reaction;nonhuman;NS3 coding region;nucleotide sequence;phylogeny;real time polymerase chain reaction;Rift Valley fever virus;sequence analysis;translation termination;virus detection;virus infection,"Schlottau, K.;Wernike, K.;Forth, L.;Holsteg, M.;Höper, D.;Beer, M.;Hoffmann, B.",2018,,10.1111/tbed.12930,0
1862,Insect iridescent virus type 6 encodes a polypeptide related to the largest subunit of eukaryotic RNA polymerase II,"Cytoplasmic DNA viruses encode a DNA-dependent RNA polymerase (DdRP) that is essential for transcription of viral genes. The amino acid sequences of known large subunits of DdRPs contain highly conserved regions. Oligonucleotide primers, deduced from two conserved domains [RQP(T/S)LH and NADFDGDE] were used in PCR experiments for the detection of the corresponding gene of the genome of insect iridescent virus type 6, also known as Chilo iridescent virus (CIV). A specific DNA product of about 150 bp could be amplified and was used as a hybridization probe against the CIV gene library to identify the corresponding gene. The gene encoding the DdRP was identified within the EcoRI fragments M (7099 bp) and L (7400 bp) of CIV DNA, between map units 0.310 and 0.347 (7990 bp). The DNA nucleotide sequence (3153 bp) of the gene encoding the largest subunit of DdRP (RPO1) was determined. Northern blot hybridization revealed the presence of a 3.4 kb RNA transcript in CIV-infected cells that hybridized to the CIV DdRP gene. This predicted viral protein consists of 1051 amino acid residues (120K) and showed considerably higher similarity to the largest subunit of eukaryotic RNA polymerase II than to the homologous proteins of vaccinia virus and African swine fever virus. Phylogenetic analysis suggested that the putative RPO1 of CIV could have evolved from RNA polymerase II after the divergence of the three types of eukaryotic RNA polymerases. The putative RPO1 of CIV lacked the C-terminal domain that is conserved in eukaryotic, eubacterial and other viral RNA polymerases and in this respect was analogous to the RNA polymerases of Archaea. It is hypothesized that the equivalent of the C-terminal domain may reside in another subunit of CIV DdRP encoded by an unidentified viral gene.",DNA directed RNA polymerase;extrachromosomal DNA;oligonucleotide;polypeptide;protein subunit;RNA polymerase II;viral protein;African swine fever virus;amino acid sequence;article;carboxy terminal sequence;DNA hybridization;eukaryote;gene library;gene mapping;genetic conservation;insect virus;nonhuman;Northern blotting;nucleotide sequence;phylogeny;priority journal;RNA transcription;Vaccinia virus;viral genetics,"Schnitzler, P.;Sonntag, K. C.;Muller, M.;Janssen, W.;Bugert, J. J.;Koonin, E. V.;Darai, G.",1994,,,0
1863,Molecular evolution of influenza viruses,"There are two different mechanisms by which influenza viruses might evolve: (1) Because the RNA genome of influenza viruses is segmented, new strains can suddenly be produced by reassortment, as happens, for example, during antigenic shift, creating new pandemic strains. (2) New viruses evolve relatively slowly by stepwise mutation and selection, for example, during antigenic or genetic drift. Influenza A viruses were found in various vertebrate species, where they form reservoirs that do not easily mix. While human influenza A viruses do not spread in birds and vice versa, the species barrier to pigs is relatively low, so that pigs might function as 'mixing vessels' for the creation of new pandemic reassortants in Southeast Asia, where the probability is greatest for double infection of pigs by human and avian influenza viruses. Phylogenetic studies revealed that about 100 years ago, an avian influenza A virus had crossed the species barrier, presumably first to pigs, and from there to humans, forming the new stable human and classical swine lineages. In 1979, again, an avian virus showed up in the North European swine population, forming another stable swine lineage. The North European swine isolates from 1979 until about 1985 were genetically extremely unstable. A hypothesis is put forward stating that a mutator mutation is necessary to enable influenza virus to cross the species barrier by providing the new host with sufficient variants from which it can select the best fitting ones. As long as the mutator mutation is still present, such a virus should be able to cross the species barrier a second time, as happened about 100 years ago. Although the most recent swine isolates from northern Germany are again genetically stable, we nevertheless should be on the lookout to see if a North European swine virus shows up in the human population in the near future.",glycoprotein;virus RNA;antigenic variation;bird;Europe;evolution;gene mutation;genetic drift;genetic stability;Influenza virus;Influenza A virus;Influenza B virus;nonhuman;phylogeny;priority journal;probability;review;Southeast Asia;pig;vertebrate;virus genome;virus mutation,"Scholtissek, C.",1995,,10.1007/bf01728660,0
1864,Analysis of influenza A virus nucleoproteins for the assessment of molecular genetic mechanisms leading to new phylogenetic virus lineages,"The nucleoprotein (NP) gene of influenza A viruses is decisive for separating two large individually evolving reservoirs in birds and humans. A phylogenetic analysis of the NP gene revealed that all mammalian influenza viruses originated--directly or indirectly--from an avian ancestor. The stable introduction of an avian influenza A virus into a mammalian species seems to be a relatively rare event, the latest one occurred in 1979 when such an avian virus was introduced into pigs in Northern Europe which gave rise to a new lineage. At least two concomitant events are required for such a new and stable introduction: (1) The new species has to become infected, and (2) a mutation in the polymerase complex has to establish a labile variant, which is prone to provide a large number of different variants, from which some can adapt rapidly to the new host (or to any unusual environments). Since such mutator mutations might be advantageous only during stress periods, variants with a less error prone polymerase might emerge again after adaptation. Examples for such fluctuations in terms of mutational and evolutionary rates are discussed in this brief review.","core protein;NP protein, Influenza A virus;nucleoprotein;RNA binding protein;animal;chemistry;genetics;human;Influenza A virus;mutation;phylogeny;review;sequence homology;virus gene","Scholtissek, C.;Ludwig, S.;Fitch, W. M.",1993,,,0
1865,Characterization of the complete genome of the Tupaia (tree shrew) adenovirus,"The members of the family Adenoviridae are widely spread among vertebrate host species and normally cause acute but innocuous infections. Special attention is focused on adenoviruses because of their ability to transform host cells, their possible application in vector technology, and their phylogeny. The primary structure of the genome of Tupaia adenovirus (TAV), which infects Tupaia spp. (tree shrew) was determined. Tree shrews are taxonomically assumed to be at the base of the phylogenetic tree of mammals and are frequently used as laboratory animals in neurological and behavior research. The TAV genome is 33,501 bp in length with a G+C content of 49.96% and has 166-bp inverted terminal repeats. Analysis of the complete nucleotide sequence resulted in the identification of 109 open reading frames (ORFs) with a coding capacity of at least 40 amino acid residues. Thirty-eight of them are predicted to encode viral proteins based on the presence of transcription and translation signals and sequence and positional conservation. Thirty viral OPFs were found to show significant similarities to known adenoviral genes, arranged into discrete early and late genome regions as they are known from mastadenoviruses. Analysis of the nucleotide content of the TAV genome revealed a significant CG dinucleotide depletion at the genome ends that suggests methylation of these genomic regions during the viral life cycle. Phylogenetic analysis of the viral gene products, including penton and hexon proteins, viral protease, terminal protein, protein VIII, DNA polymerase, protein IVa2, and 100,000-molecular-weight protein, revealed that the evolutionary lineage of TAV forms a separate branch within the phylogenetic tree of the Mastadenovirus genus.",MAJOR LATE PROMOTER;COMPLETE DNA-SEQUENCE;COMPLETE;NUCLEOTIDE-SEQUENCE;TRANSCRIPTIONAL ACTIVATOR;AVIAN ADENOVIRUS;OVINE;ADENOVIRUS;EARLY REGION;IN-VIVO;VIRUS;PROTEINS,"Schondorf, E.;Bahr, U.;Handermann, M.;Darai, G.",2003,Apr,,0
1866,"Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units","Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae.",algorithm;animal experiment;article;Bafinivirus;Carinivirus;controlled study;Coronavirinae;Deltapapillomavirus;Epsionpapillomavirus;Human parvovirus B19;metagenomics;nonhuman;nucleotide sequence;Papillomaviridae;Parvoviridae;phylogeny;Polyomavirus;reindeer;taxonomy;Torovirinae;Torovirus;United States;virus assembly;virus genome;virus identification;virus isolation;Xipapillomavirus,"Schürch, A. C.;Schipper, D.;Bijl, M. A.;Dau, J.;Beckmen, K. B.;Schapendonk, C. M. E.;Raj, V. S.;Osterhaus, A. D. M. E.;Haagmans, B. L.;Tryland, M.;Smits, S. L.",2014,,10.1371/journal.pone.0105227,0
1867,The Holstein Friesian Lethal Haplotype 5 (HH5) Results from a Complete Deletion of TBF1M and Cholesterol Deficiency (CDH) from an ERV-(LTR) Insertion into the Coding Region of APOB,"BACKGROUND: With the availability of massive SNP data for several economically important cattle breeds, haplotype tests have been performed to identify unknown recessive disorders. A number of so-called lethal haplotypes, have been uncovered in Holstein Friesian cattle and, for at least seven of these, the causative mutations have been identified in candidate genes. However, several lethal haplotypes still remain elusive. Here we report the molecular genetic causes of lethal haplotype 5 (HH5) and cholesterol deficiency (CDH). A targeted enrichment for the known genomic regions, followed by massive parallel sequencing was used to interrogate for causative mutations in a case/control approach. METHODS: Targeted enrichment for the known genomic regions, followed by massive parallel sequencing was used in a case/control approach. PCRs for the causing mutations were developed and compared to routine imputing in 2,100 (HH5) and 3,100 (CDH) cattle. RESULTS: HH5 is caused by a deletion of 138kbp, spanning position 93,233kb to 93,371kb on chromosome 9 (BTA9), harboring only dimethyl-adenosine transferase 1 (TFB1M). The deletion breakpoints are flanked by bovine long interspersed nuclear elements Bov-B (upstream) and L1ME3 (downstream), suggesting a homologous recombination/deletion event. TFB1M di-methylates adenine residues in the hairpin loop at the 3'-end of mitochondrial 12S rRNA, being essential for synthesis and function of the small ribosomal subunit of mitochondria. Homozygous TFB1M-/- mice reportedly exhibit embryonal lethality with developmental defects. A 2.8% allelic frequency was determined for the German HF population. CDH results from a 1.3kbp insertion of an endogenous retrovirus (ERV2-1-LTR_BT) into exon 5 of the APOB gene at BTA11:77,959kb. The insertion is flanked by 6bp target site duplications as described for insertions mediated by retroviral integrases. A premature stop codon in the open reading frame of APOB is generated, resulting in a truncation of the protein to a length of only <140 amino acids. Such early truncations have been shown to cause an inability of chylomicron excretion from intestinal cells, resulting in malabsorption of cholesterol. The allelic frequency of this mutation in the German HF population was 6.7%, which is substantially higher than reported so far. Compared to PCR assays inferring the genetic variants directly, the routine imputing used so far showed a diagnostic sensitivity of as low as 91% (HH5) and 88% (CDH), with a high specificity for both (>=99.7%). CONCLUSION: With the availability of direct genetic tests it will now be possible to more effectively reduce the carrier frequency and ultimately eliminate the disorders from the HF populations. Beside this, the fact that repetitive genomic elements (RE) are involved in both diseases, underline the evolutionary importance of RE, which can be detrimental as here, but also advantageous over generations.","Animals;*Apolipoproteins B/ge [Genetics];Base Sequence;*Cattle/ge [Genetics];*Cattle Diseases/ge [Genetics];*Cholesterol/df [Deficiency];DNA/ge [Genetics];DNA-Binding Proteins/df [Deficiency];*DNA-Binding Proteins/ge [Genetics];Endogenous Retroviruses/ge [Genetics];Endogenous Retroviruses/py [Pathogenicity];Female;Gene Deletion;Haplotypes;Heterozygote;High-Throughput Nucleotide Sequencing;Homozygote;Male;Methyltransferases/df [Deficiency];*Methyltransferases/ge [Genetics];Mice;Mice, Knockout;Mitochondrial Proteins/df [Deficiency];*Mitochondrial Proteins/ge [Genetics];Mutagenesis, Insertional;*Mutation;Terminal Repeat Sequences;Transcription Factors/df [Deficiency];*Transcription Factors/ge [Genetics];0 (Apolipoproteins B);0 (DNA-Binding Proteins);0 (Mitochondrial Proteins);0 (TFB1M protein, human);0 (Tfb1m protein, mouse);0 (Transcription Factors);9007-49-2 (DNA);97C5T2UQ7J (Cholesterol)","Schutz, E.;Wehrhahn, C.;Wanjek, M.;Bortfeld, R.;Wemheuer, W. E.;Beck, J.;Brenig, B.",2016,,,0
1868,Animal noroviruses,"Among enteric caliciviruses, noroviruses belong to the genus Norovirus, one of the four accepted genera in the family Caliciviridae. These single-stranded, positive-sense RNA viruses are highly variable both genetically and antigenically. Several animal enteric caliciviruses that are morphologically indistinguishable and genetically closely related to human noroviruses have been identified. The first bovine enteric noroviruses were described in Great Britain and are known as Newbury Agent 2. At least three genetic clusters of porcine noroviruses join together within genogroup II noroviruses. Human noroviruses are the most important cause of acute gastroenteritis illness in people of all ages. In the USA, they are associated with approximately 30-50% of all food-borne outbreaks. Until now, noroviruses have not been associated with gastroenteritis outbreaks in immunocompetent animals. Neither bovine nor porcine noroviruses can replicate in cell culture, although human norovirus can grow in a complex 3D culture system. However, the recently discovered murine noroviruses can replicate in cell culture and are therefore used as model viruses to study human noroviruses. This review focusses on virus classification, virion structure, pathogenesis, epidemiology, immune response and diagnosis of animal noroviruses in comparison with human noroviruses. The classification of animal enteric caliciviruses within the Norovirus genus raises the question of whether transmission from an animal reservoir to humans could occur. Answering this question is important in determining the risk of cross-species infections affecting the epidemiology and evolution of these viruses and so complicating the control of human norovirus infections.",capsid protein;single stranded RNA;acute gastroenteritis;adaptive immunity;antigenicity;Caliciviridae;cell culture;cow;disease association;electron microscopy;enteric virus;enzyme linked immunosorbent assay;epidemiological data;food contamination;gastroenteritis;gene cluster;genetic variability;genus;human;immune response;immunocompetence;infection control;infection risk;innate immunity;nonhuman;Norovirus;nucleotide sequence;pathogenesis;reverse transcription polymerase chain reaction;review;RNA virus;species difference;pig;United Kingdom;United States;virion;virogenesis;virus cell interaction;virus classification;virus culture;virus identification;virus infection;virus morphology;virus replication;virus transmission;zoonosis,"Scipioni, A.;Mauroy, A.;Vinjé, J.;Thiry, E.",2008,,10.1016/j.tvjl.2007.11.012,0
1869,Nucleotide and predicted amino acid sequence analysis of the fusion protein and hemagglutinin-neuraminidase protein genes among Newcastle disease virus isolates. Phylogenetic relationships among the Paramyxovirinae based on attachment glycoprotein sequences,"Highly virulent Newcastle disease virus (NDV) isolates are List A pathogens for commercial poultry, and reports of their isolation among member nations must be made to the Office of International Epizootes (OIE). The virus is classified as a member of the order Mononegavirales in the family Paramyxoviridae of the subfamily Paramyxovirinae. Two interactive surface glycoproteins, the fusion (F) and hemagglutinin-neuraminidase (HN) proteins, play essential roles in NDV attachment and fusion of cells during infection. Antibodies to the F or HN proteins are capable of virus neutralization; however, no full-length sequences are available for these genes from recently obtained virulent isolates. Therefore, nucleotide and predicted amino acid sequences of the F and HN protein genes from 16 NDV isolates representing highly virulent viruses from worldwide sources were obtained for comparison to older virulent isolates and vaccine strains. The F protein amino acid sequence was relatively conserved among isolates maintaining potential glycosylation sites and C residues for disulfide bonds. A dibasic amino acid motif was present at the cleavage site among more virulent isolates, while the low virulence viruses did not have this sequence. However, a Eurasian collared dove virus had a K114Q substitution at the F cleavage site unique among NDV isolates. The HN protein among NDV isolates maintained predicted catalytic and active site residues necessary for neuraminidase activity and hemagglutination. Length of the HN for the Eurasian collared dove isolate and a previously reported heat resistant virulent isolate were longer relative to other more recent virulent isolates. Phylogenetically NDV isolates separated into four groups with more recent virulent isolates forming a diverse branch, while all the avian paramyxoviruses formed their own clade distinct from other members of the Paramyxoviridae. © Springer-Verlag 2004.",amino acid;glycoprotein;HN protein;fusion protein;nucleotide;protein antibody;amino acid analysis;amino acid sequence;amino acid substitution;article;bird disease;catalysis;enzyme active site;enzyme activity;gene sequence;genetic conservation;Newcastle disease virus;nonhuman;nucleotide sequence;Paramyxoviridae;phylogeny;prediction;priority journal;protein degradation;protein function;protein glycosylation;protein motif;sequence analysis;virus classification;virus infection;virus isolation;virus neutralization;virus resistance;virus strain;virus virulence,"Seal, B. S.",2004,,10.1007/s10142-004-0113-2,0
1870,Characterization of Newcastle disease virus vaccines by biological properties and sequence analysis of the hemagglutinin-neuraminidase protein gene,"Six commercially available monovalent Newcastle disease virus (NDV) live-vaccines were examined for their biological and genomic stability in comparison to their stated parent virus. Thermostability of the hemagglutinin at 56°C for 5 min was consistently observed among the majority of the vaccine viruses. One exception was a recently developed NDV vaccine isolated from turkeys that had a thermostability of 15 min. Neuraminidase activity, as measured by elution rate of agglutinated red blood cells, varied among vaccine viruses and correlated with that of the parent isolate. Virulence as measured by intracerebral pathogenicity index ranged from 0 to 0.39 among NDV vaccine-type viruses, well within the range of avirulent lentogens. Sequence of the fusion protein cleavage site from all the NDV vaccine isolates examined was consistent with that for lentogens. The entire hemagglutinin-neurominidase gene sequence was 98% similar among all the NDV vaccine viruses examined and phylogenetic classification of commercial vaccine types correlated with their respective parent virus. Consequently, the commercially produced NDV vaccines reported here appear relatively stable when mass produced in avian embryonated eggs.",hemagglutinin;Newcastle disease vaccine;sialidase;article;controlled study;egg;hemagglutination;Newcastle disease virus;nonhuman;phylogeny;polymerase chain reaction;poultry;priority journal;reverse transcription;thermostability,"Seal, B. S.;King, D. J.;Bennett, J. D.",1996,,10.1016/0264-410x(95)00252-v,0
1871,The avian response to Newcastle disease virus,"Newcastle disease virus (NDV) is classified as a member of the superfamily Mononegavirales in the family Paramyxoviridae. This virus family is divided into two subfamilies, the Paramyxovirinae and the Pneumovirinae. In 1993 the International Committee on the Taxonomy of Viruses rearranged the order of the Paramyxovirus genus and placed NDV within the Rubulavirus genus among the Paramyxovirinae. The enveloped virus has a negative sense single- stranded RNA genome of 15,186 kb which codes for an RNA directed RNA polymerase, hemagglutinin-neuraminidase protein, fusion protein, matrix protein, phosphoprotein and nucleoprotein in the 5' to 3' direction. The virus has a wide host range with most orders of birds reported to have been infected by NDV. Isolates are characterized by virulence in chickens and are categorized into three main pathotypes depending on severity of disease. Lentogenic isolates are of low virulence while viruses of intermediate virulence are termed mesogenic. Highly virulent viruses that cause high mortality in birds are termed neurotropic or viscerotropic velogenic. Velogenic NDV are List A pathogens that require reporting to the Office of International Epizootics and outbreaks result in strict trade embargoes. The primary molecular determinant for NDV pathogenicity is the fusion protein cleavage site amino acid sequence. Vaccination for NDV is primarily by mass application of live-virus vaccines among commercial poultry. Although protection is measured by presence of antibodies to NDV, vaccinated B-cell depleted chickens are resistant to disease. Consequently, immune protection involves responses that are presently incompletely defined. (C) 2000 Elsevier Science Ltd.",HN protein;live vaccine;matrix protein;RNA directed RNA polymerase;virus fusion protein;virus nucleoprotein;virus phosphoprotein;virus RNA;amino acid sequence;animal disease;bird;chicken;fowl;Mononegavirales;Newcastle disease virus;nonhuman;Paramyxoviridae;persistent virus infection;Pneumovirinae;poultry;priority journal;protein expression;review;vaccination;veterinary medicine;virus classification;virus genome;virus transmission;virus virulence,"Seal, B. S.;King, D. J.;Sellers, H. S.",2000,,10.1016/s0145-305x(99)00077-4,0
1872,Fusion protein predicted amino acid sequence of the first US avian pneumovirus isolate and lack of heterogeneity among other US isolates,"Avian pneumovirus (APV) was first isolated from turkeys in the west-central US following emergence of turkey rhinotracheitis (TRT) during 1996. Subsequently, several APV isolates were obtained from the north-central US. Matrix (M) and fusion (F) protein genes of these isolates were examined for sequence heterogeneity and compared with European APV subtypes A and B. Among US isolates the M gene shared greater than 98% nucleotide sequence identity with only one nonsynonymous change occurring in a single US isolate. Although the F gene among US APV isolates shared 98% nucleotide sequence identity, nine conserved substitutions were detected in the predicted amino acid sequence. The predicted amino acid sequence of the US APV isolate's F protein had 72% sequence identity to the F protein of APV subtype A and 71% sequence identity to the F protein of APV subtype B. This compares with 83% sequence identity between the APV subtype A and B predicted amino acid sequences of the F protein. The US isolates were phylogenetically distinguishable from their European counterparts based on F gene nucleotide or predicted amino acid sequences. Lack of sequence heterogeneity among US APV subtypes indicates these viruses have maintained a relatively stable population since the first outbreak of TRT. Phylogenetic analysis of the F protein among APV isolates supports classification of US isolates as a new APV subtype C. Copyright (C) 2000 Elsevier Science B.V.",fusion protein;amino acid sequence;amino acid substitution;Avian metapneumovirus;controlled study;Europe;genetic heterogeneity;nonhuman;nucleotide sequence;phylogeny;Pneumovirinae;prediction;priority journal;review;rhinotracheitis;sequence homology;turkey (bird);United States;virus classification;virus gene;virus isolation,"Seal, B. S.;Sellers, H. S.;Meinersmann, R. J.",2000,,10.1016/s0168-1702(99)00133-1,0
1873,Genomic sequences of low-virulence avian paramyxovirus-1 (Newcastle disease virus) isolates obtained from live-bird markets in North America not related to commonly utilized commercial vaccine strains,"Avian paramyxovirus 1 (APMV-1), also referred to as Newcastle disease virus (NDV), variants of low virulence were isolated from chickens, ducks and other unidentified species found in live-bird markets of the northeastern United States. These isolates were characterized as APMV-1 by the hemagglutination- inhibition (HI) assay utilizing NDV-specific polyclonal antisera. However, the isolates failed to react with a monoclonal antibody that has specificity for a wide variety of APMV-1 isolates. Although only highly virulent isolates require reporting to international regulatory agencies, the ability to correctly identify APMV-1 types is important for control and regulatory purposes. Protein gel patterns of the purified isolates resembled previously reported APMV-1 and anti-NDV polyclonal sera recognized the viral proteins. For three isolates oligonucleotide primers specific for the nucleoprotein, fusion protein and polymerase genes of NDV were utilized to synthesize cDNA using viral RNA as a template. Approximately 12 kb of the genome was subsequently sequenced for the three isolates that included the nucleoprotein, phosphoprotein, matrix protein, fusion (F) protein, hemagglutinin-neuraminidase protein genes and a 5′ portion of the polymerase gene. The isolates had an F protein cleavage site sequence of ERQER/LVG indicating low-virulence viruses that phylogenetically separated with other unique NDV isolates designated as a lineage 6 genotype. Additionally, a four amino acid insert was detected in the predicted phosphoprotein which complies with the ""rule of six"" among paramyxoviruses. These APMV-1 genotypes have not been previously reported in North America and further substantiate the heterogeneous genetic nature of these commercially important pathogens found worldwide. © 2004 Elsevier B.V. All rights reserved.",complementary DNA;HN protein;fusion protein;matrix protein;monoclonal antibody;nucleoprotein;oligonucleotide;phosphoprotein;polyclonal antiserum;vaccine;viral protein;virus RNA;amino acid sequence;antibody specificity;article;bird;chicken;duck;gene sequence;genotype;hemagglutination inhibition test;Newcastle disease virus;nonhuman;North America;nucleotide sequence;phylogeny;protein gel blot analysis;structural gene;synthesis;viral genetics;virulence;virus isolation;virus strain,"Seal, B. S.;Wise, M. G.;Pedersen, J. C.;Senne, D. A.;Alvarez, R.;Scott, M. S.;King, D. J.;Yu, Q.;Kapczynski, D. R.",2005,,10.1016/j.vetmic.2004.11.013,0
1874,Evolutionary History and Phylogeography of Rabies Viruses Associated with Outbreaks in Trinidad,"Bat rabies is an emerging disease of public health significance in the Americas. The Caribbean island of Trinidad experiences periodic outbreaks within the livestock population. We performed molecular characterisation of Trinidad rabies virus (RABV) and used a Bayesian phylogeographic approach to investigate the extent to which outbreaks are a result of in situ evolution versus importation of virus from the nearby South American mainland. Trinidadian RABV sequences were confirmed as bat variant and clustered with Desmodus rotundus (vampire bat) related sequences. They fell into two largely temporally defined lineages designated Trinidad I and II. The Trinidad I lineage which included sequences from 1997-2000 (all but two of which were from the northeast of the island) was most closely related to RABV from Ecuador (2005, 2007), French Guiana (1990) and Venezuela (1993, 1994). Trinidad II comprised sequences from the southwest of the island, which clustered into two groups: Trinidad IIa, which included one sequence each from 2000 and 2007, and Trinidad IIb including all 2010 sequences. The Trinidad II sequences were most closely related to sequences from Brazil (1999, 2004) and Uruguay (2007, 2008). Phylogeographic analyses support three separate RABV introductions from the mainland from which each of the three Trinidadian lineages arose. The estimated dates for the introductions and subsequent lineage expansions suggest periods of in situ evolution within Trinidad following each introduction. These data also indicate co-circulation of Trinidad lineage I and IIa during 2000. In light of these findings and the likely vampire bat origin of Trinidadian RABV, further studies should be conducted to investigate the relationship between RABV spatiotemporal dynamics and vampire bat population ecology, in particular any movement between the mainland and Trinidad.",complementary DNA;animal tissue;article;evolutionary rate;high throughput sequencing;nonhuman;nucleotide sequence;phylogeny;phylogeography;polymerase chain reaction;Rabies virus;RNA extraction;Trinidad and Tobago;unindexed sequence,"Seetahal, J. F. R.;Velasco-Villa, A.;Allicock, O. M.;Adesiyun, A. A.;Bissessar, J.;Amour, K.;Phillip-Hosein, A.;Marston, D. A.;McElhinney, L. M.;Shi, M.;Wharwood, C. A.;Fooks, A. R.;Carrington, C. V. F.",2013,,10.1371/journal.pntd.0002365,0
1875,Public health significance of Campylobacter spp. colonisation of wild game pheasants (Phasianus colchicus) in Scotland,"Campylobacter is the most common cause of bacterial food-borne diarrhoeal disease worldwide. Chicken meat is considered the main source of human infection; however, C. jejuni and C. coli have also been reported in a range of livestock and wildlife species, including pheasants. Wild pheasant meat reaches the consumer's table because of hunting but there is a lack of information concerning the risk of Campylobacter infection in humans. This study aimed to determine the prevalence of Campylobacter in wild game pheasants in Scotland, to identify the main sequence types (STs) present and to evaluate their impact on public health. A total of 287 caecal samples from five Scottish regions were collected during the hunting season 2013/2014. Campylobacter was detected and enumerated using standard culture methods. PCR and High Throughput Multi Locus Sequence Typing (HiMLST) were used for species identification and sequence typing. In total, 36.6% of 287 caecal samples (n = 105; 95% CI: 14-59.2) were Campylobacter positive. Using PCR, 62.6% of samples (n = 99) were identified as C. coli and 37.4% as C. jejuni. HiMLST (n = 80) identified 19 different STs. ST-828 (n = 19) was the most common, followed by ST-827 (n = 12) and ST19 (n = 7). Sixteen of the 19 STs isolated are present in humans and eight are C. coli STs that account for 6.96% of human infections, although the overall risk to public health from pheasant meat is still considered to be low.",bacterial DNA;animal;bacterial load;Campylobacter;campylobacteriosis;classification;food control;food poisoning;Galliformes;genetics;geography;human;isolation and purification;microbiology;molecular epidemiology;multilocus sequence typing;pathogenicity;polymerase chain reaction;poultry;prevalence;public health;Scotland;sequence analysis;virology;wild animal,"Seguino, A.;Chintoan-Uta, C.;Smith, S. H.;Shaw, D. J.",2018,,10.1016/j.fm.2018.04.002,0
1876,"Molecular detection and analysis of Sheeppox and Orf viruses isolated from sheep from Qalubia, Egypt","In this study an outbreak with Sheeppox virus (SPPV) and Orf virus (ORFV) in one sheep herd in the Qalubia province, Egypt, was investigated. Both, SPPV and ORFV caused clinically manifest infections among sheep. The affected sheep showed skin lesions around the mouth or all over the body. Therefore, reliable diagnosis should confirm the aetiology of the infection and then reduce spread of the diseases in the affected areas. Clinical samples were investigated by virus isolation, PCR and real-time PCR assays. Furthermore, PCR-products of SPPV and ORFV isolates were sequenced and alignment to reference isolates was performed for phylogenetic analyses. The laboratory diagnosis showed that real-time PCR assay was more accurate and sensitive than conventional PCR and virus isolation. In phylogenetic analysis of the A29L gene genetic differences between SPPV field strains were not observed and the strains showed 100% homology with two SPPV isolates from Kazakhstan and one isolate from Turkey. The ORFV field strains are in the P55 gene genetically distinct from another and from other published isolates from Egypt 2006 and 2009.",virus DNA;animal;Capripoxvirus;chemistry;classification;contagious ecthyma;Egypt;genetics;isolation and purification;Orf virus;phylogeny;polymerase chain reaction;poxvirus infection;real time polymerase chain reaction;sequence alignment;sheep;sheep disease;veterinary medicine;virology,"Selim, A.;Elhaig, M.;Höche, J.;Gaede, W.",2016,,,0
1877,Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012,"One of the major problems of avian infectious bronchitis virus (IBV) is the frequent emergence of new variants. In the present study 205 tracheal swabs and organs were collected from broilers and layers chicken farms during January to August 2012 from 19 governorates all over Egypt. The chickens demonstrated respiratory signs and mortality. Out of the examined samples, 130 of which (about 64%) of suspected farms were positive for IBV with real time RT-PCR. 13 IBV-positive samples were selected for further isolation and characterization. Isolation in specific pathogen free (SPF) embryos was carried out after studies three blind successive passages and the hypervariable region of spike protein1 (SP1) was amplified by RT-PCR and sequenced to study the genetic diversity between the isolated viruses. Phylogenetic analysis of the obtained sequences of 13 isolates compared with other IBV strains from the Middle East and worldwide reveled that 11 out of the 13 isolates had close relationship the Israeli variants (IS/885 and IS/1494/06) with nucleotide homology reached up to 89.9% and 82.3%, respectively. Only two isolates had close relationship with CR/88121 and 4/91 viruses with identities of 95% and 96%, respectively. This study indicates existence of two variant groups of IBV circulating in Egypt during 2012. Group I was similar but distinguishable from Israeli variant IS/885 and group II was related to 4/91 and CR/88121 vaccine strains. There was no geographical link between the 2 groups as they were distributed all over the country. These findings necessitate the need to revise the vaccination programs and control measures for IBV. © 2013.",spike protein1;unclassified drug;virus spike protein;animal tissue;article;Avian infectious bronchitis virus;broiler;chicken;Coronavirus infection;Egypt;embryo;gene sequence;genetic variability;geographic distribution;Israel;nonhuman;nucleotide sequence;phylogeny;real time polymerase chain reaction;sequence homology;strain difference;viral genetics;virus isolation,"Selim, K.;Arafa, A. S.;Hussein, H. A.;El-Sanousi, A. A.",2013,,10.1016/j.ijvsm.2013.10.002,0
1878,… Materials: Frequency and Pathological Phenotype of Bovine Astrovirus CH13/NeuroS1 Infection in Neurologically-Diseased Cattle: Towards Assessment of …,,,"Selimovic-Hamza, S.;Boujon, C. L.;Hilbe, M.;Oevermann, A.",,,,0
1879,Frequency and Pathological Phenotype of Bovine Astrovirus CH13/NeuroS1 Infection in Neurologically-Diseased Cattle: Towards Assessment of Causality,"Next-generation sequencing (NGS) has opened up the possibility of detecting new viruses in unresolved diseases. Recently, astrovirus brain infections have been identified in neurologically diseased humans and animals by NGS, among them bovine astrovirus (BoAstV) CH13/NeuroS1, which has been found in brain tissues of cattle with non-suppurative encephalitis. Only a few studies are available on neurotropic astroviruses and a causal relationship between BoAstV CH13/NeuroS1 infections and neurological disease has been postulated, but remains unproven. Aiming at making a step forward towards assessing the causality, we collected brain samples of 97 cases of cattle diagnosed with unresolved non-suppurative encephalitis, and analyzed them by in situ hybridization and immunohistochemistry, to determine the frequency and neuropathological distribution of the BoAstV CH13/NeuroS1 and its topographical correlation to the pathology. We detected BoAstV CH13/NeuroS1 RNA or proteins in neurons throughout all parts of the central nervous system (CNS) in 34% of all cases, but none were detected in cattle of the control group. In general, brain lesions had a high correlation with the presence of the virus. These findings show that a substantial proportion of cattle with non-suppurative encephalitis are infected with BoAstV CH13/NeuroS1 and further substantiate the causal relationship between neurological disease and astrovirus infections.",astrovirus;bovine;encephalitis;neurotropic;infection;cattle;NONSUPPURATIVE ENCEPHALITIS;IDENTIFICATION;METAGENOMICS,"Selimovic-Hamza, S.;Boujon, C. L.;Hilbe, M.;Oevermann, A.;Seuberlich, T.",2017,Jan,,0
1880,Isolation of bluetongue virus serotypes new to Indonesia from sentinel cattle in west Java,,,"Sendow, I.;Daniels, P. W.;Soleha, E.;Erasmus, B.",1993,,,0
1881,Evaluation of the broad-spectrum lytic capability of bacteriophage cocktails against various Salmonella serovars and their effects on weaned pigs infected with Salmonella Typhimurium,"The broad-spectrum lytic capability of Salmonella bacteriophages against various Salmonella species was evaluated to determine their potential as an alternative for antibiotics, and the safety and preventive effects of the bacteriophages were assessed on mice and pigs. Four bacteriophage cocktails were prepared using 13 bacteriophages, and the lytic capability of the four bacteriophage cocktails was tested using Salmonella reference strains and field isolates. Bacteriophage cocktail C (SEP-1, SGP-1, STP-1, SS3eP-1, STP-2, SChP-1, SAP-1, SAP-2; ≥109 pfu/ml) showed the best lytic activity against the Salmonella reference strains (100% of 34) and field isolates (92.5% of 107). Fifty mice were then orally inoculated with bacteriophage cocktail C to determine the distribution of bacteriophages in various organs, blood and feces. The effects of bacteriophages on Salmonella infection in weaned pigs (n=15) were also evaluated through an experimental challenge with Salmonella Typhimurium after treatment with bacteriophage cocktail C. All mice exhibited distribution of the bacteriophages in all organs, blood and feces until 15 days post infection (dpi). After 35 dpi, bacteriophages were not detected in any of these specimens. As demonstrated in a pig challenge study, treatment with bacteriophage cocktail C reduced the level of Salmonella shedding in feces. The metagenomic analyses of these pig feces also revealed that bacteriophage treatment decreased the number of species of the Enterobacteriaceae family without significant disturbance to the normal fecal flora. This study showed that bacteriophages effectively controlled Salmonella in a pig challenge model and could be a good alternative for antibiotics to control Salmonella infection.",animal;bacteriolysis;bacteriophage;Bagg albino mouse;clinical trial;feces;female;metagenome;microbiology;mouse;phage therapy;pig;Salmonella enterica serovar Typhimurium;Salmonella phage;salmonellosis;swine disease;veterinary medicine;weaning,"Seo, B. J.;Song, E. T.;Lee, K.;Kim, J. W.;Jeong, C. G.;Moon, S. H.;Son, J. S.;Kang, S. H.;Cho, H. S.;Jung, B. Y.;Kim, W. I.",2018,,10.1292/jvms.17-0501,0
1882,"Africa, a reservoir of new virulent strains of Newcastle disease virus?",,Africa;chicken;farm animal;gene sequence;genotype;letter;Madagascar;Mali;morbidity;mortality;neurologic disease;Newcastle disease virus;nucleotide sequence;priority journal;reservoir;respiratory tract disease;virus detection;virus isolation,"Servan de Almeida, R.;Maminiaina, O. F.;Gil, P.;Hammoumi, S.;Molia, S.;Chevalier, V.;Koko, M.;Andriamanivo, H. R.;Traoré, A.;Samaké, K.;Diarra, A.;Grillet, C.;Martinez, D.;Albina, E.",2009,,10.1016/j.vaccine.2009.03.076,0
1883,Genetic diversity of Newcastle disease virus in Pakistan: A countrywide perspective,"Background: Newcastle disease (ND) is one of the most deadly diseases of poultry around the globe. The disease is endemic in Pakistan and recurrent outbreaks are being reported regularly in wild captive, rural and commercial poultry flocks. Though, efforts have been made to characterize the causative agent in some of parts of the country, the genetic nature of strains circulating throughout Pakistan is currently lacking. Material and methods. To ascertain the genetics of NDV, 452 blood samples were collected from 113 flocks, originating from all the provinces of Pakistan, showing high mortality (30-80%). The samples represented domesticated poultry (broiler, layer and rural) as well as wild captive birds (pigeons, turkeys, pheasants and peacock). Samples were screened with real-time PCR for both matrix and fusion genes (1792 bp), positive samples were subjected to amplification of full fusion gene and subsequent sequencing and phylogenetic analysis. Results: The deduced amino acid sequence of the fusion protein cleavage site indicated the presence of motif ( 112RK/RQRR↓F117) typical for velogenic strains of NDV. Phylogenetic analysis of hypervariable region of the fusion gene indicated that all the isolates belong to lineage 5 of NDV except isolates collected from Khyber Pakhtunkhwa (KPK) province. A higher resolution of the phylogenetic analysis of lineage 5 showed the distribution of Pakistani NDV strains to 5b. However, the isolates from KPK belonged to lineage 4c; the first report of such lineage from this province. Conclusions: Taken together, data indicated the prevalence of multiple lineages of NDV in different poultry population including wild captive birds. Such understanding is crucial to underpin the nature of circulating strains of NDV, their potential for interspecies transmission and disease diagnosis and control strategies. © 2013 Shabbir et al.; licensee BioMed Central Ltd.",amino acid sequence;bird;fusion gene;gene sequence;genetic variability;mortality;Newcastle disease virus;nonhuman;nucleotide sequence;Pakistan;phylogeny;poultry;real time polymerase chain reaction;review;unindexed sequence;virus strain,"Shabbir, M. Z.;Zohari, S.;Yaqub, T.;Nazir, J.;Shabbir, M. A. B.;Mukhtar, N.;Shafee, M.;Sajid, M.;Anees, M.;Abbas, M.;Khan, M. T.;Ali, A. A.;Ghafoor, A.;Ahad, A.;Channa, A. A.;Anjum, A. A.;Hussain, N.;Ahmad, A.;Goraya, M. U.;Iqbal, Z.;Khan, S. A.;Aslam, H. B.;Zehra, K.;Sohail, M. U.;Yaqub, W.;Ahmad, N.;Berg, M.;Munir, M.",2013,,10.1186/1743-422x-10-170,0
1884,Comparative analysis reveals frequent recombination in the parvoviruses,"Parvoviruses are small single-stranded DNA viruses that are ubiquitous in nature. Infections with both autonomous and helper-virus dependent parvoviruses are common in both human and animal populations, and many animals are host to a number of different parvoviral species. Despite the epidemiological importance of parvoviruses, the presence and role of genome recombination within or among parvoviral species has not been well characterized. Here we show that natural recombination may be widespread in these viruses. Different genome regions of both porcine parvoviruses and Aleutian mink disease viruses have conflicting phylogenetic histories, providing evidence for recombination within each of these two species. Further, the rodent parvoviruses show complex evolutionary histories for separate genomic regions, suggesting recombination at the interspecies level. © 2007 SGM.",article;DNA virus;genetic recombination;helper virus;infection;nonhuman;nucleotide sequence;Parvoviridae;phylogeny;Porcine parvovirus;priority journal;species difference;viral genetics;virus genome;virus replication,"Shackelton, L. A.;Hoelzer, K.;Parrish, C. R.;Holmes, E. C.",2007,,10.1099/vir.0.83255-0,0
1885,Phylogenetic analysis and reclassification of caprine and ovine lentiviruses based on 104 new isolates: Evidence for regular sheep-to-goat transmission and worldwide propagation through livestock trade,"We performed a phylogenetic analysis of caprine and ovine lentiviruses using long sequences in gag and pol of 104 new Swiss isolates and six available corresponding database sequences. Forty-five isolates, forming five sequence clusters, were unclassifiable by the present classification. Pairwise DNA distance analysis indicated different categories of relatedness, requiring a new classification system. We propose four principal sequence groups, A-D, which differ by 25-37%. Groups A and B are further divided into subtypes which differ by 15-27%. Group D and four of the seven group A subtypes, A3, A4, A5 and A7, are formed by new Swiss isolates. Molecular epidemiology revealed that Swiss B1 strains differed no more from French, Brazilian or US strains than from each other, suggesting virus propagation through international livestock trade. Furthermore, infection of goats by subtypes A3 or A4 was significantly associated with documented contact with sheep, which also harbor these subtypes, thus indicating regularly occurring sheep-to-goat transmission. © 2003 Elsevier Inc. All rights reserved.",DNA;Gag protein;Pol protein;amino acid sequence;article;data base;DNA determination;goat;Lentivirus;livestock;molecular dynamics;nonhuman;nucleotide sequence;phylogeny;priority journal;sheep;virus classification;virus isolation;virus strain;virus transmission,"Shah, C.;Böni, J.;Huder, J. B.;Vogt, H. R.;Mühlherr, J.;Zanoni, R.;Miserez, R.;Lutz, H.;Schüpbach, J.",2004,,10.1016/j.virol.2003.09.047,0
1886,Comparison of tissue sample processing methods for harvesting the viral metagenome and a snapshot of the RNA viral community in a turkey gut,"RNA viruses have been associated with enteritis in poultry and have been isolated from diseased birds. The same viral agents have also been detected in healthy flocks bringing into question their role in health and disease. In order to understand better eukaryotic viruses in the gut, this project focused on evaluating alternative methods to purify and concentrate viral particles, which do not involve the use of density gradients, for generating viral metagenome data. In this study, the sequence outcomes of three tissue processing methods have been evaluated and a data analysis pipeline has been established for RNA viruses from the gastrointestinal tract. In addition, with the use of the best method and increased sequencing depth, a glimpse of the RNA viral community in the gastrointestinal tract of a clinically normal 5-week old turkey is presented. The viruses from the Reoviridae and Astroviridae families together accounted for 76.3% of total viruses identified. The rarefaction curve at the species level further indicated that majority of the species diversity was included with the increased sequencing depth, implying that viruses from other viral families were present in very low abundance.",analytic method;animal tissue;article;Astroviridae;intestine;metagenome;microbial community;microbial diversity;nonhuman;Reoviridae;RNA sequence;RNA virus;Rotavirus;species richness;taxonomy;tissue processing method;turkey (bird);virus genome;virus identification;virus replication,"Shah, J. D.;Baller, J.;Zhang, Y.;Silverstein, K.;Xing, Z.;Cardona, C. J.",2014,,10.1016/j.jviromet.2014.08.011,1
1887,Development of the Intestinal RNA Virus Community of Healthy Broiler Chickens,"Several RNA viruses such as astrovirus, rotavirus, reovirus and parvovirus have been detected in both healthy and diseased commercial poultry flocks. The aim of this study was to characterize (a) the development of the RNA viral community in the small intestines of healthy broiler chickens from hatch through 6 weeks of age (market age) and (b) the contribution of the breeder source vs. bird age in development of the community structure. Intestinal tissue samples were harvested from breeders and their progeny, processed for viral RNA extraction and sequenced using Illumina Hiseq sequencing technology resulting in 100 bp PE reads. The results from this study indicated that the breeder source influenced the RNA viral community only at hatch but later environment i.e. bird age had the more significant effect. The most abundant RNA viral family detected at 2, 4 and 6 weeks of age was Astroviridae, which decreased in abundance with age while the abundance of Picornaviridae increased with age.","Age Factors;Animals;Base Sequence;*Chickens/vi [Virology];*Gastrointestinal Microbiome/ge [Genetics];Genetic Variation;High-Throughput Nucleotide Sequencing;*Intestine, Small/vi [Virology];Molecular Typing;Poultry Diseases/vi [Virology];RNA Viruses/cl [Classification];RNA Viruses/ge [Genetics];*RNA Viruses/gd [Growth & Development];*RNA, Viral/ge [Genetics];Sequence Analysis, RNA/ve [Veterinary];0 (RNA, Viral)","Shah, J. D.;Desai, P. T.;Zhang, Y.;Scharber, S. K.;Baller, J.;Xing, Z. S.;Cardona, C. J.",2016,,,1
1888,Analysis of Host-Parasite Incongruence in Papillomavirus Evolution Using Importance Sampling,"The papillomaviruses (PVs) are a family of viruses infecting several mammalian and nonmammalian species that cause cervical cancer in humans. The evolutionary history of the PVs as it associated with a wide range of host species is not well understood. Incongruities between the phylogenetic trees of various viral genes as well as between these genes and the host phylogenies suggest historical viral recombination as well as violations of strict virus-host cospeciation. The extent of recombination events among PVs is uncertain, however, and there is little evidence to support a theory of PV spread via recent host transfers. We have investigated incongruence between PV genes and hence, the possibility of recombination, using Bayesian phylogenetic methods. We find significant evidence for phylogenetic incongruence among the six PV genes E1, E2, E6, E7, L1, and L2, indicating substantial recombination. Analysis of E1 and L1 phylogenies suggests ancestral recombination events. We also describe a new method for examining alternative host-parasite association mechanisms by applying importance sampling to Bayesian divergence time estimation. This new approach is not restricted by a fixed viral tree topology or knowledge of viral divergence times, multiple parasite taxa per host may be included, and it can distinguish between prior divergence of the virus before host speciation and host transfer of the virus following speciation. Using this method, we find prior divergence of PV lineages associated with the ancestral mammalian host resulting in at least 6 PV lineages prior to speciation of this host. These PV lineages have then followed paths of prior divergence and cospeciation to eventually become associated with the extant host species. Only one significant instance of host transfer is supported, the transfer of the ancestral L1 gene between a Primate and Hystricognathi host based on the divergence times between the upsilon human type 41 and porcupine PVs.",papillomavirus;phylogenetic incongruence;importance sampling;host;transfer;relaxed clock models;Bayesian analysis;HUMAN ALPHA-PAPILLOMAVIRUS;PHYLOGENETIC ANALYSIS;GENOMIC;CHARACTERIZATION;MOLECULAR EVOLUTION;BOVINE PAPILLOMAVIRUS;MAXIMUM-LIKELIHOOD;CERVICAL-CANCER;SEQUENCE DATA;HEALTHY SKIN;DNA,"Shah, S. D.;Doorbar, J.;Goldstein, R. A.",2010,Jun,,0
1889,The fecal virome of pigs on a high-density farm,"Swine are an important source of proteins worldwide but are subject to frequent viral outbreaks and numerous infections capable of infecting humans. Modern farming conditions may also increase viral transmission and potential zoonotic spread. We describe here the metagenomics-derived virome in the feces of 24 healthy and 12 diarrheic piglets on a high-density farm. An average of 4.2 different mammalian viruses were shed by healthy piglets, reflecting a high level of asymptomatic infections. Diarrheic pigs shed an average of 5.4 different mammalian viruses. Ninety-nine percent of the viral sequences were related to the RNA virus families Picornaviridae, Astroviridae, Coronaviridae, and Caliciviridae, while 1% were related to the small DNA virus families Circoviridae, and Parvoviridae. Porcine RNA viruses identified, in order of decreasing number of sequence reads, consisted of kobuviruses, astroviruses, enteroviruses, sapoviruses, sapeloviruses, coronaviruses, bocaviruses, and teschoviruses. The near-full genomes of multiple novel species of porcine astroviruses and bocaviruses were generated and phylogenetically analyzed. Multiple small circular DNA genomes encoding replicase proteins plus two highly divergent members of the Picornavirales order were also characterized. The possible origin of these viral genomes from pig-infecting protozoans and nematodes, based on closest sequence similarities, is discussed. In summary, an unbiased survey of viruses in the feces of intensely farmed animals revealed frequent coinfections with a highly diverse set of viruses providing favorable conditions for viral recombination. Viral surveys of animals can readily document the circulation of known and new viruses, facilitating the detection of emerging viruses and prospective evaluation of their pathogenic and zoonotic potentials. © 2011, American Society for Microbiology.",circular DNA;RNA directed RNA polymerase;article;Astroviridae;asymptomatic infection;Bocaparvovirus;Circoviridae;controlled study;Coronavirinae;diarrhea;DNA virus;Enterovirus;feces analysis;gene sequence;genetic similarity;genetic variability;Kobuvirus;metagenomics;mixed infection;nematode;nonhuman;nucleotide sequence;Parvoviridae;phylogeny;Picornaviridae;pig farming;piglet;priority journal;protozoon;Sapelovirus;Sapovirus;species;pig;Teschovirus;unindexed sequence;virus detection;virus genome;virus identification;virus infection;virus isolation;virus transmission;zoonosis,"Shan, T.;Li, L.;Simmonds, P.;Wang, C.;Moeser, A.;Delwart, E.",2011,,10.1128/jvi.05217-11,1
1890,Antiviral drug discovery for the treatment of enterovirus 71 infections,"Enterovirus 71 (EV71) is a small, positive-sense, single-stranded RNA virus in the genus Enterovirus, family Picornavirus. It causes hand, foot and mouth disease in infants and children, which in a small percentage of cases progresses to central nervous system infection, ranging from aseptic meningitis to fatal encephalitis. Sporadic cases of EV71 infection occur throughout the world, but large epidemics have occurred recently in Southeast Asia and China. There are currently no approved vaccines or antiviral therapies for the prevention or treatment of EV71 infection. This paper reviews efforts to develop antiviral therapies against EV71. © 2012 Elsevier B.V.","4',6 dichloroflavan;antivirus agent;bpr 0z 101;bpr 0z 103;bpr 0z 194;lactoferrin;nf 449;pleconaril;unclassified drug;viral protein;amino terminal sequence;China;Enterovirus A71;Enterovirus 71 infection;Enterovirus infection;genotype;herpangina;Korea;mortality;prevalence;priority journal;review;Taiwan;Thailand;Viet Nam;virus classification;virus genome;virus mutation;bw 683c","Shang, L.;Xu, M.;Yin, Z.",2013,,10.1016/j.antiviral.2012.12.005,0
1891,A naturally occurring recombinant enterovirus expresses a torovirus deubiquitinase,"Enteroviruses (EVs) are implicated in a wide range of diseases in humans and animals. In this study, a novel enterovirus (enterovirus species G [EVG]) (EVG 08/NC_USA/2015) was isolated from a diagnostic sample from a neonatal pig diarrhea case and identified by using metagenomics and complete genome sequencing. The viral genome shares 75.4% nucleotide identity with a prototypic EVG strain (PEV9 UKG/410/73). Remarkably, a 582-nucleotide insertion, flanked by 3Cpro cleavage sites at the 5= and 3= ends, was found in the 2C/3A junction region of the viral genome. This insertion encodes a predicted protease with 54 to 68% amino acid identity to torovirus (ToV) papain-like protease (PLP) (ToV-PLP). Structural homology modeling predicts that this protease adopts a fold and a catalytic site characteristic of minimal PLP catalytic domains. This structure is similar to those of core catalytic domains of the foot-and-mouth disease virus leader protease and coronavirus PLPs, which act as deubiquitinating and deISGylating (interferon [IFN]-stimulated gene 15 [ISG15]-removing) enzymes on host cell substrates. Importantly, the recombinant ToV-PLP protein derived from this novel enterovirus also showed strong deubiquitination and deISGylation activities and demonstrated the ability to suppress IFN-β expression. Using reverse genetics, we generated a ToV-PLP knockout recombinant virus. Compared to the wild-type virus, the ToV-PLP knockout mutant virus showed impaired growth and induced higher expression levels of innate immune genes in infected cells. These results suggest that ToV-PLP functions as an innate immune antagonist; enterovirus G may therefore gain fitness through the acquisition of ToV-PLP from a recombination event.",deubiquitinase;papain like protease;proteinase;unclassified drug;3' untranslated region;5' untranslated region;amino acid sequence;article;catalysis;cell culture;controlled study;diarrhea;Enterovirus;enzyme activity;gene expression regulation;gene inactivation;gene insertion;gene sequence;innate immunity;metagenomics;nonhuman;phylogeny;pig;priority journal;sequence alignment;structural homology;virus attenuation;virus expression;virus genome;virus isolation;virus morphology;virus recombinant;wild type,"Shang, P.;Misra, S.;Hause, B.;Fang, Y.",2017,,10.1128/jvi.00450-17,0
1892,Molecular epidemiological investigation of porcine reproductive and respiratory syndrome virus in Northwest China from 2007 to 2010,"Porcine reproductive and respiratory syndrome (PRRS) is an economically important swine disease affecting swine worldwide. Northwest China has a sparse pig population and there is no comprehensive information currently available on PRRSV infection. In this study, we analyzed the epidemiological features and genetic diversity of PRRSV from this region. 322 field-isolated tissues or serum samples were collected from aborted pig fetuses or pigs with respiratory disease from 15 herds, twice over a period of 2 years. PRRSV infection was determined and virus strains were classified by the sequencing of GP5. We found that 35.9 % of the animals were PRRSV-positive, and the average prevalence in 2007-2008 and 2009-2010 was 46.5 and 29.3 %, respectively. To further investigate the genetic divergence of PRRSV samples collected from 2007 to 2010, 32 strains were isolated for GP5 sequencing and analysis, and phylogenetic trees were created based on GP5 amino acid sequences. All PRRSVs were of the North American genotype and belonged to the highly pathogenic HP-PRRSV subgenotype. Isolates from the Xinjiang province formed a tightly clustered branch and were closely related to an evolutionary intermediate subgroup isolate. Virus sequences from 2007 to 2008 were compared with those from 2009 to 2010 from the same herd. New mutations were found in isolates after 2009 and focused on nucleotides in the GP5 antibody decoy epitope. PRRSV strains in Northwest China from 2007 to 2010 were similar to those from other regions of China, with some regional characteristics. These results contribute to the knowledge of PRRSV epidemiology in China. © Springer Science+Business Media, LLC 2012.",amino acid sequence;amino acid substitution;animal tissue;Arterivirus;article;China;fetus;gene cluster;gene sequence;genetic conservation;genetic variability;genotype;geographic distribution;GP5 gene;molecular epidemiology;nonhuman;nucleotide sequence;open reading frame;phylogenetic tree;porcine reproductive and respiratory syndrome;priority journal;pig;virus examination;virus gene;virus isolation;virus mutation;virus strain;virus virulence,"Shang, Y.;Wang, G.;Tian, H.;Yin, S.;Du, P.;Wu, J.;Chen, Y.;Yang, S.;Jin, Y.;Zhang, K.;Liu, X.",2012,,10.1007/s11262-012-0747-4,0
1893,Genesis of avian influenza H9N2 in Bangladesh,"Avian influenza subtype H9N2 is endemic in many bird species in Asia and the Middle East and has contributed to the genesis of H5N1, H7N9 and H10N8, which are potential pandemic threats. H9N2 viruses that have spread to Bangladesh have acquired multiple gene segments from highly pathogenic (HP) H7N3 viruses that are presumably in Pakistan and currently cocirculate with HP H5N1. However, the source and geographic origin of these H9N2 viruses are not clear. We characterized the complete genetic sequences of 37 Bangladeshi H9N2 viruses isolated in 2011-2013 and investigated their inter- and intrasubtypic genetic diversities by tracing their genesis in relationship to other H9N2 viruses isolated from neighboring countries. H9N2 viruses in Bangladesh are homogenous with several mammalian host-specific markers and are a new H9N2 sublineage wherein the hemagglutinin (HA) gene is derived from an Iranian H9N2 lineage (Mideast-B Iran), the neuraminidase (NA) and polymerase basic 2 (PB2) genes are from Dubai H9N2 (Mideast-C Dubai), and the non-structural protein (NS), nucleoprotein (NP), matrix protein (MP), polymerase acidic (PA) and polymerase basic 1 (PB1) genes are from HP H7N3 originating from Pakistan. Different H9N2 genotypes that were replaced in 2006 and 2009 by other reassortants have been detected in Bangladesh. Phylogenetic and molecular analyses suggest that the current genotype descended from the prototypical H9N2 lineage (G1), which circulated in poultry in China during the late 1990s and came to Bangladesh via the poultry trade within the Middle East, and that this genotype subsequently reassorted with H7N3 and H9N2 lineages from Pakistan and spread throughout India. Thus, continual surveillance of Bangladeshi HP H5N1, H7N3 and H9N2 is warranted to identify further evolution and adaptation to humans.",matrix protein;nucleoprotein;polymerase acidic;polymerase basic 1;polymerase basic 2;sialidase;unclassified drug;virus hemagglutinin;article;Asia;Bangladesh;China;endemic species;gene sequence;genetic reassortment;genetic variability;genotype;India;Influenza A virus (H10N8);Influenza A virus (H5N1);Influenza A virus (H7N9);Influenza A virus (H9N2);Iran;marker gene;Middle East;nonhuman;Pakistan;pandemic;phylogeny;poultry;priority journal;virus isolation;virus pathogenesis,"Shanmuganatham, K.;Feeroz, M. M.;Jones-Engel, L.;Walker, D.;Alam, S. M. R.;Hasan, M. K.;McKenzie, P.;Krauss, S.;Webby, R. J.;Webster, R. G.",2014,,10.1038/emi.2014.88,0
1894,Nucleotide sequencing and phylogenic analysis of fusion (F) epitope for Egyptian pestes des petit ruminants virus (PPRV) predicting unique criteria stated as Egypt 2009,"Peste des petit ruminants virus was previously isolated and serologically identified from suspected outbreaks of PPR among sheep and goats in Qalyubia Province, Egypt at 2006. In this study, six of this PPRV isolates were confirmed by reverse transcriptase-PCR (RT-PCR) using primer set for Fusion protein (F) epitope, then cDNA were send to Institute of Animal Health Pirbright, England to analyze for their nucleotide sequences of this F protein gene and phylogenic analysis properties, by matching with other reference world recorded isolates. The gene sequenced a 322 nucleotide cDNA fragment of the fusion protein gene was obtained. The isolates showed unique phylogenic analysis had not previously been identified internationally and defined as Egypt 2009. In addition; by using the obtained sequences generated from this gene coding protein; Egyptian PPRVs were grouped phylo genetic ally belongs to lineage IV. To the author knowledge, this is the first report describing the Fusion protein (F) gene sequence, phylogenic analysis and lineage typing of Egyptian isolates of PPRVs. © 2011 Academic Journals Inc.",complementary DNA;fusion protein;article;consensus sequence;controlled study;DNA fragmentation;Egypt;epidemic;epitope mapping;gene amplification;gene sequence;goat;Measles virus;nonhuman;nucleotide sequence;phylogeny;reverse transcription;reverse transcription polymerase chain reaction;serology;sheep;virus isolation,"Sharawi, S. S. A.;Abd-El-Rahim, I. H. A.",2011,,10.3923/ijv.2011.91.99,0
1895,Molecular Epidemiology and Complete Genome Characterization of H1N1pdm Virus from India,"Background: Influenza A virus is one of world's major uncontrolled pathogen, causing seasonal epidemic as well as global pandemic. This was evidenced by recent emergence and continued prevalent 2009 swine origin pandemic H1N1 Influenza A virus, provoking first true pandemic in the past 40 years. In the course of its evolution, the virus acquired many mutations and multiple unidentified molecular determinants are likely responsible for the ability of the 2009 H1N1 virus to cause increased disease severity in humans. Availability of limited data on complete genome hampers the continuous monitoring of this type of events. Outbreaks with considerable morbidity and mortality have been reported from all parts of the country. Methods/Results: Considering a large number of clinical cases of infection complete genome based sequence characterization of Indian H1N1pdm virus and their phylogenetic analysis with respect to circulating global viruses was undertaken, to reveal the phylodynamic pattern of H1N1pdm virus in India from 2009-2011. The Clade VII was observed as a major circulating clade in phylogenetic analysis. Selection pressure analysis revealed 18 positively selected sites in major surface proteins of H1N1pdm virus. Conclusions: This study clearly revealed that clade VII has been identified as recent circulating clade in India as well globally. Few clade VII specific well identified markers undergone positive selection during virus evolution. Continuous monitoring of the H1N1pdm virus is warranted to track of the virus evolution and further transmission. This study will serve as a baseline data for future surveillance and also for development of suitable therapeutics. © 2013 Sharma et al.",membrane protein;viral protein;adult;aged;article;child;cladistics;clinical article;controlled study;coughing;cytopathogenic effect;dyspnea;female;fever;gene amplification;gene sequence;human;India;Influenza A virus (H1N1);laboratory diagnosis;male;molecular epidemiology;nucleotide sequence;pandemic influenza;phylogeny;preschool child;real time polymerase chain reaction;reverse transcription polymerase chain reaction;school child;seasonal influenza;sequence analysis;sore throat;symptomatology;virus genome;virus identification;virus isolation;virus strain,"Sharma, S.;Joshi, G.;Dash, P. K.;Thomas, M.;Athmaram, T. N.;Kumar, J. S.;Desai, A.;Vasanthapuram, R.;Patro, I. K.;Rao, P. V. L.;Parida, M.",2013,,10.1371/journal.pone.0056364,0
1896,Epidemiology of Contagious Pustular Dermatitis in Small Ruminants of Punjab,Contagious pustular dermtitic (orf) is caused by orf virus classified in the genus Parapoxvirvs of the family Poxviridae. It is nonsystemic eruptive skin disease of sheep and goats transmissible to human beings. The present paper describes the epidemiology of contagious pustular dermatitis in small ruminants of Punjab and molecular diagnosis of the disease by polymerase chain reaction (PCR),OUTBREAK;ORF,"Sharma, S.;Mahajan, V.;Hosamani, M.;Singh, R. K.;Kallesh, D. J.;Kumar, H.;Verma, S.;Sandhu, K. S.",2008,Dec,,0
1897,Response to wing-web challenge of Rous sarcoma virus subgroups in some chicken breeds,"Response to wing-web challenge (WWC) of Rous sarcoma virus (RSV) subgroups was studied in 4-8 weeks old chicks of a light breed, a heavy breed and a cross between an indigenous black plumage Bantam fowl and Australorp breed. Wing-web tumor (WWT) began to develop within one week in response to virus subgroups A (BS-RSV) and C [RSV (RAV-49)] challenge. In chicks challenged with subgroup D [RSV (RAV-50)] virus it took a minimum of 4 weeks for development of WWT. Positive response to WWC by subgroups A, C and D virus was 84%, 100% and 52%, respectively. The duration of exhibition of positive response was maximum for subgroup A virus, followed by subgroup D and minimum for subgroup C virus.",article;cellular immunity;chicken;immune response;Rous sarcoma virus;virus classification;virus envelope;virus infection;virus interference,"Sharma, S. N.",1999,,,0
1898,Comparative metagenomics of microbial traits within oceanic viral communities,"Viral genomes often contain genes recently acquired from microbes. In some cases (for example, psbA) the proteins encoded by these genes have been shown to be important for viral replication. In this study, using a unique search strategy on the Global Ocean Survey (GOS) metagenomes in combination with marine virome and microbiome pyrosequencing-based datasets, we characterize previously undetected microbial metabolic capabilities concealed within the genomes of uncultured marine viral communities. A total of 34 microbial gene families were detected on 452 viral GOS scaffolds. The majority of auxiliary metabolic genes found on these scaffolds have never been reported in phages. Host genes detected in viruses were mainly divided between genes encoding for different energy metabolism pathways, such as electron transport and newly identified photosystem genes, or translation and post-translation mechanism related. Our findings suggest previously undetected ways, in which marine phages adapt to their hosts and improve their fitness, including translation and post-translation level control over the host rather than the already known transcription level control. The ISME Journal (2011) 5, 1178-1190; doi:10.1038/ismej.2011.2; published online 10 February 2011 Subject Category: integrated genomics and post-genomics approaches in microbial ecology",cyanophage;gene transfer;metagenomics;photosynthesis;viral-host;interactions;TERMINAL METHIONINE EXCISION;AMINO-ACID-SEQUENCE;PHOTOSYNTHESIS GENES;PEPTIDE DEFORMYLASE;SAMPLING EXPEDITION;NDH-1 COMPLEXES;MARINE-ENVIRONMENT;LAMBDA-REPRESSOR;PHAGE;PROTEINS,"Sharon, I.;Battchikova, N.;Aro, E. M.;Giglione, C.;Meinnel, T.;Glaser, F.;Pinter, R. Y.;Breitbart, M.;Rohwer, F.;Beja, O.",2011,Jul,,0
1899,High prevalence and diversity of bovine astroviruses in the faeces of healthy and diarrhoeic calves in South West Scotland,"Astroviruses (AstV) are single-stranded, positive-sense RNA viruses and one of the major causes of infant diarrhoea worldwide. Diarrhoea is a common and important cause of morbidity and mortality in calves; therefore, we investigated whether the presence of AstV is associated with calf diarrhoea. We identified diverse AstV lineages from faecal samples of both healthy and diarrhoeic calves and healthy adult cattle in South West Scotland. AstV was common in calves (present in 74% (85/115) of samples) but uncommon in adult cattle (present in 15% (3/20) of samples). No association was found between the presence of AstV and calf diarrhoea or the presence of a specific AstV lineage and calf diarrhoea. AstV was strongly associated with the presence of rotavirus Group A (RVA), and a protective effect of age was evident for both AstV and RVA. Co-infections with multiple AstV lineages were detected in several calves and serial infection with different viruses could also be seen by longitudinal sampling of individuals. In summary, our study found genotypically diverse AstV in the faeces of calves in South West Scotland. However, no association was identified between AstV and calf diarrhoea, which suggests the virus does not play a primary role in the aetiology of calf diarrhoea in the group studied. (C) 2015 The Authors. Published by Elsevier B.V.",Bovine;Astrovirus;Rotavirus;Diarrhoea;PCR;VIRAL METAGENOMICS;CALF DIARRHEA;GASTROENTERITIS;ROTAVIRUS;CATTLE;PATHOGENESIS;ASSOCIATION;INFECTIONS;CHILDREN;ANIMALS,"Sharp, C. P.;Gregory, W. F.;Mason, C.;Bronsvoort, B. M. D.;Beard, P. M.",2015,Jul,,0
1900,Rapid fermentable substance modulates interactions between ruminal commensals and toll-like receptors in promotion of immune tolerance of goat rumen,"Whether dietary non-fiber carbohydrate (NFC), a rapid fermentable substance, affects immune homeostasis of rumen through the modulation of interactions of ruminal microbiota and epithelial toll-like receptors (TLRs) remains unclear. A combination of 16S rRNA amplicon sequencing and quantitative PCRs was applied to study the synergetic responses of ruminal microbiota and epithelial TLRs to the dietary NFC switch from 15 to 31% in the goat model. The results showed that the 31% NFC diet caused the radical increases on the richness and diversity of rumen microbiota. The phylum Verrucomicrobia was most significantly expanded, whereas opportunistic pathogens, namely Rikenella, Anaeroplasma, and Olsenella, were significantly decreased. In rumen epithelium, the significantly increased expressions of TLR1, 6, 10 were associated with the significantly decreased expressions of pro-inflammatory cytokines interleukin-1beta (IL-1β), IL-6, and anti-inflammatory cytokine IL-10. Constrained correlation analysis indicated that the increased abundance of commensal bacteria in Verrucomicrobia subdivision 5 contributed to the upregulation of TLR10 expression. Finally, the significantly increased concentrations of rumen short-chain fatty acids (SCFAs), coupled with the significantly upregulated expressions of epithelial genes related to SCFA absorption were observed in goats fed with 31% NFC diet. Thus, the NFC-induced expansion of rumen microbiota promoted epithelium tolerance by enhancement of the intensity of TLR10 signaling. The newly established equilibrium benefited to the transport of ruminal energy substances into the blood.",biological marker;interleukin 10;interleukin 1beta;interleukin 6;monocarboxylate transporter 1;monocarboxylate transporter 4;RNA 16S;short chain fatty acid;sodium proton exchange protein 1;sodium proton exchange protein 3;toll like receptor;toll like receptor 1;toll like receptor 10;toll like receptor 6;Anaeroplasma;animal experiment;animal tissue;article;carbohydrate diet;commensal;controlled study;cytokine production;epithelium cell;gene expression regulation;goat;immunological tolerance;male;metagenomics;microbial community;multidimensional scaling;Murine leukemia virus;nonhuman;pH;phylogenetic tree;polymerase chain reaction;rumen microorganism;upregulation;Verrucomicrobia,"Shen, H.;Lu, Z.;Chen, Z.;Wu, Y.;Shen, Z.",2016,,10.3389/fmicb.2016.01812,0
1901,"Influenza A(H5N6) Virus Reassortant, Southern China, 2014",,"Animals;Chickens/vi [Virology];China;*Ducks/vi [Virology];Genes, Viral;*Influenza A virus/ge [Genetics];*Influenza in Birds/ep [Epidemiology];Influenza in Birds/vi [Virology];Mutagenesis;*Poultry Diseases/ep [Epidemiology];Poultry Diseases/vi [Virology]","Shen, H.;Wu, B.;Chen, Y.;Bi, Y.;Xie, Q.",2015,Jul,,0
1902,Pathogenicity and genetic characterization of a duck Tembusu virus associated with egg-dropping in Muscovy ducks,"Duck Tembusu virus (DTMUV) has spread to the major duck-farming region in China, causing acute egg-production drop in Chinese duck population. In this study, we characterized a DTMUV strain (named GD2014) isolated from an egg-production drop duck farm in Guangdong province, South China. The virus was pathogenic to Muscovy duck embryos and caused severe egg production drop for laying Muscovy ducks. The genome sequence of GD2014 shared 97–99% homologies with other waterfowl-origin Tembusu viruses, and shared 89% identities with MM1775 strain isolated from mosquito. Phylogenetic analysis of entire open reading frame (ORF), E gene and NS5 gene indicated that GD2014 belonged to Ntaya group. These results have implications for understanding the orgin, emergence and pathogenicity of DTMUV as well as for the development of vaccines and diagnostics based on epidemiological data.",animal cell;animal embryo;animal tissue;article;Cairina moschata;controlled study;duck Tembusu virus;egg laying;egg production;embryo;Flavivirus;gene sequence;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;reverse transcription polymerase chain reaction;virus genome;virus isolation;virus strain;virus virulence,"Shen, H. Q.;Lin, W. C.;Wang, Z. X.;Zhang, K.;Yan, Z. Q.;Zhou, Q. F.;Qin, J. P.;Xie, Q. M.;Bi, Y. Z.;Chen, F.",2016,,10.1016/j.virusres.2016.06.016,0
1903,Isolation and phylogenetic analysis of hemagglutinin gene of H9N2 influenza viruses from chickens in South China from 2012 to 2013,"As part of our ongoing influenza surveillance program in South China, 19 field strains of H9N2 subtype avian influenza viruses (AIVs) were isolated from dead or diseased chicken flocks in Guangdong province, South China, between 2012 and 2013. Hemagglutinin (HA) genes of these strains were sequenced and analyzed and phylogenic analysis showed that 12 of the 19 isolates belonged to the lineage h9.4.2.5, while the other seven belonged to h9.4.2.6. Specifically, we found that all of the viruses isolated in 2013 belonged to lineage h9.4.2.5. The lineage h9.4.2.5 viruses contained a PSRSSR↓GLF motif at HA cleavage site, while the lineage h9.4.2.6 viruses contained a PARSSR↓GLF at the same position. Most of the isolates in lineage h9.4.2.5 lost one potential glycosylation site at residues 200-202, and had an additional one at residues 295-297 in HA1. Notably, 19 isolates had an amino acid exchange (Q226L) in the receptor binding site, which indicated that the viruses had potential affinity of binding to human like receptor. The present study shows the importance of continuing surveillance of new H9N2 strains to better prepare for the next epidemic or pandemic outbreak of H9N2 AIV infections in chicken flocks.",Influenza virus hemagglutinin;animal;avian influenza;bird disease;chemistry;chicken;China;genetics;Influenza A virus (H9N2);metabolism;phylogeny;sequence analysis;veterinary medicine;virology,"Shen, H. Q.;Yan, Z. Q.;Zeng, F. G.;Liao, C. T.;Zhou, Q. F.;Qin, J. P.;Xie, Q. M.;Bi, Y. Z.;Chen, F.",2015,,,0
1904,Genomic and evolutionary characterization of a novel influenza-C-like virus from swine,"We recently described the isolation of a novel influenza virus from swine exhibiting respiratory disease in the United States that is distantly related to human influenza C virus. Based on genetic, biochemical and morphological analysis, the virus was provisionally classified as C/swine/Oklahoma/1334/2011 (C/OK). To further understand the genetics and evolution of this novel pathogen, we performed a comprehensive analysis of its sequence and phylogeny. The results demonstrated that C/OK and human influenza C viruses share a conserved array of predicted functional domains in the viral RNA genome replication and viral entry machinery but vary at key functional sites. Furthermore, our evolutionary analysis showed that homologous genes of C/OK and human influenza C viruses diverged from each other an estimated several hundred to several thousand years ago. Taken together, the findings described in this study support and extend our previous observations that C/OK is a genetically and evolutionarily distinct influenza virus in the family Orthomyxoviridae. © 2013 Springer-Verlag Wien.",virus RNA;animal;animal disease;article;classification;cluster analysis;DNA sequence;genetics;Influenza C virus;isolation and purification;molecular evolution;molecular genetics;nucleotide sequence;orthomyxovirus infection;phylogeny;pig;swine disease;United States;virology,"Sheng, Z.;Ran, Z.;Wang, D.;Hoppe, A. D.;Simonson, R.;Chakravarty, S.;Hause, B. M.;Li, F.",2014,,10.1007/s00705-013-1815-3,0
1905,A metagenomic survey of viral abundance and diversity in mosquitoes from hubei province,"Mosquitoes as one of the most common but important vectors have the potential to transmit or acquire a lot of viruses through biting, however viral flora in mosquitoes and its impact on mosquito-borne disease transmission has not been well investigated and evaluated. In this study, the metagenomic techniquehas been successfully employed in analyzing the abundance and diversity of viral community in three mosquito samples from Hubei, China. Among 92,304 reads produced through a run with 454 GS FLX system, 39% have high similarities with viral sequences belonging to identified bacterial, fungal, animal, plant and insect viruses, and 0.02% were classed into unidentified viral sequences, demonstrating high abundance and diversity of viruses in mosquitoes. Furthermore, two novel viruses in subfamily Densovirinae and family Dicistroviridae were identified, and six torque tenosus virus1 in family Anelloviridae, three porcine parvoviruses in subfamily Parvovirinae and a Culex tritaeniorhynchus rhabdovirus in Family Rhabdoviridae were preliminarily characterized. The viral metagenomic analysis offered us a deep insight into the viral population of mosquito which played an important role in viral initiative or passive transmission and evolution during the process.",contig;nonstructural protein 1;nonstructural protein 2;adult;Anelloviridae;animal experiment;animal virus;Anopheles sinensis;archaeal virus;Armigeres subalbatus;China;contig mapping;controlled study;Culex quinquefasciatus;Culex tritaeniorhynchus;Densovirinae;Dicistroviridae;disease carrier;gene sequence;insect virus;metagenomics;microbial diversity;mosquito;mycovirus;nonhuman;nucleotide sequence;open reading frame;Parvovirinae;phylogenetic tree;plant virus;review;Rhabdoviridae;Torque tenosus virus 1;virus genome;virus identification;virus load;virus strain;virus transmission,"Shi, C.;Liu, Y.;Hu, X.;Xiong, J.;Zhang, B.;Yuan, Z.",2015,,10.1371/journal.pone.0129845,0
1906,Genomic characterization and pathogenicity of a porcine hemagglutinating encephalomyelitis virus strain isolated in China,"Porcine hemagglutinating encephalomyelitis virus (PHEV) is a member of the genus betacoronavirus within the family coronaviridae, which invades the central nervous system (CNS) via peripheral nervous system and causes encephalomyelitis or vomiting and wasting disease (VWD) in sucking piglets. Up to now, although few complete nucleotide sequences of PHEV have been reported, they are not annotated. This study aimed to illuminate genome characterization, phylogenesis and pathogenicity of the PHEV/2008 strain. The full length of the PHEV/2008 strain genome was 30,684 bp, with a G + C content of 37.27%. The genome included at a minimum of 11 predicted open reading frames (ORFs) flanked by 5′ and 3′ untranslated regions (UTR) of 211 and 289 nucleotides. The replicase polyproteins pp1a and pp1ab, which had 4382 and 7094 amino acid residues, respectively, were predicted to be cleaved into 16 subunits by two viral proteinases. Phylogenetic analysis based on the complete genome sequence revealed that PHEV/2008 strain was genetically different from other known PHEV types, which represented a novel genotype (GI-1). In addition, we found that PHEV/2008 was neurotropic and highly pathogenic to 4-week-old BALB/c mice. Taken together, this is the first detailed annotated, complete genomic sequence of a new genotype PHEV strain in China.",amino acid;polyprotein;protein pp1a;protein pp1ab;proteinase;unclassified drug;3' untranslated region;5' untranslated region;animal experiment;animal model;animal tissue;article;China;controlled study;encephalitis virus;female;gene sequence;genotype;mouse;nonhuman;nucleotide sequence;open reading frame;porcine hemagglutinating encephalomyelitis virus;prediction;priority journal;viral genetics;virus identification;virus isolation;virus strain;virus virulence,"Shi, J.;Zhao, K.;Lu, H.;Li, Z.;Lv, X.;Lan, Y.;Guan, J.;He, W.;Gao, F.",2018,,10.1007/s11262-018-1591-y,0
1907,Molecular epidemiology of PRRSV: A phylogenetic perspective,"Since its first discovery two decades ago, porcine reproductive and respiratory syndrome virus (PRRSV) has been the subject of intensive research due to its huge impact on the worldwide swine industry. Thanks to the phylogenetic analyses, much has been learned concerning the genetic diversity and evolution history of the virus. In this review, we focused on the evolutionary and epidemiological aspects of PRRSV from a phylogenetic perspective. We first described the diversity and transmission dynamics of Type 1 and 2 PRRSV, respectively. Then, we focused on the more ancient evolutionary history of PRRSV: the time of onset of all existing PRRSV and an origin hypothesis were discussed. Finally, we summarized the results from previous recombination studies to assess the potential impact of recombination on the virus epidemiology. © 2010 Elsevier B.V.",Arterivirus vaccine;ingelvac;live vaccine;nucleoprotein;primepac;unclassified drug;virus vaccine;Arterivirus;Arterivirus type 1;Arterivirus type 2;China;Eastern Europe;epidemic;genetic polymorphism;genetic variability;genotype;molecular clock;molecular dynamics;molecular epidemiology;molecular evolution;Murine leukemia virus;nonhuman;North America;open reading frame;phylogeny;phylogeography;porcine reproductive and respiratory syndrome;priority journal;restriction fragment length polymorphism;review;Russian Federation;sequence analysis;vaccination;virus characterization;virus classification;virus recombination;virus transmission;Western Europe,"Shi, M.;Lam, T. T. Y.;Hon, C. C.;Hui, R. K. H.;Faaberg, K. S.;Wennblom, T.;Murtaugh, M. P.;Stadejek, T.;Leung, F. C. C.",2010,,10.1016/j.virusres.2010.08.014,0
1908,Origin and molecular characterization of the human-infecting H6N1 influenza virus in Taiwan,"In June 2013, the first human H6N1 influenza virus infection was confirmed in Taiwan. However, the origin and molecular characterization of this virus, A/Taiwan/2/2013 (H6N1), have not been well studied thus far. In the present report, we performed phylogenetic and coalescent analyses of this virus and compared its molecular profile/characteristics with other closely related strains. Molecular characterization of H6N1 revealed that it is a typical avian influenza virus of low pathogenicity, which might not replicate and propagate well in the upper airway in mammals. Phylogenetic analysis revealed that the virus clusters with A/chicken/Taiwan/A2837/2013 (H6N1) in seven genes, except PB1. For the PB1 gene, A/Taiwan/2/2013 was clustered with a different H6N1 lineage from A/chicken/Taiwan/ A2837/2013. Although a previous study demonstrated that the PB2, PA, and M genes of A/Taiwan/2/2013 might be derived from the H5N2 viruses, coalescent analyses revealed that these H5N2 viruses were derived from more recent strains than that of the ancestor of A/Taiwan/2/2013. Therefore, we propose that A/Taiwan/2/2013 is a reassortant from different H6N1 lineages circulating in chickens in Taiwan. Furthermore, compared to avian isolates, a single P186L (H3 numbering) substitution in the hemagglutinin H6 of the human isolate might increase the mammalian receptor binding and, hence, this strain's pathogenicity in humans. Overall, human infection with this virus seems an accidental event and is unlikely to cause an influenza pandemic. However, its co-circulation and potential reassortment with other influenza subtypes are still worthy of attention. © 2013 Higher Education Press and Springer-Verlag Berlin Heidelberg.",amantadine;leucine;oseltamivir;proline;protein M2;virus hemagglutinin;amino acid substitution;article;avian influenza virus;gene mutation;Influenza A virus (H5N2);Influenza virus H6N1;nonhuman;phylogeny;poultry;priority journal;Taiwan;virus characterization;virus gene;virus genome;virus infection,"Shi, W.;Shi, Y.;Wu, Y.;Liu, D.;Gao, G. F.",2013,,10.1007/s13238-013-3083-0,0
1909,Repeated detection of H7N9 avian influenza viruses in raw poultry meat illegally brought to Japan by international flight passengers,"H7N9 highly and low pathogenic avian influenza viruses (HPAIV and LPAIV, respectively) have been isolated from duck meat products that were brought illegally into Japan by flight passengers in their hand luggage. These H7N9 virus isolates were phylogenetically closely related to those prevailing in China. Antigenic analysis revealed that the hemagglutinin of the H7N9 HPAIV isolate was slightly different from those of the H7N9 LPAIV and older H7 strains. These meat products contaminated with AIVs repeatedly brought into Japan lead to increased risks of poultry and public health. Continuous border disease control based on the detection and culling of infected poultry and meat products is, thus, essential for the prevention of introduction and spread of AIVs.",hemagglutinin;antigenicity;article;China;disease control;duck;flight;food safety;highly pathogenic avian influenza virus;infection prevention;Influenza A virus (H7N9);Japan;low pathogenic avian influenza virus;nonhuman;phylogeny;poultry meat;priority journal;public health problem;strain difference;viral contamination;virus detection;virus isolation;virus strain,"Shibata, A.;Okamatsu, M.;Sumiyoshi, R.;Matsuno, K.;Wang, Z. J.;Kida, H.;Osaka, H.;Sakoda, Y.",2018,,10.1016/j.virol.2018.08.001,0
1910,Use of S1 nuclease in deep sequencing for detection of double-stranded RNA viruses,"Metagenomic approach using next-generation DNA sequencing has facilitated the detection of many pathogenic viruses from fecal samples. However, in many cases, majority of the detected sequences originate from the host genome and bacterial flora in the gut. Here, to improve efficiency of the detection of double-stranded (ds) RNA viruses from samples, we evaluated the applicability of S1 nuclease on deep sequencing. Treating total RNA with S1 nuclease resulted in 1.5-28.4- and 10.1-208.9-fold increases in sequence reads of group A rotavirus in fecal and viral culture samples, respectively. Moreover, increasing coverage of mapping to reference sequences allowed for sufficient genotyping using analytical software. These results suggest that library construction using S1 nuclease is useful for deep sequencing in the detection of dsRNA viruses.",double stranded RNA;nuclease S1;animal;bovine;cattle disease;genetics;high throughput sequencing;metabolism;pig;procedures;Rotavirus;Rotavirus infection;swine disease;veterinary medicine;virology,"Shimada, S.;Nagai, M.;Moriyama, H.;Fukuhara, T.;Koyama, S.;Omatsu, T.;Furuya, T.;Shirai, J.;Mizutani, T.",2015,,10.1292/jvms.14-0607,0
1911,"Genetic and phylogenetic characterization of rabies virus isolates from wildlife and livestock in Paraiba, Brazil","Thirty-four rabies virus (RV) isolates from foxes (8), insectivore bats (9), cattle (14), sheep (1), a goat (1) and a donkey (1) from Paraiba state, northeastern Brazil, were genetically characterized. Sequences of 890 nts of nucleoprotein (N) genes of these isolates were analyzed and compared with those of other Brazilian isolates characterized earlier. Phylogenetic analysis revealed three genetical lineages of RV co-existing in this region. Each lineage was found to be associated with particular host species and to circulate independently of each other. The first lineage was found in foxes (Dusicyon sp.) and could be discriminated from domestic carnivore isolates from Sao Paulo, Goias and Minas Gerais in the southern and central Brazil. The second lineage was associated with insectivorous bats (Molossus spp.) and differed from vampire bat-associated RV isolates. The third lineage was found in livestock and clustered with vampire bat-associated RV isolates from Sao Paulo, Tocantins, Goias and Matto Grosso. These results indicate that RV of these genetic lineages are co-circulating in the Paraiba state and that livestock in this region are infected with vampire bat-associated RV, suggesting that the vampire bat is the main reservoir of livestock rabies in this region.",RNA;article;bat;Brazil;carnivore;bovine;controlled study;donkey;fox;gene sequence;genetic analysis;genetic trait;goat;insectivore;livestock;nonhuman;phylogeny;Rabies virus;reverse transcription polymerase chain reaction;sequence analysis;sheep;virus isolation;wildlife,"Shoji, Y.;Kobayashi, Y.;Sato, G.;Gomes, A. A. B.;Itou, T.;Ito, F. H.;Sakai, T.",2006,,,0
1912,Evidence for interspecies transmission and reassortment of influenza A viruses in pigs in Southern China,"The Asian/57, Hong Kong/68, and Russian/77 pandemics of this century appeared or reappeared in China. Interspecies transmission and genetic reassortment of influenza viruses have been implicated in the origin of these human pandemic influenza viruses. Pigs have been suspected to be the 'mixing vessel' where reassortment occurs. To investigate this possibility, 104 porcine influenza viruses collected at random from Southern China from 1976 to 1982, including 32 H3N2 isolates and 72 H1N1 isolates, were studied using dot blot hybridization, partial sequencing, and phylogenetic analysis. There were 29 of 32 H3N2 isolates characteristics of viruses originally derived from humans; the other 3 isolates were reassortants containing genes from porcine and human influenza viruses. Phylogenetic analyses of the polymerase B1 (PB1) genes showed that interspecies transmission from humans to pigs has happened multiple times in pigs in Southern China. All 72 H1N1 isolates were of porcine origin characteristic of classical porcine H1N1 influenza virus. Analysis of 624 genes of porcine influenza viruses from Southern China failed to detect any evidence for avian influenza virus genes. This contrasts to what is currently found in Europe, where the majority of porcine influenza virus isolates are of avian origin.",article;China;dot hybridization;gene sequence;genetic analysis;genotype;Influenza A virus;nonhuman;phylogeny;priority journal;species;pig;virus isolation;virus transmission,"Shu, L. L.;Lin, Y. P.;Wright, S. M.;Shortridge, K. F.;Webster, R. G.",1994,,10.1006/viro.1994.1404,0
1913,"Genetic heterogeneity of swine hepatitis e virus isolates from Yunnan province, China in 2011-2012","Background: Hepatitis E is a disease of major public-health concern mainly in developing countries. Although molecular and sero-epidemiological investigations of HEV have been performed in many provinces in China, the epidemiological data from Yunnan Province are limited and genotypes are not be fully characterized. In this study the prevalence and characteristics of hepatitis E virus (HEV) detected in pigs from Yunnan province, China was evaluated. Results: A total of 13 out of 187 pig fecal samples collected in 2011 revealed HEV positive results; likewise, 7 out of 69 samples collected in 2012 exhibited positive results. These findings indicated a total prevalence of 7.8% (20/256). Phylogenetic and molecular evolutionary analysis results revealed that nine strains were found in the samples obtained in 2011, in which 87.1% to 99.4% nucleotide sequence identity was shared among these strains; and 77.0% to 81.9%, 52.2% to 53.6%, 77.0% to 88.2% and 77.9% to 96.8% nucleotide sequence identities were shared with strains representing genotypes 1, 2, 3, and 4. Five strains were detected in the samples obtained in 2012, in which 94.2% to 99.3% nucleotide sequence identity was shared among the strains, and 81.0% to 82.5%, 81.8% to 83.2%, 81.0% to 92.7% and 81.0% to 97.8% nucleotide sequence identities were shared with strains representing the genotypes 1, 2, 3, and 4. Conclusions: Analysis of fourteen detected HEV strains revealed that three of them were subtype 4d, two were subtype 4b; the nine remaining isolated strains were subtype 4 h. These results indicated that the prevalence of HEV in the swine herds of Yunnan was quite high, additional public-health concerns should focus on pork safety.",article;China;genetic heterogeneity;genotype;Hepatitis E virus;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;pig;virus isolation,"Shu, X.;Duan, X.;Song, C.;Li, J.;Jiang, L.;Yin, G.;Li, W.",2014,,10.1186/1743-422x-11-162,0
1914,Molecular detection and characterization of West Nile virus associated with multifocal retinitis in patients from southern India,"Background: In late 2009/early 2010, approximately 2000 people were affected by a mysterious viral outbreak in a southern district of Tamil Nadu; this particularly affected those living in coastal areas. Blood samples from affected patients were sent for clinical analysis to determine the actual cause of the illness, but reports were inconclusive. Methods: The present study describes the clinical observations and laboratory investigations involving molecular methods performed on 170 of the 2000 clinically suspected cases. These were patients who were admitted to Aravind Eye Hospital, Madurai, Tamil Nadu with ocular complications. Conventional reverse transcription polymerase chain reaction (RT-PCR), real-time RT-PCR, and reverse transcription loop-mediated isothermal gene amplification (RT-LAMP) assays were used to detect West Nile virus (WNV) infection. Further investigation of the genetic diversity of the WNV implicated in ocular complications was undertaken by sequence phylogeny. Results: Out of 170 samples, 25 (15%) were positive for chikungunya IgM antibody, 10 (6%) for chikungunya antigen, and 30 (18%) were positive for dengue IgM antibody. The remaining 105 seronegative samples were further processed for WNV detection by IgM capture ELISA and molecular methods. Out of the 105 samples, 35 (33%) were positive for WNV IgM antibody, 15 (14%) were positive for WNV by RT-PCR, and 27 (26%) were found to be positive for WNV by both real-time RT-PCR and RT-LAMP assays. Comparative evaluation with acute-phase patient serum samples revealed 100% concordance between the real-time RT-PCR and RT-LAMP assays. These assays had an overall higher sensitivity than the conventional RT-PCR as they picked up 12 additional samples with a low copy number of template. Further genotyping through sequence phylogeny revealed that all the WNV isolates were grouped in lineage I. Conclusions: The association of West Nile virus with ocular infection in South India during an epidemic of mysterious fever in the first half of 2010 was clearly established through molecular approaches employing envelope gene-specific real-time RT-PCR and RT-LAMP assays followed by nucleotide sequencing. © 2011 International Society for Infectious Diseases.",immunoglobulin M antibody;virus antibody;virus antigen;adolescent;adult;article;blood sampling;chikungunya;child;clinical evaluation;clinical observation;comparative study;controlled study;dengue;enzyme linked immunosorbent assay;female;genetic variability;genotype;human;human cell;human tissue;hypertension retinopathy;India;laboratory diagnosis;loop mediated isothermal amplification;major clinical study;male;molecular diagnosis;nonhuman;nucleotide sequence;phylogeny;real time polymerase chain reaction;retina blood vessel occlusion;retina edema;retina vasculitis;retinitis;reverse transcription polymerase chain reaction;school child;sensitivity analysis;serology;virus characterization;virus detection;West Nile fever;West Nile virus,"Shukla, J.;Saxena, D.;Rathinam, S.;Lalitha, P.;Joseph, C. R.;Sharma, S.;Soni, M.;Rao, P. V. L.;Parida, M.",2012,,10.1016/j.ijid.2011.09.020,0
1915,Full genomic sequence analysis of swine genotype 3 hepatitis E virus isolated from Shanghai,"The full genomic nucleotide sequence of a previously identified genotype 3 hepatitis E virus (HEV), strain SAAS-JDY5, was obtained using RT-PCR and rapid amplification of cDNA ends (RACE). The genome consisted of 7225 nucleotides, excluding a poly-A tail at the 3′ terminus, and contained three open reading frames (ORFs), ORF-1, ORF-2 and ORF-3, encoding 1702, 660 and 113 amino acids, respectively. Phylogenetic analysis confirmed that SAAS-JDY5 belonged to genotype 3 HEV and was most closely related to the Japanese isolate wbJYG1 (AB222184). SAAS-JDY5 shared approximately 87% nucleotide similarity to human and swine strains from the United States, compared with 74-75% similarity to Asian (genotype 4) and Mexican strains (genotype 2). Alignment of the SAAS-JDY5 genomic sequence with reference sequences of the same genotype revealed one nucleotide substitution and one deletion at positions 5145 and 7189 (3′ UTR), respectively. Moreover, SAAS-JDY5 contained two additional nucleotides (AC) at the very end of the 3′-terminus preceding the poly-A tail of the genome. Comparison of the putative amino acid sequence encoded by the SAAS-JDY5 genome with sequences of other genotype 3 isolates revealed 15 unique amino acid substitutions and one deletion in ORF-1, and three substitutions in ORF-2. © 2009 Elsevier B.V. All rights reserved.",amino acid;complementary DNA;nucleotide;polyadenylic acid;amino acid sequence;amino acid substitution;article;Asia;controlled study;gene deletion;gene sequence;genotype;Hepatitis E virus;Mexico;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;reverse transcription polymerase chain reaction;sequence alignment;pig;unindexed sequence;United States;virus genome;virus strain,"Si, F. s;Zhu, Y. m;Dong, S. j;Yu, S. s;Yu, R. s;Shen, S. y;Yang, Q.;Li, Z.",2009,,10.1016/j.virusres.2009.04.009,0
1916,Evolution of a cytoplasmic tripartite motif (TRIM) protein in cows that restricts retroviral infection,"Primate tripartite motif 5α (TRIM5α) proteins mediate innate intracellular resistance to retroviruses. In humans, TRIM5 is located in a paralogous cluster that includes TRIM6, TRIM34, and TRIM22. Although TRIM6 and TRIM34 orthologs are found in other mammals, TRIM5 has to date been identified only in primates. Cow cells exhibit early blocks to infection by several retroviruses. We identify a cytoplasmic TRIM protein encoded by LOC505265 that is responsible for the restriction of infection by several lentiviruses and N-tropic murine leukemia virus in cow cells. Susceptibility of N-tropic murine leukemia virus to 505265-mediated restriction is determined primarily by residue 110 of the viral capsid protein. Phylogenetically, cow LOC505265 segregates with the TRIM5/TRIM6/TRIM34 group, but is not an ortholog of known TRIM genes. The B30.2/SPRY domain of 505265 exhibits long variable regions, a characteristic of the proteins encoded by this paralogous group, and shows evidence of positive selection. Apparently, cows have independently evolved a retroviral restriction factor from the same TRIM family that spawned TRIMS in primates. Particular features of this subset of cytoplasmic TRIM proteins may be conducive to the convergent evolution of virus-restricting factors. © 2006 by The National Academy of Sciences of the USA.",protein;protein TRIM;protein TRIM22;protein TRIM34;protein TRIM6;tripartite motif protein 5;unclassified drug;animal cell;article;cow;evolution;infection resistance;Lentivirus;Murine leukemia virus;nonhuman;nucleotide sequence;orthology;phylogeny;primate;priority journal;protein motif;Retroviridae;retrovirus infection;virus capsid;virus inhibition,"Si, Z.;Vandegraaff, N.;O'Huigin, C.;Song, B.;Yuan, W.;Xu, C.;Perron, M.;Li, X.;Marasco, W. A.;Engelman, A.;Dean, M.;Sodroski, J.",2006,,10.1073/pnas.0600771103,0
1917,"Herpesvirus strigis, a new avian herpesvirus. II. Biochemical and biophysical properties","A virus, herpesvirus strigis (HSIS), originating from dead owls was successfully cultivated in chicken embryo fibroblasts. Its replication was inhibited by IUDR. Tissue cultured virus proved sensitive to ether, chloroform, 0.5% trypsin, and to pH levels of 4.0 or lower. Infectivity was rapidly destroyed at 56°C. Negatively stained naked virions of 100 nm average diameter were seen, and enveloped virions with 160-250 nm size. The capsid was built up of hollow cylindrical capsomeres, arranged in equilateral triangles, carrying 5 capsomeres along each edge. Cubical symmetry and icosahedron structure yielded a total number of 162 capsomeres. All these biochemical and biophysical data led to the classification of HSIS virus into the genus herpesvirus. Biological properties described in a foregoing paper sustained such grouping, and indicated that the agent was a new avian herpesvirus for which the name herpesvirus strigis was proposed.",avian virus;bird;Herpesviridae;in vitro study;microorganism;theoretical study;virus isolation,"Sibalin, M.;Gerstl, F.;Pichler, L.;Buerki, F.",1974,,,0
1918,Sequence and phylogenetic analysis of highly pathogenic avian influenza H5N1 viruses isolated during 2006-2008 outbreaks in Pakistan reveals genetic diversity,"Background: Since the first outbreak recorded in northern areas of Pakistan in early 2006, highly pathogenic avian influenza H5N1 viruses were isolated from commercial poultry and wild/domestic birds from different areas of Pakistan up to July 2008. Different isolates of H5N1 were sequenced to explore the genetic diversity of these viruses. Results: Phylogenetic analysis revealed close clustering and highest sequence identity in all 8 genes to HPAI H5N1 isolates belonging to unified H5 clade 2.2, sub-lineage EMA-3 recovered from Afghanistan during the same time period. Two subgroups within Pakistani H5N1 viruses, from domestic and wild birds, were observed on the basis of their sequence homology and mutations. HPAI motif, preferred receptor specificity for α-(2, 3) linkages, potential N-linked glycosylation sites and an additional glycosylation site at the globular head of HA protein of four Pakistani H5N1 isolates. While, the amino acids associated with sensitivities to various antiviral drugs (Oseltamivir, Zanamivir, Amantadine) were found conserved for the Pakistani H5N1 isolates. Conspicuously, some important mutations observed at critical positions of antigenic sites (S141P, D155S, R162I & P181S) and at receptor binding pocket (A185T, R189K & S217P) of HA-1. A high sequence similarity between Pakistani HP H5N1 and LP H9N2 viruses was also observed. Avian like host specific markers with the exception of E627K in PB2, K356R in PA, V33I in NP, I28V in M2 and L107F in NS2 proteins were also observed. Conclusions: Various point mutations in different genes of H5 viruses from Pakistan were observed during its circulation in the field. The outbreaks started in Khyber Pakhtoon Khawa (North West) province in 2006 and spread to the Southern regions over a period of time. Though migratory birds may have a role for this continued endemicity of clade 2.2 H5N1 viruses during 2006-2008 in Pakistan, the possibility of their transmission through legal or illegal poultry trade across the borders cannot be ignored. © 2012 Siddique et al.; licensee BioMed Central Ltd.",amantadine;nonstructural protein 2;oseltamivir;zanamivir;Afghanistan;antiviral susceptibility;avian influenza virus;cladistics;gene identification;gene mutation;genetic linkage;genetic variability;glycosylation;Influenza A virus (H5N1);nonhuman;nucleotide sequence;Pakistan;phylogeny;point mutation;receptor binding;review;sequence analysis;sequence homology;unindexed sequence;virus isolation,"Siddique, N.;Naeem, K.;Abbas, M. A.;Ahmed, Z.;Malik, S. A.",2012,,10.1186/1743-422x-9-300,0
1919,Isolation and Sequence Analysis of Reassortant Low Pathogenic Avian Influenza Virus H4N6 from Duck and Chicken in Live Bird Markets from Pakistan,"The Live bird Markets (LBM) can serve as a paramount source of AIV infections. During routine Avian Influenza surveillance in Pakistan, low-pathogenic avian influenza virus subtype H4N6 was isolated first time from Khaki Campbell duck (Anal platyrhynchos) during 2010 and from broiler chicken during 2011 in the live bird markets (LBMs) from the port city of Karachi in Sindh province. Whole genome sequencing revealed introduction of a new reassortant Eurasian avian virus strain. Phylogenetically HA, NA, M, NP and PB2 genes clustered mostly with Russian strains of influenza viruses and PA gene with AI isolates from Netherlands, whereas NS and PB1 genes clustered with a Pakistani isolate of H3N1. Sequence analysis revealed a LP amino acid motif (PEKASR), avian-like receptors, conservation of amino acids at the receptor binding sites and the amino acids known to be associated with sensitivities to antiviral drugs, loss of glycosylation site in NA gene and attainment of unique PDZ domain motif (ESEI) at the C terminal of NS gene. The seroconversion against H4N6 subtype was observed mostly in the bird populations of Sindh and Khyber Pakhtoon Khawa provinces. The isolation divulged the role of LBM where mingling of different bird species provides an excellent environment for dissemination and potential reassortment of AIV. Moreover, various point mutations in these H4N6 isolates and close relationship with Pakistani H3N1 and other Eurasian strains also reflect prevailing diversity among AIVs circulating in the local LBMs. (C)2016 PVJ. All rights reserved",Avian influenza virus;H4N6;Live bird market;Pakistan;Poultry;MIGRATION;EVOLUTION;VACCINE,"Siddique, N.;Naeem, K.;Ahmed, Z.;Abbas, M. A.;Ali, A.;Rafique, S.;Rashid, F.;Begum, I.;Farooq, R.",2016,,,0
1920,Characterization and classification of virus particles associated with hepatitis A. II. Type and configuration of nucleic acid,"Virus particles banding at 1.34 g/ml in CsCl and sedimenting at 160S in sucrose gradients were isolated from fecal specimens of patients suffering from hepatitis. In the presence of 4 M urea and about 90% formamide, these particles released linear nucleic acid molecules of the kinked appearance characteristic of single-stranded RNA or single-stranded DNA. They could be distinguished from the nucleic acid of phage lambda added to the preparation as a marker for double-stranded configuration. Experiments in which the virus particles under investigation were incubated at pH 12.9 at 50 degrees C for 30 min revealed that their nucleic acid molecules were hydrolyzed as readily as the RNA genome of poliovirus type 2 analyzed in parallel. Both the single-stranded DNA of phage phiX174 and that of parvovirus LuIII, however, proved unaffected by this treatment, and the double-stranded DNA of phage lambda was denatured to single-stranded molecules. It was concluded, therefore, that the virus of human hepatitis A contains a linear genome of single-stranded RNA and has to be classified with the picornaviruses.","Coliphages/an [Analysis];Feces/mi [Microbiology];*Hepatitis A/mi [Microbiology];*Hepatovirus/an [Analysis];Hepatovirus/cl [Classification];Humans;Nucleic Acid Conformation;Picornaviridae/cl [Classification];Poliovirus/an [Analysis];*RNA, Viral/an [Analysis];0 (RNA, Viral)","Siegl, G.;Frosner, G. G.",1978,Apr,,0
1921,Urinary Virome perturbations in kidney transplantation,,,"Sigdel, T. K.;Mercer, N.;Nandoe, S.;Nicora, C. D.",2018,,,0
1922,Distinguishing the genotype 1 genes and proteins of human Wa-like rotaviruses vs. porcine rotaviruses,"Group A rotaviruses (RVAs) are 11-segmented, double-stranded RNA viruses and important causes of gastroenteritis in the young of many animal species. Previous studies have suggested that human Wa-like RVAs share a close evolutionary relationship with porcine RVAs. Specifically, the VP1-VP3 and NSP2-5/6 genes of these viruses are usually classified as genotype 1 with >. 81% nucleotide sequence identity. Yet, it remains unknown whether the genotype 1 genes and proteins of human Wa-like strains are distinguishable from those of porcine strains. To investigate this, we performed comprehensive bioinformatic analyses using all known genotype 1 gene sequences. The RVAs analyzed represent wildtype strains isolated from humans or pigs at various geographical locations during the years of 2004-2013, including 11 newly-sequenced porcine RVAs from Brazil. We also analyzed archival strains that were isolated during the years of 1977-1992 as well as atypical strains involved in inter-species transmission between humans and pigs. We found that, in general, the genotype 1 genes of typical modern human Wa-like RVAs clustered together in phylogenetic trees and were separate from those of typical modern porcine RVAs. The only exception was for the NSP5/6 gene, which showed no host-specific phylogenetic clustering. Using amino acid sequence alignments, we identified 34 positions that differentiated the VP1-VP3, NSP2, and NSP3 genotype 1 proteins of typical modern human Wa-like RVAs versus typical modern porcine RVAs and documented how these positions vary in the archival/unusual isolates. No host-specific amino acid positions were identified for NSP4, NSP5, or NSP6. Altogether, the results of this study support the notion that human Wa-like RVAs and porcine RVAs are evolutionarily related, but indicate that some of their genotype 1 genes and proteins have diverged over time possibly as a reflection of sequestered replication and protein co-adaptation in their respective hosts.",nonstructural protein 1;nonstructural protein 2;nonstructural protein 3;nonstructural protein 4;nonstructural protein 5;nonstructural protein 6;protein VP1;protein VP3;unclassified drug;viral protein;amino acid sequence;article;bioinformatics;Brazil;gene sequence;genotype 1 gene;geography;Human rotavirus;human Wa like rotavirus;nonhuman;NSP2 gene;NSP3 gene;NSP4 gene;NSP5 gene;NSP6 gene;phylogenetic tree;phylogeny;pig;porcine rotavirus;priority journal;sequence alignment;virus gene;virus isolation;virus strain;virus transmission;VP1 gene;VP2 gene;VP3 gene;wild type,"Silva, F. D. F.;Gregori, F.;McDonald, S. M.",2016,,10.1016/j.meegid.2016.05.014,0
1923,Tracking the molecular epidemiology of Brazilian Infectious bursal disease virus (IBDV) isolates,"Infectious bursal disease is a highly contagious disease of young chickens caused by Infectious bursal disease virus (IBDV). Genome segment A encodes the capsid protein (VP2), while segment B encodes the RNA-dependent RNA polymerase (VP1). In the present study, we trace the molecular epidemiology of IBDV in Brazil by analyzing 29 isolates collected in the major regions of poultry production. To genetically characterize the isolates, phylogenetic and population dynamic analyses were conducted using 68 VP1 (2634nt) and 102 VP2 (1356nt) coding sequences from IBDV isolates from different regions of the world. Furthermore, the evolution of IBDV was analyzed by characterizing the selective forces that operated during the diversification of viral isolates. We show that IBDV isolates were introduced into Brazil mainly from the Netherlands and the USA. These introductions were associated with all Brazilian poultry production regions analyzed in this work. In addition, we show that the evolution of IBDV has been shaped by a combination of very low recombination rates and relatively high rates of nucleotide substitution (2.988×10-4 for VP1 and 3.2937×10-4 for VP2), which themselves are a function of purifying selection operating on VP1 and VP2. Furthermore, our extended Bayesian skyline plot suggests that the increase in the effective population size of isolates of IBDV is consistent with its epidemiological history, with a large increase during the emergence of acute outbreaks of IBD in the 1980s. © 2012 Elsevier B.V.",protein VP1;protein VP2;amino acid sequence;amino acid substitution;article;Brazil;epidemic;gene sequence;genetic analysis;genetic correlation;genetic recombination;geographic distribution;infectious bursal disease virus;microbial diversity;molecular epidemiology;molecular evolution;molecular phylogeny;Netherlands;nonhuman;nucleotide sequence;population dynamics;population size;poultry;priority journal;purifying selection;unindexed sequence;United States;viral genetics;virus characterization;virus gene;virus isolation;virus strain;virus transmission;VP1 gene;VP2 gene,"Silva, F. M. F.;Vidigal, P. M. P.;Myrrha, L. W.;Fietto, J. L. R.;Silva, A.;Almeida, M. R.",2013,,10.1016/j.meegid.2012.09.005,0
1924,Bat coronavirus in Brazil related to appalachian ridge and porcine epidemic diarrhea viruses,,bat;Brazil;Coronavirinae;letter;metagenomics;nonhuman;phylogeny;Porcine epidemic diarrhea virus;reverse transcription polymerase chain reaction;sequence analysis;viral genetics,"Simas, P. V. M.;A.C, D. E. Souza Barnabé;Durães-Carvalho, R.;De Lima Neto, D. F.;Caserta, L. C.;Artacho, L.;Jacomassa, F. A. F.;Martini, M. C.;Dos Santos, M. M. A. B.;Felippe, P. A. N.;Ferreira, H. L.;Arns, C. W.",2015,,10.3201/eid2104.141783,0
1925,Present and Future Surveillance of Antimicrobial Resistance in Animals: Principles and Practices Review,"There is broad consensus internationally that surveillance of the levels of antimicrobial resistance (AMR) occurring in various systems underpins strategies to address the issue. The key reasons for surveillance of resistance are to determine (i) the size of the problem, (ii) whether resistance is increasing, (iii) whether previously unknown types of resistance are emerging, (iv) whether a particular type of resistance is spreading, and (v) whether a particular type of resistance is associated with a particular outbreak. The implications of acquiring and utilizing this information need to be considered in the design of a surveillance system. AMR surveillance provides a foundation for assessing the burden of AMR and for providing the necessary evidence for developing efficient and effective control and prevention strategies. The codevelopment of AMR surveillance programs in humans and animals is essential, but there remain several key elements that make data comparisons between AMR monitoring programs, and between regions, difficult. Currently, AMR surveillance relies on uncomplicated in vitro antimicrobial susceptibility methods. However, the lack of harmonization across programs and the limitation of genetic information of AMR remain the major drawbacks of these phenotypic methods. The future of AMR surveillance is moving toward genotypic detection, and molecular analysis methods are expected to yield a wealth of information. However, the expectation that these molecular techniques will surpass phenotypic susceptibility testing in routine diagnosis and monitoring of AMR remains a distant reality, and phenotypic testing remains necessary in the detection of emerging resistant bacteria, new resistance mechanisms, and trends of AMR.","Animals;Anti-Bacterial Agents/pd [Pharmacology];Bacteria/de [Drug Effects];Bacteria/ge [Genetics];Bacteria/py [Pathogenicity];Bacterial Infections/ep [Epidemiology];Bacterial Infections/mi [Microbiology];Bacterial Infections/ve [Veterinary];Drug Resistance, Bacterial/de [Drug Effects];Drug Resistance, Bacterial/ge [Genetics];*Drug Resistance, Bacterial;*Epidemiological Monitoring/ve [Veterinary];Genes, Bacterial;Humans;Livestock;Metagenomics/mt [Methods];Microbial Sensitivity Tests;Molecular Diagnostic Techniques;*Sentinel Surveillance/ve [Veterinary];Zoonoses/ep [Epidemiology];Zoonoses/mi [Microbiology];0 (Anti-Bacterial Agents)","Simjee, S.;McDermott, P.;Trott, D. J.;Chuanchuen, R.",2018,07,,0
1926,Psittacine herpesvirus infection resembling pacheco's parrot disease,"Herpesvirus was detected by electron microscopy in hepatocytes of psittacine birds that died at a Florida aviary. The virus was identified in hepatocytes of chick embryos and budgerigars that were given injections of liver suspensions from naturally infected psittacines. Infected hepatocytes had prominent intranuclear inclusions that contained naked nucleocapsids. Both naked and enveloped virions were seen in the cytoplasm of hepatocytes, and enveloped nucleocapsids occasionally were seen in the perinuclear cisternae and extracellularly. The experimental and spontaneous disease mimicked a condition in parrots described previously by Pacheco. The viral agent was classified as Herpesvirus on the bases of the character of the intranuclear inclusions, the size and conformation of the agent as determined by electron microscopy and filtration, and the sensitivity of the agent to ether.","Animals;*Bird Diseases/mi [Microbiology];Diagnosis, Differential;Filtration;Florida;Herpesviridae Infections/di [Diagnosis];Herpesviridae Infections/mi [Microbiology];*Herpesviridae Infections/ve [Veterinary];Inclusion Bodies, Viral;Liver/em [Embryology];Liver/mi [Microbiology];Liver/pa [Pathology];Microscopy, Electron;Parrots;*Psittaciformes","Simpson, C. F.;Hanley, J. E.;Gaskin, J. M.",1975,Apr,,0
1927,"Genetic characterization of orf virus associated with an outbreak of severe orf in goats at a farm in Lusaka, Zambia (2015)","Orf or contagious ecthyma is a neglected and economically important zoonotic disease caused by a dermatotropic parapoxvirus that commonly affects domestic small ruminants. Although orf is globally distributed, there is a paucity of information on the disease in many African countries. Here, a suspected severe outbreak of orf in goats at a farm in Lusaka was investigated. Orf virus (ORFV) infection was confirmed by PCR amplification of viral DNA (RNA polymerase, B2L and virus interferon-resistance genes) in clinical samples. Some detected genes were sequenced and phylogenetically analyzed. This is the first report on molecular characterization of ORFV in goats in Zambia.",virus DNA;animal;contagious ecthyma;genetics;goat;goat disease;high throughput sequencing;isolation and purification;livestock;Orf virus;pathogenicity;phylogeny;polymerase chain reaction;virology;zoonosis,"Simulundu, E.;Mtine, N.;Kapalamula, T. F.;Kajihara, M.;Qiu, Y.;Ngoma, J.;Zulu, V.;Kwenda, G.;Chisanga, C.;Phiri, I. K.;Takada, A.;Mweene, A. S.",2017,,10.1007/s00705-017-3352-y,0
1928,Potential for the cross-species transmission of swine torque teno viruses,,,"Singh, G.;Ramamoorthy, S.",2018,,,0
1929,Identification of the MicroRNA repertoire in TLR-ligand challenged bubaline PBMCs as a model of bacterial and viral infection,"In the present study, we used high-throughput sequencing, miRNA-seq, to discover and explore the expression profiles of known and novel miRNAs in TLR ligand-stimulated vis-à-vis non-stimulated (i.e. Control) peripheral blood mononuclear cells (PBMCs) isolated from blood of healthy Murrah buffaloes. Six small RNA (sRNA) libraries were multiplexed in Ion Torrent PI chip and sequenced on Ion Proton System. The reads obtained were aligned to the Bos taurus genome (UMD3.1 assembly), which is phylogenetically closest species to buffalo (Bubalus bubalis). A total of 160 bovine miRNAs were biocomputationally identified in buffalo PBMCs and 130 putatively novel miRNAs (not enlisted in the bovine mirBase) were identified. All of these 290 miRNAs identified across the six treatment and control samples represent the repertoire of novel miRNAs for the buffalo species. The expression profiles of these miRNAs across the samples have been represented by sample dendrogram and heatmap plots. The uniquely expressed miRNAs in each treatment and control groups were identified. A few miRNAs were expressed at very high levels while the majority of them were moderately expressed. The miRNAs bta-miR-103 and -191 were found to be highly abundant and expressed in all the samples. Other abundantly expressed miRNAs include bta-miR-19b, -29b, -15a, -19a, -30d, -30b-5p and members of let family (let 7a-5p, let 7g & let 7f) in LPS and CpG treated PBMCS and bta-miR-191, -103 & -19b in Poly I:C stimulated PBMCs. Only one novel miRNA (bta-miR-11039) out of 130 identified putatively novel miRNAs, was expressed in all the six samples and differentially expressed (>2- fold) miRNAs were identified. Six of the differentially expressed miRNAs across the groups (bta-miR-421, bta-let-7i, bta-miR-138, bta-miR-21-5p, bta-miR-222 and bta-miR-27b) were subsequently confirmed by TaqMan quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, the target genes of differentially expressed miRNAs were enriched for the roles in innate immunity and TLR signaling pathways. This maiden study on profiling and cataloguing of bubaline miRNAs expressed in TLR-ligand stimulated PBMCs will provide an important reference point for future studies on regulatory roles of miRNAs in immune system of buffaloes.",bta let 7i;bta miR 103;bta miR 11039;bta miR 138;bta miR 15a;bta miR 191;bta miR 19a;bta miR 19b;bta miR 21 5p;bta miR 222;bta miR 27b;bta miR 29b;bta miR 30b 5p;bta miR 30d;bta miR 421;CpG oligodeoxynucleotide;let 7a 5p;let 7f;let 7g;lipopolysaccharide;microRNA;polyinosinic polycytidylic acid;toll like receptor;unclassified drug;animal cell;article;bacterial infection;buffalo;cell stimulation;controlled study;female;gene expression;innate immunity;nonhuman;peripheral blood mononuclear cell;reverse transcription polymerase chain reaction;signal transduction;taurine cattle;virus infection;water buffalo,"Singh, J.;Mukhopadhyay, C. S.;Kaur, S.;Malhotra, P.;Sethi, R. S.;Choudhary, R. K.",2016,,10.1371/journal.pone.0156598,0
1930,Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers,"Individual weight gain in broiler growers appears to vary, which may in part be due to variation in their gut microbiota. In this paper we analyse the fecal microbiota of low and high feed conversion ratio (FCR) broilers. After shotgun sequencing of the fecal microbiome, we used the SEED database to identify the microbial diversity and metabolic potential in low and high FCR birds. The domain-level breakdown of our samples was bacteria (>95 %), eukaryotes (>2 %), archaea (>0.2 %), and viruses (>0.2 %). At the phylum level, Proteobacteria (78.83 % in low and 52.04 % in high FCR), Firmicutes (11.97 % in low and 27.53 % in high FCR) and Bacteroidetes (7.10 % in low FCR and 17.53 % in high FCR) predominated in the fecal microbial community. Poultry fecal metagenomes revealed the sequences related to 33 genera in both low and high FCR with significantly different proportion. Functional analysis revealed that genes for the metabolism of carbohydrates, amino acids and derivatives and protein metabolism were most abundant in SEED subsystem in both samples. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Indeed, genes associated with sulphur assimilation, flagellum and flagellar motility were over represented in low FCR birds. This information could help in developing strategies to improve feed efficiency and feed formulation for broiler chickens. © 2013 Institute of Plant Genetics, Polish Academy of Sciences, Poznan.",RNA 16S;amino acid metabolism;animal experiment;archaeon;article;Bacteroidetes;carbohydrate metabolism;eukaryote;feces analysis;female;Firmicutes;gene conversion;gene sequence;male;metagenomics;microbial community;microbial diversity;microbiome;nonhuman;polymerase chain reaction;protein metabolism;Proteobacteria;pyrosequencing;virus,"Singh, K. M.;Shah, T. M.;Reddy, B.;Deshpande, S.;Rank, D. N.;Joshi, C. G.",2014,,10.1007/s13353-013-0179-4,0
1931,"Complete sequence analyses of enterovirus 71 strains from fatal and non-fatal cases of the hand, foot and mouth disease outbreak in Singapore (2000)","Enterovirus 71 (EV71) is a major aetiological agent of hand, foot and mouth disease (HFMD). In recent years, several outbreaks in East Asia were associated with neurological complications and numerous deaths. An outbreak in Singapore in October 2000 afflicted thousands of children, resulting in four fatal cases from three of whom EV71 was isolated. The genomes of two representative EV71 strains isolated from a fatal case and a surviving patient were completely sequenced, and their nucleotide and amino acid sequences compared with known EV71 strains. The two outbreak strains were classified under genogroup B, together with those previously isolated in Singapore, Malaysia and Japan. Comparative sequence analysis of the two Singapore strains revealed 99% nucleotide similarity, while their deduced amino acid sequences were almost identical except for residue 1506 in the 3A non-structural region. Given that the outbreak involved closely related genetic variants of EV71, the broad spectrum of disease severity may be attributed to critical factors such as varying viral inoculation doses or differing host immune responses following infection, but is less likely to be due to the emergence of EV71 strains with heightened virulence.",amino acid sequence;article;death;disease severity;Enterovirus A71;epidemic;gene sequence;genetic variability;hand foot and mouth disease;human;immune response;inoculation;Japan;Malaysia;neurological complication;nonhuman;nucleotide sequence;promoter region;sequence analysis;Singapore;virus classification;virus gene;virus genome;virus isolation;virus strain;virus survival;virus virulence,"Singh, S.;Poh, C. L.;Chow, V. T. K.",2002,,,0
1932,Complex virome in feces from Amerindian children in isolated Amazonian villages,"The number of viruses circulating in small isolated human populations may be reduced by viral extinctions and rare introductions. Here we used viral metagenomics to characterize the eukaryotic virome in feces from healthy children from a large urban center and from three Amerindian villages with minimal outside contact. Numerous human enteric viruses, mainly from the Picornaviridae and Caliciviridae families, were sequenced from each of the sites. Multiple children from the same villages shed closely related viruses reflecting frequent transmission clusters. Feces of isolated villagers also contained multiple viral genomes of unknown cellular origin from the Picornavirales order and CRESS-DNA group and higher levels of nematode and protozoan DNA. Despite cultural and geographic isolation, the diversity of enteric human viruses was therefore not reduced in these Amazonian villages. Frequent viral introductions and/or increased susceptibility to enteric infections may account for the complex fecal virome of Amerindian children in isolated villages.",GENETIC DIVERSITY;STOOL SAMPLES;FECAL VIROME;METAGENOMIC ANALYSIS;VIRAL PATHOGENS;ENTERIC VIROME;ACUTE DIARRHEA;SWINE FECES;VIRUSES;AMERICA,"Siqueira, J. D.;Dominguez-Bello, M. G.;Contreras, M.;Lander, O.;Caballero-Arias, H.;Deng, X. T.;Noya-Alarcon, O.;Delwart, E.",2018,Oct,,0
1933,"ENDEMIC INFECTION OF STRANDED SOUTHERN SEA OTTERS (ENHYDRA LUTRIS NEREIS) WITH NOVEL PARVOVIRUS, POLYOMAVIRUS, AND ADENOVIRUS","Over the past century, the southern sea otter (SSO; Enhydra lutris nereis) population has been slowly recovering from near extinction due to overharvest. The SSO is a threatened subspecies under federal law and a fully protected species under California law, US. Through a multiagency collaborative program, stranded animals are rehabilitated and released, while deceased animals are necropsied and tissues are cryopreserved to facilitate scientific study. Here, we processed archival tissues to enrich particle-associated viral nucleic acids, which we randomly amplified and deeply sequenced to identify viral genomes through sequence similarities. Anelloviruses and endogenous retroviral sequences made up over 50% of observed viral sequences. Polyomavirus, parvovirus, and adenovirus sequences made up most of the remaining reads. We characterized and phylogenetically analyzed the full genome of sea otter polyomavirus 1 and the complete coding sequence of sea otter parvovirus 1 and found that the closest known viruses infect primates and domestic pigs ( Sus scrofa domesticus), respectively. We tested archived tissues from 69 stranded SSO necropsied over 14 yr (2000-13) by PCR. Polyomavirus, parvovirus, and adenovirus infections were detected in 51, 61, and 29% of examined animals, respectively, with no significant increase in frequency over time, suggesting endemic infection. We found that 80% of tested SSO were infected with at least one of the three DNA viruses, whose tissue distribution we determined in 261 tissue samples. Parvovirus DNA was most frequently detected in mesenteric lymph node, polyomavirus DNA in spleen, and adenovirus DNA in multiple tissues (spleen, retropharyngeal and mesenteric lymph node, lung, and liver). This study describes the virome in tissues of a threatened species and shows that stranded SSO are frequently infected with multiple viruses, warranting future research to investigate associations between these infections and observed lesions.",Adenoviridae;animal;California;isolation and purification;otter;Parvoviridae;Polyomavirus;virology,"Siqueira, J. D.;Ng, T. F.;Miller, M.;Li, L.;Deng, X.;Dodd, E.;Batac, F.;Delwart, E.",2017,,10.7589/2016-04-082,0
1934,Assessing pathogenicity potential of waterfowl-origin type A influenza viruses in chickens,"Intravenous pathogenicity index (IVPI) tests on 29 wild duck-origin type A influenza viruses, two turkey-origin type A influenza viruses, and one chicken-origin type A influenza virus resulted in indices ranging from 0.0 to 0.49. Most of the wild duck-origin viruses and the two turkey-origin viruses had indices of 0.0, indicating they are not pathogenic. Six of the duck-origin viruses had indices ranging from 0.25 to 0.49, and the IVPI for A/chicken/Alabama/75 (H4N8) was 0.49, indicating they had low pathogenic potential. An IVPI of 1.25 up to the maximum score of 3.0 is necessary for a type A influenza virus to be classified as highly pathogenic. Gross lesions observed in chickens dying following intravenous viral challenge included kidney swelling with more prominent lobular patterns, but visceral urate deposits were not present. The usefulness of the IVPI test in evaluating the pathogenicity potential of nonpathogenic and low-pathogenic strains of avian influenza virus may be limited.",animal;article;avian influenza;chicken;duck;germfree animal;Influenza A virus;isolation and purification;kidney;microbiology;mortality;pathogenicity;pathology;United States;wild animal,"Slemons, R. D.;Condobery, P. K.;Swayne, D. E.",1991,,,0
1935,Hazards of disease transfer from marine mammals to land mammals: review and recent findings,"In a 5-year study (1972-1977) of microbial agents isolated from both clinically normal and diseased marine mammals, it was shown that certain disease agents are widespread in a diversity of ocean populations and that some are also transmissible to a number of terrestrial mammal species. Leptospira interrogans serovar pomona has been isolated repeatedly from 2 species of pinnipeds (Zalophus californianus califonianus and Callorhinus ursinus). Some of the more important bacterial pathogens for land mammals that were isolated from wild marine mammals are Pseudomonas mallei, Clostridium chauvoei, C novyi, Neisseria mucosa var heidelbergensis, Klebsiella pneumoniae, Salmonella spp, and Pasteurella multocida. Numerous serotypes of viruses classified as caliciviruses were isolated from a variety of marine mammals. Some of these are known to infect several land mammal species including swine horses, and primates. For this reason., precautions should be taken to ensure that disease agents shed by captive marine mammals are not transmitted to susceptible terrestrial mammals, including animal handlers and other human beings.","Animals;Caliciviridae/ip [Isolation & Purification];*Caniformia/mi [Microbiology];*Dolphins/mi [Microbiology];Leptospira/ip [Isolation & Purification];Seals, Earless/mi [Microbiology]","Smith, A. W.;Vedros, N. A.;Akers, T. G.;Gilmartin, W. G.",1978,Nov 01,,0
1936,Genetic variability and the classification of hepatitis E virus,"The classification of hepatitis E virus (HEV) variants is currently in transition without agreed definitions for genotypes and subtypes or for deeper taxonomic groupings into species and genera that could incorporate more recently characterized viruses assigned to the Hepeviridae family that infect birds, bats, rodents, and fish. These conflicts arise because of differences in the viruses and genomic regions compared and in the methodology used. We have reexamined published sequences and found that synonymous substitutions were saturated in comparisons between and within virus genotypes. Analysis of complete genome sequences or concatenated ORF1/ORF2 amino acid sequences indicated that HEV variants most closely related to those infecting humans can be consistently divided into six genotypes (types 1 to 4 and two additional genotypes from wild boar). Variants isolated from rabbits, closely related to genotype 3, occupy an intermediate position. No consistent criteria could be defined for the assignment of virus subtypes. Analysis of amino acid sequences from these viruses with the more divergent variants from chickens, bats, and rodents in three conserved subgenomic regions (residues 1 to 452 or 974 to 1534 of ORF1 or residues 105 to 458 of ORF2) provided consistent support for a division into 4 groups, corresponding to HEV variants infecting humans and pigs, those infecting rats and ferrets, those from bats, and those from chickens. This approach may form the basis for a future genetic classification of HEV into four species, with the more divergent HEV-like virus from fish (cutthroat trout virus) representing a second genus. © 2013, American Society for Microbiology.",article;gene sequence;genetic variability;genome analysis;genotype;Hepatitis E virus;molecular phylogeny;nonhuman;nucleotide sequence;priority journal;sequence analysis;unindexed sequence;virus classification;virus genome,"Smith, D. B.;Purdy, M. A.;Simmonds, P.",2013,,10.1128/jvi.02762-12,0
1937,Classification and genomic diversity of enterically transmitted hepatitis viruses,"Hepatitis A virus (HAV) and hepatitis E virus (HEV) are significant human pathogens and are responsible for a substantial proportion of cases of severe acute hepatitis worldwide. Genetically, both viruses are heterogeneous and are classified into several genotypes that differ in their geographical distribution and risk group association. There is, however, little evidence that variants of HAV or HEV differ antigenically or in their propensity to cause severe disease. Genetically more divergent but primarily hepatotropic variants of both HAV and HEV have been found in several mammalian species, those of HAV being classified into eight species within the genus Hepatovirus in the virus family Picornaviridae. HEV is classified as a member of the species Orthohepevirus A in the virus family Hepeviridae, a species that additionally contains viruses infecting pigs, rabbits, and a variety of other mammalian species. Other species (Orthohepevirus B–D) infect a wide range of other mammalian species including rodents and bats.",article;genetic variability;genotype;Hepatitis A virus;hepatitis virus;Hepatovirus;Hepeviridae;nonhuman;Picornaviridae;taxonomy;virus classification;virus genome;virus transmission,"Smith, D. B.;Simmonds, P.",2018,,10.1101/cshperspect.a031880,0
1938,Consensus proposals for classification of the family Hepeviridae,"The family Hepeviridae consists of positive-stranded RNA viruses that infect a wide range of mammalian species, as well as chickens and trout. A subset of these viruses infects humans and can cause a self-limiting acute hepatitis that may become chronic in immunosuppressed individuals. Current published descriptions of the taxonomical divisions within the family Hepeviridae are contradictory in relation to the assignment of species and genotypes. Through analysis of existing sequence information, we propose a taxonomic scheme in which the family is divided into the genera Orthohepevirus (all mammalian and avian hepatitis E virus (HEV) isolates) and Piscihepevirus (cutthroat trout virus). Species within the genus Orthohepevirus are designated Orthohepevirus A (isolates from human, pig, wild boar, deer, mongoose, rabbit and camel), Orthohepevirus B (isolates from chicken), Orthohepevirus C (isolates from rat, greater bandicoot, Asian musk shrew, ferret and mink) and Orthohepevirus D (isolates from bat). Proposals are also made for the designation of genotypes within the human and rat HEVs. This hierarchical system is congruent with hepevirus phylogeny, and the three classification levels (genus, species and genotype) are consistent with, and reflect discontinuities in the ranges of pairwise distances between amino acid sequences. Adoption of this system would include the avoidance of host names in taxonomic identifiers and provide a logical framework for the assignment of novel variants.",amino acid sequence;article;consensus;evolutionary rate;Hepatitis E virus;Hepevirus;host range;maximum likelihood method;nonhuman;nucleotide sequence;Orthohepevirus a;Orthohepevirus b;Orthohepevirus c;phylogeny;virus classification;virus genome,"Smith, D. B.;Simmonds, P.;Jameel, S.;Emerson, S. U.;Harrison, T. J.;Meng, X. J.;Okamoto, H.;Van der Poel, W. H. M.;Purdy, M. A.",2014,,10.1099/vir.0.068429-0,0
1939,"Nomenclature updates resulting from the evolution of avian influenza A(H5) virus clades 2.1.3.2a, 2.2.1, and 2.3.4 during 2013-2014","AIM: The A/goose/Guangdong/1/96-like hemagglutinin (HA) genes of highly pathogenic avian influenza (HPAI) A(H5) viruses have continued to rapidly evolve since the most recent update to the H5 clade nomenclature by the WHO/OIE/FAO H5N1 Evolution Working Group. New clades diverging beyond established boundaries need to be identified and designated accordingly. METHOD: Hemagglutinin sequences deposited in publicly accessible databases up to December 31, 2014, were analyzed by phylogenetic and average pairwise distance methods to identify new clades that merit nomenclature changes. RESULTS: Three new clade designations were recommended based on division of clade 2.1.3.2a (Indonesia), 2.2.1 (Egypt), and 2.3.4 (widespread detection in Asia, Europe, and North America) that includes newly emergent HPAI virus subtypes H5N2, H5N3, H5N5, H5N6, and H5N8. CONCLUSION: Continued global surveillance for HPAI A(H5) viruses in all host species and timely reporting of sequence data will be critical to quickly identify new clades and assess their potential impact on human and animal health.","Animals;*Biological Evolution;Birds;Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];Humans;*Influenza A virus/cl [Classification];*Influenza A virus/ge [Genetics];Influenza A virus/ip [Isolation & Purification];*Influenza in Birds/vi [Virology];Influenza, Human/vi [Virology];Molecular Sequence Data;Phylogeny;*Poultry Diseases/vi [Virology];0 (Hemagglutinin Glycoproteins, Influenza Virus)","Smith, G. J.;Donis, R. O.;World Health Organization/World Organisation for Animal, H. F.;Agriculture Organization, H. E. W. G.",2015,Sep,,0
1940,Dating the emergence of pandemic influenza viruses,"Pandemic influenza viruses cause significant mortality in humans. In the 20th century, 3 influenza viruses caused major pandemics: the 1918 H1N1 virus, the 1957 H2N2 virus, and the 1968 H3N2 virus. These pandemics were initiated by the introduction and successful adaptation of a novel hemagglutinin subtype to humans from an animal source, resulting in antigenic shift. Despite global concern regarding a new pandemic influenza, the emergence pathway of pandemic strains remains unknown. Here we estimated the evolutionary history and inferred date of introduction to humans of each of the genes for all 20th century pandemic influenza strains. Our results indicate that genetic components of the 1918 H1N1 pandemic virus circulated in mammalian hosts, i.e., swine and humans, as early as 1911 and was not likely to be a recently introduced avian virus. Phylogenetic relationships suggest that the A/Brevig Mission/1/1918 virus (BM/1918) was generated by reassortment between mammalian viruses and a previously circulating human strain, either in swine or, possibly, in humans. Furthermore, seasonal and classic swine H1N1 viruses were not derived directly from BM/1918, but their precursors co-circulated during the pandemic. Mean estimates of the time of most recent common ancestor also suggest that the H2N2 and H3N2 pandemic strains may have been generated through reassortment events in unknown mammalian hosts and involved multiple avian viruses preceding pandemic recognition. The possible generation of pandemic strains through a series of reassortment events in mammals over a period of years before pandemic recognition suggests that appropriate surveillance strategies for detection of precursor viruses may abort future pandemics.",article;controlled study;genetic reassortment;Influenza virus;Influenza A virus (H1N1);Influenza A virus (H2N2);Influenza A virus (H3N2);molecular evolution;nonhuman;pandemic;phylogeny;priority journal;virus cell interaction;virus gene;virus strain;virus transmission,"Smith, G. J. D.;Bahl, J.;Vijaykrishna, D.;Zhang, J.;Poon, L. L. M.;Chen, H.;Webster, R. G.;Peiris, J. S. M.;Guan, Y.",2009,,10.1073/pnas.0904991106,0
1941,Bats and their virome: An important source of emerging viruses capable of infecting humans,"Bats are being increasingly recognized as an important reservoir of zoonotic viruses of different families, including SARS coronavirus, Nipah virus, Hendra virus and Ebola virus. Several recent studies hypothesized that bats, an ancient group of flying mammals, are the major reservoir of several important RNA virus families from which other mammalian viruses of livestock and humans were derived. Although this hypothesis needs further investigation, the premise that bats carry a large number of viruses is commonly accepted. The question of whether bats have unique biological features making them ideal reservoir hosts has been the subject of several recent reviews. In this review, we will focus on the public health implications of bat derived zoonotic viral disease outbreaks, examine the drivers and risk factors of past disease outbreaks and outline research directions for better control of future disease events.",article;bat;Ebola hemorrhagic fever;Ebolavirus;ecology;epidemic;Hendra virus;Hendra virus infection;human;infection control;infection prevention;Marburg hemorrhagic fever;Marburgvirus;Nipah virus;Nipah virus infection;nonhuman;priority journal;rabies;Rabies virus;Reoviridae;reovirus infection;risk factor;SARS coronavirus;severe acute respiratory syndrome;virus;virus cell interaction;virus transmission;zoonosis,"Smith, I.;Wang, L. F.",2013,,10.1016/j.coviro.2012.11.006,0
1942,Identification and isolation of a novel herpesvirus in a captive mob of eastern grey kangaroos (Macropus giganteus),"A novel herpesvirus was detected in a captive mob of eastern grey kangaroos (Macropus giganteus) during diagnostic workup for individuals with ulcerative cloacitis. Virus was initially detected in tissues using a consensus herpesvirus PCR. No viral inclusions or particles had been evident in routine histologic or transmission electron microscopic sections of cloacal lesions. Virus was isolated from samples and transmission electron microscopy of the resulting isolates confirmed that the virus was morphologically consistent with a herpesvirus. Nucleotide sequencing of the PCR product from tissue samples and from the isolates revealed that the virus was in the subfamily Gammaherpesvirinae and was distinct from other known herpesviruses. The correlation between the lesions and the novel virus remains unknown. Two herpesviruses, both in the subfamily Alphaherpesvirinae, have previously been described in macropods and are known to cause systemic clinical disease. This is the first reported gammaherpesvirus within the order Marsupialia, and may provide valuable information regarding the evolution and phylogeny of this virus family. Based on current herpesvirus nomenclature convention, the authors propose the novel herpesvirus be named Macropodid herpesvirus 3 (MaHV-3).","Amino Acid Sequence;Animals;Animals, Domestic;Base Sequence;Bayes Theorem;DNA, Viral/ch [Chemistry];DNA, Viral/ip [Isolation & Purification];Female;*Gammaherpesvirinae/cl [Classification];*Gammaherpesvirinae/ip [Isolation & Purification];Herpesviridae Infections/di [Diagnosis];*Herpesviridae Infections/ve [Veterinary];Herpesviridae Infections/vi [Virology];Immunohistochemistry/ve [Veterinary];*Macropodidae/vi [Virology];Male;Microscopy, Electron, Transmission/ve [Veterinary];Molecular Sequence Data;*Phylogeny;Polymerase Chain Reaction/mt [Methods];Polymerase Chain Reaction/ve [Veterinary];Sequence Alignment/ve [Veterinary];Sequence Analysis, DNA/ve [Veterinary];0 (DNA, Viral)","Smith, J. A.;Wellehan, J. F., Jr.;Pogranichniy, R. M.;Childress, A. L.;Landolfi, J. A.;Terio, K. A.",2008,Jun 22,,0
1943,Re-Assembly and Analysis of an Ancient Variola Virus Genome,"We report a major improvement to the assembly of published short read sequencing data from an ancient variola virus (VARV) genome by the removal of contig-capping sequencing tags and manual searches for gap-spanning reads. The new assembly, together with camelpox and taterapox genomes, permitted new dates to be calculated for the last common ancestor of all VARV genomes. The analysis of recently sequenced VARV-like cowpox virus genomes showed that single nucleotide polymorphisms (SNPs) and amino acid changes in the vaccinia virus (VACV)-Cop-O1L ortholog, predicted to be associated with VARV host specificity and virulence, were introduced into the lineage before the divergence of these viruses. A comparison of the ancient and modern VARV genome sequences also revealed a measurable drift towards adenine + thymine (A + T) richness.","Base Composition;DNA, Viral/ch [Chemistry];DNA, Viral/ge [Genetics];Evolution, Molecular;*Genome, Viral;Host Specificity;Orthopoxvirus/ge [Genetics];Orthopoxvirus/py [Pathogenicity];Phylogeny;Polymorphism, Single Nucleotide;*Variola virus/ge [Genetics];Variola virus/py [Pathogenicity];0 (DNA, Viral)","Smithson, C.;Imbery, J.;Upton, C.",2017,09 08,,0
1944,"Novel gyroviruses, including chicken anaemia virus, in clinical and chicken samples from South Africa",,,"Smuts, H. E. M.",2014,,,0
1945,A review of the strain diversity and pathogenesis of chicken astrovirus,"Although a relatively recently emerged virus, identified only in 2004 as a separate species of avian astrovirus, chicken astrovirus (CAstV) has been associated with poor growth of broiler flocks, enteritis and diarrhea and is a candidate pathogen in cases of runting stunting syndrome. More recently CAstV has been implicated in cases of two other diseases of broilers as the sole etiological agent, namely severe kidney disease of young broilers with visceral gout and the “White Chicks” hatchery disease. Examination of the strains of CAstV associated with the two latter diseases reveals they are closely related genetically. This review will discuss the pathogenesis of CAstV in relation to strain diversity and the effects of vertical versus horizontal transmission, virus load, co-infections and age of bird at infection, all factors that may impact upon disease severity.",RNA directed RNA polymerase;amino acid sequence;Astroviridae;bird disease;diarrhea;disease severity;dysbiosis;enteritis;enzyme linked immunosorbent assay;genetic variation;growth retardation;hatchery disease;hepatitis;metagenomics;microbial diversity;mixed infection;mortality;multiplex polymerase chain reaction;nonhuman;review;stunting syndrome;virus infection;virus load;virus strain;virus transmission,"Smyth, V. J.",2017,,10.3390/v9020029,0
1946,Sequence analysis of the foot and mouth disease virus type O/IRN/2007 VP1 gene from Iranian isolate,"The foot and mouth disease virus (FMDV) causes a vesicular and contagious disease of clovenhoofed animals. In this study, the virus was isolated from vesicles of the infected cattle using cell culture and serotyped by ELISA test. The extracted RNA from the infected cells was reverse transcribed and amplified using VP1 gene-specific primer pairs by means of one-step RT-PCR. The purified VP1 gene was sub-cloned into the uniqe KpnI and BamHI cloning sites of the pcDNA3.1+ vector. The DH5α strain of E. coli was transformed by the vector. The sequences of sub-cloned FMDV type O/IRN/2007 VP1 were aligned with FMDV type O/UKG/2001 VP1 using MegAlign software. Nucleotide sequence comparisons were made using the BLAST software available from the NCBI website. The amino acid sequences of three sub-cloned FMDV type O/IRN/2007 VP1 were also aligned with three other similar sequences using MegAlign software. Nineteen of the most similar VP1 nucleotide sequences (by BLASTN program), FMDV O/IRN/2007 VP1 sequence, twenty isolates of FMDV-O VP1 in Iran and eight topotypes of FMDV type O were aligned by Mega5 to create a FMDV-O VP1-based sequence similarity tree. The nucleotide sequence comparison indicated that FMDV O/ IRN/2007 VP1 had the greatest nucleotide sequence similarity to the VP1 gene of FMDV O1/Manisa/ Turkey/69 (99 %), FMDV O1/Manisa/Netherlands (98 %) and FMDV O1/Manisa/iso87/Turkey (98 %). It was also observed that the highest identity between FMDV O/IRN/2007 VP1 sequence and other nucleotide sequences of FMDV type O VP1 genes isolated in Iran during 1997-2004 was about 91 %. © 2006 -2013 Folia Biologica.",virus RNA;amino acid sequence;animal cell;article;cell vacuole;software;controlled study;enzyme linked immunosorbent assay;foot and mouth disease;Foot and mouth disease virus;Iran;molecular cloning;Netherlands;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;RNA extraction;sequence alignment;sequence analysis;sequence homology;Turkey (republic);virus gene;virus isolation;virus typing;vp1 gene;MegAlign,"Soleimanjahi, H.;Sedeh, F. M.;Jalilian, A. R.;Mahravani, H.",2013,,,0
1947,Sequence and phylogenetic analysis of neuraminidase genes of H9N2 avian influenza viruses isolated from commercial broiler chicken in Iran (2008 and 2009),"A total of 512 tissue samples collected from 30 farms located in various states of Iran during 2008-2009 as part of a program to monitor avian influenza viruses (AIVs) infection in Iran's poultry population. To determine the genetic relationship of Iranian viruses, neuraminidase (NA) genes from ten isolates of H9N2 viruses isolated from commercial chickens in Iran during 2008-2009 were amplified and sequenced. The viruses' neuraminidase gene was >90% similar to those of A/Quail/Hong Kong/G1/97 (H9N2) sublineage. The neuraminidase stalk regions in these Viruses had no deletion as compared to that of chicken/Beijing/1/94 sublineage (Beijing-like viruses) and the two human isolates A/HK/1073/99, A/HK/1074/99. Phylogenetic analysis of neuraminidase (NA) gene showed that it shares a common ancestor A/Quail/Hong Kong/G1/97 isolate which had contributed the internal genes of the H5N1 virus. The results of this study indicated that No (Beijing-like) virus and (Korean-like) virus were found in chickens in Iran, and the NA genes of H9N2 influenza viruses circulating in Iran during the past years were well conserved and the earlier Iranian isolates may be considered to represent such a progenitor. © 2011 Springer Science+Business Media B.V.",sialidase;viral protein;animal;article;avian influenza;chicken;classification;DNA sequence;genetics;Influenza A virus (H9N2);Iran;isolation and purification;molecular evolution;molecular genetics;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;sequence homology;virology,"Soltanialvar, M.;Shoushtari, H.;Bozorgmehrifard, M.;Charkhkar, S.;Akbarnejad, F.",2012,,10.1007/s11250-011-9913-2,0
1948,Molecular characterization of hemagglutinin and neuraminidase genes of H9N2 avian influenza viruses isolated from commercial broiler chicken in Iran,"A total of 512 tissue samples collected from 30 farms located in various states of Iran during 2008-2009 as part of a program to monitor AIV infection in Iran poultry population. Avian influenza virus was isolated from poultry farms with history of respiratory illness and increased mortality. Nucleotide sequence analysis of five representative isolates confirmed that all isolates possessed one type of amino acid motif (R-S-S-R/GL) at cleavage site of HA, Deduced amino acid sequences showed the presence of L226 (234 in H9 numbering) in all five Iranian isolates which indicates a preference to binding of a (2-6) sialic acid receptors. The viruses' surface glycoproteins genes were >90% similar to those of A/Quail/Hong Kong/Gl/97 (H9N2) lineage. The neuraminidase stalks regions in these viruses had no deletion as compared to that A/Dk/HK/ Y280/97 lineage (Ck/Bei-like viruses) and the 2 human isolates A/HK/1073/99, A/HK/1074/99. The hemadsorbmg site of neuraminidase had up to 3 amino acid substitutions and is different from those of earlier Iranian viruses. Phylogenetic analysis HA and NA genes showed that they share a common ancestor Qa/HK/Gl/97 isolate which had contributed internal genes of H5N1 virus. © 2010 Asian Network for Scientific Information.",hemagglutinin;receptor;sialic acid receptor;sialidase;unclassified drug;virus glycoprotein;amino acid sequence;amino acid substitution;animal tissue;article;chicken;controlled study;hemadsorption;Influenza A virus (H5N1);Influenza A virus (H9N2);Iran;mortality;nonhuman;nucleotide sequence;phylogeny;poultry;protein cleavage;protein motif;receptor affinity;respiratory tract disease;virus isolation,"Soltanialvar, M.;Shoushtari, H.;Bozorgmehrifard, M.;Charkhkar, S.;Eshratabadi, F.",2010,,10.3923/jbs.2010.145.150,0
1949,Molecular epidemiology of pseudorabies virus in Yunnan and the sequence analysis of its gD gene,"Outbreaks of pseudorabies (PRs) have occurred in Yunnan, China, which caused significant economic loss. To determine the prevalence and origin of PR in Yunnan, especially among vaccinated pigs, overall 791 samples of blood, tissue, semen, and sera were analyzed by serological methods, PCR, and sequence analysis of gD gene. Detection with viral gI antibody or PCR showed that the yearly positive rates of PR virus (PRV) in Yunnan from 2010 to 2014 were 48.15, 21.26, 2.17, 5.22, and 0.35%, respectively, with an average of 15.43%. In general, the incidence declined through the period of 2010–2014 probably due to the application of PRV eradication strategies. A phylogenetic tree was constructed based on the complete sequence of gD gene, with all strains clustered into two independent clades, i.e., Asian and European–American clades. The virus isolates from Henan, Tianjin, Heilongjiang, Sichuan, Shandong, Fujian, Xinjiang, Hubei, Guangdong, and Yunnan fell into Asian group, which harbored South Korea isolate. Four Yunnan virus isolates together with South Korean Namyangju fell into in the European–American clade. It showed that PR was pandemic as there was not a clear clue about the geographical origin of the PRV isolates in China since 2010.",virus DNA;animal tissue;article;boar (male pig);China;cladistics;controlled study;female;gD gene;gene amplification;gene sequence;incidence;male;molecular epidemiology;nonhuman;phylogenetic tree;phylogeny;pig;polymerase chain reaction;prevalence;Pseudorabies virus;sow (swine);virus gene;virus strain,"Song, C.;Gao, L.;Bai, W.;Zha, X.;Yin, G.;Shu, X.",2017,,10.1007/s11262-017-1429-z,0
1950,Detection and classification of infectious bronchitis viruses isolated in Korea by dot-immunoblotting assay using monoclonal antibodies,"Dot-immunoblotting assay (DIA) using five monoclonal antibodies (MAbs) to infectious bronchitis virus (IBV) was used to detect and classify the viruses propagated in embryonated chicken eggs. Using a group-specific MAb 3F5, 10 reference strains and 12 Korean isolates of IBV were successfully detected by DIA, and the lowest virus titer of IBV detected by DIA was approximately less than 103.8 mean embryo infective dose/mi. For evaluating the diagnostic efficiency, DIA was compared with the conventional infectious bronchitis (IB) diagnostic method. IBV antigens in allantoic fluid from embryonated eggs inoculated with IB-suspected field samples were specifically detected by DIA within only one or two egg passages, whereas the conventional embryonated egg inoculation method required four to seven egg passages for confirming IBV infection. These results indicated that DIA could significantly reduce time and cost for IB diagnosis. For examining the possibility of classifying IBV by DIA, four strain-specific MAbs, 3A4, 2A3, 6F7, and 2C6, were used. According to the MAb reacting patterns to the IBV antigens, the 10 IBV reference strains were classified into six groups; seven strains belonged to three different groups, and the other three strains each belonged to an individual group. In the case of 12 Korean isolates of IBV, they were classified in six groups. Among the six groups, the MAb reacting patterns of three groups matched those of the IBV reference strains, but the others did not. These data suggest that at least three variant serotypes of IBV exist in Korea.",monoclonal antibody;animal;animal disease;antibody specificity;article;Avian infectious bronchitis virus;bird disease;chick embryo;chicken;classification;fetus membrane;immunoblotting;isolation and purification;Korea;methodology;prenatal development;virology;virus infection,"Song, C. S.;Kim, J. H.;Lee, Y. J.;Kim, S. J.;Izumiya, Y.;Tohya, Y.;Jang, H. K.;Mikami, T.",1998,,,0
1951,Epidemiological classification of infectious bronchitis virus isolated in Korea between 1986 and 1997,"Forty Korean isolates and four reference strains of infectious bronchitis virus (IBV) were classified by reverse transcriptase-polymerase chain reaction and restriction fragment length polymorphism (RFLP) analysis. Each Korean isolate was isolated from different types of commercial chicken flocks between 1986 and 1997. RFLP patterns of an amplified DNA fragment (1722 bp) containing the S1 gene of IBV digested by restriction enzyme HaeIII showed that the 40 Korean isolates were classified into five genotypes, I to V. Six of them belonged to genotype I which had the same HaeIII and XcmI cleavage patterns with Massachusetts type (H120 and M41) but the other four genotypes had a different HaeIII cleavage pattern from the four reference IBV strains used in this study. Genotype III seemed to be the major type as 29 of the 40 isolates belonged to this type which was consistently found in the chicken flocks since 1990. On the other hand, genotypes II, IV and V were found in the field only in 1986, 1995 and 1995, respectively. Five isolates selected from each of the five genotypes were inoculated into 1-day-old specific-pathogen-free chicks to evaluate their pathogenicity. Genotype III induced 50% mortality as well as severe renal urate deposition on the kidneys but the other four genotypes only showed respiratory distress at 1 to 2 days after inoculation. Live H120 vaccine protected chicks against challenge with isolates selected from genotype I, but not genotypes IV to V. A live KM91p120 strain selected from major genotype III did protect chicks against challenge with isolates from genotype III, in addition to other genotypes, including two recent isolates of genotypes IV and V.",,"Song, C. S.;Lee, Y. J.;Kim, J. H.;Sung, H. W.;Lee, C. W.;Izumiya, Y.;Miyazawa, T.;Jang, H. K.;Mikami, T.",1998,,,0
1952,Profiling of novel microRNAs elicited by EV71 and CA16 infection in human bronchial epithelial cells using high-throughput sequencing,"Enterovirus 71 (EV71) and coxsackievirus A16 (CA16) are two major etiologic agents associated with hand, foot, and mouth disease (HFMD) worldwide. Despite that they both belong to the Enterovirus genus of the Picornaviridae family, there are many differences in the infection process of these viruses. However, the underlying mechanisms have not been elucidated. Multiple studies indicated that microRNAs (miRNAs) can play critical roles in the host-pathogen interaction. Our previous study reported that EV71 and CA16 infection leads to differential expression of miRNAs in human bronchial epithelial (16HBE) cells. Herein, we aimed to further explore the expression profile and possible roles of other differentially expressed miRNAs in 16HBE cells following EV71 and CA16 infections using high-throughput sequencing. We describe 44 novel differentially expressed miRNAs in all samples. Among these miRNAs, 7 novel differentially expressed miRNAs show an opposite expression trend during the progression of EV71 and CA16 infections. Subsequently, bioinformatics analyses, including Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, were used to identify the biological processes, molecular functions, cellular components, and pathways involved. The top 10 significant GO and Pathway annotations indicated that 849 target genes are involved in cell development, such as nervous system development, multicellular organism development, and developmental biology. Finally, the genes identified in both the GO and Pathway analysis were used to construct a co-expression network to further identify the potential function of these co-expressed genes. Thus, our data may be beneficial in guiding further studies on the molecular mechanism of developmental regulation in HFMD pathogenesis caused by EV71 and CA16. In addition, it provided new candidate biomarkers or therapeutic targets for HFMD.",DNA;gonadorelin receptor;microRNA;microRNA 1;microRNA 10;microRNA 11;microRNA 12;microRNA 13;microRNA 14;microRNA 15;microRNA 16;microRNA 17;microRNA 18;microRNA 19;microRNA 2;microRNA 20;microRNA 21;microRNA 22;microRNA 23;microRNA 24;microRNA 25;microRNA 26;microRNA 27;microRNA 3;microRNA 4;microRNA 5;microRNA 6;microRNA 7;microRNA 8;microRNA 9;unclassified drug;16HBE14o- cell line;algorithm;angiogenesis;article;controlled study;Coxsackie virus infection;Coxsackievirus A16;DNA binding;Enterovirus A71;Enterovirus infection;epithelium cell;gene expression;gene identification;high throughput sequencing;human;human cell;priority journal;reverse transcription polymerase chain reaction;RNA sequence;Wnt signaling,"Song, J.;Hu, Y.;Jiang, X.;Zhu, W.;Wu, Z.;Dong, S.",2018,,10.1016/j.virusres.2018.02.008,0
1953,miR-1303 regulates BBB permeability and promotes CNS lesions following CA16 infections by directly targeting MMP9,"Coxsackievirus A16 (CA16) is a member of the Picornaviridae family and causes mild and self-limiting hand, foot, and mouth disease (HFMD) in infants and young children. CA16 infection can also progress to central nervous system (CNS) complications; however, the underlying mechanism by which CA16 penetrates the blood-brain barrier (BBB) and then causes CNS damage remains unclear. This study aimed to explore the mechanism of CA16 neurotropic tropism by establishing an in vitro BBB model with CA16 infection and an in vivo CA16 rhesus monkey infant infection model. The results showed that CA16 infection induced increased permeability of the BBB accompanied by upregulation of matrix metalloproteinase 9 (MMP9) expression. Subsequently, high-throughput miRNA sequencing technology and bioinformatics analysis revealed that miR-1303 may regulate BBB permeability by targeting MMP9. Next, we used dual-luciferase, qRT-PCR, and western blot assays to provide evidence of MMP9 targeting by miR-1303. Further experiments revealed that CA16 infection promoted the degradation of junctional complexes (Claudin4, Claudin5, VE-Cadherin, and ZO-1), likely by downregulating miR-1303 and upregulating MMP9. Finally, EGFP-CA16 infection could enter the CNS by facilitating the degradation of junctional complexes, eventually causing neuroinflammation and injury to the CNS, which was confirmed using the in vivo rhesus monkey model. Our results indicate that CA16 might penetrate the BBB and then enter the CNS by downregulating miR-1303, which disrupts junctional complexes by directly regulating MMP9 and ultimately causing pathological CNS changes. These results provide new therapeutic targets in HFMD patients following CA16 infection.",claudin 4;claudin 5;gelatinase B;microRNA;microRNA 1303;protein ZO1;tissue inhibitor of metalloproteinase 1;unclassified drug;vascular endothelial cadherin;animal experiment;animal model;article;blood brain barrier;cell proliferation;central nervous system disease;controlled study;Coxsackievirus A16;Enterovirus A71;Enterovirus infection;enzyme linked immunosorbent assay;flow cytometry;hand foot and mouth disease;high throughput sequencing;human;human cell;HUVEC cell line;immunofluorescence;in vitro study;infant;nonhuman;priority journal;protein degradation;protein expression;reverse transcription polymerase chain reaction;rhesus monkey;RNA sequence;thalamus;upregulation;viral tropism;virus load;virus titration;Western blotting,"Song, J.;Hu, Y.;Li, H.;Huang, X.;Zheng, H.;Hu, Y.;Wang, J.;Jiang, X.;Li, J.;Yang, Z.;Fan, H.;Guo, L.;Shi, H.;He, Z.;Yang, F.;Wang, X.;Dong, S.;Li, Q.;Liu, L.",2018,,10.1038/s41426-018-0157-3,0
1954,Different microRNA profiles reveal the diverse outcomes induced by EV71 and CA16 infection in human umbilical vein endothelial cells using high-throughput sequencing,"Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) remain the predominant pathogens in hand, foot, and mouth disease (HFMD), but the factors underlying the pathogenesis of EV71 and CA16 infections have not been elucidated. Recently, the functions of microRNAs (miRNAs) in pathogen-host interactions have been highlighted. In the present study, we performed comprehensive miRNA profiling in EV71- And CA16-infected human umbilical vein endothelial cells (HUVECs) at multiple time points using high-throughput sequencing. The results showed that 135 known miRNAs exhibited remarkable differences in expression. Of these, 30 differentially expressed miRNAs presented opposite trends in EV71- And CA16- infected samples. Subsequently, we mainly focused on the 30 key differentially expressed miRNAs through further screening to predict targets. Gene ontology (GO) and pathway analysis of the predicted targets showed the enrichment of 14 biological processes, 9 molecular functions, 8 cellular components, and 85 pathways. The regulatory networks of these miRNAs with predicted targets, GOs, pathways, and co-expression genes were determined, suggesting that miRNAs display intricate regulatory mechanisms during the infection phase. Consequently, we specifically analyzed the hierarchical GO categories of the predicted targets involved in biological adhesion. The results indicated that the distinct changes induced by EV71 and CA16 infection may be partly linked to the function of the blood-brain barrier. Taken together, this is the first report describing miRNA expression profiles in HUVECs with EV71 and CA16 infections using high-throughput sequencing. Our data provide useful insights that may help to elucidate the different host-pathogen interactions following EV71 and CA16 infection and offer novel therapeutic targets for these infections.",microRNA;article;blood brain barrier;controlled study;Coxsackievirus A16;Enterovirus A71;gene expression;gene ontology;gene regulatory network;hand foot and mouth disease;high throughput sequencing;host pathogen interaction;human;human cell;prediction;protein expression;protein function;regulatory mechanism;umbilical vein endothelial cell,"Song, J.;Hu, Y.;Li, J.;Zheng, H.;Wang, J.;Guo, L.;Ning, R.;Li, H.;Yang, Z.;Fan, H.;Liu, L.",2017,,10.1371/journal.pone.0177657,0
1955,High-Throughput Sequencing of Putative Novel microRNAs in Rhesus Monkey Peripheral Blood Mononuclear Cells following EV71 and CA16 Infection,"Objectives: Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) remain the major pathogens in hand, foot, and mouth disease (HFMD) cases, but the mechanisms of the different pathogeneses that follow EV71 and CA16 infection remain largely unknown. Methods: Herein, we utilized microRNA (miRNA) deep sequencing to investigate the roles of novel differentially expressed miRNAs in peripheral blood mononuclear cells (PBMCs) infected with EV71 and CA16. Results: The results identified 13 novel differentially expressed miRNAs in each group. Additionally, the target genes were predicted by the miRanda and RNAhybrid programs, and a total of 2,501 targets were found in the two databases. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that these targets were mainly involved in cell development and were associated with nervous system development, system development, multicellular organism development, the Wnt signaling pathway, the PDGF signaling pathway, and the EGF receptor signaling pathway. Finally, a coexpression regulatory network was built with the key targets to further extrapolate the functional interactions of the targets and their coexpressed genes. Conclusion: Our results not only revealed potential biomarkers or targets for the diagnosis and treatment of HFMD, but also provided new insights to explore the mechanisms of EV71 and CA16 pathogenesis.",epidermal growth factor receptor;microRNA;microRNA 1;microRNA 10;microRNA 11;microRNA 12;microRNA 13;microRNA 2;microRNA 3;microRNA 4;microRNA 5;microRNA 6;microRNA 7;microRNA 8;microRNA 9;platelet derived growth factor;unclassified drug;animal cell;article;cell maturation;controlled study;Coxsackievirus A16;Enterovirus A71;gene expression;gene function;gene ontology;hand foot and mouth disease;high throughput sequencing;in vitro study;nervous system development;nonhuman;peripheral blood mononuclear cell;priority journal;quantitative analysis;reverse transcription polymerase chain reaction;rhesus monkey;RNA analysis;signal transduction;Wnt signaling,"Song, J.;Jiang, X.;Hu, Y.;Li, H.;Zhang, X.;Xu, J.;Li, W.;Zheng, X.;Dong, S.",2018,,10.1159/000493798,0
1956,Evidence of human-to-swine transmission of the pandemic (H1N1) 2009 influenza virus in South Korea,"As the pandemic (H1N1) 2009 influenza virus continues to infect human populations globally, reports on epidemiologically linked animal infections are also on the rise. Since December 2009, pandemic (H1N1) 2009-like viruses have been isolated in pigs from different swine farms of South Korea. Genetic and phylogenetic analyses of viral segments demonstrated several events of human-to-swine transmission with no apparent signs of reassortment. These events were also supported by serological surveillance in pig sera collected from April to December, suggesting that reverse transmission probably started between June and July with a drastic increase in prevalence the following months. Although molecular characterization indicates that the swine isolates are generally stable, some viruses are genetically evolving, most notably in their surface proteins. Animal studies (ferrets and mice) reveal that swine pandemic isolates epitomize biological properties attributed to the currently circulating human pandemic viruses, including replication kinetics and efficient transmission, indicating their potential to return to circulation among humans. Overall, these results indicate widespread human-to-animal transmission of pandemic (H1N1) 2009 influenza viruses in South Korea. With the significant role of pigs in the ecology of influenza viruses, these transmission events should be closely monitored and minimized to prevent the risk of generating viruses with greater human health concerns. Copyright © 2010, American Society for Microbiology. All Rights Reserved.",membrane protein;animal experiment;article;genetic analysis;genetic reassortment;Influenza virus;mouse;nonhuman;nucleotide sequence;pandemic influenza;phylogeny;prevalence;priority journal;South Korea;virus isolation;virus replication;virus transmission,"Song, M. S.;Lee, J. H.;Pascua, P. N. Q.;Baek, Y. H.;Kwon, H. I.;Park, K. J.;Choi, H. W.;Shin, Y. K.;Song, J. Y.;Kim, C. J.;Choi, Y. K.",2010,,10.1128/jcm.00053-10,0
1957,Chilo iridescent virus encodes a putative helicase belonging to a distinct family within the 'DEAD/H' superfamily: Implications for the evolution of large DNA viruses,"The complete nucleotide sequence of the EcoRI DNA fragment M (7099 bp; 0.310-0.345 map units) of the genome of insect iridescent virus type 6-Chilo iridescent virus (CIV)-was determined. A 606 codon open reading frame located in this region encoded a protein (p69) related to a distinct family of putative DNA and/or RNA helicases belonging to the 'DEAD/H' superfamily. Unique sequence signatures were derived that allowed selective retrieval of the putative helicases of the new family from amino acid sequence databases. The family includes yeast, Drosophila, mammalian, and bacterial proteins involved in transcription regulation and in repair of damaged DNA. It is hypothesized that p69 of CIV may be a DNA or RNA helicase possibly involved in viral transcription. A distant relationship was observed to exist between this family of helicases and another group of proteins that consists of putative helicases of poxviruses, African swine fever virus, and yeast mitochondrial plasmids. It is shown that p69 of CIV is much more closely related to cellular helicases than any of the other known viral helicases. Phylogenetic analysis suggested an independent origin for the p69 gene and the genes encoding other viral helicases.",amino acid;helicase;nucleotide;RNA helicase;virus DNA;viral protein;African swine fever virus;amino acid sequence;article;DNA sequence;DNA virus;Iridovirus;nonhuman;Northern blotting;nucleotide sequence;phylogeny;plasmid;Poxviridae;priority journal;virus gene;virus transcription;yeast,"Sonntag, K. C.;Schnitzler, P.;Koonin, E. V.;Darai, G.",1994,,,0
1958,Small RNA deep sequencing identifies viral microRNAs during malignant catarrhal fever induced by alcelaphine herpesvirus 1,"Alcelaphine herpesvirus 1 (AlHV-1) is a γ-herpesvirus (γ-HV) carried asymptomatically by wildebeest. Upon cross-species transmission, AlHV-1 induces a fatal lymphoproliferative disease named malignant catarrhal fever (MCF) in many ruminants, including cattle, and the rabbit model. Latency has been shown to be essential for MCF induction. However, the mechanisms causing the activation and proliferation of infected CD8+T cells are unknown. Many γ-HVs express microRNAs (miRNAs). These small non-coding RNAs can regulate expression of host or viral target genes involved in various pathways and are thought to facilitate viral infection and/or mediate activation and proliferation of infected lymphocytes. The AlHV-1 genome has been predicted to encode a large number of miRNAs. However, their precise contribution in viral infection and pathogenesis in vivo remains unknown. Here, using cloning and sequencing of small RNAs we identified 36 potential miRNAs expressed in a lymphoblastoid cell line propagated from a calf infected with AlHV-1 and developing MCF. Among the sequenced candidate miRNAs, 32 were expressed on the reverse strand of the genome in two main clusters. The expression of these 32 viral miRNAs was further validated using Northern blot and quantitative reverse transcription PCR in lymphoid organs of MCF-developing calves or rabbits. To determine the concerted contribution in MCF of 28 viral miRNAs clustered in the non-protein-coding region of the AlHV-1 genome, a recombinant virus was produced. The absence of these 28 miRNAs did not affect viral growth in vitro or MCF induction in rabbits, indicating that the AlHV-1 miRNAs clustered in this non-protein-coding genomic region are dispensable for MCF induction.",microRNA;microRNA 291b 3p;microRNA 31 5p;RNA;small RNA;unclassified drug;Alcelaphine herpesvirus 1;animal cell;animal experiment;animal model;animal tissue;article;CD8+ T lymphocyte;controlled study;disease severity;gene expression;high throughput sequencing;in vitro study;lymphadenopathy;lymphoblastoid cell line;lymphocyte count;lymphoid tissue;malignant catarrhal fever;molecular cloning;nonhuman;Northern blotting;priority journal;quantitative analysis;Leporidae;reverse transcription polymerase chain reaction;RNA isolation;RNA sequence;Southern blotting;virogenesis;virus genome;virus load;virus replication,"Sorel, O.;Tuddenham, L.;Myster, F.;Palmeira, L.;Kerkhofs, P.;Pfeffer, S.;Vanderplasschen, A.;Dewals, B. G.",2015,,10.1099/jgv.0.000272,0
1959,Adult fulminant subacute sclerosing panencephalitis: Pathological and molecular studies - A case report,"Subacute sclerosing panencephalitis is an uncommon progressive neurological disorder caused by a persistent defective-measles virus, typically affecting children. We describe a case of fulminant subacute sclerosing panencephalitis in a 25-year-old male. Brain tissue biopsy showed histologic evidence of encephalitis with eosinophilic intranuclear inclusion bodies (Cowdry Type A and B), intracytoplasmic inclusion bodies, perivascular lymphoplasmacytic infiltration and gliosis. Immunohistochemical studies were positive using an anti-measles antibody. Reverse transcriptase-PCR detected measles virus RNA and phylogenetic analysis indicated a C2 genotype. The rare adult-onset form is often atypical and difficult to diagnose and should be included in the differential diagnosis of subacute ""unexplained"" neurological diseases and uncommon infectious disorders. © 2009 Dustri-Verlag Dr. K. Feistle.",aciclovir;antibiotic agent;carbamazepine;clonazepam;etiracetam;phenobarbital;phenytoin;virus RNA;adult;article;brain angiography;brain biopsy;case report;cell inclusion;cell nucleus inclusion body;cerebrospinal fluid analysis;differential diagnosis;electroencephalogram;genotype;histology;human;human tissue;immunohistochemistry;male;nuclear magnetic resonance imaging;onset age;phylogeny;priority journal;reverse transcription polymerase chain reaction;subacute sclerosing panencephalitis;tonic clonic seizure,"Souraud, J. B.;Faivre, A.;Waku-Kouomou, D.;Gaillard, T.;Aouad, N.;Meaudre, E.;Wild, F. T.;Fouet, B.;Soulard, R.",2009,,,0
1960,Pathological and molecular findings of avian avulavirus type 1 outbreak in pigeons (Columba livia) of southern Brazil,"The Newcastle disease, caused by avian avulavirus type 1 strains (APMV-1) is an important avian disease involved into high rates of mortality and economic losses. Several outbreaks have been reported over the last 30 years in Columbiformes in different parts of the world, caused by a adapted variant strain of AAvV-1, called pigeon paramyxovirus type 1 (PPMV-1). A high mortality associated with an outbreak was analyzed in free-living pigeons (Columba livia) in a public square in Porto Alegre in Southern Brazil. A total of 24 pigeons moribund or freshly dead, within five weeks interval were submitted to necropsy, histopathological, immunohistochemical (anti-Newcastle), and RT-PCR followed by sequencing of the amplification products analysis. They presented neurological signs, non-suppurative encephalitis and encephalomyelitis, and mononuclear inflammatory infiltrate in different organs. Immunohistochemical analysis in nine pigeons tissue showed that anti-Newcastle was expressed in brain, kidney, liver and pancreas. The RT-PCR test for the M protein of Newcastle disease virus was positive in six pigeons. The differential diagnosis of Influenza, West Nile, Mycoplasma gallisepticum and Mycoplasma synoviae in all pigeons presented negative results. The sequence of amino acids in the cleavage site region of the F protein was 112RRQKRF117 classifying the strain as virulent. The phylogenetic analysis classified this virus strain into Class II and VI genotype.",fusion protein;M protein;peroxidase;animal experiment;animal tissue;article;autopsy;Avulavirus infection;cell vacuole;clinical feature;Columba livia;differential diagnosis;encephalitis;encephalomyelitis;enzyme activity;gene amplification;gliosis;hepatomegaly;histopathology;hyperemia;inflammatory infiltrate;influenza;lymphoplasmacytic meningitis;meningitis;microscopy;mortality;Mycoplasma gallisepticum;Mycoplasma synoviae;neuronophagia;Newcastle disease;nonhuman;pathology;perivascular lymphoplasmacytic cuffing;phylogeny;reverse transcription polymerase chain reaction;splenomegaly;West Nile virus,"Souza, S. O.;Fredo, G.;Dupont, P. M.;Leite-Filho, R. V.;Teifke, J. P.;Pavarini, S. P.;Canal, C. W.;Driemeier, D.",2018,,10.1590/1678-5150-pvb-5528,0
1961,Viral diversity of Rhipicephalus microplus parasitizing cattle in southern Brazil,"Ticks are ectoparasites spread worldwide and are well known as vectors of many viruses of great importance to human and animal health. However, the viral diversity in ticks is still poorly understood, particularly in South America. Here we characterized the viral diversity present in Rhipicephalus microplus parasitizing cattle in the southern region of Brazil using metagenomics. Our study revealed the presence of viruses that had not been previously described in the region, including lihan tick virus (Phenuiviridae family) and wuhan tick virus 2 (Chuviridae family), as well as expands the biogeography of jingmen tick virus (Flaviviridae family) in Brazil. Also, we described three novel tymoviruses (Tymovirales order), named guarapuava tymovirus-like 1 to 3. We described the genomic and phylogenetic characterization of these viruses. Our study sheds light on the viral diversity of Rhipicephalus microplus in South America, and also expands the biogeography of tick viruses that were previously described only in Asia.",article;Asia;biogeography;Brazil;Flaviviridae;human;metagenomics;nonhuman;Rhipicephalus (Boophilus) microplus;Tymovirus,"Souza, W. M.;Fumagalli, M. J.;Torres Carrasco, A. O.;Romeiro, M. F.;Modha, S.;Seki, M. C.;Gheller, J. M.;Daffre, S.;Nunes, M. R. T.;Murcia, P. R.;Acrani, G. O.;Figueiredo, L. T. M.",2018,,10.1038/s41598-018-34630-1,0
1962,Characterization of low-pathogenicity H5N1 avian influenza viruses from North America,"Wild-bird surveillance in North America for avian influenza (AI) viruses with a goal of early identification of the Asian H5N1 highly pathogenic AI virus has identified at least six low-pathogenicity H5N1 AI viruses between 2004 and 2006. The hemagglutinin (HA) and neuraminidase (NA) genes from all 6 H5N1 viruses and an additional 38 North American wild-bird-origin H5 subtype and 28 N1 subtype viruses were sequenced and compared with sequences available in GenBank by phylogenetic analysis. Both HA and NA were phylogenetically distinct from those for viruses from outside of North America and from those for viruses recovered from mammals. Four of the H5N1 AI viruses were characterized as low pathogenicity by standard in vivo pathotyping tests. One of the H5N1 viruses, A/MuteSwan/MI/451072-2/06, was shown to replicate to low titers in chickens, turkeys, and ducks. However, transmission of A/MuteSwan/MI/451072-2/06 was more efficient among ducks than among chickens or turkeys based on virus shed. The 50% chicken infectious dose for A/MuteSwan/MI/451072-2/06 and three other wild-waterfowl-origin H5 viruses were also determined and were between 10 5.3 and 107.5 50% egg infective doses. Finally, seven H5 viruses representing different phylogenetic clades were evaluated for their antigenic relatedness by hemagglutination inhibition assay, showing that the antigenic relatedness was largely associated with geographic origin. Overall, the data support the conclusion that North American H5 wild-bird-origin AI viruses are low-pathogenicity wild-bird-adapted viruses and are antigenically and genetically distinct from the highly pathogenic Asian H5N1 virus lineage. Copyright © 2007, American Society for Microbiology. All Rights Reserved.",animal experiment;animal model;animal tissue;antigenicity;article;chicken;cladistics;controlled study;duck;gene sequence;genetic linkage;hemagglutination inhibition;Influenza A virus (H5N1);nonhuman;North America;nucleotide sequence;phylogeny;priority journal;sequence analysis;turkey (bird);virus characterization;virus identification;virus shedding;virus strain;virus transmission;virus virulence,"Spackman, E.;Swayne, D. E.;Suarez, D. L.;Senne, D. A.;Pedersen, J. C.;Killian, M. L.;Pasick, J.;Handel, K.;Pillai, S. P. S.;Lee, C. W.;Stallknecht, D.;Slemons, R.;Ip, H. S.;Deliberto, T.",2007,,10.1128/jvi.01368-07,0
1963,"Prevalence and phylogenetic analysis of hepatitis E virus in pigs, wild boars, roe deer, red deer and moose in Lithuania","BACKGROUND: Hepatitis E virus (HEV) is one of the major causes of acute viral hepatitis worldwide. In Europe, food-borne zoonotic transmission of HEV genotype 3 has been associated with domestic pigs and wild boar. Controversial data are available on the circulation of the virus in animals that are used for human consumption, and to date, no gold standard has yet been defined for the diagnosis of HEV-associated hepatitis. To investigate the current HEV infection status in Lithuanian pigs and wild ungulates, the presence of viral RNA was analyzed by nested reverse transcription polymerase chain reaction (RT-nPCR) in randomly selected samples, and the viral RNA was subsequently genotyped. RESULTS: In total, 32.98 and 22.55% of the domestic pig samples were HEV-positive using RT-nPCR targeting the ORF1 and ORF2 fragments, respectively. Among ungulates, 25.94% of the wild boar samples, 22.58% of the roe deer samples, 6.67% of the red deer samples and 7.69% of the moose samples were positive for HEV RNA using primers targeting the ORF1 fragment. Using primers targeting the ORF2 fragment of the HEV genome, viral RNA was only detected in 17.03% of the wild boar samples and 12.90% of the roe deer samples. Phylogenetic analysis based on a 348-nucleotide-long region of the HEV ORF2 showed that all obtained sequences detected in Lithuanian domestic pigs and wildlife belonged to genotype 3. In this study, the sequences identified from pigs, wild boars and roe deer clustered within the 3i subtype reference sequences from the GenBank database. The sequences obtained from pig farms located in two different counties of Lithuania were of the HEV 3f subtype. The wild boar sequences clustered within subtypes 3i and 3h, clearly indicating that wild boars can harbor additional subtypes of HEV. For the first time, the ORF2 nucleotide sequences obtained from roe deer proved that HEV subtype 3i can be found in a novel host. CONCLUSION: The results of the viral prevalence and phylogenetic analyses clearly demonstrated viral infection in Lithuanian pigs and wild ungulates, thus highlighting a significant concern for zoonotic virus transmission through both the food chain and direct contact with animals. Unexpected HEV genotype 3 subtype diversity in Lithuania and neighboring countries revealed that further studies are necessary to understand the mode of HEV transmission between animals and humans in the Baltic States region.",virus RNA;animal;classification;deer;genetics;genotype;hepatitis E;Hepatitis E virus;Lithuania;phylogeny;pig;prevalence;swine disease;veterinary medicine;virology,"Spancerniene, U.;Grigas, J.;Buitkuviene, J.;Zymantiene, J.;Juozaitiene, V.;Stankeviciute, M.;Razukevicius, D.;Zienius, D.;Stankevicius, A.",2018,,10.1186/s13028-018-0367-7,0
1964,Physical and chemical characterization of an avian reovirus,"The avian viral agent S1133 has previously been classified serologically as a member of the avian reovirus group. This viral agent grows in chicken embryo fibroblast cells, bands at a density of 1.37 g/ml in CsCl equilibrium density gradients, has a particle diameter of 75 nm, and has a morphology similar to that of human reovirus type 3. Its nucleic acid is comprised of double stranded RNA and adenosine rich oligonucleotides. The dsRNA is distributed among 10 segments with molecular weights of 2.7 x 106, 2.6 x 106, 2.4 x 106, 1.7 x 106, 1.5 x 106, 1.3 x 106, 1.2 x 106, 0.80 x 106, 0.74 x 106, and 0.68 x 106 for the largest (L1) to the smallest (S4) segment, respectively, as determined by polyacrylamide gel electrophoresis. These 10 segments migrate differently on polyacrylamide gels compared to those of human reovirus type 3. The capsid proteins of avian reovirus consist of eight species of polypeptides as determined by polyacrylamide gel electrophoresis. These are λ1, λ2, λ3, μ1, μ2, sigma1, sigma2, and sigma3 with molecular weights of 140, 125, 115, 85, 72, 40, 36, and 32 x 103, respectively. Only polypeptide sigma2, which resides in the inner capsid or core, comigrated with the sigma2 polypeptide of type 3 reovirus. Antiserum against type 3 reovirus did not neutralize avian reovirus. Avian reovirus core particles were found to possess a transcriptase and a methylase activity.",viral protein;virus RNA;cell culture;classification;in vitro study;microorganism;Reoviridae;theoretical study;virus;virus characterization;virus classification,"Spandidos, D. A.;Graham, A. F.",1976,,,0
1965,Dynamic equilibrium of Marek's disease genomes during in vitro serial passage,"Attenuation of Gallid herpesvirus-2 (GaHV-2), the causative agent of Marek's disease, can occur through serial passage of a virulent field isolate in avian embryo fibroblasts. In order to gain a better understanding of the genes involved in attenuation and associate observed changes in phenotype with specific genetic variations, the genomic DNA sequence of a single GaHV-2 virulent strain (648A) was determined at defined passage intervals. Biological characterization of these ""interval-isolates"" in chickens previously indicated that the ability to induce transient paralysis was lost by passages 40 and the ability to induce persistent neurological disease was lost after passage 80, coincident with the loss of neoplastic lesion formation. Deep sequencing of the interval-isolates allowed for a detailed cataloguing of the mutations that exist within a single passage population and the frequency with which a given mutation occurs across passages. Gross genetic alterations were identified in both novel and well-characterized genes and cis-acting regions involved in replication and cleavage/packaging. Deletions in genes encoding the virulence factors vLipase, vIL8, and RLORF4, as well as a deletion in the promoter of ICP4, appeared between passages 61 and 101. Three mutations in the virus-encoded telomerase which predominated in late passages were also identified. Overall, the frequency of mutations fluctuated greatly during serial passage and few genetic changes were absolute. This indicates that serial passage of GaHV-2 results in the generation of a collection of genomes with limited sequence heterogeneity.","Animals;Chick Embryo;*DNA, Viral/ge [Genetics];Fibroblasts/vi [Virology];*Genome, Viral;Genotype;*Herpesvirus 2, Gallid/ge [Genetics];Herpesvirus 2, Gallid/ph [Physiology];High-Throughput Nucleotide Sequencing/mt [Methods];*Marek Disease/vi [Virology];Mutagenesis, Insertional;Nuclear Proteins/ge [Genetics];Nucleic Acid Conformation;Oncogene Proteins, Viral/ge [Genetics];Open Reading Frames;Promoter Regions, Genetic;Sequence Analysis, DNA;Sequence Deletion;Serial Passage;Trans-Activators/ge [Genetics];Virus Cultivation/mt [Methods];Virus Replication;0 (DNA, Viral);0 (Nuclear Proteins);0 (Oncogene Proteins, Viral);0 (Trans-Activators);0 (vIL-8 protein, Marek's disease virus);147979-89-3 (ICP4 protein, Gallid herpesvirus 2)","Spatz, S. J.;Volkening, J. D.;Gimeno, I. M.;Heidari, M.;Witter, R. L.",2012,Dec,,0
1966,Dual natural infection with bovine viral diarrhea virus-1 and-2 in a stillborn calf: Tissue distribution and molecular characterization,"Dual infections with both bovine viral diarrhea virus (BVDV)-1 and-2 seem to be unusual. The aim of this study was to describe an infection with both BVDV genotypes in a stillborn calf. Virus isolation and phylogenetic analyses of the 5´UTR and NS5B regions confirmed the presence of BVDV-1b and-2b in spleen and lung, whereas BVDV-2b was also detected in brain, heart, liver, kidney and, fluid of cavities. These results confirm that dual infections with both BVDV-1 and BVDV-2 species can occur naturally and their tissue distribution can be different.",ExoProStar;GoTaq;Illustra;SYBR Green;nonstructural protein 5B;5' untranslated region;animal experiment;animal tissue;article;autopsy;Border disease virus;bovine viral diarrhea;Bovine viral diarrhea virus 1;bovine viral diarrhea virus 1 infection;Bovine viral diarrhea virus 2;bovine viral diarrhea virus 2 infection;calf (bovine);GenBank;genotype;mixed infection;molecular diagnosis;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;reverse transcription polymerase chain reaction;RNA extraction;sequence alignment;stillbirth;tissue characterization;tissue distribution;virus isolation,"Spetter, M. J.;Uriarte, E. L. L.;Altamiranda, E. A. G.;Leunda, M. R.;Pereyra, S. B.;Verna, A. E.;Odeón, A. C.",2018,,10.4314/ovj.v8i4.23,0
1967,Serologic and virologic studies of selected cattle with antibodies to bovine herpesviruses,"In order to investigate the specificity of low titer antibodies to BHV 1, twelve cattle were subjected to stress and dexamethasone treatment. They were monitored virologically by inoculating cell cultures with naso-pharyngeal-, ocular- and vaginal- or preputial swabs and serologically by assessing the prevalence and incidence of antibodies to bovine, caprine-, porcine-, and equine herpesviruses and to bovine leukemia virus. Antibodies were classified as specific for BHV 1 if the animals excreted IBR virus, or if the antibodies neutralized BHV 1 and reacted with BHV 1 antigens, or if they reacted additionally with CapHV antigens. Animals whose sera recognized BHV 1 and BHV 2 but not other herpesviruses, were judged to have experienced both infections. Nine of the twelve animals had specific BHV 1 antibodies. With three animals the question for specificity of their antibodies remains open. Two animals experienced several herpesvirus infections. Therefore, the induction of crossreacting antibodies, directed against epitopes common to herpesviruses, could not be ruled out. The sera of one animal reacted with BHV 1 and BHV 4 antigens in ELISA tests. They did, however, not neutralize BHV 1.",virus antibody;animal;antibody specificity;article;bovine;cattle disease;cross reaction;female;immunology;Bovine herpesvirus 1;isolation and purification;male,"Spirig, C.;Ackermann, M.;Müller, H. K.;Bruckner, L.;Kihm, U.",1989,,,0
1968,Orf virus infection in sheep or goats,"Orf virus, a member of the genus Parapoxvirus, is the causative agent of contagious ecthyma ('Orf'). It is a pathogen with worldwide distribution, causing significant financial losses in livestock production. The disease mainly affects sheep and goats, but various other ruminants and mammals have been reported to be infected as well. It is also a zoonotic disease, affecting mainly people who come in direct or indirect contact with infected animals (e.g. farmers, veterinarians). The disease is usually benign and self-limiting, although in many cases, especially in young animals, it can be persistent and even fatal. Production losses caused by Orf virus are believed to be underestimated, as it is not a notifiable disease. This review of literature presents all latest information regarding the virus; considerations regarding treatment and prevention will be also discussed.",antivirus agent;antiviral therapy;article;clinical feature;contagious ecthyma;goat;incineration;nonhuman;Orf virus;pathogenesis;phylogeny;vaccination;virus classification;virus genome;virus isolation;virus morphology;virus transmission,"Spyrou, V.;Valiakos, G.",2015,,10.1016/j.vetmic.2015.08.010,0
1969,Characterization of infectious bursal disease viruses from four layer flocks in the United States,"Twenty bursal samples were obtained from four infectious bursal disease virus (IBDV)-vaccinated layer flocks experiencing problems with immune suppression that was thought to be infectious bursal disease. All the samples were found to be positive for IBDV by reverse transcriptase polymerase chain reaction (RT-PCR). Restriction fragment length polymorphism analysis of the samples identified them as classic molecular group 3 and group 4 viruses. Two samples from each of the four flocks were sequenced, and within a flock, these sequences were identical; however, between flocks, some differences were observed. One virus from each of the four flocks was selected for further analysis. The VP2 hypervariable sequence region of samples GA-1, H-30, and CS-2-35 had nucleotide and amino acid similarities with the D78 and Vi Bursa G classic vaccines that were used in those flocks. The sequence of HPR-2 was similar to the Bursa Vac 4 vaccine used in that flock and the STC virulent classic IBDV strain. The deduced amino acid sequence of these isolates revealed that all the isolates had proline at position 222, which is characteristic of U.S. classic viruses. The phylogenetic analysis of these isolates on the basis of the VP2 hypervariable amino acid sequence clustered GA-1, H-30, and CS-2-35 with the D78 vaccine and HPR-2 with STC. The pathogenicity of these isolates was tested in specific-pathogen-free chickens. Bursa-body weight (B-BW) ratios and histopathologic lesion scores in the bursa were determined. Gross lesions were observed in the bursa, and the B-BW ratios of the birds infected with all four wild-type viruses were significantly different compared with the D78 vaccine and uninoculated control groups. Histopathology of the bursa from groups infected with GA-1, H-30, CS-2-35, and HPR-2 showed different degrees of follicular depletion and necrosis. A very slight lymphoid depletion was observed in the D78-infected group at 5 days postinoculation, and no microscopic lesions were observed in this group at 8 days postinoculation or at any time in the uninoculated control group. The bursa collected from the field virus and D78-infected birds at necropsy revealed the presence of IBDV via RT-PCR, and the VP-2 hypervariable nucleotide sequences of the GA-1, H-30, CS-2-35, HPR-2, and D78 samples were identical to the original viral isolates and vaccine, respectively.","viral protein;VP2 protein, infectious bursal disease virus;amino acid sequence;animal;animal disease;article;bird disease;chemistry;chicken;egg laying;female;genetics;infectious bursal disease virus;isolation and purification;molecular genetics;phylogeny;United States;virology;virus infection","Sreedevi, B.;LeFever, L. J.;Sommer-Wagner, S. E.;Jackwood, D. J.",2007,,10.1637/7923-020607-regr1.1,0
1970,Phylogenetic analysis of poly and non structural protein in Japanese Encephalitis virus with other related viral families,"BACKGROUND: Japanese encephalitis (JE) causes inflammation of brain. The mortality rate due to JE is 30% while 10 -15 % of patients make full recovery. The disease spreads through infected mosquito bites breeding in rice fields and feeds on pigs, birds, and ducks. PURPOSE: As proteins show important structure to function relationship the study was designed to carry out the identification of poly and non-structural proteins in the infective virus group using different strains of Japanese encephalitis virus i.e. JAOARS982, Nakayama Strain SA (V), Strain SA-14. METHODS: With reference to non structural proteins we obtained protein sequences of the following Japanese encephalitis virus groups: Japanese encephalitis virus, Weatnile virus, Kunjin virus. Further comparative and phylogenetic analysis was performed to explore evolutionary relationship among these groups. RESULTS: Results of phylogeny of alignment score was found to be 375184 using multiple alignment, Jal view, ClustalW (1.83) and ClustalW2. However, the analysis among the non-structural proteins of Japanese Encephalitis Virus, Westnile Virus, and Kunjin Virus revealed the phylogeny alignment score to be 875 through multiple sequence alignment and Tree view respectively. CONCLUSION: Phylogenetic analysis revealed that these four strains are interrelated as well as showing high similarity with the other viruses of this group due to conserved regions among their sequences.",,"Srivastava, P.;Trivedi, A. C.;Tiwari, A.;Verma, A.;Pant, A. B.",2010,Apr,,0
1971,Animal models of Ebolavirus infection,"Ebola virus is a highly pathogenic member of the family Filoviridae that causes a severe hemorrhagic disease in humans and NHP. The 2013-2016 West African outbreak has increased interest in the development and refinement of animal models of Ebola virus disease. These models are used to test countermeasures and vaccines, gain scientific insights into the mechanisms of disease progression and transmission, and study key correlates of immunology. Ebola virus is classified as a BSL4 pathogen and Category A agent, for which the United States government requires preparedness in case of bioterrorism. Rodents, such as Syrian golden hamsters (Mesocricetus auratus), mice (Mus musculus), and Guinea pigs (Cavia porcellus), are the most common research species. However, NHP, especially macaques, are favored for Ebola virus disease research due to similarities with humans regarding the pathogenesis, clinical presentation, laboratory findings, and causes of fatality. To satisfy the regulatory requirements for approval of countermeasures against high-consequence pathogens, the FDA instituted the Animal Rule, which permits efficacy studies in animal models in place of human clinical data when such studies are not feasible or ethical. This review provides a comprehensive summary of various animal models and their use in Ebola virus disease research.",animal model;baboon;Callitrichinae;Chlorocebus aethiops;Ebola hemorrhagic fever;Ebolavirus;experimental infection;experimental model;guinea pig model;hamster model;macaque model;medical research;mouse model;nonhuman;review,"St Claire, M. C.;Ragland, D. R.;Bollinger, L.;Jahrling, P. B.",2017,,,0
1972,Genetic heterogeneity of classical swine fever virus in Central Europe,"The aim of this work was to genetically characterize Central European isolates of classical swine fever virus (CSFV) and to evaluate the applicability of molecular analysis in the epizootiology of CSFV infections. Thirty four viruses, derived from Central European pigs or wild boar, were examined. All of these viruses were detected by each of three sets of oligonucleotide primers which had been designed for the specific RT-PCR amplification of different genomic regions. Comparative sequence analysis of the PCR products showed that they were of a genetic type common in Western Europe. Further discrimination of virus isolates was possible, into subgroups that largely coincided with their regions of origin in Poland, Slovakia, Hungary and Estonia. The discriminatory ability of the technique was improved by the analysis of a composite dataset consisting of all of the sequence data from all of the viruses. Using this approach we were able to distinguish between all of the viruses and to group them in a manner that precisely matched their geographical origins, apart from a single Estonian isolate which grouped with viruses from Eastern Poland.",article;DNA sequence;genetic heterogeneity;nonhuman;Pestivirus;phylogeny;priority journal;reverse transcription polymerase chain reaction;sequence analysis;species difference;swine disease;virus characterization;virus isolation,"Stadejek, T.;Vilček, Š;Lowings, J. P.;Ballagi-Pordány, A.;Paton, D. J.;Belák, S.",1997,,10.1016/s0168-1702(97)00118-4,0
1973,"Comparative sequence analysis of the 5' noncoding region of classical swine fever virus strains from Europe, Asia, and America",Polymerase chain reaction was utilized to determine the sequence of a 280 base pair fragment from cDNAs of the 5' noncoding region of 29 isolates of classical swine fever virus. Phylogenetic analysis of the sequences revealed low level genomic variation that correlated with the geographic origins of the isolates.,virus DNA;animal;article;Asia;cell line;classification;comparative study;Europe;genetics;isolation and purification;molecular genetics;nucleotide sequence;Pestivirus;phylogeny;sequence homology;species difference;pig;Western Hemisphere,"Stadejek, T.;Warg, J.;Ridpath, J. F.",1996,,,0
1974,First detection of porcine circovirus type 3 on commercial pig farms in Poland,"Porcine circovirus type 3 (PCV3) is a novel circovirus species recently discovered in USA and China in cases of porcine dermatitis and nephropathy syndrome, reproductive failure, respiratory disease and multisystemic inflammation. This study reports on the first identification of PCV3 in Europe, in serum from pigs from Polish farms. A total of 1,050 serum samples were collected between 2014 and 2017 from sows and 3–20 weeks old pigs from 14 commercial farms representing different regions of Poland, different size and health status. The samples were pooled by 4–6 and tested with real-time PCR for PCV3. PCV3 DNA was detected in 12 of 14 farms (85.7%). On the PCV3-positive farms, the virus was detected in 5.9% to 65% serum pools. PCV3 was most common among weaned pigs and finishers (26.1% and 28.0% of serum pools, respectively). Sequence analysis of 359 nucleotide fragment of ORF2 showed highest identity of 99.7% to PCV3-US/SD2016 from USA. Our results indicate that PCV3 is a common virus among Polish pigs but no links to unexplained disease conditions were established.",agricultural land;animal experiment;article;China;Circoviridae infection;Circovirus;DNA extraction;high throughput sequencing;nonhuman;Poland;Porcine circovirus 3;real time polymerase chain reaction;sequence analysis;United States;viral skin disease;virus detection,"Stadejek, T.;Woźniak, A.;Miłek, D.;Biernacka, K.",2017,,10.1111/tbed.12672,0
1975,Markers of Venezuelan encephalitis virus which distinguish enzootic strains of subtype I-D from those of I-E,"Strains of Venezuelan encephalitis virus isolated from enzootic habitats during interepizootic periods in Middle America and northern South America can be distinguished from each other antigenically by hemagglutination inhibition. This test has provided the basis for the classification of these virus strains into subtypes I-E and I-D, respectively. Virus strains of these two subtypes have been found to differ profoundly with respect to virulence for English short hair guinea pigs. Studies are described which confirm that virus strains of the I-D subtype are guinea pig virulent, and that virulence is not the result of cocycling subpopulations of epizootic subtype I-AB or I-C virions. Two additional markers were found which distinguish subtype I-D and I-E Venezuelan encephalitis virus strains. Firstly, hydroxylapatite chromatography of intact virions at pH 6.5 showed differential elution of I-D and I-E prototype strains. Virions of subtype I-D strains eluted at 0.08 to 0.11 M phosphate, while those of subtype I-E strains eluted at 0.15 to 0.20 M phosphate. Secondly, the isoelectric points of the E1 envelope glycoproteins of the I-D and I-E prototype strains were significantly different; pH 6.85 to 7.00 and pH 7.25 to 7.30, respectively. There was no significant difference in the isoelectric points of the E2 envelope glycoproteins. These distinguishing characteristics most likely reflect a fundamental difference in virion surface structure.",radioisotope;virus antigen;virus glycoprotein;animal experiment;experimental infection;guinea pig;hemagglutination inhibition;isoelectric focusing;isoelectric point;nonhuman;priority journal;Venezuelan equine encephalitis virus;virulence;virus isolation,"Stanick, D. R.;Wiebe, M. E.;Scherer, W. F.",1985,,,0
1976,Detection and molecular characterization of porcine reproductive and respiratory syndrome virus in Lithuanian wild boar populations,"BACKGROUND: Porcine reproductive and respiratory syndrome virus (PRRSV) is recognized worldwide as an important and economically devastating pathogen in pig production. Although PRRSV is widespread in domestic swine, there is a lack of information regarding PRRSV infection in European wild boars (Sus scrofa). Currently available information does not provide conclusive evidence that wild boars are a reservoir of PRRSV. Nevertheless, wild boars may be likely to become infected by domestic swine through occasional direct or indirect contact. Furthermore, wild boars can act as a reservoir for infectious diseases of domestic pigs. Therefore, the objectives of the present study were to determine the virus prevalence and further explore the epidemiology and diversity of PRRSV strains present in Lithuanian wild boars over a 5-year period. A total of 1597 tissue and serum samples from wild boars inhabiting 44 districts and ten counties in Lithuania were analysed using conventional nested reverse transcription polymerase chain reaction (RT-PCR) and real-time Taqman RT-PCR for the detection of PRRSV-specific open reading frame (ORF) 1 and 6 sequences. RESULTS: PRRSV was highly prevalent in Lithuanian wild boar populations, with an average rate of 18.66 % using conventional RT-PCR and 19.54 % using real-time RT-PCR. PRRSV was detected in 36.71 and 41.77 % of 237 hunting grounds tested by conventional RT-nPCR and real-time RT-PCR, respectively. No statistically significant differences in PRRSV prevalence were observed by geographic area in the ten Lithuanian counties. Animals infected with PRRSV were identified in all age groups; however, significantly higher prevalence rates were identified in subadult and adult wild boars than in juveniles up to 12 months old. No positive results were obtained using conventional PCR with Type 2 specific primers. Phylogenetic analysis of the partial ORF5 region revealed that ten wild boars harboured virus sequences belonging to genetic subtypes 3 and 4 and may therefore pose a serious threat to Lithuanian pig farms in which only subtype two strains are circulating. CONCLUSIONS: The results of virus prevalence and phylogenetic analyses strongly support the role of wild boars as a possible natural reservoir for PRRSV in Lithuania.",animal;classification;genetic variation;genetics;isolation and purification;molecular typing;phylogeny;pig;porcine reproductive and respiratory syndrome;Porcine reproductive and respiratory syndrome virus;prevalence;virology;wild animal,"Stankevicius, A.;Buitkuviene, J.;Sutkiene, V.;Spancerniene, U.;Pampariene, I.;Pautienius, A.;Oberauskas, V.;Zilinskas, H.;Zymantiene, J.",2016,,10.1186/s13028-016-0232-5,0
1977,"Analysis of influenza A viruses of subtype H1 from wild birds, turkeys and pigs in Germany reveals interspecies transmission events","Background Despite considerable host species barriers, interspecies transmissions of influenza A viruses between wild birds, poultry and pigs have been demonstrated repeatedly. In particular, viruses of the subtypes H1 and H3 were transmitted between pigs and poultry, predominantly turkeys, in regions with a high population density of both species. The recovery of a swine influenza H1N1 virus from a turkey flock in Germany in 2009 prompted us to investigate molecularly the subtype H1 viruses recently detected in wild birds, pigs and poultry. Objectives The goal of this study was to investigate the relationship between H1N1 viruses originating from wild and domestic animals of Germany and to identify potential trans-species transmission or reassortment events. Methods Hemagglutinin and neuraminidase gene or full-length genome sequences were generated from selected, current H1N1 viruses from wild birds, pigs and turkeys. Phylogenetic analyses were combined with genotyping and analyses of the deduced amino acid sequences with respect to biologically active sites. Antigenic relationships were assessed by hemagglutination inhibition reactions. Results Phylogenetic analysis of the hemagglutinin sequences showed that viruses from distinct H1 subgroups co-circulate among domestic animals and wild birds. In addition, these viruses comprised different genotypes and were distinguishable antigenically. An H1N1 virus isolated from a turkey farm in northern Germany in 2009 showed the highest similarity with the avian-like porcine H1N1 influenza viruses circulating in Europe since the late 1970s. Conclusions The data demonstrate the genetic and antigenic heterogeneity of H1 viruses currently circulating in domestic and wild animals in Germany and points to turkeys as a possible bridge between avian and mammalian hosts. © 2011 Blackwell Publishing Ltd.",amino acid;hemagglutinin;virus sialidase;amino acid sequence;antigenicity;article;avian influenza virus;cell strain;disease transmission;gene amplification;gene sequence;genetic analysis;genetic heterogeneity;genotype;Germany;Influenza A virus (H1N1);interspecies transmission;nonhuman;nucleotide sequence;phylogeny;priority journal;receptor binding;reverse transcription polymerase chain reaction;sampling;serology;pig;turkey (bird);unindexed sequence;virus detection;virus gene;virus isolation;wild bird,"Starick, E.;Fereidouni, S. R.;Lange, E.;Grund, C.;Vahlenkamp, T.;Beer, M.;Harder, T. C.",2011,,10.1111/j.1750-2659.2011.00201.x,0
1978,Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand,"In recent years, innovations in molecular techniques and sequencing technologies have resulted in a rapid expansion in the number of known viral sequences, in particular those with circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA genomes. CRESS DNA viruses are present in the virome of many ecosystems and are known to infect a wide range of organisms. A large number of the recently identified CRESS DNA viruses cannot be classified into any known viral families, indicating that the current view of CRESS DNA viral sequence space is greatly underestimated. Animal faecal matter has proven to be a particularly useful source for sampling CRESS DNA viruses in an ecosystem, as it is cost-effective and non-invasive. In this study a viral metagenomic approach was used to explore the diversity of CRESS DNA viruses present in the faeces of domesticated and wild animals in New Zealand. Thirty-eight complete CRESS DNA viral genomes and two circular molecules (that may be defective molecules or single components of multicomponent genomes) were identified from forty-nine individual animal faecal samples. Based on shared genome organisations and sequence similarities, eighteen of the isolates were classified as gemycircularviruses and twelve isolates were classified as smacoviruses. The remaining eight isolates lack significant sequence similarity with any members of known CRESS DNA virus groups. This research adds significantly to our knowledge of CRESS DNA viral diversity in New Zealand, emphasising the prevalence of CRESS DNA viruses in nature, and reinforcing the suggestion that a large proportion of CRESS DNA viruses are yet to be identified.",Anas platyrhynchos;article;chicken;circular replication associated protein encoding single stranded DNA virus;controlled study;DNA virus;dog;domestic pig;domestic sheep;fallow deer;feces analysis;gene sequence;Lepus europaeus;llama;New Zealand;nonhuman;priority journal;taurine cattle;Trichosurus vulpecula;virus genome;virus identification;virus isolation;virus replication;wild animal,"Steel, O.;Kraberger, S.;Sikorski, A.;Young, L. M.;Catchpole, R. J.;Stevens, A. J.;Ladley, J. J.;Coray, D. S.;Stainton, D.;Dayaram, A.;Julian, L.;van Bysterveldt, K.;Varsani, A.",2016,,10.1016/j.meegid.2016.05.008,1
1979,"Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections","Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L) and small (S) genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on viral ecology, diversity, and disease potential.","Animals;Animals, Zoo/bl [Blood];Animals, Zoo/me [Metabolism];Animals, Zoo/vi [Virology];Arenaviridae Infections/me [Metabolism];Arenaviridae Infections/pa [Pathology];*Arenaviridae Infections/ve [Veterinary];Arenaviridae Infections/vi [Virology];*Arenavirus/ge [Genetics];Arenavirus/ip [Isolation & Purification];Arenavirus/ph [Physiology];Base Sequence;Boidae/vi [Virology];Cells, Cultured;*Disease Transmission, Infectious/ve [Veterinary];*Gene Rearrangement;Genome, Viral;Liver/me [Metabolism];Liver/pa [Pathology];Liver/vi [Virology];Molecular Sequence Data;Pets/bl [Blood];Pets/me [Metabolism];Pets/vi [Virology];Phylogeny;RNA, Viral/bl [Blood];RNA, Viral/ch [Chemistry];RNA, Viral/me [Metabolism];*Recombination, Genetic;Snakes/bl [Blood];Snakes/me [Metabolism];*Snakes/vi [Virology];United States;Virus Replication;0 (RNA, Viral)","Stenglein, M. D.;Jacobson, E. R.;Chang, L. W.;Sanders, C.;Hawkins, M. G.;Guzman, D. S.;Drazenovich, T.;Dunker, F.;Kamaka, E. K.;Fisher, D.;Reavill, D. R.;Meola, L. F.;Levens, G.;DeRisi, J. L.",2015,May,,0
1980,Isolation and cloning of two variant papillomaviruses from domestic pigs: Sus scrofa papillomaviruses type 1 variants a and b,"The healthy skin of two female domestic pigs (Sus scrofa domestica) was sampled with cotton-tipped swabs. Total genomic DNA was extracted from the samples and subjected to PCR with degenerate papillomavirus (PV)-specific primers. Similarity searches performed with BLASTN showed that partial E1 and L1 sequences of two novel PVs were amplified. Subsequently, the complete genomes of these Sus scrofa papillomaviruses (SsPVs) were amplified by longtemplate PCR, cloned and sequenced using a transposon insertion method. They contained the typical PV open reading frames (ORFs) E1, E2, E4, E6, L1 and L2, but the E7 ORF was absent in both viruses. Pairwise nucleotide sequence alignment of the L1 ORFs of the SsPVs showed 98.5% similarity, classifying these viruses as SsPV type 1 'variants' (SsPV-1a and -1b). Based on a concatenated alignment of the E1, E2, L1 and L2 ORFs of SsPV-1 variants a and b, and 81 other human and animal PV type species, a neighbour-joining phylogenetic tree was constructed. This phylogenetic analysis showed that the SsPV-1a and -1b variants did not cluster with the other PVs of artiodactyls (cloven-hoofed) host species, but clustered on the edge of the genus Alphapapillomavirus, very near to the root of this genus. © 2008 SGM.",genomic DNA;glycoprotein E1;papillomavirus e2 protein;Papillomavirus E4 protein;papillomavirus E6 protein;Papillomavirus L1 protein;Papillomavirus L2 protein;protein E7;unclassified drug;Alphapapillomavirus;amino acid sequence;article;Artiodactyla;controlled study;DNA sequence;gene cluster;gene sequence;genetic transformation;molecular cloning;nonhuman;nucleotide sequence;Papillomaviridae;Papilloma virus type 1a;Papilloma virus type 1b;Papilloma virus type 81;papovavirus;phylogeny;polymerase chain reaction;priority journal;pig;transposon;unindexed sequence;virus isolation,"Stevens, H.;Rector, A.;van der Kroght, K.;van Ranst, M.",2008,,10.1099/vir.0.2008/003186-0,0
1981,Small RNA cloning and sequencing strategy affects host and viral microRNA expression signatures,"The establishment of the microRNA (miRNA) expression signatures is the basic element to investigate the role played by these regulatory molecules in the biology of an organism. Marek's disease virus 1 (MDV-1) is an avian herpesvirus that naturally infects chicken and induces T cells lymphomas. During latency, MDV-1, like other herpesviruses, expresses a limited subset of transcripts. These include three miRNA clusters. Several studies identified the expression of virus and host encoded miRNAs from MDV-1 infected cell cultures and chickens. But a high discrepancy was observed when miRNA cloning frequencies obtained from different cloning and sequencing protocols were compared. Thus, we analyzed the effect of small RNA library preparation and sequencing on the miRNA frequencies obtained from the same RNA samples collected during MDV-1 infection of chicken at different steps of the oncoviral pathogenesis. Qualitative and quantitative variations were found in the data, depending on the strategy used. One of the mature miRNA derived from the latency-associated-transcript (LAT), mdv1-miR-M7-5p, showed the highest variation. Its cloning frequency was 50% of the viral miRNA counts when a small scale sequencing approach was used. Its frequency was 100 times less abundant when determined through the deep sequencing approach. Northern blot analysis showed a better correlation with the miRNA frequencies found by the small scale sequencing approach. By analyzing the cellular miRNA repertoire, we also found a gap between the two sequencing approaches. Collectively, our study indicates that next-generation sequencing data considered alone are limited for assessing the absolute copy number of transcripts. Thus, the quantification of small RNA should be addressed by compiling data obtained by using different techniques such as microarrays, qRT-PCR and NB analysis in support of high throughput sequencing data. These observations should be considered when miRNA variations are studied prior addressing functional studies. © 2014 Elsevier B.V.",microRNA;animal cell;animal experiment;animal model;article;cell isolation;chicken;gene expression;high throughput sequencing;host;in vitro study;in vivo study;Marek disease;molecular cloning;nonhuman;Northern blotting;peripheral lymphocyte;priority journal;qualitative analysis;quantitative analysis;reverse transcription polymerase chain reaction;RNA extraction;RNA sequence;virus expression;virus pathogenesis,"Stik, G.;Muylkens, B.;Coupeau, D.;Laurent, S.;Dambrine, G.;Messmer, M.;Chane-Woon-Ming, B.;Pfeffer, S.;Rasschaert, D.",2014,,10.1016/j.jbiotec.2014.04.005,0
1982,Molecular and biological characteristics of avian polyomaviruses: Isolates from different species of birds indicate that avian polyomaviruses form a distinct subgenus within the polyomavirus genus,"The isolation and characterization of two avian polyomaviruses, from chicken (BFDV-2) and a parrot (BFDV-3), is reported. Both isolates are closely related to the non-mammalian polyomavirus budgerigar fledgling disease virus (BFDV) isolated from budgerigars (now called BFDV-1), and all three viral genomes are shown to have the same basic size of 4981 bp. A 151 bp insertion was, however, observed in the non-coding region of BFDV-2 which represented an exact duplication of the left half of the non-coding region, including the putative early promoter and amino terminus of the large T antigen. With a further 15 base pairs exchanged elsewhere throughout the three genomes, these viruses have distinct degrees of tropism for various avian species. The production of antibodies directed against a β-galactosidase-large T antigen fusion protein of BFDV-1 is described. These antibodies detected the large T antigen, with an M(r) of approximately 80K, and the small t antigen, with an M(r) of approximately 24K, in cells infected with BFDV isolates. Whereas these antibodies bind with low affinity to the large T antigen of simian virus 40 (SV40), SV40- or mouse polyomavirus-specific antibodies will not bind to the BFDV large T antigen. Antibodies directed against BFDV structural polypeptides exhibit broad, reciprocal cross-reactivities with all three structural proteins of mammalian polyomaviruses. The significance of polyomavirus infections in various avian species is discussed. Based on unique structural and biological properties we propose that these viruses should be placed in a distinct subgenus (Avipolyomavirus) within the polyomaviruses.",cross reacting antibody;fusion protein;protein antibody;virus large T antigen;viral protein;amino terminal sequence;animal cell;animal tissue;antibody affinity;article;bird;chicken;embryo;gene insertion;molecular weight;nonhuman;Polyomavirus;priority journal;promoter region;Simian virus 40;virus cell interaction;virus classification;virus gene;virus genome;virus infection;virus infectivity;virus isolation,"Stoll, R.;Luo, D.;Kouwenhoven, B.;Hobom, G.;Muller, H.",1993,,,0
1983,Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association,"Genetic variation in an infectious disease pathogen can be driven by ecological niche dissimilarities arising from different host species and different geographical locations. Whole genome sequencing was used to compare E. coli O157 isolates from host reservoirs (cattle and sheep) from Scotland and to compare genetic variation of isolates (human, animal, environmental/food) obtained from Scotland, New Zealand, Netherlands, Canada and the USA. Nei's genetic distance calculated from core genome single nucleotide polymorphisms (SNPs) demonstrated that the animal isolates were from the same population. Investigation of the Shiga toxin bacteriophage and their insertion sites (SBI typing) revealed that cattle and sheep isolates had statistically indistinguishable rarefaction profiles, diversity and genotypes. In contrast, isolates from different countries exhibited significant differences in Nei's genetic distance and SBI typing. Hence, after successful international transmission, which has occurred on multiple occasions, local genetic variation occurs, resulting in a global patchwork of continental and trans-continental phylogeographic clades. These findings are important for three reasons: first, understanding transmission and evolution of infectious diseases associated with multiple host reservoirs and multi-geographic locations; second, highlighting the relevance of the sheep reservoir when considering farm based interventions; and third, improving our understanding of why human disease incidence varies across the world.",animal;bacteriophage;bovine;Escherichia coli infection;Escherichia coli O157;genetic variation;genetics;genome;high throughput sequencing;host pathogen interaction;human;isolation and purification;microbiology;New Zealand;phylogeography;sheep;single nucleotide polymorphism,"Strachan, N. J.;Rotariu, O.;Lopes, B.;MacRae, M.;Fairley, S.;Laing, C.;Gannon, V.;Allison, L. J.;Hanson, M. F.;Dallman, T.;Ashton, P.;Franz, E.;van Hoek, A. H.;French, N. P.;George, T.;Biggs, P. J.;Forbes, K. J.",2015,,10.1038/srep14145,0
1984,Detection and subtyping of foot-and-mouth disease virus in infected cattle by polymerase chain reaction and amplified VP1 sequencing,Fast and accurate detection of foot-and-mouth disease (FMD) outbreaks is needed to limit spread of the disease by proper vaccination. The use of the polymerase chain reaction (PCR) has revolutionized the way in which viral diseases are diagnosed. Sequence analysis of the amplified VP1 sequence can enable the classification of FMD virus detected in the morbid animal. PCR assays were carried out to identify the virus and its serotype in suspect animals from 2 outbreaks of FMD type O virus. Sequence analysis of the amplified VP1 cDNA showed 78% homology with O1K and over 95% homology between the samples. These findings suggest that the 2 outbreaks were due to infection with the same virus serosubtype.,capsid protein;primer DNA;virus antigen;amino acid sequence;animal;animal disease;Aphthovirus;article;biosynthesis;bovine;chemistry;comparative study;epidemic;foot and mouth disease;genetics;isolation and purification;methodology;molecular genetics;nucleotide sequence;polymerase chain reaction;sequence homology;virus capsid,"Stram, Y.;Molad, T.;Chai, D.;Gelman, B.;Yadin, H.",1995,,,0
1985,Expanding the conversation on high-throughput virome sequencing standards to include consideration of microbial contamination sources,,,"Strong, M. J.;Lin, Z.;Flemington, E. K.",2014,,,0
1986,Increased phylogenetic diversity of bovine viral diarrhoea virus type 1 isolates in England and Wales since 2001,"Currently, there are two recognised genotypes of Bovine viral diarrhoea virus (BVDV), type 1 and type 2. These genotypes are divided into subtypes based on phylogenetic analysis, namely a-p for BVDV-1 and a-c for BVDV-2. Within this study, the genetic heterogeneity of BVDV-1 in England and Wales was investigated and compared to the situation in 1996/1997. Viral RNA was extracted from 316 blood samples collected between 2004 and 2009 that were previously identified as BVDV-1 positive. A region of the 5' untranslated region (UTR) was amplified by RT-PCR and the PCR products were sequenced. Phylogenetic analysis of the 5'UTR demonstrated the existence of five subtypes of BVDV-1 circulating in England and Wales, namely BVDV-1a (244 samples), BVDV-1b (50), BVDV-1e (3), BVDV-1f (1) and BVDV-1i (18). Phylogenetic analysis of the nucleotide sequence for the Npro region of the viral genome supported the classification obtained with the 5'UTR. Given the fact that only three subtypes were detected in 1999 this report supports the notion that the restocking of cattle from continental Europe, after the mass culling during the Foot-and-Mouth outbreak in 2001 and slaughter of cattle due to bovine tuberculosis infection, has increased the genetic diversity of BVDV-1 subtypes in England and Wales in the past 10years. © 2012 Elsevier B.V.",virus RNA;5' untranslated region;article;blood sampling;Bovine viral diarrhea virus 1;gene amplification;genetic variability;nonhuman;nucleotide sequence;Pestivirus;phylogeny;reverse transcription polymerase chain reaction;RNA extraction;sequence analysis;unindexed sequence;United Kingdom;virus classification;virus detection;virus isolation;SERELISA,"Strong, R.;Errington, J.;Cook, R.;Ross-Smith, N.;Wakeley, P.;Steinbach, F.",2013,,10.1016/j.vetmic.2012.09.006,0
1987,Infectious Pustular Vulvovaginitis Virus Infection of Bulls,,"Animals;*Biopsy;Cattle;*Cattle Diseases;*Classification;Female;*Herpesvirus 1, Bovine;Male;*Pathology;*Research;*Serologic Tests;*Terminology as Topic;*Vertebrates;*Virus Diseases;*Viruses","Studdert, M. J.;Barker, C. A.;Savan, M.",1964,Mar,,0
1988,A novel psittacid herpesvirus found in African grey parrots (Psittacus erithacus erithacus),"DNA from a novel alphaherpesvirus was amplified from a cloacal papilloma, a cutaneous papilloma, and the normal cloacal mucosa of African grey parrots (Psittacus erithacus erithacus). Phylogenetically, the virus was most closely related to the psittacid herpesvirus, but demonstrated sufficient nucleotide and amino acid diversity to be considered a new alphaherpesvirus. It is proposed that the previously described psittacid herpesvirus be designated as psittacid herpesvirus 1 (PsHV-1), and this new species be classified as psittacid herpesvirus 2 (PsHV-2). It is speculated that PsHV-2 co-evolved with the African grey parrot and should therefore be present in these birds in the wild. © 2005 Houghton Trust Ltd.",virus DNA;animal;animal disease;article;bird disease;cloaca;genetics;Herpesviridae;isolation and purification;papilloma;parrot;phylogeny;virology,"Styles, D. K.;Tomaszewski, E. K.;Phalen, D. N.",2005,,10.1080/03079450500059032,0
1989,"Phylogenetic analysis of gansu sheeppox virus isolates based on P32, GPCR, and RPO30 genes","Two outbreaks of sheeppox in sheep have occurred in Gansu Province, China. The P32, GPCR, and RPO30 genes were used as markers for differential diagnosis. We confirmed that the outbreaks were caused by sheeppox virus. Sequence and phylogenetic analysis of the P32, GPCR, and RPO30 genes revealed a close relationship between the 2 isolates and Chinese sheeppox viruses. Because ill sheep were imported from Jingyuan, another county of Gansu Province, our results strongly suggest the importance of veterinary surveillance prior to transportation.",animal cell;animal tissue;article;Capripoxvirus;China;gene amplification;gene sequence;genetic analysis;GPCR gene;inoculation;marker gene;muscle;nonhuman;P32 gene;phylogeny;RP030 gene;sheep;strain identification;tail;udder;virus gene;virus identification;virus isolation,"Su, H. L.;Jia, H. J.;Yin, C.;Jing, Z. Z.;Luo, X. N.;Chen, Y. X.",2015,,10.4238/2015.March.13.17,0
1990,Hepatic rupture hemorrhage syndrome in chickens caused by a novel genotype avian hepatitis E virus,"Since 2016, severe outbreaks of hepatic rupture hemorrhage syndrome (HRHS) have emerged in chickens in several Chinese provinces and caused huge economic losses to the poultry industry, but the etiological characteristics and pathogenic potential of it has remained unclear. This study sequenced the partial helicase and capsid gene of the potentially novel avian hepatitis E virus (HEV) isolated from chickens with HRHS and tested the pathogenicity of it on SPF chicks, while the appearance of clinical signs, histopathological changes, viral distribution, viremia and viral shedding were monitored for 14 days post-infection (dpi). Analysis revealed that the HRHS related avian HEV belongs to a novel genotype, and infected chicks developed the typical symptoms of HRHS. Thus, this study successfully developed an experimental infection model for studying the pathogenicity and role of the novel avian HEV in HRHS. Meanwhile, the novel avian HEV mainly existed in the liver and spleen, inducing a rapid viremia and chronic viral shedding in infected chicks, and could cause 40% mortality before 14 dpi. In conclusion, this study found the novel genotype avian HEV and confirmed its role in HRHS.","Animals;Antibodies, Viral/bl [Blood];Chickens/vi [Virology];China/ep [Epidemiology];Disease Models, Animal;Genes, Viral/ge [Genetics];*Genotype;Hemorrhage;Hepatitis E/bl [Blood];*Hepatitis E/ve [Veterinary];Hepatitis E/vi [Virology];Hepatitis, Viral, Animal/bl [Blood];Hepatitis, Viral, Animal/ep [Epidemiology];*Hepatitis, Viral, Animal/vi [Virology];*Hepevirus/ge [Genetics];Hepevirus/py [Pathogenicity];High-Throughput Nucleotide Sequencing;*Liver/pa [Pathology];Liver/vi [Virology];*Liver Diseases/ve [Veterinary];Liver Diseases/vi [Virology];Poultry Diseases/vi [Virology];Rupture, Spontaneous/ve [Veterinary];Rupture, Spontaneous/vi [Virology];Viremia/pa [Pathology];Virus Shedding;0 (Antibodies, Viral)","Su, Q.;Li, Y.;Meng, F.;Cui, Z.;Chang, S.;Zhao, P.",2018,Aug,,0
1991,Characterization of H7N2 Avian Influenza Virus in Wild Birds and Pikas in Qinghai-Tibet Plateau Area,"Qinghai Lake is a major migrating bird breeding site that has experienced several recent highly pathogenic avian influenza virus (HPAIV) epizootics. From 2006 to 2009 we studied Qinghai's wild birds and pikas for evidence of AIV infections. We sampled 941 healthy wild animals and isolated seventeen H7N2 viruses (eight from pikas and nine from wild birds). The H7N2 viruses were phylogenetically closely related to each other and to viruses isolated in Hong Kong in the 1970s. We determined the pathogenicity of the H7N2 viruses by infecting chickens and mice. Our results suggest that pikas might play an important role in the ecology of AIVs, acting as intermediate hosts in which viruses become more adapted to mammals. Our findings of AI infection in pikas are consistent with previous observations and raise the possibility that pikas might play a previously unrecognized role in the ecology of AIVs peridomestic aquatic environments.",animal;avian influenza;bird;Hong Kong;Influenza A virus (H7N2);lagomorph;lake;pathogenicity;phylogeny;virology;wild animal,"Su, S.;Xing, G.;Wang, J.;Li, Z.;Gu, J.;Yan, L.;Lei, J.;Ji, S.;Hu, B.;Gray, G. C.;Yan, Y.;Zhou, J.",2016,,10.1038/srep30974,0
1992,Overexpression of the Rybp Gene Inhibits Differentiation of Bovine Myoblasts into Myotubes,"RING1 and YY1 binding protein (Rybp) genes inhibit myogenesis in mice, but there are no reports on the effects of these genes in cattle. The aim of this study is to investigate the roles of the Rybp gene on bovine skeletal muscle development and myoblast differentiation. In the present study, the Rybp gene was overexpressed in bovine myoblasts via adenovirus. RNA-seq was performed to screen differentially expressed genes (DEGs). The results showed that overexpressing the Rybp gene inhibits the formation of myotubes. The morphological differences in myoblasts began on the second day and were very significant 6 days after adenovirus induction. A total of 1311 (707 upregulated and 604 downregulated) DEGs were screened using RNA-seq between myoblasts with added negative control adenoviruses (AD-NC) and Rybp adenoviruses (AD-Rybp) after 6 days of induction. Gene ontology (GO) and KEGG analysis revealed that the downregulated DEGs were mainly involved in biological functions related to muscle, and, of the 32 pathways, those associated with muscle development were significantly enriched for the identified DEGs. This study can not only provide a theoretical basis for the regulation of skeletal muscle development in cattle by exploring the roles of the Rybp gene in myoblast differentiation, but it can also lay a theoretical foundation for molecular breeding of beef cattle.","Adenoviridae/me [Metabolism];Animals;Cattle;*Cell Differentiation/ge [Genetics];Cell Shape;Cluster Analysis;Gene Expression Profiling;Gene Ontology;High-Throughput Nucleotide Sequencing;*Intracellular Signaling Peptides and Proteins/ge [Genetics];Intracellular Signaling Peptides and Proteins/me [Metabolism];*Muscle Fibers, Skeletal/cy [Cytology];Muscle Fibers, Skeletal/me [Metabolism];*Myoblasts/cy [Cytology];Myoblasts/me [Metabolism];Recombination, Genetic/ge [Genetics];Reproducibility of Results;0 (Intracellular Signaling Peptides and Proteins)","Su, X.;Zhao, Y.;Wang, Y.;Zhang, L.;Zan, L.;Wang, H.",2018,Jul 18,,0
1993,Isolation and genetic characterization of a novel adeno-associated virus from Muscovy ducks in China,"Adeno-associated virus (AAV; genus Dependoparvovirus, family Parvoviridae) was first discovered in 1965 as a contaminant in adenovirus preparations. The AAVs are generally considered non-pathogenic, and they have the ability to attenuate the replication of other more pathogenic viruses, which makes them attractive as potential therapeutics or preventative measures. This study characterized a novel AAV isolated from Muscovy ducks in China. The novel virus (MHH-05-2015) was isolated after propagating a field isolate of the DAdV-3 virus (a type 3 duck adenovirus) in duck embryo fibroblasts. The full genome sequence of MHH-05-2015 was determined, and the nucleotide and amino acid sequences were compared to other avian AAVs. The genomic distribution of the structural and non-structural protein-coding genes in MHH-05-2015 was conserved and consistent with the other AAVs. Compared to previously isolated avian AAVs, MHH-05-2015 had approximately 63 to 64% sequence identity. Phylogenetic analysis indicated that MHH-05-2015 clustered separately from other avian AAVs, suggesting that MHH-05-2015 was not directly descended from other Dependoparvovirus family members. These results suggest that MHH-05-2015 is a new subtype of AAV that is distinct from other avian AAVs.",animal;bird disease;China;classification;Dependoparvovirus;DNA sequence;duck;genetics;isolation and purification;parvovirus infection;phylogeny;sequence analysis;veterinary medicine;virology,"Su, X. N.;Liu, J. J.;Zhou, Q. F.;Zhang, X. H.;Zhao, L. C.;Xie, Q. M.;Chen, W. G.;Chen, F.",2017,,10.3382/ps/pex235,0
1994,Companion animals symposium: microbes and gastrointestinal health of dogs and cats Review,"Recent molecular studies have revealed complex bacterial, fungal, archaeal, and viral communities in the gastrointestinal tract of dogs and cats. More than 10 bacterial phyla have been identified, with Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, and Actinobacteria constituting more than 99% of all gut microbiota. Microbes act as a defending barrier against invading pathogens, aid in digestion, provide nutritional support for enterocytes, and play a crucial role in the development of the immune system. Of significance for gastrointestinal health is their ability to ferment dietary substrates into short-chain fatty acids, predominantly to acetate, propionate, and butyrate. However, microbes can have also a detrimental effect on host health. Specific pathogens (e.g., Salmonella, Campylobacter jejuni, and enterotoxigenic Clostridium perfringens) have been implicated in acute and chronic gastrointestinal disease. Compositional changes in the small intestinal microbiota, potentially leading to changes in intestinal permeability and digestive function, have been suggested in canine small intestinal dysbiosis or antibiotic-responsive diarrhea. There is mounting evidence that microbes play an important role in the pathogenesis of canine and feline inflammatory bowel disease (IBD). Current theories for the development of IBD favor a combination of environmental factors, the intestinal microbiota, and a genetic susceptibility of the host. Recent studies have revealed a genetic susceptibility for defective bacterial clearance in Boxer dogs with granulomatous colitis. Differential expression of pathogen recognition receptors (i.e., Toll-like receptors) were identified in dogs with chronic enteropathies. Similarly to humans, a microbial dysbiosis has been identified in feline and canine IBD. Commonly observed microbial changes are increased Proteobacteria (i.e., Escherichia coli) with concurrent decreases in Firmicutes, especially a reduced diversity in Clostridium clusters XIVa and IV (i.e., Lachnospiraceae, Ruminococcaceae, Faecalibacterium spp.). This would indicate that these bacterial groups, important short-chain fatty acid producers, may play an important role in promoting intestinal health.",Animals;Cat Diseases/mi [Microbiology];*Cats/mi [Microbiology];Dog Diseases/mi [Microbiology];*Dogs/mi [Microbiology];Gastrointestinal Diseases/mi [Microbiology];Gastrointestinal Diseases/ve [Veterinary];*Gastrointestinal Tract/mi [Microbiology];*Metagenome/ph [Physiology];*Pets/mi [Microbiology],"Suchodolski, J. S.",2011,May,,0
1995,Viruses detected in the caecum contents of healthy pigs representing a new genetic cluster in genogroup II of the genus 'Norwalk-like viruses',"Viruses of the genus 'Norwalk-like viruses' (NLVs) detected in humans have been genetically classified into two major genetic groups, genogroups I and II (GI and GII), which together are made up of at least 14 genetic subgroups. However, a comparable classification of NLVs in other species remains to be carried out. We sequenced a 2-kb region from within the RNA polymerase gene to the 3′ end of open reading frame 2 (ORF2) of two NLV strains previously detected in the caecum contents of healthy pigs. The sequences of the entire ORF2 of these two NLV strains were analyzed for their genetic relationships to 15 human strains, which have already been reported and used as references for the genetic classification of human NLV strains, and additional two strains; one, a human strain which has recently been reported and appears to represent a new genetic subgroup of GII; and the other, an animal NLV strain. Analysis of a matrix showing pairwise identities and topology of a neighbor-joining tree showed that the two swine strains could be classified into a new genetic subgroup of GII on the basis of the amino acid sequences of the entire capsid protein. Grouping of the two swine strains was well corroborated by results of similar analyses of nucleotide sequences of the entire ORF2 and of a 510 base region at the 3′ end of ORF1. © 2002 Elsevier Science B.V. All rights reserved.",capsid protein;RNA polymerase;amino acid sequence;article;cecum;gene cluster;gene sequence;genotype;human;neighbor joining method;nonhuman;Norwalk virus;nucleotide sequence;open reading frame;priority journal;promoter region;pig;viral genetics;virus classification;virus detection;virus identification;virus strain,"Sugieda, M.;Nakajima, S.",2002,,10.1016/s0168-1702(02)00107-7,0
1996,Differentiation of respiratory syncytial virus subgroups with cDNA probes in a nucleic acid hybridization assay,"A new approach to respiratory syncytial (RS) virus subgroup determination was developed by using a simple nucleic acid filter hybridization technique. By this method, virus-infected cells are bound and fixed in a single step, and the viral RNA in the fixed-cell preparation is characterized directly by its ability to hybridize to cDNA probes specific for either the A or B subgroups of RS virus. The subgroup-specific probes were constructed from cDNA clones that corresponded to a portion of the extracellular domain of the RS virus G protein of either a subgroup B RS virus (8/60) or a subgroup A RS virus (A2). The cDNA probes were labeled with 32P and used to analyze RS virus isolates collected over a period of three decades. Replicate templates of infected cell preparations were hybridized with either the subgroup A or B probe. The subgroup assignments of 40 viruses tested by nucleic acid hybridization were in agreement with the results of subgroup determinations based on their reactivities with monoclonal antibodies, which previously has been the only method available for determining the subgroup classification of RS virus isolates. The nucleic acid hybridization assay has the advantage of providing broad-based discrimination of the two subgroups on the basis of nucleic acid homology, irrespective of minor antigenic differences that are detected in assays in which monoclonal antibodies are used. The nucleic acid hybridization technique provides a reliable method for RS virus subgroup characterization.",radioisotope;animal cell;article;bovine;cell culture;diagnosis;DNA hybridization;DNA probe;human;human cell;nonhuman;normal human;priority journal;Human respiratory syncytial virus,"Sullender, W. M.;Anderson, L. J.;Anderson, K.;Wertz, G. W.",1990,,,0
1997,Evaluation of an epitope-blocking enzyme-linked immunosorbent assay for the detection of antibodies to influenza A virus in domestic and wild avian and mammalian species,"An epitope-blocking enzyme-linked immunosorbent assay (bELISA) was developed for the detection of antibodies to influenza A virus in taxonomically diverse domestic and wild vertebrate species. In contrast to the bELISAs published previously that require reagent production, manipulation by the end-user, or have not been evaluated for use with both mammalian and avian species, this assay is performed using commercially available recombinant nucleoprotein antigen and corresponding nucleoprotein-specific monoclonal antibody and has been shown to work with multiple avian and mammalian species. The efficacy of the bELISA as a serum screening assay was compared to the agar gel immunodiffusion (AGID) assay using 251 serum samples obtained from experimentally infected mallards (Anas platyrhynchos) and raccoons (Procyon lotor). The concordance between the AGID assay and bELISA was 94.1% (95% CI=89.9, 98.3) for raccoons, and 71.2% (95% CI=63.5, 78.9) for mallards and 82.8% (95% CI=78.2, 87.3) overall. The bELISA was more sensitive than the AGID assay as demonstrated by the detection of antibodies to influenza A virus at earlier time points in experimental infection studies and at higher serial dilutions. The efficacy of the bELISA to monitor natural influenza A virus exposure was also compared to the AGID assay using an additional 745 serum samples from six avian species and six mammalian species. This bELISA provides a rapid, reliable, and inexpensive technique for large-scale surveillance of influenza A virus exposure in taxonomically diverse vertebrate species.","Animals;*Antibodies, Viral/bl [Blood];Birds;*Enzyme-Linked Immunosorbent Assay/mt [Methods];*Influenza A virus/im [Immunology];*Influenza in Birds/im [Immunology];Mammals;*Orthomyxoviridae Infections/im [Immunology];Sensitivity and Specificity;0 (Antibodies, Viral)","Sullivan, H. J.;Blitvich, B. J.;VanDalen, K.;Bentler, K. T.;Franklin, A. B.;Root, J. J.",2009,Oct,,0
1998,Viral metagenomics analysis of picobirnavirus-positive feces from children with sporadic diarrhea in China,"Picobirnaviruses (PBVs) infect humans and a wide range of animals and may cause diarrhea. The aim of this study was to investigate PBV infection and its association with diarrhea. Here, seven PBV RT-PCR-positive fecal samples from diarrheic children and four fecal samples from healthy children as controls were analyzed by viral metagenomics. The results indicated that all the seven diarrheic fecal samples contain high titers of PBV sequences, while three of the controls were negative, and one had low titers of PBV. Three of the diarrheic fecal samples were also positive for other viruses, including anellovirus, human gyrovirus, human parechovirus, and porcine stool-associated circular virus. PBV sequences from the seven patients were assembled, generating seven large contigs with the complete ORF of RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis of the amino acid sequences of RdRp indicated that the seven PBVs in the present study belonged to three different genogroups. Our data suggest that PBV might have been the cause of diarrhea in these seven children.",child;China;diarrhea;feces;human;isolation and purification;metagenomics;phylogeny;Picobirnavirus;preschool child;RNA virus infection;virology;virus genome,"Sun, G.;Zang, Q.;Gu, Y.;Niu, G.;Ding, C.;Zhang, P.",2016,,10.1007/s00705-015-2726-2,0
1999,Epidemiological and genetic characteristics of swine pseudorabies virus in mainland China between 2012 and 2017,"The outbreak of pseudorabies (PR) in many Bartha-K61 vaccinated farms in China in late 2011 has seriously damaged the pig industry of one of the largest producers of pork products in the world. To understand the epidemiological characteristics of the pseudorabies virus (PRV) strains currently prevalent in China, a total of 16,256 samples collected from pig farms suspected of PRV infection in 27 Provinces of China between 2012 and 2017 were evaluated for detection of PRV. Since the extensive use of gE-deleted PRV vaccine in China, the PRV-gE was applied for determining wild-type virus infection by PCR. Of the 16,256 samples detected, approximately 1,345 samples were positive for the detection of PRV-gE, yielding an average positive rate of 8.27%. The positive rates of PRV detection from 2012 to 2017 were 11.92% (153/1284), 12.19% (225/1846), 6.70% (169/2523), 11.10% (269/2424), 5.57% (147/2640), and 6.90% (382/5539), respectively. To understand the genetic characteristics of the PRV strains currently circulating, 25 PRV strains isolated from those PRV-gE positive samples were selected for further investigation. Phylogenetic analysis based on gB, gC, and gE showed that PRV strains prevalent in China had a remarkably distinct evolutionary relationship with PRVs from other countries, which might explain the observation that Bartha-K61 vaccine was unable to provide full protection against emergent strains. Sequence alignments identified many amino acid changes within the gB, gC, and gE proteins of the PRVs circulating in China after the outbreak compared to those from other countries or those prevalent in China before the outbreak; those changes also might affect the protective efficacy of previously used vaccines in China, as well as being associated in part with the increased virulence of the current PRV epidemic strains in China.",glycoprotein B;glycoprotein E;protein C;agar gel electrophoresis;animal experiment;animal tissue;article;China;comparative study;genetic analysis;genetic trait;nonhuman;pathogenicity;phylogeny;pig;polymerase chain reaction;prevalence;pseudorabies;Pseudorabies virus;sequence alignment;virulence;virus detection;virus isolation;virus load;virus mutation,"Sun, Y.;Liang, W.;Liu, Q.;Zhao, T.;Zhu, H.;Hua, L.;Peng, Z.;Tang, X.;Stratton, C. W.;Zhou, D.;Tian, Y.;Chen, H.;Wu, B.",2018,,10.7717/peerj.5785,0
2000,"Novel triple-reassortant H1N1 swine influenza viruses in pigs in Tianjin, Northern China","Pigs are susceptible to both human and avian influenza viruses and therefore have been proposed to be mixing vessels for the generation of pandemic influenza viruses through reassortment. In this study, for the first time, we report the isolation and genetic analyses of three novel triple-reassortant H1N1 swine influenza viruses from pigs in Tianjin, Northern China. Phylogenetic analysis showed that these novel viruses contained genes from the 2009 pandemic H1N1 (PB2, PB1, PA and NP), Eurasian swine (HA, NA and M) and triple-reassortant swine (NS) lineages. This indicated that the reassortment among the 2009 pandemic H1N1, Eurasian swine and triple-reassortant swine influenza viruses had taken place in pigs in Tianjin and resulted in the generation of new viruses. Furthermore, three human-like H1N1, two classical swine H1N1 and two Eurasian swine H1N1 viruses were also isolated during the swine influenza virus surveillance from 2009 to 2013, which indicated that multiple genetic lineages of swine H1N1 viruses were co-circulating in the swine population in Tianjin, China. The emergence of novel triple-reassortant H1N1 swine influenza viruses may be a potential threat to human health and emphasizes the importance of further continuous surveillance.",article;China;gene;genetic analysis;genetic reassortment;Influenza A virus (H1N1);nonhuman;phylogeny;pig;swine influenza virus;triple reassortant H1N1 swine influenza virus,"Sun, Y. F.;Wang, X. H.;Li, X. L.;Zhang, L.;Li, H. H.;Lu, C.;Yang, C. L.;Feng, J.;Han, W.;Ren, W. K.;Tian, X. X.;Tong, G. Z.;Wen, F.;Li, Z. J.;Gong, X. Q.;Liu, X. M.;Ruan, B. Y.;Yan, M. H.;Yu, H.",2016,,10.1016/j.vetmic.2015.12.006,0
2001,Separate evolution of virulent Newcastle disease viruses from Mexico and Central America,"An outbreak of Newcastle disease (ND) in poultry was reported in Belize in 2008. The characteristics of three virulent Newcastle disease virus (NDV) isolates from this outbreak (NDV-Belize-3/08, NDV-Belize-4/08, and NDV-Belize-12/08) were assessed by genomic analysis and by clinicopathological characterization in specific-pathogen-free (SPF) chickens. The results showed that all three strains belong to NDV genotype V and are virulent, as assessed by the intracerebral pathogenicity index and the polybasic amino acid sequence at the fusion protein cleavage site. In 4-week-old SPF chickens, NDV-Belize-3/08 behaved as a typical velogenic viscerotropic NDV strain, causing severe necrohemorrhagic lesions in the lymphoid organs, with systemic virus distribution. Phylogenetic analysis of multiple NDV genotype V representatives revealed that genotype V can be divided into three subgenotypes, namely, Va, Vb, and Vc, and that all tested Belizean isolates belong to subgenotype Vb. Furthermore, these isolates are nearly identical to a 2007 isolate from Honduras and appear to have evolved separately from other contemporary viruses circulating in Mexico, clustering into a new clade within NDV subgenotype Vb. Copyright © 2014, American Society for Microbiology. All Rights Reserved.",3' untranslated region;amino acid sequence;article;Central America;chicken;DNA base composition;epidemic;evolutionary rate;genotype;Mexico;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;priority journal;protein cleavage;RNA isolation;RNA sequence;sequence alignment;virus isolation;virus strain;virus virulence,"Susta, L.;Hamal, K. R.;Miller, P. J.;Cardenas-Garcia, S.;Brown, C. C.;Pedersen, J. C.;Gongora, V.;Afonso, C. L.",2014,,10.1128/jcm.00066-14,0
2002,Swine as the possible source of hepatitis E virus transmission to humans in Thailand,"This report describes a study that provides evidence of HEV transmission from pigs to humans in Thailand by applying molecular genetics analysis. It was found that viruses recovered from Thai patients are closely related to genotype 3 and swine hepatitis E virus in Thailand. Based on analysis of a 302-base-pair ORF2 fragment, the strains investigated belong to subgroup 3e and are closely related to European strains. Based on the results obtained, swine are suspected to be a source of HEV transmission to humans in Thailand. © 2010 Springer-Verlag.","ORF2 protein, Hepatitis E virus;viral protein;virus RNA;animal;animal disease;article;classification;cluster analysis;disease transmission;DNA sequence;genetics;genotype;hepatitis E;Hepatitis E virus;human;isolation and purification;molecular genetics;nucleotide sequence;phylogeny;sequence homology;pig;swine disease;Thailand;virology;zoonosis","Suwannakarn, K.;Tongmee, C.;Theamboonlers, A.;Komolmit, P.;Poovorawan, Y.",2010,,10.1007/s00705-010-0751-8,0
2003,Potency of an inactivated influenza vaccine prepared from A/duck/Mongolia/245/2015 (H10N3) against H10 influenza virus infection in a mouse model,"The H10N8 influenza virus became a threat to public health when cases of fatal infections were identified in China in 2013 and 2014. Thus, genetic and antigenic characterization of H10 influenza viruses and development of an appropriate vaccine are essential to prepare for a future pandemic by H10 influenza viruses. However, current information regarding these properties of H10 influenza viruses circulating in birds is limited. In this study, genetic analysis of H10 influenza viruses revealed that the viruses recently circulating in wild birds in East Asia are genetically close to human H10N8 influenza viruses. Furthermore, the antigenicity of H10 influenza viruses was stable among the viruses circulating in birds. An inactivated vaccine was prepared from A/duck/Mongolia/245/2015 (H10N3), which is genetically and antigenically close to the human H10 influenza viruses. The vaccine induced sufficient neutralizing antibodies against homologous and heterologous viruses in mice. The inactivated vaccine induced protective immunity sufficient to reduce the impact of challenges with A/duck/Hokkaido/W87/2007 (H10N2), which is pathogenic strain in mice. This study demonstrates that the inactivated whole virus particle vaccine prepared from viruses isolated from wild birds would be useful against a future pandemic influenza by H10 influenza viruses.",inactivated vaccine;influenza vaccine;neutralizing antibody;animal experiment;animal model;article;bioinformatics;body weight loss;chicken;drug potency;embryo;genetic analysis;hemagglutination inhibition test;ID50 (median infectious dose);immunization;influenza;Influenza A virus (A/duck/Mongolia/245/2015(H10N3));Influenza A virus (A/duck/Mongolia/66/2015 (H10N2));Influenza A virus (A/duck/Mongolia/709/2015 (H10N7));Influenza A virus (A/duck/Mongolia/97/2014 (H10N4));Influenza A virus (A/duck/Mongolia/97/2014 (H10N6));Influenza A virus (H10N8);Influenza A virus;Influenza A/chicken/Germany/N/1949 (H10N7);Influenza A/duck/Alaska/658/1991 (H10N7);Influenza A/duck/Hokkaido/18/2000 (H10N4);Influenza A/duck/Hokkaido/W87/2007 (H10N2);Influenza A/duck/Hong Kong/786/1979 (H10N3);Influenza A/duck/Mongolia/245/2015 (H10N3);Influenza A/duck/Mongolia/97/2014 (H10N6);Influenza A/duck/Shimane/45/1997 (H10N7);Influenza A/duck/Vietnam/OIE-0483/2012 (H10N7);mouse;nonhuman;phylogeny;serodiagnosis;virus infectivity;virus titration,"Suzuki, M.;Okamatsu, M.;Fujimoto, Y.;Hiono, T.;Matsuno, K.;Kida, H.;Sakoda, Y.",2018,,10.14943/jjvr.66.1.29,0
2004,Double stranded RNA of Ibaraki virus,"Ibaraki virus was isolated by Omori et al. (1969a,b) from diseased cattle exhibiting clinical symptoms of paralysis of the upper region of the digestive organs. This virus is an RNA virus and resembles bluetongue virus in biological (Omori et al., 1969a,b; Matsumoto et al., 1970) and physicochemical (Inaba et al., 1970) properties. The diameter of the virion is 55 nm, and the capsid consists of 32 capsomers (Saito et al., 1972; Ito et al., 1973). There is no evidence for serological cross-reaction between Ibaraki virus and bluetongue virus (Inaba et al., 1970). It is not known whether Ibaraki virus RNA is single- stranded or double-stranded; hence, the classification of Ibaraki virus is uncertain. The present paper presents evidence that this virus contains double-stranded RNA. It should therefore be classified in the same group as bluetongue virus, that is, as an orbivirus.",virus RNA;ibaraki virus;in vitro study;microorganism;Orbivirus;theoretical study;virus classification,"Suzuki, Y.;Saito, Y.;Nakagawa, S.",1977,,,0
2005,"Past, present and future of hepatitis E virus infection: Zoonotic perspectives","The origin of hepatitis E virus (HEV) is not fully understood, but it is considered an emerging zoonotic pathogen. To date, HEV has been isolated from many animal species. The family Hepeviridae consists of two genera. The genus Orthohepevirus includes four distinct species (A, B, C, and D), each with distinct genotypes. Within the Orthohepevirus A species, HEV-1 and HEV-2 host ranges are restricted to humans, whereas genotypes 3 and 4 primarily infect a wide range of diverse animal species, in addition to being zoonotic to humans. Swine and wild boar species were previously thought to be the primary natural HEV reservoir, but recently rabbits have also been identified as major carriers. Moreover, increasing the number of HEV infections within the food supply chain underscore the important role of farming and food processing practices in limiting virus transmission. Notably, a Chinese commercial vaccine has the potential to protect humans and possibly animal reservoirs from HEV infection. This review summarizes the status of HEV infection worldwide in different animal species and outlines various modes of zoonotic transmission, with reference to cross-species transmission and recent vaccine developments.",hepatitis E vaccine;deer;drug effect;enzyme linked immunosorbent assay;European wild boar;farming system;food processing;hepatitis E;Hepatitis E virus;Hepatitis E virus genotype 1;Hepatitis E virus genotype 2;Hepatitis E virus genotype 3;Hepatitis E virus genotype 4;host range;human;infection prevention;nonhuman;priority journal;review;vaccination;virus carrier;virus classification;virus isolation;virus strain;virus transmission;zoonosis,"Syed, S. F.;Zhao, Q.;Umer, M.;Alagawany, M.;Ujjan, I. A.;Soomro, F.;Bangulzai, N.;Baloch, A. H.;Abd El-Hack, M.;Zhou, E. M.;Arain, M. A.",2018,,10.1016/j.micpath.2018.03.051,0
2006,Studies on Swine Enteroviruses. Ii. Morphology of the Cytopathic Changes Produced in Swine-Kidney Monolayers,,"Animals;*Classification;*Enterovirus;*Enteroviruses, Porcine;*Kidney;*Research Design;Swine;*Tissue Culture Techniques;*Virus Cultivation","Szent Ivanyi, T.",1963,,,0
2007,A wide extent of inter-strain diversity in virulent and vaccine strains of Alphaherpesviruses,"Alphaherpesviruses are widespread in the human population, and include herpes simplex virus 1 (HSV-1) and 2, and varicella zoster virus (VZV). These viral pathogens cause epithelial lesions, and then infect the nervous system to cause lifelong latency, reactivation, and spread. A related veterinary herpesvirus, pseudorabies (PRV), causes similar disease in livestock that result in significant economic losses. Vaccines developed for VZV and PRV serve as useful models for the development of an HSV-1 vaccine. We present full genome sequence comparisons of the PRV vaccine strain Bartha, and two virulent PRV isolates, Kaplan and Becker. These genome sequences were determined by high-throughput sequencing and assembly, and present new insights into the attenuation of a mammalian alphaherpesvirus vaccine strain. We find many previously unknown coding differences between PRV Bartha and the virulent strains, including changes to the fusion proteins gH and gB, and over forty other viral proteins. Inter-strain variation in PRV protein sequences is much closer to levels previously observed for HSV-1 than for the highly stable VZV proteome. Almost 20% of the PRV genome contains tandem short sequence repeats (SSRs), a class of nucleic acids motifs whose length-variation has been associated with changes in DNA binding site efficiency, transcriptional regulation, and protein interactions. We find SSRs throughout the herpesvirus family, and provide the first global characterization of SSRs in viruses, both within and between strains. We find SSR length variation between different isolates of PRV and HSV-1, which may provide a new mechanism for phenotypic variation between strains. Finally, we detected a small number of polymorphic bases within each plaque-purified PRV strain, and we characterize the effect of passage and plaque-purification on these polymorphisms. These data add to growing evidence that even plaque-purified stocks of stable DNA viruses exhibit limited sequence heterogeneity, which likely seeds future strain evolution. © 2011 Szpara et al.",fusion protein;nucleic acid;proteome;pseudorabies vaccine;viral protein;Alphaherpesvirus;amino acid sequence;article;DNA binding;gene sequence;genetic heterogeneity;genetic polymorphism;Herpesviridae;high throughput sequencing;mammal;nonhuman;nucleotide sequence;phenotype;protein interaction;Pseudorabies virus;short tandem repeat;transcription regulation;virus genome;virus isolation;virus virulence,"Szpara, M. L.;Tafuri, Y. R.;Parsons, L.;Shamim, S. R.;Verstrepen, K. J.;Legendre, M.;Enquist, L. W.",2011,,10.1371/journal.ppat.1002282,0
2008,A new microplate neutralization test for typing of herpes simplex virus,"A microplate serum neutralization test for estimation of complement-requiring neutralizing (CRN) antibody was established as the first step for simplification of typing of herpes simplex virus (HSV). When guinea pigs were immunized with type 2 HSV, the late sera could mostly differentiate the types of HSV better than hyperimmune rabbit sera, the CRN titer against the heterologous type 1 HSV being much lower than the homologous titer. Sera of guinea pigs immunized with type 1 HSV showed about the same level of cross reaction against type 2 HSV as did rabbit antisera. Guinea pig sera having minimal levels of cross reaction were selected, and their high dilution (1:160) and complement were added to serial 10-fold dilutions of virus in the microplate titration of virus infectivity. Selective reduction of virus titer by either antiserum could determine the type of HSV. No equivocal intermediate case was found among a number of stock strains including many fresh isolates. The typing result coincided with that determined by a modification of Yang et al's method based on virus titers obtained with Vero and primary chick embryo cells. The typing based on plaquing in chick embryo cells sometimes failed to identify type 1 HSV.",complement;virus antibody;animal experiment;cell culture;Herpesviridae;in vitro study;methodology;virus classification;virus inhibition,"Tada, A.;Yoshino, K.",1978,,,0
2009,Bovine viral diarrhea virus 1 is classified into different subgenotypes depending on the analyzed region within the viral genome,"Phylogenetic analyses of bovine viral diarrhea virus (BVDV) were performed based on the nucleotide sequences of the 5′ untranslated region (5′-UTR) and E2-coding gene. Thirty-six BVDV detected from naturally infected cattle in the northern region of Japan were divided into three genotypes, BVDV1a, BVDV1b and BVDV2, in a 5′-UTR phylogenetic tree. In a phylogenetic tree constructed from the E2-coding gene, BVDV1c was identified and the viruses classified in BVDV1c were included in BVDV1a in the 5′-UTR phylogenetic tree. Moreover, BVDV1a and BVDV1b in the E2-phylogenetic tree clustered closer together than in the 5′-UTR tree. These results suggested that phylogenetic analysis of the E2 gene was more useful for identification of subgenotypes within BVDV1. © 2004 Elsevier B.V. All rights reserved.",nucleotide;5' untranslated region;animal cell;animal experiment;article;Bovine viral diarrhea virus 1;cattle disease;controlled study;gene cluster;genetic analysis;genetic code;genome;genotype;Japan;nonhuman;nucleotide sequence;phylogeny;viral genetics;virus classification;virus identification;virus infection,"Tajima, M.",2004,,10.1016/j.vetmic.2003.11.011,0
2010,Molecular characterization of a novel hepatitis E virus (HEV) strain obtained from a wild boar in Japan that is highly divergent from the previously recognized HEV strains,"Although a consensus classification system for hepatitis E virus (HEV) genotypes is currently unavailable, HEV variants (JBOAR135-Shiz09 and wbJOY_06) from wild boars (Sus scrofa leucomystax) have provisionally been classified into two novel genotypes (5 and 6). While performing a survey of HEV infections among 566 wild boars that were captured in Japan between January 2010 and August 2013, we found 24 boars (4.2%) with ongoing HEV infections: 13 had genotype 3 HEV, 10 had genotype 4 HEV and the remaining boar possessed a novel HEV variant (designated wbJNN_13). The entire wbJNN_13 genome comprised 7247 nucleotides excluding the poly(A) tail, and was highly divergent from known genotype 1 to 4 HEV isolates derived from humans, swine, wild boars, deer, mongoose and rabbits by 22.4-28.2%, JBOAR135-Shiz09 and wbJOY_06 by 19.6-21.9% and rat, ferret, bat and avian HEV isolates by 40.9-46.1% over the entire genome. Phylogenetic trees confirmed that wbJNN_13 is distantly related to all known HEV isolates. A Simplot analysis revealed no significant recombination among the existing HEV strains. These results indicate the presence of at least three genetic lineages of presumably boar-indigenous HEV strains. Further studies to fully understand the extent of the genomic heterogeneity of HEV variants infecting wild boars are warranted. © 2013 Elsevier B.V.",hepatitis E antibody;nucleotide;animal experiment;article;bat;bird;controlled study;deer;Mustela putorius furo;genetic heterogeneity;genotype;hepatitis E;Hepatitis E virus;Japan;mongoose;neighbor joining method;nonhuman;nucleotide sequence;phylogenetic tree;priority journal;rat;pig;unindexed sequence;virus strain;European wild boar,"Takahashi, M.;Nishizawa, T.;Nagashima, S.;Jirintai, S.;Kawakami, M.;Sonoda, Y.;Suzuki, T.;Yamamoto, S.;Shigemoto, K.;Ashida, K.;Sato, Y.;Okamoto, H.",2014,,10.1016/j.virusres.2013.12.014,0
2011,Phylogenetic characterization of H5N1 avian influenza viruses isolated in Indonesia from 2003-2007,"The wide distribution of H5N1 highly pathogenic avian influenza viruses is a global threat to human health. Indonesia has had the largest number of human infections and fatalities caused by these viruses. To understand the enzootic conditions of the viruses in Indonesia, twenty-four H5N1 viruses isolated from poultry from 2003 to 2007 were phylogenetically characterized. Although previous studies exclusively classified the Indonesian viruses into clades 2.1.1-2.1.3, our phylogenetic analyses showed a new sublineage that did not belong to any of the present clades. In addition, novel reassortant viruses were identified that emerged between this new sublineage and other clades in 2005-2006 on Java Island. H5N1 viruses were introduced from Java Island to Sulawesi, Kalimantan, and Sumatra Island on multiple occasions from 2003-2007, causing the geographical expansion of these viruses in Indonesia. These findings identify Java Island as the epicenter of the Indonesian H5N1 virus expansion. © 2009 Elsevier Inc. All rights reserved.",article;controlled study;genotype;geographic distribution;Indonesia;Influenza A virus (H5N1);molecular evolution;nonhuman;nucleotide sequence;phylogeny;poultry;priority journal;virogenesis;virus assembly;virus classification;virus gene;virus identification;virus isolation;virus replication,"Takano, R.;Nidom, C. A.;Kiso, M.;Muramoto, Y.;Yamada, S.;Sakai-Tagawa, Y.;Macken, C.;Kawaoka, Y.",2009,,10.1016/j.virol.2009.04.024,0
2012,Agar gel precipitin line patterns and pathogenicity of infectious bursal disease viruses,Twenty-nine strains of infectious bursal disease virus could be classified into three groups by the agar gel precipitin line patterns using two representative base antigens of F539 and G691 strains. The precipitin line of the first group (16 strains including F539) did not fuse with that of G691 base antigen and spur was seen. The line of the second group (2 strains) did not fuse with those of both base antigens. The line of the third group (11 strains including G691) did not fuse with that of F539 base antigen. Every strain of the first group was highly pathogenic for chickens showing a mortality of 40% or more.,virus antigen;animal;animal disease;article;bird disease;chicken;classification;immunology;infectious bursal disease virus;Japan;microbiology;pathogenicity;serodiagnosis;virus infection,"Takase, K.;Uchimura, T.;Katsuki, N.;Yamamoto, M.",1993,,,0
2013,"Novel Reassortant Avian Influenza A(H5N1) Virus in Human, Southern Vietnam, 2014",,"Animals;Genes, Viral;Humans;*Influenza A Virus, H5N1 Subtype/cl [Classification];*Influenza A Virus, H5N1 Subtype/ge [Genetics];Influenza in Birds/ep [Epidemiology];Influenza in Birds/vi [Virology];*Influenza, Human/di [Diagnosis];Influenza, Human/ep [Epidemiology];Influenza, Human/mo [Mortality];*Influenza, Human/vi [Virology];Male;Middle Aged;Multilocus Sequence Typing;Phylogeny;Poultry/vi [Virology];*Reassortant Viruses;Vietnam/ep [Epidemiology]","Takayama, I.;Hieu, N. T.;Shirakura, M.;Nakauchi, M.;Fujisaki, S.;Takahashi, H.;Nagata, S.;Long, N. T.;Odagiri, T.;Tashiro, M.;Kageyama, T.",2016,Mar,,0
2014,A thymus cell marker in murine leukemia virus-induced lymphomas of rats,"A specific marker for an immature population of thymus cells in the rat was shown by the rosette formation between thymus cells and guinea pig erythrocytes. This method was used to classify murine leukemia virus-induced rat lymphomas. Eight of nine Gross virus-induced rat lymphoma lines, which originated in the thymus, formed rosettes; whereas Friend, Rauscher, or Moloney virus-induced rat lymphoma lines, which originated in either the thymus, spleen or mesenteric lymph nodes, did not form rosettes. The percentage of the total cells which formed rosettes in the Gross lymphoma lines decreased with in vivo passages. If the tumor cells were exposed to trypsin treatment, then the tumor cells would form rosettes. Lymphoma lines which lacked rosette-forming cells did not show rosette formation after trypsin treatment. An immunofluorescence test showed that none of the lymphoma lines induced by Gross, Friend, Rauscher, or Moloney viruses carried the surface immunoglobulin characteristic of B-cells. These results suggest that Gross lymphomas may be derived from the thymic cortex and that Friend, Rauscher, or Moloney lymphomas may be derived from either mature thymus cells (non-rosette-forming cells) or from a subpopulation of the B-cell series which does not have the surface immunoglobulin G receptor.",cell marker;animal experiment;in vitro study;lymphoma;mouse;Murine leukemia virus;rat;thymocyte;thymus,"Takeichi, N.;Suzuki, K.;Kobayashi, H.",1979,,,0
2015,Influenza A viruses of swine (IAV-S) in Vietnam from 2010 to 2015: Multiple introductions of A(H1N1)pdm09 viruses into the pig population and diversifying genetic constellations of enzootic IAV-S,"Active surveillance of influenza A viruses of swine (IAV-S) involving 262 farms and 10 slaughterhouses in seven provinces in northern and southern Vietnam from 2010 to 2015 yielded 388 isolates from 32 farms; these viruses were classified into H1N1, H1N2, and H3N2 subtypes. Whole-genome sequencing followed by phylogenetic analysis revealed that the isolates represented 15 genotypes, according to the genetic constellation of the eight segments. All of the H1N1 viruses were entirely A(H1N1) pdm09 viruses, whereas all of the H1N2 and H3N2 viruses were reassortants among 5 distinct ancestral viruses: H1 and H3 triple-reassortant (TR) IAV-S that originated from North American pre-2009 human seasonal H1, human seasonal H3N2, and A(H1N1)pdm09 viruses. Notably, 93% of the reassortant IAV-S retained M genes that were derived from A(H1N1)pdm09, suggesting some advantage in terms of their host adaptation. Bayesian Markov chain Monte Carlo analysis revealed that multiple introductions of A(H1N1)pdm09 and TR IAV-S into the Vietnamese pig population have driven the genetic diversity of currently circulating Vietnamese IAV-S. In addition, our results indicate that a reassortant IAV-S with human-like H3 and N2 genes and an A(H1N1)pdm09 origin M gene likely caused a human case in Ho Chi Minh City in 2010. Our current findings indicate that human-to-pig transmission as well as cocirculation of different IAV-S have contributed to diversifying the gene constellations of IAV-S in Vietnam.",adaptation;article;controlled study;gene sequence;genetic reassortment;genetic variability;genotype;H3 gene;influenza A (H1N1);Influenza A virus (H1N1);Influenza A virus (H1N2);Influenza A virus (H3N2);M gene;N2 gene;nonhuman;North American;phylogeny;priority journal;swine disease;urban area;Viet Nam;viral genetics;virus cell interaction;virus classification;virus gene;virus genome;virus isolation;virus strain;virus transmission,"Takemae, N.;Harada, M.;Nguyen, P. T.;Nguyen, T.;Nguyen, T. N.;To, T. L.;Nguyen, T. D.;Pham, V. P.;Le, V. T.;Do, H. T.;Vo, H. V.;Tin Le, Q. V.;Tran, T. M.;Nguyen, T. D.;Thai, P. D.;Nguyen, D. H.;Thi Le, A. Q.;Nguyen, D. T.;Uchida, Y.;Saito, T.",2017,,10.1128/jvi.01490-16,0
2016,Full genome analysis of a European-type genotype 3 hepatitis E virus variant obtained from a Japanese patient with autochthonous acute hepatitis E,"A unique European-type HEV strain (HE-JA12-0725) classifiable into subgenotype 3f was recovered from a 66-year-old Japanese female with autochthonous acute hepatitis E, and its entire genomic sequence was determined and characterized. The HE-JA12-0725 strain shared the highest identity of 92.7% with a Spanish swine isolate (EU723514) over the entire genome and possessed a long hypervariable region sequence of 111 amino acids, identical to the 3f strains of European origin. The patient had consumed pork liver obtained via home delivery in Japan approximately two months before the disease onset. These results suggest the circulation of rare 3f HEV strains in Japan.",acute hepatitis;aged;amino acid sequence;article;case report;disease severity;female;genome analysis;hepatitis E;Hepatitis E virus;Hepatitis E virus genotype 3;human;Japanese (people);liver;nonhuman;phylogeny;pork;virus genome;virus strain,"Takeuchi, S.;Yamazaki, Y.;Sato, K.;Takizawa, D.;Yamada, M.;Okamoto, H.",2015,,10.1002/jmv.24191,0
2017,Evaluating methods for Avian avulavirus-1 whole genome sequencing,"Background: Avian avulavirus-1 (AAvV-1, previously Newcastle Disease Virus) is responsible for poultry and wild birds' disease outbreaks. Numerous whole genome sequencing methods were reported for this virus. These methods included cloning, specific primers amplification, shotgun PCR approaches, Sequence Independent Single Primer Amplification and next generation sequencing platform kits. Methods: Three methods were used to sequence 173 Israeli Avian avulavirus-1 field isolates and one vaccine strain (VH). The sequencing was performed on Proton and Ion Torrent Personal Genome Machine and to a lesser extent, Illumina MiSeq and NextSeq sequencers. Target specific primers (SP) and Sequence Independent Single Primer Amplification (SISPA) products sequenced via the Ion torrent sequencer had a high error rate and truncated genomes. All the next generation sequencing platform sequencing kits generated high sequence accuracy and near-complete genomic size. Results: A high level of mutations was observed in the intergenic regions between the avian avulavirus-1 genes. Within genes, multiple regions are more mutated than the Fusion region currently used for typing. Conclusions: Our findings suggest that the whole genome sequencing by the Ion torrent sequencing kit is sufficient. However, when higher fidelity is desired, the Illumina NextSeq and Proton torrent sequencing kits were found to be preferable.",article;Avulavirus;controlled study;epidemic;gene amplification;gene mutation;genetic analyzer;machine;Newcastle disease virus;next generation sequencing;nonhuman;whole genome sequencing;proton;vaccine,"Tal, S.;Ben Izhak, M.;Wachtel, C.;Wiseman, A.;Braun, T.;Yechezkel, E.;Golan, E.;Hadas, R.;Turjeman, A.;Banet-Noach, C.;Bronstein, M.;Lublin, A.;Berman, E.;Raviv, Z.;Pirak, M.;Klement, E.;Louzoun, Y.",2019,,10.1016/j.gene.2019.100004,0
2018,Evaluation of the broad-range PCR-electrospray ionization mass spectrometry (PCR/ESI-MS) system and virus microarrays for virus detection,"Advanced nucleic acid-based technologies are powerful research tools for novel virus discovery but need to be standardized for broader applications such as virus detection in biological products and clinical samples. We have used well-characterized retrovirus stocks to evaluate the limit of detection (LOD) for broad-range PCR with electrospray ionization mass spectrometry (PCR/ESI-MS or PLEX-ID), RT-PCR assays, and virus microarrays. The results indicated that in the absence of background cellular nucleic acids, PLEX-ID and RT-PCR had a similar LOD for xenotropic murine retrovirus-related virus (XMRV; 3.12 particles per μL) whereas sensitivity of virus detection was 10-fold greater using virus microarrays. When virus was spiked into a background of cellular nucleic acids, the LOD using PLEX-ID remained the same, whereas virus detection by RT-PCR was 10-fold less sensitive, and no virus could be detected by microarrays. Expected endogenous retrovirus (ERV) sequences were detected in cell lines tested and known species-specific viral sequences were detected in bovine serum and porcine trypsin. A follow-up strategy was developed using PCR amplification, nucleotide sequencing, and bioinformatics to demonstrate that an RD114-like retrovirus sequence that was detected by PLEX-ID in canine cell lines (Madin-Darby canine kidney (MDCK) and Cf2Th canine thymus) was due to defective, endogenous gammaretrovirus-related sequences. © 2014 by the authors; licensee MDPI, Basel, Switzerland.",virus RNA;animal cell;article;Avian leukosis virus;bioinformatics;controlled study;electrospray mass spectrometry;endogenous retrovirus;evolutionary rate;follow up;high throughput sequencing;human cell;limit of detection;microarray analysis;phylogeny;polymerase chain reaction;Simian virus 40;virus detection,"Taliaferro, L. P.;Galvin, T. A.;Ma, H.;Shaheduzzaman, S.;Williams, D. K.;Glasner, D. R.;Khan, A. S.",2014,,10.3390/v6051876,0
2019,Circulation of very virulent avian infectious bursal disease virus in Finland,"In the spring of 2014 infectious bursal disease (IBD) was confirmed in a Finnish layer flock exhibiting clinical signs and increased mortality. Organ and blood samples were sent for diagnosis to the Finnish Food Safety Authority Evira. IBD virus (IBDV) was detected in RT–PCR studies. Altogether hens from six layer farms associated with increased mortality (7–10%, worst case 30%) were diagnosed with IBD during 2014. Antibodies were also detected with IBD-ELISA tests in hens on two farms. Phylogenetic analysis showed that the causative agent of the 2014 IBD outbreak was a non-reassortant very virulent type IBDV. The representative virus strains from previous IBD outbreaks in 1978, 1987 and 1993 were also included in the analysis. The strains isolated in 2014 and 1993 were very similar indicating circulation of a very virulent IBDV for over 20 years in the country. In spite of the comprehensive phylogenetic analysis, the definitive origin of the viruses from 2014 and previous outbreaks remains unclear.",animal tissue;antibody detection;article;blood sampling;controlled study;enzyme linked immunosorbent assay;epidemic;Finland;hen;infectious bursal disease;infectious bursal disease virus;mortality rate;nonhuman;phylogeny;reverse transcription polymerase chain reaction;serology;virus detection;virus strain;virus virulence,"Tammiranta, N.;Ek-Kommonen, C.;Rossow, L.;Huovilainen, A.",2018,,10.1080/03079457.2018.1503642,0
2020,A generic assay for whole-genome amplification and deep sequencing of enterovirus A71,"Enterovirus A71 (EV-A71) has emerged as the most important cause of large outbreaks of severe and sometimes fatal hand, foot and mouth disease (HFMD) across the Asia-Pacific region. EV-A71 outbreaks have been associated with (sub)genogroup switches, sometimes accompanied by recombination events. Understanding EV-A71 population dynamics is therefore essential for understanding this emerging infection, and may provide pivotal information for vaccine development. Despite the public health burden of EV-A71, relatively few EV-A71 complete-genome sequences are available for analysis and from limited geographical localities. The availability of an efficient procedure for whole-genome sequencing would stimulate effort to generate more viral sequence data. Herein, we report for the first time the development of a next-generation sequencing based protocol for whole-genome sequencing of EV-A71 directly from clinical specimens. We were able to sequence viruses of subgenogroup C4 and B5, while RNA from culture materials of diverse EV-A71 subgenogroups belonging to both genogroup B and C was successfully amplified. The nature of intra-host genetic diversity was explored in 22 clinical samples, revealing 107 positions carrying minor variants (ranging from 0 to 15 variants per sample). Our analysis of EV-A71 strains sampled in 2013 showed that they all belonged to subgenogroup B5, representing the first report of this subgenogroup in Vietnam. In conclusion, we have successfully developed a high-throughput next-generation sequencing-based assay for whole-genome sequencing of EV-A71 from clinical samples.",virus RNA;amplicon;article;controlled study;depp sequencing;Enterovirus;Enterovirus A71;gene amplification;genetic procedures;genetic variability;high throughput sequencing;molecular dynamics;next generation sequencing;nonhuman;priority journal;reverse transcription polymerase chain reaction;RNA sequence;sequence analysis;species diversity;virus genome;virus identification;virus strain;whole genome sequencing,"Tan, L. V.;Tuyen, N. T. K.;Thanh, T. T.;Ngan, T. T.;Van, H. M. T.;Sabanathan, S.;Van, T. T. M.;Thanh, L. T. M.;Nguyet, L. A.;Geoghegan, J. L.;Ong, K. C.;Perera, D.;Hang, V. T. T.;Ny, N. T. H.;Anh, N. T.;Ha, D. Q.;Qui, P. T.;Viet, D. C.;Tuan, H. M.;Wong, K. T.;Holmes, E. C.;Chau, N. V.;Thwaites, G.;van Doorn, H. R.",2015,,10.1016/j.jviromet.2015.02.011,0
2021,"Virome profiling of rodents in Xinjiang Uygur Autonomous Region, China: isolation and characterization of a new strain of Wenzhou virus",,,"Tan, Z.;Yu, H.;Xu, L.;Zhao, Z.;Zhang, P.;Qu, Y.;He, B.;Tu, C.",2019,,,0
2022,Suppression of coronavirus replication by cyclophilin inhibitors,"Coronaviruses infect a variety of mammalian and avian species and cause serious diseases in humans, cats, mice, and birds in the form of severe acute respiratory syndrome (SARS), feline infectious peritonitis (FIP), mouse hepatitis, and avian infectious bronchitis, respectively. No effective vaccine or treatment has been developed for SARS-coronavirus or FIP virus, both of which cause lethal diseases. It has been reported that a cyclophilin inhibitor, cyclosporin A (CsA), could inhibit the replication of coronaviruses. CsA is a well-known immunosuppressive drug that binds to cellular cyclophilins to inhibit calcineurin, a calcium-calmodulin-activated serine/threonine-specific phosphatase. The inhibition of calcineurin blocks the translocation of nuclear factor of activated T cells from the cytosol into the nucleus, thus preventing the transcription of genes encoding cytokines such as interleukin-2. Cyclophilins are peptidyl-prolyl isomerases with physiological functions that have been described for many years to include chaperone and foldase activities. Also, many viruses require cyclophilins for replication; these include human immunodeficiency virus, vesicular stomatitis virus, and hepatitis C virus. However, the molecular mechanisms leading to the suppression of viral replication differ for different viruses. This review describes the suppressive effects of CsA on coronavirus replication. © 2013 by the authors; licensee MDPI, Basel, Switzerland.",calcineurin;cyclophilin;cyclophilin A;cyclophilin B;cyclophilin inhibitor;cyclosporine;nonstructural protein 1;transcription factor NFAT;antiviral activity;Arterivirus;Coronavirus infection;drug mechanism;drug protein binding;Equine arteritis virus;human;microbial diversity;nonhuman;porcine reproductive and respiratory syndrome;protein expression;protein function;protein protein interaction;review;severe acute respiratory syndrome;signal transduction;virus classification;virus inhibition;virus recombinant;virus replication,"Tanaka, Y.;Sato, Y.;Sasaki, T.",2013,,10.3390/v5051250,0
2023,"Characterization of Akabane virus from domestic bamboo rat, Southern China","To identify the causative agents in 3 large-scale outbreaks of encephalitis and death among farmed bamboo rats (Rhizomys pruinosus). The routine bacterial culture and identification were performed. There were no significant pathogenic bacteria isolated from the brain, heart, liver, spleen, lung, or kidney of diseased bamboo rats. Using PCR-based methods, we excluded the following as causative agent: pox virus, herpesvirus, adenovirus, lymphocytic choriomeningitis virus, rabies virus, and sendai virus. Furthermore, the homogenate from the diseased bamboo rats was subjected to viral metagenomic analysis which revealed 48506 filtered viral reads annotated to Akabane virus (AKAV) with > 75% nucleotide identity, suggesting the presence of AKAVs in bamboo rats. Five novel AKAV isolates were successfully isolated and characterized. Furthermore the newly isolated AKAV isolate was used to demonstrate that it can reproduce the severe encephalitic and pneumonic disease in bamboo rats and mice. The findings add to the better understanding of AKAV epidemiology and to the prevention and control of Akabane diseases in China.",Akabane virus;Bamboo rat;NEUTRALIZING ANTIBODIES;CULICOIDES-BREVITARSIS;EPIZOOTIC ABORTION;CATTLE;DISTANCE;JAPAN,"Tang, H. B.;Chen, F. L.;Rao, G. B.;Bai, A. B.;Jiang, J. J.;Du, Y. C.;Ren, P. F.;Liu, J. F.;Qin, S. M.;Yang, L.;Wu, J. M.",2017,Aug,,0
2024,Metagenomics for the discovery of novel human viruses,"Modern laboratory techniques for the detection of novel human viruses are greatly needed as physicians and epidemiologists increasingly deal with infectious diseases caused by new or previously unrecognized pathogens. There are many clinical syndromes in which viruses are suspected to play a role, but for which traditional microbiology techniques routinely fail in uncovering the etiologic agent. In addition, new viruses continue to challenge the human population owing to the encroachment of human settlements into animal and livestock habitats, globalization, climate change, growing numbers of immunocompromised people and bioterrorism. Metagenomics-based tools, such as microarrays and high-throughput sequencing are ideal for responding to these challenges. Pan-viral microarrays, containing representative sequences from all known viruses, have been used to detect novel and distantly-related variants of known viruses. Sequencing-based methods have also been successfully employed to detect novel viruses and have the potential to detect the full spectrum of viruses, including those present in low numbers. © 2010 Future Medicine Ltd.",nucleic acid;climate change;high throughput screening;Influenza A virus (H1N1);metagenomics;microarray analysis;microbiology;nonhuman;nucleic acid amplification;polymerase chain reaction;priority journal;review;SARS coronavirus;serology;virus detection;virus infection,"Tang, P.;Chiu, C.",2010,,10.2217/fmb.09.120,0
2025,"Molecular evolution of Japanese encephalitis virus isolates from swine in Oita, Japan during 1980-2009","In order to identify the patterns of genetic change of Japanese encephalitis virus (JEV) strains circulating in Oita, the complete envelope (E) gene has been sequenced for 35 isolates from swine in a 30-year span. Based on nucleotide and deduced amino acid sequences, the genetic variation was examined, phylogeny was estimated and selection pressures were also analyzed. This study demonstrated that the major genotype (G) of JEV isolates had shifted from GIII to GI in the mid-1990s in Oita. The intensities of selection acting on the Oita GIII and GI strains were found to be almost same. It suggests that the intensity of selection might not be the reason for such a genotype shift observed in Oita. Pairwise comparisons revealed the high conservation of the E gene at the protein level. Compared with the Oita GIII strains, all the Oita GI strains shared four amino acid changes at E129 (T-M), E222 (A-S), E327 (S-T) and E366 (A-S). Among all 70 JEV isolates involved in this paper, the GI strains shared only one amino acid change at E222 (A-S) in comparison with the GIII strains. No strong evidence for positive selection was found, the JEV evolution has generally been subject to strong purifying selection, but one ongoing evolutionary pathway was found to be under relaxed purifying selection in Oita. This study is a localized example of JEV molecular evolution in nature. © 2009 Elsevier B.V. All rights reserved.",amino acid sequence;amino acid substitution;animal cell;article;controlled study;genetic conservation;genetic selection;genetic variability;genotype;Japan;Japanese encephalitis virus;molecular evolution;nonhuman;nucleotide sequence;phylogeny;priority journal;strain difference;pig;virus envelope;virus isolation;virus strain,"Tang, W. F.;Ogawa, M.;Eshita, Y.;Aono, H.;Makino, Y.",2010,,10.1016/j.meegid.2009.12.005,0
2026,Isolation and characterization of H3N2 influenza A virus from turkeys,"Five 34-wk-old turkey breeder layer flocks in separate houses of 2550 birds each in a single farm in Ohio experienced a drop in egg production from late January to early February 2004. Tracheal swabs (n = 60), cloacal swabs (n = 50), and convalescent sera (n = 110) from the flocks were submitted to the laboratory for diagnostics. Virus isolation was attempted in specific-pathogen free embryonating chicken eggs and Vero and MDCK cells. Virus characterization was performed using agar gel immunodiffusion, the hemagglutination test, the hemagglutination inhibition test, the virus neutralization test, reverse transcription-polymerase chain reaction, sequencing, and phylogenetic analysis. A presumptive influenza virus was successfully propagated and isolated on the first passage in MDCK cells, but initially not in Vero cells or specific-pathogen free chicken embryos. After two passages in MDCK cells, it was possible to propagate the isolate in specific-pathogen free chicken embryos. Preliminary sequence analysis of the isolated virus confirmed that it was influenza A virus with almost 100% (235/236) identity with the matrix gene of a swine influenza A virus, A/Swine/Illinois/100084/01 (H1N2). Howevet, it was not possible to subtype the virus using conventional serotyping methods. The results of genetic characterization of the isolated virus showed that it was the H3N2 subtype and was designated as A/Turkey/OH/313053/04 (H3N2). Phylogenetic analysis of the eight gene segments of the virus showed that A/Turkey/OH/313053/04 (H3N2) isolate was most closely related to the triple-reassortant H3N2 swine viruses [A/Swine/WI/ 14094/99 (H3N2)] that have been circulating among pigs in the United States since 1998, which contains gene segments from avian, swine, and human viruses. The A/Turkey/OH/313053/04 (H3N2) isolated from turkeys in this study was classified as a low pathogenic avian influenza A virus because it only caused a drop in egg production with minor other clinical signs and no mortality.",primer DNA;animal;animal disease;article;Cercopithecus;chick embryo;classification;comparative study;DNA sequence;genetics;germfree animal;hemagglutination test;immunodiffusion;Influenza A virus;Influenza A virus (H3N2);molecular genetics;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;serodiagnosis;turkey (bird);United States;Vero cell line;virology,"Tang, Y.;Lee, C. W.;Zhang, Y.;Senne, D. A.;Dearth, R.;Byrum, B.;Perez, D. R.;Suarez, D. L.;Saif, Y. M.",2005,,,0
2027,Detection and characterization of two co-infection variant strains of avian orthoreovirus (ARV) in young layer chickens using next-generation sequencing (NGS),"Using next-generation sequencing (NGS) for full genomic characterization studies of the newly emerging avian orthoreovirus (ARV) field strains isolated in Pennsylvania poultry, we identified two co-infection ARV variant strains from one ARV isolate obtained from ARV-affected young layer chickens. The de novo assembly of the ARV reads generated 19 contigs of two different ARV variant strains according to 10 genome segments of each ARV strain. The two variants had the same M2 segment. The complete genomes of each of the two variant strains were 23,493 bp in length, and 10 dsRNA segments ranged from 1192 bp (S4) to 3958 bp (L1), encoding 12 viral proteins. Sequence comparison of nucleotide (nt) and amino acid (aa) sequences of all 10 genome segments revealed 58.1-100% and 51.4-100% aa identity between the two variant strains, and 54.3-89.4% and 49.5-98.1% aa identity between the two variants and classic vaccine strains. Phylogenetic analysis revealed a moderate to significant nt sequence divergence between the two variant and ARV reference strains. These findings have demonstrated the first naturally occurring co-infection of two ARV variants in commercial young layer chickens, providing scientific evidence that multiple ARV strains can be simultaneously present in one host species of chickens.",animal;Avian orthoreovirus;bird disease;chicken;duck;genetics;high throughput sequencing;isolation and purification;mixed infection;pathogenicity;phylogeny;virology;virus genome,"Tang, Y.;Lin, L.;Sebastian, A.;Lu, H.",2016,,10.1038/srep24519,0
2028,Genomic characterization of a novel avian arthritis orthoreovirus variant by next-generation sequencing,"By using next-generation sequencing (NGS) technology, we have identified a divergent avian orthoreovirus (ARV) field variant (Reo/PA/Broiler/15511/13, or PA15511), isolated from broiler chickens with viral arthritis in Pennsylvania in 2013. The complete genome of the PA15511 field strain was 23,495 bp in length with 10 dsRNA segments encoding 12 viral proteins. The lengths of the genomic segments ranged from 1192 bp (S4) to 3958 bp (L1). Genomic analysis has revealed that this virus is distinct from reference ARV strains and meets criteria for a new or novel strain.",animal;Avian orthoreovirus;bird disease;chicken;genetics;genomics;high throughput sequencing;isolation and purification;molecular genetics;phylogeny;physiology;reovirus infection;veterinary medicine;virology;virus genome,"Tang, Y.;Lu, H.",2015,,10.1007/s00705-015-2547-3,0
2029,Genomic characterization of a turkey reovirus field strain by Next-Generation Sequencing,"The genome of a turkey arthritis reovirus (TARV) field strain (Reo/PA/Turkey/22342/13), isolated from a turkey flock in Pennsylvania (PA) in 2013, has been sequenced using Next-Generation Sequencing (NGS) on the Illumina MiSeq platform. The genome of the PA TARV field strain was 23,496bp in length with 10 dsRNA segments encoding 12 viral proteins. The lengths of the genomic segments ranged from 1192bp (S4) to 3959bp (L1). The 5' and 3' conserved terminal sequences of the PA TARV field strain were similar to the two Minnesota (MN) TARVs (MN9 and MN10) published recently and avian orthoreovirus (ARV) reference strains. Phylogenetic analysis of the nucleotide sequences of all 10 genome segments revealed that there was a low to significant nucleotide sequence divergence between the PA TARV field strain and reference TARV and ARV strains. Analysis of the PA TARV sequence indicates that this PA TARV field strain is a unique strain and is different from the TARV MN9 or MN10 in M2 segment genes and ARV S1133 vaccine strain.","Animals;Conserved Sequence/ge [Genetics];*Genome, Viral;*High-Throughput Nucleotide Sequencing/mt [Methods];Open Reading Frames;Orthoreovirus, Avian/cl [Classification];*Orthoreovirus, Avian/ge [Genetics];Orthoreovirus, Avian/ip [Isolation & Purification];Pennsylvania;Phylogeny;Polymorphism, Single Nucleotide;Poultry Diseases/vi [Virology];Sequence Analysis, RNA;*Turkeys/vi [Virology];*Viral Proteins/ge [Genetics];0 (Viral Proteins)","Tang, Y.;Lu, H.;Sebastian, A.;Yeh, Y. T.;Praul, C. A.;Albert, I. U.;Zheng, S. Y.",2015,Jun,,0
2030,Open reading frames 1a and 1b of the porcine reproductive and respiratory syndrome virus (PRRSV) collaboratively initiate viral minus-strand RNA synthesis,"The porcine reproductive and respiratory syndrome virus (PRRSV) causes a persistent threat to the swine industry, especially when highly pathogenic PRRSV (HP-PRRSV) emerges. Previous studies have indicated that PRRSV RNA synthesis was correlated with HP-PRRSV virulence. PRRSV RNA synthesis includes genomic RNA and sub-genomic mRNA, and these processes require minus-strand RNA as a template. However, the mechanisms involved in PRRSV minus-strand RNA synthesis are not fully understood. A mini-genome system can be used to assess viral replication mechanisms and to evaluate the effects of potential antiviral drugs on viral replicase activities. In this study, we developed a mini-genome system that uses firefly luciferase as a reporter. Based on this system, we found that PRRSV RNA-dependent RNA polymerase nsp9 alone failed to activate virus minus-strand RNA synthesis. We also demonstrated that combinations of open reading frames 1a (ORF1a) and ORF1b are necessary for viral minus-strand RNA synthesis.","Animals;Base Sequence;Chromosome Mapping/mt [Methods];*High-Throughput Nucleotide Sequencing/mt [Methods];Molecular Sequence Data;*Open Reading Frames/ge [Genetics];*Porcine respiratory and reproductive syndrome virus/ge [Genetics];*RNA, Viral/ge [Genetics];Swine;*Transcription Elongation, Genetic/ph [Physiology];*Virus Activation/ge [Genetics];0 (RNA, Viral)","Tang, Y. D.;Fang, Q. Q.;Liu, J. T.;Wang, T. Y.;Wang, Y.;Tao, Y.;Liu, Y. G.;Cai, X. H.",2016,09 02,,0
2031,Combining Comprehensive Analysis of Off-Site Lambda Phage Integration with a CRISPR-Based Means of Characterizing Downstream Physiology,"During its lysogenic life cycle, the phage genome is integrated into the host chromosome by site-specific recombination. In this report, we analyze lambda phage integration into noncanonical sites using next-generation sequencing and show that it generates significant genetic diversity by targeting over 300 unique sites in the host Escherichia coli genome. Moreover, these integration events can have important phenotypic consequences for the host, including changes in cell motility and increased antibiotic resistance. Importantly, the new technologies that we developed to enable this study-sequencing secondary sites using next-generation sequencing and then selecting relevant lysogens using clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based selection-are broadly applicable to other phage-bacterium systems.<b>IMPORTANCE</b> Bacteriophages play an important role in bacterial evolution through lysogeny, where the phage genome is integrated into the host chromosome. While phage integration generally occurs at a specific site in the host chromosome, it is also known to occur at other, so-called secondary sites. In this study, we developed a new experimental technology to comprehensively study secondary integration sites and discovered that phage can integrate into over 300 unique sites in the host genome, resulting in significant genetic diversity in bacteria. We further developed an assay to examine the phenotypic consequence of such diverse integration events and found that phage integration can cause changes in evolutionarily relevant traits such as bacterial motility and increases in antibiotic resistance. Importantly, our method is readily applicable to other phage-bacterium systems.","Anti-Bacterial Agents/pd [Pharmacology];*Bacteriophage lambda/ge [Genetics];*CRISPR-Cas Systems;DNA, Viral/ge [Genetics];Drug Resistance, Bacterial;Escherichia coli/de [Drug Effects];Escherichia coli/ge [Genetics];*Escherichia coli/vi [Virology];Genetic Variation;Genome, Bacterial;Genome, Viral;High-Throughput Nucleotide Sequencing;*Lysogeny/ge [Genetics];*Recombination, Genetic;0 (Anti-Bacterial Agents);0 (DNA, Viral)","Tanouchi, Y.;Covert, M. W.",2017,09 19,,0
2032,A metagenomic approach to characterize temperate bacteriophage populations from Cystic Fibrosis and non-Cystic Fibrosis bronchiectasis patients,"Pseudomonas aeruginosa (Pa), normally a soil commensal, is an important opportunistic pathogen in Cystic Fibrosis (CF) and non-Cystic Fibrosis Bronchiectasis (nCFBR). Persistent infection correlates with accelerated decline in lung function and early mortality. The horizontal transfer of DNA by temperate bacteriophages can add gene function and selective advantages to their bacterial host within the constrained environment of the lower lung. In this study, we chemically induce temperate bacteriophages from clonal cultures of Pa and identify their mixed viral communities employing metagenomic approaches. We compared 92 temperate phage metagenomes stratified from these clinical backgrounds (47 CF and 45 nCFBR Pa isolates) using MG-RAST and GeneWise2. KEGG analysis shows the complexity of temperate phage accessory gene carriage increases with duration and severity of the disease. Furthermore, we identify the presence of Ig-like motifs within phage structural genes linked to bacterial adhesion and carbohydrate binding including Big_2, He_Pig, and Fn3. This study provides the first clinical support to the proposed bacteriophage adherence to mucus (BAM) model and the evolution of phages interacting at these mucosal surfaces over time.",carbohydrate binding protein;immunoglobulin;norfloxacin;adult;amino acid sequence;article;bacteriophage;bacterium adherence;bioinformatics;bronchiectasis;child;cystic fibrosis;disease duration;disease severity;gene location;human;major clinical study;metagenomics;next generation sequencing;open reading frame;polymerase chain reaction;principal component analysis;prophage;Pseudomonas aeruginosa;signal transduction;structural gene,"Tariq, M. A.;Everest, F. L. C.;Cowley, L. A.;De Soyza, A. D.;Holt, G. S.;Bridge, S. H.;Perry, A.;Perry, J. D.;Bourke, S. J.;Cummings, S. P.;Lanyon, C. V.;Barr, J. J.;Smith, D. L.",2015,,10.3389/fmicb.2015.00097,0
2033,"Genetically Different Highly Pathogenic Avian Influenza A(H5N1) Viruses in West Africa, 2015","To trace the evolution of highly pathogenic influenza A(H5N1) virus in West Africa, we sequenced genomes of 43 viruses collected during 2015 from poultry and wild birds in 5 countries. We found 2 co-circulating genetic groups within clade 2.3.2.1c. Mutations that may increase adaptation to mammals raise concern over possible risk for humans.","Africa, Western/ep [Epidemiology];Animals;*Genetic Variation;Genome, Viral;Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];Humans;Influenza A Virus, H5N1 Subtype/cl [Classification];*Influenza A Virus, H5N1 Subtype/ge [Genetics];Influenza A Virus, H5N1 Subtype/py [Pathogenicity];*Influenza in Birds/ep [Epidemiology];*Influenza in Birds/vi [Virology];Mutation;Phylogeny;*Poultry/vi [Virology];Virulence;Whole Genome Sequencing;0 (Hemagglutinin Glycoproteins, Influenza Virus)","Tassoni, L.;Fusaro, A.;Milani, A.;Lemey, P.;Awuni, J. A.;Sedor, V. B.;Dogbey, O.;Commey, A. N.;Meseko, C.;Joannis, T.;Minoungou, G. L.;Ouattara, L.;Haido, A. M.;Cisse-Aman, D.;Couacy-Hymann, E.;Dauphin, G.;Cattoli, G.;Monne, I.",2016,12,,0
2034,Fifth annual meeting on Retroviruses,"The fifth annual meeting on retrovirus of the RNA tumor virus group was held in October, 1977. Over 100 scientists from France, Belgium and Switzerland and a few others from Great-Britain, Italy and United States attended this meeting. They they discussed their projects and the interpretation of their results on: Virus cell interaction (cellular alterations, oncornavirus and cell differentiation, endogenous viruses); morphogenesis and genetic analysis; cellular restriction to virus infection; and proviral DNA (characterization and gene expression). Some topics also concerned research in human and bovine leukemias.",abstract report;animal experiment;classification;etiology;in vitro study;leukemia virus;lymphatic system;Orthoretrovirinae;virus classification,"Tavitian, A.",1978,,,0
2035,The epidemiology of peste des petits ruminants in the Sultanate of Oman,"Virological and serological evidence was obtained to show that peste des petits ruminants virus was widely distributed in Omani sheep and goats. There was no evidence for the concomitant presence of rinderpest virus in these species. Two virus isolates were classified as peste des petits ruminants virus on the basis of their pathogenicity in experimental animals and their specific hybridisation with nucleic acid probes. However, neutralisation tests and polyacrylamide gel analysis of their nucleocapsid proteins showed that they were not identical to the highly conserved African strains of this virus.","Age Factors;Animals;Antibodies, Viral/an [Analysis];DNA Probes;*Goat Diseases/ep [Epidemiology];Goats;Immunodiffusion;Neutralization Tests;Nucleic Acid Hybridization;Oman/ep [Epidemiology];Prevalence;RNA, Viral/an [Analysis];*Rinderpest/ep [Epidemiology];Rinderpest virus/ge [Genetics];Rinderpest virus/im [Immunology];Rinderpest virus/ip [Isolation & Purification];Rinderpest virus/py [Pathogenicity];Sheep;*Sheep Diseases/ep [Epidemiology];Viral Proteins/an [Analysis];Virulence;0 (Antibodies, Viral);0 (DNA Probes);0 (RNA, Viral);0 (Viral Proteins)","Taylor, W. P.;al Busaidy, S.;Barrett, T.",1990,May,,0
2036,"Virology, serology, and demography of hepatitis e viremic blood donors in South East England","BACKGROUND Hepatitis E virus (HEV) Genotype 3 (G3) in England comprises two principal phylogenetic groups (Group 1 and Group 2) and can be transmitted by transfusion. Unselected screening identified 79 viremic donors; 76 participated in a follow-up study. STUDY DESIGN AND METHODS Viral RNA dynamics, phylogenetics, and seroconversion were characterized in the donors. Detailed demographic, travel, clinical, and lifestyle questionnaires were undertaken. RESULTS The majority of viremic individuals (57/79) were seronegative at time of donation but all seroconverted. Viremia was short-lived, with a median of 6.5 weeks to confirmed viral clearance. All infections were acquired in the United Kingdom and were G3, with Group 2 viruses predominating (43/54; 80%). Infection was associated with some clinical symptoms both at and after donation (8/77; 10%). Viral loads and symptoms were more pronounced in Group 1 infections. There was no serologic evidence of reinfection. Donors were more commonly male (p = 0.002); both male and female donors were older than comparator donors. Animal contact was unlikely to be the source of infection. Consumption of chicken and pig meat was common to all infected donors; processed pig meat was most commonly purchased from one particular retail chain. CONCLUSION Viremic donors represent primary infection in older members of the community and reflect a widespread zoonotic in the United Kingdom. The two phylogenetic groups of HEV G3 display different pathogenicity and the more common Group 2 appears less adapted to humans. There are no objective demographic criteria that can identify donors at enhanced HEV risk.",virus RNA;adult;article;blood donor;chicken meat;clinical feature;England;female;follow up;food intake;food preference;hepatitis E;human;infection risk;lifestyle;major clinical study;male;middle aged;nonhuman;phylogeny;pork;processed meat;reinfection;screening;seroconversion;travel;United Kingdom;viral clearance;viremia;virus load,"Tedder, R. S.;Tettmar, K. I.;Brailsford, S. R.;Said, B.;Ushiro-Lumb, I.;Kitchen, A.;Morgan, D.;Lattimore, S.;Tossell, J.;Ijaz, S.;Hewitt, P. E.",2016,,10.1111/trf.13498,0
2037,Increased Prevalence of Anellovirus in Pediatric Patients with Fever,"The Anelloviridae family consists of non-enveloped, circular, single-stranded DNA viruses. Three genera of anellovirus are known to infect humans, named TTV, TTMDV, and TTMV. Although anelloviruses were initially thought to cause non-A-G viral hepatitis, continued research has shown no definitive associations between anellovirus and human disease to date. Using high-throughput sequencing, we investigated the association between anelloviruses and fever in pediatric patients 2-36 months of age. We determined that although anelloviruses were present in a large number of specimens from both febrile and afebrile patients, they were more prevalent in the plasma and nasopharyngeal (NP) specimens of febrile patients compared to afebrile controls. Using PCR to detect each of the three species of anellovirus that infect humans, we found that anellovirus species TTV and TTMDV were more prevalent in the plasma and NP specimens of febrile patients compared to afebrile controls. This was not the case for species TTMV which was found in similar percentages of febrile and afebrile patient specimens. Analysis of patient age showed that the percentage of plasma and NP specimens containing anellovirus increased with age until patients were 19-24 months of age, after which the percentage of anellovirus positive patient specimens dropped. This trend was striking for TTV and TTMDV and very modest for TTMV in both plasma and NP specimens. Finally, as the temperature of febrile patients increased, so too did the frequency of TTV and TTMDV detection. Again, TTMV was equally present in both febrile and afebrile patient specimens. Taken together these data indicate that the human anellovirus species TTV and TTMDV are associated with fever in children, while the highly related human anellovirus TTMV has no association with fever.",TT VIRUS-INFECTION;CHICKEN-ANEMIA-VIRUS;ACUTE RESPIRATORY-DISEASES;HUMAN DNA VIRUS;MINI VIRUS;NONHUMAN-PRIMATES;MONONUCLEAR-CELLS;EARLY;ACQUISITION;ENTIRE GENOMES;LIVER-DISEASE,"TeKippe, E. M.;Wylie, K. M.;Deych, E.;Sodergren, E.;Weinstock, G.;Storch, G. A.",2012,Nov,,0
2038,Viral metagenomics on animals as a tool for the detection of zoonoses prior to human infection?,"Many human viral infections have a zoonotic, i.e., wild or domestic animal, origin. Several zoonotic viruses are transmitted to humans directly via contact with an animal or indirectly via exposure to the urine or feces of infected animals or the bite of a bloodsucking arthropod. If a virus is able to adapt and replicate in its new human host, human-to-human transmissions may occur, possibly resulting in an epidemic, such as the A/H1N1 flu pandemic in 2009. Thus, predicting emerging zoonotic infections is an important challenge for public health officials in the coming decades. The recent development of viral metagenomics, i.e., the characterization of the complete viral diversity isolated from an organism or an environment using high-throughput sequencing technologies, is promising for the surveillance of such diseases and can be accomplished by analyzing the viromes of selected animals and arthropods that are closely in contact with humans. In this review, we summarize our current knowledge of viral diversity within such animals (in particular blood-feeding arthropods, wildlife and domestic animals) using metagenomics and present its possible future application for the surveillance of zoonotic and arboviral diseases. © 2014 by the authors; licensee MDPI, Basel, Switzerland.",Alphavirus;arthropod;bacteriophage;bat;Bunyaviridae;Circoviridae;Culex;degenerate oligonucleotide primed polymerase chain reaction;Densovirinae;Dicistroviridae;disease surveillance;DNA sequence;early diagnosis;Ebolavirus;Flavivirus;Hantavirus;Henipavirus;high throughput sequencing;horse;human;Inoviridae;Japanese encephalitis;Lentivirus;meal;meat;metagenomics;microbial diversity;Nanoviridae;nonhuman;nucleic acid amplification;Orthobunyavirus;Papillomaviridae;parasite vector;piglet;polymerase chain reaction;Poxviridae;Reoviridae;review;Rhabdoviridae;rodent;rolling circle amplification;sequence Independent single primer amplification;severe acute respiratory syndrome;pig;Togaviridae;Tymoviridae;virus infection;European wild boar;zoonosis,"Temmam, S.;Davoust, B.;Berenger, J. M.;Raoult, D.;Desnues, C.",2014,,10.3390/ijms150610377,0
2039,Faustovirus-like asfarvirus in hematophagous biting midges and their vertebrate hosts,"Faustovirus, a new Asfarviridae-related giant virus, was recently isolated in Vermamoeba vermiformis, a protist found in sewage water in various geographical locations and occasionally reported in human eye infection cases. As part of a global metagenomic analysis of viral communities existing in biting midges, we report here for the first time the identification and isolation of a Faustovirus-like virus in hematophagous arthropods and its detection in their animal hosts. The DNA virome analysis of three pools of Culicoides sp., engorged female Culicoides imicola and non-engorged male/female C. imicola biting midges collected in Senegal, revealed the presence of amoeba-infecting giant viruses and, among them, a majority of sequences related to Faustovirus. Phylogenetic analyses conducted on several structural genes of Faustovirus confirmed the clustering of the arthropod-borne Faustovirus with sewage-borne Faustoviruses, with a distinct geographical clustering of Senegalese Faustovirus strains. Transmission electron microscopy identified viral particles with morphologies and diameters which were compatible with Faustovirus. The presence of infectious arthropod-borne Faustovirus was finally confirmed by successful isolation on V. vermiformis amoeba. Global proteomic analysis of biting midges identified that arthropods' blood meal originating from cattle, rodents and humans. Further screening of cattle sera and rodent tissue resulted in prevalence of Faustovirus being estimated at 38% in rodents and 14% in cattle, suggesting a possible origin of Faustovirus presence in arthropods via the ingestion of contaminated blood meal. Viral loads were the highest in rodents' urine and kidney samples, suggesting a possible excretion of viral particles into the environment. Faustovirus DNA polymerase-related sequences were also detected in more than 9 and 11% of febrile patients and healthy Senegalese human sera, respectively. Our study thus, highlights the need to investigate the role of arthropods, wildlife, and domestic animals in the lifecycle of amoeba-infecting giant viruses and, in particular, the environmental cycle of Faustovirus.",DNA directed DNA polymerase;amoeba (life cycle stage);animal experiment;animal model;animal tissue;article;Asfarviridae;bite;domestic animal;female;gene sequence;human versus animal comparison;male;metagenomics;nonhuman;open reading frame;phylogeny;proteomics;real time polymerase chain reaction;sanguivore;structural gene;transmission electron microscopy;virus identification;virus load;virus strain;Western blotting,"Temmam, S.;Monteil-Bouchard, S.;Sambou, M.;Aubadie-Ladrix, M.;Azza, S.;Decloquement, P.;Bou Khalil, J. Y.;Baudoin, J. P.;Jardot, P.;Robert, C.;Scola, B. L.;Mediannikov, O. Y.;Raoult, D.;Desnues, C.",2015,,10.3389/fmicb.2015.01406,0
2040,"Genetic characterization of coronaviruses from domestic ferrets, Japan",We detected ferret coronaviruses in 44 (55.7%) of 79 pet ferrets tested in Japan and classified the viruses into 2 genotypes on the basis of genotype-specific PCR. Our results show that 2 ferret coronaviruses that cause feline infectious peritonitis-like disease and epizootic catarrhal enteritis are enzootic among ferrets in Japan.,"Animals;Coronavirus/cl [Classification];*Coronavirus/ge [Genetics];Coronavirus/ip [Isolation & Purification];Coronavirus Infections/ep [Epidemiology];*Coronavirus Infections/ve [Veterinary];Coronavirus Infections/vi [Virology];Diarrhea/ep [Epidemiology];*Diarrhea/ve [Veterinary];Diarrhea/vi [Virology];Enteritis/ep [Epidemiology];*Enteritis/ve [Veterinary];Enteritis/vi [Virology];Feces/vi [Virology];*Ferrets/vi [Virology];Genotype;Humans;Japan/ep [Epidemiology];Molecular Typing;Pets;Phylogeny;RNA, Viral/cl [Classification];*RNA, Viral/ge [Genetics];Reverse Transcriptase Polymerase Chain Reaction;0 (RNA, Viral)","Terada, Y.;Minami, S.;Noguchi, K.;Mahmoud, H. Y.;Shimoda, H.;Mochizuki, M.;Une, Y.;Maeda, K.",2014,Feb,,0
2041,Avian poxvirus infection in flamingos (Phoenicopterus roseus) in a Zoo in Japan,"Two diseased flamingos (Phoenicopterus roseus) with nodular lesions (pock) characteristic of poxvirus infection were found in a zoo in Japan. Avian poxvirus was isolated from the lesions (upper beak) of the affected birds and was genetically characterized by polymerase chain reaction, nucleotide sequencing, and phylogenetic analysis. Based on the phylogenetic analysis, the virus isolated from these flamingos was genetically close to those isolated from pigeons, suggesting the possibility of interspecies transmission. © 2010 American Association of Avian Pathologists.",animal;animal disease;article;bird;bird disease;case report;fatality;Fowlpox virus;genetics;Japan;phylogeny;poxvirus infection;virology;zoo animal,"Terasaki, T.;Kaneko, M.;Mase, M.",2010,,10.1637/9040-082609-Case.1,0
2042,Characterization of Newcastle disease virus isolates obtained from Eurasian collared doves (Streptopelia decaocto) in Italy,"Eurasian collared doves (Streptopelia decaocto) are thought to originate from India and they have colonized, throughout the centuries, the Middle East and, more recently, Mediterranean countries such as Italy and Spain. In the present paper we report of the isolation and characterization of Newcastle disease viruses (NDV) obtained from Eurasian collared doves during 2000-2001, and compare them to isolates obtained from feral pigeons (Columba livia) during the same period. All isolates could be classified as avian paramyxovirus type 1 (APMV1) and belonged to the pigeon variant group (PPMV1), as their haemagglutinating activity was inhibited by mAb 161/617 which is specific for PPMV1. The intracerebral pathogenicity indices ranged from 0.68 to 1.38 and all isolates contained multiple basic amino acids at the deduced cleavage site of the fusion protein, which is a typical feature of virulent viruses. Phylogenetic analysis of the isolates indicate that 18/20 of these form a separate cluster from the isolates obtained from pigeons in the same period. These findings suggest that different lineages are circulating in feral pigeon populations, and that a separate lineage affects Eurasian collared doves.",virus fusion protein;amino acid sequence;animal;article;bird disease;chemistry;genetics;isolation and purification;Italy;Newcastle disease virus;phylogeny;Columbidae;species difference;virology,"Terregino, C.;Cattoli, G.;Grossele, B.;Bertoli, E.;Tisato, E.;Capua, I.",2003,,10.1080/0307,0
2043,Heterologous viral expression systems in fosmid vectors increase the functional analysis potential of metagenomic libraries,"The extraordinary potential of metagenomic functional analyses to identify activities of interest present in uncultured microorganisms has been limited by reduced gene expression in surrogate hosts. We have developed vectors and specialized E. coli strains as improved metagenomic DNA heterologous expression systems, taking advantage of viral components that prevent transcription termination at metagenomic terminators. One of the systems uses the phage T7 RNA-polymerase to drive metagenomic gene expression, while the other approach uses the lambda phage transcription anti-termination protein N to limit transcription termination. A metagenomic library was constructed and functionally screened to identify genes conferring carbenicillin resistance to E. coli. The use of these enhanced expression systems resulted in a 6-fold increase in the frequency of carbenicillin resistant clones. Subcloning and sequence analysis showed that, besides β-lactamases, efflux pumps are not only able contribute to carbenicillin resistance but may in fact be sufficient by themselves to convey carbenicillin resistance.",bacterial DNA;bacteriophage T7 RNA polymerase;beta lactamase;carbenicillin;DNA directed RNA polymerase;viral protein;antibiotic resistance;article;Enterobacteria phage lambda;Enterobacteria phage T7;Escherichia coli;gene expression;gene library;gene vector;genetic transcription;genetics;metabolism;metagenomics;methodology;molecular cloning,"Terrón-González, L.;Medina, C.;Limón-Mortés, M. C.;Santero, E.",2013,,,0
2044,"Identification of a novel aviadenovirus, designated pigeon adenovirus 2 in domestic pigeons (Columba livia)","The young pigeon disease syndrome (YPDS) affects mainly young pigeons of less than one year of age and leads to crop stasis, vomitus, diarrhea, anorexia and occasionally death. This disease is internationally a major health problem because of its seasonal appearance during competitions such as homing pigeon races or exhibitions of ornamental birds. While the etiology of YPDS is still unclear, adenoviruses are frequently discussed as potential causative agents. Electron microscopy of feces from a YPDS outbreak revealed massive shedding of adenovirus-like particles. Whole genome sequencing of this sample identified a novel adenovirus tentatively named pigeon adenovirus 2 (PiAdV-2). Phylogenetic and comparative genome analysis suggest PiAdV-2 to belong to a new species within the genus Aviadenovirus, for which we propose the name Pigeon aviadenovirus B. The PiAdV-2 genome shares 54.9% nucleotide sequence identity with pigeon adenovirus 1 (PiAdV-1). In a screening of further YPDS-affected flocks two variants of PiAdV-2 (variant A and B) were detected which shared 97.6% nucleotide identity of partial polymerase sequences, but only 79.7% nucleotide identity of partial hexon sequences. The distribution of both PiAdV-2 variants was further investigated in fecal samples collected between 2008 and 2015 from healthy or YPDS-affected racing pigeons of different lofts. Independent of their health status, approximately 20% of young and 13% of adult pigeon flocks harbored PiAdV-2 variants. Birds were free of PiAdV-1 or other aviadenoviruses as determined by PCRs targeting the aviadenovirus polymerase or the PiAdV-1 fiber gene, respectively. In conclusion, there is no indication of a correlation between YPDS outbreaks and the presence of PiAdV-2 or other aviadenoviruses, arguing against an causative role in this disease complex.","Animals;Animals, Domestic;*Aviadenovirus/cl [Classification];*Aviadenovirus/ge [Genetics];Aviadenovirus/ul [Ultrastructure];Base Sequence;Bird Diseases/ep [Epidemiology];Bird Diseases/vi [Virology];*Columbidae/vi [Virology];Computational Biology/mt [Methods];Gene Order;Genes, Viral;Genome, Viral;Genomics/mt [Methods];Germany;High-Throughput Nucleotide Sequencing;Phylogeny;Polymerase Chain Reaction","Teske, L.;Rubbenstroth, D.;Meixner, M.;Liere, K.;Bartels, H.;Rautenschlein, S.",2017,01 02,,0
2045,"Characterization of a genetically heterogeneous porcine rotavirus C, and other viruses present in the fecal virome of a non-diarrheic Belgian piglet","Next-generation sequencing (NGS) technologies are becoming increasingly accessible, leading to an expanded interest in the composition of the porcine enteric virome. In the present study, the fecal virome of a non-diarrheic Belgian piglet was determined. Although the virome of only a single piglet was analyzed, some interesting data were obtained, including the second complete genome of a pig group C rotavirus (RVC). This Belgian strain was only distantly related to the only other completely characterized pig RVC strain, Cowden. Its relatedness to RVC strains from other host species was also analyzed and the porcine strain found in our study was only distantly related to RVCs detected in humans and cows. The gene encoding the outer capsid protein VP7 belonged to the rare porcine G3 genotype, which might be serologically distinct from most other pig RVC strains. A putative novel RVC VP6 genotype was identified as well. A group A rotavirus strain also present in this fecal sample contained the rare pig genotype combination G11P[27], but was only partially characterized. Typical pig RVA genotypes I5, A8, and T7 were found for the viral proteins VP6, NSP1, and NSP3, respectively. Interestingly, the fecal virome of the piglet also contained an astrovirus and an enterovirus, of which the complete genomes were characterized. Results of the current study indicate that many viruses may be present simultaneously in fecal samples of non-diarrheic piglets. In this study, these viruses could not be directly associated with any disease, but still they might have had a potential subclinical impact on pig growth performance. The fast evolution of NGS will be a powerful tool for future diagnostics in veterinary practice. Its application will certainly lead to better insights into the relevance of many (sub)clinical enteric viral infections, that may have remained unnoticed using traditional diagnostic techniques. This will stimulate the development of new and durable prophylactic measures to improve pig health and production.",NSP1 protein;NSP3 protein;NSP5 protein;protein VP1;protein VP2;protein VP3;protein VP4;protein VP6;protein VP7;unclassified drug;viral protein;article;Astroviridae;controlled study;Enterovirus;feces analysis;genetic variability;genome analysis;genotype;infection risk;molecular evolution;nonhuman;phylogenetic tree;piglet;priority journal;risk assessment;Rotavirus C;strain difference;virus characterization;virus detection;virus genome;virus strain;virus transmission,"Theuns, S.;Conceição-Neto, N.;Zeller, M.;Heylen, E.;Roukaerts, I. D. M.;Desmarets, L. M. B.;Van Ranst, M.;Nauwynck, H. J.;Matthijnssens, J.",2016,,10.1016/j.meegid.2016.05.018,1
2046,Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus,"Enteric diseases in swine are often caused by different pathogens and thus metagenomics are a useful tool for diagnostics. The capacities of nanopore sequencing for viral diagnostics were investigated here. First, cell culture-grown porcine epidemic diarrhea virus and rotavirus A were pooled and sequenced on a MinION. Reads were already detected at 7 seconds after start of sequencing, resulting in high sequencing depths (19.2 to 103.5X) after 3 h. Next, diarrheic feces of a one-week-old piglet was analyzed. Almost all reads (99%) belonged to bacteriophages, which may have reshaped the piglet's microbiome. Contigs matched Bacteroides, Escherichia and Enterococcus phages. Moreover, porcine kobuvirus was discovered in the feces for the first time in Belgium. Suckling piglets shed kobuvirus from one week of age, but an association between peak of viral shedding (10<sup>6.42</sup>-10<sup>7.01</sup> copies/swab) and diarrheic signs was not observed during a follow-up study. Retrospective analysis showed the widespread (n = 25, 56.8% positive) of genetically moderately related kobuviruses among Belgian diarrheic piglets. MinION enables rapid detection of enteric viruses. Such new methodologies will change diagnostics, but more extensive validations should be conducted. The true enteric pathogenicity of porcine kobuvirus should be questioned, while its subclinical importance cannot be excluded.",,"Theuns, S.;Vanmechelen, B.;Bernaert, Q.;Deboutte, W.;Vandenhole, M.;Beller, L.;Matthijnssens, J.;Maes, P.;Nauwynck, H. J.",2018,Jun 29,,1
2047,Molecular characterization of positive-strand RNA viruses: pestiviruses and the porcine reproductive and respiratory syndrome virus (PRRSV),"Molecular characterization has become an important tool for the analysis of viruses including their classification. The manuscript focuses on the molecular analysis of two members of the genus pestivirus (hog cholera virus, HCV and bovine viral diarrhea virus, BVDV) and of the recently discovered porcine reproductive and respiratory syndrome virus (PRRSV). The first protein encoded within the single large pestivirus ORF is a nonstructural protein with autoproteolytic activity. The cleavage site between the protease and the capsid protein p14 has been predicted previously, but recent experimental data indicate that processing occurs at a different site. The capsid protein is followed by a putative internal signal sequence and three glycoproteins which are part of the virion envelope. According to a new proposal for the nomenclature of the structural proteins of pestiviruses they are termed C, E0, E1 and E2. The genomes of BVDV pairs isolated from animals which came down with mucosal disease were analyzed. The genomes from cytopathogenic (cp) BVD viruses may contain insertions highly homologous to cellular sequences. In addition, cp BVDV may differ from its non cytopathogenic (noncp) counterpart by mere rearrangement of viral sequences. The disease PRRS, which emerged a few years ago, is caused by a single strand RNA virus; the viral genome is of positive polarity and has a size of 15 kb. Data concerning morphology, morphogenesis and virion composition suggested already that PRRSV belongs to a group of so-called arteriviruses which comprises equine arteritis virus (EAV), lactate dehydrogenase elevating virus (LDV) and simian hemorrhagic fever virus (SHFV). This conclusion has now been confirmed by analysis of genome organization, gene expression strategy and by comparison of deduced protein sequences.",amino acid sequence;animal;genetics;molecular genetics;Pestivirus;review;pig,"Thiel, H. J.;Meyers, G.;Stark, R.;Tautz, N.;Rümenapf, T.;Unger, G.;Conzelmann, K. K.",1993,,,0
2048,Case reports of hemorrhagic diathesis in calves with bovine diarrhea virus infection,Clinical and pathological findings in six veal calves suffering from haemorrhagic diathesis are reported. Further pathological and virological results were highly suggestive of mucosal disease (BVD). No virus isolation or classification was possible. The post mortem results indicated that the virus might have been cytopathogenic. The cases are discussed and compared with similar field and experimental publications dealing with thrombocytopenia in veal calves in the USA. These are the first reports of cases published in Germany.,animal;animal disease;article;bleeding disorder;case report;bovine;cattle disease;cecum;diarrhea;female;male;pathology;Peyer patch;ruminant stomach;small intestine,"Thiel, W.",1993,,,0
2049,Estimation of hepatitis E virus (HEV) pig seroprevalence using ELISA and Western blot and comparison between human and pig HEV sequences in Belgium,"Zoonotic transmission of hepatitis E virus (HEV) is of special concern, particularly in high income countries were waterborne infections are less frequent than in developing countries. High HEV seroprevalences can be found in European pig populations. The aims of this study were to obtain prevalence data on HEV infection in swine in Belgium and to phylogenetically compare Belgian human HEV sequences with those obtained from swine. An ELISA screening prevalence of 73% (95% CI 68.8-77.5) was determined in Belgian pigs and a part of the results were re-evaluated by Western blot (WB). A receiver operating characteristic curve analysis was performed and scenarios varying the ELISA specificity relative to WB were analysed. The seroprevalences estimated by the different scenarios ranged between 69 and 81% and are in agreement with the high exposure of the European pig population to HEV. Pig HEV sequences were genetically compared to those detected in humans in Belgium and a predominance of genotype 3 subtype f was shown in both swine and humans. The high HEV seroprevalence in swine and the close phylogenetic relationships between pig and human HEV sequences further support the risk for zoonotic transmission of HEV between humans and pigs. © 2014 Elsevier B.V.",immunoglobulin G;immunoglobulin M;article;Belgium;comparative study;controlled study;enzyme linked immunosorbent assay;gene sequence;genotype;hepatitis E;Hepatitis E virus;hepatitis e virus genotype 3f;human;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;screening test;seroprevalence;pig;swine disease;Western blotting,"Thiry, D.;Mauroy, A.;Saegerman, C.;Thomas, I.;Wautier, M.;Miry, C.;Czaplicki, G.;Berkvens, D.;Praet, N.;van der Poel, W.;Cariolet, R.;Brochier, B.;Thiry, E.",2014,,10.1016/j.vetmic.2014.06.004,0
2050,Molecular biology of bovine herpesvirus type 4,"Bovine herpesvirus type 4 (BHV-4) is a ubiquitous virus of cattle. Its genome is a 144 ± 6 kb double-stranded DNA consisting of a unique central part (L-DNA) flanked at both ends by tandem repeats called polyrepetitive DNA (prDNA or H-DNA). The overall arrangement of genes has been obtained by the analysis of homologies between short BHV-4 DNA sequences and corresponding genes of Epstein-Barr virus (EBV) and herpesvirus saimiri (HVS). The gene expression is temporally regulated. Glycoprotein precursor p(gp10/gp17) is expressed as gamma 1 polypeptide. Glycoproteins gp1, gp8, gp11 and their precursors are gamma 2 proteins. The analysis of strain variations allows the definition of two types of strains, based on the DNA patterns: the Movar 33/63-like and the DN 599-like strains. Only the M40 strain, isolated in India, fails to fit this classification. The genomic variations have been compiled to build a dendrogram showing three levels of divergence between BHV-4 strains or isolates. The available molecular data indicate that the BHV-4 genome shares much similarity with the DNA of EBV and HVS, two representative members of the gammaherpesvirinae. BHV-4 may therefore be classified in the subfamily gammaherpesvirinae.",animal cell;animal model;Bovine herpesvirus 1;bovine;conference paper;controlled study;DNA sequence;herpes simplex;molecular biology;nonhuman;veterinary medicine;virus classification,"Thiry, E.;Bublot, M.;Dubuisson, J.;Van Bressem, M. F.;Lequarre, A. S.;Lomonte, P.;Vanderplasschen, A.;Pastoret, P. P.",1992,,10.1016/0378-1135(92)90037-t,0
2051,The origin of lentivirus research: Maedi-visna virus,"Maedi and visna are contagious sheep diseases which were introduced into Iceland in 1933 by imported sheep of Karakul breed. Maedi, a slowly progressing pneumonia, and the central nervous system disease visna were shown to be transmissible in sheep and most likely caused by a virus. In 1957, visna virus was isolated in tissue culture from sheep brain and maedi virus was isolated the following year from sheep lungs. Both viruses showed similar cytopathic effect in tissue culture. Electron microscope studies of ultrathin sections from visna virus infected cells demonstrated spherical particles, 70-100 nm in diameter, which were formed by budding from the cell membrane. Later studies showed identical particles in maedi virus infected cultures. These, and several other comparative studies, strongly indicated that maedi and visna were caused by strains of the same virus, later named maedi-visna virus (MVV). Comparative studies in tissue culture suggested that MVV was related to RNA tumor viruses of animals, the oncornaviruses. This was later supported by the finding that MVV is an RNA virus. A few months after reverse transcriptase was demonstrated in oncornaviruses, the enzyme was also found in MVV virions. Thus, MVV was classified as a retrovirus together with the oncornaviruses. However, MVV is not oncogenic in vivo or in vitro and was in 1975 placed in a subgroup of retroviruses named lentiviruses, which cause cytopathic effect in vitro and slowly progressing inflammatory disease in animals, but are nononcogenic. In the early 1980s, the causative agent of AIDS was found to be a non-oncogenic retrovirus and was classified as a lentivirus. Thus, HIV became the first human lentivirus. © 2013 Bentham Science Publishers.",article;cell count;cell structure;contact examination;cytopathogenic effect;incubation time;inflammation;lung disease;nonhuman;pleocytosis;pneumonia;sheep;tissue culture;transmission electron microscopy;viral clearance;virogenesis;virus classification;virus isolation;virus release;virus replication;virus transmission;Visna virus,"Thormar, H.",2013,,,0
2052,"Prevalence and diversity of H9N2 avian influenza in chickens of Northern Vietnam, 2014","Despite their classification as low pathogenicity avian influenza viruses (LPAIV), A/H9N2 viruses cause significant losses in poultry in many countries throughout Asia, the Middle East and North Africa. To date, poultry surveillance in Vietnam has focused on detection of influenza H5 viruses, and there is limited understanding of influenza H9 epidemiology and transmission dynamics. We determined prevalence and diversity of influenza A viruses in chickens from live bird markets (LBM) of 7 northern Vietnamese provinces, using pooled oropharyngeal swabs collected from October to December 2014. Screening by real time RT-PCR revealed 1207/4900 (24.6%) of pooled swabs to be influenza A virus positive; overall prevalence estimates after accounting for pooling (5 swabs/pools) were 5.8% (CI 5.4-6.0). Subtyping was performed on 468 pooled swabs with M gene Ct<26. No influenza H7 was detected; 422 (90.1%) were H9 positive; and 22 (4.7%) were H5 positive. There was no evidence was of interaction between H9 and H5 virus detection rates. We sequenced 17 whole genomes of A/H9N2, 2 of A/H5N6, and 11 partial genomes. All H9N2 viruses had internal genes that clustered with genotype 57 and were closely related to Chinese human isolates of A/H7N9 and A/H10N8. Using a nucleotide divergence cutoff of 98%, we identified 9 distinct H9 genotypes. Phylogenetic analysis suggested multiple introductions of H9 viruses to northern Vietnam rather than in-situ transmission. Further investigations of H9 prevalence and diversity in other regions of Vietnam are warranted to assess H9 endemicity elsewhere in the country.","Animals;*Chickens/vi [Virology];Genome, Viral;Genotype;Hemagglutinin Glycoproteins, Influenza Virus/ch [Chemistry];Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];High-Throughput Nucleotide Sequencing;*Influenza A Virus, H9N2 Subtype/cl [Classification];*Influenza A Virus, H9N2 Subtype/ge [Genetics];*Influenza in Birds/ep [Epidemiology];*Influenza in Birds/vi [Virology];Models, Molecular;Mutation;Phylogeny;Phylogeography;Prevalence;Protein Conformation;Public Health Surveillance;Vietnam/ep [Epidemiology];0 (Hemagglutinin Glycoproteins, Influenza Virus)","Thuy, D. M.;Peacock, T. P.;Bich, V. T. N.;Fabrizio, T.;Hoang, D. N.;Tho, N. D.;Diep, N. T.;Nguyen, M.;Hoa, L. N. M.;Trang, H. T. T.;Choisy, M.;Inui, K.;Newman, S.;Trung, N. V.;van Doorn, R.;To, T. L.;Iqbal, M.;Bryant, J. E.",2016,10,,0
2053,Chimeric porcine reproductive and respiratory syndrome viruses reveal full function of genotype 1 envelope proteins in the backbone of genotype 2,"Porcine reproductive and respiratory syndrome virus (PRRSV) is classified into two genotypes, type 1 and type 2, which share only about 60% genetic identity. Here, we report viable chimeric viruses in which the envelope protein genes from ORF2a to ORF5 of vSHE (type 1) were swapped into the genetic backbone of vAPRRS (type 2). We found that the envelope proteins of genotype 1 were fully functional in genotype 2 PRRSV, and the rescued chimeric progeny viruses showed robust genetic stability and similar replication properties to the parental strains in vitro. To our knowledge, this is the first study to report the substitution of complete ORFs between different genotypes of porcine arterivirus. These findings pave the way to further elucidate the structure-function relationship of PRRSV envelope proteins, and may enable the development of novel marker vaccines that can be used to differentiate vaccinated from infected animals. © 2010 Elsevier Inc.",protein ORF2a;protein ORF2b;protein ORF3;protein ORF4;protein orf5;unclassified drug;virus envelope protein;Arterivirus;article;chimera;controlled study;gene replication;genetic stability;genotype;in vitro study;nonhuman;nucleotide sequence;priority journal;progeny;protein function;protein structure;virus strain,"Tian, D.;Zheng, H.;Zhang, R.;Zhuang, J.;Yuan, S.",2011,,10.1016/j.virol.2010.12.048,0
2054,Genome sequence of a novel reassortant H3N2 avian influenza virus in southern China,"The distribution and prevalence of H3 subtype influenza viruses in avian and mammalian hosts constitutes a potential threat to both human and avian health. We report a complete genome sequence of a novel reassortant H3N2 avian influenza virus. Phylogenetic analysis showed that HA and NA showed the highest sequence homologies with those of A/white-backed munia/Hong Kong/4519/2009 (H3N2). However, the internal genes had the highest sequence homologies with those of H6 and H7 subtypes. The data provide further evidence of the existence of a natural reassortant H3N2 strain in southern China.","Animals;Base Sequence;*Bird Diseases/vi [Virology];China;*Genome, Viral;Influenza A Virus, H3N2 Subtype/cl [Classification];*Influenza A Virus, H3N2 Subtype/ge [Genetics];Influenza A Virus, H3N2 Subtype/ip [Isolation & Purification];Molecular Sequence Data;Phylogeny;Reassortant Viruses/cl [Classification];*Reassortant Viruses/ge [Genetics];Reassortant Viruses/ip [Isolation & Purification];Viral Proteins/ge [Genetics];0 (Viral Proteins)","Tian, J.;Zhang, C.;Qi, W.;Xu, C.;Huang, L.;Li, H.;Liao, M.",2012,Sep,,0
2055,Immunodominant E2 (gp53) sequences of highly virulent bovine viral diarrhea group II viruses indicate a close resemblance to a subgroup of border disease viruses,"The genes for the E2 envelope protein, which elicits virus-neutralizing antibodies, from members of the newly described group II of bovine viral diarrhea viruses (BVDVs) were cloned and sequenced. These BVDVs included a thrombocytopenic strain from the United States, a fetal bovine serum contaminant, a strain from Western Canada, and two highly virulent strains, causing high mortality rates, from Quebec. The nucleotide and amino acid sequences of these E2s had only a 60-65% homology with group I BVDV E2s but >90% homology with the E2 of a subgroup of sheep border disease viruses. The E2 gene of the NADL strain was expressed and monospecific antibodies were raised in calves and rabbits. The virus-neutralizing titers of these antisera were 15- to 80-fold lower for the heterologous group of BVDVs as compared to those for the homologous BVDVs.",monoclonal antibody;virus envelope protein;amino acid sequence;article;Bovine viral diarrhea virus 1;controlled study;nonhuman;nucleotide sequence;priority journal;taxonomy;virus characterization;virus classification,"Tijssen, P.;Pellerln, C.;Lecomte, J.;Van Den Hurk, J.",1996,,10.1006/viro.1996.0123,0
2056,Invasion of exotic bovine ephemeral fever virus into Taiwan in 2013-2014,"Bovine ephemeral fever virus is a member of the family Rhabdoviridae and bovine ephemeral fever has frequently affected cattle population in Taiwan since 1967. During the outbreaks in 2013 and 2014, exotic bovine ephemeral fever viruses were detected by reverse transcription polymerase chain reaction and nucleotide sequencing. Sequence comparison showed that the exotic viruses shared 99.0-99.4% nucleotide identities (99.4-100.0% amino acid identities) with Chinese viruses and, on the contrary, 96.2-97.2% nucleotide identities (97.8-98.6% amino acid identities) with indigenous Taiwanese viruses. Additionally, our phylogenetic analysis also supported that the newly invaded bovine ephemeral fever viruses were closely related to the Chinese strains. These exotic 2013-2014 viruses have become prevalent and displaced indigenous virus strains since their appearance.",amino acid sequence;article;Bovine ephemeral fever virus;nonhuman;nucleotide sequence;reverse transcription polymerase chain reaction;Taiwan;virus detection,"Ting, L. J.;Lee, M. S.;Lin, Y. L.;Cheng, M. C.;Lee, F.",2016,,10.1016/j.vetmic.2015.10.025,0
2057,Crimean-Congo hemorrhagic fever in Tajikistan Review,"Crimean-Congo hemorrhagic fever (CCHF) is a pathogenic tick-borne disease caused by a single-stranded negative-sense RNA virus classified within the Nairovirus genus of the family Bunyaviridae. Cases of CCHF have been registered in Tajikistan since the disease was first brought to medical attention in 1944. However, historical Tajik manuscripts describe the features of hemorrhagic fever associated with ticks, indicating that the disease might have been known in this region for many years before it was officially characterized. Here we review the historical context of CCHF in Tajikistan, much of which has been described over several decades in the Russian literature, and include reports of recent outbreaks in Tajikistan.","Adult;Animals;Arachnid Vectors/vi [Virology];Cattle;Disease Outbreaks;Female;*Hemorrhagic Fever Virus, Crimean-Congo/im [Immunology];Hemorrhagic Fever, Crimean/di [Diagnosis];Hemorrhagic Fever, Crimean/ep [Epidemiology];Hemorrhagic Fever, Crimean/th [Therapy];Hemorrhagic Fever, Crimean/vi [Virology];*Hemorrhagic Fever, Crimean;Humans;Male;Middle Aged;Tajikistan/ep [Epidemiology];Ticks/vi [Virology]","Tishkova, F. H.;Belobrova, E. A.;Valikhodzhaeva, M.;Atkinson, B.;Hewson, R.;Mullojonova, M.",2012,Sep,,0
2058,Targeted 16S rRNA high-throughput sequencing to characterize microbial communities during composting of livestock mortalities,"Aim A comprehensive understanding of the microbial community is necessary to ensure a significant reduction in pathogens during the composting process. Methods and Results Two biosecure, static composting systems containing cattle mortalities were constructed at subzero temperatures. Temperature at each sampling site was measured continuously and samples were grouped as either <= 50 or >= 55 degrees C, based on temperature exposure required for effective pathogen inactivation during composting. High-throughput 454 sequencing was used to characterize the bacterial communities within each sample. Clustering of bacterial communities was observed according to temperature. However, neither richness nor diversity differed between temperature groups. Firmicutes was the most abundant phylum within both temperature groups but was more pronounced (63 center dot 6%) in samples >= 55 degrees C (P<0 center dot 05). Similarly, members of Clostridia, Clostridium sensu stricto (3 center dot 64%), Clostridium XI (0 center dot 59%), UF (Clostridiaceae 1) (5 center dot 29%) and UF (Clostridiales Incertae Sedis XI) (6 center dot 20%), were prominent at >= 55 degrees C (P<0 center dot 05), likely a reflection of spore survival and/or anaerobic microenvironments within passively aerated compost piles. Members of Thermobifida (3 center dot 54%), UO (Actinomycetales) (12 center dot 29%) and UO (Bacillales) (19 center dot 49%) were also prominent at >= 55 degrees C (P<0 center dot 05). Conclusion Substantial spatial diversity exists within bacterial communities in field-scale compost piles. Localized temperature at the site of sampling may be one of the factors contributing to this phenomenon. Significance and Impact of the Study This is the first study to describe the microbial community profile with the use of targeted 16S rRNA high-throughput sequencing in passively aerated composted livestock mortalities.",thermophilic;pyrosequencing;spatial variability;mortalities;cattle;16S rRNA;microbial community;compost;BACTERIAL COMMUNITIES;DIVERSITY;MANURE;CARCASSES;ACTINOMYCETE;DEGRADATION;DYNAMICS;VIRUS;PILES;SOIL,"Tkachuk, V. L.;Krause, D. O.;Knox, N. C.;Hamm, A. C.;Zvomuya, F.;Ominski, K. H.;McAllister, T. A.",2014,May,,0
2059,An extensive repetoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination,"Several pathogenic strains of Escherichia coli exploit type III secretion to inject ""effector proteins"" into human cells, which then subvert eukaryotic cell biology to the bacterium's advantage. We have exploited bioinformatics and experimental approaches to establish that the effector repertoire in the Sakai strain of enterohemorrhagic E. coli (EHEC) O157:H7 is much larger than previously thought. Homology searches led to the identification of >60 putative effector genes. Thirteen of these were judged to be likely pseudogenes, whereas 49 were judged to be potentially functional. In total, 39 proteins were confirmed experimentally as effectors: 31 through proteomics and 28 through translocation assays. At the protein level, the EHEC effector sequences fall into >20 families. The largest family, the NIeG family, contains 14 members in the Sakai strain alone. EHEC also harbors functional homologs of effectors from plant pathogens (HopPtoH, HopW, AvrA) and from Shigella (OspD, OspE, OspG), and two additional members of the Map/IpgB family. Genes encoding proven or predicted effectors occur in >20 exchangeable effector loci scattered throughout the chromosome. Crucially, the majority of functional effector genes are encoded by nine exchangeable effector loci that lie within lambdoid prophages. Thus, type III secretion in E. coli is linked to a vast phage ""metagenome,"" acting as a crucible for the evolution of pathogenicity. © 2006 by The National Academy of Sciences of the USA.",bacterial protein;effector protein;protein;protein avrA;protein hopptoh;protein hopw;protein ipgb;protein map;protein ospd;protein OspE;protein OspG;unclassified drug;article;bacterial gene;bacterial genetics;bacterial strain;bacterial virulence;Enterobacteria phage lambda;bioinformatics;enterohemorrhagic Escherichia coli;Escherichia coli O157;experimental study;gene identification;gene sequence;nonhuman;plant disease;priority journal;protein family;proteomics;pseudogene;sequence homology;Shigella,"Tobe, T.;Beatson, S. A.;Taniguchi, H.;Abe, H.;Bailey, C. M.;Fivian, A.;Younis, R.;Matthews, S.;Marches, O.;Frankel, G.;Hayashi, T.;Pallen, M. J.",2006,,10.1073/pnas.0604891103,0
2060,Full-Genome Sequence of Porcine Circovirus type 3 recovered from serum of sows with stillbirths in Brazil,"Two full-genome sequences of porcine circovirus type 3 (PCV3) are reported. The genomes were recovered from pooled serum samples from sows who had just delivered litters with variable numbers of stillbirths. The two circular genomes (PCV3-BR/RS/6 and PCV3-BR/RS/8) are 2,000 nucleotides long and contain two open reading frames (ORFs) oriented in opposite directions that encode the putative capsid (Cap) and replicase (Rep) proteins. The intergenic region contains a stem-loop motif, as reported for other circoviruses. Rolling circle replication motifs and putative helicase domains were identified in the Rep coding region. The degree of overall nucleotide similarity between the genomes reported here and those available at GenBank was higher than 97%. No PCV3 sequence was detected in pooled serum samples from sows which had no stillbirths on the same farms. However, further studies are necessary to confirm the association between PCV3 and the occurrence of stillbirths.",amino acid sequence;article;Brazil;carditis;Circovirus;gene sequence;maximum likelihood method;nonhuman;nucleotide sequence;open reading frame;phylogeny;sequence homology;sow (swine);stillbirth;whole genome sequencing,"Tochetto, C.;Lima, D. A.;Varela, A. P. M.;Loiko, M. R.;Paim, W. P.;Scheffer, C. M.;Herpich, J. I.;Cerva, C.;Schmitd, C.;Cibulski, S. P.;Santos, A. C.;Mayer, F. Q.;Roehe, P. M.",2018,,10.1111/tbed.12735,1
2061,Circoviruses: immunosuppressive threats to avian species: a review,"Circoviruses are small, non-enveloped, icosahedral viruses that are unique among animal viruses in having circular, single-stranded DNA genomes. Their genomes are also the smallest possessed by animal viruses. The circovirus family currently comprises three members, chicken anaemia virus, porcine circovirus, and psittacine beak and feather disease virus, with pigeon circovirus being classified as a tentative member. Infections with each of the four circoviruses are associated with potentially fatal diseases in which virus-induced damage to lymphoid tissue and immunosuppression are common features. Experience with other animal virus families suggests that additional animal species will be infected by, as yet undiscovered, circoviruses and that these may display similar tissue tropism and disease-causing potential. Recent reports describing the association of circovirus-like viruses with immunodeficiency-related diseases of geese and southern black-backed gulls suggest that circovirus infections of avian species may be more common than previously recognized, and prompt the question of whether novel circoviruses infect poultry to cause clinical and/or subclinical diseases that may be economically important. This review has three purposes. First, it is designed to summarize the currently available information about the classified circoviruses and viruses that are regarded as circovirus-like. Second, it aims to alert the readership to the possibility that other avian species, including commercial poultry, may be infected with novel circoviruses. Finally, possible methods for discovering novel circoviruses and for controlling infections by such viruses are suggested.",,"Todd, D.",2000,Oct,,0
2062,Morphogenesis of a cytomegalovirus from an American bison affected with malignant catarrhal fever,"A herpesvirus isolated from several organs of an American bison affected with malignant catarrhal fever was cultured in bovine foetal spleen cells and studied by electron microscopy. The fine structural features of the mature virion and the mode of virus morphogenesis were found to be similar to herpesviruses classified in the subgroup cytomegalovirus. The capsids were granular, hexagonal in shape and contained pleomorphic cores in thin sections. Envelopment of the capsids occurred primarily by budding on cytoplasmic membranes which appeared to be formed as extended vesicles of the Golgi apparatus; budding on nuclear membranes was only rarely observed. Cytoplasmic inclusions consisting of granular threads and amorphous electron-dense material were found in association with virions during the late stages of infection. The formation of cytoplasmic inclusions, the morphogenesis and ultrastructure of the virus are all consistent with classification of this virus as a cytomegalovirus.",cell culture;Cytomegalovirus;electron microscopy;in vitro study;Ovine herpesvirus 2;mammal;virogenesis;virus classification;virus inclusion;virus isolation,"Todd, W. J.;Storz, J.",1983,,,0
2063,Differentiation between vaccine and wild-type varicella-zoster virus genotypes by high-resolution melt analysis of single nucleotide polymorphisms,"Background: The analysis of single nucleotide polymorphisms (SNPs) of varicella-zoster virus (VZV) has enabled differentiation between wild-type genotypes from the Oka vaccine strain (V-Oka). Objectives: To genotype VZV strains in Australia using high-resolution melt (HRM) analysis of SNPs in five gene targets. Study design: Extracted DNA from 78 samples obtained from patients with chickenpox and zoster were genotyped by HRM analysis of SNPs in five open reading frames (ORFs): 1 (685 G > A), 21 (33 725 C > T), 37 (66 288 G > A), 60 (101 464 C > A) and 62 (106 262 T > C) using a double-stranded (ds) DNA saturating dye, LC Green Plus. Results: For each genotype, melt curve temperature (Tm) shifts differentiated the nucleotide present at that locus (P < 0.0001) with melting curve shifts between alleles ranging from 0.56 °C (ORF 37) to 3.34 °C (ORF 62). The most common genotypes detected were the European Type C (59%) and B (18%) strains. This was followed by the African/Asian Type A (14%) and Japanese J1 (9%), strains, both prevalent in the Northern Territory and Western Australia. Conclusions: HRM analysis of SNPs showed that the European B and C genotypes were most prevalent in Australia, with genotypes A and J strains also present. HRM analysis using a dsDNA dye provides a useful tool in classifying varicella-zoster viruses. © 2008 Elsevier B.V. All rights reserved.",chickenpox vaccine;double stranded DNA;dye;oka vaccine;unclassified drug;varicella zoster vaccine;virus vaccine;African American;allele;article;Asian;Australia;chickenpox;controlled study;DNA extraction;gene locus;gene targeting;genotype;herpes zoster;human;human cell;Japanese (people);major clinical study;molecular epidemiology;nucleic acid base substitution;nucleotide sequence;open reading frame;prevalence;priority journal;single nucleotide polymorphism;statistical significance;temperature;Varicella zoster virus;virus strain;wild type;varilrix;varivax,"Toi, C. S.;Dwyer, D. E.",2008,,10.1016/j.jcv.2008.03.027,0
2064,Discovery of a novel nidovirus in cattle with respiratory disease,"The family Coronaviridae represents a diverse group of vertebrate RNA viruses, all with genomes greater than 26 000 nt. Here, we report the discovery and genetic characterization of a novel virus present in cattle with respiratory disease. Phylogenetic characterization of this virus revealed that it clusters within the subfamily Torovirinae, in the family Coronaviridae. The complete genome consists of only 20 261 nt and represents the smallest reported coronavirus genome. We identified seven ORFs, including the canonical nidovirus ORF1a and ORF1b. Analysis of polyprotein 1ab revealed that this virus, tentatively named bovine nidovirus (BoNV), shares the highest homology with the recently described python-borne nidoviruses and contains several conserved nidovirus motifs, but does not encode the NendoU or O-MT domains that are present in other viruses within the family Coronaviridae. In concert with its reduced genome, the atypical domain architecture indicates that this virus represents a unique lineage within the order Nidovirales.",amino acid sequence;animal tissue;article;bovine;controlled study;genome size;high throughput sequencing;immunoprecipitation;Nidovirales;nonhuman;phylogeny;priority journal;protein glycosylation;respiratory tract disease;virus classification;virus genome,"Tokarz, R.;Sameroff, S.;Hesse, R. A.;Hause, B. M.;Desai, A.;Jain, K.;Ian Lipkin, W.",2015,,10.1099/vir.0.000166,1
2065,"Virome analysis of Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis ticks reveals novel highly divergent vertebrate and invertebrate viruses",,,"Tokarz, R.;Williams, S. H.;Sameroff, S.;Leon, M. S.",2014,,,0
2066,Phylogenetic study of viral isolates of swine and human hepatitis E virus,,DNA fragment;virus DNA;virus RNA;article;controlled study;DNA extraction;genotype;hepatitis E;Hepatitis E virus;human;molecular phylogeny;nonhuman;nucleotide sequence;reverse transcription polymerase chain reaction;RNA extraction;sequence analysis;species difference;pig;viral genetics;virus gene;virus isolation;virus transmission,"Tolari, F.;Del Chiaro, L.;Card, R.;Mazzei, M.;Bandecchi, P.;Banks, M.",2006,,10.1007/s11259-006-0059-z,0
2067,Birds and viruses at a crossroad--surveillance of influenza A virus in Portuguese waterfowl,"During recent years, extensive amounts of data have become available regarding influenza A virus (IAV) in wild birds in northern Europe, while information from southern Europe is more limited. Here, we present an IAV surveillance study conducted in western Portugal 2008-2009, analyzing 1653 samples from six different species of waterfowl, with the majority of samples taken from Mallards (Anas platyrhynchos). Overall 4.4% of sampled birds were infected. The sampling results revealed a significant temporal variation in the IAV prevalence, including a pronounced peak among predominantly young birds in June, indicating that IAV circulate within breeding populations in the wetlands of western Portugal. The H10N7 and H9N2 subtypes were predominant among isolated viruses. Phylogenetic analyses of the hemagglutinin and neuraminidase sequences of H10N7, H9N2 and H11N3 virus showed that sequences from Portugal were closely related to viral sequences from Central Europe as well as to IAVs isolated in the southern parts of Africa, reflecting Portugal's position on the European-African bird migratory flyway. This study highlights the importance of Portugal as a migratory crossroad for IAV, connecting breeding stationary waterfowl with birds migrating between continents which enable transmission and spread of IAV.","Animal Migration;Animals;Animals, Wild/ge [Genetics];Animals, Wild/vi [Virology];*Birds/vi [Virology];Female;Influenza A Virus, H10N7 Subtype/ge [Genetics];*Influenza A Virus, H10N7 Subtype/ip [Isolation & Purification];Influenza A Virus, H9N2 Subtype/ge [Genetics];*Influenza A Virus, H9N2 Subtype/ip [Isolation & Purification];Influenza in Birds/ep [Epidemiology];*Influenza in Birds/vi [Virology];Phylogeny;Portugal/ep [Epidemiology]","Tolf, C.;Bengtsson, D.;Rodrigues, D.;Latorre-Margalef, N.;Wille, M.;Figueiredo, M. E.;Jankowska-Hjortaas, M.;Germundsson, A.;Duby, P. Y.;Lebarbenchon, C.;Gauthier-Clerc, M.;Olsen, B.;Waldenstrom, J.",2012,,,0
2068,Birds and Viruses at a Crossroad - Surveillance of Influenza A Virus in Portuguese Waterfowl,"During recent years, extensive amounts of data have become available regarding influenza A virus (IAV) in wild birds in northern Europe, while information from southern Europe is more limited. Here, we present an IAV surveillance study conducted in western Portugal 2008-2009, analyzing 1653 samples from six different species of waterfowl, with the majority of samples taken from Mallards (Anas platyrhynchos). Overall 4.4% of sampled birds were infected. The sampling results revealed a significant temporal variation in the IAV prevalence, including a pronounced peak among predominantly young birds in June, indicating that IAV circulate within breeding populations in the wetlands of western Portugal. The H10N7 and H9N2 subtypes were predominant among isolated viruses. Phylogenetic analyses of the hemagglutinin and neuraminidase sequences of H10N7, H9N2 and H11N3 virus showed that sequences from Portugal were closely related to viral sequences from Central Europe as well as to IAVs isolated in the southern parts of Africa, reflecting Portugal's position on the European-African bird migratory flyway. This study highlights the importance of Portugal as a migratory crossroad for IAV, connecting breeding stationary waterfowl with birds migrating between continents which enable transmission and spread of IAV. © 2012 Tolf et al.",virus hemagglutinin;virus sialidase;Africa;amino acid sequence;Anas platyrhynchos;article;breeding;disease surveillance;waterfowl;geographic distribution;Influenza A virus;Influenza A virus (H10N7);Influenza virus A H11N3;Influenza A virus (H9N2);nonhuman;nucleotide sequence;phylogeny;population migration;Portugal;Portuguese waterfowl;prevalence;sequence analysis;strain difference;unindexed sequence;virus isolation;virus strain;virus transmission;wetland,"Tolf, C.;Bengtsson, D.;Rodrigues, D.;Latorre-Margalef, N.;Wille, M.;Figueiredo, M. E.;Jankowska-Hjortaas, M.;Germundsson, A.;Duby, P. Y.;Lebarbenchon, C.;Gauthier-Clerc, M.;Olsen, B.;Waldenström, J.",2012,,10.1371/journal.pone.0049002,0
2069,Development of an RT-qPCR assay for the specific detection of a distinct genetic lineage of the infectious bursal disease virus,"The infectious bursal disease virus (IBDV) is a major health threat to the world's poultry industry despite intensive controls including proper biosafety practices and vaccination. IBDV (Avibirnavirus, Birnaviridae) is a non-enveloped virus with a bisegmented double-stranded RNA genome. The virus is traditionally classified into classic, variant and very virulent strains, each with different epidemiological relevance and clinical implications. Recently, a novel worldwide spread genetic lineage was described and denoted as distinct (d) IBDV. Here, we report the development and validation of a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay for the specific detection of dIBDVs in the global poultry industry. The assay employs a TaqMan-MGB probe that hybridizes with a unique molecular signature of dIBDV. The assay successfully detected all the assessed strains belonging to the dIBDV genetic lineage, showing high specificity and absence of cross-reactivity with non-dIBDVs, IBDV-negative samples and other common avian viruses. Using serial dilutions of in vitro-transcribed RNA we obtained acceptable PCR efficiencies and determination coefficients, and relatively small intra- and inter-assay variability. The assay demonstrated a wide dynamic range between 103 and 108 RNA copies/reaction. This rapid, specific and quantitative assay is expected to improve IBDV surveillance and control worldwide and to increase our understanding of the molecular epidemiology of this economically detrimental poultry pathogen.","double stranded RNA;primer DNA;viral protein;VP2 protein, infectious bursal disease virus;animal;bird disease;birnavirus infection;bursa Fabricii;chicken;classification;DNA probe;genetics;infectious bursal disease virus;isolation and purification;procedures;reverse transcription polymerase chain reaction;sensitivity and specificity;sequence alignment;veterinary medicine;virology","Tomás, G.;Hernández, M.;Marandino, A.;Techera, C.;Grecco, S.;Hernández, D.;Banda, A.;Panzera, Y.;Pérez, R.",2017,,10.1080/03079457.2016.1228827,0
2070,"Contagious Ecthyma, Rangiferine Brucellosis, and Lungworm Infection in a Muskox ( Ovibos moschatus ) from the Canadian Arctic, 2014","An adult male muskox ( Ovibos moschatus ), harvested on 26 August 2014 on Victoria Island, Nunavut, in the Canadian Arctic, had proliferative dermatitis on the muzzle and fetlocks suggestive of contagious ecthyma or orf (Parapoxvirus). Histopathologic features of the lesions were consistent with this diagnosis. Orf virus DNA, phylogenetically similar to an isolate from a captive muskox of the Minnesota Zoo, US, was detected in the lesions by PCR using Parapoxvirus primers. Additionally, there was a metaphyseal abscess with a cortical fistula in the right metacarpus from which Brucella suis biovar 4 was isolated and identification supported by PCR. Brucella spp. antibodies were detected in serum. Finally, 212 nodules were dissected from the lungs. Fecal analysis and lung examination demonstrated co-infection with the lungworms Umingmakstrongylus pallikuukensis and Varestrongylus eleguneniensis. The zoonotic potential of orf and rangiferine brucellosis adds an important public health dimension to this case, particularly given that muskoxen are a valuable source of food for Arctic residents. Careful examination of these pathogens at a population level is needed as they may contribute to muskox population decline and potentially constitute a driver of food insecurity for local communities. This case underscores the importance of wildlife health surveillance as a management tool to conserve wildlife populations and maintain food security in subsistence-oriented communities.",animal;Arctic;brucellosis;Canada;case report;contagious ecthyma;genetics;lung infection;male;microbiology;nematodiasis;Orf virus;parasitology;pathology;phylogeny;ruminant;veterinary medicine;virology,"Tomaselli, M.;Dalton, C.;Duignan, P. J.;Kutz, S.;van der Meer, F.;Kafle, P.;Surujballi, O.;Turcotte, C.;Checkley, S.",2016,,10.7589/2015-12-327,0
2071,Detection and heterogeneity of herpesviruses causing Pacheco's disease in parrots,"Pacheco's disease (PD) is a common, often fatal, disease of parrots. We cloned a virus isolate from a parrot that had characteristic lesions of PD. Three viral clones were partially sequenced, demonstrating that this virus was an alphaherpesvirus most closely related to the gallid herpesvirus 1. Five primer sets were developed from these sequences. The primer sets were used with PCR to screen tissues or tissue culture media suspected to contain viruses from 54 outbreaks of PD. The primer sets amplified DNA from all but one sample. Ten amplification patterns were detected, indicating that PD is caused by a genetically heterogeneous population of viruses. A single genetic variant (psittacid herpesvirus variant 1) amplified with all primer sets and was the most common virus variant (62.7%). A single primer set (23F) amplified DNA from all of the positive samples, suggesting that PCR could be used as a rapid postmortem assay for these viruses. PCR was found to be significantly more sensitive than tissue culture for the detection of psittacid herpesviruses.",virus DNA;animal tissue;article;autopsy;bird disease;controlled study;diagnostic accuracy;genetic analysis;genetic heterogeneity;Herpesviridae;intermethod comparison;nonhuman;nucleotide sequence;parrot;polymerase chain reaction;priority journal;sequence analysis;tissue culture;viral genetics;virus classification;virus culture;virus detection,"Tomaszewski, E.;Wilson, V. G.;Wigle, W. L.;Phalen, D. N.",2001,,10.1128/jcm.39.2.533-538.2001,0
2072,Molecular phylogeny of the psittacid herpesviruses causing Pacheco's disease: Correlation of genotype with phenotypic expression,"Fragments of 419 bp of the UL16 open reading frame from 73 psittacid herpesviruses (PsHVs) from the United States and Europe were sequenced. All viruses caused Pacheco's disease, and serotypes of the European isolates were known. A phylogenetic tree derived from these sequences demonstrated that the PsHVs that cause Pacheco's disease comprised four major genotypes, with each genotype including between two and four variants. With the exception of two viruses, the serotypes of the virus isolates could be predicted by the genotypes. Genotypes 1 and 4 corresponded to serotype 1 isolates, genotype 2 corresponded to serotype 2 isolates, and genotype 3 corresponded to serotype 3 isolates. The single serotype 4 virus mapped to genotype 4. DNA from a virus with a unique serotype could not be amplified with primers that amplified DNA from all other PsHVs, and its classification remains unknown. Viruses representing all four genotypes were found in both the United States and Europe, and it was therefore predicted that serotypes 1, 2, and 3 were present in the United States. Serotype 4 was represented by a single European isolate that could not be genetically distinguished from serotype 1 viruses; therefore, the presence of serotype 4 in the United States could not be predicted. Viruses of genotype 4 were found to be the most commonly associated with Pacheco's disease in macaws and conures and were least likely to be isolated in chicken embryo fibroblasts in the United States. All four genotypes caused deaths in Amazon parrots, but genotype 4 was associated with Pacheco's disease only in Amazons in Europe. Genotypes 2, 3, and 4, but not 1, were found in African grey parrots. Although parrots from the Pacific distribution represent a relatively small percentage of the total number of birds with Pacheco's disease, all four genotypes were found to cause disease in these species.",animal disease;article;bird disease;death;Europe;genotype;Herpesviridae;nonhuman;nucleotide sequence;open reading frame;pacheco disease;parrot;phenotype;phylogeny;priority journal;psittacine;serotype;United States;virus infection;virus isolation,"Tomaszewski, E. K.;Kaleta, E. F.;Phalen, D. N.",2003,,10.1128/jvi.77.20.11260-11267.2003,0
2073,Characterization of the Dynamic Transcriptome of a Herpesvirus with Long-read Single Molecule Real-Time Sequencing,"Herpesvirus gene expression is co-ordinately regulated and sequentially ordered during productive infection. The viral genes can be classified into three distinct kinetic groups: immediate-early, early, and late classes. In this study, a massively parallel sequencing technique that is based on PacBio Single Molecule Real-time sequencing platform, was used for quantifying the poly(A) fraction of the lytic transcriptome of pseudorabies virus (PRV) throughout a 12-hour interval of productive infection on PK-15 cells. Other approaches, including microarray, real-time RT-PCR and Illumina sequencing are capable of detecting only the aggregate transcriptional activity of particular genomic regions, but not individual herpesvirus transcripts. However, SMRT sequencing allows for a distinction between transcript isoforms, including length- and splice variants, as well as between overlapping polycistronic RNA molecules. The non-amplified Isoform Sequencing (Iso-Seq) method was used to analyse the kinetic properties of the lytic PRV transcripts and to then classify them accordingly. Additionally, the present study demonstrates the general utility of long-read sequencing for the time-course analysis of global gene expression in practically any organism.",transcriptome;viral protein;animal;cell line;cytology;eukaryotic cell;gene expression profiling;gene expression regulation;genetics;genomics;high throughput sequencing;physiology;pig;procedures;Pseudorabies virus;virology;virus genome,"Tombácz, D.;Balázs, Z.;Csabai, Z.;Moldován, N.;Szűcs, A.;Sharon, D.;Snyder, M.;Boldogkői, Z.",2017,,10.1038/srep43751,0
2074,Metagenomic assessment of adventitious viruses in commercial bovine sera,"Animal serum is an essential supplement for cell culture media. Contamination of animal serum with adventitious viruses has led to major regulatory action and product recalls. We used metagenomic methods to detect and characterize viral contaminants in 26 bovine serum samples from 12 manufacturers. Across samples, we detected sequences with homology to 20 viruses at depths of up to 50,000 viral reads per million. The viruses detected represented nine viral families plus four taxonomically unassigned viruses and had both RNA genomes and DNA genomes. Sequences ranged from 28% to 96% similar at the amino acid level to viruses in the GenBank database. The number of viruses varied from zero to 11 among samples and from one to 11 among suppliers, with only one product from one supplier being entirely “clean.” For one common adventitious virus, bovine viral diarrhea virus (BVDV), abundance estimates calculated from metagenomic data (viral reads per million) closely corresponded to Ct values from quantitative real-time reverse transcription polymerase chain reaction (rtq-PCR), with metagenomics being approximately as sensitive as rtq-PCR. Metagenomics is useful for detecting taxonomically and genetically diverse adventitious viruses in commercial serum products, and it provides sensitive and quantitative information.",article;blood sampling;Bovine viral diarrhea virus 1;calculation;controlled study;genome analysis;metagenomics;nonhuman;population abundance;priority journal;quantitative analysis;real time polymerase chain reaction;reverse transcription polymerase chain reaction;sequence analysis;sequence homology;viral contamination;virus detection;virus genome,"Toohey-Kurth, K.;Sibley, S. D.;Goldberg, T. L.",2017,,10.1016/j.biologicals.2016.10.009,0
2075,Sequencing approach to analyze the role of quasispecies for classical swine fever,"Classical swine fever virus (CSFV) is a positive-sense RNA virus with a high degree of genetic variability among isolates. High diversity is also found in virulence, with strains covering the complete spectrum from avirulent to highly virulent. The underlying genetic determinants are far from being understood. Since RNA polymerases of RNA viruses lack any proof-reading activity, different genome variations called haplotypes, occur during replication. A set of haplotypes is referred to as a viral quasispecies. Genetic variability can be a fitness advantage through facilitating of a more effective escape from the host immune response. In order to investigate the correlation of quasispecies composition and virulence in vivo, we analyzed next-generation sequencing data of CSFV isolates of varying virulence. Viral samples from pigs infected with the highly virulent isolates ""Koslov"" and ""Brescia"" showed higher quasispecies diversity and more nucleotide variability, compared to samples of pigs infected with low and moderately virulent isolates.","Animals;*Classical Swine Fever/vi [Virology];*Classical Swine Fever Virus/cl [Classification];*Classical Swine Fever Virus/ge [Genetics];Classical Swine Fever Virus/ip [Isolation & Purification];Classical Swine Fever Virus/py [Pathogenicity];*Genetic Variation;Haplotypes;High-Throughput Nucleotide Sequencing;RNA, Viral/ge [Genetics];Swine;Virulence;0 (RNA, Viral)","Topfer, A.;Hoper, D.;Blome, S.;Beer, M.;Beerenwinkel, N.;Ruggli, N.;Leifer, I.",2013,Mar 30,,0
2076,Genetic typing of bovine viral diarrhoea virus: Most Slovenian isolates are of genotypes 1d and 1f,"A selection of 43 bovine viral diarrhoea viruses isolated from mainly persistently infected cattle on 23 Slovenian farms between 1997 and 2001 were characterised genetically. Viral RNA was extracted from infected cell cultures, reverse transcribed and amplified by PCR with primers targeting the 5′-UTR and the Npro gene, followed by direct sequencing of purified PCR products obtained for both genomic regions. The Npro sequences provided the best genetic resolution, and gave also higher statistical support for phylogenetic classification of the viruses. Thirty-eight of the Slovenian isolates were of genetic subtypes 1d and 1f, four were 1b, and one subtype 1g. No BVDV type 2 viruses were found. This genetic prevalence matched those previously reported for neighbouring countries, as opposed to findings reported for more distant European countries, e.g. France, Spain and the UK. From eight cattle herds several virus isolates were analysed; with one exception all isolates from each herd were of the same genetic group. Extended sequencing of the Npro and part of the C gene of virus isolates with identical 5′-UTR sequences allowed differentiation between isolates obtained at different times from one herd. © 2004 Elsevier B.V. All rights reserved.",virus RNA;5' untranslated region;animal cell;Bovine viral diarrhea virus 1;bovine;cell culture;controlled study;France;gene amplification;gene sequence;genome analysis;genotype;herd;molecular phylogeny;nonhuman;nucleotide sequence;reverse transcription polymerase chain reaction;review;RNA extraction;Slovenia;Spain;United Kingdom;virus classification;virus genome;virus isolation;virus typing,"Toplak, I.;Sandvik, T.;Barlič-Maganja, D.;Grom, J.;Paton, D. J.",2004,,10.1016/j.vetmic.2003.12.004,0
2077,Biological and molecular characterization of avian influenza virus (H9N2) isolates from Iran,"Three Influenza A virus (H9N2) isolates obtained from three separate broiler flocks with variable mortality rates were cloned twice in embryonated SPF chicken eggs by limiting dilution. Biological properties of these isolates were examined in 4-week-old SPF chickens and chick embryo fibroblast (CEF) cultures. The isolates neither caused mortality in the inoculated chickens nor produced CPE in cell cultures, indicating low pathogenicity. PCR products of 486 bp containing the sequences for hemagglutinin (HA) cleavage site, which were generated from the isolates, were subjected to nucleotide sequencing. Sequence analysis of the HA region containing the cleavage site of the isolates showed a similar sequence motif (PARSSRG) but different flanking regions. Phylogenetic analysis of deduced amino acid sequences revealed that the isolates were closely related to those isolated earlier, indicating a common source. Moreover, the amino acid sequences of the recent isolates were very similar to those from Saudi Arabia, Germany and Pakistan. It is postulated that, except for some Chinese isolates, the pathogenicity of Iranian isolates seems to be similar to that of other Eurasian isolates. It is possible that an elevation in mortality rate under field condition could be caused by coinfection of recent isolates with the bacteria such as mycoplasma, Escherichia coli, and Ornithobacterium rhinotracheale rather than by an emerging a pathogenic H9N2 subtype of the virus.",hemagglutinin;amino acid sequence;article;avian influenza;chick embryo;chicken;controlled study;Germany;Influenza virus;Influenza A virus;Iran;mortality;nonhuman;nucleotide sequence;Pakistan;phylogeny;Saudi Arabia;sequence analysis;virus isolation,"Toroghi, R.;Momayez, R.",2006,,,0
2078,Emergence of amantadine-resistant avian influenza H5N1 virus in India,"This study reports the genetic characterization of highly pathogenic avian influenza (HPAI) virus (subtype H5N1) isolated from poultry in West Bengal, India. We analyzed all the eight genome segments of two viruses isolated from chickens in January 2010 to understand their genetic relationship with other Indian H5N1 isolates and possible connection between different outbreaks. The hemagglutinin (HA) gene of the viruses showed multiple basic amino acids at the cleavage site, a marker for high virulence in chickens. Of greatest concern was that the viruses displayed amino acid substitution from serine-to-asparagine at position 31 ofM2 ion channel protein suggesting emergence of amantadine-resistant mutants not previously reported in HPAI H5N1 outbreaks in India. Amino acid lysine at position 627 of the PB2 protein highlights the risk the viruses possess to mammals. In the phylogenetic trees, the viruses clustered within the lineage of avian isolates from India (2008-2009) and avian and human isolates from Bangladesh (2007-2009) in all the genes. Both these viruses were most closely related to the viruses from 2008 in West Bengal within the subclade 2.2.3 of H5N1 viruses. © Springer Science+Business Media, LLC 2010.",amantadine;asparagine;lysine;serine;virus hemagglutinin;amino acid substitution;antiviral resistance;article;chicken;controlled study;embryo;gene cluster;genome analysis;India;Influenza A virus (H5N1);molecular phylogeny;nonhuman;nucleotide sequence;priority journal;protein cleavage;sequence analysis;sequence homology;virus gene;virus genome;virus hemagglutinin gene;virus identification;virus isolation;virus mutant;virus virulence,"Tosh, C.;Murugkar, H. V.;Nagarajan, S.;Tripathi, S.;Katare, M.;Jain, R.;Khandia, R.;Syed, Z.;Behera, P.;Patil, S.;Kulkarni, D. D.;Dubey, S. C.",2011,,10.1007/s11262-010-0534-z,0
2079,First genetic characterization of Peste des Petits Ruminants from Niger: On the advancing front of the Asian virus lineage,"Peste des Petits Ruminants (PPR) is a serious transboundary infectious disease of small ruminants. The causal agent, PPR virus (PPRV), can be separated into four genetically distinct lineages using phylogenetic analysis. In recent decades, lineage IV of PPRV has dramatically extended its geographic distribution from Asia to the Middle East and to Africa, where it has progressively replaced other PPRV lineages. Lineages I and II are historically distributed in West Africa. Currently, lineage II appears to dominate the region, whereas the last recorded occurrence of lineage I dates back to 1994. Recent studies reported the presence of lineage IV in Nigeria, suggesting that this lineage is expanding in West Africa. In Niger, a close neighbour of Nigeria, PPRV has never been genetically characterized, despite reports of PPR incidence. In this study, pathological samples collected from sick goats were collected in 2013 during a suspected PPR outbreak in southern Niger close to the Nigerian border were compared to samples collected in a previous investigation in October 2001 in south-western Niger. These strains were characterized by sequencing and phylogenetic analysis to identify their genetic lineage. Our results show that in 2001, lineages I and II were cocirculating in south-western Niger, whereas the strain that caused the outbreak in 2013 belonged to lineage IV and is closely related to strains identified in Nigeria. These results confirm the progression of lineage IV in West Africa. The process of PPRV lineage replacement and its implications for the epidemiology and the control of the disease in this region are unclear and should be the subject of further studies in the field.",article;controlled study;gene sequence;genetic lineage;genetic parameters;genetic stability;geographic distribution;goat;nonhuman;nucleotide sequence;peste des petits ruminants;phylogenetic tree;reverse transcription polymerase chain reaction;RNA extraction;virus characterization;virus isolation;virus virulence,"Tounkara, K.;Bataille, A.;Adombi, C. M.;Maikano, I.;Djibo, G.;Settypalli, T. B. K.;Loitsch, A.;Diallo, A.;Libeau, G.",2018,,10.1111/tbed.12901,0
2080,Genetic and biological characterisation of an avian-like H1N2 swine influenza virus generated by reassortment of circulating avian-like H1N1 and H3N2 subtypes in Denmark,"Background: The influenza A virus subtypes H1N1, H1N2 and H3N2 are the most prevalent subtypes in swine. In 2003, a reassorted H1N2 swine influenza virus (SIV) subtype appeared and became prevalent in Denmark. In the present study, the reassortant H1N2 subtype was characterised genetically and the infection dynamics compared to an ""avian-like"" H1N1 virus by an experimental infection study. Methods. Sequence analyses were performed of the H1N2 virus. Two groups of pigs were inoculated with the reassortant H1N2 virus and an ""avian-like"" H1N1 virus, respectively, followed by inoculation with the opposite subtype four weeks later. Measurements of HI antibodies and acute phase proteins were performed. Nasal virus excretion and virus load in lungs were determined by real-time RT-PCR. Results: The phylogenetic analysis revealed that the reassorted H1N2 virus contained a European ""avian-like"" H1-gene and a European ""swine-like"" N2-gene, thus being genetically distinct from most H1N2 viruses circulating in Europe, but similar to viruses reported in 2009/2010 in Sweden and Italy. Sequence analyses of the internal genes revealed that the reassortment probably arose between circulating Danish ""avian-like"" H1N1 and H3N2 SIVs. Infected pigs developed cross-reactive antibodies, and increased levels of acute phase proteins after inoculations. Pigs inoculated with H1N2 exhibited nasal virus excretion for seven days, peaking day 1 after inoculation two days earlier than H1N1 infected pigs and at a six times higher level. The difference, however, was not statistically significant. Pigs euthanized on day 4 after inoculation, had a high virus load in all lung lobes. After the second inoculation, the nasal virus excretion was minimal. There were no clinical sign except elevated body temperature under the experimental conditions. Conclusions: The ""avian-like"" H1N2 subtype, which has been established in the Danish pig population at least since 2003, is a reassortant between circulating swine ""avian-like"" H1N1 and H3N2. The Danish H1N2 has an ""avian-like"" H1 and differs from most other reported H1N2 viruses in Europe and North America/Asia, which have H1-genes of human or ""classical-swine"" origin, respectively. The variant seems, however, also to be circulating in countries like Sweden and Italy. The infection dynamics of the reassorted ""avian-like"" H1N2 is similar to the older ""avian-like"" H1N1 subtype. © 2013 Trebbien et al.; licensee BioMed Central Ltd.",acute phase protein;cross reacting antibody;animal experiment;animal model;antibody detection;article;controlled study;Denmark;genetic reassortment;Influenza A virus (H1N1);Influenza A virus (H1N2);Influenza A virus (H3N2);nonhuman;phylogeny;sequence analysis;Spanish influenza;viral genetics;virus excretion;virus load;virus strain,"Trebbien, R.;Bragstad, K.;Larsen, L. E.;Nielsen, J.;Bøtner, A.;Heegaard, P. M.;Fomsgaard, A.;Viuff, B.;Hjulsager, C. K.",2013,,10.1186/1743-422x-10-290,0
2081,Neuropathological survey reveals underestimation of the prevalence of neuroinfectious diseases in cattle in Switzerland,"Neuroinfectious diseases in livestock represent a severe threat to animal health, but their prevalence is not well documented and the etiology of disease often remains unidentified. The aims of this study were to generate baseline data on the prevalence of neuroinfectious diseases in cattle in Switzerland by neuropathological survey, and to identify disease-associated pathogens. The survey was performed over a 1-year period using a representative number of brainstem samples (n = 1816) from fallen cattle. In total, 4% (n = 73) of the animals had significant lesions, the most frequent types of which were indicative of viral (n = 27) and bacterial (n = 31) etiologies. Follow-up diagnostics by immunohistochemistry, PCR protocols and next-generation sequencing identified infection with Listeria monocytogenes (n = 6), ovine herpesvirus 2 (n = 7), bovine astrovirus CH13 (n = 2), bovine herpesvirus 6 (n = 6), bovine retrovirus CH15 (n = 2), posavirus 1 (n = 2), and porcine astroviruses (n = 2). A retrospective questionnaire-based investigation indicated that animals' owners observed clinical signs of neurological disease in about one-third of cases with lesions, which was estimated to correspond to approximately 85 cases per year in the adult fallen cattle population in Switzerland. This estimate stands in sharp contrast to the number of cases reported to the authorities and reveals a gap in disease surveillance. Systematic neuropathological examination and follow-up molecular testing of neurologically diseased cattle could significantly enhance the efficiency of disease detection for the purposes of estimating the prevalence of endemic diseases, identifying new or re-emerging pathogens, and providing ""early warnings"" of disease outbreaks.",Cattle;Neurology;Zoonosis;Infectious disease;Surveillance;Neurovirology;MALIGNANT CATARRHAL FEVER;REAL-TIME PCR;NONSUPPURATIVE ENCEPHALITIS;LISTERIA-MONOCYTOGENES;BSE SURVEILLANCE;SMALL RUMINANTS;ASTROVIRUS;IDENTIFICATION;HERPESVIRUS;VIROME,"Truchet, L.;Walland, J.;Wuthrich, D.;Boujon, C. L.;Posthaus, H.;Bruggmann, R.;Schupbach-Regula, G.;Oevermann, A.;Seuberlich, T.",2017,Sep,,0
2082,High-throughput sequencing reveals differing immune responses in the intestinal mucosa of two inbred lines afflicted with necrotic enteritis,"We investigated the necrotic enteritis (NE)-induced transcripts of immune-related genes in the intestinal mucosa of two highly inbred White Leghorn chicken lines, line 6.3 and line 7.2, which share the same MHC haplotype and show different levels of NE susceptibility using high-throughput RNA sequencing (RNA-Seq) technology. NE was induced by the previously described co-infection model using Eimeria maxima and Clostridium perfringens. The RNA-Seq generated over 38 million sequence reads for Marek's disease (MD)-resistant line 6.3 and over 40 million reads for the MD-susceptible line 7.2. Alignment of these sequences with the Gallus gallus genome database revealed the expression of over 29,900 gene transcripts induced by NE in these two lines, among which 7,841 genes were significantly upregulated and 2,919 genes were downregulated in line 6.3 chickens and 6,043 genes were significantly upregulated and 2,764 genes were downregulated in NE-induced line 7.2 compared with their uninfected controls. Analysis of 560 differentially expressed genes (DEGs) using the gene ontology database revealed annotations for 246 biological processes, 215 molecular functions, and 81 cellular components. Among the 53 cytokines and 96 cytokine receptors, 15 cytokines and 29 cytokine receptors were highly expressed in line 6.3, whereas the expression of 15 cytokines and 15 cytokine receptors was higher in line 7.2 than in line 6.3 (fold change >= 2, p<0.01). In a hierarchical cluster analysis of novel mRNAs, the novel mRNA transcriptome showed higher expression in line 6.3 than in line 7.2, which is consistent with the expression profile of immune-related target genes. In qRT-PCR and RNA-Seq analysis, all the genes examined showed similar responses to NE (correlation coefficient R=0.85-0.89, p<0.01) in both lines 6.3 and 7.2. This study is the first report describing NE-induced DEGs and novel transcriptomes using RNA-seq data from two inbred chicken lines showing different levels of NE susceptibility. These findings provide important insights into our current knowledge of host-pathogen interaction and the nature of host genes that can serve as NE resistance markers for molecular breeding.","Animals;Chickens/im [Immunology];Clostridium Infections/im [Immunology];Clostridium Infections/ve [Veterinary];Clostridium perfringens/im [Immunology];Coccidiosis/im [Immunology];Coccidiosis/ve [Veterinary];Coinfection/mi [Microbiology];Coinfection/ps [Parasitology];Coinfection/ve [Veterinary];Eimeria;Enteritis/im [Immunology];Enteritis/me [Metabolism];Enteritis/pa [Pathology];*Enteritis/ve [Veterinary];High-Throughput Nucleotide Sequencing/ve [Veterinary];Immunity, Active/ge [Genetics];Immunity, Active/im [Immunology];*Intestinal Mucosa/im [Immunology];Intestinal Mucosa/me [Metabolism];Intestinal Mucosa/pa [Pathology];Necrosis;*Poultry Diseases/im [Immunology];Poultry Diseases/me [Metabolism];Poultry Diseases/pa [Pathology]","Truong, A. D.;Hong, Y. H.;Lillehoj, H. S.",2015,Aug 15,,0
2083,Analysis of heterogenous populations of antihemagglutinating antibodies in hyperimmune sera against influenza virus by indirect solid-phase radioimmunoassay Russian,"Populations of antihemagglutinating antibodies in hyperimmune rabbit sera to influenza A/PR8/34, A/Moscow/PAN/52, and A/Swine Iowa/15/31 viruses were examined by indirect competitive solid phase radioimmunoassay (SPRIA). Under conditions of competitive assay with immobilized virus homologous to the serum under test, not all subpopulations of cross-reacting antibodies in the sera are identified. Competition in the system of immobilized heterologous virus identifies a fuller spectrum of cross-reacting antibody. A composite analysis of the sera under both variants of competition showed each of the sera to contain a heterogenous population of antibodies interacting to various extents with determinants of a number of heterologous viruses classified, according to 1971 Nomenclature, as viruses with H0, H1, and Hsw1 hemagglutinin subtypes. The identification of cross-reacting antibodies permitted a conclusion on the existence of both antigenic determinants on the surface of hemagglutinin molecules of the viruses under study and an analysis of their variability. The pattern of changes of similar determinants in transition from viruses of one subtype to viruses of another subtype is characteristic of the drift type.","*Antibodies, Viral/an [Analysis];Cross Reactions;Epitopes/an [Analysis];*Hemagglutinins, Viral/im [Immunology];Humans;*Immune Sera/im [Immunology];*Influenza A virus/im [Immunology];*Influenza, Human/im [Immunology];Radioimmunoassay/mt [Methods];0 (Antibodies, Viral);0 (Epitopes);0 (Hemagglutinins, Viral);0 (Immune Sera)","Trushinskaia, G. N.;Rovnova, Z. I.;Berezina, O. N.;Grigor'eva, T. A.;Isaeva, E. I.",1981,Sep-Oct,,0
2084,Analysis of heterogenous population of antihemagglutinating antibody in hyperimmune rabbit sera against influenza virus by indirect solid phase radioimmunoassay,"Populations of antihemagglutinating antibodies in hyperimmune rabbit sera to influenza A/PR8/34, A/Moscow/PAN/52, and A/Swine Iowa/15/31 viruses were examined by indirect competitive solid phase radioimmunoassay (SPRIA). Under conditions of competitive assay with immobilized virus homologous to the serum under test, not all subpopulations of cross-reacting antibodies in the sera are identified. Competition in the system of immobilized heterologous virus identifies a fuller spectrum of cross reacting antibody. A composite analysis of the sera under both variants of competition showed each of the sera to contain a heterogenous population of antibodies interacting to various extents with determinants of a number of heterologous viruses classified, according to 1971 Nomenclature, as viruses with H0, H1, and Hsw1 hemagglutinin subtypes. The identification of cross-reacting antibodies permitted a conclusion as to the existence of both antigenic determinants on the surface of hemagglutinin molecules of the viruses under study and an analysis of their variability. The pattern of changes of similar determinants in transition from viruses of one subtype to viruses of another subtype is characteristic of the drift type.",hemagglutination inhibiting antibody;radioisotope;virus antibody;human cell;Influenza A virus;radioimmunoassay,"Trushinskaya, G. N.;Rovnova, Z. I.;Berezina, O. N.",1981,,,0
2085,Relevant oncogenic viruses in veterinary medicine: original pathogens and animal models for human disease,"Oncogenic viruses are important pathogens in farm and companion animals. These original pathogens are classified in various virus families, such as Retroviridae, Papillomaviridae, and Herpesviridae. Besides a role as pathogens for its original host, animal viruses serve as valuable models for viruses affecting humans, such as hepatitis B virus, and issues of immunity, therapy, but also basic pathophysiological mechanisms, can often only be addressed in those animal systems.",animal;animal disease;disease model;domestic animal;human;neoplasm;review;tumor virus;virology;virus infection,"Truyen, U.;Löchelt, M.",2006,,,0
2086,There is nothing permanent except change. The emergence of new virus diseases,"The sudden appearance of apparently new viruses with pathogenic potential is of fundamental importance in medical microbiology and a constant threat to humans and animals. The emergence of a 'new' pathogen is not an isolated event, as for instance the frequent appearance of new influenza virus strains demonstrates. Often the new virus strains co-circulate with the older strains in a susceptible population, but a replacement of the older strains has been also observed. In rare instances the new viruses can cause dramatic epidemics or pandemics, such as those observed with the human immunodeficiency virus, canine parvovirus, or most recently, with the agent of bovine spongiform encephalopathy in the United Kingdom. The mechanisms of the emergence are not always clearly understood, but an altered host range appears to be a common event. Whether a true change in host range occurs, or whether the virus adapted to the host and replicated more efficiently, is often unknown. This review tries to summarize the facts that are known about a wide variety of 'new' viruses of mammals, such as the simian, human and feline lentiviruses, the feline coronaviruses, the feline parvoviruses, the carnivore morbilliviruses, the influenza A viruses, and the transmissible spongiform encephalopathies. A particular emphasis will be put on the genetic mechanisms that might have taken place and that might have been responsible for their sudden appearance.",evolution;genetic analysis;nonhuman;review;virus classification;virus infection,"Truyen, U.;Parrish, C. R.;Harder, T. C.;Kaaden, O. R.",1995,,10.1016/0378-1135(95)92531-f,0
2087,Molecular epidemiological studies on foot-and-mouth disease type O Taiwan viruses from the 1997 epidemic,"Sequence diversity was assessed of the complete VP1 gene directly amplified from 49 clinical specimens during an explosive foot-and-mouth disease (FMD) outbreak in Taiwan. Type O Taiwan FMD viruses are genetically highly homogenous, as seen by the minute divergence of 0.2-0.9% revealed in 20 variants. The O/HCP-0314/TW/97 and O/TCP-022/TW/97 viral variants dominated FMD outbreaks and were prevalent in most affected pig-raising areas. Comparison of deduced amino acid sequences around the main neutralizable antigenic sites on the VP1 polypeptide showed no significant antigenic variation. However, the O/CHP-158/TW/97 variant had an alternative critical residue at position 43 in antigenic site 3, which may be due to selective pressure in the field. Two vaccine production strains (O1/Manisa/Turkey/69 and O1/Campos/Brazil/71) probably provide partial heterologous protection of swine against O Taiwan viruses. The type O Taiwan variants clustered in sublineage A1 of four main lineages in the phylogenetic tree. The O/Hong Kong/9/94 and O/1685/Moscow/Russia/95 viruses in sublineage A2 are closely related to the O Taiwan variants. The causative agent for the 1997 epidemic presumably originated from a single common source of type O FMD viruses prevalent in neighboring areas. Copyright (C) 2000 Elsevier Science B.V.",foot and mouth disease vaccine;virus RNA;amino acid sequence;animal experiment;article;controlled study;foot and mouth disease;Foot and mouth disease virus;gene amplification;gene sequence;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;sequence analysis;pig;Taiwan,"Tsai, C. P.;Pan, C. H.;Liu, M. Y.;Lin, Y. L.;Chen, C. M.;Huang, T. S.;Cheng, I. C.;Jong, M. H.;Yang, P. C.",2000,,10.1016/s0378-1135(00)00182-6,0
2088,New H1N2 and H3N1 influenza viruses in Taiwanese pig herds,,,"Tsai, C. P.;Pan, M. J.",2003,,,0
2089,Emergence of a sylvatic enzootic formosan ferret badger-associated rabies in Taiwan and the geographical separation of two phylogenetic groups of rabies viruses,"Taiwan had been declared rabies-free in humans and domestic animals for five decades until July 2013, when surprisingly, three Formosan ferret badgers (FB) were diagnosed with rabies. Since then, a variety of wild carnivores and other wildlife species have been found dead, neurologically ill, or exhibiting aggressive behaviors around the island. To determine the affected animal species, geographic areas, and environments, animal bodies were examined for rabies by direct fluorescent antibody test (FAT). The viral genomes from the brains of selected rabid animals were sequenced for the phylogeny of rabies viruses (RABV). Out of a total of 1016 wild carnivores, 276/831 (33.2%) Formosan FBs were FAT positive, with occasional biting incidents in 1 dog and suspected spillover in 1 house shrew. All other animals tested, including dogs, cats, bats, mice, house shrews, and squirrels, were rabies-negative. The rabies was badger-associated and confined to nine counties/cities in sylvatic environments. Phylogeny of nucleoprotein and glycoprotein genes from 59 Formosan FB-associated RABV revealed them to be clustered in two distinct groups, TWI and TWII, consistent with the geographic segregation into western and eastern Taiwan provided by the Central Mountain Range and into northern rabies-free and central-southern rabies-affected regions by a river bisecting western Taiwan. The unique features of geographic and genetic segregation, sylvatic enzooticity, and FB-association of RABV suggest a logical strategy for the control of rabies in this nation.",article;Meles;Melogale;fluorescent antibody technique;gene segregation;gene sequence;nonhuman;phylogeny;rabies;Rabies virus;Taiwan;virus genome,"Tsai, K. J.;Hsu, W. C.;Chuang, W. C.;Chang, J. C.;Tu, Y. C.;Tsai, H. J.;Liu, H. F.;Wang, F. I.;Lee, S. H.",2016,,10.1016/j.vetmic.2015.10.030,0
2090,An Evolutionarily Young Polar Bear (Ursus maritimus) Endogenous Retrovirus Identified from Next Generation Sequence Data,"Transcriptome analysis of polar bear (Ursus maritimus) tissues identified sequences with similarity to Porcine Endogenous Retroviruses (PERV). Based on these sequences, four proviral copies and 15 solo long terminal repeats (LTRs) of a newly described endogenous retrovirus were characterized from the polar bear draft genome sequence. Closely related sequences were identified by PCR analysis of brown bear (Ursus arctos) and black bear (Ursus americanus) but were absent in non-Ursinae bear species. The virus was therefore designated UrsusERV. Two distinct groups of LTRs were observed including a recombinant ERV that contained one LTR belonging to each group indicating that genomic invasions by at least two UrsusERV variants have recently occurred. Age estimates based on proviral LTR divergence and conservation of integration sites among ursids suggest the viral group is only a few million years old. The youngest provirus was polar bear specific, had intact open reading frames (ORFs) and could potentially encode functional proteins. Phylogenetic analyses of UrsusERV consensus protein sequences suggest that it is part of a pig, gibbon and koala retrovirus clade. The young age estimates and lineage specificity of the virus suggests UrsusERV is a recent cross species transmission from an unknown reservoir and places the viral group among the youngest of ERVs identified in mammals.",Animals;*Endogenous Retroviruses/ge [Genetics];*Endogenous Retroviruses/ip [Isolation & Purification];Female;*High-Throughput Nucleotide Sequencing;Male;Open Reading Frames;Phylogeny;Polymerase Chain Reaction;Proviruses/ge [Genetics];Proviruses/ip [Isolation & Purification];Sequence Homology;Terminal Repeat Sequences;*Ursidae/ge [Genetics];*Ursidae/vi [Virology],"Tsangaras, K.;Mayer, J.;Alquezar-Planas, D. E.;Greenwood, A. D.",2015,Nov 24,,0
2091,Identification of a novel bat papillomavirus by metagenomics,"The discovery of novel viruses in animals expands our knowledge of viral diversity and potentially emerging zoonoses. High-throughput sequencing (HTS) technology gives millions or even billions of sequence reads per run, allowing a comprehensive survey of the genetic content within a sample without prior nucleic acid amplification. In this study, we screened 156 rectal swab samples from apparently healthy bats (n = 96), pigs (n = 9), cattles (n = 9), stray dogs (n = 11), stray cats (n = 11) and monkeys (n = 20) using a HTS metagenomics approach. The complete genome of a novel papillomavirus (PV), Miniopterus schreibersii papillomavirus type 1 (MscPV1), with L1 of 60% nucleotide identity to Canine papillomavirus (CPV6), was identified in a specimen from a Common Bent-wing Bat (M. schreibersii). It is about 7.5kb in length, with a G+C content of 45.8% and a genomic organization similar to that of other PVs. Despite the higher nucleotide identity between the genomes of MscPV1 and CPV6, maximum-likelihood phylogenetic analysis of the L1 gene sequence showed that MscPV1 and Erethizon dorsatum papillomavirus (EdPV1) are most closely related. Estimated divergence time of MscPV1 from the EdPV1/MscPV1 common ancestor was approximately 60.2-91.9 millions of years ago, inferred under strict clocks using the L1 and E1 genes. The estimates were limited by the lack of reliable calibration points from co-divergence because of possible host shifts. As the nucleotide sequence of this virus only showed limited similarity with that of related animal PVs, the conventional approach of PCR using consensus primers would be unlikely to have detected the novel virus in the sample. Unlike the first bat papillomavirus RaPV1, MscPV1 was found in an asymptomatic bat with no apparent mucosal or skin lesions whereas RaPV1 was detected in the basosquamous carcinoma of a fruit bat Rousettus aegyptiacus. We propose MscPV1 as the first member of the novel Dyolambda-papillomavirus genus. © 2012 Tse et al.",article;bat;Canine papillomavirus 6;cat;bovine;controlled study;DNA base composition;dog;Dyolambda papillomavirus;Erethizon dorsatum papillomavirus 1;estimated divergence time;gene e1;genetic parameters;genetic variability;genome analysis;Haplorhini;high throughput sequencing;L1 gene;last common ancestor;maximum likelihood method;metagenomics;Miniopterus schreibersii;Miniopterus schreibersii papillomavirus type 1;nonhuman;nucleotide sequence;Papillomaviridae;Rousettus aegyptiacus;sequence analysis;sequence homology;pig;virus detection;virus gene;virus identification,"Tse, H.;Tsang, A. K. L.;Tsoi, H. W.;Leung, A. S. P.;Ho, C. C.;Lau, S. K. P.;Woo, P. C. Y.;Yuen, K. Y.",2012,,10.1371/journal.pone.0043986,0
2092,Discovery and genomic characterization of a novel ovine partetravirus and a new genotype of bovine partetravirus,"Partetravirus is a recently described group of animal parvoviruses which include the human partetravirus, bovine partetravirus and porcine partetravirus (previously known as human parvovirus 4, bovine hokovirus and porcine hokovirus respectively). In this report, we describe the discovery and genomic characterization of partetraviruses in bovine and ovine samples from China. These partetraviruses were detected by PCR in 1.8% of bovine liver samples, 66.7% of ovine liver samples and 71.4% of ovine spleen samples. One of the bovine partetraviruses detected in the present samples is phylogenetically distinct from previously reported bovine partetraviruses and likely represents a novel genotype. The ovine partetravirus is a novel partetravirus and phylogenetically most related to the bovine partetraviruses. The genome organization is conserved amongst these viruses, including the presence of a putative transmembrane protein encoded by an overlapping reading frame in ORF2. Results from the present study provide further support to the classification of partetraviruses as a separate genus in Parvovirinae. © 2011 Tse et al.",virus DNA;article;Bovine partetravirus;China;controlled study;genome analysis;genotype;genus;nonhuman;nucleotide sequence;Ovine partetravirus;Parvoviridae;phylogeny;polymerase chain reaction;sequence analysis;virus classification;virus detection;virus genome;virus strain,"Tse, H.;Tsoi, H. W.;Teng, J. L. L.;Chen, X. C.;Liu, H.;Zhou, B.;Zheng, B. J.;Woo, P. C. Y.;Lau, S. K. P.;Yuen, K. Y.",2011,,10.1371/journal.pone.0025619,0
2093,A novel activation mechanism of avian influenza virus H9N2 by furin,"Avian influenza virus H9N2 is prevalent in waterfowl and has become endemic in poultry in Asia and the Middle East. H9N2 influenza viruses have served as a reservoir of internal genes for other avian influenza viruses that infect humans, and several cases of human infection by H9N2 influenza viruses have indicated its pandemic potential. Fortunately, an extensive surveillance program enables close monitoring of H9N2 influenza viruses worldwide and has generated a large repository of virus sequences and phylogenetic information. Despite the large quantity of sequences in different databases, very little is known about specific virus isolates and their pathogenesis. Here, we characterize a low-pathogenicity avian influenza virus, A/chicken/Israel/810/2001 (H9N2) (Israel810), which is representative of influenza virus strains that have caused severe morbidity and mortality in poultry farms. We show that under certain circumstances the Israel810 hemagglutinin (HA) can be activated by furin, a hallmark of highly pathogenic avian influenza virus. We demonstrate that Israel810 HA can be cleaved in cells with high levels of furin expression and that a mutation that eliminates a glycosylation site in HA1 allows the Israel810 HA to gain universal cleavage in cell culture. Pseudoparticles generated from Israel810 HA, or the glycosylation mutant, transduce cells efficiently. In contrast, introduction of a polybasic cleavage site into Israel810 HA leads to pseudoviruses that are compromised for transduction. Our data indicate a mechanism for an H9N2 evolutionary pathway that may allow it to gain virulence in a distinct manner from H5 and H7 influenza viruses. © 2014, American Society for Microbiology.",furin;Influenza virus hemagglutinin;proteinase;amino acid sequence;article;cleavage site;enzyme activation;glycosylation;human;Influenza A virus (H5N1);Influenza A virus (H7N1);Influenza A virus (H9N2);morbidity;mortality;nonhuman;nucleotide sequence;priority journal;protein binding;protein degradation;protein expression;protein stability;restriction site;virus activation;virus virulence,"Tse, L. V.;Hamilton, A. M.;Friling, T.;Whittaker, G. R.",2014,,10.1128/jvi.02648-13,0
2094,"Similarities and differences between the E5 oncoproteins of bovine papillomaviruses type 1 and type 4: Cytoskeleton, motility and invasiveness in E5-transformed bovine and mouse cells","Bovine papillomaviruses (BPVs) are oncogenic viruses. In cattle, BPV-1/2 is associated with urinary bladder cancer and BPV-4 with upper GI tract cancer. BPV E5 is a small hydrophobic protein localised in the endoplasmic reticulum (ER) and Golgi apparatus (GA). E5 is the major transforming protein of BPVs, capable of inducing cell transformation in cultured mouse fibroblasts and, in cooperation with E7, in primary bovine cells. E5-induced cell transformation is accompanied by activation of several cellular protein kinases, including growth factor receptors, and alkalinisation of endosomes and GA. We have reported that BPV E5 causes swelling and fragmentation of the GA and extensive vacuolisation of the cytoplasm. We now show that E5 from both BPV-1 and BPV-4 disturbs the actin cytoskeleton and focal adhesions in transformed bovine cells, where these morphological and behavioural characteristics are accompanied by hyperphosphorylation of the cellular phosphotyrosine kinase c-src. Both BPV-1 and BPV-4 E5 increase the motility of transformed mouse cells, but only BPV-1 E5 causes transformed mouse cells to penetrate a matrigel matrix. BPV-1 transformed mouse cells, but not BPV-4 transformed mouse cells, have hyperhpsphorylated c-src. © 2005 Elsevier B.V. All rights reserved.",actin;protein e5;protein kinase p60;protein tyrosine kinase;unclassified drug;viral protein;alkalinization;animal cell;article;cell function;cell invasion;cell motility;cell transformation;cell vacuole;controlled study;cytoplasm;cytoskeleton;endosome;enzyme phosphorylation;fibroblast;focal adhesion;mouse;nonhuman;Papillomaviridae;priority journal;protein analysis;protein function;virus classification,"Tsirimonaki, E.;Ullah, R.;Marchetti, B.;Ashrafi, G. H.;McGarry, L.;Ozanne, B.;Campo, M. S.",2006,,10.1016/j.virusres.2005.08.003,0
2095,Dynamics of envelope evolution in clade C SHIV-infected pig-tailed macaques during disease progression analyzed by ultra-deep pyrosequencing,"Understanding the evolution of the human immunodeficiency virus type 1 (HIV-1) envelope during disease progression can provide tremendous insights for vaccine development, and simian-human immunodeficiency virus (SHIV) infection of non-human primate provides an ideal platform for such studies. A newly developed clade C SHIV, SHIV-1157ipd3N4, which was able to infect rhesus macaques, closely resembled primary HIV-1 in transmission and pathogenesis, was used to infect several pig-tailed macaques. One of the infected animals subsequently progressed to AIDS, whereas one remained a non-progressor. The viral envelope evolution in the infected animals during disease progression was analyzed by a bioinformatics approach using ultra-deep pyrosequencing. Our results showed substantial envelope variations emerging in the progressor animal after the onset of AIDS. These envelope variations impacted the length of the variable loops and charges of different envelope regions. Additionally, multiple mutations were located at the CD4 and CCR5 binding sites, potentially affecting receptor binding affinity, viral fitness and they might be selected at late stages of disease. More importantly, these envelope mutations are not random since they had repeatedly been observed in a rhesus macaque and a human infant infected by either SHIV or HIV-1, respectively, carrying the parental envelope of the infectious molecular clone SHIV-1157ipd3N4. Moreover, similar mutations were also observed from other studies on different clades of envelopes regardless of the host species. These recurring mutations in different envelopes suggest that there may be a common evolutionary pattern and selection pathway for the HIV-1 envelope during disease progression.","*Acquired Immunodeficiency Syndrome/ge [Genetics];Amino Acid Sequence;Animals;Base Sequence;Binding Sites/ge [Genetics];CD4 Antigens/me [Metabolism];CD4-Positive T-Lymphocytes/im [Immunology];Cell Count;Disease Progression;*Evolution, Molecular;Genetic Variation;*HIV-1/ge [Genetics];High-Throughput Nucleotide Sequencing;Macaca nemestrina;Molecular Sequence Data;Mutation/ge [Genetics];Phylogeny;Receptors, CCR5/me [Metabolism];*Simian Immunodeficiency Virus/ge [Genetics];*Viral Envelope Proteins/ge [Genetics];Viral Envelope Proteins/me [Metabolism];0 (CD4 Antigens);0 (Receptors, CCR5);0 (Viral Envelope Proteins)","Tso, F. Y.;Tully, D. C.;Gonzalez, S.;Quince, C.;Ho, O.;Polacino, P.;Ruprecht, R. M.;Hu, S. L.;Wood, C.",2012,,,0
2096,Genetic diversity and recombination of enterovirus G strains in Japanese pigs: High prevalence of strains carrying a papain-like cysteine protease sequence in the enterovirus G population,"To study the genetic diversity of enterovirus G (EV-G) among Japanese pigs, metagenomics sequencing was performed on fecal samples from pigs with or without diarrhea, collected between 2014 and 2016. Fifty-nine EV-G sequences, which were >5,000 nucleotides long, were obtained. By complete VP1 sequence analysis, Japanese EV-G isolates were classified into G1 (17 strains), G2 (four strains), G3 (22 strains), G4 (two strains), G6 (two strains), G9 (six strains), G10 (five strains), and a new genotype (one strain). Remarkably, 16 G1 and one G2 strain identified in diarrheic (23.5%; four strains) or normal (76.5%; 13 strains) fecal samples possessed a papain-like cysteine protease (PL-CP) sequence, which was recently found in the USA and Belgium in the EV-G genome, at the 2C–3A junction site. This paper presents the first report of the high prevalence of viruses carrying PL-CP in the EV-G population. Furthermore, possible inter- and intragenotype recombination events were found among EV-G strains, including G1-PL-CP strains. Our findings may advance the understanding of the molecular epidemiology and genetic evolution of EV-Gs.",cysteine proteinase;papain;papain like cysteine protease;protein VP1;unclassified drug;article;controlled study;diarrhea;Enterovirus G;Enterovirus G1;Enterovirus G10;Enterovirus G2;Enterovirus G3;Enterovirus G4;Enterovirus G6;Enterovirus G9;genetic recombination;genetic variability;Japan;metagenomics;next generation sequencing;nonhuman;pig;prevalence;virus genome;VP1 gene,"Tsuchiaka, S.;Naoi, Y.;Imai, R.;Masuda, T.;Ito, M.;Akagami, M.;Ouchi, Y.;Ishii, K.;Sakaguchi, S.;Omatsu, T.;Katayama, Y.;Oba, M.;Shirai, J.;Satani, Y.;Takashima, Y.;Taniguchi, Y.;Takasu, M.;Madarame, H.;Sunaga, F.;Aoki, H.;Makino, S.;Mizutani, T.;Nagai, M.",2018,,10.1371/journal.pone.0190819,1
2097,Identification of a novel bovine enterovirus possessing highly divergent amino acid sequences in capsid protein,"Background: Bovine enterovirus (BEV) belongs to the species Enterovirus E or F, genus Enterovirus and family Picornaviridae. Although numerous studies have identified BEVs in the feces of cattle with diarrhea, the pathogenicity of BEVs remains unclear. Previously, we reported the detection of novel kobu-like virus in calf feces, by metagenomics analysis. In the present study, we identified a novel BEV in diarrheal feces collected for that survey. Complete genome sequences were determined by deep sequencing in feces. Secondary RNA structure analysis of the 5′ untranslated region (UTR), phylogenetic tree construction and pairwise identity analysis were conducted. Results: The complete genome sequences of BEV were genetically distant from other EVs and the VP1 coding region contained novel and unique amino acid sequences. We named this strain as BEV AN12/Bos taurus/JPN/2014 (referred to as BEV-AN12). According to genome analysis, the genome length of this virus is 7414 nucleotides excluding the poly (A) tail and its genome consists of a 5′UTR, open reading frame encoding a single polyprotein, and 3′UTR. The results of secondary RNA structure analysis showed that in the 5′UTR, BEV-AN12 had an additional clover leaf structure and small stem loop structure, similarly to other BEVs. In pairwise identity analysis, BEV-AN12 showed high amino acid (aa) identities to Enterovirus F in the polyprotein, P2 and P3 regions (aa identity ≥82.4%). Therefore, BEV-AN12 is closely related to Enterovirus F. However, aa sequences in the capsid protein regions, particularly the VP1 encoding region, showed significantly low aa identity to other viruses in genus Enterovirus (VP1 aa identity ≤58.6%). In addition, BEV-AN12 branched separately from Enterovirus E and F in phylogenetic trees based on the aa sequences of P1 and VP1, although it clustered with Enterovirus F in trees based on sequences in the P2 and P3 genome region. Conclusions: We identified novel BEV possessing highly divergent aa sequences in the VP1 coding region in Japan. According to species definition, we proposed naming this strain as ""Enterovirus K"", which is a novel species within genus Enterovirus. Further genomic studies are needed to understand the pathogenicity of BEVs.",capsid protein;protein VP1;3' untranslated region;5' untranslated region;amino acid sequence;article;Bovine enterovirus;controlled study;Enterovirus E;Enterovirus F;Enterovirus K;Japan;nonhuman;nucleotide sequence;open reading frame;phylogenetic tree;RNA structure;virus genome;virus isolation,"Tsuchiaka, S.;Rahpaya, S. S.;Otomaru, K.;Aoki, H.;Kishimoto, M.;Naoi, Y.;Omatsu, T.;Sano, K.;Okazaki-Terashima, S.;Katayama, Y.;Oba, M.;Nagai, M.;Mizutani, T.",2017,,10.1186/s12866-016-0923-0,0
2098,Evidence of serologic diversity within group C rotaviruses,"The Cowden strain of porcine group C rotavirus and the Shintoku strain of bovine group C rotavirus were classified as different serotypes by two-way cross-neutralization tests. Two neutralization patterns against the Cowden and Shintoku strains were observed when hyperimmune or convalescent-phase antisera to three noncultivatable porcine group C rotaviruses and a human group C rotavirus were used in one-way cross-neutralization tests. Antisera to two porcine group C rotaviruses and the human group C rotavirus neutralized the Cowden strain at high titers but did not neutralize the Shintoku strain, suggesting that these three strains are serotypically related to the Cowden strain. The remaining antisera to a porcine group C rotavirus (HF strain) reacted with the Cowden and Shintoku group C rotaviruses in cell culture immunofluorescence tests but did not neutralize either virus in one-way cross-neutralization, suggesting that the HF strain belongs to a third serotype. However, confirmation of these findings requires additional analysis by two-way cross-neutralization. Our findings support the existence of at least two distinct serotypes of group C rotaviruses, and possibly a third, among animals and humans. The serotypic similarity observed between the Cowden strain and a human group C rotavirus suggests that the cultivatable Cowden strain and antiserum to this virus may provide important reagents for the diagnosis of group C rotaviruses in humans.",antiserum;neutralizing antibody;antibody titer;cell culture;cow;experimental infection;gnotobiotics;human;immunofluorescence;immunoreactivity;nonhuman;note;priority journal;Rotavirus;serotype;pig;virus classification;virus infection;virus neutralization,"Tsunemitsu, H.;Jiang, B.;Yamashita, Y.;Oseto, M.;Ushijima, H.;Saif, L. J.",1992,,,0
2099,"Porcine rotavirus C in pigs with gastroenteritis on Thai swine farms, 2011–2016",,,"Tuanthap, S.;Phupolphan, C.;Luengyosluechakul, S.",2018,,,0
2100,"Porcine rotavirus C in pigs with gastroenteritis on Thai swine farms, 2011-2016","Swine are economically important food animals, but highly contagious porcine epidemic diarrhea virus (PEDV) and rotavirus can afflict pig herds and contribute significantly to piglet morbidity and mortality. While there have been studies on rotavirus group A (RVA) in Thailand, reports of rotavirus group C (RVC) are limited. Here, we aimed to identify the prevalence of RVC circulating on Thai commercial swine farms. We analyzed 769 feces and intestine mucosal contents of pigs affected with diarrhea between 2011 and 2016 using RT-PCR specific for the PEDV spike (S), rotavirus glycoprotein (G) VP7, and protease-sensitive protein (P) VP4 genes. We found that 6.6% (51/769) of samples tested positive for RVC, of which 11 samples were co-infected with RVA and four samples were co-infected with PEDV. Three samples tested positive for all three viruses. Phylogenetic analysis of the VP7 gene showed that the most frequent RVC genotype was G1, which grouped with the prototypic RVC Cowden strain. While G6 and G9 were also common, G3 was relatively rare. Analysis of the VP4 gene revealed that the most common P type was P[5], followed by P[4], P[7], and P[1]. In all, there were six G/P combinations (G6P[5], G1P[1], G1P[4], G1P[5], G9P[4], and G9P[7]), of which G6P[5] was the most predominant.",proteinase;rotavirus glycoprotein;unclassified drug;virus glycoprotein;article;cell cycle G1 phase;feces analysis;gastroenteritis;gene expression;gene frequency;genotyping technique;nonhuman;nucleic acid analysis;phylogeny;pig;pig farming;Porcine epidemic diarrhea virus;prevalence;protein expression;reverse transcription polymerase chain reaction;Rotavirus C;sequence analysis;Thailand;virus spike,"Tuanthap, S.;Phupolphan, C.;Luengyosluechakul, S.;Duang-In, A.;Theamboonlers, A.;Wattanaphansak, S.;Vongpunsawad, S.;Amonsin, A.;Poovorawan, Y.",2018,,10.7717/peerj.4724,0
2101,"Seroepidemiology of Bivens Arm virus infections of cattle in Florida, St Croix and Puerto Rico","Bivens Arm virus (BAV) is a newly discovered rhabdovirus infecting cattle and water buffalo in Florida. The virus is classified as a member of the Tibrogargan group, members of which have hitherto been found only in Australasia. They are considered to be transmitted by Culicoides species. Bivens Arm virus was first isolated from Culicoides insignis which suggests that BAV is also transmitted by this genus. A serological survey of two small groups of cattle raised in St. Croix and puerto Rico, in the Caribbean, established that antibody to BAV, or a closely related virus, exists on both islands. A retrospective analysis of seroconversions to BAV in sentinel calves in Florida, relative to populations of potential Culicoides vectors, failed to demonstrate any statistically significant correlation.",neutralizing antibody;virus vector;antibody titer;article;bovine;cell culture;insect;nonhuman;Rhabdoviridae;seasonal variation;seroconversion;serology;virus infection;virus neutralization,"Tuekam, T.;Greiner, E. C.;Gibbs, E. P. J.",1991,,10.1016/0378-1135(91)90087-v,0
2102,Antigenic relationship between influenza A viruses of human and animal origin,"Reciprocal antigenic relationships between 17 influenza A viruses of human, porcine, equine and avian origin were investigated by haemagglutination-inhibition (HI) and strain-specific complement-fixation (CF). Cross-reactions were observed between the following strains: (a) Equi/1/Prague/1/56, Fowl plague (Dutch strain) and Turkey/England/1/63 (Langham strain); (b) Equi/2/Miami/1/63, Quail/Italy/1117/65, Pheasant/Italy/647/66, Duck/England/1/62 and Turkey/Canada/1/63; (c) A2/Singapore/1/57 and Turkey/Massachussets/65; (d) Swine/S15/30 and Chicken/Scotland/1/59. The results of HI tests performed with post-infection sera showed on the whole narrower specificity than those of HI with hyperimmune sera or those of strain-specific CF. There is clearly no sharp demarcation of antigenic subtypes of influenza A viruses, and studies over a yet wider range of strains are likely to disclose a continuous spectrum of antigenic variation for the whole group. The authors suggest that, in practice, host specificity rather than antigenic specificity may have to be used as the main criterion in classifying influenza A viruses.",Antigens;Complement Fixation Tests;Hemagglutination Inhibition Tests;Humans;*Orthomyxoviridae/cl [Classification];Orthomyxoviridae/im [Immunology];Serotyping;Species Specificity;0 (Antigens),"Tumova, B.;Pereira, H. G.",1968,,,0
2103,Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing,"The feline gastrointestinal microbiota have direct influence on feline health and also human health as a reservoir for potential zoonotic pathogens and antibiotic resistant bacterial strains. In order to describe the feline gastrointestinal microbial diversity, fecal samples from cats have been characterized using both culture-dependent and culture-independent methods. However, data correlating total microbial composition and their functions are lacking. Present descriptive study evaluated both phylogenetic and metabolic diversity of the feline intestinal microbiota using GS Junior titanium shotgun pyrosequencing. A total of 152,494 pyrosequencing reads (5405 assembled contigs) were generated and classified into both phylogenetic and metabolic profiles of the feline intestinal microbiota. The Bacteroides/Chlorobi group was the most predominant bacterial phylum comprising ~. 68% of total classified diversity, followed by Firmicutes (~. 13%) and Proteobacteria (~. 6%) respectively. Archaea, fungi and viruses made up the minor communities in the overall microbial diversity. Interestingly, this study also identified a range of potential enteric zoonotic pathogens (0.02-1.25%) and genes involved in antimicrobial resistance (0.02-0.7%) in feline fecal materials. Based on clustering among nine gastrointestinal metagenomes from five different monogastric hosts (dog, human, mice, cat and chicken), the cat metagenome clustered closely together with chicken in both phylogenetic and metabolic level (> 80%). Future studies are required to provide deeper understandings on both intrinsic and extrinsic effects such as impact of age, genetics and dietary interventions on the composition of the feline gastrointestinal microbiome. © 2012 Elsevier B.V.",genomic DNA;meticillin;quinoline derived antiinfective agent;tetracycline;antibiotic resistance;archaeon;article;Bacillus;bacterium culture;Bacteroides;Campylobacter;cat;chicken;Chlorobi;Clostridium;controlled study;correlation analysis;DNA extraction;dog;Escherichia coli;feces analysis;Firmicutes;fungus;Helicobacter;host;intestine flora;Listeria;metagenome;metagenomics;microbial diversity;nonhuman;phylogeny;priority journal;Proteobacteria;pyrosequencing;Salmonella;Shigella;species difference;species diversity;Staphylococcus;Streptococcus;Vibrio;virus;Yersinia;zoonosis,"Tun, H. M.;Brar, M. S.;Khin, N.;Jun, L.;Hui, R. K. H.;Dowd, S. E.;Leung, F. C. C.",2012,,10.1016/j.mimet.2012.01.001,0
2104,"Highly pathogenic avian influenza A(H5N8) virus, democratic republic of the Congo, 2017","In 2017, highly pathogenic avian influenza A(H5N8) virus was detected in poultry in the Democratic Republic of the Congo. Whole-genome phylogeny showed the virus clustered with H5N8 clade 2.3.4.4B strains from birds in central and southern Asia. Emergence of this virus in central Africa represents a threat for animal health and food security.",virus hemagglutinin;virus nucleoprotein;article;autopsy;avian influenza (H5N8);avian influenza (H5N8) infection;avian influenza virus;chicken;clinical feature;Congo;diarrhea;duck;dyspnea;geographic distribution;influenza;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;poultry;real time polymerase chain reaction;virus identification;virus transmission;weakness;whole genome sequencing,"Twabela, A. T.;Tshilenge, G. M.;Sakoda, Y.;Okamatsu, M.;Bushu, E.;Kone, P.;Wiersma, L.;Zamperin, G.;Drago, A.;Zecchin, B.;Monne, I.",2018,,10.3201/eid2407.172123,0
2105,"Phylogenetic analysis of Japanese encephalitis virus: envelope gene based analysis reveals a fifth genotype, geographic clustering, and multiple introductions of the virus into the Indian subcontinent","We report the analysis of the complete nucleotide sequence for the Indian isolate (P20778; Genbank Accession number AF080251) of Japanese encephalitis virus (JEV). The phylogenetic tree topology obtained using thirteen complete genome sequences of JEV was reproduced with the envelope, NS1, NS3, and NS5 genes and revealed extensive divergence between the two Indian strains included. A more exhaustive analysis of JEV evolution using 107 envelope sequences available for isolates from different geographic locations worldwide revealed five distinct genotypes of JEV, displaying a minimum nucleotide divergence of 7% with high bootstrap support values. The tree also revealed overall clustering of strains based on geographic location, as well as multiple introductions of JEV into the Indian subcontinent. Nonsynonymous nucleotide divergence rates of the envelope gene estimated that the ancestor common to all JEV genotypes arose within the last three hundred years.","Aedes/vi [Virology];Amino Acid Sequence;Animals;Base Sequence;Cell Line;Cluster Analysis;DNA, Complementary/ge [Genetics];Encephalitis Virus, Japanese/ch [Chemistry];*Encephalitis Virus, Japanese/cl [Classification];*Encephalitis Virus, Japanese/ge [Genetics];Encephalitis, Japanese/ge [Genetics];*Evolution, Molecular;*Genes, env/ge [Genetics];*Genetic Variation;Genotype;Humans;India;Molecular Sequence Data;*Phylogeny;RNA, Viral/ge [Genetics];Reverse Transcriptase Polymerase Chain Reaction;Sequence Homology, Amino Acid;Sequence Homology, Nucleic Acid;Swine;0 (DNA, Complementary);0 (RNA, Viral)","Uchil, P. D.;Satchidanandam, V.",2001,Sep,,0
2106,Studies on Cotia virus; an unclassified poxvirus,"This paper is a report of studies on Cotia virus; this had been first isolated in 1965 in Brazil and was subsequently shown to be a poxvirus. Cotia virus grew in a wide range of cell cultures and on the chick chorio-allantois (CAM). Its growth characteristics are similar to those of other poxviruses. Microscopy showed virus factories or type B inclusions appearing before infectious progeny virus could be demonstrated. Type A inclusions appeared later, after development of progeny virus; these were shown by electron microscopy to differ from the type A inclusions of cowpox and other poxviruses and they have been termed Cotia bodies. Immunofluorescent staining also showed ring structures which appeared before the development of Cotia bodies. The growth of Cotia virus in human embryo lung (HEL) cells was sensitive to inhibitors of DNA and protein synthesis but was resistant to a concentration of rifampicin which inhibited vaccinia virus. Sharing of antigens between the Cotia virus and vaccinia virus was shown by gel precipitation tests and immunofluorescent staining. There was no cross neutralization between Cotia virus and vaccinia virus nor did anti-Cotia sera neutralize representatives of other poxvirus groups.",animal experiment;cell culture;classification;cytopathogenic effect;geographic distribution;in vitro study;mouse;newborn;Poxviridae;virus characterization;virus classification;virus inclusion;virus infection;virus isolation,"Ueda, Y.;Dumbell, K. R.;Tsuruhara, T.;Tagaya, I.",1978,,,0
2107,Use of DOP-PCR in non-specific virus detection,"Detection and identification of pathogens in any given sample without any knowledge about the pathogen requires the combination of sample purification and generic signal amplification. Our universal virusdetection assay combines virus capsid purification with a generic polymerase chain reaction (PCR) optimized for virus-sized genomes. As a general strategy, biochemical and physical purification by targeted digestion of contaminating host nucleic acids precedes nucleic acid extraction. RNA is transcribed into cDNA; cDNA and the DNA are then used as templates for degenerate oligonucleotide primer PCR (DOP-PCR). This PCR uses a pool of related but different primers, combining degenerate and specific annealing conditions. PCR products can be identified by cloning and sequencing, by microarray, or by high-throughput sequencing. We detected enveloped and non-enveloped DNA and RNA viruses by DOP-PCR in cell culture as well as in clinical samples. The assay has the ability to detect single- and double-stranded genomes, circular genomes, segmented genomes, and linear genomes. Both, large virus genomes such as herpesvirus and very small virus genomes (e.g., circovirus) can be sensitively detected in the same assay. The DOP-PCR assay can be used to identify viruses either directly from biological specimens or from cell culture. A strong feature of the DOP-PCR is its ability to amplify viral sequences without prior knowledge of those sequences, increasing the likelihood of finding mutated or novel viruses. In combination with high-throughput sequencing, the DOP-PCR is a very sensitive tool that can potentially be used for the characterization of a given sample. ©PDA, Inc. 2011.",complementary DNA;double stranded DNA;oligonucleotide;primer DNA;primer RNA;Adeno associated virus;animal cell;bovine viral diarrhea;cell culture;Circovirus;cloning;coliphage;conference paper;controlled study;Coronavirinae;degenerate oligonucleotide primer polymerase chain reaction;DNA microarray;DNA sequence;endogenous retrovirus;Enterovirus;Epstein Barr virus;Human alphaherpesvirus 1;Herpes simplex virus 2;Herpesviridae;high throughput sequencing;human;Human metapneumovirus;Influenza A virus;Nodaviridae;nonhuman;Norovirus;Parvoviridae;Poliomyelitis virus;polymerase chain reaction;RNA transcription;Simian virus 40;Varicella zoster virus;Vesivirus;virus capsid;virus detection;virus envelope;virus genome;virus purification;water contamination,"Uhlenhaut, C.;McClenahan, S.;Krause, P. R.",2011,,10.5731/pdajpst.2011.00842,0
2108,"Complete nucleotide sequence of IT-227/82, an avian paramyxovirus type-1 strain of pigeons (Columba livia)","This paper describes the complete genome sequence of IT-227/82, a strain of avian paramyxovirus type-1 of pigeon (PPMV-1). IT-227/82 is an antigenic variant of Newcastle disease virus (NDV) of chickens. The genome is 15,192 nucleotides (nt) long, similarly to the previously published NDV strain ZJ1. It is, however, six nt longer than the genomes of NDV strains LaSota/46 and Beaudette C. The six-nt insertion was located in the 5′ non-coding region of the nucleoprotein (NP) gene. The presence of this six-nt insertion showed no correlation with the virulence or the reservoir of the NDV strains sequenced so far. The genome length of 15,186 or 15,192 nt can be connected however, to ""old"" (I, II, III and IV) and ""new"" (V, VI, VII and VIII) NDV genotypes, respectively. Comparison of open reading frames indicated that the PPMV-1 strain IT-227/82 encodes the longest W protein, (227 amino acids). The length of the W protein showed remarkable differences even within genotypes and cannot be regarded, therefore, as a phylogenetic feature. The haemagglutinin-neuraminidase protein of strain IT-227/82 consists of 571 amino acids, similarly to genotypes IV, V and VII NDV strains, while genotype I and II strains have longer HN proteins, 616 and 577 amino acids, respectively. The length of the haemagglutinin-neuraminidase protein possesses phylogenetic importance. © Springer Science+Business Media, Inc. 2006.",amino acid;HN protein;nucleoprotein;animal cell;antigenic variation;article;Avulavirus;chicken;gene insertion;genotype;Newcastle disease virus;nonhuman;nucleotide sequence;open reading frame;phylogeny;Columbidae;priority journal;virus genome;virus strain,"Ujvári, D.",2006,,10.1007/s11262-005-5845-0,0
2109,Identification and subgrouping of pigeon type Newcastle disease virus strains by restriction enzyme cleavage site analysis,"A host variant of Newcastle disease virus (NDV, genus Avulavirus, family Paramyxoviridae) is responsible for an autonomous disease in pigeons. It emerged in the late 1970s in the Mediterranean region. Despite great genetic diversity the vast majority of strains belong to a monophyletic group (sublineage VIb) within genotype VI of NDV strains that were indigenous in the region at that time. To date only a monoclonal antibody assay is available for the specific identification of pigeon type strains. A specific genetic assay is described suitable for the identification of pigeon isolates. Cleavage site analysis of a 1349 bp amplicon of the fusion protein gene was carried out using restriction enzymes (RE) HinfI, BstOI and RsaI. RE analysis of over 100 strains isolated between 1978 and 2002 deriving from 16 countries has revealed nine RE-patterns, which were progressive site variants of the parental (group VI) genotype. In spite of substantial site variation, extant pigeon viruses lacked a BstOI cleavage site at nucleotide 1601 shared by other NDV strains of chicken origin. RE analysis is a simple and reliable method both for the identification and subgrouping of pigeon type viruses. © 2005 Elsevier B.V. All rights reserved.",restriction endonuclease;virus RNA;amplicon;article;genetic analysis;genetic variability;genotype;immunoassay;monophyly;Newcastle disease virus;nonhuman;phylogeny;Columbidae;priority journal;restriction mapping;virus classification;virus identification;virus isolation;virus strain,"Ujvári, D.;Wehmann, E.;Herczeg, J.;Lomniczi, B.",2006,,10.1016/j.jviromet.2005.07.012,0
2110,Genetic characterization of bovine viral diarrhoea (BVD) viruses: Confirmation of the presence of BVD genotype 2 in Africa,"Bovine viral diarrhoea virus (BVDV) has emerged as one of the economically important pathogens in cattle populations, with a worldwide distribution and causing a complex of disease syndromes. Two genotypes, BVDV 1 and 2, exist and are discriminated on the basis of the sequence of the 5′ non-coding region (5' NCR) using real-time PCR. Real-time PCR is more sensitive, specific, and less time-consuming than conventional PCR, and it has less risk of cross-contamination of samples. Limited information exists on BVDV genetic subtypes in South Africa. The aim of this study was to determine the genotypes of BVDV currently circulating in South African feedlots. A total of 279 specimens (219 tissue samples, 59 trans-tracheal aspirates and 1 blood sample) were collected from dead and living cattle with lesions or clinical signs compatible with BVDV infection. Pooled homogenates from the same animals were prepared, and total RNA was extracted. A screening test was performed on the pooled samples, and positive pools were investigated individually. A Cador BVDV Type 1/2 RT-PCR Kit (QIAGEN, Hilden, Germany) was used for the real-time PCR assay on a LightCycler® V2. 0 real-time PCR machine (Roche Diagnostics, Mannheim, Germany). The results were read at 530 and 640 nm for BVDV 1 and 2, respectively. Bovine viral diarrhoea virus was detected in a total of 103 samples that included 91 tissue samples, 1 blood sample and 11 trans-tracheal aspirates. Eighty-five (82. 5 %) of the strains were genotype 1 and 18 (17. 5 %) were genotype 2. Comparing the sequencing data, genotypes 1 and 2 from the field strains did not cluster with vaccine strains currently used in feedlots in South Africa. The present study revealed the presence of BVDV genotype 2 in cattle in South Africa based on the high sequence similarity between genotype 2 field strains and strain 890 from North America. The presence of genotype 2 viruses that phylogenetically belong to different clusters and coexist in feedlots is consistent with the possibility of multiple virus introductions. These results represent the first documented evidence for the presence of BVDV genotype 2 in African cattle. © 2012 Springer-Verlag.",Africa;animal;article;Bovine viral diarrhea virus 1;bovine viral diarrhea;bovine;classification;genetic variability;genetics;genotype;isolation and purification;molecular genetics;phylogeny;virology,"Ularamu, H. G.;Sibeko, K. P.;Bosman, A. B.;Venter, E. H.;van Vuuren, M.",2013,,10.1007/s00705-012-1478-5,0
2111,Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq()),"Sequence-independent methods for viral discovery have been widely used for whole genome sequencing of viruses. Different protocols for viral enrichment, library preparation and sequencing have increasingly been more available and at lower costs. However, no study to date has focused on optimization of viral sample preparation for commercial deep sequencing. Accordingly, the aim of the present study was to evaluate an In-House enzymatic protocol for double-stranded DNA (dsDNA) synthesis and also compare the use of a commercially available kit protocol (Nextera XT, Illumina Inc, San Diego, CA, USA) and its combination with a library quantitation kit (Kapa, Kapa Biosystems, Wilmington, MA, USA) for deep sequencing (Illumina Miseq). Two RNA viruses (canine distemper virus and dengue virus) and one ssDNA virus (porcine circovirus type 2) were tested with the optimized protocols. The tested method for dsDNA synthesis has shown satisfactory results and may be used in laboratory setting, particularly when enzymes are already available. Library preparation combining commercial kits (Nextera XT and Kapa) has yielded more reads and genome coverage, probably due to a lack of small fragment recovering at the normalization step of Nextera XT. In addition, libraries may be diluted or concentrated to provide increase on genome coverage with Kapa quantitation.","*Circovirus/ge [Genetics];DNA/bi [Biosynthesis];DNA, Viral/ch [Chemistry];DNA, Viral/ge [Genetics];*DNA, Viral/ip [Isolation & Purification];*Dengue Virus/ge [Genetics];*Distemper Virus, Canine/ge [Genetics];*High-Throughput Nucleotide Sequencing/mt [Methods];Humans;RNA, Viral/ch [Chemistry];RNA, Viral/ge [Genetics];*RNA, Viral/ip [Isolation & Purification];0 (DNA, Viral);0 (RNA, Viral);9007-49-2 (DNA)","Ullmann, L. S.;de Camargo Tozato, C.;Malossi, C. D.;da Cruz, T. F.;Cavalcante, R. V.;Kurissio, J. K.;Cagnini, D. Q.;Rodrigues, M. V.;Biondo, A. W.;Araujo, J. P., Jr.",2015,Aug,,0
2112,Characterization of complete genome sequence of genotype VI and VII velogenic Newcastle disease virus from Japan,"The complete genome sequences of three strains of Newcastle disease virus (NDV) isolated from vaccinated commercial layer flocks in Japan in the span of three decades were characterized. All strains had genome lengths of 15,192 nucleotides consisting of six genes in the order of 3′-NP-P/V/W-M-F-HN-L- 5′. The general genomic characteristics of the Japanese field strains were consistent with previously characterized class II NDV, except for those belonging to early genotypes (genotype I-IV), which lack the six nucleotide insertion at nucleotide positions 1,648-1,653 of the nucleoprotein (NP) gene. Phylogenetic analysis showed that the Japanese strains could be classified into genotypes VIc and VIIe using the complete genome sequence and the complete coding sequence of the fusion (F) gene according to the unified NDV classification system. Characterization of functional domains and neutralizing epitopes of the F and hemagglutinin-neuraminidase (HN) proteins of Japanese field strains revealed a total of 31 amino acid substitutions, as compared to vaccine strains Ishii and B1, which were widely used in Japan. Although virus neutralization (VN) test showed that poor flock immunity due to vaccination failure or partial and non-uniform immunization maybe the major factors involved in the mechanism of breakthrough infection of the Japanese field strains, approximately two to threefold decrease in the VN titers of the field NDV strains possessing a point mutation (E347K or E347G) at the linear epitope of the HN protein was observed, as compared to vaccine strain B1 and field strain 2440/69, which lack the point mutation. This study may be a useful reference in characterizing future ND outbreaks in vaccinated chickens and as a genetic map for future investigations regarding vaccine designs, reverse genetics systems, and development of molecular diagnostic tools to prevent future ND outbreaks in vaccinated poultry flocks. © 2014 Springer Science+Business Media.",HN protein;virus nucleoprotein;amino acid substitution;article;chicken;controlled study;drug design;fusion gene;gene insertion;genome size;Japan;molecular diagnostics;Newcastle disease;Newcastle disease virus;Newcastle disease virus genotype VI;Newcastle disease virus genotype VII;nonhuman;nucleoprotein gene;nucleotide sequence;phylogeny;point mutation;poultry;priority journal;protein domain;reverse genetics;sequence analysis;strain difference;unindexed sequence;vaccine failure;virus characterization;virus classification;virus genome;virus immunity;virus isolation;virus neutralization;virus strain,"Umali, D. V.;Ito, H.;Shirota, K.;Katoh, H.;Ito, T.",2014,,10.1007/s11262-014-1075-7,0
2113,Molecular epidemiology of Newcastle disease virus isolates from vaccinated commercial poultry farms in non-epidemic areas of Japan,"Background: Newcastle Disease (ND) is a highly contagious and economically devastating disease of poultry. At present, limited molecular epidemiological data are available regarding the causes of ND outbreaks in vaccinated commercial poultry farms. Knowing the genomic characteristics of Newcastle disease virus (NDV) infecting commercial poultry operations in spite of vaccination might give important insights on the infection dynamics of these viruses. In addition, molecular analyses at the subgenotype level and studies on the relationship of Japanese NDVs with other isolates from around the world are lacking. Therefore, in the present study, a molecular epidemiological investigation was conducted to characterize nine NDVs isolated from vaccinated commercial poultry flocks in five different Prefectures in non-epidemic areas of Japan between 1969 and 2002. Methods. Nucleotide sequencing and phylogenetic studies were performed to characterize the complete fusion (F)-protein gene, 3-prime end of the nucleoprotein (NP)-gene and 5-prime end of the RNA dependent RNA polymerase (L)-gene. Sequence data were compared with 180 NDV strains from GenBank representing different NDV genotypes and subgenotypes from different regions of the world at different time periods. Deduced amino acids were analyzed for homologies, recombination and mutation. Recombination events were estimated using Recombination Detection Program (RDP) version 3.44. Phylogenetic trees were constructed to determine evolutionary relationships among strains. Results: Mean death time (MDT: 48-56 hr), Intracerebral Pathogenicity Index (ICPI: 1.7-1.9) and deduced amino acid sequences of the F0 proteolytic cleavage site (§ssup§112§esup§RRQKR§ssup§116§esup§) revealed that all nine field isolates were velogenic. Phylogenetic analysis showed that these isolates could be classified into two genetic lineages and three sublineages namely genotypes VIa (lineage 4a), VId (lineage 4d) and VIId (lineage 5d). No recombination events were observed but a point mutation in one of the neutralizing epitope of the F-protein was identified in the field isolates from Japan. Conclusions: All field isolates from vaccinated commercial poultry in non-epidemic areas of Japan were part of much bigger outbreaks in provinces and regions and, in some cases, continents. In general, four ND panzootics occurred in Japan and that these outbreaks were mostly characterized by co-circulation of genetically distinct virus lineages due to involvements of infected wild birds. The point mutation identified in the field isolates from Japan may be due to escape from vaccine pressure. The identification of such mutation may be useful for future site-directed mutagenesis to understand the dynamics of NDV infection in vaccinated chickens. © 2013 Umali et al.; licensee BioMed Central Ltd.",epitope;fusion protein;nucleoprotein;RNA directed RNA polymerase;amino acid sequence;amino acid substitution;article;China;gene mutation;Japan;molecular epidemiology;neighbor joining method;Newcastle disease;Newcastle disease virus;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;poultry farming;reverse transcription polymerase chain reaction;systematic review;Taiwan;time of death;virus isolation;virus strain,"Umali, D. V.;Ito, H.;Suzuki, T.;Shirota, K.;Katoh, H.;Ito, T.",2013,,10.1186/1743-422x-10-330,0
2114,Molecular characterization and phylogenetic analysis of newcastle disease virus isolated from clinical cases of newcastle disease in commercial layer farms in the Philippines,"Newcastle Disease (ND) is an economically devastating disease of poultry. At present, limited data are available regarding the molecular characteristics of Newcastle disease virus (NDV) from the Philippines. Clinical and molecular characterizations were performed on five clinical cases of ND in vaccinated commercial layer farms from four provinces in the Philippines, namely Bulacan, Pampanga, Zamboanga del Sur and Davao Del Sur. Clinical signs observed on affected flocks were conjunctivitis, gasping, tracheal rales, facial swelling, lethargy, greenish diarrhea, torticollis and paralysis. Disease onset ranged from 21 to 124 days with mortality rates of 15 to 61%. Gross morphological lesions identified were presence of serous exudates in the infraorbital sinuses, hemorrhagic trachea, inflamed spleen, liver and kidneys and petechial hemorrhages in the proventriculus and cecal tonsils. Nucleotide sequencing showed that all field strains were velogenic with FO proteolytic cleavage site of 112RRRKRz.ast;F117 and 112RRQKRz.ast;F117 patterns. Phylogenetic analysis showed that all field NDV strains belong to class II genotype VII, subgenotypes Vila, Vllh and Vili. Evolutionary divergence showed that the field NDV strains were closely related (up to 99% similarity) to the newly identified subgenotypes of virulent NDVs currently emerging in Southeast Asia and the Middle East.",Newcastle disease vaccine;amino acid sequence;animal experiment;animal tissue;article;capillary electrophoresis;cecal tonsil;conjunctivitis;controlled study;depression;diarrhea;disease surveillance;DNA extraction;food intake;molecular biology;mortality rate;neighbor joining method;Newcastle disease virus;nonhuman;opisthotonus;phylogeny;proventriculus;reverse transcription polymerase chain reaction;RNA extraction;sampling;Sanger sequencing;sequence analysis;torticollis;vaccination;virus classification,"Umali, D. V.;Lopez, A. L. M.;Torres, M. I. P.;Umandal, M. C.;Katoh, H.",2017,,,0
2115,Screening human cell lines for viral infections applying RNA-Seq data analysis,"Monitoring viral infections of cell cultures is largely neglected although the viruses may have an impact on the physiology of cells and may constitute a biohazard regarding laboratory safety and safety of bioactive agents produced by cell cultures. PCR, immunological assays, and enzyme activity tests represent common methods to detect virus infections. We have screened more than 300 Cancer Cell Line Encyclopedia RNA sequencing and 60 whole exome sequencing human cell lines data sets for specific viral sequences and general viral nucleotide and protein sequence assessment applying the Taxonomer bioinformatics tool developed by IDbyDNA. The results were compared with our previous findings from virus specific PCR analyses. Both, the results obtained from the direct alignment method and the Taxonomer alignment method revealed a complete concordance with the PCR results: twenty cell lines were found to be infected with five virus species. Taxonomer further uncovered a bovine polyomavirus infection in the breast cancer cell line SK-BR-3 most likely introduced by contaminated fetal bovine serum. RNA-Seq data sets were more sensitive for virus detection although a significant proportion of cell lines revealed low numbers of virus specific alignments attributable to low level nucleotide contamination during RNA preparation or sequencing procedure. Low quality reads leading to Taxonomer false positive results can be eliminated by trimming the sequence data before analysis. One further important result is that no viruses were detected that had never been shown to occur in cell cultures. The results prove that the currently applied testing of cell cultures is adequate for the detection of contamination and for the risk assessment of cell cultures. The results emphasize that next generation sequencing is an efficient tool to determine the viral infection status of human cells.",amino acid sequence;article;bioinformatics;cell screening;controlled study;diagnostic accuracy;false positive result;fetal bovine serum;gene expression;hepatitis B;hepatitis C;human;human cell;Human immunodeficiency virus infection;measurement accuracy;next generation sequencing;nonhuman;nucleotide sequence;papillomavirus infection;polymerase chain reaction;polyomavirus infection;risk assessment;RNA analysis;SK-BR-3 cell line;virus detection;virus gene;virus genome;virus infection;whole exome sequencing,"Uphoff, C. C.;Pommerenke, C.;Denkmann, S. A.;Drexler, H. G.",2019,,10.1371/journal.pone.0210404,0
2116,Bovine ephemeral fever,"Ephemeral fever remains a viral disease of considerable importance to many countries including Australia. The virus has been only partly characterised and still awaits final classification. Although BEF virus was first thought to contain 6 structural proteins there is increasing evidence to suggest that it contains the 5 proteins characteristic of the Rhabdoviridae. Although BEF is thought to be arthropod borne, the vector has yet to be identified but it is clear from the distribution of BEF that more than one vector is capable of transmitting the disease. Despite rigorous investigation of the clinical signs and the pathology of ephemeral fever, little progress has been made on the pathogenesis of the disease. This has been partly due to the difficulty of propagating BEF virus in vitro and the inability to define the site of replication. However, there is mounting evidence to suggest that BEF is immunopathologic in nature and that the clinical expression of the disease is influenced by the release of one or more mediators of inflammation. The disease is characterised by a number of haematological and biochemical changes and early and prolonged treatment with phenylbutazone is capable of reversing a number of these changes. The intravenous administration of calcium can now be considered a justifiable addition to the treatment regimen together with prolonged phenylbutazone therapy. The vaccines currently available are prepared from either live attenuated or killed virus and may be less than reliable. There appears to be a need for a reliable, inexpensive, cold-chain independent alternative vaccine.",animal;Australia;bovine;cattle disease;classification;immunology;microbiology;review;Rhabdoviridae,"Uren, M. F.",1989,,,0
2117,Unmapped reads from cattle RNAseq data: A source for missing and misassembled sequences in the reference assemblies and for detection of pathogens in the host,"Usually, reads from transcriptome sequencing data unmapped to the target species' reference genome are disregarded. A recent RNAseq project on the new fatal disease Bovine Neonatal Pancytopenia had indicated an unexplained immune response signature to a double-stranded RNA virus. To unravel its background, contigs were de novo assembled from unmapped RNAseq reads and aligned against the bovine genome assemblies and multispecies NCBI databases. Lack of genuine virus sequence contigs rejected the hypothesis of a live virus being causal for the unexplained immune response. Alignment data also demonstrated incomplete bovine reference genome assemblies. In addition, we found that several parasite and virus genome reference assemblies in NCBI were contaminated with bovine DNA and confirmed recombination of bovine DNA into BVD virus strains. Exploring unmapped reads can extract useful biological information regarding the presence of microorganisms and can highlight issues with reference genome assemblies of host and pathogen species.","Animals;*Cattle/ge [Genetics];Cattle/mi [Microbiology];Cattle/ps [Parasitology];Cattle/vi [Virology];Computational Biology;Female;*Genome;*High-Throughput Nucleotide Sequencing/st [Standards];*Sequence Analysis, RNA/st [Standards]","Usman, T.;Hadlich, F.;Demasius, W.;Weikard, R.;Kuhn, C.",2017,01,,0
2118,"Sequencing and sequence analysis of partial nucleoprotein (N) gene and phylogenetic analysis of rabies virus field isolates from Gujarat state, India","The present study was undertaken with an aim of characterization of rabies virus (genus Lyssavirus of the family Rhabdoviridae under the order Mononegavirales) by sequencing of partial nucleoprotein (N) gene of rabies virus and phylogenetic analysis to know the genotype and lineage of rabies virus present in Gujarat state of India. A total of 32 samples (18 brain samples and 14 saliva samples) were aseptically collected from live and dead animals (viz. dog, buffalo, cow, goat, donkey and hyena) for rabies virus detection. Out of 32 samples, 24 samples were found positive by Reverse Transcriptase Polymerase Chain Reactions and from these 24 positive samples, 20 samples were selected for sequencing having good concentration of gene product. ClustalW alignment of nucleotide sequences and amino acid sequences of field rabies isolates revealed 95.20–100 and 97.95–100% similarity among themselves, respectively. Multiple sequence alignment of field rabies isolates and reference vaccine strains [Pasteur strain and Challenge Virus Strain (CVS)] indicated single nucleotide mutations at total 91 positions and amino acid mutations at total 17 different positions. Phylogenetic analysis of N gene sequences using our 20 field rabies isolates and 21 other reported isolates in Genbank resulted in 3 phylogenetic clusters. All the field rabies isolates showed same genetic lineage among themselves and with other earlier reported Indian rabies isolates placing them in Arctic like lineage of Genotype 1 Rabies virus. However, they were at genetic distance with reference Pasteur and CVS strains, which grouped in different phylogenetic cluster.",amino acid;nucleoprotein;nucleotide;rabies vaccine;viral protein;amino acid sequence;article;brain;buffalo;concentration (parameter);cow;dog;donkey;gene product;gene sequence;genetic distance;genotype;goat;Gujarat;hyena;molecular phylogeny;nonhuman;nucleotide sequence;proteomics;Rabies virus;reverse transcription polymerase chain reaction;saliva;sequence alignment;sequence analysis;virus detection;virus gene;virus isolation;virus mutation;virus strain,"Vagheshwari, D. H.;Bhanderi, B. B.;Mathakiya, R. A.;Jhala, M. K.",2017,,10.1007/s13337-017-0387-3,0
2119,Global Distribution of Human Protoparvoviruses,"Development of next-generation sequencing and metagenomics has revolutionized detection of novel viruses. Among these viruses are 3 human protoparvoviruses: bufavirus, tusavirus, and cutavirus. These viruses have been detected in feces of children with diarrhea. In addition, cutavirus has been detected in skin biopsy specimens of cutaneous T-cell lymphoma patients in France and in 1 melanoma patient in Denmark. We studied seroprevalences of IgG against bufavirus, tusavirus, and cutavirus in various populations (n = 840), and found a striking geographic difference in prevalence of bufavirus IgG. Although prevalence was low in adult populations in Finland (1.9%) and the United States (3.6%), bufavirus IgG was highly prevalent in populations in Iraq (84.8%), Iran (56.1%), and Kenya (72.3%). Conversely, cutavirus IgG showed evenly low prevalences (0%-5.6%) in all cohorts, and tusavirus IgG was not detected. These results provide new insights on the global distribution and endemic areas of protoparvoviruses.",HUMAN BUFAVIRUS;ACUTE DIARRHEA;DOMESTIC PIGS;PARVOVIRUSES;VIRUSES;FECES;IDENTIFICATION;CHILDREN;CHINA,"Vaisanen, E.;Mohanraj, U.;Kinnunen, P. M.;Jokelainen, P.;Al-Hello, H.;Barakat, A. M.;Sadeghi, M.;Jalilian, F. A.;Majlesi, A.;Masika, M.;Mwaengo, D.;Anzala, O.;Delwart, E.;Vapalahti, O.;Hedman, K.;Soderlund-Venermo, M.",2018,Jul,,0
2120,"Epidemiology of two human protoparvoviruses, bufavirus and tusavirus","Two human parvoviruses were recently discovered by metagenomics in Africa, bufavirus (BuV) in 2012 and tusavirus (TuV) in 2014. These viruses have been studied exclusively by PCR in stool and detected only in patients with diarrhoea, although at low prevalence. Three genotypes of BuV have been identified. We detected, by in-house EIA, BuV1-3 IgG antibodies in 7/228 children (3.1%) and 10/180 adults (5.6%), whereas TuV IgG was found in one child (0.4%). All children and 91% of the adults were Finnish, yet interestingly 3/6 adults of Indian origin were BuV-IgG positive. By competition EIA, no cross-reactivity between the BuVs was detected, indicating that the BuV genotypes represent distinct serotypes. Furthermore, we analysed by BuV qPCR stool and nasal swab samples from 955 children with gastroenteritis, respiratory illness, or both, and found BuV DNA in three stools (0.3%) and for the first time in a nasal swab (0.1%). This is the first study documenting the presence of BuV and TuV antibodies in humans. Although the seroprevalences of both viruses were low in Finland, our results indicate that BuV infections might be widespread in Asia. The BuV-specific humoral immune responses appeared to be strong and long-lasting, pointing to systemic infection in humans.",GENETIC DIVERSITY;HUMAN BOCAVIRUSES;ERYTHROVIRUS B19;ACUTE DIARRHEA;DOMESTIC PIGS;PARVOVIRUS;IDENTIFICATION;INFECTION;CHILDREN;FECES,"Vaisanen, E.;Paloniemi, M.;Kuisma, I.;Lithovius, V.;Kumar, A.;Franssila, R.;Ahmed, K.;Delwart, E.;Vesikari, T.;Hedman, K.;Soderlund-Venermo, M.",2016,Dec,,0
2121,S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification,"Infectious bronchitis virus (IBV) is the causative agent of a highly contagious disease that results in severe economic losses to the global poultry industry. The virus exists in a wide variety of genetically distinct viral types, and both phylogenetic analysis and measures of pairwise similarity among nucleotide or amino acid sequences have been used to classify IBV strains. However, there is currently no consensus on the method by which IBV sequences should be compared, and heterogeneous genetic group designations that are inconsistent with phylogenetic history have been adopted, leading to the confusing coexistence of multiple genotyping schemes. Herein, we propose a simple and repeatable phylogeny-based classification system combined with an unambiguous and rationale lineage nomenclature for the assignment of IBV strains. By using complete nucleotide sequences of the S1 gene we determined the phylogenetic structure of IBV, which in turn allowed us to define 6 genotypes that together comprise 32 distinct viral lineages and a number of inter-lineage recombinants. Because of extensive rate variation among IBVs, we suggest that the inference of phylogenetic relationships alone represents a more appropriate criterion for sequence classification than pairwise sequence comparisons. The adoption of an internationally accepted viral nomenclature is crucial for future studies of IBV epidemiology and evolution, and the classification scheme presented here can be updated and revised novel S1 sequences should become available.",Africa;article;Australia;Avian infectious bronchitis virus;Europe;gene sequence;genetic variability;genotype;Middle East;New Zealand;nonhuman;North America;nucleotide sequence;phylogeny;priority journal;S1 gene;South America;virus classification;virus gene;virus recombination,"Valastro, V.;Holmes, E. C.;Britton, P.;Fusaro, A.;Jackwood, M. W.;Cattoli, G.;Monne, I.",2016,,10.1016/j.meegid.2016.02.015,0
2122,Genetic typing and prevalence of Border disease virus (BDV) in small ruminant flocks in Spain,"Between 2001 and 2002, samples from 1413 animals in 21 Spanish small ruminant flocks, most of them with animals showing clinical signs compatible with Border disease (BD), were screened for the presence of Pestivirus antigen and antibodies by an indirect peroxidase monolayer assay (IPMA) and the virus neutralization test (VNT), respectively. Although all flocks harboured seropositive animals, virus could only be isolated from animals in five of the flocks. Between 4 and 11 months later all animals older than 6 months in three of the flocks were resampled. At this time, 51-83% of them had neutralizing antibodies. The prevalence of persistently infected (PI) animals within two of the flocks was 0.3 and 0.6%, respectively. The third flock presumably had eliminated all the PI animals. Fourteen virus isolates were obtained. The 5′ untranslated region (5′UTR) was amplified by RT-PCR and directly sequenced. Phylogenetic analyses classified them as a group of Border disease viruses (BDV), separated from BDV-1, but showing a relatively low bootstrap value. Three of the 14 isolates were in the same subgroup as a set of formerly characterised Spanish isolates from the Basque Country, which were allocated to subgroup BDV-C. In addition, they were in the group with an isolate from chamois, which is currently allocated in group BDV-4. Because of its close relation to the chamois isolate, these isolates were tentatively reallocated in a subgroup BDV-4a. The remaining isolates generated a new subgroup, related but not in the same cluster as the chamois isolate, and was therefore tentatively assigned to a new subgroup BDV-4b. Our results show that classification and nomenclature of BDV needs to be harmonised. © 2006 Elsevier B.V. All rights reserved.",neutralizing antibody;peroxidase;virus antibody;virus antigen;5' untranslated region;article;clinical feature;controlled study;enzyme assay;gene sequence;genetic trait;genotype;groups by age;herd;nonhuman;nucleotide sequence;Pestivirus;phylogeny;prevalence;reverse transcription polymerase chain reaction;sampling;screening;separation technique;serodiagnosis;sheep disease;Spain;statistical analysis;virus classification;virus isolation;virus neutralization,"Valdazo-González, B.;Álvarez-Martínez, M.;Greiser-Wilke, I.",2006,,10.1016/j.vetmic.2006.06.008,0
2123,"Interspecies transmission of Rotaviruses among ruminants, dogs and humans: Current facts and remarks","Rotaviruses are considered to be a major cause of diarrhoea to humans as well as a wide variety of animals and may cause serious economic losses in livestock animals, especially swine and ruminants. This fact, along with the genetic diversity that characterizes members of the Rotavirus group, raised concerns regarding the potential of virus interspecies transmission among various species of animals and humans. Regarding the presence and the epidemiology of Rotaviruses in ruminants in association with closely related humans and dogs, research is limited and few data have been presented in recent years. In this review we present all the latest information regarding the distribution of genotypes of Rotavirus strains in ruminants, dogs and humans.",Cryptosporidium;diarrhea;disease burden;disease surveillance;dog;genetic variability;genome analysis;genotype;human;metagenomics;mortality rate;nonhuman;prevalence;review;Rotavirus;ruminant;virus identification;virus transmission,"Valiakos, G.;Chatzopoulos, D. C.;Tsokana, C. N.",2017,,10.12681/jhvms.15596,0
2124,Anaplasma marginale superinfection attributable to pathogen strains with distinct genomic backgrounds,"Strain superinfection occurs when a second pathogen strain infects a host already infected with a primary strain. The selective pressures that drive strain divergence, which underlies superinfection, and allow penetration of a new strain into a host population are critical knowledge gaps relevant to shifts in infectious disease epidemiology. In regions of endemicity with a high prevalence of infection, broad population immunity develops against Anaplasma marginale, a highly antigenically variant rickettsial pathogen, and creates strong selective pressure for emergence of and superinfection with strains that differ in their Msp2 variant repertoires. The strains may emerge either by msp2 locus duplication and allelic divergence on an existing genomic background or by introduction of a strain with a different msp2 allelic repertoire on a distinct genomic background. To answer this question, we developed a multilocus typing assay based on high-throughput sequencing of non-msp2 target loci to distinguish among strains with different genomic backgrounds. The technical error level was statistically defined based on the percentage of perfect sequence matches of clones of each target locus and validated using experimental single strains and strain pairs. Testing of A. marginale-positive samples from tropical regions where A. marginale infection is endemic identified individual infections that contained unique alleles for all five targeted loci. The data revealed a highly significant difference in the number of strains per animal in the tropical regions compared to infections in temperate regions and strongly supported the hypothesis that transmission of genomically distinct A. marginale strains predominates in high-prevalence areas of endemicity.","*Anaplasma marginale/cl [Classification];*Anaplasma marginale/ge [Genetics];Anaplasma marginale/im [Immunology];Anaplasma marginale/ip [Isolation & Purification];*Anaplasmosis/mi [Microbiology];Animals;*Antigens, Bacterial/ge [Genetics];Antigens, Bacterial/im [Immunology];*Bacterial Outer Membrane Proteins/ge [Genetics];Bacterial Outer Membrane Proteins/im [Immunology];Cattle;*Cattle Diseases/mi [Microbiology];DNA, Bacterial/ch [Chemistry];DNA, Bacterial/ge [Genetics];*Genetic Variation;Genotype;Multilocus Sequence Typing;Superinfection/mi [Microbiology];*Superinfection/ve [Veterinary];0 (Antigens, Bacterial);0 (Bacterial Outer Membrane Proteins);0 (DNA, Bacterial);0 (msp2 protein, Anaplasma marginale)","Vallejo Esquerra, E.;Herndon, D. R.;Alpirez Mendoza, F.;Mosqueda, J.;Palmer, G. H.",2014,Dec,,0
2125,What's in a strain? Viral metagenomics identifies genetic variation and contaminating circoviruses in laboratory isolates of pigeon paramyxovirus type 1,"We used next generation sequencing on random amplified viral nucleic acids to determine the genome sequence of 11 pigeon paramyxovirus type 1 (PPMV-1) isolates from Belgium (period 1998-2011). The PPMV-1 deep sequence data allowed identification of sequence variability in multiple PPMV-1 isolates, including one STOP codon in the Matrix gene which was present in 15% of the viral population of one isolate. Notably, mutations that were previously associated with pathogenicity in chickens were identified as minor sequence variants in one parent laboratory strain. A phylogenetic analysis of the consensus PPMV-1 genome sequences was performed. In addition to providing nearly complete paramyxovirus genome sequences, our sequence-independent approach identified the presence of pigeon circovirus (PiCV) sequences in four of these viral stocks. Real-time quantitative RT-PCR analysis specific for PMV-1 and PiCV showed that these contaminations were present in seven viral stocks consisting of allantoic fluids and was occasionally also detected in stocks passaged in embryonated chicken eggs. Phylogenetic analysis of the PiCV consensus genome sequences showed a circulation of PiCV covering the full genetic diversity of known PiCV.This study shows the value of novel sequence independent technologies for access to sequence information for the control of reference virus stocks and other biological materials, as co-infecting viruses or sequence variants from the original sample may persist in the stocks without being identified by the routine virus-specific diagnostic tools. The exact role of PiCV in pigeon disease - in particular Newcastle disease - and its potential interference with PPMV-1 diagnostics remains to be investigated. © 2012 Elsevier B.V.",nucleic acid;article;Belgium;chicken;Circovirus;codon;gene amplification;gene mutation;gene sequence;genetic variability;metagenomics;nonhuman;Paramyxoviridae;phylogeny;pigeon paramyxovirus type 1;priority journal;real time polymerase chain reaction;reverse transcription polymerase chain reaction;sequence analysis;virus isolation;virus virulence,"Van Borm, S.;Rosseel, T.;Steensels, M.;Van den Berg, T.;Lambrecht, B.",2013,,10.1016/j.virusres.2012.11.017,0
2126,Complete coding sequence of a novel picorna-like virus in a blackbird infected with Usutu virus,"Using random high-throughput RNA sequencing, the complete coding sequence of a novel picorna-like virus (a 9,228-nt contig containing 212,202 reads) was determined from a blackbird (Turdus merula) infected with Usutu virus. This sequence shares only 36% amino acid sequence identity with its closest homolog, arivirus 1, (an unclassified member of the order Picornavirales), and shares its dicistronic genome arrangement. The new virus was therefore tentatively named ""blackbird arilivirus"" (ari-like virus). The nearly complete genome sequence consists of at least 9,228 nt and contains two open reading frames (ORFs) encoding the nonstructural polyprotein (2235 amino acids) and structural polyprotein (769 amino acids). Two TaqMan RT-qPCR assays specific for ORF1 confirmed the presence of high levels of this novel virus in the original sample. Nucleotide composition analysis suggests that blackbird arilivirus is of dietary (plant) origin.",animal;Belgium;bird disease;chromosomal mapping;classification;Flavivirus;Flavivirus infection;genetics;isolation and purification;mixed infection;open reading frame;Passeriformes;phylogeny;Picornaviridae;picornavirus infection;plant;veterinary medicine;virology;virus genome;whole genome sequencing,"Van Borm, S.;Steensels, M.;Mathijs, E.;Yinda, C. K.;Matthijnssens, J.;Lambrecht, B.",2018,,10.1007/s00705-018-3761-6,0
2127,"Genital warts in Burmeister's porpoises: Characterization of Phocoena spinipinnis papillomavirus type 1 (PsPV-1) and evidence for a second, distantly related PsPV","We identified sequences from two distantly related papillomaviruses in genital warts from two Burmeister's porpoises, including a PV antigen-positive specimen, and characterized Phocoena spinipinnis papillomavirus type 1 (PsPV-1). The PsPV-1 genome comprises 7879 nt and presents unusual features. It lacks an E7, an E8 and a bona fide E5 open reading frame (ORF) and has a large E6 ORF. PsPV-1 L1 ORF showed the highest percentage of nucleotide identity (54-55%) with human papillomavirus type 5, bovine papillomavirus type 3 (BPV-3) and Tursiops truncatus papillomavirus type 2 (TtPV-2). This warrants the classification of PsPV-1 as the prototype of the genus Omikronpapillomavirus. PsPV-1 clustered with TtPV-2 in the E6 and E1 E2 phylogenetic trees and with TtPV-2 and BPV-3 in the L2L1 tree. This supports the hypothesis that PV evolution may not be monophyletic across ali genes. © 2007 SGM.",protein E5;protein E6;protein E7;protein E8;unclassified drug;viral protein;article;cluster analysis;condyloma;controlled study;DNA virus;nonhuman;nucleotide sequence;Omikronpapilloma virus;open reading frame;Papillomaviridae;Papilloma virus 1;Papilloma virus 2;Papilloma virus 3;Papilloma virus 5;phylogeny;porpoise;priority journal;sequence analysis;taxonomic rank;virus characterization;virus classification;virus genome,"Van Bressem, M. F.;Cassonnet, P.;Rector, A.;Desaintes, C.;Van Waerebeek, K.;Alfaro-Shigueto, J.;Van Ranst, M.;Orth, G.",2007,,10.1099/vir.0.82694-0,0
2128,Phylogenetic analysis of the first complete hepatitis E virus (HEV) genome from Africa,"Hepatitis E virus (HEV) is globally distributed, transmitted enterically and between humans and animals. Phylogenetic analysis has identified five distinct HEV genotypes. The first full-length sequence of an African strain (Chad) is presented and compared to 31 complete HEV genomes available, including the fulminant hepatitis strain from India, swine strains and a strain from Morocco. The two African strains are more closely related to genotype 1 than to any other genotypes and together they possibly form a sub-genotype or sixth genotype. The first evidence for recombination between divergent HEV strains is presented. © 2003 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.",Africa;article;controlled study;gene sequence;genetic analysis;genotype;Hepatitis E virus;nonhuman;nucleotide sequence;phylogeny;priority journal;species comparison;virus gene;virus genome;virus recombination;virus strain,"Van Cuyck, H.;Juge, F.;Roques, P.",2003,,10.1016/s0928-8244(03)00241-4,0
2129,Development and validation of a genotype 3 recombinant protein-based immunoassay for hepatitis E virus serology in swine,"Hepatitis E virus (HEV) is classified within the family Hepeviridae, genus Hepevirus. HEV genotype 3 (Gt3) infections are endemic in pigs in Western Europe and in North and South America and cause zoonotic infections in humans. Several serological assays to detect HEV antibodies in pigs have been developed, at first mainly based on HEV genotype 1 (Gt1) antigens. To develop a sensitive HEV Gt3 ELISA, a recombinant baculovirus expression product of HEV Gt3 open reading frame-2 was produced and coated onto polystyrene ELISA plates. After incubation of porcine sera, bound HEV antibodies were detected with anti-porcine anti-IgG and anti-IgM conjugates. For primary estimation of sensitivity and specificity of the assay, sets of sera were used from pigs experimentally infected with HEV Gt3. For further validation of the assay and to set the cutoff value, a batch of 1100 pig sera was used. All pig sera were tested using the developed HEV Gt3 assay and two other serologic assays based on HEV Gt1 antigens. Since there is no gold standard available for HEV antibody testing, further validation and a definite setting of the cutoff of the developed HEV Gt3 assay were performed using a statistical approach based on Bayes' theorem. The developed and validated HEV antibody assay showed effective detection of HEV-specific antibodies. This assay can contribute to an improved detection of HEV antibodies and enable more reliable estimates of the prevalence of HEV Gt3 in swine in different regions.",recombinant protein;animal cell;article;baculovirus expression system;cell lysate;culture medium;development;diagnostic accuracy;diagnostic test accuracy study;enzyme linked immunosorbent assay;genotype;Hepatitis E virus;immunoassay;nonhuman;nucleotide sequence;polyacrylamide gel electrophoresis;protein expression;sensitivity and specificity;pig;validation study;Western blotting,"van der Poel, W. H. M.;Pavio, N.;van der Goot, J.;van Es, M.;Martin, M.;Engel, B.",2014,,10.1590/1414-431x20133249,0
2130,Micro neuraminidase-inhibition assay for classification of influenza A virus neuraminidases,"A neuraminidase-inhibition (NI) assay performed in microtiter plates is described. This micro-NI assay is a modification of the NI assay recommended by the World Health Organization. It reduces the quantity of reagents required and permits antigenic classification of many isolates simultaneously. To determine the accuracy and sensitivity of this micro-NI assay, 110 influenza A viruses, representing all subtypes, based upon the nine known neuraminidases (NAs), were classified by both the micro-NI and macro-NI assays in two separate laboratories. The NAs were identified accurately by the micro-NI assay. Virus mixtures were detected by both assays, although the macro-NI was clearly more sensitive. The micro-NI assay was also suitable for testing sera for the presence of antibodies to the NAs. Although the micro-NI assay did not provide the quantitation of the macro-NI assay, it did prove to be a rapid method for virus classification and antibody studies on influenza A viruses.",sialidase;virus antibody;virus antigen;animal;animal disease;article;classification;comparative study;duck;Influenza A virus;isolation and purification;methodology;microbiology;serotyping,"Van Deusen, R. A.;Hinshaw, V. S.;Senne, D. A.;Pellacani, D.",1983,,,0
2131,"One world, one health. Humans, animals and the environment are inextricably linked--a fact that needs to be remembered and exploited in our modern approach to health",,"Animals;*Biodiversity;Birds;Cats;Cattle;Disease Reservoirs/ps [Parasitology];Disease Reservoirs/vi [Virology];Health;Humans;*Influenza in Birds/tm [Transmission];*Influenza, Human/tm [Transmission];Metagenome/ph [Physiology];Toxoplasmosis/pc [Prevention & Control];*Toxoplasmosis/tm [Transmission];Toxoplasmosis, Animal/pc [Prevention & Control];*Toxoplasmosis, Animal/tm [Transmission];Tuberculosis, Pulmonary/tm [Transmission];*Tuberculosis, Pulmonary/ve [Veterinary];Zoonoses","van Helden, P. D.;van Helden, L. S.;Hoal, E. G.",2013,Jun,,0
2132,"Complete nucleotide sequence of the new simian T-lymphotropic virus, STLV-PH969 from a hamadryas baboon, and unusual features of its long terminal repeat","A third type of primate T-lymphotropic virus, PTLV-L, with STLV-PH969 as a prototype, has recently been isolated from an African baboon (Papio hamadryas). Classification of this virus has been based on partial sequence analysis of cDNA from a virus-producing cell line, PH969. We obtained the complete nucleotide sequence of this virus with a proviral genome of 8,916 bp. All major genes, homologous in all human T-cell lymphotropic virus (HTLV)-related viruses, and their corresponding mRNAs, including appropriate splicing, were identified. One additional nonhomologous open reading frame in the proximal pX region is accessible for translation through alternative splicing. Sequence comparison shows that STLV-PH969 is equidistantly related to HTLV type 1 (HTLV-1) and HTLV-2. In all coding regions, the similarity tends to be the lowest between STLV-PH969 and HTLV-1. However, in the long terminal repeat (LTR) region, the lowest similarity was found between STLV- PH969 and HTLV-2. The U3-R and R-U5 boundaries of the STLV-PH969 LTR were experimentally determined at nucleotides 268 and 52.4, respectively. This 695-bp LTR is 60 and 73 bp shorter than the LTRs of HTLV-1 and HTLV-2, respectively, but its general organization is similar to the one found in the HTLV-bovine leukemia virus genus. In the long region between the polyadenylation signal and the poly(A) site, sequence similarity with the HTLV-1 Rex-responsive element (RexRE) core and secondary structure prediction suggest the presence of a RexRE. The presence of three 21-bp repeats is conserved within the U3 region of HTLV-1, HTLV-2, and BLV. Only two direct repeats with similarity to these Tax-responsive elements were found in the STLV-PH969 LTR, which might suggest differences in the Tax-mediated transactivation of this virus. We conclude that STLV-PH969 has all the genes and genomic regions to suggest a replication cycle comparable to that of HTLV-1 and HTLV-2.",polyadenylic acid;alternative RNA splicing;amino acid sequence;animal cell;article;baboon;Human T-lymphotropic virus 1;Human T-lymphotropic virus 2;long terminal repeat;nonhuman;open reading frame;polyadenylation;polymerase chain reaction;priority journal;Retroviridae;RNA splicing;sequence analysis;sequence homology;TATA box;transactivation;virus genome;virus isolation;virus replication,"Van Marianne, B.;Goubau, P.;Rousseau, R.;Desmyter, J.;Vandamme, A. M.",1997,,,0
2133,Genetic heterogeneity in the foot-and-mouth disease virus Leader and 3C proteinases,"The Leader and 3C proteinases of foot-and-mouth disease virus (FMDV) are responsible for almost all the proteolytic processing events of the viral polyprotein precursor. Investigation into the genetic heterogeneity of the regions encoding these proteins from isolates of six FMDV serotypes revealed the 3C proteinase to be more conserved than the Leader proteinase. Maximum likelihood analysis indicated similar phylogenetic groupings for the non-structural protein coding regions of both the Leader and 3C. These groupings were different from the structural VP1 protein coding region which, as shown previously, grouped according to serotype. Two distinct clades were apparent for both the Leader and 3C coding regions: one comprising of serotypes A, O and C together with SAT (South African Territories) isolates from eastern Africa. The other clade consisted of SAT isolates originating from southern Africa. Only one virus isolate, obtained from a buffalo in Uganda, did not conform to this phylogenetic pattern. This SAT 1 virus grouped with types A, O and C in the Leader analysis, but with the southern African SAT types in the 3C analysis, implicating intertypic recombination. The leader proteinases of southern African SAT type isolates differed from those present in European type isolates, particularly in the self-processing region. A three-dimensional structure was modeled for the Leader proteinase of one of the SAT type viruses, ZIM/7/83/2, and compared with the previously elucidated crystal structure of O1Kaufbeuren Leader proteinase. The active sites of the two leaders were found to superimpose closely, despite the observed sequence variation between the two molecules. Comparison of the 3C proteinase P1 cleavage sites suggested that the FMDV 3C proteinase may possess a broader substrate specificity, as observed in hepatitis A virus 3C proteinase. © 2002 Elsevier Science B.V. All rights reserved.",enzyme precursor;proteinase;virus enzyme;Africa;article;controlled study;crystal structure;enzyme active site;enzyme specificity;enzyme structure;Foot and mouth disease virus;genetic heterogeneity;geographic distribution;Hepatitis A virus;nonhuman;nucleotide sequence;phylogeny;priority journal;protein degradation;sequence homology;serotype;virus isolation,"Van Rensburg, H.;Haydon, D.;Joubert, F.;Bastos, A.;Heath, L.;Nel, L.",2002,,10.1016/s0378-1119(02)00471-7,0
2134,Origin of the 1918 Spanish influenza virus: A comparative genomic analysis,"To test the avian-origin hypothesis of the 1918 Spanish influenza virus we surveyed influenza sequences from a broad taxonomic distribution and collected 65 full-length genomes representing avian, human and ""classic"" swine H1N1 lineages in addition to numerous other swine (H1N2, H3N1, and H3N2), human (H2N2, H3N2, and H5N1), and avian (H1N1, H4N6, H5N1, H6N1, H6N6, H6N8, H7N3, H8N4, H9N2, and H13N2) subtypes. Amino acids from all eight segments were concatenated, aligned, and used for phylogenetic analyses. In addition, the genes of the polymerase complex (PB1, PB2, and PA) were analyzed individually. All of our results showed the Brevig-Mission/1918 strain in a position basal to the rest of the clade containing human H1N1s and were consistent with a reassortment hypothesis for the origin of the 1918 virus. Our genome phylogeny further indicates a sister relationship with the ""classic"" swine H1N1 lineage. The individual PB1, PB2, and PA phylogenies were consistent with reassortment/recombination hypotheses for these genes. These results demonstrate the importance of using a complete-genome approach for addressing the avian-origin hypothesis and predicting the emergence of new pandemic influenza strains. © 2008 Elsevier Inc. All rights reserved.",concatenated DNA;article;comparative study;genetics;human;Influenza A virus;phylogeny;Spain;virus genome,"Vana, G.;Westover, K. M.",2008,,10.1016/j.ympev.2008.02.003,0
2135,An ecological and conservation perspective on advances in the applied virology of zoonoses,"The aim of this manuscript is to describe how modern advances in our knowledge of viruses and viral evolution can be applied to the fields of disease ecology and conservation. We review recent progress in virology and provide examples of how it is informing both empirical research in field ecology and applied conservation. We include a discussion of needed breakthroughs and ways to bridge communication gaps between the field and the lab. In an effort to foster this interdisciplinary effort, we have also included a table that lists the definitions of key terms. The importance of understanding the dynamics of zoonotic pathogens in their reservoir hosts is emphasized as a tool to both assess risk factors for spillover and to test hypotheses related to treatment and/or intervention strategies. In conclusion, we highlight the need for smart surveillance, viral discovery efforts and predictive modeling. A shift towards a predictive approach is necessary in today's globalized society because, as the 2009 H1N1 pandemic demonstrated, identification post-emergence is often too late to prevent global spread. Integrating molecular virology and ecological techniques will allow for earlier recognition of potentially dangerous pathogens, ideally before they jump from wildlife reservoirs into human or livestock populations and cause serious public health or conservation issues. © 2011 by the authors; licensee MDPI, Basel, Switzerland.",active immunization;climate change;disease carrier;disease surveillance;genetic variability;human;infection risk;metagenomics;molecular phylogeny;nonhuman;review;risk assessment;species conservation;virus cell interaction;virus identification;virus infection;virus mutation;zoonosis,"Vandegrift, K. J.;Wale, N.;Epstein, J. H.",2011,,10.3390/v3040379,0
2136,Comparative genome sequencing identifies a prophage-associated genomic island linked to host adaptation of Lawsonia intracellularis infections,"Lawsonia intracellularis is an obligate intracellular bacterium and the causative agent of proliferative enteropathy (PE). The disease is endemic in pigs, emerging in horses and has also been reported in a variety of other animal species, including nonhuman primates. Comparing the whole genome sequences of a homologous porcine L. intracellularis isolate cultivated for 10 and 60 passages in vitro, we identified a 18-kb prophage-associated genomic island in the passage 10 (pathogenic variant) that was lost in the passage 60 (non-pathogenic variant). This chromosomal island comprises 15 genes downstream from the prophage DLP12 integrase gene. The prevalence of this genetic element was evaluated in 12 other L. intracellularis isolates and in 53 infected animals and was found to be conserved in all porcine isolates cultivated for up to 20 passages and was lost in isolates cultivated for more than 40 passages. Furthermore, the prophage region was also present in 26 fecal samples derived from pigs clinically affected with both acute and chronic forms of the disease. Nevertheless, equine L. intracellularis isolates evaluated did not harbor this genomic island regardless of the passage in vitro. Additionally, fecal samples from 21 clinically affected horses and four wild rabbits trapped in horse farms experiencing PE outbreaks did not show this prophage-associated island. Although the presence of this prophage-associated island was not essential for a virulent L. intracellularis phenotype, this genetic element was porcine isolate-specific and potentially contributed to the ecological specialization of this organism for the swine host.",animal;Desulfovibrionaceae infection;enteropathy;feces;genetics;genomic island;high throughput sequencing;horse;horse disease;Lawsonia;microbiology;pathogenicity;physiology;polymerase chain reaction;prophage;pig;swine disease;veterinary medicine;virulence,"Vannucci, F. A.;Kelley, M. R.;Gebhart, C. J.",2013,,10.1186/1297-9716-44-49,0
2137,Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae,"With the advent of metagenomics approaches, a large diversity of known and unknown viruses has been identified in various types of environmental, plant, and animal samples. One such widespread virus group is the recently established family Genomoviridae which includes viruses with small (similar to 2-2.4 kb), circular ssDNA genomes encoding rolling- circle replication initiation proteins (Rep) and unique capsid proteins. Here, we propose a sequence-based taxonomic framework for classification of 121 new virus genomes within this family. Genomoviruses display similar to 47% sequence diversity, which is very similar to that within the well-established and extensively studied family Geminiviridae (46% diversity). Based on our analysis, we establish a 78% genome-wide pairwise identity as a species demarcation threshold. Furthermore, using a Rep sequence phylogeny-based analysis coupled with the current knowledge on the classification of geminiviruses, we establish nine genera within the Genomoviridae family. These are Gemycircularvirus (n = 73), Gemyduguivirus (n = 1), Gemygorvirus (n = 9), Gemykibivirus (n = 29), Gemykolovirus (n = 3), Gemykrogvirus (n = 3), Gemykroznavirus (n = 1), Gemytondvirus (n = 1), Gemyvongvirus (n = 1). The presented taxonomic framework offers rational classification of genomoviruses based on the sequence information alone and sets an example for future classification of other groups of uncultured viruses discovered usingmetagenomics approaches.",Genomoviridae;CRESS DNA viruses;replication-associated protein;ssDNA;viruses;REPLICATION INITIATOR PROTEIN;NECROTIC YELLOWS VIRUS;LEAF CURL;GEMINIVIRUS;MOLECULAR CHARACTERIZATION;REP PROTEIN;SSDNA VIRUSES;PHYLOGENETIC EVIDENCE;ENDONUCLEASE DOMAIN;PORCINE PARVOVIRUS;CONSERVED SEQUENCE,"Varsani, A.;Krupovic, M.",2017,Jan,,0
2138,Smacoviridae: a new family of animal-associated single-stranded DNA viruses,"Smacoviruses have small (similar to 2.3-2.9 kb), circular single-stranded DNA genomes encoding rolling circle replication-associated proteins (Rep) and unique capsid proteins. Although smacoviruses are prevalent in faecal matter of various vertebrates, including humans, none of these viruses have been cultured thus far. Smacoviruses display similar to 45% genome-wide sequence diversity, which is very similar to that found within other families of circular Rep-encoding single-stranded (CRESS) DNA viruses, including members of the families Geminiviridae (46% diversity) and Genomoviridae (47% diversity). Here, we announce the creation of a new family Smacoviridae and describe a sequence-based taxonomic framework which was used to classify 83 smacovirus genomes into 43 species within six new genera, Bovismacovirus (n=3), Cosmacovirus (n=1), Dragsmacovirus (n=1), Drosmacovirus (n=3), Huchismacovirus (n=7), and Porprismacovirus (n=28). As in the case of genomoviruses, the species demarcation is based on the genome-wide pairwise identity, whereas genera are established based on the Rep amino acid sequence identity coupled with strong phylogenetic support. A similar sequence-based taxonomic framework should guide the classification of an astonishing diversity of other uncultured and currently unclassified CRESS DNA viruses discovered by metagenomic approaches.",MAXIMUM-LIKELIHOOD PHYLOGENIES;SSDNA VIRUSES;FECAL VIROME;PIG FECES;IDENTIFICATION;PICOBIRNAVIRUSES;DIVERSITY;TAXONOMY;REVEALS;SAMPLES,"Varsani, A.;Krupovic, M.",2018,Jul,,0
2139,A new varient of influenza virus-h1n1 swine flu virus,"In 2009 a swine -origin H1N1 virus strain commonly referred as Swine flu caused the 2009 flu Pandemic. Most of the cold climatic countries affected by the disease. On average 41,000 people died each year in the U.S between 1979 and 2001 from Influenza. Influenza commonly referred to as the flu is an infectious disease caused by RNA viruses of the family Orthomyxoviridae that affects birds and mammals. This virus is mainly classified into three types 1) Influenza virus A 2) Influenza virus B 3) Influenza virus C. Swine flu belongs to the Influenza virus A(H1N1). The virus particle is 80-120 nanometers. It can be difficult to distinguish between the common cold and Influenza in the early stages of swine flu but a flu can be identified by high fever with a sudden onset and extreme fatigue. Transmitted by three main ways direct transmission, the air bone route and direct personal contact (like hand shake). As Influenza virus can persist outside the body, it can also be transmitted by contaminated surfaces such as bank notes, door knobs etc. H1N1 easily spread rarely fatal. H1N1one of the mechanisms is belived to be the inhibition of adrenocorticotropic hormone (ACTH) resulting in lowered cortisol level. Influenza viruses can be inactivated by sunlight, disinfectants and detergents. Commonly used antivirals are oseltamivir & zanamivir these are neuraminidase inhibitors and amantadine & rimantadine block a viral ion channel & prevent virus from infecting cells. Vaccines like Mono Valent Vaccines Live Intranasal, Mono Valent Vaccines for Intramuscular injection, fluzone etc.",antivirus agent;ayurvedic drug;hemagglutinin;oseltamivir;sialidase;swine influenza vaccine;zanamivir;allopathy;application site swelling;Ayurveda;chemoprophylaxis;child care;coughing;cultural anthropology;drug efficacy;drug hypersensitivity;drug safety;fever;hand washing;headache;human;immunopotentiation;India;infection control;influenza vaccination;Influenza A virus (H1N1);myalgia;pain;pandemic;practice guideline;review;rhinorrhea;seasonal influenza;seasonal variation;society;sore throat;spring;summer;sunlight;swine influenza;symptom;treatment indication;violence;virus attachment;virus morphology;virus nomenclature;virus replication;virus transmission;vomiting;wheezing;winter,"Veeranjaneyulu, T. N.;Seerishna, B.;Kiran, T. N. R.;Madhulatha, A. V. S.;Bindu, A. H.",2011,,,0
2140,Autochthonous hepatitis E-virus infection as cause of acute hepatitis in Germany - A case report,"There is an increasing body of evidence that hepatitis E virus (HEV) triggers acute hepatitis not only in tropical and subtropical regions of Asia, Africa, and America with low sanitary standards but also in highly industrialized countries. We here report on two patients from Thuringia (Germany) with a HEV infection without a recent stay abroad. All other common causes of hepatitis were excluded. Transaminases were significantly incresed in both cases, while icterus could be proven in one patient, only. Both patients fully recovered in the long-term course. Epidemiological and phylogenetic data from viral analyses suggest that HEV infection has to be considered as a zoonosis. It is likely that viral transmission from animals to humans occurs through insufficiently cooked meat or entrails, e. g., from pigs or wild animals. In summary, HEV infection is a relevant differential diagnosis in acute non-A/B/C viral hepatitis. Further studies are required for the identification of other transmission pathways, pathogen reservoirs as well as novel concepts for prophylaxis, especially for patients at risk for hepatic diseases. © 2010 Georg Thieme Verlag KG Stuttgart · New York.",aminotransferase;acute hepatitis;aminotransferase blood level;article;case report;differential diagnosis;disease course;disease duration;epidemiological data;Germany;hepatitis E;Hepatitis E virus;human;jaundice;laboratory test;meat;phylogeny;risk factor;pig;virus detection;virus transmission;zoonosis,"Veitt, R.;Reichardt, M.;Wenzel, J.;Jilg, W.",2011,,10.1055/s-0029-1245767,0
2141,Phylodynamics of parapoxvirus genus in Mexico (2007–2011),"In this study we report for the first time the phylodynamics of the parapoxvirus (PPV) genus in Mexico. Based on the analysis by PCR of 124 epithelial samples collected between 2007 and 2011 from naturally infected goats, sheep and cows in Mexico, we found that different PPV were present in 21 out of the 24 states sampled during this study. Our phylogenetic analysis confirmed the presence of different PPV species in Mexico, and their phylogenetic relationship with other PPV circulating in the US and Canada. Furthermore, we describe the existence of two different ORFV phylogenetic groups that are clearly host associated (sheep or goat). Evidence of directional selection at five specific amino acid residues in the enveloped glycoprotein B2L might help to support this host predilection. Collectively, the results generated in this study highlight the importance of PPV genus in Mexico and open the possibility for future studies describing with more detail the importance of this genus in North America.",alanine;asparagine;aspartic acid;leucine;serine;virus DNA;virus envelope protein;animal tissue;article;B2L gene;bovine;Bovine papular stomatitis virus;controlled study;epithelium;Foot and mouth disease virus;genetic variability;geographic distribution;goat;host range;Mexico;nonhuman;Orf virus;Parapoxvirus;phylogeny;polymerase chain reaction;priority journal;Pseudocowpox virus;sheep;Vesiculovirus;viral genetics;virus gene,"Velazquez-Salinas, L.;Ramirez-Medina, E.;Bracht, A. J.;Hole, K.;Brito, B. P.;Gladue, D. P.;Carrillo, C.",2018,,10.1016/j.meegid.2018.07.005,0
2142,Avian influenza viruses in wild birds: Virus evolution in a multihost ecosystem,"Wild ducks and gulls are the major reservoirs for avian influenza A viruses (AIVs). The mechanisms that drive AIV evolution are complex at sites where various duck and gull species from multiple flyways breed, winter, or stage. The Republic of Georgia is located at the intersection of three migratory flyways: the Central Asian flyway, the East Africa/West Asia flyway, and the Black Sea/Mediterranean flyway. For six complete study years (2010 to 2016), we collected AIV samples from various duck and gull species that breed, migrate, and overwinter in Georgia. We found a substantial subtype diversity of viruses that varied in prevalence from year to year. Low-pathogenic AIV (LPAIV) subtypes included H1N1, H2N3, H2N5, H2N7, H3N8, H4N2, H6N2, H7N3, H7N7, H9N1, H9N3, H10N4, H10N7, H11N1, H13N2, H13N6, H13N8, and H16N3, and two highly pathogenic AIVs (HPAIVs) belonging to clade 2.3.4.4, H5N5 and H5N8, were found. Whole-genome phylogenetic trees showed significant host species lineage restriction for nearly all gene segments and significant differences in observed reassortment rates, as defined by quantification of phylogenetic incongruence, and in nucleotide sequence diversity for LPAIVs among different host species. Hemagglutinin clade 2.3.4.4 H5N8 viruses, which circulated in Eurasia during 2014 and 2015, did not reassort, but analysis after their subsequent dissemination during 2016 and 2017 revealed reassortment in all gene segments except NP and NS. Some virus lineages appeared to be unrelated to AIVs in wild bird populations in other regions, with maintenance of local AIVs in Georgia, whereas other lineages showed considerable genetic interrelationships with viruses circulating in other parts of Eurasia and Africa, despite relative undersampling in the area.",hemagglutinin;sialidase;Africa;article;avian influenza virus;bird;controlled study;duck;ecosystem;evolution;gene structure;gene transfer;genetic reassortment;genetic trait;genetic variability;host range;low pathogenic avian influenza;microbial diversity;molecular phylogeny;nonhuman;nucleotide sequence;prevalence;priority journal;quantitative analysis;United States;virus virulence;whole genome sequencing;wild type,"Venkatesh, D.;Poen, M. J.;Bestebroer, T. M.;Scheuer, R. D.;Vuong, O.;Chkhaidze, M.;Machablishvili, A.;Mamuchadze, J.;Ninua, L.;Fedorova, N. B.;Halpin, R. A.;Lin, X.;Ransier, A.;Stockwell, T. B.;Wentworth, D. E.;Kriti, D.;Dutta, J.;van Bakel, H.;Puranik, A.;Slomka, M. J.;Essen, S.;Brown, I. H.;Fouchier, R. A. M.;Lewis, N. S.",2018,,10.1128/jvi.00433-18,0
2143,Molecular characterization of Belgian pseudorabies virus isolates from domestic swine and wild boar,"Aujeszky's disease is an economically important disease in domestic swine caused by suid herpesvirus 1, also called pseudorabies virus (PRV). In several European countries, including Belgium, the virus has successfully been eradicated from the domestic swine population. The presence of PRV in the wild boar population however poses a risk for possible reintroduction of the virus into the domestic pig population. It is therefore important to assess the genetic relatedness between circulating strains and possible epidemiological links. In this study, nine historical Belgian domestic swine isolates that circulated before 1990 and five recent wild boar isolates obtained since 2006 from Belgium and the Grand Duchy of Luxembourg were genetically characterized by restriction fragment length polymorphism (RFLP) analysis and phylogenetic analysis. While all wild boar isolates were characterized as type I RFLP genotypes, the RFLP patterns of the domestic swine isolates suggest that a shift from genotype I to genotype II might have occurred in the 1980s in the domestic population. By phylogenetic analysis, Belgian wild boar isolates belonging to both clade A and B were observed, while all domestic swine isolates clustered within clade A. The joint phylogenetic analysis of both wild boar and domestic swine strains showed that some isolates with identical sequences were present within both populations, raising the question whether these strains represent an increased risk for reintroduction of the virus into the domestic population. © 2014 Elsevier B.V.",animal tissue;article;cladistics;genotype;nonhuman;nucleotide sequence;phylogeny;Pseudorabies virus;restriction fragment length polymorphism;pig;virus isolation;European wild boar,"Verpoest, S.;Cay, A. B.;De Regge, N.",2014,,10.1016/j.vetmic.2014.05.001,0
2144,The capacity of UL49.5 proteins to inhibit TAP is widely distributed among members of the genus varicellovirus,"The lifelong infection by varicelloviruses is characterized by a fine balance between the host immune response and immune evasion strategies used by these viruses. Virus-derived peptides are presented to cytotoxic T lymphocytes by major histocompatibility complex (MHC) class I molecules. The transporter associated with antigen processing (TAP) transports the peptides from the cytosol into the endoplasmic reticulum, where the loading of MHC-I molecules occurs. The varicelloviruses bovine herpesvirus 1 (BoHV-1), pseudorabies virus, and equid herpesviruses 1 and 4 have been found to encode a UL49.5 protein that inhibits TAP-mediated peptide transport. To investigate to what extent UL49.5-mediated TAP inhibition is conserved within the family of Alphaherpesvirinae, the homologs of another five varicelloviruses, one mardivirus, and one iltovirus were studied. The UL49.5 proteins of BoHV-5, bubaline herpesvirus 1, cervid herpesvirus 1, and felid herpesvirus 1 were identified as potent TAP inhibitors. The varicella-zoster virus and simian varicellovirus UL49.5 proteins fail to block TAP; this is not due to the absence of viral cofactors that might assist in this process, since cells infected with these viruses did not show reduced TAP function either. The UL49.5 homologs of the mardivirus Marek's disease virus 1 and the iltovirus infectious laryngotracheitis virus did not block TAP, suggesting that the capacity to inhibit TAP via UL49.5 has been acquired by varicelloviruses only. A phylogenetic analysis of viruses that inhibit TAP through their UL49.5 proteins reveals an interesting hereditary pattern, pointing toward the presence of this capacity in defined clades within the genus Varicellovirus. Copyright © 2011, American Society for Microbiology. All Rights Reserved.",major histocompatibility antigen class 1;transporter associated with antigen processing 1;UL49.5 protein;unclassified drug;viral protein;Alphaherpesvirinae;animal cell;article;Bovine herpesvirus 1;cervid herpesvirus 1;controlled study;cytosol;endoplasmic reticulum;Equid herpesvirus 1;felid herpesvirus 1;Felidae;Human alphaherpesvirus 1;Herpesviridae;human;human cell;Iltovirus;laryngotracheobronchitis;major histocompatibility complex;Mardivirus;nonhuman;nucleotide sequence;phylogeny;priority journal;protein function;protein localization;protein transport;Pseudorabies virus;sequence homology;simian;Varicella zoster virus;Varicellovirus;virus infection;virus load,"Verweij, M. C.;Lipińska, A. D.;Koppers-Lalic, D.;Van Leeuwen, W. F.;Cohen, J. I.;Kinchington, P. R.;Messaoudi, I.;Bieńkowska-Szewczyk, K.;Ressing, M. E.;Rijsewijk, F. A. M.;Wiertz, E. J. H. J.",2011,,10.1128/jvi.01621-10,0
2145,Detection and Genotyping of Classical Swine Fever Virus Isolates in Serbia,"Classical swine fever (CSF) is a highly contagious disease of pigs leading to significant economic losses worldwide. Classical swine fever virus can be classified into three genogroups, each consisting of three or four subgroups. However, there is a lack of knowledge on the genotypes of CSFV isolates in Republic of Serbia. This study, based on the sequences analysis of partial E2 gene and 5' non coding region (NCR) of 15 CSFV isolated during 2006-2008 from domestic pigs, revealed that all were clustered into genetic group 2.3. Additionally, we showed that the two most often used real time RT-PCR assays were able to detect all local CSF viruses circulated in Serbia in the last years during intensive vaccination campaign against CSF",Classical swine fever virus;genotyping;real time RT-PCR;Serbia;POLYMERASE-CHAIN-REACTION;HOG-CHOLERA VIRUS;RT-PCR;MOLECULAR;EPIDEMIOLOGY;PESTIVIRUSES;DISEASE;ASSAY;DISCRIMINATION;STRAINS;GENOME,"Vesna, M.;Sonja, R.;Valcic, A. M.;Ivovic, V.;Jelena, M. Z.;Radosavljevic, V.",2013,,,0
2146,Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds,"We present an optimised metagenomics method for detection and characterisation of all virus types including single and double stranded DNA/RNA and enveloped and non-enveloped viruses. Initial evaluation included both spiked and non-spiked bird faecal samples as well as non-spiked human faecal samples. From the non-spiked bird samples (Australian Muscovy duck and Pacific black ducks) we detected 21 viruses, and we also present a summary of a few viruses detected in human faecal samples. We then present a detailed analysis of selected virus sequences in the avian samples that were somewhat similar to known viruses, and had good quality (Q20 or higher) and quantity of next-generation sequencing reads, and was of interest from a virological point of view, for example, avian coronavirus and avian paramyxovirus 6. Some of these viruses were closely related to known viruses while others were more distantly related with 70% or less identity to currently known/sequenced viruses. Besides detecting viruses, the technique also allowed the characterisation of host mitochondrial DNA present and thus identifying host species, while ribosomal RNA sequences provided insight into the ""ribosomal activity microbiome""; of gut parasites; and of food eaten such as plants or insects, which we correlated to non-avian host associated viruses.",,"Vibin, J.;Chamings, A.;Collier, F.;Klaassen, M.;Nelson, T. M.;Alexandersen, S.",2018,Jun 06,,0
2147,Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis,"We analyzed viral nucleic acids in stool samples collected from 35 South Asian children with nonpolio acute flaccid paralysis (AFP). Sequence-independent reverse transcription and PCR amplification of capsid-protected, nuclease-resistant viral nucleic acids were followed by DNA sequencing and sequence similarity searches. Limited Sanger sequencing (35 to 240 subclones per sample) identified an average of 1.4 distinct eukaryotic viruses per sample, while pyrosequencing yielded 2.6 viruses per sample. In addition to bacteriophage and plant viruses, we detected known enteric viruses, including rotavirus, adenovirus, picobirnavirus, and human enterovirus species A (HEV-A) to HEV-C, as well as numerous other members of the Picornaviridae family, including parechovirus, Aichi virus, rhinovirus, and human cardiovirus. The viruses with the most divergent sequences relative to those of previously reported viruses included members of a novel Picornaviridae genus and four new viral species (members of the Dicistroviridae, Nodaviridae, and Circoviridae families and the Bocavirus genus). Samples from six healthy contacts of AFP patients were similarly analyzed and also contained numerous viruses, particularly HEV-C, including a potentially novel Enterovirus genotype. Determining the prevalences and pathogenicities of the novel genotypes, species, genera, and potential new viral families identified in this study in different demographic groups will require further studies with different demographic and patient groups, now facilitated by knowledge of these viral genomes.",TAURA-SYNDROME VIRUS;PORCINE CIRCOVIRUS;VIRAL COMMUNITY;HUMAN FECES;INFECTION;SEQUENCE;GUT;DICISTROVIRIDAE;ENTEROVIRUS-71;EPIDEMIOLOGY,"Victoria, J. G.;Kapoor, A.;Li, L. L.;Blinkova, O.;Slikas, B.;Wang, C. L.;Naeem, A.;Zaidi, S.;Delwart, E.",2009,May,,0
2148,Viral nucleic acids in live-attenuated vaccines: Detection of minority variants and an adventitious virus,"Metagenomics and a panmicrobial microarray were used to examine eight live-attenuated viral vaccines. Viral nucleic acids in trivalent oral poliovirus (OPV), rubella, measles, yellow fever, varicella-zoster, multivalent measles/mumps/rubella, and two rotavirus live vaccines were partially purified, randomly amplified, and pyrosequenced. Over half a million sequence reads were generated covering from 20 to 99% of the attenuated viral genomes at depths reaching up to 8,000 reads per nucleotides. Mutations and minority variants, relative to vaccine strains, not known to affect attenuation were detected in OPV, mumps virus, and varicella-zoster virus. The anticipated detection of endogenous retroviral sequences from the producer avian and primate cells was confirmed. Avian leukosis virus (ALV), previously shown to be noninfectious for humans, was present as RNA in viral particles, while simian retrovirus (SRV) was present as genetically defective DNA. Rotarix, an orally administered rotavirus vaccine, contained porcine circovirus-1 (PCV1), a highly prevalent nonpathogenic pig virus, which has not been shown to be infectious in humans. Hybridization of vaccine nucleic acids to a panmicrobial microarray confirmed the presence of endogenous retroviral and PCV1 nucleic acids. Deep sequencing and microarrays can therefore detect attenuated virus sequence changes, minority variants, and adventitious viruses and help maintain the current safety record of live-attenuated viral vaccines. Copyright © 2010, American Society for Microbiology. All Rights Reserved.",biopolio;chickenpox vaccine;live vaccine;measles mumps rubella vaccine;measles vaccine;nucleic acid;nucleotide;oral poliomyelitis vaccine;Rotavirus vaccine;rubella vaccine;unclassified drug;varicella zoster vaccine;virus RNA;virus vaccine;yellow fever vaccine;article;Avian leukosis virus;Circovirus;fowl;genome analysis;Herpesviridae;Measles virus;metagenomics;microarray analysis;Mumps virus;nonhuman;nucleic acid analysis;nucleotide sequence;primate;priority journal;Retroviridae;Rotavirus;sequence analysis;virus detection;virus genome;virus mutation;virus particle;virus strain;Yellow fever virus;attenuvax;meruvax;mmr ii;rotarix;rotateq;varivax;yf vax,"Victoria, J. G.;Wang, C.;Jones, M. S.;Jaing, C.;McLoughlin, K.;Gardner, S.;Delwart, E. L.",2010,,10.1128/jvi.02690-09,0
2149,Full-genome characterization by deep sequencing of rotavirus A isolates from outbreaks of neonatal diarrhoea in pigs in Spain,"Since early 2017, in Spain there was an apparent increase in reports on rotavirus involvement in neonatal diarrhoea outbreaks, affecting also adult sows. In this study, 16 unrelated outbreaks of diarrhoea in suckling pigs and sows, where rotavirus A was the only pathogen detected, were investigated. Deep-sequencing was performed on total RNA from twenty-four positive faecal samples. Genotyping, phylogenetic and bayesian analyses showed that all isolates had a common ancestor of porcine, or human porcine-like, origin. The new strain was introduced in the population shortly before the onset of the outbreaks. Besides, a high diversification of the VP7 and VP4 genes occurred in a short time. Isolates presented a high number of amino acid changes in the neutralizing epitopes compared to vaccine sequences. The present report illustrates how a new rotavirus A strain may disseminate rapidly and the extremely high diversification that this pathogen may undergo in a short period.","Animals;*Animals, Newborn/vi [Virology];Antigens, Viral/ge [Genetics];Bayes Theorem;Capsid Proteins/ge [Genetics];Diarrhea/ve [Veterinary];*Disease Outbreaks/ve [Veterinary];Epitopes/ge [Genetics];Feces;Female;Genetic Variation;*Genome, Viral;High-Throughput Nucleotide Sequencing/mt [Methods];Humans;Phylogeny;*Rotavirus/ge [Genetics];Rotavirus/ip [Isolation & Purification];*Rotavirus Infections/ep [Epidemiology];Rotavirus Infections/ve [Veterinary];Rotavirus Infections/vi [Virology];Spain/ep [Epidemiology];Swine;*Swine Diseases/ep [Epidemiology];Swine Diseases/vi [Virology];0 (Antigens, Viral);0 (Capsid Proteins);0 (Epitopes);0 (VP4 protein, Rotavirus);0 (VP7 protein, Rotavirus)","Vidal, A.;Clilverd, H.;Cortey, M.;Martin-Valls, G. E.;Franzo, G.;Darwich, L.;Martin, M.;Mateu, E.",2018,Dec,,1
2150,Application of Standard and Molecular Methods for the Diagnosis of Newcastle Disease,"Four pooled samples of whole poultry carcasses with their internal organs were used to determine the presence of Newcastle disease (ND) virus. Samples were collected from one epizootiological area in the Republic of Serbia during January 2007. Newcastle disease virus strains were isolated from four samples. The identification of isolated strains was done by using the hemagglutination and hemagglutination-inhibition tests. The nucleic acid of the ND virus was identified in all the four samples It was confirmed that all the isolated strains were velogenic strains. Analysis of the nucleotide sequences of the gene encoding the F cleavage site of the fusion F protein showed the presence of motifs (112)RRQKRFIG(119), characteristic for the velogenic strains of the ND virus. Phylogenetic analysis of the F gene sequences revealed that all isolated strains of the virus belong to class II and genotype VIId.",Newcastle disease virus;RT-PCR;Real Time RT-PCR;AVIAN PARAMYXOVIRUS SEROTYPE-1;POLYMERASE CHAIN-REACTION;VIRUS;DIFFERENTIATION;PATHOGENICITY;SEQUENCE;TYPE-1;PCR,"Vidanovic, D.;Sekler, M.;Polacek, V.;Vaskovic, N.;Asanin, R.;Milic, N.;Nisavic, J.",2012,,,0
2151,"Tripping over emerging pathogens around the world: A phylogeographical approach for determining the epidemiology of Porcine circovirus-2 (PCV-2), considering global trading","Porcine circovirus-2 (PCV-2) is an emerging virus associated with a number of different syndromes in pigs known as Porcine Circovirus Associated Diseases (PCVAD). Since its identification and characterization in the early 1990s, PCV-2 has achieved a worldwide distribution, becoming endemic in most pig-producing countries, and is currently considered as the main cause of losses on pig farms. In this study, we analyzed the main routes of the spread of PCV-2 between pig-producing countries using phylogenetic and phylogeographical approaches. A search for PCV-2 genome sequences in GenBank was performed, and the 420 PCV-2 sequences obtained were grouped into haplotypes (group of sequences that showed 100% identity), based on the infinite sites model of genome evolution. A phylogenetic hypothesis was inferred by Bayesian Inference for the classification of viral strains and a haplotype network was constructed by Median Joining to predict the geographical distribution of and genealogical relationships between haplotypes. In order to establish an epidemiological and economic context in these analyses, we considered all information about PCV-2 sequences available in GenBank, including papers published on viral isolation, and live pig trading statistics available on the UN Comtrade database (http://comtrade.un.org/). In these analyses, we identified a strong correlation between the means of PCV-2 dispersal predicted by the haplotype network and the statistics on the international trading of live pigs. This correlation provides a new perspective on the epidemiology of PCV-2, highlighting the importance of the movement of animals around the world in the emergence of new pathogens, and showing the need for effective sanitary barriers when trading live animals. © 2011 Elsevier B.V.",viral protein;Argentina;article;Austria;Belgium;Brazil;Canada;China;Circovirus;Croatia;Cuba;Denmark;France;gene sequence;genotype;Greece;haplotype;Hungary;India;Indonesia;Japan;Malaysia;Netherlands;nonhuman;phylogeny;phylogeography;Porcine circovirus 2;Portugal;priority journal;Romania;Serbia;Slovakia;South Africa;South Korea;Spain;Sweden;Taiwan;United States;virus gene;virus strain,"Vidigal, P. M. P.;Mafra, C. L.;Silva, F. M. F.;Fietto, J. L. R.;Silva Júnior, A.;Almeida, M. R.",2012,,10.1016/j.virusres.2011.10.019,0
2152,Hepadnavirus detected in bile and liver samples from domestic pigs of commercial abattoirs,"Background: Preliminary studies showed the prevalence of a virus similar to human hepatitis B virus (HBV-like) in swine from farms in China and the molecular evidence of Hepadnavirus infection in domestic pigs herds in Brazil. In this study, we genetically characterize the swine Hepadnavirus strains in swine from slaughterhouses located in certified abattoirs from Rio de Janeiro State, Brazil and evaluate its hepatotropic potential. Results: Bile and liver samples from swine were positive for partial genome amplification (ORF S and ORF C), direct sequencing and viral load quantification. Sequencing of the gene encoding the surface antigen allowed classification of Hepadnavirus into genotypes, similar to HBV genotype classification. Indirect immunofluorescence confirmed the presence of HBsAg antigen in liver tissue sections. Conclusions: So far our data suggest that commercial swine house an HBV-like virus and this relevant finding should be considered in studies on the origin and viral evolution.",hepatitis B surface antigen;animal tissue;article;bile;Brazil;controlled study;domestic pig;gene amplification;genetic analysis;genotype;Hepadnaviridae;human;immunofluorescence;liver;nonhuman;open reading frame;phylogeny;slaughterhouse;viral tropism;virus classification;virus detection;virus gene;virus load,"Vieira, Y. R.;Dos Santos, D. R. L.;Portilho, M. M.;Velloso, C. E. P.;Arissawa, M.;Villar, L. M.;Pinto, M. A.;De Paula, V. S.",2014,,10.1186/s12866-014-0315-2,0
2153,"Hendra and Nipah infection: Pathology, models and potential therapies","The Paramyxoviridae family comprises of several genera that contain emerging or re-emerging threats for human and animal health with no real specific effective treatment available. Hendra and Nipah virus are members of a newly identified genus of emerging paramyxoviruses, Henipavirus. Since their discovery in the 1990s, henipaviruses outbreaks have been associated with high economic and public health threat potential. When compared to other paramyxoviruses, henipaviruses appear to have unique characteristics. Henipaviruses are zoonotic paramyxoviruses with a broader tropism than most other paramyxoviruses, and can cause severe acute encephalitis with unique features among viral encephalitides. There are currently no approved effective prophylactic or therapeutic treatments for henipavirus infections. Although ribavirin was empirically used and seemed beneficial during the biggest outbreak caused by one of these viruses, the Nipah virus, its efficacy is disputed in light of its lack of efficacy in several animal models of henipavirus infection. Nevertheless, because of its highly pathogenic nature, much effort has been spent in developing anti-henipavirus therapeutics. In this review we describe the unique features of henipavirus infections and the different strategies and animal models that have been developed so far in order to identify and test potential drugs to prevent or treat henipavirus infections. Some of these components have the potential to be broad-spectrum antivirals as they target effectors of viral pathogenecity common to other viruses. We will focus on small molecules or biologics, rather than vaccine strategies, that have been developed as anti-henipaviral therapeutics. © 2011 Bentham Science Publishers Ltd.",5 ethynyl 4 imidazolecarboxamide 1 riboside;azauridine;chloroquine;chlorpromazine;galectin 1;gliotoxin;glycine dehydrogenase (decarboxylating);human monoclonal antibody;lj001;monoclonal antibody;murine monoclonal antibody;palivizumab;pirazofurin;polyinosinic polycytidylic acid;protein f;protein G;quinolone derivative;rhodanine;ribavirin;small interfering RNA;unclassified drug;viral protein;Africa;antiviral therapy;Australia;Bangladesh;bat;blood brain barrier;cell fusion;clinical trial (topic);disease model;epidemic;genetic procedures;Ghana;Hendra virus;Hendra virus infection;high throughput screening;human;India;Malaysia;morbidity;mortality;Nipah virus;Nipah virus infection;nonhuman;open reading frame;pathology;pseudotyping;review;Southeast Asia;virus classification;virus morphology;virus particle;virus transmission;virus virulence,"Vigant, F.;Lee, B.",2011,,,0
2154,Analysis of the crow lung transcriptome in response to infection with highly pathogenic H5N1 avian influenza virus,"The highly pathogenic avian influenza (HPAI) H5N1 virus, currently circulating in Asia, causes severe disease in domestic poultry as well as wild birds like crow. However, the molecular pathogenesis of HPAIV infection in crows and other wild birds is not well known. Thus, as a step to explore it, a comprehensive global gene expression analysis was performed on crow lungs, infected with HPAI H5N1 crow isolate (A/Crow/India/11TI11/2011) using high throughput next generation sequencing (NGS) (GS FLX Titanium XLR70). The reference genome of crow is not available, so RNA seq analysis was performed on the basis of a de novo assembled transcriptome. The RNA seq result shows, 4052 genes were expressed uniquely in noninfected, 6277 genes were expressed uniquely in HPAIV infected sample and of the 6814 genes expressed in both samples, 2279 genes were significantly differentially expressed. Our transcriptome profile data allows for the ability to understand the molecular mechanism behind the recent lethal HPAIV outbreak in crows which was, until recently, thought to cause lethal infections only in gallinaceous birds such as chickens, but not in wild birds. The pattern of differentially expressed genes suggest that this isolate of H5N1 virus evades the host innate immune response by attenuating interferon (IFN)-inducible signalling possibly by down regulating the signalling from type I IFN (IFNAR1 and IFNAR2) and type II IFN receptors, upregulation of the signalling inhibitors suppressor of cytokine signalling 1 (SOCS1) and SOCS3 and altering the expression of toll-like receptors (TLRs). This may be the reason for disease and mortality in crows.",complementary DNA;contig;interferon receptor;suppressor of cytokine signaling 1;suppressor of cytokine signaling 3;transcriptome;animal tissue;article;Corvus;exon;gene expression;gene ontology;genetic analysis;immune evasion;immune response;influenza A (H5N1);innate immunity;intron;lung;next generation sequencing;nonhuman;priority journal;signal transduction;upregulation,"Vijayakumar, P.;Mishra, A.;Ranaware, P. B.;Kolte, A. P.;Kulkarni, D. D.;Burt, D. W.;Raut, A. A.",2015,,10.1016/j.gene.2015.01.016,0
2155,Evaluation of envelope glycoprotein Erns of an atypical bovine pestivirus as antigen in a microsphere immunoassay for the detection of antibodies against bovine viral diarrhea virus 1 and atypical bovine pestivirus,"Atypical bovine pestiviruses are related antigenically and phylogenetically to bovine viral diarrhea viruses (BVDV-1 and BVDV-2), and may cause the same clinical manifestations in animals. Glycoprotein Erns of an atypical bovine pestivirus Th/04_KhonKaen was produced in a baculovirus expression system and was purified by affinity chromatography. The recombinant Erns protein was used as an antigen in a microsphere immunoassay for the detection of antibodies against BVDV-1 and atypical bovine pestivirus. The diagnostic performance of the new method was evaluated by testing a total of 596 serum samples, and the assay was compared with enzyme-linked immunosorbent assay (ELISA). Based on the negative/positive cut-off median fluorescence intensity (MFI) value of 2800, the microsphere immunoassay had a sensitivity of 100% and specificity of 100% compared to ELISA. The immunoassay was able to detect antibodies against both BVDV-1 and the atypical pestivirus. This novel microsphere immunoassay has the potential to be multiplexed for simultaneous detection of antibodies against different bovine pathogens in a high-throughput and economical way. © 2012 Elsevier B.V.",glycoprotein E;recombinant protein;virus antibody;antibody detection;antigenicity;article;atypical bovine pestivirus;baculovirus expression system;blood sampling;Bovine viral diarrhea virus 1;bovine viral diarrhea;controlled study;cow;diagnostic test accuracy study;diagnostic value;enzyme linked immunosorbent assay;fluorescence;immunoassay;immunogenicity;intermethod comparison;microsphere immunoassay;nonhuman;Pestivirus;Pestivirus infection;priority journal;process optimization;protein expression;protein purification;sensitivity and specificity,"Vijayaraghavan, B.;Xia, H.;Harimoorthy, R.;Liu, L.;Belák, S.",2012,,10.1016/j.jviromet.2012.06.017,0
2156,Pathotyping of a Newcastle disease virus isolated from peacock (Pavo cristatus),This report describes Newcastle disease in peacock and the isolation and characterization of the virus. The virus had an intracerbral pathogenicity index of 1.71 and mean death time of 47 h. The isolate had multiple basic amino acids at the fusion protein cleavage site sequence ((110)GGRRQRRFIG(119)) with a phenylalanine at residue 117. Biological and molecular characterization revealed that the virus is velogenic. Phylogenetic analysis placed the isolate in genotype II.,animal;article;case report;classification;Galliformes;genetics;genotype;Newcastle disease;Newcastle disease virus;pathology;phylogeny;virology,"Vijayarani, K.;Muthusamy, S.;Tirumurugaan, K. G.;Sakthivelan, S. M.;Kumanan, K.",2010,,10.1007/s11250-009-9436-2,0
2157,Complete genomic sequence of human coronavirus OC43: Molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event,"Coronaviruses are enveloped, positive-stranded RNA viruses with a genome of approximately 30 kb. Based on genetic similarities, coronaviruses are classified into three groups. Two group 2 coronaviruses, human coronavirus OC43 (HCoV-OC43) and bovine coronavirus (BCoV), show remarkable antigenic and genetic similarities. In this study, we report the first complete genome sequence (30,738 nucleotides) of the prototype HCoV-OC43 strain (ATCC VR7S9). Complete genome and open reading frame (ORF) analyses were performed in comparison to the BCoV genome. In the region between the spike and membrane protein genes, a 290-nucleotide deletion is present, corresponding to the absence of BCoV ORFs ns4.9 and ns4.8. Nucleotide and amino acid similarity percentages were determined for the major HCoV-OC43 ORFs and for those of other group 2 coronaviruses. The highest degree of similarity is demonstrated between HCoV-OC43 and BCoV in all ORFs with the exception of the E gene. Molecular clock analysis of the spike gene sequences of BCoV and HCoV-OC43 suggests a relatively recent zoonotic transmission event and dates their most recent common ancestor to around 1890. An evolutionary rate in the order of 4 × 10 -4 nucleotide changes per site per year was estimated. This is the first animal-human zoonotic pair of coronaviruses that can be analyzed in order to gain insights into the processes of adaptation of a nonhuman coronavirus to a human host, which is important for understanding the interspecies transmission events that led to the origin of the severe acute respiratory syndrome outbreak. Copyright © 2005, American Society for Microbiology. All Rights Reserved.",membrane protein;amino acid sequence;article;Coronavirinae;gene sequence;host;human;molecular clock;nonhuman;nucleotide sequence;open reading frame;priority journal;RNA virus;severe acute respiratory syndrome;virus classification;virus e gene;virus envelope;virus gene;virus strain;virus transmission;zoonosis,"Vijgen, L.;Keyaerts, E.;Moës, E.;Thoelen, I.;Wollants, E.;Lemey, P.;Vandamme, A. M.;Van Ranst, M.",2005,,10.1128/jvi.79.3.1595-1604.2005,0
2158,Distribution and genetic characterization of Enterovirus G and Sapelovirus A in six Spanish swine herds,,,"Vilar, M. J.;Peralta, B.;García-Bocanegra, I.;Simon-Grifé, M.",2016,,,0
2159,Organization and diversity of the 3'-noncoding region of classical swine fever virus genome,"Specific PCR primers were selected to amplify a 359 bp DNA fragment flanking the 3'-part of the polymerase gene and the 3'-noncoding (3'-NC) region of the genome of classical swine fever virus (CSFV). In RT-PCR the selected fragment was amplified from the genomes of 27 viral strains collected from Europe, America and Asia over a period of a half century as well as from three vaccine strains of CSFV. Eight PCR products were sequenced using an automatic sequencing device. Nucleotide sequence analysis was performed by computer programs DNASTAR and PHYLIP. The comparative studies revealed that the 3'-NC region contains a variable region of nucleotides which is located immediately after the stop codon TGA or TAA. Furthermore, a strongly conserved constant region was identified near to the extreme 3'-terminus. Two imperfect repeated sequences were found both in the variable and in the constant regions. In addition, the variable region was characterized by the occurrence of a 50 bp long poly AT track. Phylogenetic analysis with different mathematical approaches (MegAlign, Neighbor-Joining method, Maximum Likelihood, Parsimony) revealed that the studied CSFV strains were clustered into two main phylogenetic groups. Group I was comprised of the reference strain Brescia, together with old American and European field isolates and a Brazilian vaccine strain. Group II included the reference strain Alfort (Tubingen) and recent European field strains. The Congenital Tremor strain formed a distinct lineage which, although being highly divergent, was more closely related to group I than to group II. In conclusion, the present phylogenetic grouping yielded very similar results as previous studies based on comparison of the E2 (gp55) region. The agreement of the phylogenetic analysis in the two distinct regions confirms the reliability of the genetic grouping of CSFV strains into two main genogroups.",DNA fragment;article;software;DNA flanking region;nucleotide sequence;Pestivirus;phylogeny;priority journal;reverse transcription polymerase chain reaction;stop codon;virus genome,"Vilček, Š;Belák, S.",1997,,10.1023/a:1007971110065,0
2160,Genetic diversity of BVDV: Consequences for classification and molecular epidemiology,"Genetic typing of bovine viral diarrhoea virus (BVDV) is important for the precise classification of viruses as well as for the development of molecular epidemiology. BVDV isolates were usually typed based on comparison of genomic sequences from the 5′-untranslated region (5′-UTR), Npro and E2 region. Recently we have identified 11 genetic groups (subgenotypes) of BVDV-1. Our further experiments confirmed a new subgenotype, BVDV-1k, isolated from cattle in Switzerland. BVDV isolates from India were typed as BVDV-1b whereas BVDV-1c is a predominant subgenotype in Australia. The results of genetic typing of BVDV indicate that distribution of subgenotypes has no relationship to the geographic origin of viral isolates. © 2005 Elsevier B.V. All rights reserved.",animal;Bovine viral diarrhea virus 1;bovine;cattle disease;classification;conference paper;epidemiology;genetic variability;genetics;genotype;virology,"Vilcek, S.;Durkovic, B.;Kolesarova, M.;Paton, D. J.",2005,,10.1016/j.prevetmed.2005.08.004,0
2161,Genetic diversity of recent bovine viral diarrhoea viruses from the southeast of Austria (Styria),"To characterise the bovine virus diarrhoea virus (BVDV) isolates circulating in the southeastern region of Austria, namely in the province of Styria, 71 blood samples collected between 1998 and 2000 from persistently infected cattle in 62 herds were subjected to genetic typing. For this, 288bp fragments from the 5′ untranslated region (5′-UTR) were amplified by polymerase chain reaction after reverse transcription (RT-PCR). The products were sequenced and used for phylogenetic analysis. Seventy virus isolates were typed as BVDV species 1 (BVDV-1). Only one isolate was typed as BVDV species 2 (BVDV-2), representing the first isolate of this pestivirus genotype found in Austria. In addition, phylogenetic analysis revealed that viruses belonging to five genetic groups within BVDV-1 are circulating in Styria. Most viruses (53) were found in group BVDV-1f, nine viruses in BVDV-1h, four viruses in BVDV-1b, three viruses in BVDV-1d and one virus in BVDV-1g. No virus was found in genetic group BVDV-1a, which is dominant in the UK and widely distributed in USA. Likewise, the BVDV isolates predominating in a neighbouring country, namely Germany, belonged to different genogroups than those circulating in Styria. We conclude that in a particular region and environment certain BVDV-1 genetic groups predominate. New groups, including BVDV-2, can be introduced, e.g. by trade of animals. The low incidence of BVDV-2 in Styria is in concert with the sporadic occurrence of these viruses in other regions of Europe. © 2002 Elsevier Science B.V. All rights reserved.",gene product;5' untranslated region;article;Austria;base pairing;blood sampling;bovine;cattle disease;controlled study;diarrhea;gene sequence;genetic variability;genotype;herd;nonhuman;Pestivirus;phylogeny;reverse transcription polymerase chain reaction;virus isolation,"Vilcek, S.;Greiser-Wilke, I.;Durkovic, B.;Obritzhauser, W.;Deutz, A.;Köfer, J.",2003,,10.1016/s0378-1135(02)00296-1,0
2162,Molecular characterization of ovine pestiviruses,"Forty-two ovine pestivirus isolates, collected over a period of 18 years, were compared by phylogenetic analysis. The viruses were mostly field isolates from Britain; two others originated from Sweden and two from New Zealand. RT-PCR products were obtained from two genomic regions, one within the 5'-noncoding (5'-NC) region, and the other encompassing parts of the p20 (N(pro)) and C coding regions. Direct sequencing of the 5'-NC PCR products, followed by computer-assisted phylogenetic analysis, divided the ovine pestiviruses into three main genotypes. The results demonstrated that sheep may naturally be infected not only with border disease virus (BDV), but also with bovine viral diarrhoea virus (BVDV) types I and II. The BDV isolates segregated into two principal subtypes represented by the Moredun strain from Scotland and the 137/4 strain from England. The BVDV-I group was composed of three clusters, two of them represented by BVDV reference strains NADL and Osloss, respectively, and the third by ovine isolates D1120/1 and D1432/P. The grouping of ovine pestiviruses, based on comparative nucleotide sequence analysis of the 5'-NC region, was confirmed by comparative analysis of the p20 (NP(pro)) and C coding regions, performed both at the nucleotide and at the amino acid level. The presence of three genotypes in sheep, including BVDV-I and BVDV-II, indicates the inadequacy of the current host-species-based nomenclature and classification of pestiviruses.",amino acid sequence;animal disease;article;Bovine viral diarrhea virus 1;computer analysis;genotype;New Zealand;nonhuman;nucleotide sequence;Pestivirus;phylogeny;priority journal;reverse transcription polymerase chain reaction;sequence homology;sheep;Sweden;United Kingdom;virus classification;virus genome;virus isolation,"Vilček, Š;Nettleton, P. F.;Paton, D. J.;Belák, S.",1997,,,0
2163,Genetic variability of classical swine fever virus,"The genetic variability of classical swine fever virus was studied by comparative nucleotide sequence analysis of 76 virus isolates, collected during a half century from three continents. Parts of the E2 (gp55) and the polymerase gene coding regions of the viral genome were amplified by RT-PCR and DNA fragments of 254 and 207 bp, respectively, were sequenced. The comparative sequence analysis of the E2 region revealed two main phylogenetic groups of CSFV, indicating that the virus apparently evolved from two ancestor nodes. Group I (represented by Brescia strain) consisted of old and recent American and Asian viruses, as well as old English isolates from the 1950s. This group was subdivided into three subgroups, termed I.A I.C. Group II (represented by Alfort strain) consisted of relatively recent isolates from Europe, together with strain Osaka, which was isolated in Japan from a pig of European origin. Based on genetic distances the group was divided into subgroups II.A and II.B. Malaysian isolates were branched into both groups, indicating multiple origins for contemporaneous outbreaks in that country. All ten vaccine strains tested were branched in group I, implying a common ancestor. The Japanese Kanagawa strain, isolated in 1974, and the British Congenital Tremor strain from 1964 were the most distinct variants of CSFV in our collection. The comparison of the nucleotide sequences of the polymerase coding region of 32 European strains distinguished subgroups II.A and II.B which were similar to the corresponding subgroups of the E2 phylogenetic tree. Thus, the results revealed that the E2 region and the polymerase coding regions seem to be appropriate for the grouping of CSFV isolates from all over the world, distinguishing two major groups of the virus. The reliability of these regions for phylogenetic analysis is indicated by the similarity of the results obtained from the two separate parts of the CSFV genome.",animal cell;article;classification;genetic variability;nonhuman;nucleotide sequence;Pestivirus;phylogeny;priority journal;reliability;sequence analysis;strain difference;virus morphology,"Vilček, Š;Stadejek, T.;Ballagi-Pordány, A.;Lowings, J. P.;Paton, D. J.;Belák, S.",1996,,10.1016/0168-1702(96)01326-3,0
2164,Hepatitis E virus genotype 3 diversity: Phylogenetic analysis and presence of subtype 3b in wild boar in Europe,"An increasing number of indigenous cases of hepatitis E caused by genotype 3 viruses (HEV-3) have been diagnosed all around the word, particularly in industrialized countries. Hepatitis E is a zoonotic disease and accumulating evidence indicates that domestic pigs and wild boars are the main reservoirs of HEV-3. A detailed analysis of HEV-3 subtypes could help to determine the interplay of human activity, the role of animals as reservoirs and cross species transmission. Although complete genome sequences are most appropriate for HEV subtype determination, in most cases only partial genomic sequences are available. We therefore carried out a subtype classification analysis, which uses regions from all three open reading frames of the genome. Using this approach, more than 1000 published HEV-3 isolates were subtyped. Newly recovered HEV partial sequences from hunted German wild boars were also included in this study. These sequences were assigned to genotype 3 and clustered within subtype 3a, 3i and, unexpectedly, one of them within the subtype 3b, a first non-human report of this subtype in Europe.",article;blood sampling;controlled study;Europe;gene sequence;genetic variability;Hepatitis E virus;Hepatitis E virus genotype 3;nonhuman;open reading frame;phylogeny;real time polymerase chain reaction;reverse transcription polymerase chain reaction;RNA extraction;sequence alignment;virus genome;European wild boar,"Vina-Rodriguez, A.;Schlosser, J.;Becher, D.;Kaden, V.;Groschup, M. H.;Eiden, M.",2015,,10.3390/v7052704,0
2165,Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing,"Although nearly one fifth of all human cancers have an infectious aetiology, the causes for the majority of cancers remain unexplained. Despite the enormous data output from high-throughput shotgun sequencing, viral DNA in a clinical sample typically constitutes a proportion of host DNA that is too small to be detected. Sequence variation among virus genomes complicates application of sequence-specific, and highly sensitive, PCR methods. Therefore, we aimed to develop and characterize a method that permits sensitive detection of sequences despite considerable variation. We demonstrate that our low-stringency in-solution hybridization method enables detection of <100 viral copies. Furthermore, distantly related proviral sequences may be enriched by orders of magnitude, enabling discovery of hitherto unknown viral sequences by high-throughput sequencing. The sensitivity was sufficient to detect retroviral sequences in clinical samples. We used this method to conduct an investigation for novel retrovirus in samples from three cancer types. In accordance with recent studies our investigation revealed no retroviral infections in human B-cell lymphoma cells, cutaneous T-cell lymphoma or colorectal cancer biopsies. Nonetheless, our generally applicable method makes sensitive detection possible and permits sequencing of distantly related sequences from complex material.",DNA probe;messenger RNA;virus DNA;animal;gene library;genetics;HEK293 cell line;high throughput sequencing;human;human genome;Human immunodeficiency virus 1;metabolism;neoplasm;nucleotide sequence;pig;procedures;provirus;real time polymerase chain reaction;Retroviridae;virology,"Vinner, L.;Mourier, T.;Friis-Nielsen, J.;Gniadecki, R.;Dybkaer, K.;Rosenberg, J.;Langhoff, J. L.;Cruz, D. F.;Fonager, J.;Izarzugaza, J. M.;Gupta, R.;Sicheritz-Ponten, T.;Brunak, S.;Willerslev, E.;Nielsen, L. P.;Hansen, A. J.",2015,,10.1038/srep13201,0
2166,Nucleotide sequence analysis of variable region of VP2 gene of two infectious bursal disease virus isolates from commercial poultry farms,"Two infectious bursal disease virus (IBDV) isolates were obtained from commercial poultry farms with a history of severe outbreaks. A 474-bp product encompassing hypervariable region of IBDV VP2 gene was amplified by reverse transcription-polymerase chain reaction (RT-PCR). The nucleotide sequences of two isolates, VMB1 and VMB2, were determined and compared with those of twenty IBDV strains, including seven very virulent, four classical virulent, four classical attenuated, three antigenic variants and two avirulent serotype 2 strains. The two isolates showed a similarity of 96.5-98.4% with very virulent strains, 84.6-94.6% with classical virulent strains, 90.0-91.4% with classical attenuated strains, 83.0-91.9% with antigenic variants and 65.8-68.7% with avirulent strains. The deduced amino acid sequences of the two isolates showed amino acid substitutions of V256I, N279D, L294I and N299S, specific for very virulent strains. Phylogenetic analysis showed that the two isolates, along with a reported very virulent Indian strain, were closely related to European, Japanese and Chinese very virulent strains indicating their evolutionary origin.",virus RNA;amino acid sequence;article;genetic variability;infectious bursal disease virus;nonhuman;nucleotide sequence;phylogeny;poultry;reverse transcription polymerase chain reaction;virus gene;virus isolation;virus virulence,"Viswas, K. N.;Muniyappa, L.;Suryanarayana, V. V. S.;Byregowda, S. M.",2002,,,0
2167,Experimental infection of conventional nursing pigs and their dams with Porcine deltacoronavirus,"Porcine deltacoronavirus (PDCoV) is a newly identified virus that has been detected in swine herds of North America associated with enteric disease. The aim of this study was to demonstrate the pathogenicity, course of infection, virus kinetics, and aerosol transmission of PDCoV using 87 conventional piglets and their 9 dams, including aerosol and contact controls to emulate field conditions. Piglets 2-4 days of age and their dams were administered an oronasal PDCoV inoculum with a quantitative real-time reverse transcription (qRT)-PCR quantification cycle (Cq) value of 22 that was generated from a field sample having 100% nucleotide identity to USA/Illinois121/2014 determined by metagenomic sequencing and testing negative for other enteric disease agents using standard assays. Serial samples of blood, serum, oral fluids, nasal and fecal swabs, and tissues from sequential autopsy, conducted daily on days 1-8 and regular intervals thereafter, were collected throughout the 42-day study for qRT-PCR, histopathology, and immunohistochemistry. Diarrhea developed in all inoculated and contact control pigs, including dams, by 2 days post-inoculation (dpi) and in aerosol control pigs and dams by 3-4 dpi, with resolution occurring by 12 dpi. Mild to severe atrophic enteritis with PDCoV antigen staining was observed in the small intestine of affected piglets from 2 to 8 dpi. Mesenteric lymph node and small intestine were the primary sites of antigen detection by immunohistochemistry, and virus RNA was detected in these tissues to the end of the study. Virus RNA was detectable in piglet fecal swabs to 21 dpi, and dams to 14-35 dpi.",virus RNA;animal;controlled study;Coronaviridae;Coronavirus infection;diarrhea;female;genetics;immunohistochemistry;mortality;newborn;pathogenicity;pathology;pig;randomized controlled trial;real time polymerase chain reaction;survival analysis;swine disease;veterinary medicine;virology,"Vitosh-Sillman, S.;Loy, J. D.;Brodersen, B.;Kelling, C.;Doster, A.;Topliff, C.;Nelson, E.;Bai, J.;Schirtzinger, E.;Poulsen, E.;Meadors, B.;Anderson, J.;Hause, B.;Anderson, G.;Hesse, R.",2016,,10.1177/1040638716654200,0
2168,Novel hemotropic mycoplasmas are widespread and genetically diverse in vampire bats,"Bats (Order: Chiroptera) have been widely studied as reservoir hosts for viruses of concern for human and animal health. However, whether bats are equally competent hosts of non-viral pathogens such as bacteria remains an important open question. Here, we surveyed blood and saliva samples of vampire bats from Peru and Belize for hemotropic Mycoplasma spp. (hemoplasmas), bacteria that can cause inapparent infection or anemia in hosts. 16S rRNA gene amplification of blood showed 67% (150/223) of common vampire bats (Desmodus rotundus) were infected by hemoplasmas. Sequencing of the 16S rRNA gene amplicons revealed three novel genotypes that were phylogenetically related but not identical to hemoplasmas described from other (non-vampire) bat species, rodents, humans, and non-human primates. Hemoplasma prevalence in vampire bats was highest in non-reproductive and young individuals, did not differ by country, and was relatively stable over time (i.e., endemic). Metagenomics from pooled D. rotundus saliva from Peru detected non-hemotropic Mycoplasma species and hemoplasma genotypes phylogenetically similar to those identified in blood, providing indirect evidence for potential direct transmission of hemoplasmas through biting or social contacts. This study demonstrates vampire bats host several novel hemoplasmas and sheds light on risk factors for infection and basic transmission routes. Given the high frequency of direct contacts that arise when vampire bats feed on humans, domestic animals, and wildlife, the potential of these bacteria to be transmitted between species should be investigated in future work.",adult;amplicon;anemia;Belize;bite;blood;Desmodus rotundus;domestic animal;genotype;human;metagenomics;Mycoplasma;nonhuman;Peru;phylogeny;prevalence;primate;risk factor;rodent;saliva;social behavior;wildlife;endogenous compound;RNA 16S,"Volokhov, D. V.;Becker, D. J.;Bergner, L. M.;Camus, M. S.;Orton, R. J.;Chizhikov, V. E.;Altizer, S. M.;Streicker, D. G.",2017,,10.1017/s095026881700231x,0
2169,Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study,"BACKGROUND: During the pandemic outbreak of the 2009 swine influenza (A(H1N1)pdm09), 32 fatal cases occurred in Norway and 19 of these were included in this study. OBJECTIVES: We characterised pulmonary changes in these fatal Norwegian cases. PATIENTS AND METHODS: Upon hospitalisation, detailed clinical information and specimens from the upper and lower respiratory pathways were collected. At post-mortem, lung tissue was collected, formalin-fixed and paraffin-embedded. Immunohistochemical and light microscopic examination was performed to visualise the local expression of the A(H1N1)pdm09 virus. Reverse transcription-polymerase chain reaction (RT-PCR) and pyrosequencing of the non-fixed specimens allowed the identification of mutations in the influenza virus surface glycoprotein (haemagglutinin gene) particularly at position 222. RESULTS AND CONCLUSIONS: The overall course of illness lasted from 2 to 40 days (median 9 days). Diffused alveolar damage (DAD) was evident in 11 cases, 4 of which had no apparent underlying illness. Obesity was prominent in 12 cases, where three individuals were classified as otherwise healthy. The HA D222G mutation was detected in six cases, 3 of which had no underlying illness. Immunohistochemistry showed the A(H1N1)pdm09 virus to be prominent at the site of inflammation both in close proximity to and inside alveolar structures in the lung tissue. In addition to a possible role for the HA D222G mutation, our findings indicate that host factors and underlying conditions in the infected individuals are fundamental for disease outcome in many cases. This study increases our understanding of determinants for the clinical outcome of pandemic influenza, which could guide future treatment.","Adolescent;Adult;Aged;Child;Female;High-Throughput Nucleotide Sequencing;Hospitalization;Host-Pathogen Interactions;Humans;Immunohistochemistry;*Influenza A Virus, H1N1 Subtype/ge [Genetics];Influenza A Virus, H1N1 Subtype/im [Immunology];Influenza A Virus, H1N1 Subtype/ip [Isolation & Purification];Influenza, Human/co [Complications];*Influenza, Human/mo [Mortality];*Influenza, Human/pa [Pathology];Influenza, Human/vi [Virology];Lung/im [Immunology];*Lung/pa [Pathology];*Lung/vi [Virology];Male;Middle Aged;Mutation;Norway/ep [Epidemiology];Obesity/co [Complications];Obesity/vi [Virology];Pandemics;RNA, Viral/ge [Genetics];Real-Time Polymerase Chain Reaction;Young Adult;0 (RNA, Viral)","Voltersvik, P.;Aqrawi, L. A.;Dudman, S.;Hungnes, O.;Norwegian Lung Pathology, G.;Bostad, L.;Brokstad, K. A.;Cox, R. J.",2016,11,,0
2170,"99th Dahlem Conference on Infection, Inflammation and Chronic Inflammatory Disorders: Farm lifestyles and the hygiene hypothesis","About 15 years have gone by since Strachan first proposed the idea that infections and unhygienic contact may confer protection from the development of allergic illnesses. The so-called 'hygiene hypothesis' has since undergone numerous modifications in the field of epidemiology, clinical science and immunology. Three main areas of research have been brought forward: to explore the role of overt viral and bacterial infections for the inception of allergic diseases; to investigate the significance of environmental exposure to microbial compounds on the development of allergies; and to study the effect of both exposures on underlying innate and adaptive immune responses. A concept unifying these various aspects has not been found, but various pieces of a complex interplay between immune responses of the host, characteristics of the invading microorganism, the level and variety of the environmental exposure and the interactions between an exposed subject's genetic background and the environmental exposures becomes apparent. A natural experiment relating to the hygiene hypothesis is the recurrent observation of a protective effect of growing up on a farm for asthma and allergies. This has been shown in a large number of epidemiological studies across the world among children and adults. The timing and duration of exposure are likely to play a critical role. The largest reduction in risk has been demonstrated for those exposed prenatally and continuously thereafter until adulthood. The protective factors in these farming environments have not been unravelled completely. Findings from various studies suggest that the contact with farm animals, at least in childhood, confers protection. Also the consumption of unprocessed cow's milk directly from the farm has been shown to protect from childhood asthma and allergies. Increased levels of microbial substances may, at least in part, contribute to the 'farm effect'. However, only few studies have measured microbial exposures in these environments and the results obtained so far suggest that the underlying protective microbial exposure(s) have not been identified, but a number of studies using metagenomic approaches are currently under way. The mechanisms by which such environmental exposures confer protection from respiratory allergies are also not well understood. There is good evidence for the involvement of innate immune responses, but translation into protective mechanisms for asthma and allergies is lacking. Furthermore, a number of gene x environment interactions have been observed. © 2010 British Society for Immunology.",adaptive immunity;adulthood;asthma;bacterial infection;childhood;clinical research;conference paper;disease course;environment;environmental exposure;farm animal;farming system;gene;genetics;hepatitis A;host;hygiene hypothesis;hypothesis;immunology;innate immunity;lifestyle;metagenomics;microorganism;milk;observational study;prenatal exposure;priority journal;protection;respiratory tract allergy;risk reduction;science;virus infection,"Von Mutius, E.",2010,,10.1111/j.1365-2249.2010.04138.x,0
2171,The possible role that buffalo played in the recent outbreaks of foot-and-mouth disease in South Africa,"African buffalo (Syncerus caffer) act as maintenance hosts for foot-and-mouth disease (FMD) in southern Africa. A single buffalo can become infected with all three of the endemic serotypes of FMD virus (SAT-1, SAT-2, and SAT-3) and pose a threat of infection to other susceptible cloven-hoofed animals. The floods of 2000 in southern Africa damaged the Kruger National Park (KNP) game fence extensively, and there were several accounts of buffalo that had escaped from the park. The VP1 gene, which codes for the major antigenic determinant of the FMD virus, was used to determine phylogenetic relationships between virus isolates obtained from the outbreaks and those previously obtained from buffalo in the KNP. These results demonstrate that buffalo were most probably the source of the outbreaks, indicating that disease control using fencing as well as vaccination is extremely important to ensure that FMD does not become established in domestic livestock.",protein VP1;Africa;animal cell;animal housing;animal tissue;buffalo;bovine;conference paper;epidemic;flooding;foot and mouth disease;Foot and mouth disease virus;host;infection control;livestock;nonhuman;phylogeny;vaccination;virus gene,"Vosloo, W.;Boshoff, K.;Dwarka, R.;Bastos, A.",2002,,,0
2172,"Genome variation in the SAT types of foot-and-mouth disease viruses prevalent in buffalo (Syncerus caffer) in the Kruger National Park and other regions of Southern Africa, 1986-93","Dideoxy nucleotide sequencing of a portion of the 1D gene of SAT-type foot-and-mouth disease viruses (FMDV) was used to derive phylogenetic relationships between viruses recovered from the oesophageo-pharyngeal secretions of buffalo in the Kruger National Park as well as several other wildlife areas in southern Africa. The three serotypes differed from one another by more than 40% while intratypic variation did not exceed 29%. Within each type, isolates from particular countries were more closely related to one another than to isolates from other countries lending credence to previous observations that FMDV evolve independently in different regions of the subcontinent.",article;buffalo;cattle disease;foot and mouth disease;Foot and mouth disease virus;nonhuman;nucleotide sequence;phylogeny;serotype;South Africa,"Vosloo, W.;Kirkbride, E.;Bengis, R. G.;Keet, D. F.;Thomson, G. R.",1995,,,0
2173,What should be the correct name for the chickenpox virus?,,chickenpox;human;laboratory diagnosis;letter;microbiological examination;nomenclature;nonhuman;species difference;taxonomic identification;Varicella zoster virus;virus classification;virus identification;virus pathogenesis,"Votava, M.",2003,,,0
2174,Phylogenetic analysis of the polyprotein coding region of an infectious South African bursal disease virus (IBDV) strain,"Infectious bursal disease virus (IBDV) causes Gumboro disease, which is highly contagious and immunosuppressive in young chickens. A virulent form of IBDV reached South Africa in 1989 and to date there has been little molecular information available for this strain. In this study, the polyprotein coding region of the South African strain SA-KZN95 was sequenced and analysed along with 52 representative sequences of other serotype I and II strains. We explored the relative impact of recombination on phylogenetic reconstruction using a multidimensional scaling approach. Phylogenetic analyses consistently placed the South African isolate within the very virulent IBDV clade. Selection analyses were also conducted to identify evolutionarily relevant amino acid residues. Previously, 19 residues in the polyprotein were shown to be potentially diagnostic for the different IBDV pathotypes. This study identified an additional two unique residues in the polyprotein which may be used as genetic signatures in future viral identifications. Better strain identification would aid in the development and application of vaccines. © 2013 Elsevier B.V.",amino acid;polyprotein;protein VP2;protein VP3;protein VP4;article;cladistics;infectious bursal disease virus;molecular phylogeny;nonhuman;nucleotide sequence;open reading frame;pathotype;priority journal;protein analysis;sequence alignment;sequence analysis;serotype;South Africa;virus isolation;virus strain;virus virulence,"Vukea, P. R.;Willows-Munro, S.;Horner, R. F.;Coetzer, T. H. T.",2014,,10.1016/j.meegid.2013.11.017,0
2175,Human spermidine synthase: Cloning and primary structure,"Using a synthetic deoxyoligonucleotide mixture constructed for a tryptic peptide of the bovine enzyme as a probe, cDNA coding for the full-length subunit of spermidine synthase was isolated from a human decidual cDNA library constructed on phage λgt11. After subcloning into the Eco RI site of pBR322 and propagation, both strands of the insert were sequenced using a shotgun strategy. Starting from the first start codon, which was immediately preceded by a GC-rich region including four overlapping CCGCC consensus sequences, an open reading frame for a 302-amino-acid polypeptide was resolved. This peptide had an M(r) of 33,827, started with methionine, and ended with serine. The identity of the isolated cDNA was confirmed by comparison of the deduced amino acid sequence with resolved sequences of the tryptic peptides of bovine spermidine synthase. The coding strand of the cDNA revealed no special regulatory or ribosome-binding signals within 82 nucleotides preceding the start codon and no polyadenylation signal within 247 nucleotides following the stop codon. The coding region, containing a 13-nucleotide repeat close to the 5' end, was longer than, and very different from, that of the bacterial counterpart. This region seems to be of retroviral origin and shows marked homology with sequences found in a variety of human, mammalian, avian, and viral genes and mRNAs. By computer analysis, the first 200 nucleotides of the 5' end of the coding strand appear able to form a very stable secondary structure with a free energy change of -157.6 kcal/mole. In Northern blot hybridization experiments, the labeled cDNA specifically recognized a 1.5-kb poly(A)+RNA from cultured human and murine cell lines.",spermidine synthase;amino acid sequence;article;genetic engineering;human;molecular cloning;priority journal,"Wahlfors, J.;Alhonen, L.;Kauppinen, L.;Hyvonen, T.;Janne, J.;Eloranta, T. O.",1990,,,0
2176,Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus,"Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well-supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV.",,"Wainaina, J. M.;Kubatko, L.;Harvey, J.;Ateka, E.;Makori, T.;Karanja, D.;Boykin, L. M.;Kehoe, M. A.",2019,,,0
2177,"In vivo characterisation of two Australian isolates of Marek's disease virus including pathology, viral load and neuropathotyping based on clinical signs","OBJECTIVE: To evaluate the pathogenicity of Australian Marek's disease virus (MDV) isolate MPF23 (1985) against the reference strain MPF57 based on pathology, viral load and neuropathotyping on the basis of clinical signs. PROCEDURE: Two MDV challenge isolates (MPF57 or MPF23) were administered to unvaccinated specific-pathogen free (SPF) layer chicks on day 5 after hatch at three challenge doses (500, 2000 or 8000 plaque-forming units (pfu)/chick). Mortality, body weight, immune organ weights, MDV load in peripheral blood lymphocytes (PBL) and clinical signs were measured to 56 days post challenge (dpc). RESULTS: MPF23 was the more pathogenic of the two viruses, inducing higher mortality (81% vs 62%) and incidence of MD lesions (100% vs 76%). MPF23 induced earlier, more sustained and more severe neurological signs in the period 26-56 dpc. However, there were few differences during the 0-23 dpc used in the neuropathotyping classification under test. The observed pattern during this earlier period classified both viruses as neuropathotype B, consistent with a very virulent pathotype. MDV load in PBL at 7 and 44 dpc did not differ between virus isolates, but the load at 7 dpc was significantly and negatively associated with time to euthanasia or death. CONCLUSION: MPF23 appears to be as, or more, virulent than the MDV strains isolated over the subsequent two decades. The neuropathotyping system developed in the USA did not clearly differentiate between the two isolates under test; however, extension of the period of assessment of clinical signs beyond 26 dpc did reveal clear differences.",animal;Australia;bird disease;blood;chicken;classification;comparative study;disease model;isolation and purification;Kaplan Meier method;Mardivirus;Marek disease;mortality;pathogenicity;pathology;pathophysiology;polymerase chain reaction;veterinary medicine;virology;virus load,"Wajid, S. J.;Walkden-Brown, S. W.;Vanselow, B. A.;Islam, A. F.;Renz, K. G.",2015,,10.1111/avj.12342,0
2178,ICTV virus taxonomy profile: Rhabdoviridae,"The family Rhabdoviridae comprises viruses with negative-sense (–) single-stranded RNA genomes of 10.8–16.1 kb. Virions are typically enveloped with bullet-shaped or bacilliform morphology but can also be non-enveloped filaments. Rhabdoviruses infect plants and animals including mammals, birds, reptiles and fish, as well as arthropods which serve as single hosts or act as biological vectors for transmission to animals or plants. Rhabdoviruses include important pathogens of humans, livestock, fish and agricultural crops. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of Rhabdoviridae, which is available at www.ictv.global/report/rhabdoviridae.",article;nonhuman;priority journal;Rhabdoviridae;taxonomy;virion;virus genome;virus replication,"Walker, P. J.;Blasdell, K. R.;Calisher, C. H.;Dietzgen, R. G.;Kondo, H.;Kurath, G.;Longdon, B.;Stone, D. M.;Tesh, R. B.;Tordo, N.;Vasilakis, N.;Whitfield, A. E.;Lefkowitz, E. J.;Davison, A. J.;Siddell, S. G.;Simmonds, P.;Sabanadzovic, S.;Smith, D. B.;Orton, R. J.",2018,,10.1099/jgv.0.001020,0
2179,A global genomic characterization of nairoviruses identifies nine discrete genogroups with distinctive structural characteristics and host-vector associations,"Nairoviruses are primarily tick-borne bunyaviruses, some of which are known to cause mild-to-severe febrile illness in humans or livestock. We describe the genome sequences of 11 poorly characterized nairoviruses that have ecological associations with either birds (Farallon, Punta Salinas, Sapphire II, Zirqa, Avalon, Clo Mor, Taggert, and Abu Hammad viruses), rodents (Qalyub and Bandia viruses), or camels (Dera Ghazi Khan virus). Global phylogenetic analyses of proteins encoded in the L, M, and S RNA segments of these and 20 other available nairovirus genomes identified nine well-supported genogroups (Nairobi sheep disease, Thiafora, Sakhalin, Keterah, Qalyub, Kasokero, Dera Ghazi Khan, Hughes, and Tamdy). Genogroup-specific structural variations were evident, particularly in the M segment encoding a polyprotein from which virion envelope glycoproteins (Gn and Gc) are generated by proteolytic processing. Structural variations include the extension, abbreviation, or absence sequences encoding an O-glycosylated mucin-like protein in the N-terminal domain, distinctive patterns of conserved cysteine residues in the GP38-like domain, insertion of sequences encoding a double-membrane-spanning protein (NSm) between the Gn and Gc domains, and the presence of an alternative long open reading frame encoding a viroporin-like transmembrane protein (Gx). We also observed strong genogroup-specific associations with categories of hosts and tick vectors.",cysteine;membrane protein;polyprotein;virus envelope protein;amino terminal sequence;article;bird;camel;gene sequence;genetic variation;host pathogen interaction;Nairovirus;nonhuman;open reading frame;phylogenetic tree;protein degradation;protein domain;protein glycosylation;structural genomics;virion;virus genome,"Walker, P. J.;Widen, S. G.;Wood, T. G.;Guzman, H.;Tesh, R. B.;Vasilakis, N.",2016,,10.4269/ajtmh.15-0917,0
2180,The history of bluetongue and a current global overview,"Bluetongue (BT) was first reported more than 125 years ago when European breeds of sheep were introduced into southern Africa. BT viruses (BTV) have been identified in many tropical and temperate areas of the world. BT, the disease, is a phenomenon of ruminants in the temperate zones. There is little clinical disease in the tropical and subtropical areas of the world. At least 24 serotypes of BTV have been described. While the viruses are classified antigenically and taxonomically as BTV, each serotype is unique and may not cause BT, the disease. The BTVs are transmitted among ruminants by competent vector species of the genus Culicoides, i.e. biting gnats or midges. BTV serotypes exist with vector species of Culicoides in predictable, but finite, geographic and ecological cycles or ecosystems around the world. Despite the almost certain movement of livestock and Culicoides species between these ecosystems, there is little evidence that introduced BTV serotypes have been established in these ecosystems. Rather, periodic cyclic extensions and remissions of these virus-vector ecosystems permit the viruses and the disease to move into and recede from adjacent non-endemic areas in a pattern characteristic of many other known arthropod-borne viruses (arboviruses). Earlier publications suggested that a carrier state occurred in cattle infected as foetuses with BTV. No subsequent natural experiences or research support the hypothesis which has not been validated. The conclusions of the research are not accepted by the scientific community. It is logical, therefore, to propose that regulatory restrictions against the movement of cattle from BTV-affected countries be relaxed or eliminated.",,"Walton, T. E.",2004,Jul-Sep,,0
2181,Detection of African swine fever virus-like sequences in ponds in the Mississippi Delta through metagenomic sequencing,"Metagenomic characterization of water virome was performed in four Mississippi catfish ponds. Although differing considerably from African swine fever virus (ASFV), 48 of 446,100 sequences from 12 samples were similar enough to indicate that they represent new members in the family Asfarviridae. At present, ASFV is the only member of Asfarviridae, and this study presents the first indication of a similar virus in North America. At this point, there is no indication that the identified virus(es) pose a threat to human or animal health, and further study is needed to characterize their potential risks to both public health and agricultural development. © 2013 Springer Science+Business Media New York.",African swine fever virus;agricultural management;animal health;article;catfish;gene sequence;health hazard;metagenomics;nonhuman;North America;pond;priority journal;public health;risk assessment;sequence analysis;species differentiation;United States;virus detection;virus gene;virus identification,"Wan, X. F.;Barnett, J. L.;Cunningham, F.;Chen, S.;Yang, G.;Nash, S.;Long, L. P.;Ford, L.;Blackmon, S.;Zhang, Y.;Hanson, L.;He, Q.",2013,,10.1007/s11262-013-0878-2,0
2182,Perspective on emergence and re-emergence of amantadine resistant influenza A viruses in domestic animals in China,"In China, approximately 20% of the animal original influenza A viruses have molecular markers of amantadine resistance. Through phylogenetic data analyses and geospatial statistical analyses, this study suggests emergence of amantadine resistance in animal influenza could be due to selection pressures in China, for example, amantadine usage in some areas. © 2013 Elsevier B.V.",amantadine;antiviral resistance;article;bird;China;domestic animal;drug utilization;genetic selection;Influenza A virus;Influenza A virus (H5N1);Influenza A virus (H9N2);nonhuman;phylogeny;priority journal;pig,"Wan, X. F.;Carrel, M.;Long, L. P.;Alker, A. P.;Emch, M.",2013,,10.1016/j.meegid.2013.09.004,0
2183,Identification of novel and differentially expressed MicroRNAs in goat enzootic nasal adenocarcinoma,"Background: MicroRNAs (miRNAs) post-transcriptionally regulate a variety of genes involved in eukaryotic cell growth, development, metabolism and other biological processes, and numerous miRNAs are implicated in the initiation and progression of cancer. Enzootic nasal adenocarcinoma (ENA), an epithelial tumor induced in goats and sheep by enzootic nasal tumor virus (ENTV), is a chronic, progressive, contact transmitted disease. Methods: In this work, small RNA Illumina high-throughput sequencing was used to construct a goat nasal miRNA library. This study aimed to identify novel and differentially expressed miRNAs in the tumor and para-carcinoma nasal tissues of Nanjiang yellow goats with ENA. Results: Four hundred six known miRNAs and 29 novel miRNAs were identified. A total of 116 miRNAs were significantly differentially expressed in para-carcinoma nasal tissues and ENA (54 downregulated; 60 upregulated; two only expressed in control group); Target gene prediction and functional analysis revealed that 6176 non-redundancy target genes, 1792 significant GO and 97 significant KEGG pathway for 121 miRNAs (116 significant expression miRNAs and five star sequence) were predicted. GO and KEGG pathway analysis revealed the majority of target genes in ENA are involved in cell proliferation, signal transduction and other processes associated with cancer. Conclusions: This is the first large-scale identification of miRNAs in Capra hircus ENA and provides a theoretical basis for investigating the complicated miRNA-mediated regulatory networks involved in the pathogenesis and progression of ENA.",microRNA;animal disease;animal tissue;article;carcinogenesis;cell proliferation;controlled study;domestic goat;down regulation;enzootic nasal adenocarcinoma;gene expression;gene expression regulation;genetic association;high throughput sequencing;nonhuman;nose cancer;RNA analysis;RNA sequence;RNA stability;sequence alignment;sequence analysis;signal transduction;upregulation;validation process,"Wang, B.;Ye, N.;Cao, S. J.;Wen, X. T.;Huang, Y.;Yan, Q. G.",2016,,10.1186/s12864-016-3238-5,0
2184,Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes,"BACKGROUND: Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases. In this study, changes of resistome expression were determined and related to active microbiome profiles during the dynamic composting process. This was achieved by integrating metagenomic and time series metatranscriptomic data for the evolving microbial community during composting. RESULTS: Composting noticeably reduced the aggregated expression level of the manure resistome, which primarily consisted of genes encoding for tetracycline, vancomycin, fluoroquinolone, beta-lactam, and aminoglycoside resistance, as well as efflux pumps. Furthermore, a varied transcriptional response of resistome to composting at the ARG levels was highlighted. The expression of tetracycline resistance genes (tetM-tetW-tetO-tetS) decreased during composting, where distinctive shifts in the four phases of composting were related to variations in antibiotic concentration. Composting had no effect on the expression of sulfonamide and fluoroquinolone resistance genes, which increased slightly during the thermophilic phase and then decreased to initial levels. As indigenous populations switched greatly throughout the dynamic composting, the core resistome persisted and their reservoir hosts' composition was significantly correlated with dynamic active microbial phylogenetic structure. Hosts for sulfonamide and fuoroquinolone resistance genes changed notably in phylognetic structure and underwent an initial increase and then a decrease in abundance. By contrast, hosts for tetracycline resistance genes (tetM-tetW-tetO-tetS) exhibited a constant decline through time. CONCLUSIONS: The transcriptional patterns of a core resistome over the course of composting were identified, and microbial phylogeny was the key determinant in defining the varied transcriptional response of resistome to this dynamic biological process. This research demonstrated the benefits of composting for manure treatment. It reduced the risk of emerging environmental contaminants such as tetracyclines, tetracycline resistance genes, and clinically relevant pathogens carrying ARGs, as well as RNA viruses and bacteriophages.",antiinfective agent;animal;antibiotic resistance;bacterial gene;bacteriophage;composting;drug effect;genetic transcription;genetics;livestock;manure;metagenomics;microbiology;microflora;phylogeny;RNA virus;tetracycline resistance,"Wang, C.;Dong, D.;Strong, P. J.;Zhu, W.;Ma, Z.;Qin, Y.;Wu, W.",2017,,10.1186/s40168-017-0324-0,0
2185,Comprehensive virome analysis reveals the complexity and diversity of the viral spectrum in pediatric patients diagnosed with severe and mild hand-foot-and-mouth disease,"The management of hand-foot-and-mouth disease(HFMD) epidemic is difficult due to the frequent emergence of non-EV71 and non-CVA16 enteroviruses and some cases testing negative for HFMD-associated causative agents. To clarify the virus spectrum of mild and severe HFMD, a comprehensive virome analysis of 238 samples was performed using next-generation sequencing (NGS). The data revealed total thirteen mammalian- and plant- virus families and diverse viral populations including enteroviruses, common respiratory viruses, diarrhea-related viruses, plant viruses and anelloviruses. A total of 18 viruses from 7 virus families were identified in severe cases, versus 37 viruses from 12 virus families in mild cases. Moreover, complicated mixed-infections of enteroviruses with common respiratory viruses were mainly found in severe cases(P = 0.013), while diarrhea-related viruses were mainly found in mild cases(P < 0.001). This study provides the preliminary understanding of viromes both in mild and severe cases, which may benefit the detection of etiologic agents and prevention of HFMD.",Anelloviridae;article;child;disease severity;Enterovirus;Enterovirus infection;female;hand foot and mouth disease;human;infant;male;microbial diversity;next generation sequencing;nucleotide sequence;phylogeny;plant virus;preschool child;priority journal;respiratory virus;screening test;validation process;virus detection;virus diagnosis,"Wang, C.;Zhou, S.;Xue, W.;Shen, L.;Huang, W.;Zhang, Y.;Li, X.;Wang, J.;Zhang, H.;Ma, X.",2018,,10.1016/j.virol.2018.02.004,0
2186,"Isolation, complete genome sequencing, and phylogenetic analysis of the first Chuzan virus in China","A Chuzan virus (CHUV), defined as GX871 here, was isolated from blood from a sentinel cattle firstly in China, and its full-length genome was sequenced in this study. The GX871 genome included 10 segments and 18914 bp, one base fewer than the CHUV prototype strain K-47 due to a one-base deletion in the 5′ non-coding region of segment 8. A frameshift mutation was detected in a short coding region (1010–1026 nt) corresponding to the VP1 protein; this frameshift resulted in a five-amino acid mutation from 336CVLSY340 to 336YGAKL340. In addition, there were a one-base deletion at 1713 nt and a one-base insertion at 1682 nt in the 3′ non-coding region of segment 5. Based on phylogenetic analysis of the deduced VP2 amino acid sequences, Palyam serogroup viruses were classified into three groups. The Chinese CHUV isolate GX871 was categorized into the same group as CHUV prototype strain K-47. The phylogenetic tree was divided into three clusters according to the geographical distribution of the partial nucleotide sequences of VP7, and this arrangement might define the geographical gene pool of CHUV.",protein VP1;protein VP7;amino acid substitution;animal cell;article;blood culture;bovine;China;Chuzan virus;controlled study;frameshift mutation;gene cluster;gene deletion;gene insertion;gene pool;genetic variability;genome analysis;genome size;geographic distribution;molecular phylogeny;nonhuman;nucleotide sequence;Palyam virus;phylogenetic tree;priority journal;sequence analysis;virus genome;virus isolation;virus strain,"Wang, F.;Lin, J.;Chang, J.;Cao, Y.;Qin, S.;Wu, J.;Yu, L.",2016,,10.1007/s11262-015-1282-x,0
2187,Plasma virome of cattle from forest region revealed diverse small circular ssDNA viral genomes,"Background: Free-range cattle are common in the Northeast China area, which have close contact with farmers and may carry virus threatening to cattle and farmers. Methods: Using viral metagenomics we analyzed the virome in plasma samples collected from 80 cattle from the forested region of Northeast China. Results: The virome of cattle plasma is composed of the viruses belonging to the families including Parvoviridae, Papillomaviridae, Picobirnaviridae, and divergent viral genomes showing sequence similarity to circular Rep-encoding single stranded (CRESS) DNA viruses. Five such CRESS-DNA genomes were full characterized, with Rep sequences related to circovirus and gemycircularvirus. Three bovine parvoviruses belonging to two different genera were also characterized. Conclusion: The virome in plasma samples of cattle from the forested region of Northeast China was revealed, which further characterized the diversity of viruses in cattle plasma.",circular DNA;single stranded DNA;animal tissue;article;blood sampling;bovine;China;Circovirus;controlled study;DNA virus;forest;metagenomics;nonhuman;nucleotide sequence;Papillomaviridae;Parvoviridae;Picobirnaviridae;virus genome,"Wang, H.;Li, S.;Mahmood, A.;Yang, S.;Wang, X.;Shen, Q.;Shan, T.;Deng, X.;Li, J.;Hua, X.;Cui, L.;Delwart, E.;Zhang, W.",2018,,10.1186/s12985-018-0923-9,1
2188,"Novel phlebovirus with zoonotic potential isolated from ticks, Australia","Recently discovered tick-borne phleboviruses have been associated with severe disease and death among persons in Asia and the United States. We report the discovery of a novel tick phlebovirus in Tasmania State, Australia, that is closely related to those zoonotic viruses found in Asia and North America.","Animals;*Bird Diseases/ep [Epidemiology];Bird Diseases/vi [Virology];Birds;*Disease Outbreaks;Disease Vectors;*Genome, Viral;High-Throughput Nucleotide Sequencing;Humans;Phlebotomus Fever/ep [Epidemiology];*Phlebotomus Fever/ve [Veterinary];Phlebotomus Fever/vi [Virology];Phlebovirus/cl [Classification];*Phlebovirus/ge [Genetics];Phlebovirus/ip [Isolation & Purification];Phylogeny;*RNA, Viral/ge [Genetics];Tasmania;*Ticks/vi [Virology];0 (RNA, Viral)","Wang, J.;Selleck, P.;Yu, M.;Ha, W.;Rootes, C.;Gales, R.;Wise, T.;Crameri, S.;Chen, H.;Broz, I.;Hyatt, A.;Woods, R.;Meehan, B.;McCullough, S.;Wang, L. F.",2014,Jun,,0
2189,Identification of the progenitors of Indonesian and Vietnamese avian influenza A (H5N1) viruses from southern China,"The transmission of highly pathogenic avian influenza H5N1 virus to Southeast Asian countries triggered the first major outbreak and transmission wave in late 2003, accelerating the pandemic threat to the world. Due to the lack of influenza surveillance prior to these outbreaks, the genetic diversity and the transmission pathways of H5N1 viruses from this period remain undefined. To determine the possible source of the wave 1 H5N1 viruses, we recently conducted further sequencing and analysis of samples collected in live-poultry markets from Guangdong, Hunan, and Yunnan in southern China from 2001 to 2004. Phylogenetic analysis of the hemagglutinin and neuraminidase genes of 73 H5N1 isolates from this period revealed a greater genetic diversity in southern China than previously reported. Moreover, results show that eight viruses isolated from Yunnan in 2002 and 2003 were most closely related to the clade 1 virus sublineage from Vietnam, Thailand, and Malaysia, while two viruses from Hunan in 2002 and 2003 were most closely related to viruses from Indonesia (clade 2.1). Further phylogenetic analyses of the six internal genes showed that all 10 of those viruses maintained similar phylogenetic relationships as the surface genes. The 10 progenitor viruses were genotype Z and shared high similarity (≥99%) with their corresponding descendant viruses in most gene segments. These results suggest a direct transmission link for H5N1 viruses between Yunnan and Vietnam and also between Hunan and Indonesia during 2002 and 2003. Poultry trade may be responsible for virus introduction to Vietnam, while the transmission route from Hunan to Indonesia remains unclear. Copyright © 2008, American Society for Microbiology. All Rights Reserved.",hemagglutinin;sialidase;article;avian influenza;China;gene;gene isolation;gene sequence;genetic variability;genotype;hemagglutinin gene;Indonesia;Influenza A virus (H5N1);Malaysia;neuraminidase gene;nonhuman;nucleotide sequence;phylogeny;poultry;priority journal;Thailand;time series analysis;Viet Nam;virus isolation;virus transmission,"Wang, J.;Vijaykrishna, D.;Duan, L.;Bahl, J.;Zhang, J. X.;Webster, R. G.;Peiris, J. S. M.;Chen, H.;Smith, G. J. D.;Guan, Y.",2008,,10.1128/jvi.02468-07,0
2190,Transcriptomic Analysis Identifies Candidate Genes and Gene Sets Controlling the Response of Porcine Peripheral Blood Mononuclear Cells to Poly I:C Stimulation,"Polyinosinic-polycytidylic acid (poly I:C), a synthetic dsRNA analog, has been demonstrated to have stimulatory effects similar to viral dsRNA. To gain deep knowledge of the host transcriptional response of pigs to poly I:C stimulation, in the present study, we cultured and stimulated peripheral blood mononuclear cells (PBMC) of piglets of one Chinese indigenous breed (Dapulian) and one modern commercial breed (Landrace) with poly I:C, and compared their transcriptional profiling using RNA-sequencing (RNA-seq). Our results indicated that poly I:C stimulation can elicit significantly differentially expressed (DE) genes in Dapulian (g = 290) as well as Landrace (g = 85). We also performed gene set analysis using the Gene Set Enrichment Analysis (GSEA) package, and identified some significantly enriched gene sets in Dapulian (g = 18) and Landrace (g = 21). Most of the shared DE genes and gene sets were immune-related, and may play crucial rules in the immune response of poly I:C stimulation. In addition, we detected large sets of significantly DE genes and enriched gene sets when comparing the gene expression profile between the two breeds, including control and poly I:C stimulation groups. Besides immune-related functions, some of the DE genes and gene sets between the two breeds were involved in development and growth of various tissues, which may be correlated with the different characteristics of the two breeds. The DE genes and gene sets detected herein provide crucial information towards understanding the immune regulation of antiviral responses, and the molecular mechanisms of different genetic resistance to viral infection, in modern and indigenous pigs.","Animals;Breeding;Chromosome Mapping;Computational Biology/mt [Methods];Gene Expression Profiling;*Gene Expression Regulation/de [Drug Effects];Gene Ontology;Genetic Association Studies;High-Throughput Nucleotide Sequencing;*Leukocytes, Mononuclear/de [Drug Effects];*Leukocytes, Mononuclear/me [Metabolism];Molecular Sequence Annotation;*Poly I-C/pd [Pharmacology];Reproducibility of Results;Swine;*Transcriptome;O84C90HH2L (Poly I-C)","Wang, J.;Wang, Y.;Wang, H.;Wang, H.;Liu, J. F.;Wu, Y.;Guo, J.",2016,05 03,,0
2191,Characterization of emerging Newcastle disease virus isolates in China,"Abstract Background: Newcastle disease (ND) is a devastating worldwide disease of poultry characterized by increased respiration, circulatory disturbances, hemorrhagic enteritis, and nervous signs. Sequence analysis shows several amino acid residue substitutions at neutralizing epitopes on the F and HN proteins of recent Shaanxi strains. Both Cross protection and cross serum neutralization tests revealed that the traditional vaccine strains were unable to provide full protection for the flocks. Methods: To better understand the epidemiology of Newcastle disease outbreak, a portion of the F gene and the full-length HN gene were amplified from Shaanxi isolates by reverse transcription-polymerase chain reaction (RT-PCR) and then conducted sequence and phylogenetic analyzes. In pathogenicity analysis, both high intra-cerebral pathogenicity index (ICPI) and mean death time (MDT) tests of chicken embryo were carried out. Furthermore, a cross-protection experiment in which specific-pathogen-free chickens vaccinated with a LaSota vaccine strain were challenged by the recent Shaanxi strain was also performed. Results: Nine Newcastle disease (ND) virus (NDV) isolates which were recovered from ND outbreaks in chicken flocks in China were genotypically and pathotypically characterized. Amino acid sequence analysis revealed that all the recent Shaanxi-isolated NDVs have <sup>112</sup>R-R-Q-K-R-F<sup>117</sup> for the C-terminus of the F2 protein and exhibit high ICPI and MDT of chicken embryos, suggesting that they were all classified as velogenic type of NDVs. Phylogenetic analysis of these isolates showed that they belong to subgenotype VIId that have been implicated in the recent outbreaks in northwestern China. The percentage of amino acid sequence identity of F protein between recent Shaanxi stains and five vaccine strains was in the range of 81.9 %-88.1 %, while the percentage of amino acid sequence identity of HN protein between recent Shaanxi strains and vaccine strains was in the range of 87.4 %-91.2 %. Furthermore, a number of amino acid residue substitutions at neutralizing epitopes on the F and HN proteins of these isolates were observed, which may lead to the change of antibody recognition and neutralization capacity. A cross-protection experiment indicated that specific-pathogen-free chickens vaccinated with a LaSota vaccine strain was not capable of providing full protection for the flocks that were challenged by the recent Shaanxi strain. Conclusions: Taken together, our findings reveal that recent Shannxi NDVstrains exhibit antigenic variations that could be responsible for recent outbreaks of NDVs in northwestern China.",live vaccine;Newcastle disease vaccine;amino acid sequence;amino acid substitution;animal experiment;animal model;antigenic variation;article;carboxy terminal sequence;chicken;China;controlled study;cross protection;embryo;epidemic;F gene;genotype;hemagglutination inhibition test;molecular evolution;molecular recognition;Newcastle disease;Newcastle disease virus;NH gene;nonhuman;phylogeny;reverse transcription polymerase chain reaction;virus gene;virus isolation;virus neutralization;virus virulence,"Wang, J. Y.;Liu, W. H.;Ren, J. J.;Tang, P.;Wu, N.;Wu, H. Y.;Ching, C. D.;Liu, H. J.",2015,,10.1186/s12985-015-0351-z,0
2192,Genome sequence characterization of pigeon circoviruses in China,"Pigeon circovirus (PiCV) was detected by PCR in pigeons from China. Altogether, 48 out of 244 pigeons tested positive for PiCV (positive rate, 19.67%), suggesting that the virus was prevalent in China. From the 48 PiCV-positive samples, about 2040bp complete genome fragments were obtained by full length genome amplification and sequenced with a next-generation sequencing platform. Characteristics of the ORFs from different PiCV strains tested in this study were analyzed. Several insertion, deletion or substitutions were discovered during the analysis of the nucleotide sequence compared with sequences reported previously. In phylogenetic tree analysis, 48 sequences isolated in this study could be further divided into five clades (A, B, C, D, and F), clade E includes reference sequences only. Two major groups were found in the six clades, distinguished by ATA and ATG initiation codons. Most of the viruses isolated in the study were in the ATG group, with fewer in the ATA branch.","Amino Acid Sequence;Animals;Base Sequence;Bird Diseases;China/ep [Epidemiology];Chromosome Mapping;Circoviridae Infections/ep [Epidemiology];Circoviridae Infections/tm [Transmission];*Circoviridae Infections/ve [Veterinary];Circoviridae Infections/vi [Virology];Circovirus/cl [Classification];*Circovirus/ge [Genetics];Circovirus/ip [Isolation & Purification];*Columbidae/vi [Virology];Feces/vi [Virology];*Genome, Viral;High-Throughput Nucleotide Sequencing;Molecular Epidemiology;Mutation;Open Reading Frames;*Phylogeny;Prevalence;*Viral Proteins/ge [Genetics];0 (Viral Proteins)","Wang, K. C.;Zhuang, Q. Y.;Qiu, Y.;Wang, T.;Chen, J. M.",2017,04 02,,0
2193,"New variant of porcine epidemic diarrhea virus, United States, 2014",,"Animals;*Coronavirus Infections/ve [Veterinary];Evolution, Molecular;Genetic Variation;Genome, Viral;History, 21st Century;Phylogeny;*Porcine epidemic diarrhea virus/cl [Classification];Porcine epidemic diarrhea virus/ge [Genetics];Swine;*Swine Diseases/ep [Epidemiology];Swine Diseases/hi [History];Swine Diseases/vi [Virology];United States/ep [Epidemiology]","Wang, L.;Byrum, B.;Zhang, Y.",2014,May,,0
2194,Classification of duck hepatitis virus into three genotypes based on molecular evolutionary analysis,"The nucleotide sequences of the complete VP1, VP0, VP3, and partial 3D regions of seven duck hepatitis virus (DHV) serotype 1 (DHV-1) strains isolated in China between 2001 and 2007 and one DHV-1 strain originally obtained from ATCC were determined and compared with previously available DHV sequences in GenBank. Phylogenetic analysis on the basis of VP1 sequences demonstrated three distinct genetic groups. There was an excellent concordance among the genetic groups assigned based on the complete VP0, VP3, and the partial 3D regions. In view of the growing importance of molecular techniques in diagnosis, we propose that the three genetic groups should be termed DHV types A, B, and C. All DHV-1 strains grouped in genotype A, whereas the new serotype strains isolated in Taiwan and the new serotype strains isolated in South Korea clustered into genotypes B and C, respectively, suggesting a potential genetic correlates of serotype. In pairwise comparisons of complete VP1, VP0, and VP3 nucleotide and amino acid sequences and the partial 3D nucleotide sequence, DHVs of the same genotype were clearly distinguished from those of heterologous genotypes. Analysis of the amino acid sequences of the three capsid proteins demonstrated the presence of conserved elements that form the eight-stranded β-barrel structures, as well as intervening domains that vary in sequence between strains of different genotypes as seen in other picorna viruses. © 2008 Springer Science+Business Media, LLC.",protein VP0;protein VP1;protein VP3;viral protein;amino acid sequence;article;China;embryo;genetic correlation;genotype;hepatitis virus;molecular evolution;nonhuman;nucleotide sequence;phylogeny;Picornaviridae;priority journal;sequence analysis;serotype;South Korea;Taiwan;virus strain,"Wang, L.;Pan, M.;Fu, Y.;Zhang, D.",2008,,10.1007/s11262-008-0233-1,0
2195,Characterization of miRNAs involved in response to poly(I:C) in porcine airway epithelial cells,"MicroRNAs (miRNA) have been implicated in a variety of pathological conditions including infectious diseases. Knowledge of the miRNAs affected by poly(I:C), a synthetic analog of viral double-stranded RNA, in porcine airway epithelial cells (PAECs) contributes to understanding the mechanisms of swine viral respiratory diseases, which bring enormous economic loss worldwide every year. In this study, we used high throughput sequencing to profile miRNA expression in PAECs treated with poly(I:C) as compared to the untreated control. This approach revealed 23 differentially expressed miRNAs (DEMs), five of which have not been implicated in viral infection before. Nineteen of the 23 miRNAs were down-regulated including members of the miR-17-92 cluster, a well-known polycistronic oncomir and extensively involved in viral infection in humans. Target genes of DEMs, predicted using bioinformatic methods and validated by luciferase reporter analysis on two representative DEMs, were significantly enriched in several pathways including transforming growth factor-β signaling. A large quantity of sequence variations (isomiRs) were found including a substitution at position 5, which was verified to redirect miRNAs to a new spectrum of targets by luciferase reporter assay together with bioinformatics analysis. Twelve novel porcine miRNAs conserved in other species were identified by homology analysis together with cloning verification. Furthermore, the expression analysis revealed the potential importance of three novel miRNAs in porcine immune response to viruses. Overall, our data contribute to clarifying the mechanisms underlying the host immune response against respiratory viruses in pigs, and enriches the repertoire of porcine miRNAs.",polyinosinic polycytidylic acid;transcriptome;transforming growth factor beta;untranslated RNA;animal;cell culture;cytology;epithelium cell;immunology;metabolism;pig;respiratory system;signal transduction;virology,"Wang, L.;Wang, J. K.;Han, L. X.;Zhuo, J. S.;Du, X.;Liu, D.;Yang, X. Q.",2017,,10.1111/age.12524,0
2196,Isolation of a reassortant H1N2 swine Flu strain of type “Swine-Human-Avian” and its genetic variability analysis,,,"Wang, L. B.;Chen, Q. Y.;Wu, X. M.;Che, Y. L.",2018,,,0
2197,A novel enterovirus species identified from severe diarrheal goats,"Backgrounds The Enterovirus genus of the family of Picornaviridae consists of 9 species of Enteroviruses and 3 species of Rhinoviruses based on the latest virus taxonomy. Those viruses contribute significantly to respiratory and digestive disorders in human and animals. Out of 9 Enterovirus species, Enterovirus E-G are closely related to diseases affecting on livestock industry. While enterovirus infection has been increasingly reported in cattle and swine, the enterovirus infections in small ruminants remain largely unknown. Methods Virology, molecular and bioinformatics methods were employed to characterize a novel enterovirus CEV-JL14 from goats manifesting severe diarrhea with morbidity and mortality respectively up to 84% and 54% in China. Results CEV-JL14 was defined and proposed as a new Enterovirus species L within the genus of Enterovirus of the family Picornaviridae. CEV-JL14 had a complete genome sequence of 7461 nucleotides with an ORF encoding 2172 amino acids, and shared 77.1% of genomic sequence identity with TB4-OEV, an ovine enterovirus. Comparison of 5'-UTR and structural genes of CEV-JL14 with known Enterovirus species revealed highly genetic variations among CEV-JL14 with known Enterovirus species. VP1 nucleotide sequence identities of CEV-14 were 51.8%-53.5% with those of Enterovirus E and F, 30.9%-65.3% with Enterovirus G, and 43.8-51. 5% with Enterovirus A-D, respectively. CEV-JL14 was proposed as a novel species within the genus of Enterovirus according to the current ICTV demarcation criteria of enteroviruses. Conclusions CEV-JL14 clustered phylogenetically to neither Enterovirus E and F, nor to Enterovirus G. It was defined and proposed as novel species L within the genus of Enterovirus. This is the first report of caprine enterovirus in China, the first complete genomic sequence of a caprine enterovirus revealed, and the unveiling of significant genetic variations between ovine enterovirus and caprine enterovirus, thus broadening the current understanding of enteroviruses.",protein VP1;5' untranslated region;animal cell;animal tissue;article;bioinformatics;China;controlled study;coughing;diarrhea;disease severity;dyspnea;Enterovirus;Enterovirus A;Enterovirus B;Enterovirus C;Enterovirus D;Enterovirus E;Enterovirus F;Enterovirus G;Enterovirus L;epidemic;fever;gene sequence;genetic variation;genome sequence;goat;molecular biology;morbidity;mortality;nonhuman;nucleotide sequence;open reading frame;respiratory distress;structural gene;virology;virus genome;virus identification;virus infectivity;virus isolation,"Wang, M.;He, J.;Lu, H.;Liu, Y.;Deng, Y.;Zhu, L.;Guo, C.;Tu, C.;Wang, X.",2017,,10.1371/journal.pone.0174600,0
2198,Metagenomic insights into the contribution of phages to antibiotic resistance in water samples related to swine feedlot wastewater treatment,"In this study, we examined the types of antibiotic resistance genes (ARGs) possessed by bacteria and bacteriophages in swine feedlot wastewater before and after treatment using a metagenomics approach. We found that the relative abundance of ARGs in bacterial DNA in all water samples was significantly higher than that in phages DNA (>10.6-fold), and wastewater treatment did not significantly change the relative abundance of bacterial- or phage-associated ARGs. We further detected the distribution and diversity of the different types of ARGs according to the class of antibiotics to which they confer resistance, the tetracycline resistance genes were the most abundant resistance genes and phages were more likely to harbor ATP-binding cassette transporter family and ribosomal protection genes. Moreover, the colistin resistance gene mcr-1 was also detected in the phage population. When assessing the contribution of phages in spreading different groups of ARGs, β-lactamase resistance genes had a relatively high spreading ability even though the abundance was low. These findings possibly indicated that phages not only could serve as important reservoir of ARG but also carry particular ARGs in swine feedlot wastewater, and this phenomenon is independent of the environment.",ABC transporter;bacterial DNA;beta lactamase;colistin;lake water;agricultural land;antibiotic resistance;article;bacterial genetics;bacteriophage;China;controlled study;metagenomics;nonhuman;pig;tetracycline resistance;waste water management;whole genome sequencing,"Wang, M.;Xiong, W.;Liu, P.;Xie, X.;Zeng, J.;Sun, Y.;Zeng, Z.",2018,,10.3389/fmicb.2018.02474,0
2199,Complete sequence and evolutionary genomic analysis of the Pseudomonas aeruginosa transposable bacteriophage D3112,"Bacteriophage D3112 represents one of two distinct groups of transposable phage found in the clinically relevant, opportunistic pathogen Pseudomonas aeruginosa. To further our understanding of transposable phage in P. aeruginosa, we have sequenced the complete genome of D3112. The genome is 37,611 bp, with an overall G+C content of 65%. We have identified 53 potential open reading frames, including three genes (the c repressor gene and early genes A and B) that have been previously characterized and sequenced. The organization of the putative coding regions corresponds to published genetic and transcriptional maps and is very similar to that of enterobacteriophage Mu. In contrast, the International Committee on Taxonomy of Viruses has classified D3112 as a lambda-like phage on the basis of its morphology. Similarity-based analyses identified 27 open reading frames with significant matches to proteins in the NCBI databases. Forty-eight percent of these were similar to Mu-like phage and prophage sequences, including proteins responsible for transposition, transcriptional regulation, virion morphogenesis, and capsid formation. The tail proteins were highly similar to prophage sequences in Escherichia coli and phage Phi12 from Staphylococcus aureus, while proteins at the right end were highly similar to proteins in Xylella fastidiosa. We performed phylogenetic analyses to understand the evolutionary relationships of D3112 with respect to Mu-like versus lambda-like bacteriophages. Different results were obtained from similarity-based versus phylogenetic analyses in some instances. Overall, our findings reveal a highly mosaic structure and suggest that extensive horizontal exchange of genetic material played an important role in the evolution of D3112.","Bacteriophages/cl [Classification];*Bacteriophages/ge [Genetics];Bacteriophages/py [Pathogenicity];Base Composition;Base Sequence;*DNA Transposable Elements;*Genome, Viral;Open Reading Frames;Phylogeny;*Pseudomonas aeruginosa/vi [Virology];0 (DNA Transposable Elements)","Wang, P. W.;Chu, L.;Guttman, D. S.",2004,Jan,,0
2200,Nucleotide sequence analysis of E2 major protective antigen encoding region of 12 strains of hog cholera virus(HCV),"cDNA fragments, of HCV envelope glycoprotein E2 major gene of 11 field strains isolated in China in different time and 1 French reference strain(Thiveral) were amplified respectively with RT-PCR method and sequenced. The fragments amplified located by the 5' 2485 to 2708 of E2 major domains B and C and encoded 75 amino acid residues of E2 glycoprotein. All the products amplifield by RT-PCR from 12 strains in the study were same size of 224 bp. Comparing 12 sequences with other 9 references strains sequence reported before using software DNAstar, it was found that Hog Cholera Virus could be classified in two groups by analysis of phylogenetic tree. Strains Brescia, Gpe, Ald, Thiverval, C, CW, HCLV, HCVSM, BJCY1/96, BJTX3/96, BJSY2/96, HeNXH2/98, HeNZZ1/82 and GDGZ1/95 were assigned to group A and were 85.7%-100% for nucleotide sequence and 83.8%-100% for amino acid sequence in homology; but strains HCVF98, HCVF94, HeBHH2/95, LN1/84, SZGM1/85, SCCD1/79 and Alfort were assigned to group B and were 84.3%-100% for nucleotide sequence and 85.1%-100% for amino acid sequence in homology; and 21 strains of HCV were 78.1%-100% for nucleotide sequence and for 78.4%-100% amino acid sequence in homology. Homology were 99.1% for nucleotide sequence and 100% for amino acid sequence between strains HCLV in our study and strains C reported by Rijn's in the Netherlands. It's showed our method of sequencing is reliable. There were obvious differences between the two groups in sequences of envelope glycoprotein E2 major gene, especially in the amino acid substitutions of sites 713 and 729 respectively, and it is showed the two groups of HCV field strains might vary genetically in some extents. The results of other report of challenging of the partial field strains showed that the Chinese stock vaccine virus(HCLV) has good immunity.","complementary DNA;glycoprotein E2, classical swine fever virus;virus envelope protein;amino acid sequence;amino acid substitution;article;genetics;immunology;molecular genetics;nucleotide sequence;Pestivirus;phylogeny;reverse transcription polymerase chain reaction;sequence homology","Wang, Q.;Wang, Z.;Zhao, Y.;Li, B.;Qiu, H.",2000,,,0
2201,Prevalence of noroviruses and sapoviruses in swine of various ages determined by reverse transcription-PCR and microwell hybridization assays,"Noroviruses (NoVs) and sapoviruses (SaVs) are emerging enteric pathogens that cause diarrhea in humans and animals. Porcine genogroup II (GII) NoVs replicate in pigs, but their pathogenesis is undefined. The porcine SaV/GIII/Cowden/80/US strain causes diarrhea and intestinal lesions in pigs. Recently, genetically diverse porcine NoVs (genotypes 11, 18, and 19 within GII) and SaVs comprising at least two genogroups (GIII and GVI?/JJ681-like) and two unclassified strains (G?/QW19 and G?/LL26) were identified; however, their prevalence has not been reported. To investigate the prevalence of porcine NoVs and SaVs, 621 fecal samples were collected from swine of various ages from seven swine farms and one slaughterhouse in three states in the United States. Fecal samples were tested by reverse transcription-PCR and microwell hybridization assays with porcine NoV- and SaV-specific primers and probes, respectively. Porcine GII NoVs were detected exclusively from finisher pigs with an overall prevalence of 20%. Porcine GIII SaVs were detected in 62% of pigs, with the highest prevalence in postweaning pigs and lowest in nursing pigs. Porcine GVI?/JJ681-like SaVs and the G?/QW19-like SaVs were detected infrequently in pigs. The G?/LL26-like SaVs were detected mainly in younger pigs. Because some porcine NoVs and SaVs are genetically or antigenically related to human strains and recombinants within NoVs or SaVs occur for human and pig strains, the high prevalence and subclinical infection rate of these viruses in pigs raise questions of whether pigs may be reservoirs for human strains or for the emergence of new human and porcine recombinants. Copyright © 2006, American Society for Microbiology. All Rights Reserved.",primer RNA;age;article;bioassay;diarrhea;disease carrier;feces analysis;finisher swine;genotype;host;hybridization;infection rate;intestine injury;microwell hybridization assay;molecular phylogeny;nonhuman;Norovirus;Norovirus G LL26;Norovirus G QW19;Norovirus genogroup II;Norovirus genogroup III;Norovirus genogroup VI JJ681 like;Norovirus genotype 11;Norovirus genotype 18;Norovirus genotype 19;Norovirus SaV GIII Cowden 80 US;nursing swine;pig farming;postweaning swine;prevalence;priority journal;reservoir host;reverse transcription polymerase chain reaction;RNA probe;Sapovirus;slaughterhouse;swine disease;United States;virus classification;virus infection;virus recombinant;virus replication;virus strain,"Wang, Q. H.;Souza, M.;Funk, J. A.;Zhang, W.;Saif, L. J.",2006,,10.1128/jcm.02634-05,0
2202,Classification of emergent U.S. strains of porcine epidemic diarrhea virus by phylogenetic analysis of nucleocapsid and ORF3 genes,,China;letter;nonhuman;nucleotide sequence;ORF3 gene;phylogenetic tree;phylogeny;Porcine epidemic diarrhea virus;priority journal;unindexed sequence;virus gene;virus isolation;virus nucleocapsid;virus strain;virus virulence,"Wang, S.;Cheng, X.;Chen, S.;Lin, F.;Jiang, B.;Zhu, X.;Li, Z.;Wang, J.;Chen, S.",2014,,10.1128/jcm.01708-14,0
2203,Calculation of evolutionary correlation between individual genes and full-length genome: A method useful for choosing phylogenetic markers for molecular epidemiology,"Individual genes or regions are still commonly used to estimate the phylogenetic relationships among viral isolates. The genomic regions that can faithfully provide assessments consistent with those predicted with full-length genome sequences would be preferable to serve as good candidates of the phylogenetic markers for molecular epidemiological studies of many viruses. Here we employed a statistical method to evaluate the evolutionary relationships between individual viral genes and full-length genomes without tree construction as a way to determine which gene can match the genome well in phylogenetic analyses. This method was performed by calculation of linear correlations between the genetic distance matrices of aligned individual gene sequences and aligned genome sequences. We applied this method to the phylogenetic analyses of porcine circovirus 2 (PCV2), measles virus (MV), hepatitis E virus (HEV) and Japanese encephalitis virus (JEV). Phylogenetic trees were constructed for comparisons and the possible factors affecting the method accuracy were also discussed in the calculations. The results revealed that this method could produce results consistent with those of previous studies about the proper consensus sequences that could be successfully used as phylogenetic markers. And our results also suggested that these evolutionary correlations could provide useful information for identifying genes that could be used effectively to infer the genetic relationships. Copyright: © 2013 Wang et al.",article;Circovirus;consensus sequence;gene sequence;genetic distance;genetic marker;Hepatitis E virus;Japanese encephalitis virus;Measles virus;molecular epidemiology;molecular evolution;molecular phylogeny;nonhuman;phylogenetic marker;phylogenetic tree;Porcine circovirus 2;virus gene;virus genome,"Wang, S.;Luo, X.;Wei, W.;Zheng, Y.;Dou, Y.;Cai, X.",2013,,10.1371/journal.pone.0081106,0
2204,Analysis of codon usage preference in hemagglutinin genes of the swine-origin influenza A (H1N1) virus,"Background The swine-origin influenza A (H1N1) virus (S-OIV) has come to the forefront since 2009 and was identified as a new reassortant strain. The hemagglutinin (HA) glycoprotein mediates virus binding, contains antigenic regions recognized by neutralizing antibodies, and is associated with viral cross-species infection and adaption. The comparison study of codon usage preferences in influenza viral genomes was less extensive. In this study, we used codon usage pattern analyses to validate the adaption and origins of S-OIV. Methods Codon usage pattern was used to estimate the host adaption of S-OIVs. Phylogenetic analysis of the HA gene was conducted to understand the phylogeny of H1N1 viruses isolated from different hosts. Amino acid signature pattern on antigenic sites of HA was analyzed to understand the antigenic characteristics. Results Results of phylogenetic analyses of HA gene indicate that S-OIVs group in identical clusters. The synonymous codon usage pattern analyses indicate that the effective number of codons versus GC content at the third codon position in the HA1 gene slightly differ from those in swine H1N1 and gradually adapted to human. Our data indicate that S-OIV evolution occurred according to positive selection within these antigenic regions. A comparison of antigenic site amino acids reveals similar signature patterns between S-OIV and 1918 human influenza strains. Conclusion This study proposes a new and effective way to gain a better understanding of the features of the S-OIV genome and evolutionary processes based on the codon usage pattern. It is useful to trace influenza viral origins and cross-species virus transmission.",hemagglutinin;amino acid substitution;article;bird;codon;codon usage;DNA base composition;human;Influenza A virus (H1N1);lower respiratory tract;molecular evolution;nonhuman;phylogenetic tree;phylogeny;pig;receptor binding;viral genetics;virus genome,"Wang, S. F.;Su, M. W.;Tseng, S. P.;Li, M. C.;Tsao, C. H.;Huang, S. W.;Chu, W. C.;Liu, W. T.;Chen, Y. M. A.;Huang, J. C.",2016,,10.1016/j.jmii.2014.08.011,0
2205,"Divergent Pathogenic Properties of Circulating Coxsackievirus A6 Associated with Emerging Hand, Foot, and Mouth Disease","Coxsackievirus A6 (CV-A6) is an emerging pathogen associated with hand, foot, and mouth disease (HFMD). Its genetic characterization and pathogenic properties are largely unknown. Here, we report 39 circulating CV-A6 strains isolated in 2013 from HFMD patients in northeast China. Three major clusters of CV-A6 were identified and related to CV-A6, mostly from Shanghai, indicating that domestic CV-A6 strains were responsible for HFMD emerging in northeast China. Four full-length CV-A6 genomes representing each cluster were sequenced and analyzed further. Bootscanning tests indicated that all four CV-A6-Changchun strains were most likely recombinants between the CV-A6 prototype Gdula and prototype CV-A4 or CV-A4-related viruses, while the recombination pattern was related to, yet distinct from, the strains isolated from other regions of China. Furthermore, different CV-A6 strains showed different capabilities of viral replication, release, and pathogenesis in a mouse model. Further analyses indicated that viral protein 2C contributed to the diverse pathogenic abilities of CV-A6 by causing autophagy and inducing cell death. To our knowledge, this study is the first to report lethal and nonlethal strains of CV-A6 associated with HFMD. The 2C protein region may play a key role in the pathogenicity of CV-A6 strains.<b>IMPORTANCE</b> Hand, foot, and mouth disease (HFMD) is a major and persistent threat to infants and children. Besides the most common pathogens, such as enterovirus A71 (EV-A71) and coxsackievirus A16 (CV-A16), other enteroviruses are increasingly contributing to HFMD. The present study focused on the recently emerged CV-A6 strain. We found that CV-A6 strains isolated in Changchun City in northeast China were associated with domestic origins. These Changchun viruses were novel recombinants of the CV-A6 prototype Gdula and CV-A4. Our results imply that measures to control CV-A6 transmission are urgently needed. Further analyses revealed differing pathogenicities in strains isolated in a neonatal mouse model. One of the possible causes has been narrowed down to the viral protein 2C, using phylogenetic studies, viral sequences, and direct tests on cultured human cells. Thus, the viral 2C protein is a promising target for antiviral drugs to prevent CV-A6-induced tissue damage.","Animals;Cell Line, Tumor;China;Disease Models, Animal;Disease Outbreaks;*Enterovirus A, Human/cl [Classification];*Enterovirus A, Human/ge [Genetics];Enterovirus A, Human/ip [Isolation & Purification];Hand, Foot and Mouth Disease/pa [Pathology];*Hand, Foot and Mouth Disease/vi [Virology];Humans;Mice;Mice, Inbred ICR;Phylogeny;*Reassortant Viruses/ge [Genetics];Reassortant Viruses/py [Pathogenicity];*Recombination, Genetic/ge [Genetics]","Wang, S. H.;Wang, A.;Liu, P. P.;Zhang, W. Y.;Du, J.;Xu, S.;Liu, G. C.;Zheng, B. S.;Huan, C.;Zhao, K.;Yu, X. F.",2018,06 01,,0
2206,Discovery of a highly divergent coronavirus in the Asian house shrew from China illuminates the origin of the alphacoronaviruses,"Although shrews are one of the largest groups of mammals little is known about their role in the evolution and transmission of viral pathogens including coronaviruses. We captured 266 Asian house shrews (Suncus murinus) in Jiangxi and Zhejiang provinces, China, during 2013-2015. Coronavirus (CoV) RNA was detected in 24 Asian house shrews, with an overall prevalence of 9.02%. Complete viral genome sequences were successfully recovered from the RNA positive samples. The newly discovered shrew CoV fell into four lineages reflecting their geographic origins, indicative of largely allopatric evolution. Notably, these viruses were most closely related to alphacoronaviruses, but sufficiently divergent that they should be considered a novel member of the genus Alphacoronavirus, which we denote Wencheng shrew virus (WESV). Phylogenetic analysis revealed that WESV was a highly divergent member of the alphacoronaviruses and, more dramatically, that the S gene of WESV fell in a cluster that was genetically distinct from that of known coronaviruses. The divergent position of WESV suggests that coronaviruses have a long association with Asian house shrews. In addition, the genome of WESV contains a distinct NS7 gene that exhibits no sequence similarity to any known viruses. Together, these data suggest that shrews are natural reservoirs for coronaviruses and may have played an important and long-term role in CoV evolution.<b>IMPORTANCE</b> The subfamily Coronavirinae contains several notorious human and animal pathogens, including severe acute respiratory syndrome coronavirus, Middle East respiratory syndrome coronavirus, and porcine epidemic diarrhea virus. Because of their genetic diversity and phylogenetic relationships it has been proposed that the alphacoronaviruses likely have their ultimate ancestry in those viruses residing in bats. Here, we described a novel alphacoronavirus (Wencheng shrew virus, WESV) that was sampled from Asian house shrews in China. Notably, WESV is a highly divergent member of the alphacoronaviruses and possesses an S gene that is genetically distinct from that of all known coronaviruses. In addition, the genome of WESV contains a distinct NS7 gene that exhibits no sequence similarity to any known viruses. Together, these data suggest that shrews are important and long-standing hosts for coronaviruses that merit additional research and surveillance.",,"Wang, W.;Lin, X. D.;Liao, Y.;Guan, X. Q.;Guo, W. P.;Xing, J. G.;Holmes, E. C.;Zhang, Y. Z.",2017,Jun 21,,0
2207,The Evidence of Clade 7.1 Avian Influenza Virus (H5N1) in Qinghai Lake,"The highly pathogenic influenza A virus subtype H5N1 spread throughout Asia since 2003, reached to Europe in 2005, and the Middle East, as well as Africa and caused a global concern for a potential pandemic threat last decade. A Clade 2.3.2 H5N1 virus became dominate in the Qinghai Lake region in 2009 with sporadic mammal cases of infection and transferred to Russia and Europe through wild migratory birds. Currently, HPAI H5N1 of clades 2.3.4, 2.3.2, and 7 are the dominant co-circulating H5N1 viruses in poultry in Asia. 2.3.2 Clade is dominant in wild birds through the world whereas there is no evident data about Clade 7 circulation in wild birds. We detected HPAI H5N1 virus of Clade 7.1 in Qinghai Lake, that closely related to Shanxi-like and Vietnam viruses co-circulating in poultry. This is the first report of Clade 7.1 H5N1 in wild birds. Based on phylogenetic analyses, the virus can be originated from Clade 7.1 virus gene pool that spread in Vietnam and Chinese poultry and could spread with migratory birds to Qinghai Lake. The Qinghai Lake continues to be significant hotspot for H5N1 surveillance since the regular outbreaks occurred there in wild birds and mammals. Based on these facts and findings, the related researchers should pay more attention to the Qinghai Lake basin as significant hotspot for H5N1 avian influenza surveillance since the regular H5N1 outbreaks occurred there in wild birds with sporadic mammal cases of infection.",Highly Pathogenic Avian Influenza;H5N1;Clade 7.1;Qinghai Lake;Wild;Birds;WILD BIRDS;MIGRATORY BIRDS;POULTRY;CHINA;ALIGNMENT;OUTBREAK,"Wang, W.;Sharshov, K.;Li, Z.;Zheng, S. S.;Sun, H.;Yang, F.;Wang, X. L.;Li, L. X.",2016,Dec,,0
2208,Genetic characterization of a novel duck-origin picornavirus with six 2A proteins,"A novel virus was detected from diseased ducks and completely determined. The virus was shown to have a picornavirus-like genome layout. Interestingly, the genome contained a total of up to six 2As, including four 2As (2A1-2A4) each having an NPGP motif, an AIG1-like 2A5, and a parechovirus-like 2A6. The 5′UTR was predicted to possess a hepacivirus/pestivirus-like internal ribosome entry site (IRES). However, the subdomain IIIe consisted of a 3 nt stem and five unpaired bases, distinct from those found in all other HP-like IRESs. The virus was most closely related to duck hepatitis A virus, with amino acid identities of 37.7 %, 39 % and 43.7 % in the P1, P2 and P3 regions, respectively. Based on these investigations, together with phylogenetic analyses, the virus could be considered as the founding member of a novel picornavirus genus that we tentatively named 'Aalivirus', with 'Aalivirus A' as the type species.",amino acid;nonstructural protein 2;nonstructural protein 2A;nonstructural protein 2A1;nonstructural protein 2A2;nonstructural protein 2A3;nonstructural protein 2A4;nonstructural protein 2A5;unclassified drug;viral protein;5' untranslated region;amino acid sequence;animal cell;article;controlled study;duck;Duck hepatitis A virus;gene expression;Hepatitis A virus;Hepatitis C virus;internal ribosome entry site;nonhuman;nucleotide sequence;Pestivirus;Picornaviridae;priority journal;unindexed sequence;viral genetics;virus detection;virus gene;virus genome;virus replication;virus strain,"Wang, X.;Liu, N.;Wang, F.;Ning, K.;Li, Y.;Zhang, D.",2014,,10.1099/vir.0.063313-0,0
2209,Genomic characterization and pathogenicity of a strain of type 1 porcine reproductive and respiratory syndrome virus,"The emergence of type 1 porcine reproductive and respiratory syndrome virus (PRRSV) has been noticed recently in China. In the present study, the complete genomic characterization of a strain of type 1 PRRSV (designated GZ11-G1) was described and its pathogenicity for piglets was analyzed. The results showed that the complete genome of GZ11-G1 with a size of 15,094 nt, excluding the poly (A) tails, shared 80.2–96.3% identity with the representative strains of type 1 PRRSV, and in particular, it had highest homology (96.3%) with Amervac PRRS, a live vaccine virus of type 1 PRRSV and SHE, a rescued virus from an infectious clone of Amervac PRRS virus. Compared with the vaccine virus, the nonstructural and structural proteins of GZ11-G1 displayed extensive amino acid variations except for its ORF5a. GZ11-G1 was clustered with the strains of type 1 PRRSV including Cresa3267, Cresa3249, Cresa3256, Olot/91, 9625/2012, ESP-1991-Olot91 and Amervac PRRS vaccine virus by further phylogenetic analysis. Moreover, GZ11-G1 was shown to cause fever, higher viremia and lung and lymph node lesions in piglets. Our findings indicate that GZ11-G1 is genetically related to type 1 PRRSV strains within the cluster formed by Cresa3267, Cresa3249, Cresa3256, Olot/91, 9625/2012, ESP-1991-Olot91 and Amervac PRRS vaccine virus, and it is a pathogenic for piglets. This study aids in understanding the genetic variation and evolution of type 1 PRRSV.",amino acid;polyadenylic acid;viral protein;amino acid sequence;animal cell;animal experiment;animal model;article;controlled study;fever;genetic similarity;genome analysis;genome size;lung lesion;lymphadenopathy;nonhuman;nucleotide sequence;phylogeny;piglet;porcine reproductive and respiratory syndrome;Porcine reproductive and respiratory syndrome virus;priority journal;sequence homology;viremia;virus characterization;virus genome;virus strain;virus virulence,"Wang, X.;Yang, X.;Zhou, R.;Zhou, L.;Ge, X.;Guo, X.;Yang, H.",2016,,10.1016/j.virusres.2016.09.006,0
2210,RNA-Seq analysis of duck embryo fibroblast cell gene expression during the early stage of egg drop syndrome virus infection,"Egg drop syndrome virus (EDSV), a member of the family Adenoviridae and an economically important pathogen with a broad host range, leads to markedly decreased egg production. However, the molecular mechanism underlying the host-EDSV interaction remains unclear. Here, we performed high-throughput RNA sequencing (RNA-Seq) to study the dynamic changes in host gene expression at 6, 12, and 24 hours post-infection in duck embryo fibroblasts (DEFs) infected with EDSV. Atotal of 441 differentially expressed genes (DEGs) were identified after EDSV infection. Gene Ontology category and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that these DEGs were associated with multiple biological functions, including signal transduction, host immunity, virus infection, cell apoptosis, cell proliferation, and pathogenicity-related and metabolic process signaling pathways. We screened and identified 12 DEGs for further examination by using qRT-PCR. The qRT-PCR and RNA-Seq results were highly consistent. This study analyzed viral infection and host immunity induced by EDSV infection from a novel perspective, and the results provide valuable information regarding the mechanisms underlying host-EDSV interactions, which will prove useful for the future development of antiviral drugs or vaccines for poultry, thus benefiting the entire poultry industry.",apoptosis;article;cell proliferation;controlled study;duck;fibroblast;gene expression;gene ontology;immunity;metabolism;nonhuman;pathogenicity;poultry;real time polymerase chain reaction;RNA sequence;signal transduction;syndrome;virus infection;antivirus agent;vaccine,"Wang, X. P.;Qi, X. F.;Yang, B.;Chen, S. Y.;Wang, J. Y.",2019,,10.3382/ps/pey318,0
2211,Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers,"BACKGROUND: Avian influenza virus (AIV) outbreaks are worldwide threats to both poultry and humans. Our previous study suggested microRNAs (miRNAs) play significant roles in the regulation of host response to AIV infection in layer chickens. The objective of this study was to test the hypothesis if genetic background play essential role in the miRNA regulation of AIV infection in chickens and if miRNAs that were differentially expressed in layer with AIV infection would be modulated the same way in broiler chickens. Furthermore, by integrating with parallel mRNA expression profiling, potential molecular mechanisms of host response to AIV infection can be further exploited. RESULTS: Total RNA isolated from the lungs of non-infected and low pathogenic H5N3 infected broilers at four days post-infection were used for both miRNA deep sequencing and mRNA microarray analyses. A total of 2.6 M and 3.3 M filtered high quality reads were obtained from infected and non-infected chickens by Solexa GA-I Sequencer, respectively. A total of 271 miRNAs in miRBase 16.0 were identified and one potential novel miRNA was discovered. There were 121 miRNAs differentially expressed at the 5% false discovery rate by Fisher's exact test. More miRNAs were highly expressed in infected lungs (108) than in non-infected lungs (13), which was opposite to the findings in layer chickens. This result suggested that a different regulatory mechanism of host response to AIV infection mediated by miRNAs might exist in broiler chickens. Analysis using the chicken 44 K Agilent microarray indicated that 508 mRNAs (347 down-regulated) were differentially expressed following AIV infection. CONCLUSIONS: A comprehensive analysis combining both miRNA and targeted mRNA gene expression suggests that gga-miR-34a, 122-1, 122-2, 146a, 155, 206, 1719, 1594, 1599 and 451, and MX1, IL-8, IRF-7, TNFRS19 are strong candidate miRNAs or genes involved in regulating the host response to AIV infection in the lungs of broiler chickens. Further miRNA or gene specific knock-down assay is warranted to elucidate underlying mechanism of AIV infection regulation in the chicken.",Animals;*Chickens/ge [Genetics];Chickens/vi [Virology];High-Throughput Nucleotide Sequencing;Influenza A virus/py [Pathogenicity];*Influenza in Birds/ge [Genetics];Influenza in Birds/vi [Virology];*Lung/vi [Virology];*MicroRNAs/ge [Genetics];Microarray Analysis;Molecular Sequence Data;*Transcriptome;0 (MicroRNAs),"Wang, Y.;Brahmakshatriya, V.;Lupiani, B.;Reddy, S. M.;Soibam, B.;Benham, A. L.;Gunaratne, P.;Liu, H. C.;Trakooljul, N.;Ing, N.;Okimoto, R.;Zhou, H.",2012,Jun 22,,0
2212,Adelaide River virus nucleoprotein gene: Analysis of phylogenetic relationships of ephemeroviruses and other rhabdoviruses,"The nucleotide sequence of the Adelaide River virus (ARV) genome was determined from the 3' terminus to the end of the nucleoprotein (N) gene. The 3' leader sequence comprises 50 nucleotides and shares a common terminal trinucleotide (3' UGC-), a conserved U-rich domain and a variable AU-rich domain with other animal rhabdoviruses. The N gene comprises 1355 nucleotides from the transcription start sequence (AACAGG) to the poly(A) sequence [CATG(A)7] and encodes a polypeptide of 429 amino acids. The N protein has a calculated molecular mass of 49429 Da and a pI of 5.4 and, like the bovine ephemeral fever virus (BEFV) N protein, features a highly acidic C-terminal domain. Analysis of amino acid sequence relationships between all available rhabdovirus N proteins indicated that ARV and BEFV are closely related viruses (48.3% similarity) which share higher sequence similarity to vesiculoviruses than to lyssaviruses. Phylogenetic trees based on a multiple sequence alignment of all available rhabdovirus N protein sequences demonstrated clustering of viruses according to genome organization, host range and established taxonomic relationships.",polyadenylic acid;virus nucleoprotein;amino acid sequence;article;carboxy terminal sequence;molecular genetics;molecular weight;nonhuman;nucleotide sequence;phylogeny;priority journal;Rabies virus;Rhabdoviridae;sequence homology;Vesiculovirus;virus classification;virus gene,"Wang, Y.;Cowley, J. A.;Walker, P. J.",1995,,,0
2213,The fecal virome of red-crowned cranes,,,"Wang, Y.;Yang, S.;Liu, D.;Zhou, C.;Li, W.;Lin, Y.;Wang, X.",2018,,,0
2214,Comprehensive analysis of amino acid sequence diversity at the F protein cleavage site of Newcastle disease virus in fusogenic activity,"Newcastle disease virus (NDV) is a contagious agent of Newcastle disease in avian species and seriously affects the poultry industry. The cleavage site of the viral F protein (Fcs) is a key determinant of membrane fusion and viral virulence. In this study, we investigated the precise effect of variable amino acid sequences of the Fcs on fusogenic activity. Based on viral pathogenicity, the Fcs sequences of natural isolates (n = 1572) are classified into eight types of virulent Fcs (VFcs) with the motif “G/R/K-R-Q/R/K-R/K-R↓F” and ten types of the avirulent Fcs (AFcs) with the motif “G/R/E-R/K/Q-Q-G/E-R↓L”. The VFcs is only found in the Class II cluster of viral classification and not in Class I. The AFcs exists in both Class I and II isolates. The VFc and AFc types present an evolutionary relationship with temporal distribution and host species. Using a fusion assay in vitro, VFcs-1 “RRQKR↓F” and VFcs-2 “RRQRR↓F” show the highest efficiency in triggering membrane fusion. The neutral residue Q at the P3 position of the VFcs plays an enhancing role compared to effect of the basic residues R and K. A single residue K at P3 or P5 is less efficient of the fusogenic activity in the VFcs with all basic residues. Moreover, the cleavage efficiencies of F0 proteins with different types of Fcs motifs do not appear to affect membrane fusion. Our findings offer insight into the effect of amino acid variation of the Fcs on the fusion triggered by NDV.",virus fusion protein;amino acid sequence;article;cell membrane;coevolution;controlled study;genotype;geographic distribution;in vitro study;membrane fusion;mutant;Newcastle disease virus;nonhuman;plasmid;protein cleavage;protein expression;sequence analysis;virus isolation;virus strain;virus virulence;wild type,"Wang, Y.;Yu, W.;Huo, N.;Wang, W.;Guo, Y.;Wei, Q.;Wang, X.;Zhang, S.;Yang, Z.;Xiao, S.",2017,,10.1371/journal.pone.0183923,0
2215,Full-length and defective enterovirus G genomes with distinct torovirus protease insertions are highly prevalent on a Chinese pig farm,"Recombination occurs frequently between enteroviruses (EVs) which are classified within the same species of the Picornaviridae family. Here, using viral metagenomics, the genomes of two recombinant EV-Gs (strains EVG 01/NC_CHI/2014 and EVG 02/NC_CHI/2014) found in the feces of pigs from a swine farm in China are described. The two strains are characterized by distinct insertion of a papain-like protease gene from toroviruses classified within the Coronaviridae family. According to recent reports the site of the torovirus protease insertion was located at the 2C/3A junction region in EVG 02/NC_CHI/2014. For the other variant EVG 01/NC_CHI/2014, the inserted protease sequence replaced the entire viral capsid protein region up to the VP1/2A junction. These two EV-G strains were highly prevalent in the same pig farm with all animals shedding the full-length genome (EVG 02/NC_CHI/2014) while 65% also shed the capsid deletion mutant (EVG 01/NC_CHI/2014). A helper-defective virus relationship between the two co-circulating EV-G recombinants is hypothesized.",capsid protein;proteinase;viral protein;agricultural land;animal;China;classification;Enterovirus infection;feces;gene deletion;genetic reassortment;genetic recombination;genetic variation;genetics;metabolism;metagenomics;phylogeny;Picornaviridae;pig;prevalence;procedures;swine disease;Torovirus;Torovirus infection;veterinary medicine;virology;virus genome,"Wang, Y.;Zhang, W.;Liu, Z.;Fu, X.;Yuan, J.;Zhao, J.;Lin, Y.;Shen, Q.;Wang, X.;Deng, X.;Delwart, E.;Shan, T.;Yang, S.",2018,,10.1007/s00705-018-3875-x,1
2216,Hepatitis E virus,"Since the sequence of hepatitis E virus (HEV) was determined from a patient with enterically transmitted non-A, non-B hepatitis in 1989, similar sequences have been isolated from many different animals, including pigs, wild boars, deer, rabbits, bats, rats, chicken, and trout. All of these sequences have the same genomic organization, which contains open reading frames (ORFs) 1, 2, and 3, although their genomic sequences are variable. Some have proposed that they be classified as new family, Hepeviridae, which would be further divided into different genera and species according to their sequence variability. The size of these virus particles generally ranged from 27 to 34 nm. However, HEV virions produced in cell culture differ in structure from the viruses found in feces. Those from cell culture have a lipid envelope and a little ORF3 on their surfaces, whereas the viruses isolated from feces lack lipid envelope and ORF3. Surprisingly, most of the secreted ORF2 protein from both these sources is not associated with HEV RNA.",amino acid sequence;gene structure;Hepatitis E virus;human;molecular cloning;nonhuman;phylogenetic tree;priority journal;sequence alignment;virus classification;virus genome;virus morphology;virus transmission,"Wang, Y.;Zhao, C.;Qi, Y.;Geng, Y.",2016,,10.1007/978-94-024-0942-0_1,0
2217,Genotyping of Newcastle disease viruses isolated from 2002 to 2004 in China,"The main function region of the fusion (F) protein gene of 124 strains of Newcastle disease virus isolated from 2002 to 2004 in China was amplified and sequenced for further phylogenetic and residue substitutive analysis. Most of the isolates were classified into genotype VIIc, VIId, VIf, and VIb, while others into genotype IX, III, or II. The genotype IX, a unique genotype which includes strain F48, the first Chinese virulent NDV strain isolated in 1948, were still found inducing sporadic infections in certain areas. Subgenotype VIIc, VIId, and VIIe viruses, which were distributed in clusters in the phylogenetic tree distinct from members of subgenotypes Vila and VIIb, were responsible for most outbreaks in China and circulated predominantly in China in recent years. Strain NDV03-026, an isolate of the genotype II which was normally lentogenic, was found carrying 112RRQKRF117 motif at the cleavage site of F protein as the virulent strain. © 2006 New York Academy of Sciences.",animal tissue;bird disease;Chinese;conference paper;controlled study;disease transmission;embryo;epidemic;genotype;Newcastle disease virus;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;protein degradation;virus classification;virus isolation;virus strain,"Wang, Z.;Liu, H.;Xu, J.;Bao, J.;Zheng, D.;Sun, C.;Wei, R.;Song, C.;Chen, J.",2006,,10.1196/annals.1373.027,0
2218,H13 influenza viruses in wild birds have undergone genetic and antigenic diversification in nature,"Among 16 haemagglutinin (HA) subtypes of avian influenza viruses (AIVs), H13 AIVs have rarely been isolated in wild waterfowl. H13 AIVs cause asymptomatic infection and are maintained mainly in gull and tern populations; however, the recorded antigenic information relating to the viruses has been limited. In this study, 2 H13 AIVs, A/duck/Hokkaido/W345/2012 (H13N2) and A/duck/Hokkaido/WZ68/2012 (H13N2), isolated from the same area in the same year in our surveillance, were genetically and antigenically analyzed with 10 representative H13 strains including a prototype strain, A/gull/Maryland/704/1977 (H13N6). The HA genes of H13 AIVs were phylogenetically divided into 3 groups (I, II, and III). A/duck/Hokkaido/W345/2012 (H13N2) was genetically classified into Group III. This virus was distinct from a prototype strain, A/gull/Maryland/704/1977 (H13N6), and the virus, A/duck/Hokkaido/WZ68/2012 (H13N2), both belonging to Group I. Antigenic analysis indicated that the viruses of Group I were antigenically closely related to those of Group II, but distinct from those of Group III, including A/duck/Hokkaido/W345/2012 (H13N2). In summary, our study indicates that H13 AIVs have undergone antigenic diversification in nature.",antigenic diversification;antigenicity;article;avian influenza virus;avian influenza virus (H13);disease surveillance;genetic variability;HA gene;nonhuman;phylogeny;priority journal;strain difference;virus classification;virus gene;virus isolation;virus strain;waterfowl;wild species,"Wang, Z. J.;Kikutani, Y.;Nguyen, L. T.;Hiono, T.;Matsuno, K.;Okamatsu, M.;Krauss, S.;Webby, R.;Lee, Y. J.;Kida, H.;Sakoda, Y.",2018,,10.1007/s11262-018-1573-0,0
2219,Molecular characterization of the first G24P 14 rotavirus strain detected in humans,"Here we report the genome of a novel rotavirus A (RVA) strain detected in a stool sample collected during routine surveillance by the Centers for Disease Control and Prevention's New Vaccine Surveillance Network. The strain, RVA/human-wt/USA/2012741499/2012/G24P[14], has a genomic constellation of G24-P[14]-I2-R2-C2-M2-A3-N2-T9-E2-H3. The VP2, VP3, VP7 and NSP3 genes cluster phylogenetically with bovine strains. The other genes occupy mixed clades containing animal and human strains. Strain RVA/human-wt/USA/2012741499/2012/G24P[14] most likely is the product of interspecies transmission and reassortment events. This is the second report of the G24 genotype and the first report of the G24P[14] genotype combination in humans.","Animals;Cattle;Child, Preschool;*Genome, Viral;*Genotype;High-Throughput Nucleotide Sequencing;Humans;Male;*Phylogeny;Reassortant Viruses/cl [Classification];*Reassortant Viruses/ge [Genetics];Rotavirus/cl [Classification];*Rotavirus/ge [Genetics];Rotavirus Infections/vi [Virology];Texas;*Viral Nonstructural Proteins/ge [Genetics];0 (Viral Nonstructural Proteins)","Ward, M. L.;Mijatovic-Rustempasic, S.;Roy, S.;Rungsrisuriyachai, K.;Boom, J. A.;Sahni, L. C.;Baker, C. J.;Rench, M. A.;Wikswo, M. E.;Payne, D. C.;Parashar, U. D.;Bowen, M. D.",2016,09,,0
2220,Antigenic analysis of highly pathogenic avian influenza virus H5N1 sublineages co-circulating in Egypt,"Highly pathogenic avian influenza virus H5N1 has spread across Eurasia and Africa, and outbreaks are now endemic in several countries, including Indonesia, Vietnam and Egypt. Continuous circulation of H5N1 virus in Egypt, from a single infected source, has led to significant genetic diversification with phylogenetically separable sublineages, providing an opportunity to study the impact of genetic evolution on viral phenotypic variation. In this study, we analysed the phylogeny of H5 haemagglutinin (HA) genes in influenza viruses isolated in Egypt from 2006 to 2011 and investigated the effect of conserved amino acid mutations in the HA genes in each of the sublineages on their antigenicity. The analysis showed that viruses in at least four sublineages still persisted in poultry in Egypt as of 2011. Using reverse genetics to generate HA-reassortment viruses with specific HA mutations, we found antigenic drift in the HA in two influenza virus sublineages, compared with the other currently co-circulating influenza virus sublineages in Egypt. Moreover, the two sublineages with significant antigenic drift were antigenically distinguishable. Our findings suggested that phylogenetically divergent H5N1 viruses, which were not antigenically cross-reactive, were co-circulating in Egypt, indicating that there was a problem in using a single influenza virus strain as seed virus to produce influenza virus vaccine in Egypt and providing data for designing more efficacious control strategies in H5N1-endemic areas. © 2012 SGM.",hemagglutinin;influenza vaccine;neutralizing antibody;animal experiment;animal model;antibody titer;antigen antibody reaction;antigenicity;article;cross reaction;Egypt;glycosylation;hemagglutination inhibition;immunogenicity;infection control;influenza vaccination;Influenza A virus (H5N1);mouse;nonhuman;phylogeny;priority journal;viral genetics;virus isolation;virus mutation;virus recombinant;virus strain,"Watanabe, Y.;Ibrahim, M. S.;Ellakany, H. F.;Kawashita, N.;Daidoji, T.;Takagi, T.;Yasunaga, T.;Nakaya, T.;Ikuta, K.",2012,,10.1099/vir.0.044032-0,0
2221,Multiple genotypes of nonpathogenic H6N2 influenza viruses isolated from chickens in California,"From February 2000 through September 2001, a limited number of H6N2 influenza viruses were isolated from chickens in California. This report describes the genetic characterization of nine of these H6N2 viruses. All of the viruses analyzed had phylogenetically similar hemagglutinin (HA) and neuraminidase molecules that suggested the viruses shared a recent common ancestor. The analysis of the HA sequence of these viruses with all available H6 viruses from different hosts and locations showed that these genes do not separate into well-defined North American and Eurasian lineages. The neuraminidase genes of the California viruses contain an 18 amino acid deletion, a possible adaptation to growth in chickens. Analysis of the remaining gene segments of the California viruses revealed that three distinct genotypes of H6N2 viruses were present.",,"Webby, R. J.;Woolcock, P. R.;Krauss, S. L.;Walker, D. B.;Chin, P. S.;Shortridge, K. F.;Webster, R. G.",2003,,,0
2222,"Antigenic drift, antigenic shift and interferon antagonists: How bunyaviruses counteract the immune system","Members of the Bunyaviridae family are amongst the most widespread viruses in the world. They can be found on every inhabited continent at virtually every latitude, and are able to infect a wide range of arthropods, plants and mammals including humans. More than 300 named viruses are contained within the family Bunyaviridae (Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses (2000) 599), and several members cause significant disease in humans or domestic animals. Despite being recognised as an emerging threat, relatively little is known about their virulence mechanisms. Here, we try to summarise the current state of knowledge about how the viruses of the Bunyaviridae succeed in establishing infection in the face of a powerful immune system. © 2002 Elsevier Science B.V. All rights reserved.",gene product;genomic RNA;arthropod;Bunyaviridae;crush syndrome;domestic animal;encephalitis;fever;Hantavirus pulmonary syndrome;hemorrhagic fever;human;immune system;mammal;nonhuman;outcomes research;plant;priority journal;respiratory tract disease;review;taxonomy;virus cell interaction;virus classification;virus gene;virus identification;virus transmission;virus virulence,"Weber, F.;Elliott, R. M.",2002,,10.1016/s0168-1702(02)00125-9,0
2223,Characterization of dog serum virome from Northeastern Brazil,"Domestic dogs share habitats with human, a fact that makes them a potential source of zoonotic viruses. Moreover, knowledge regarding possible bloodborne pathogens is important due to the increasing application of blood transfusion in dogs. In the present study, we evaluated the serum virome of 520 dogs using throughput sequencing (HTS). The serum samples were pooled and sequenced using an Illumina MiSeq platform. Our unbiased method identified prevalent canine pathogens as canine protoparvovirus 1 (canine parvovirus 2), undersearched agents as canine bocaparvovirus 1 (minute virus of canines) and canine circovirus, circular viruses closely related to viruses recently found in human samples, and new parvovirus and anelloviruses. The dog virome described in the present work furthers the knowledge concerning the viral population in domestic animals. The present data includes information regarding viral agents that are potentially transmitted through blood transfusion among dogs.",single stranded DNA;article;blood sampling;Brazil;canine bocaparvovirus 1;canine circovirus;Canine parvovirus;canine protoparvovirus 1;Circovirus;DNA library;DNA sequence;high throughput sequencing;metagenomics;molecular phylogeny;nonhuman;nucleotide sequence;priority journal;real time polymerase chain reaction;Sanger sequencing;virus genome;virus transmission,"Weber, M. N.;Cibulski, S. P.;Olegário, J. C.;da Silva, M. S.;Puhl, D. E.;Mósena, A. C. S.;Alves, C. D. B. T.;Paim, W. P.;Baumbach, L. F.;Mayer, F. Q.;Fernandes, A. R. F.;Azevedo, S. S.;Canal, C. W.",2018,,10.1016/j.virol.2018.09.023,0
2224,"Evaluation of the serum virome in calves persistently infected with Pestivirus A, presenting or not presenting mucosal disease","Bovine viral diarrhea virus 1, reclassified as Pestivirus A, causes an economically important cattle disease that is distributed worldwide. Pestivirus A may cause persistent infection in that calves excrete the virus throughout their lives, spreading the infection in the herd. Many persistently infected (PI) calves die in the first 2 years of life from mucosal disease (MD) or secondary infections, probably as a consequence of virus-induced immune depression. Here, high-throughput sequencing (HTS) was applied for evaluation of the total virome in sera of (i) PI calves displaying clinically apparent MD (n = 8); (ii) PI calves with no signs of MD (n = 8); and (iii) control, Pestivirus A-free calves (n = 8). All the groups were collected at the same time and from the same herd. Serum samples from calves in each of the groups were pooled, submitted to viral RNA/DNA enrichment, and sequenced by HTS. Viral genomes of Pestivirus A, Ungulate erythroparvovirus 1, bosavirus (BosV), and hypothetical circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses were identified. Specific real-time PCR assays were developed to determine the frequency of occurrence of such viruses in each of the groups. The absolute number of distinct viral genomes detected in both PI calf groups was higher than in the control group, as revealed by higher number of reads, contigs, and genomes, representing a wider range of taxons. Genomes representing members of the family Parvoviridae, such as U. erythroparvovirus 1 and BosV, were most frequently detected in all the three groups of calves. Only in MD-affected PI calves, we found two previously unreported Hypothetical single-stranded DNA genomes clustered along with CRESS-DNA viruses. These findings reveal that parvoviruses were the most frequently detected viral genomes in cattle serum; its frequency of detection bears no statistical correlation with the status of calves in relation to Pestivirus A infection, since clinically normal or MD-affected/non-affected PI calves were infected with similar U. erythroparvovirus 1 genome loads. Moreover, MD-affected PI calves were shown to support viremia of CRESS-DNA viral genomes; however, the meaning of such correlation remains to be established.",single stranded DNA;virus RNA;article;bovine;Bovine viral diarrhea virus 1;cattle disease;controlled study;Erythroparvovirus;gene cluster;gene sequence;genetic code;high throughput sequencing;mucosal disease;nonhuman;persistent infection;Pestivirus infection;priority journal;real time polymerase chain reaction;virus genome,"Weber, M. N.;Cibulski, S. P.;Silveira, S.;Siqueira, F. M.;Mósena, A. C. S.;da Silva, M. S.;Olegário, J. C.;Varela, A. P. M.;Teixeira, T. F.;Bianchi, M. V.;Driemeier, D.;Pavarini, S. P.;Mayer, F. Q.;Roehe, P. M.;Canal, C. W.",2018,,10.1007/s11262-018-1599-3,0
2225,First Evidence of Bovine Viral Diarrhea Virus Infection in Wild Boars,"Background: The farming of wild boars has growing due to the interest of the human consumption of this exotic meat. Such a development may pose an increased risk of disease transmission between boars and domestic animals. The wild boar population has increased in South America in the last years due the absence of predator causing economic losses due to direct damage to crops and risk of disease transmission. The genus Pestivirus within the family Flaviviridae are composed by four recognized species by the International Committee on the Taxonomy of Viruses (ICTV): classical swine fever virus (CSFV), border disease virus (BDV), bovine viral diarrhea virus type 1 (BVDV-1) and 2 (BVDV-2). Other putative species denoted as atypical pesitiviruses have been reported as 'HoBi'-like virus, giraffe pestivirus, Bungowannah pestivirus, Pronghorn antelope virus, atypical porcine pestivirus (APPV), Norwegian rat pestivirus (NrPV) and Rhinolophus affinis bat pestivirus (RaPestV-1). CSFV is commonly detected in wild boars, but despite positive serology, bovine viral diarrhea virus (BVDV) was never detected in this animal species. Thereby, the present communication describes the first detection of BVDV in the lungs of captive boars using RT-PCR and DNA sequencing. Materials, Methods & Results: Forty lung samples from farmed wild boars were collected after slaughter in a commercial abattoir. The organs were crushed separately, centrifuged, and the supernatant was stored for further analysis. The total RNA was isolated using a phenol-based protocol and RT-PCR protocol that amplified 118 bp of 5' untranslated region (5' UTR) was carried out. One out 40 samples resulted positive. The positive sample had partial fragments of 5' UTR and N terminal autoprotease (N-pro) sequenced and analyzed. The strain LV Java/ 2012 presented 99% of identity in 5' UTR and 98% in N-pro region with a BVDV-2 previously reported in bovines in Southern Brazil. In both 5' UTR and Npro phylogenetic analysis, the strain LV Java/ 2015 clustered with BVDV-2 strains and was most closely related to subtype 2b identified in bovines in Southern Brazil grouping in the same terminal node. Discussion: Wild boars are commonly associated to pathogen transmission to domestic animals. This animal species is considered a reservoir of the pestivirus CSFV and important keys in CSFV control and eradication programs in Europe. Despite indirect presence of BVDV was reported in wild boars by serology tests, the direct detection of the viral agent was never reported. The present study showed the presence of BVDV-2 genomic segments obtained by RT-PCR followed by DNA sequencing in captive wild boars. The reported data suggests a possible importance of this animal species in the epidemiology of ruminant pestiviruses which could interfere in control and eradication programs of these important pathogens for cattle worldwide. The strain LV Java/ 2012 was closely related to BVDV-2b and presented highest identity with a strain detected in cattle from Southern Brazil. This data suggests that wild boars and bovines could be sharing this pathogen due the similarity of the strains and that both were reported in the same region. It can lead to need of inclusion of wild swines in BVDV control programs since boars can circulate between different regions and carry this pathogen to different cattle herds. The present study reported the first molecular evidence of BVDV in wild boars in the literature. The data generated herein suggests a possible importance of boars in the epidemiology of ruminant pestiviruses.",BVDV;wild boar;pestivirus;RT-PCR;PESTIVIRUS;PIGS;IDENTIFICATION,"Weber, M. N.;Pino, E. H. M.;Souza, C. K.;Mosena, A. C. S.;Sato, J. P. H.;de Barcellos, Desn;Canal, C. W.",2016,Oct,,0
2226,Evolution of influenza a viruses in wild birds,"The emergence of highly pathogenic (HP) H5 influenza A viruses in Asia and the increase of HP H7 viruses in Europe and the Americas focused greater attention on the ecology of influenza in wild birds. Influenza virus surveillance studies in wild bird populations in the Americas, Europe, and Asia confirmed that wild aquatic birds are the reservoir for all known influenza A viruses. Phylogenetic analysis groups the influenza viruses in wild aquatic birds into two distinct superfamilies-one in the Americas and one in Eurasia. The separation of viruses into American and Eurasian clades implies that transmission of HP H5 into the Americas by wild birds is likely to be a rare event. The rapid evolution of the Eurasian H5NI viruses makes them a continued threat to poultry and humans world-wide.",avian influenza virus;ecology;evolution;H5N1;highly pathogenic avian;influenza;AVIAN INFLUENZA;AQUATIC BIRDS;NORTH-AMERICA;FERAL DUCKS;HEMAGGLUTININ;GENES;RECOMBINATION;PATHOGENICITY;PERSISTENCE;SHOREBIRDS,"Webster, R. G.;Krauss, S.;Hulse-Post, D.;Sturm-Ramirez, K.",2007,Jul,,0
2227,The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract,"BACKGROUND: Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown. RESULTS: To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14 L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se. However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity. CONCLUSIONS: This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations.","Animals;Bacterial Outer Membrane Proteins/ge [Genetics];Bacterial Secretion Systems/ge [Genetics];Bacteriophages;Basal Metabolism/ge [Genetics];Chromosomes, Bacterial;Gastrointestinal Tract/mi [Microbiology];Gene Order;Gene Transfer, Horizontal;Genetic Structures;*Genome, Bacterial;Genomics/mt [Methods];*Genomics;High-Throughput Nucleotide Sequencing;Host-Pathogen Interactions;*Lactobacillus reuteri/ge [Genetics];Lactobacillus reuteri/ip [Isolation & Purification];Lactobacillus reuteri/me [Metabolism];Lactobacillus reuteri/vi [Virology];Multigene Family;Phylogeny;Pseudogenes;Swine;0 (Bacterial Outer Membrane Proteins);0 (Bacterial Secretion Systems)","Wegmann, U.;MacKenzie, D. A.;Zheng, J.;Goesmann, A.;Roos, S.;Swarbreck, D.;Walter, J.;Crossman, L. C.;Juge, N.",2015,Dec 01,,0
2228,Genetic dynamic analysis of the influenza A H5N1 NS1 gene in China,"The direct precursors of the A/Goose/Guangdong/1/1996 (GS/GD) virus lineage and its reassortants have been established geographically and ecologically. To investigate the variation and evolutionary dynamics of H5N1 viruses, whole-genome viral sequences (n = 164) were retrieved from the NCBI Influenza Virus Resource. Here, we present phylogenetic evidence for intrasubtype reassortments among H5N1 viruses isolated from China during 1996-2012. On the basis of phylogenetic analysis, we identified four major groups and further classified the reassortant viruses into three subgroups. Putative mosaic structures were mostly found in the viral ribonucleoprotein (vRNP) complexes and 91.0% (10/11) mosaics were obtained from terrestrial birds. Sequence variability and selection pressure analyses revealed that both surface glycoproteins (HA and NA) and nonstructural protein 1 (NS1) have higher dN/dS ratio and variability than other internal proteins. Furthermore, we detected 47 positively selected sites in genomic segments with the exception of PB2 and M1 genes. Hemagglutinin (HA) and neuraminidase (NA) are considered highly variable due to host immune pressure, however, it is not known what drives NS1 variability. Therefore, we performed a thorough analysis of the genetic variation and selective pressure of NS1 protein (462 available NS1 sequences). We found that most of positively selected sites and variable amino acids were located in the C-terminal effector domain (ED) of NS1. In addition, we focused on the NS1-RNA and NS1-protein interactions that were involved in viral replication mechanisms and host immune response. Transcriptomic analysis of H5N1-infected monkey lungs showed that certain PI3K-related genes were up-regulated.","Animals;Birds/vi [Virology];China;*Genetic Testing;Genome, Viral;Haplorhini/vi [Virology];Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];Humans;*Influenza A Virus, H5N1 Subtype/ge [Genetics];*Influenza in Birds/ge [Genetics];Influenza in Birds/im [Immunology];Influenza in Birds/vi [Virology];*Influenza, Human/ge [Genetics];Influenza, Human/im [Immunology];Influenza, Human/vi [Virology];Lung/im [Immunology];Lung/me [Metabolism];Lung/vi [Virology];Neuraminidase/ge [Genetics];*Phosphatidylinositol 3-Kinases/ge [Genetics];*Phylogeny;*Viral Nonstructural Proteins/ge [Genetics];Virus Replication;0 (Hemagglutinin Glycoproteins, Influenza Virus);0 (INS1 protein, influenza virus);0 (Viral Nonstructural Proteins)","Wei, K.;Chen, Y.;Lin, Y.;Pan, Y.",2014,,,0
2229,Global genetic variation and transmission dynamics of H9N2 avian influenza virus,"The H9N2 influenza viruses are extensively circulating in the poultry population, and variable genotypes can be generated through mutation, recombination and reassortment, which may be better adapted to infect a new host, resist drug treatment or escape immune pressure. The LPAI H9N2 viruses have the potential to evolve towards high levels of virulence in human. Some studies about the regional dispersal were reported, but global dissemination and the drivers of the virus are poorly understood, particularly at the genome scale. Here, we have analysed all eight gene segments of 168 H9N2 genomes sampled randomly aiming to provide a panoramic framework for better understanding the genesis and genetic variation of the viruses, and utilized phylogeography and spatial epidemiology approaches to uncover the effects of the genetic variation, predictors and spread of H9N2 viruses. We found that more frequent reassortment events involve segments PA, NP and NS, and 21 isolates have possible mosaic structure resulting from recombination events. Estimates of gene-specific global dN/dS ratios showed that all genes were subject to purifying selection. However, a total of 13 sites were detected under positive selection by at least two of three methods, which located within segments HA, NA, M2, NS1 and PA. Additionally, we inferred that NA segment has the highest rate of nucleotide substitution, and its tMRCA estimate is the youngest than the remaining segments’ inference. About the spatial history, air transportation of human was identified as the predominant driver of global viral migration using GLM analysis, and economic factors and geographical distance were the modest predictors. Higher migration rates were estimated between five pairs of regions (>0.01) indicating the frequent migration of the viruses between discrete geographical locations. Further, our Markov jumps analysis showed that viral migration is more frequent between Southern China and Northern China, and high rate of gene flow was observed between America and East Asia. Moreover, the America together with Southeast Asia acted as the primary hubs of global transmission, forming the trunk of evolutionary tree. These findings suggested a complex interaction between virus evolution, epidemiology and human behaviour.",article;avian influenza virus;evolutionary rate;genetic reassortment;genetic recombination;genetic variation;geographic distribution;influenza A;Influenza A virus (H9N2);migration;nonhuman;phylogenetic tree;phylogeography;virus transmission,"Wei, K.;Li, Y.",2018,,10.1111/tbed.12733,0
2230,Re-emergence of a genotype VIII virulent Newcastle disease virus isolated from Chinese game fowl after 13 years,"Circulation of dominant genotypes VI and VII of Newcastle disease virus (NDV) is causing significant economic losses to the poultry industry in China. However, reports of Newcastle disease (ND) outbreaks caused by genotype VIII strains of NDV are rare. In this study, a virulent genotype VIII strain of NDV, designated GXGB2011, was isolated from a vaccinated game fowl flock showing clinic signs of infection in Pinxiang county, Guangxi, China. The whole genome of the isolate was completely sequenced and was found to be comprised of 15,192 nucleotides (nt), encoding the six structural proteins in the order of 3′-NP-P-M-F-HN-L-5′. The pattern of cleavage site 112RRQKR↓F117 in the fusion (F) protein and the intracerebral pathogenicity index (ICPI) value of 1.5 showed that the strain GXGB2011 was a velogenic NDV. The results of the challenge experiment with the 5-week-old SPF chickens showed that the strain was highly pathogenic with 100% morbidity and mortality of the challenged birds. Based on the detection of virus in different organs of the infected birds, the highest viral load in caecal tonsils was observed and viral levels in immune organs were higher than those in the respiratory organs. Bayesian reconstruction of complete genomes based on the sequences of 66 NDV reference strains showed that the strain belonged to the genotype VIII of NDV. Phylogenetic analysis showed that the strain was more closely related to the foreign strains gamefowl/U.S.(CA)/24225/98, 1ITTY94060 and IT-147/94 rather than to the first domestic strains of the emergence genotype VIII in Qinghai, China during 1979–1985. In summary, the results of the study demonstrated the re-emergence of a highly pathogenic virulent isolate of genotype VIII of NDV. These results indicate the risk that this genotype VIII of NDV may spread to commercial chickens from game fowl.",animal experiment;article;cecal tonsil;controlled study;genome;genotype;germfree chicken;Guangxi;morbidity;mortality;Newcastle disease;nonhuman;pathogenicity;phylogeny;respiratory system;virus load;nucleotide;structural protein,"Wei, T.;Deng, Q.;Zhai, G.;He, C.;Li, H.;Zhang, Y.;Zeng, R.;Mo, M.;Huang, T.;Wei, P.",2019,,10.1111/tbed.13129,0
2231,Genetic and pathobiologic characterization of pandemic H1N1 2009 influenza viruses from a naturally infected swine herd,"Since its initial identification in Mexico and the United States, concerns have been raised that the novel H1N1 influenza virus might cause a pandemic of severity comparable to that of the 1918 pandemic. In late April 2009, viruses phylogenetically related to pandemic H1N1 influenza virus were isolated from an outbreak on a Canadian pig farm. This outbreak also had epidemiological links to a suspected human case. Experimental infections carried out in pigs using one of the swine isolates from this outbreak and the human isolate A/Mexico/InDRE4487/2009 showed differences in virus recovery from the lower respiratory tract. Virus was consistently isolated from the lungs of pigs infected with A/Mexico/InDRE4487/2009, while only one pig infected with A/swine/Alberta/OTH-33-8/2008 yielded live virus from the lung, despite comparable amounts of viral RNA and antigen in both groups of pigs. Clinical disease resembled other influenza virus infections in swine, albeit with somewhat prolonged virus antigen detection and delayed viral-RNA clearance from the lungs. There was also a noteworthy amount of genotypic variability among the viruses isolated from the pigs on the farm. This, along with the somewhat irregular pathobiological characteristics observed in experimentally infected animals, suggests that although the virus may be of swine origin, significant viral evolution may still be ongoing. Copyright © 2010, American Society for Microbiology. All Rights Reserved.",virus antigen;virus RNA;animal experiment;animal tissue;antigen detection;article;controlled study;disease course;experimental infection;gene sequence;genetic analysis;genetic variability;herd;influenza;Influenza A virus (H1N1);lower respiratory tract infection;lung clearance;mutation rate;natural host;nonhuman;nucleotide sequence;pandemic;pathogenicity;phylogenetic tree;pig farming;priority journal;pig;virus isolation;virus mutation;virus replication,"Weingartl, H. M.;Berhane, Y.;Hisanaga, T.;Neufeld, J.;Kehler, H.;Emburry-Hyatt, C.;Hooper-McGreevy, K.;Kasloff, S.;Dalman, B.;Bystrom, J.;Alexandersen, S.;Li, Y.;Pasick, J.",2010,,10.1128/jvi.02118-09,0
2232,The proposed family Toroviridae: Agents of enteric infections,,viral protein;virus RNA;bovine;classification;diagnosis;digestive system;electron microscopy;electrophoresis;horse;human;newborn;newborn diarrhea;priority journal;RNA virus;Torovirus;virus classification,"Weiss, M.;Horzinek, M. C.",1987,,10.1007/bf01310058,0
2233,Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus,"Coronaviruses are a family of enveloped, single-stranded, positive-strand RNA viruses classified within the Nidovirales order. This coronavirus family consists of pathogens of many animal species and of humans, including the recently isolated severe acute respiratory syndrome coronavirus (SARS-CoV). This review is divided into two main parts; the first concerns the animal coronaviruses and their pathogenesis, with an emphasis on the functions of individual viral genes, and the second discusses the newly described human emerging pathogen, SARS-CoV. The coronavirus part covers (i) a descnption of a group of coronaviruses and the diseases they cause, including the prototype coronavirus, murine hepatitis virus, which is one of the recognized animal models for multiple sclerosis, as well as viruses of veterinary importance that infect the pig, chicken, and cat, and a summary of the human viruses; (ii) a short summary of the replication cycle of coronaviruses in cell culture; (iii) the development and application of reverse genetics systems; and (iv) the roles of individual coronavirus proteins in replication and pathogenesis. The SARS-CoV part covers the pathogenesis of SARS, the developing animal models for infection, and the progress in vaccine development and antiviral therapies. The data gathered on the animal coronaviruses continue to be helpful in understanding SARS-CoV. Copyright © 2005, American Society for Microbiology. All Rights Reserved.",alpha interferon;calpastatin;cytokine;DNA vaccine;envelope protein;esterase;gamma interferon;interleukin 2;interleukin 4;interleukin 5;M protein;membrane protein;messenger RNA;monoclonal antibody;neutralizing antibody;nucleocapsid protein;nucleoside analog;peginterferon alpha2b;proteinase inhibitor;recombinant alpha interferon;ribavirin;RNA directed RNA polymerase;small interfering RNA;tumor necrosis factor;virus hemagglutinin;viral protein;virus RNA;virus spike protein;animal model;cat;Coronavirinae;Mustela putorius furo;human;life cycle;nonhuman;open reading frame;pathogenesis;protein analysis;review;rodent;SARS coronavirus;severe acute respiratory syndrome;vaccination;virion;virus genome;virus infection;virus replication,"Weiss, S. R.;Navas-Martin, S.",2005,,10.1128/mmbr.69.4.635-664.2005,0
2234,Investigation of potential causes for the development of porcine ear necrosis: different study designs--comparable results? German,"During the last years two studies for the investigation of the etiology of porcine ear necrosis were carried out at the Clinic for Swine of the University of Veterinary Medicine Vienna. In study 1, parameters, which are discussed in this context, were collected by veterinary practitioners by completing specially designed questionnaires in farms with symptoms of the porcine ear necrosis syndrome. In study 2, samples of piglets and feed were collected for laboratory analysis of the most important infectious agents as well as mycotoxins. In the present manuscript, the results of both projects were compared. Even if the selection criteria of both studies differed, the affected age class was comparable (5.5 to ten weeks of life in study 1 and six to ten weeks of life in study 2). The herd-specific prevalence of the porcine ear necrosis syndrome varied considerably with percentages between 2 and 10, respectively, to 100%. The evaluation of questionnaires in study 1 showed that 51% of the farms had problems with cannibalism. Particles of plant material, which were frequently seen on the histologic slides of study 2, could have got into the tissue by chewing the ears of the pen mates or cannibalism. Whereas in study 1 the negative effect of parameters as high pig density, suboptimal climate, missing enrichment material and bad quality of feed and water were considered, in study 2 all these factors were checked at sample collection and ruled out as precursor for cannibalism. In both studies bacterial agents proved to be a crucial co-factor for the expansion of the necroses to deeper tissue layers, whereas viral pathogens were classified less important. In both projects it was not possible to estimate the direct impact of infectious agents and mycotoxins as direct trigger of the necroses as well as their participation as co-factors or precursor in the sense of an immunosuppression or previous damage of blood vessels or tissue.","Animals;Ear Diseases/et [Etiology];*Ear Diseases/ve [Veterinary];Ear, External/in [Injuries];*Ear, External/pa [Pathology];Necrosis/ve [Veterinary];*Research Design;Swine;*Swine Diseases/et [Etiology];Syndrome","Weissenbacher-Lang, C.;Voglmayr, T.;Weissenbock, H.;Pyrek, R.;Waxenecker, F.;Hofstetter, U.;Hoelzle, K.;Hoelzle, L. E.;Welle, M.;Bruns, G.;Ritzmann, M.",2013,Sep-Oct,,0
2235,Genomic analysis of some Japanese isolates of Getah virus,"Using the reverse transcription-polymerase chain reaction (RT-PCR) and direct sequencing, capsid protein and non-structural protein 1 (nsP1) regions of Sagiyama virus and eight Getah virus strains were analysed. The viruses were isolated from Malaysia and various areas of Japan over a period of 30 years. Based on the available published sequence data, oligonucleotide primers were designed for RT-PCR and the sequences were determined. Our findings showed that though there were differences in the nucleotide sequences in the nsP1 region, there was 100% amino acid homology. On the other hand, in the capsid region, the nucleotide differences caused a major difference in the amino acid sequence. Therefore, the difference in the capsid region is one of the useful markers in the genetic classification between Sagiyama virus and strains of Getah virus, and might be responsible for the serological difference in complement fixation test. The genomic differences among the Getah virus strains are due to time factor rather than geographical distribution.","Alphavirus/ch [Chemistry];*Alphavirus/ge [Genetics];Alphavirus/ip [Isolation & Purification];Amino Acid Sequence;Animals;Base Sequence;Capsid/ch [Chemistry];*Capsid/ge [Genetics];Culex/vi [Virology];Genetic Markers;*Genetic Variation;Genome, Viral;Horses/vi [Virology];Japan;Molecular Sequence Data;Reverse Transcriptase Polymerase Chain Reaction/ve [Veterinary];Sequence Alignment/ve [Veterinary];Sequence Homology, Amino Acid;Swine/vi [Virology];Viral Nonstructural Proteins/ch [Chemistry];*Viral Nonstructural Proteins/ge [Genetics];0 (Genetic Markers);0 (Viral Nonstructural Proteins)","Wekesa, S. N.;Inoshima, Y.;Murakami, K.;Sentsui, H.",2001,Nov 08,,0
2236,"Purification, morphology and partial characterization of a reovirus-like agent associated with neonatal calf diarrhea","Studies have been conducted on a virus which has recently been implicated as an etiological agent in widely disseminated cases of calf diarrhea. The virus was isolated from feces and intestinal mucosa from experimentally infected calves and from cell cultures which had been inoculated with material from infected calves. The virus was purified by differential centrifugation, nuclease treatment, extraction with Genetron 113 and cesium chloride (CsC1) gradient. Purified and non-purified samples were studied by electron microscopy. Both types of preparations contained unenveloped particles approximately 64 nm in diameter with a hexagonal core region 36 nm in diameter. Subunits of the capsids appeared to be arranged in accordance with cubic synmetry. Essential lipids were not associated with the virus. The buoyant density of purified virus was 1.359. Viral nucleic acid was determined by chemical methods to be ribonucleic acid (RNA). The morphology and some chemical characteristics appear to be similar to those of the reovirus group. However, the exact classification of this virus and its relationship to other groups remains to be established.","Animals;Bacteriological Techniques;Cattle;*Cattle Diseases/mi [Microbiology];Culture Media;DNA, Viral/an [Analysis];Diarrhea/mi [Microbiology];*Diarrhea/ve [Veterinary];Ethers/pd [Pharmacology];Feces/mi [Microbiology];Intestinal Mucosa/mi [Microbiology];Lipids/an [Analysis];Microbial Sensitivity Tests;Microscopy, Electron;RNA Viruses/an [Analysis];RNA Viruses/cl [Classification];RNA Viruses/gd [Growth & Development];*RNA Viruses/ip [Isolation & Purification];RNA, Viral/an [Analysis];*Virus Diseases/ve [Veterinary];0 (Culture Media);0 (DNA, Viral);0 (Ethers);0 (Lipids);0 (RNA, Viral)","Welch, A. B.",1971,Jul,,0
2237,Avipoxviruses: Infection biology and their use as vaccine vectors,"Avipoxviruses (APVs) belong to the Chordopoxvirinae subfamily of the Poxviridae family. APVs are distributed worldwide and cause disease in domestic, pet and wild birds of many species. APVs are transmitted by aerosols and biting insects, particularly mosquitoes and arthropods and are usually named after the bird species from which they were originally isolated. The virus species Fowlpox virus (FWPV) causes disease in poultry and associated mortality is usually low, but in flocks under stress (other diseases, high production) mortality can reach up to 50%. APVs are also major players in viral vaccine vector development for diseases in human and veterinary medicine. Abortive infection in mammalian cells (no production of progeny viruses) and their ability to accommodate multiple gene inserts are some of the characteristics that make APVs promising vaccine vectors. Although abortive infection in mammalian cells conceivably represents a major vaccine bio-safety advantage, molecular mechanisms restricting APVs to certain hosts are not yet fully understood. This review summarizes the current knowledge relating to APVs, including classification, morphogenesis, host-virus interactions, diagnostics and disease, and also highlights the use of APVs as recombinant vaccine vectors. © 2011 Weli and Tryland; licensee BioMed Central Ltd.",avipoxvirus vector;fowlpox virus vaccine;unclassified drug;virus vaccine;virus vector;autopsy;avian influenza virus;Canine distemper virus;classification;drug mechanism;drug safety;electron microscopy;equine influenza;Feline leukemia virus;fowlpox;Fowlpox virus;gene insertion;genetic variability;histopathology;Influenza virus;mammal cell;morphogenesis;mortality;nonhuman;pathogenicity;progeny;Rabies virus;Reticuloendotheliosis virus;review;serology;vaccination;viral genetics;virus cell interaction;virus genome;virus isolation;virus replication;West Nile virus,"Weli, S. C.;Tryland, M.",2011,,10.1186/1743-422x-8-49,0
2238,Types and strains: Their essential role in understanding protein aggregation in neurodegenerative diseases,"Protein misfolding and aggregation is a key event in diseases like Alzheimer's disease (AD) or Parkinson's disease (PD) and is associated with neurodegeneration. Factors that initiate protein misfolding and the role of protein aggregation in the pathophysiology of disease pose major challenges to the neuroscientific community. Interestingly, although the accumulation of the same misfolded protein, e.g., a-synuclein is detectable in all idiopathic PD patients, the disease spectrum covers a variety of different clinical presentations and disease courses. In a more recent attempt this clinical variance is being explained in analogy to prion diseases by different protein aggregate conformations. In prion diseases a relationship between protein aggregate conformation properties and the clinical disease course was shown by relating different prion types to a dementia and an ataxic disease course in Creutzfeldt-Jakob patients. This principle is currently transferred to AD, PD and other neurodegenerative diseases with protein aggregation. However, differences in protein aggregate conformation are frequently addressed as disease strains. The term ""strain"" also derives from prion research and evolved by adopting the virus terminology at a time when transmissible spongiform encephalopathies (TSEs; later called prion diseases) were assumed to be caused by a virus. The problem is that in virus taxonomy the term ""type"" refers to properties of the disease agent itself and the term ""strain"" refers to host associated factors that interact with the disease agent and may moderately modify the clinical disease presentation. Strain factors can be discovered only after transmission and passaging of the agent in a host of a different species. The incorrect use of the terminology confuses disease agent and host factors and hampers the understanding of the pathophysiology of protein aggregate-associated neurodegenerative diseases. In this review article the discoveries are reviewed that explain how the terms ""type"" and ""strain"" emerged for unconventional disease agents. This may help to avoid confusion in the terminology of protein aggregation diseases and to reflect correctly the impact of protein aggregate conformation as well as host factor contribution on different clinical variations of AD, PD and other neurodegenerative diseases.",alpha synuclein;amyloid beta protein;prion protein;tau protein;amino acid sequence;Creutzfeldt Jakob disease;degenerative disease;diffuse Lewy body disease;disease predisposition;disease transmission;heterozygosity;human;inbred mouse strain;incubation time;nerve degeneration;Parkinson disease;prion disease;protein aggregation;protein cleavage;protein conformation;protein function;protein misfolding;protein motif;review;scrapie;virus strain,"Wemheuer, W. M.;Wrede, A.;Schulz-Schaeffer, W. J.",2017,,10.3389/fnagi.2017.00187,0
2239,Comments on duck circovirus (DuCV) genotype definition,"A standardised methodology has been used to define genotypes based on pairwise sequence comparisons (PASC). PASC is a widely accepted method in virus taxonomy, which is based on the histogram of pairwised differences among sequences. Recently, Zhang et al. (2013) concluded that the average p-distance of duck circovirus (DuCV) between genotypes 1 and 2 was 0.170, and subtype distance thresholds were 0.032 in DuCV-1 and 0.018 in DuCV-2, respectively. However, there might be some concerns on the methodology application to define the genotype of DuCV. Taking into account the concerns mentioned above, our authors conducted the PASC analyses of 54 capsid gene (ORF2) and genomic sequences including all the sequences from Zhang et al. (2013). Our results confirmed the existence of two DuCV genotypes (1 and 2) and, we suggest that DuCV ORF2 and genomic distance genotype thresholds were 0.061 and 0.038, respectively. © 2014 Elsevier B.V.",Circovirus;duck circovirus;genotype;letter;nonhuman;open reading frame;priority journal;taxonomy;virus capsid,"Wen, H.;Wu, Y.;Yang, C.;Zhang, X.;Lian, C.;Chen, H.;Han, L.",2014,,10.1016/j.gene.2014.01.004,0
2240,Characterization of porcine and some ruminant pestiviruses by cross-neutralization,"Serologic relationships between 11 pestivirus strains that originated from pigs and five that originated from cattle or sheep were studied by cross-neutralization. Experiments were performed with pig and sheep sera raised against the strains. The results were analysed by a computerized taxonomic procedure. The 16 viruses were classified into four distinct serologic groups. All hog cholera virus (HCV) strains were classified in one group; the other three groups consisted of strains that can infect pigs, but that are identified as bovine viral diarrhoea virus (BVDV) or border disease virus (BDV), or showed a closer relationship to BVDV and BDV than to HCV.","Animals;*Antibodies, Monoclonal/im [Immunology];Border Disease/mi [Microbiology];*Cattle/mi [Microbiology];Cell Line;Classical Swine Fever Virus/cl [Classification];Classical Swine Fever Virus/im [Immunology];Classical Swine Fever Virus/py [Pathogenicity];Neutralization Tests/ve [Veterinary];*Pestivirus/cl [Classification];Pestivirus/im [Immunology];Pestivirus/py [Pathogenicity];*Sheep/mi [Microbiology];*Swine/mi [Microbiology];Virulence;0 (Antibodies, Monoclonal)","Wensvoort, G.;Terpstra, C.;de Kluyver, E. P.",1989,Aug,,0
2241,Detection of hepatitis E virus (HEV) from porcine livers in Southeastern Germany and high sequence homology to human HEV isolates,"Background: Hepatitis E virus (HEV) has been identified as an emerging cause of infectious hepatitis over the last years in developed countries. In contrast to travel associated hepatitis E, zoonotic sources of infection are suspected for autochthonous cases in Europe. Objective: Since pigs are known reservoirs of HEV, we tested porcine livers sold as food in Southeastern Germany for the presence of hepatitis E virus RNA. Study design: We purchased 200 porcine liver samples in 81 butcher shops and grocery stores in Regensburg, Germany. Nucleic acid preparations were tested for the presence of HEV RNA by quantitative real-time PCR (RT-qPCR). HEV isolates from positive samples were characterized by partial sequencing of ORF1 and ORF2 regions in the HEV genome and by phylogenetic analysis. Results: Specimens from eight (4%) of 200 purchased pig livers had detectable HEV RNA amounts. Sequence determination and phylogenetic analysis allowed two novel isolates to be classified as HEV genotype 3, subgenotype 3a (swR437) and 3c (swR269), respectively. Both novel swine HEV isolates showed high sequence homology to isolates obtained from patients with acute HEV infection from the same geographic region. Conclusions: These results support the suggested role of undercooked pig products in food as a source of zoonotic HEV infection for humans. It remains to be clarified if this mechanism of transmission is responsible for the surprisingly high anti-HEV IgG prevalence recently observed in some European countries and the USA. © 2011 Elsevier B.V.",liver extract;virus RNA;adult;animal tissue;article;clinical article;controlled study;diagnostic test accuracy study;female;food intake;Germany;hepatitis E;Hepatitis E virus;Hepevirus;human;male;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;quantitative analysis;real time polymerase chain reaction;sequence homology;pig;virus detection;virus genome;virus isolation,"Wenzel, J. J.;Preiß, J.;Schemmerer, M.;Huber, B.;Plentz, A.;Jilg, W.",2011,,10.1016/j.jcv.2011.06.006,0
2242,Schmallenberg Virus: A Novel Virus of Veterinary Importance,"In late 2011, unspecific clinical symptoms such as fever, diarrhea, and decreased milk production were observed in dairy cattle in the Dutch/German border region. After exclusion of classical endemic and emerging viruses by targeted diagnostic systems, blood samples from acutely diseased cows were subjected to metagenomics analysis. An insect-transmitted orthobunyavirus of the Simbu serogroup was identified as the causative agent and named Schmallenberg virus (SBV). It was one of the first detections of the introduction of a novel virus of veterinary importance to Europe using the new technology of next-generation sequencing. The virus was subsequently isolated from identical samples as used for metagenomics analysis in insect and mammalian cell lines and disease symptoms were reproduced in calves experimentally infected with both, this culture-grown virus and blood samples of diseased cattle. Since its emergence, SBV spread very rapidly throughout the European ruminant population causing mild unspecific disease in adult animals, but also premature birth or stillbirth and severe fetal malformation when naive dams were infected during a critical phase of gestation. In the following years, SBV recirculated regularly to a larger extend; in the 2014 and 2016 vector seasons the virus was again repeatedly detected in the blood of adult ruminants, and in the following winter and spring months, a number of malformed calves and lambs was born. The genome of viruses present in viremic adult animals showed a very high sequence stability; in sequences generated between 2012 and 2016, only a few amino acid substitutions in comparison to the initial SBV isolate could be detected. In contrast, a high sequence variability was identified in the aminoterminal part of the glycoprotein Gc-encoding region of viruses present in the brain of malformed newborns. This mutation hotspot is independent of the region or host species from which the samples originated and is potentially involved in immune evasion mechanisms.",animal;bovine;bunyavirus infection;cattle disease;classification;Europe;genetic variation;genetics;high throughput sequencing;insect;isolation and purification;metagenomics;mutation;Orthobunyavirus;procedures;sheep;sheep disease;veterinary medicine;virology,"Wernike, K.;Beer, M.",2017,,10.1016/bs.aivir.2017.07.001,0
2243,"Schmallenberg Virus Recurrence, Germany, 2014","Schmallenberg virus (SBV) emerged in Germany in 2011, spread rapidly across Europe, and almost disappeared in 2013. However, since late summer 2014, new cases have occurred in adult cattle. Full-genome analysis revealed some amino acid substitution differences from the first SBV sample. Viremia developed in experimentally infected sheep and cattle for 4-6 days.","Animals;Bunyaviridae Infections/ep [Epidemiology];*Bunyaviridae Infections/ve [Veterinary];Bunyaviridae Infections/vi [Virology];Cattle;Cattle Diseases/ep [Epidemiology];*Cattle Diseases/vi [Virology];Female;Germany/ep [Epidemiology];*Orthobunyavirus/ge [Genetics];Recurrence;Sheep, Domestic","Wernike, K.;Hoffmann, B.;Conraths, F. J.;Beer, M.",2015,Jul,,0
2244,Detection and typing of highly pathogenic porcine reproductive and respiratory syndrome virus by multiplex real-time RT-PCR,"Porcine reproductive and respiratory syndrome (PRRS) causes economic losses in the pig industry worldwide, and PRRS viruses (PRRSV) are classified into the two distinct genotypes ""North American (NA, type 2)"" and ""European (EU, type 1)"". In 2006, a highly pathogenic NA strain of PRRSV (HP-PRRSV), characterized by high fever as well as high morbidity and mortality, emerged in swine farms in China. Therefore, a real-time reverse transcription polymerase chain reaction (RT-qPCR) assay specific for HP-PRRSV was developed and combined with type 1- and type 2-specific RT-qPCR systems. Furthermore, an internal control, based on a heterologous RNA, was successfully introduced. This final multiplex PRRSV RT-qPCR, detecting and typing PRRSV, had an analytical sensitivity of less than 200 copies per μl for the type 1-assay and 20 copies per μl for the type 2- and HP assays and a high diagnostic sensitivity. A panel of reference strains and field isolates was reliably detected and samples from an animal trial with a Chinese HP-PRRS strain were used for test validation. The new multiplex PRRSV RT-qPCR system allows for the first time the highly sensitive detection and rapid differentiation of PRRSV of both genotypes as well as the direct detection of HP-PRRSV. © 2012 Wernike et al.",virus RNA;animal experiment;animal model;Arterivirus;article;China;controlled study;genotype;nonhuman;nucleotide sequence;real time polymerase chain reaction;reproducibility;reverse transcription polymerase chain reaction;sensitivity analysis;sensitivity and specificity;pig;validation process;virus detection;virus isolation;virus strain;virus typing,"Wernike, K.;Hoffmann, B.;Dauber, M.;Lange, E.;Schirrmeier, H.;Beer, M.",2012,,10.1371/journal.pone.0038251,0
2245,West Nile Virus: An Update on Recent Developments,"West Nile Virus arrived in North America just over 12 years ago, and since that time, much has been learned about its pathology and transmission of infection and the factors affecting prevalence. Key developments uncovered critical risk factors for severe neurologic disease and revealed successful host defense strategies. At present, only equine vaccines are available; human vaccines remain in various stages of clinical trials. This review discusses the advances in and limitations of the current research related to the emergence and continued dissemination of West Nile virus throughout the Americas. © 2012 Elsevier Inc.",chimerivax;unclassified drug;West Nile vaccine;article;cohort analysis;disease severity;experimental model;horse;host resistance;human;infection risk;information dissemination;medical research;neurologic disease;nonhuman;passive immunization;pathology;prevalence;risk factor;trend study;vaccination;virus classification;virus transmission;West Nile fever;West Nile virus;Western Hemisphere,"Wertheimer, A. M.",2012,,10.1016/j.clinmicnews.2012.04.001,0
2246,Molecular evolution of viral fusion and matrix protein genes and phylogenetic relationships among the Paramyxoviridae,"Phylogenetic relationships among the Paramyxoviridae, a broad family of viruses whose members cause devastating diseases of wildlife, livestock, and humans, were examined with both fusion (F) and matrix (M) protein-coding sequences. Neighbor-joining trees of F and M protein sequences showed that the Paramyxoviridae was divided into the two traditionally recognized subfamilies, the Paramyxovirinae and the Pneumovirinae. Within the Paramyxovirinae, the results also showed groups corresponding to three currently recognized genera: Respirovirus, Morbillivirus, and Rubulavirus. The relationships among the three genera of the Paramyxovirinae were resolved with M protein sequences and there was significant bootstrap support (100%) showing that members of the genus Respirovirus and the genus Morbillivirus were more closely related to each other than to members of the genus Rubulavirus. Both F and M phylogenies showed that Newcastle disease virus (NDV) was more closely related to the genus Rubulavirus than to the other two genera but were consistent with the proposal (B. S. Seal et al., 2000, Virus Res. 66, 1-11) that NDV be classified as a separate genus within the Paramyxovirinae. Both F and M phylogenies were also consistent with the proposal (L. Wang et al., 2000, J. Virol 74, 9972-9979) that Hendra virus be classified as a new genus closely related and basal to the genus Morbillivirus. Rinderpest was most closely related to measles and a more derived virus than to canine distemper virus, phocine distemper virus, or dolphin morbillivirus. © 2001 Academic Press.",,"Westover, K. M.;Hughes, A. L.",2001,,10.1006/mpev.2001.0999,0
2247,Exudative cloacitis in the kakapo (Strigops habroptilus) potentially linked to Escherichia coli infection,"METHODS: Metagenomics using unbiased RNA or DNA sequencing was applied to faecal material from an 11-year-old female kakapo with exudative cloacitis, and a pool of eight birds (male and female aged 1-20 years) with no current signs or history of the disease. Faecal material from the diseased bird was collected pre- and post-treatment. For RNA sequencing, extracted RNA/DNA was subject to DNase, and the remaining RNA reverse transcribed to cDNA and subject to multiple displacement amplification prior to sequencing. RESULTS: No significant alignment to any known avian virus sequence was obtained from any faecal samples. However significant BLAST alignments to five bacteriophages known to infect enterobacteria were obtained. Strong evidence was obtained for the presence of the bacteriophage Escherichia phage TL-2011b, a bacteriophage known to occur in Escherichia coli causing outbreaks of foodborne disease in humans, in the sample from the diseased bird, but not the non-diseased pool. Differences in E. coli community structure between the diseased bird and the non-diseased pool were also apparent. CONCLUSIONS: Escherichia coli infection of human origin is suggested as a possible cause of exudative cloacitis, although confirmatory work is required to test this hypothesis. AIM: To investigate the initiating causes of cloacitis (inflammation of the cloaca) in kakapo (Strigops habroptilus).",animal;bird disease;case report;cloaca;Escherichia coli infection;female;microbiology;parrot;pathology;veterinary medicine,"White, D. J.;Hall, R. J.;Jakob-Hoff, R.;Wang, J.;Jackson, B.;Tompkins, D. M.",2015,,10.1080/00480169.2014.960905,0
2248,"Discovery and complete genome sequence of a novel circovirus-like virus in the endangered rowi kiwi, Apteryx rowi","Circoviruses are circular, non-enveloped, single-stranded DNA viruses around 2000 nucleotides (nt) in length and include the pathogenic species, Porcine circovirus 1 and Beak and feather disease virus, capable of causing significant morbidity and mortality. This group of viruses may be robust to degradation by external environments, and avian circoviruses are known to move between closely related hosts. Using a de novo metagenomic approach, followed by confirmatory PCR, we identify for the first time a circular Rep-encoding single-stranded (CRESS) DNA virus in New Zealand kiwi, Apteryx spp., derived from faecal matter of the rowi kiwi (A. rowi) showing signs of verminous dermatitis. The entire 2085 nt genome was cloned and sequenced and contains both capsid and replicase genes, as well as a conserved 9 nt motif. Phylogenetic analyses place it within Circoviridae, adjacent to other environmental CRESS-DNA viruses, and most closely related to badger circovirus-like virus (Meles meles circovirus-like virus). As the rowi is the most critically endangered kiwi, it is vital to understand the role of rowi kiwi circovirus-like virus as a possible pathogen and also any potential cross-species transmission.",Apteryx rowi;article;bird;Circoviridae;circovirus like virus;controlled study;gene sequence;genome analysis;next generation sequencing;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;priority journal;replicase gene;virus capsid;virus gene;virus genome;virus identification;virus replication;virus transmission,"White, D. J.;Hall, R. J.;Wang, J.;Moore, N. E.;Park, D.;McInnes, K.;Gartrell, B. D.;Tompkins, D. M.",2016,,10.1007/s11262-016-1342-x,0
2249,Serologic evidence of exposure to influenza D virus among persons with occupational contact with cattle,"Background: Influenza D virus (IDV), a novel influenza virus with proposed classification: family Orthomyxoviridae, genus Influenzavirus D, species Influenza D virus, has been associated with influenza-like illness in cattle and swine. More recently, anti-IDV antibodies have also been detected in small ruminants. A seroprevalence of approximately 1.3% has been estimated for the general human population. Objectives: To gain insights on the zoonotic potential of IDV to human adults with occupational exposure to cattle in north central Florida. Study: A cross-sectional serological study was performed on human serum samples from 35 cattle-exposed and 11 non-cattle-exposed adults to screen for IDV antibodies using hemagglutination inhibition (HI) and microneutralization (MN) assays. Results: A seroprevalence of 91% was detected via HI assay, and 97% by MN assay among individuals working with cattle in Florida. Among non-cattle-exposed individuals, seropositivity determined via MN assay (only) was lower (18%). Conclusions: IDV poses a zoonotic risk to cattle-exposed workers, based on detection of high seroprevalence (94-97%). Whereas it is still unknown whether IDV causes disease in humans, our studies indicate that the virus may be an emerging pathogen among cattle-workers.",virus antibody;adult;aged;antibody screening;article;blood sampling;calf (bovine);clinical article;controlled clinical trial;controlled study;cross-sectional study;female;Florida;hemagglutination inhibition;human;Human parainfluenza virus 1;influenza;influenza d;male;nonhuman;occupational exposure;pig;priority journal;serology;seroprevalence,"White, S. K.;Ma, W.;McDaniel, C. J.;Gray, G. C.;Lednicky, J. A.",2016,,10.1016/j.jcv.2016.05.017,0
2250,Characterization of Unknown Orthobunya-Like Viruses from India,"Next-generation sequencing (NGS) of agents causing idiopathic human diseases has been crucial in the identification of novel viruses. This study describes the isolation and characterization of two novel orthobunyaviruses obtained from a jungle myna and a paddy bird from Karnataka State, India. Using an NGS approach, these isolates were classified as Cat Que and Balagodu viruses belonging to the Manzanilla clade of the Simbu serogroup. Closely related viruses in the Manzanilla clade have been isolated from mosquitos, humans, birds, and pigs across a wide geographic region. Since Orthobunyaviruses exhibit high reassortment frequency and can cause acute, self-limiting febrile illness, these data suggest that human and livestock infections of the Oya/Cat Que/Manzanilla virus may be more widespread and/or under-reported than anticipated. It therefore becomes imperative to identify novel and unknown viruses in order to understand their role in human and animal pathogenesis. The current study is a step forward in this regard and would act as a prototype method for isolation, identification and detection of several other emerging viruses.","Animals;*Bunyaviridae Infections/vi [Virology];Chick Embryo;*Genome, Viral;High-Throughput Nucleotide Sequencing;Humans;India;Mice;*Orthobunyavirus/cl [Classification];*Orthobunyavirus/ge [Genetics];Orthobunyavirus/ip [Isolation & Purification];Passeriformes/vi [Virology];Phylogeny;*RNA, Viral;Serogroup;Simbu virus/ge [Genetics];Swine/vi [Virology];0 (RNA, Viral)","Whitmer, S. L. M.;Yadav, P. D.;Sarkale, P.;Chaubal, G. Y.;Francis, A.;Klena, J.;Nichol, S. T.;Stroher, U.;Mourya, D. T.",2018,08 24,,0
2251,"Prevalence of Antibodies to Hepatitis E Virus among Apparently Healthy Humans and Pigs in Bali, Indonesia: Identification of A Pig Infected with A Genotype 4 Hepatitis E Virus","In Indonesia where hepatitis E virus (HEV) is believed to be highly endemic, only three outbreaks of HEV transmission have been documented to date in restricted areas (West Kalimantan and East Java). A total of 1,115 serum samples collected from apparently healthy individuals in Bali, Lombok, and Surabaya in Indonesia in 1996 where epidemic HEV transmissions have never been reported, were tested for IgG class antibodies to HEV (anti-HEV). In Bali, anti-HEV was detected in 20% (54/276) of the tested population, in remarkable contrast with 4% (17/446) in Lombok and 0.5% (2/393) in Surabaya. On the other hand, antibodies to hepatitis A virus were highly prevalent in all three regions (95% in Bali, 90% in Lombok, and 89% in Surabaya). Although the majority of the population in Indonesia is Moslem, Balinese people are mostly Hindu and have a habit of consuming pork. Therefore, serum samples were obtained from the 99 farm pigs in Bali and tested for anti-HEV and HEV RNA. The sera from 71 pigs (72%) were positive for anti-HEV and a 2-month-old pig had detectable HEV RNA. The swine HEV isolate recovered from the viremic pig was named SB66-Bali. The SB66-Bali isolate was most closely related to the genotype 4 isolates from China, India, Japan, and Taiwan, but shared only 82.6-90.0% identity in the common 241-412 nucleotides within open reading frame 2 (ORF2). These results indicate that a presumably indigenous HEV strain(s) is circulating in Bali, Indonesia and that HEV infection may occur via zoonosis even in developing countries. © 2004 Wiley-Liss, Inc.",hepatitis A antibody;hepatitis E antibody;immunoglobulin G;unclassified drug;virus antibody;adolescent;adult;article;China;developing country;epidemic;female;food intake;genotype;geographic distribution;hepatitis E;Hepatitis E virus;Hepatitis E virus 4;Hepatitis E virus SB66 Bali;human;Indonesia;Japan;male;meat;nonhuman;normal human;nucleotide sequence;open reading frame;phylogeny;religion;sequence homology;seroprevalence;species endemicity;pig;swine disease;Taiwan;unindexed sequence;virus isolation;virus strain;virus transmission;zoonosis,"Wibawa, I. D. N.;Muljono, D. H.;Mulyanto;Suryadarma, I. G. A.;Tsuda, F.;Takahashi, M.;Nishizawa, T.;Okamoto, H.",2004,,10.1002/jmv.20059,0
2252,Matrix gene of influenza A viruses isolated from wild aquatic birds: Ecology and emergence of influenza A viruses,"Wild aquatic birds are the primary reservoir of influenza A viuses, but little is known about the viruses' gene pool in wild birds. Therefore, we investigated the ecology and emergence of influenza viruses by conducting phylogenetic analysis of 70 matrix (M) genes of influenza viruses isolated from shorebirds and gulls in the Delaware Bay region and from ducks in Alberta, Canada, during > 18 years of surveillance. In our analysis, we included 61 published M genes of isolates from various hosts. We showed that M genes of Canadian duck viruses and those of shorebird and gull viruses in the Delaware Bay shared ancestors with the M genes of North American poultry viruses. We found that North American and Eurasian avian-like lineages are divided into sublineages, indicating that multiple branches of virus evolution may be maintained in wild aquatic birds. The presence of non-H13 gull viruses in the gull-like lineage and of H13 gull viruses in other avian lineages suggested that gulls' M genes do not preferentially associate with the H13 subtype or segregate into a distinct lineage. Some North American avian influenza viruses contained M genes closely related to those of Eurasian avian viruses. Therefore, there may be interregional mixing of the two clades. Reassortment of shorebird M and HA genes was evident, but there was no correlation among the HA or NA subtype, M gene sequence, and isolation time. Overall, these results support the hypothesis that influenza viruses in wild waterfowl contain distinguishable lineages of M genes.",aquatic environment;article;bird;Canada;cell line;duck;gene isolation;gene sequence;genetic line;hypothesis;Influenza A virus;nonhuman;nucleotide sequence;phylogeny;poultry;priority journal;shorebird;United States;virus gene;virus isolation;wildlife,"Widjaja, L.;Krauss, S. L.;Webby, R. J.;Xie, T.;Webster, R. G.",2004,,10.1128/jvi.78.16.8771-8779.2004,0
2253,A new emerging genotype subgroup within PCV-2b dominates the PMWS epizooty in Switzerland,"Postweaning multisystemic wasting syndrome (PMWS) is among the most important emerging pig diseases worldwide. Initially, the insidious nature of the disease made it difficult to pinpoint the pathogen. The presence of porcine circovirus type 2 (PCV2) in all PMWS diseased animals led to its acceptance, possibly together with an unknown factor, as the causative agent for PMWS. Also, presence of PCV2 in healthy individuals did not facilitate the understanding of the disease. Phylogenetic classification separates PCV2 viruses into at least two major groups. With the aid of a signature motif, a short amino acid motif encoded within the capsid protein, the viruses are determined as belonging to PCV-2a or PCV-2b. Recently, this classification received more attention, as it seemed to define PCV-2b to be more virulent. This simplification, however, could not be confirmed experimentally. Hence, we investigated whether virus genetic shift was an initiator for the PMWS epizooty in Switzerland. Piglet lymphoid tissues from 1973 to 2005 were investigated by histology, immunohistochemistry (IHC) and PCR. For genotype classification, a sequence amplificate of 137 bp was used encompassing the signature motif. The onset of Swiss PMWS epizooty exhibited a marked shift in PMWS diseased and subclinically infected piglets to PCV-2b and specifically to one genotype subgroup. Complementary to these observations, healthy piglets also defined by IHC as negative are positive in the PCR reaction and are void of any PCV-2b virus during epizooty. Consequently, our data support PCV2 genome plasticity as a major contributing factor for PMWS disease manifestation. © 2008 Elsevier B.V. All rights reserved.",animal experiment;animal tissue;article;Circoviridae;Circoviridae 2;controlled study;epizootiology;gene sequence;genotype;histopathology;immunohistochemistry;lymphoid tissue;nonhuman;nucleotide sequence;polymerase chain reaction;postweaning multisystemic wasting syndrome;pig;Switzerland;viral genetics,"Wiederkehr, D. D.;Sydler, T.;Buergi, E.;Haessig, M.;Zimmermann, D.;Pospischil, A.;Brugnera, E.;Sidler, X.",2009,,10.1016/j.vetmic.2008.10.028,0
2254,Cowpox virus infection in an 11-year-old girl,"We describe an 11-year-old girl with a cowpox virus infection, who presented with a 14-day-old crusted, ulcerated nodule on the chin/neck and a 6-day-old eroded blister on the left leg. The girl lived in a rural environment, had close contact to several cats from the neighborhood, and had an atopic predisposition. The presence of orthopox virus in the lesion on the left leg was demonstrated by electron microscopy (negative staining, transmission electron microscopy) and virus isolation. Classification as a cowpox virus was determined by polymerase chain reaction (PCR), followed by restriction enzyme digestion of the PCR product.",article;bullous skin disease;case report;cat;child;clinical feature;cowpox;Cowpox virus;electron microscopy;female;human;Orthopoxvirus;polymerase chain reaction;priority journal;school child;skin infection;virus classification;virus isolation;virus pathogenesis,"Wienecke, R.;Wolff, H.;Schaller, M.;Meyer, H.;Plewig, G.",2000,,,0
2255,Molecular detection and characterization of picobirnaviruses in piglets with diarrhea in Thailand,"Picobirnavirus (PBV) is a small, bi-segmented, double-stranded RNA virus. Taxonomically, the genus Picobirnavirus belongs to the Picobirnaviridae family. PBV infects a wide range of hosts and causes opportunistic infections, but its role in diarrheal disease remains unclear. To determine the prevalence and genetic diversity of porcine PBVs in Northern Thailand, 380 fecal samples collected from diarrheic and non-diarrheic piglets, raised in 22 pig farms, were tested for the presence of PBV. Reverse-transcription PCR (RT-PCR) was performed using primer sets specific to the RNA-dependent RNA polymerase (RdRp) gene. PBV was detected in 86 of 265 (32.5%) diarrheic piglets and in 26 of 115 (22.6%) non-diarrheic piglets. All the PBV strains detected in this study belonged to genogroup I and a high proportion of PBV-positive piglets were co-infected with group A rotavirus (RVA) and bocavirus (BoV). Phylogenetic analysis of representative genogroup I strains revealed remarkably high similarity between strains; these formed a monophyletic cluster with 97-100% sequence identity in the RdRp gene. The strains were also closely related to genogroup I PBV Chinese porcine strain. The findings indicate that PBV infection is common in piglets with and without diarrhea in Northern Thailand.",animal;classification;diarrhea;feces;genetics;isolation and purification;phylogeny;physiology;Picobirnavirus;pig;RNA virus infection;swine disease;Thailand;veterinary medicine;virology,"Wilburn, L.;Yodmeeklin, A.;Kochjan, P.;Saikruang, W.;Kumthip, K.;Khamrin, P.;Maneekarn, N.",2017,,10.1007/s00705-016-3190-3,0
2256,Influenza-A viruses in ducks in northwestern Minnesota: Fine scale spatial and temporal variation in prevalence and subtype diversity,"Waterfowl from northwestern Minnesota were sampled by cloacal swabbing for Avian Influenza Virus (AIV) from July - October in 2007 and 2008. AIV was detected in 222 (9.1%) of 2,441 ducks in 2007 and in 438 (17.9%) of 2,452 ducks in 2008. Prevalence of AIV peaked in late summer. We detected 27 AIV subtypes during 2007 and 31 during 2008. Ten hemagglutinin (HA) subtypes were detected each year (i.e., H1, 3-8, and 10-12 during 2007; H1-8, 10 and 11 during 2008). All neuraminidase (NA) subtypes were detected during each year of the study. Subtype diversity varied between years and increased with prevalence into September. Predominant subtypes during 2007 (comprising ≥5% of subtype diversity) included H1N1, H3N6, H3N8, H4N6, H7N3, H10N7, and H11N9. Predominant subtypes during 2008 included H3N6, H3N8, H4N6, H4N8, H6N1, and H10N7. Additionally, within each HA subtype, the same predominant HA/NA subtype combinations were detected each year and included H1N1, H3N8, H4N6, H5N2, H6N1, H7N3, H8N4, H10N7, and H11N9. The H2N3 and H12N5 viruses also predominated within the H2 and H12 subtypes, respectively, but only were detected during a single year (H2 and H12 viruses were not detected during 2007 and 2008, respectively). Mallards were the predominant species sampled (63.7% of the total), and 531 AIV were isolated from this species (80.5% of the total isolates). Mallard data collected during both years adequately described the observed temporal and spatial prevalence from the total sample and also adequately represented subtype diversity. Juvenile mallards also were adequate in describing the temporal and spatial prevalence of AIV as well as subtype diversity.",Influenza virus hemagglutinin;virus sialidase;article;avian influenza virus;cloacal swab;controlled study;duck;waterfowl;genetic variability;geographical variation (species);Influenza A virus;Influenza A virus (H10N7);Influenza virus A H11N9;Influenza A virus (H1N1);Influenza virus A H3N6;Influenza A virus (H3N8);Influenza virus A H4N6;Influenza A virus (H5N2);Influenza virus A H6N1;Influenza A virus (H7N3);Influenza virus A H8N4;juvenile animal;Anas platyrhynchos;microbiological examination;nonhuman;seasonal variation;summer;United States;virus classification;virus detection;virus isolation,"Wilcox, B. R.;Knutsen, G. A.;Berdeen, J.;Goekjian, V.;Poulson, R.;Goyal, S.;Sreevatsan, S.;Cardona, C.;Berghaus, R. D.;Swayne, D. E.;Yabsley, M. J.;Stallknecht, D. E.",2011,,10.1371/journal.pone.0024010,0
2257,Virus–virus interactions and host ecology are associated with RNA virome structure in wild birds,,,"Wille, M.;Eden, J. S.;Shi, M.;Klaassen, M.;Hurt, A. C.",2018,,,0
2258,Virus-virus interactions and host ecology are associated with RNA virome structure in wild birds,"Little is known about the factors that shape the ecology of RNA viruses in nature. Wild birds are an important case in point, as other than influenza A virus, avian samples are rarely tested for viruses, especially in the absence of overt disease. Using bulk RNA-sequencing (""meta-transcriptomics""), we revealed the viral diversity present in Australian wild birds through the lens of the ecological factors that may determine virome structure and abundance. A meta-transcriptomic analysis of four Anseriformes (waterfowl) and Charadriiformes (shorebird) species sampled in temperate and arid Australia revealed the presence of 27 RNA virus genomes, 18 of which represent newly described species. The viruses identified included a previously described gammacoronavirus and influenza A viruses. Additionally, we identified novel virus species from the families Astroviridae, Caliciviridae, Reoviridae, Rhabdoviridae, Picobirnaviridae and Picornaviridae. We noted differences in virome structure that reflected underlying differences in location and influenza A infection status. Red-necked Avocets (Recurvirostra novaehollandiae) from Australia's arid interior possessed the greatest viral diversity and abundance, markedly higher than individuals sampled in temperate Australia. In Ruddy Turnstones (Arenaria interpres) and dabbling ducks (Anas spp.), viral abundance and diversity were higher and more similar in hosts that were positive for influenza A infection compared to those that were negative for this virus, despite samples being collected on the same day and from the same location. This study highlights the extent and diversity of RNA viruses in wild birds and lays the foundation for understanding the factors that determine virome structure in wild populations.",adult;article;Astroviridae;Australia;Caliciviridae;Charadriiformes;controlled study;disease course;ecology;Gammacoronavirus;host pathogen interaction;human;human tissue;Influenza A virus;nonhuman;Picobirnaviridae;Picornaviridae;Reoviridae;Rhabdoviridae;RNA sequence;shorebird;transcriptomics;virus genome;waterfowl,"Wille, M.;Eden, J. S.;Shi, M.;Klaassen, M.;Hurt, A. C.;Holmes, E. C.",2018,,10.1111/mec.14918,0
2259,A divergent hepatitis D-like agent in birds,"Hepatitis delta virus (HDV) is currently only found in humans and is a satellite virus that depends on hepatitis B virus (HBV) envelope proteins for assembly, release, and entry. Using meta-transcriptomics, we identified the genome of a novel HDV-like agent in ducks. Sequence analysis revealed secondary structures that were shared with HDV, including self-complementarity and ribozyme features. The predicted viral protein shares 32% amino acid similarity to the small delta antigen of HDV and comprises a divergent phylogenetic lineage. The discovery of an avian HDV-like agent has important implications for the understanding of the origins of HDV and sub-viral agents.",complementary RNA;ribozyme;acetylation;amino acid sequence;Anas (genus);animal experiment;article;bioinformatics;gene mapping;genetic similarity;genotype;Hepatitis delta virus;hydrophobicity;isoelectric point;methylation;nonhuman;nucleotide sequence;open reading frame;phylogeny;protein processing;protein secondary structure;RNA extraction;RNA sequence;sequence alignment;sequence analysis;transcriptomics;virus genome;virus like agent;waterfowl,"Wille, M.;Netter, H. J.;Littlejohn, M.;Yuen, L.;Shi, M.;Eden, J. S.;Klaassen, M.;Holmes, E. C.;Hurt, A. C.",2018,,10.3390/v10120720,0
2260,Viral Diversity of House Mice in New York City,"The microbiome of wild Mus musculus (house mouse), a globally distributed invasive pest that resides in close contact with humans in urban centers, is largely unexplored. Here, we report analysis of the fecal virome of house mice in residential buildings in New York City, NY. Mice were collected at seven sites in Manhattan, Queens, Brooklyn, and the Bronx over a period of 1 year. Unbiased highthroughput sequencing of feces revealed 36 viruses from 18 families and 21 genera, including at least 6 novel viruses and 3 novel genera. A representative screen of 15 viruses by PCR confirmed the presence of 13 of these viruses in liver. We identified an uneven distribution of diversity, with several viruses being associated with specific locations. Higher mouse weight was associated with an increase in the number of viruses detected per mouse, after adjusting for site, sex, and length. We found neither genetic footprints to known human viral pathogens nor antibodies to lymphocytic choriomeningitis virus. IMPORTANCE Mice carry a wide range of infectious agents with zoonotic potential. Their proximity to humans in the built environment is therefore a concern for public health. Laboratory mice are also the most common experimental model for investigating the pathobiology of infectious diseases. In this survey of mice trapped in multiple locations within New York City over a period of 1 year, we found a diverse collection of viruses that includes some previously not associated with house mice and others that appear to be novel. Although we found no known human pathogens, our findings provide insights into viral ecology and may yield models that have utility for clinical microbiology.",environmental microbiology;microbial ecology;microbial genetics;New;York City;veterinary microbiology;mouse virome;viral diversity;LYMPHOCYTIC CHORIOMENINGITIS VIRUS;MUS-MUSCULUS;BROWN-RATS;BOCAVIRUS;MOUSE;IDENTIFICATION;DOMESTICUS;FAMILY;PIG;ASTROVIRUSES,"Williams, S. H.;Che, X. Y.;Garcia, J. A.;Klena, J. D.;Lee, B.;Muller, D.;Ulrich, W.;Corrigan, R. M.;Nichol, S.;Jain, K.;Lipkin, W. I.",2018,Mar-Apr,,0
2261,Meeting report: 2013 PDA Virus & TSE Safety Forum,"The report provides a summary of the presentations and discussions at the Virus & TSE Safety Forum 2013 organized by the Parenteral Drug Association (PDA) and held in Berlin, Germany, from June 4 to 6, 2013. The conference was accompanied by a workshop, ""Virus Spike Preparations and Virus Removal by Filtration: New Trends and Developments"". The presentations and the discussion at the workshop are summarized in a separate report that will be published in this issue of the journal as well. As with previous conferences of this series, the PDA Virus & TSE Safety Forum 2013 provided again an excellent opportunity to exchange information and opinions between the industry, research organizations, and regulatory bodies. Updates on regulatory considerations related to virus and transmissible spongiform encephalopathy (TSE) safety of biopharmaceuticals were provided by agencies of the European Union (EU), the United States (US), and Singapore. The epidemiology and detection methods of new emerging pathogens like hepatitis E virus and parvovirus (PARV 4) were exemplified, and the risk of contamination of animal-derived raw materials like trypsin was considered in particular. The benefit of using new sequence-based virus detection methods was discussed. Events of bioreactor contaminations in the past drew the attention to root cause investigations and preventive actions, which were illustrated by several examples. Virus clearance data of specific unit operations were provided; the discussion focused on the mechanism of virus clearance and on the strategic concept of viral clearance integration. As in previous years, the virus safety section was followed by a TSE section that covered recent scientific findings that may influence the risk assessment of blood and cell substrates. These included the realization that interspecies transmission of TSE by blood components in sheep is greater than predicted by assays in transgenic mice. Also, the pathogenesis and possibility of productive TSE infection of cell substrates were considered, and cell-based assays that may be suitable for use in TSE clearance studies were discussed. The current report provides an overview about the outcomes of the 2013 PDA Virus & TSE Safety Forum, a unique event in this field. ©PDA, Inc. 2014.",foot and mouth disease vaccine;hepatitis E antibody;immunoglobulin F(ab) fragment;live vaccine;poloxamer;polysorbate 80;prion protein;propofol;Rotavirus vaccine;virus RNA;von Willebrand factor;Anelloviridae;anion exchange chromatography;Astroviridae;BHK cell line;blood donor;blood safety;blood transfusion;Bovine herpesvirus 1;bovine spongiform encephalopathy;cell death;CHO cell line;Circovirus;clinical trial (topic);conference paper;cytopathogenic effect;erythrocyte;follicular dendritic cell;gamma irradiation;genetic transfection;genotype;heat treatment;hepatitis;Hepatitis A virus;Hepatitis B virus;Hepatitis C virus;Hepatitis E virus;Hepatitis G virus;Herpesviridae;high throughput sequencing;human;Human immunodeficiency virus;Human parvovirus B19;immunofluorescence;intravenous drug abuse;leukocyte;metagenomics;nonhuman;Parvoviridae;patient safety;Picornaviridae;plasmapheresis;Polyomavirus;prion disease;Pseudorabies virus;risk assessment;safety;thrombotic thrombocytopenic purpura;ultraviolet C radiation;viral clearance;viral contamination;virus;virus detection;virus genome;virus inactivation;virus load;virus particle;virus spike,"Willkommen, H.;Blümel, J.;Brorson, K.;Chen, D.;Chen, Q.;Gröner, A.;Hubbard, B. R.;Kreil, T. R.;Ruffing, M.;Ruiz, S.;Scott, D.;Silvester, G.",2014,,10.5731/pdajpst.2014.00980,0
2262,"Internet-accessed sexually transmitted infection (e-STI) testing and results service: A randomised, single-blind, controlled trial","Background: Internet-accessed sexually transmitted infection testing (e-STI testing) is increasingly available as an alternative to testing in clinics. Typically this testing modality enables users to order a test kit from a virtual service (via a website or app), collect their own samples, return test samples to a laboratory, and be notified of their results by short message service (SMS) or telephone. e-STI testing is assumed to increase access to testing in comparison with face-to-face services, but the evidence is unclear. We conducted a randomised controlled trial to assess the effectiveness of an e-STI testing and results service (chlamydia, gonorrhoea, HIV, and syphilis) on STI testing uptake and STI cases diagnosed. Methods and findings: The study took place in the London boroughs of Lambeth and Southwark. Between 24 November 2014 and 31 August 2015, we recruited 2,072 participants, aged 16–30 years, who were resident in these boroughs, had at least 1 sexual partner in the last 12 months, stated willingness to take an STI test, and had access to the internet. Those unable to provide consent and unable to read English were excluded. Participants were randomly allocated to receive 1 text message with the web link of an e-STI testing and results service (intervention group) or to receive 1 text message with the web link of a bespoke website listing the locations, contact details, and websites of 7 local sexual health clinics (control group). Participants were free to use any other services or interventions during the study period. The primary outcomes were self-reported STI testing at 6 weeks, verified by patient record checks, and self-reported STI diagnosis at 6 weeks, verified by patient record checks. Secondary outcomes were the proportion of participants prescribed treatment for an STI, time from randomisation to completion of an STI test, and time from randomisation to treatment of an STI. Participants were sent a £10 cash incentive on submission of self-reported data. We completed all follow-up, including patient record checks, by 17 June 2016. Uptake of STI testing was increased in the intervention group at 6 weeks (50.0% versus 26.6%, relative risk [RR] 1.87, 95% CI 1.63 to 2.15, P < 0.001). The proportion of participants diagnosed was 2.8% in the intervention group versus 1.4% in the control group (RR 2.10, 95% CI 0.94 to 4.70, P = 0.079). No evidence of heterogeneity was observed for any of the pre-specified subgroup analyses. The proportion of participants treated was 1.1% in the intervention group versus 0.7% in the control group (RR 1.72, 95% CI 0.71 to 4.16, P = 0.231). Time to test, was shorter in the intervention group compared to the control group (28.8 days versus 36.5 days, P < 0.001, test for difference in restricted mean survival time [RMST]), but no differences were observed for time to treatment (83.2 days versus 83.5 days, P = 0.51, test for difference in RMST). We were unable to recruit the planned 3,000 participants and therefore lacked power for the analyses of STI diagnoses and STI cases treated. Conclusions: The e-STI testing service increased uptake of STI testing for all groups including high-risk groups. The intervention required people to attend clinic for treatment and did not reduce time to treatment. Service innovations to improve treatment rates for those diagnosed online are required and could include e-treatment and postal treatment services. e-STI testing services require long-term monitoring and evaluation. Trial registration: ISRCTN Registry ISRCTN13354298.",virus DNA;adult;article;controlled study;cross-sectional study;female;gene locus;genital herpes;genotype;Herpes simplex virus 2;high throughput sequencing;human;Human immunodeficiency virus infection;major clinical study;male;phylogeny;prevalence;single nucleotide polymorphism,"Wilson, E.;Free, C.;Morris, T. P.;Syred, J.;Ahamed, I.;Menon-Johansson, A. S.;Palmer, M. J.;Barnard, S.;Rezel, E.;Baraitser, P.",2017,,10.1371/journal.pmed.1002479,0
2263,Diagnostic Tools for Bluetongue and Epizootic Hemorrhagic Disease Viruses Applicable to North American Veterinary Diagnosticians Review,"This review provides an overview of current and potential new diagnostic tests for bluetongue (BT) and epizootic hemorrhagic disease (EHD) viruses compiled from international participants of the Orbivirus Gap Analysis Workshop, Diagnostic Group. The emphasis of this review is on diagnostic tools available to North American veterinary diagnosticians. Standard diagnostic tests are readily available for BT/EHD viruses, and there are described tests that are published in the World Organization for Animal Health (OIE) Terrestrial Manual. There is however considerable variation in the diagnostic approach to these viruses. Serological assays are well established, and many laboratories are experienced in running these assays. Numerous nucleic acid amplification assays are also available for BT virus (BTV) and EHD virus (EHDV). Although there is considerable experience with BTV reverse-transcriptase PCR (RT-PCR), there are no standards or comparisons of the protocols used by various state and federal veterinary diagnostic laboratories.","Animals;*Bluetongue/di [Diagnosis];Bluetongue virus/ge [Genetics];Bluetongue virus/im [Immunology];*Bluetongue virus/ip [Isolation & Purification];Genotype;*Genotyping Techniques/ve [Veterinary];Hemorrhagic Disease Virus, Epizootic/ge [Genetics];Hemorrhagic Disease Virus, Epizootic/im [Immunology];*Hemorrhagic Disease Virus, Epizootic/ip [Isolation & Purification];High-Throughput Nucleotide Sequencing/ve [Veterinary];North America;Reoviridae Infections/di [Diagnosis];*Reoviridae Infections/ve [Veterinary];Reverse Transcriptase Polymerase Chain Reaction/ve [Veterinary];Sequence Analysis, DNA/ve [Veterinary];Sheep","Wilson, W. C.;Daniels, P.;Ostlund, E. N.;Johnson, D. E.;Oberst, R. D.;Hairgrove, T. B.;Mediger, J.;McIntosh, M. T.",2015,Jun,,0
2264,Virus risk mitigation for raw materials: A European perspective,,live vaccine;neutralizing antibody;Rotavirus vaccine;trypsin;virus antibody;Adeno associated virus;Bocaparvovirus;Bovine viral diarrhea virus 1;bovine;Circovirus;culture medium;drug manufacture;gamma irradiation;high temperature procedures;human;device material;metagenomics;nonhuman;Norovirus;nucleotide sequence;Parvoviridae;pH;polymerase chain reaction;raw material;Reoviridae;risk reduction;serum;short survey;ultraviolet C radiation;Vesivirus;viral contamination;virus detection;virus inactivation;virus infectivity;virus replication,"Wisher, M.",2013,,,0
2265,Classification of Marek's disease viruses according to pathotype: Philosophy and methodology,"The concept of pathotype in Marek's disease (MD) probably dates from the recognition of a more virulent form of the disease in the late 1950s (Benton & Cover, 1957). Distinctions between MD virus strains were further expanded with the description of the vv pathotype in the early 1980s and of the vv + pathotype in the 1990s. Pathotype designations reflect important biological properties that correlate with the break-through of vaccinal immunity in the field. However, pathotyping methods applied by various laboratories have not been uniform, preventing critical comparison of results. Better uniformity of pathotyping procedures is desirable. The Avian Disease and Oncology Laboratory (ADOL) method is based on induction of lymphoproliferative lesions in vaccinated chickens. This method has been used to pathotype more than 45 isolates and is the basis for the current pathotype classification of MD virus strains. Its limitations include requirements for a specific type of chickens (15 x 7 ab+), large numbers of animals, and a statistical method to compare lesion responses to those of JM/102W and Md5 control strains. Because of these limitations, it has not been and is not likely to be used in other laboratories. Comparability in pathotyping can be improved by the comparison of field isolates with standard prototype strains such as JM/102W, Md5 and 648A (American Type Culture Collection) or their equivalents. Data may be generated by different in vivo procedures that measure tumour induction, neurological disease (both neoplastic and non-neoplastic lesions), or solely non-neoplastic criteria (such as lymphoid organ weights or virus replication). Methods based on neoplastic criteria, especially when generated in MD-immunized chickens, will probably correlate most closely with that of the ADOL method and be most relevant to evolution of MD virus in the field. Based on data from several trials, a modification of the ADOL method that utilizes fewer chickens and can be conducted with commercial specific pathogen free strains is proposed. The modified method is based on ""best fit"" comparisons with prototype strains, and is expected to provide results generally comparable with the original method. A variety of other alternative criteria (see earlier) are also evaluated both for primary pathotyping and as adjuncts to other pathotyping methods. Advantages and disadvantages of alternative methods are presented. © 2005 Houghton Trust Ltd.",Marek disease vaccine;animal;Gallid alphaherpesvirus 2;bird disease;chicken;classification;genetic predisposition;genetics;pathogenicity;review;virology;virulence,"Witter, R. L.;Calnek, B. W.;Buscaglia, C.;Gimeno, I. M.;Schat, K. A.",2005,,10.1080/03079450500059255,0
2266,Equine Parvovirus: Initial isolation and partial characterization,"A viral agent was isolated from the fetal liver of an aborted equine fetus. The isolate hemagglutinated red blood cells from guinea pig, rhesus monkey and rooster. By hemagglutination inhibition tests, the isolate was shown to be antigenically distinct from parvoviruses of bovine and canine origin. Specific hemagglutination inhibiting antibody against the viral isolate was exhibited by 26 of 136 horse sera tested. The isolated virus showed properties compatible with those of an autonomous parvovirus including size, morphology, stability to ether treatment and heating to 56°C, the presence of a 5300 base DNA genome, characteristic protein composition and density (1.405 g/mL). The virus was classified as an equine parovovirus.",virus DNA;classification;fetus;horse;nonhuman;Parvoviridae;priority journal;virus characterization;virus isolation,"Wong, F. C.;Spearman, J. G.;Smolenski, M. A.;Loewen, P. C.",1985,,,0
2267,Application of enteric viruses for fecal pollution source tracking in environmental waters,"Microbial source tracking (MST) tools are used to identify sources of fecal pollution for accurately assessing public health risk and implementing best management practices (BMPs). This review focuses on the potential of enteric viruses for MST applications. Following host infection, enteric viruses replicate and are excreted in high numbers in the hosts' feces and urine. Due to the specificity in host infection, enteric viruses have been considered one of the most accurate library-independent culture-independent MST tools. In an assessment of molecular viral assays based on sensitivity, specificity and the density of the target virus in fecal-impacted samples, human adenovirus and human polyomavirus were found to be the most promising human-specific viral markers. However, more research is needed to identify promising viral markers for livestock because of cross-reactions that were observed among livestock species or the limited number of samples tested for specificity. Other viral indicators of fecal origin, F+ RNA coliphage and pepper mild mottle virus, have also been proposed as potential targets for developing MST markers. Enhancing the utility of enteric viruses for MST applications through next generation sequencing (NGS) and virus concentration technology is discussed in the latter part of this review. The massive sequence databases generated by shotgun and gene-targeted metagenomics enable more efficient and reliable design of MST assays. Finally, recent studies revealed that alternative virus concentration methodologies may be more cost-effective than standard technologies such as 1MDS; however, improvements in the recovery efficiency and consistency are still needed. Overall, developments in metagenomic information combined with efficient concentration methodologies, as well as high host-specificity, make enteric viruses a promising tool in MST applications. © 2012 .",environmental water;river water;sea water;tap water;unclassified drug;virus RNA;water;Astroviridae;coliphage;direct nucleic acid extraction;DNA sequence;enteric virus;extraction;fecal pollution source tracking;feces analysis;filter;gene targeting;gene technology;glass wool filter;hepatitis A;host range;human;Human adenovirus C;membrane filter;metagenomics;nanoceram filter;next generation sequencing;nonhuman;Norovirus;nucleic acid analysis;pepper mild mottle virus;pollution monitoring;polymerase chain reaction;Polyomavirus;priority journal;quantitative analysis;review;risk assessment;Rotavirus;sensitivity and specificity;sequence database;ultracentrifugation;ultrafiltration;urinary excretion;virus cell interaction;virus detection;virus replication;water pollution indicator,"Wong, K.;Fong, T. T.;Bibby, K.;Molina, M.",2012,,10.1016/j.envint.2012.02.009,0
2268,Cloning and sequencing of full-length cDNA of classical swine fever virus LPC strain,"The cDNAs of classical swine fever virus (LPC vaccine strain) were cloned by transcriptase-polymerase chain reaction, and their nucleotide sequences were determined. In this work, we obtained the sequence information of the 786 bases of the 5′-terminal region, 6049 bases of the middle region, and 1648 bases of the 3′-terminal region. Taking our previous results and present data together, the entire genomic sequence of LPC strain was completed (12344 nucleotides in length). The genome of LPC has a large open reading frame that can encode a polypetide of 3897 amino acids, and are flanked by untranslated regions (UTR), 373 bases at the 5′-end and 278 bases at the 3′-end. Phylogenetic analysis based on genomic sequences of several viruses suggested that the LPC strain is closer to Chinese, Riems, HCLV, Alfort/187, Brescia, and Alfort strains in order. After further analysis, we found that an insertion of 13 nucleotides, TTT(C/T)CTTTTTTTT, in the 3′-UTR of LPC, Chinese, and HCLV strains. Immediately downstream to the 13 nucleotides, a unique sequence of LPC consisting of 28 thymidine was observed.",amino acid;complementary DNA;nucleotide;thymidine;virus DNA;3' untranslated region;5' untranslated region;amino acid sequence;article;gene sequence;genetic analysis;molecular cloning;nonhuman;nucleotide sequence;open reading frame;Pestivirus;phylogeny;priority journal;reverse transcription polymerase chain reaction;sequence analysis;viral genetics;virus strain,"Wong, M. L.;Peng, B. Y.;Liu, J. J.;Chang, T. J.",2001,,10.1023/a:1011856608580,0
2269,Neutralizing DNA aptamers against swine influenza H3N2 viruses,"Triple reassortant influenza A viruses (IAVs) of swine, particularly the North American H3N2 subtype, circulate in swine herds and may reassort and result in the emergence of novel zoonotic strains. Current diagnostic tools rely on isolation of the viruses, followed by serotyping by hemagglutination or genome sequencing, both of which can be expensive and time-consuming. Thus, novel subtype-specific ligands and methods are needed for rapid testing and subtyping of IAVs in the field. To address this need, we selected DNA aptamers against the recombinant HA protein from swine IAV H3 cluster IV using systematic evolution of ligands by exponential enrichment (SELEX). Four candidate aptamers (HA68, HA7, HA2a, and HA2b) were identified and characterized. The dissociation constants (Kd) of aptamers HA68, HA7, HA2a, and HA2b against recombinant H3 protein were 7.1, 22.3, 16.0, and 3.7 nM, respectively. The binding site of HA68 to H3 was identified to be between nucleotide residues 8 and 40. All aptamers inhibited H3 hemagglutination. HA68 was highly specific to all four lineages within the North American H3N2 subtype. Further, the other three aptamers specifically identified live viruses belonging to the phylogenetic clusters I, II/III, and IV especially the virus that closely related to the recent H3N2 variant (H3N2v). Aptamer HA68 was also able to bind and detect H3N2v isolated from recent human cases. In conclusion, we provide subtype-specific aptamers against H3N2 IAVs of swine that can now be used in rapid detection and typing protocols for field applications. Copyright © 2013, American Society for Microbiology. All Rights Reserved.",aptamer;DNA aptamer;Influenza virus hemagglutinin;ligand;recombinant Influenza virus H3 hemagglutinin;unclassified drug;virus DNA;article;combinatorial chemistry;controlled study;dissociation constant;human;Influenza A virus (H1N1);Influenza A virus (H3N2);nonhuman;nucleotide binding site;phylogeny;priority journal;strain difference;swine influenza virus;taxonomic rank;virus classification;virus hemagglutination;virus identification;virus isolation;virus strain;virus typing,"Wongphatcharachai, M.;Wang, P.;Enomoto, S.;Webby, R. J.;Gramer, M. R.;Amonsin, A.;Sreevatsan, S.",2013,,10.1128/jcm.02118-12,0
2270,Metagenomic analysis of viromes of dromedary camel fecal samples reveals large number and high diversity of circoviruses and picobirnaviruses,"The recent discovery of Middle East Respiratory Coronavirus and another novel dromedary camel coronavirus UAE-HKU23 in dromedaries has boosted interest in search of novel viruses in dromedaries. In this study, fecal samples of 203 dromedaries in Dubai were pooled and deep sequenced. Among the 7330 assembled viral contigs, 1970 were assigned to mammalian viruses. The largest groups of these contigs matched to Picobirnaviridae, Circoviridae, Picornaviridae, Parvoviridae, Astroviridae and Hepeviridae. Many of these viral families were previously unknown to dromedaries. In addition to the high abundance of contigs from Circoviridae (n=598 with 14 complete genomes) and Picobirnaviridae (n=1236), a high diversity of contigs from these two families was found, with the 14 Circoviridae complete genomes forming at least five clusters and contigs from both genogroup I and genogroup II potentially novel picobirnaviruses. Further studies comparing the incidence of these viral families in healthy and sick dromedaries will reveal their pathogenic potential. (C) 2014 Elsevier Inc. All rights reserved.",Metagenomic analysis;Dromedary camel;Novel virus;RESPIRATORY SYNDROME CORONAVIRUS;CALIFORNIA SEA LIONS;STRANDED-RNA;GENOME;MIDDLE-EAST;GENOGROUP-I;MAMMALIAN VIRUSES;SAUDI-ARABIA;VIRAL;FLORA;PIGS;FECES,"Woo, P. C. Y.;Lau, S. K. P.;Teng, J. L. L.;Tsang, A. K. L.;Joseph, M.;Wong, E. Y. M.;Tang, Y.;Sivakumar, S.;Bai, R.;Wernery, R.;Wernery, U.;Yuen, K. Y.",2014,Dec,,0
2271,High Diversity of Genogroup I Picobirnaviruses in Mammals,"In a molecular epidemiology study using 791 fecal samples collected from different terrestrial and marine mammals in Hong Kong, genogroup I picobirnaviruses (PBVs) were positive by RT-PCR targeting the partial RdRp gene in specimens from five cattle, six monkeys, 17 horses, nine pigs, one rabbit, one dog, and 12 California sea lions, with 11, 9, 23, 17, 1, 1, and 15 sequence types in the positive specimens from the corresponding animals, respectively. Phylogenetic analysis showed that the PBV sequences from each kind of animal were widely distributed in the whole tree with high diversity, sharing 47.4-89.0% nucleotide identities with other genogroup I PBV strains based on the partial RdRp gene. Nine complete segment 1 (viral loads 1.7 x 10(4) to 5.9 x 10(6)/ml) and 15 segment 2 (viral loads 4.1 x 10(3) to 1.3 x 10(6)/ml) of otarine PBVs from fecal samples serially collected from California sea lions were sequenced. In the two phylogenetic trees constructed using ORF2 and ORF3 of segment 1, the nine segment 1 sequences were clustered into four distinct clades (C1-C4). In the tree constructed using RdRp gene of segment 2, the 15 segment 2 sequences were clustered into nine distinct clades (R1-R9). In four sea lions, PBVs were detected in two different years, with the same segment 1 Glade (C3) present in two consecutive years from one sea lion and different clades present in different years from three sea lions. A high diversity of PBVs was observed in a variety of terrestrial and marine mammals. Multiple sequence types with significant differences, representing multiple strains of PBV, were present in the majority of PBV-positive samples from different kinds of animals.",diversity;picobirnaviruses;mammals;genogroup I;sea lion;COMPLETE GENOME SEQUENCE;GENETIC DIVERSITY;FECAL VIROME;WASTE-WATER;VIRUSES;CORONAVIRUS;INFECTION;REVEALS;PIGS;IDENTIFICATION,"Woo, P. C. Y.;Teng, J. L. L.;Bai, R.;Wong, A. Y. P.;Martelli, P.;Hui, S. W.;Tsang, A. K. L.;Lau, C. C. Y.;Ahmed, S. S.;Yip, C. C. Y.;Choi, G. K. Y.;Li, K. S. M.;Lam, C. S. F.;Lau, S. K. P.;Yuen, K. Y.",2016,Nov,,0
2272,Resolving Bovine viral diarrhea virus subtypes from persistently infected U.S. beef calves with complete genome sequence,"Bovine viral diarrhea virus (BVDV) is classified into 2 genotypes, BVDV-1 and BVDV-2, each of which contains distinct subtypes with genetic and antigenic variation. To effectively control BVDV by vaccination, it is important to know which subtypes of the virus are circulating and how their prevalence is changing over time. Accordingly, the purpose of our study was to estimate the current prevalence and diversity of BVDV subtypes from persistently infected (PI) beef calves in the central United States. Phylogenetic analysis of the 5'-UTR (5' untranslated region) for 119 virus strains revealed that a majority (82%) belonged to genotype 1b, and the remaining strains were distributed between genotypes 1a (9%) and 2 (8%); however, BVDV-2 subtypes could not be confidently resolved. Therefore, to better define the variability of U.S. BVDV isolates and further investigate the division of BVDV-2 isolates into subtypes, complete genome sequences were obtained for these isolates as well as representatives of BVDV-1a and -1b. Phylogenetic analyses of the complete coding sequence provided more conclusive genetic classification and revealed that U.S. BVDV-2 isolates belong to at least 3 distinct genetic groups that are statistically supported by both complete and individual coding gene analyses. These results show that a more complex set of BVDV-2 subtypes has been circulating in this region than was previously thought.",5' untranslated region;animal;bovine;bovine viral diarrhea;Bovine viral diarrhea virus 1;Bovine viral diarrhea virus 2;genetics;genotype;isolation and purification;newborn;nucleotide sequence;phylogeny;red meat;virology,"Workman, A. M.;Heaton, M. P.;Harhay, G. P.;Smith, T. P.;Grotelueschen, D. M.;Sjeklocha, D.;Brodersen, B.;Petersen, J. L.;Chitko-McKown, C. G.",2016,,10.1177/1040638716654943,0
2273,Revised and updated nomenclature for highly pathogenic avian influenza A (H5N1) viruses,"The divergence of the hemagglutinin gene of A/goose/Guangdong/1/1996-lineage H5N1 viruses during 2011 and 2012 (807 new sequences collected through December 31, 2012) was analyzed by phylogenetic and p-distance methods to define new clades using the pre-established nomenclature system. Eight new clade designations were recommended based on division of clade 1.1 (Mekong River Delta), 2.1.3.2 (Indonesia), 2.2.2 (India/Bangladesh), 2.2.1.1 (Egypt/Israel), and 2.3.2.1 (Asia). A simplification to the previously defined criteria, which adds a letter rather than number to the right-most digit of fifth-order clades, was proposed to facilitate this and future updates.","Animals;Birds;*Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];*Influenza A virus/cl [Classification];Influenza A virus/ge [Genetics];Influenza A virus/ip [Isolation & Purification];Influenza A virus/py [Pathogenicity];*Influenza in Birds/vi [Virology];Molecular Sequence Data;Phylogeny;Virulence;0 (Hemagglutinin Glycoproteins, Influenza Virus)","World Health Organization/World Organisation for Animal, H. F.;Agriculture Organization, H. N. E. W. G.",2014,May,,0
2274,Genetic characterization of an adapted pandemic 2009 H1N1 influenza virus that reveals improved replication rates in human lung epithelial cells,"The 2009 influenza pandemic originated from a swine-origin H1N1 virus, which, although less pathogenic than anticipated, may acquire additional virulence-associated mutations in the future. To estimate the potential risk, we sequentially passaged the isolate A/Hamburg/04/2009 in A549 human lung epithelial cells. After passage 6, we observed a 100-fold increased replication rate. High-throughput sequencing of viral gene segments identified five dominant mutations, whose contribution to the enhanced growth was analyzed by reverse genetics. The increased replication rate was pinpointed to two mutations within the hemagglutinin (HA) gene segment (HA1 D130E, HA2 I91L), near the receptor binding site and the stem domain. The adapted virus also replicated more efficiently in mice in vivo. Enhanced replication rate correlated with increased fusion pH of the HA protein and a decrease in receptor affinity. Our data might be relevant for surveillance of pre-pandemic strains and development of high titer cell culture strains for vaccine production.",hemagglutinin;amino acid sequence;animal cell;animal experiment;animal model;animal tissue;article;binding site;controlled study;embryo;female;gene mutation;gene segment;gene structure;genetic analysis;genetic variability;HA gene;high throughput sequencing;human;human cell;in vivo study;Influenza A virus (H1N1);lung alveolus epithelium cell;mouse;nonhuman;pH;priority journal;protein structure;receptor affinity;receptor binding;reverse genetics;virogenesis;virus culture;virus gene;virus replication;virus titration,"Wörmann, X.;Lesch, M.;Welke, R. W.;Okonechnikov, K.;Abdurishid, M.;Sieben, C.;Geissner, A.;Brinkmann, V.;Kastner, M.;Karner, A.;Zhu, R.;Hinterdorfer, P.;Anish, C.;Seeberger, P. H.;Herrmann, A.;Meyer, T. F.;Karlas, A.",2016,,10.1016/j.virol.2016.02.002,0
2275,Does the complexity of the rumen microbial ecology preclude methane mitigation?,"Ruminant livestock are responsible for production of a portion of greenhouse gases, particularly methane (61 Tg/yr) which is believed to contribute to global warming and climate change. Methane is an end product of fermentation of plant material by the microbial ecosystem in the rumen. Methanogenesis is undertaken by methanogenic archaea and is a mechanism by which H(2) is removed from fermentation in order to regenerate biochemical co-factors such as NAD+. The microbial ecosystem is very complex and involves thousands of species of bacteria (10(10)-10(11) cells/ml), archaea (10(7)-10(9) cells/ml), protozoa (10(4)-10(6) cells/ml), fungi (10(3)-10(6) cells/ml), and viruses (10(9)-10(10) cells/ml), which interact with the feed, their host and each other. This ecosystem is relatively poorly understood, particularly inter-species interactions and interactions with the host. Less than 15% of the microbial species in the gastrointestinal tract have been cultured and characterised. However, knowledge of this ecosystem is accumulating, particularly with the advent of molecular biology and culture independent technologies. New high throughput sequencing methodologies, such as pyrosequencing, will greatly improve the rate of knowledge acquisition and techniques such as Stable Isotope Probing will enhance our ability to understand species inter-relationships. While we can expect an increase in our knowledge of this complex ecosystem, and an improved ability to predictably lower CH(4) emissions, examples of successful reductions already exist, including use of feeds (e.g., cereal grains) and chemical additives (e.g., 2-bromo-ethane sulfonate, bromochloromethane). Achieving meaningful reductions in CH(4) emissions may be possible with advances in our knowledge of the intricacies of this complex ecosystem. This paper is part of the special issue entitled: Greenhouse Gases in Animal Agriculture Finding a Balance between Food and Emissions, Guest Edited by T.A. McAllister, Section Guest Editors: K.A. Beauchemin, X. Hao, S. McGinn and Editor for Animal Feed Science and Technology, P.H. Robinson. (C) 2011 Elsevier B.V. All rights reserved.",Rumen microbiome;Archaea;Methanogens;Methane;Pyrosequencing;DIRECTED PCR PRIMERS;PRODUCTUS ATCC 35244;RUMINAL METHANOGENESIS;REDUCTIVE ACETOGENESIS;PHYLOGENETIC ANALYSIS;MOLECULAR DIVERSITY;COCONUT OIL;SHEEP;CATTLE;EMISSIONS,"Wright, A. D. G.;Klieve, A. V.",2011,Jun,,0
2276,Molecular characterization of H1N1 influenza A viruses from human cases in North America,"Subtypes of H1N1 influenza virus can be found in humans in North America, while they are also associated with the infection of swine. Characterization of the genotypes of viral strains in human populations is important to understand the source and distribution of viral strains. Genomic and protein sequences of 10 isolates of the 2009 outbreak of influenza A (H1N1) virus in North America were obtained from GenBank database. To characterize the genotypes of these viruses, phylogenetic trees of genes PB2, PB1, PA, HA, NP, NA, NS and M were constructed by Phylip3.67 program and N-Linked glycosylation sites of HA, NA, PB2, NS1 and M2 proteins were analyzed online by NetNGlyc1.0 program. Phylogenetic analysis indicated that these isolates are virtually identical but may be recombinant viruses because their genomic fragments come from different viruses. The isolates also contain a characteristic lowly pathogenic amino acid motif at their HA cleavage sites (IPSIQSRa dagger""GL), and an E residue at position 627 of the PB2 protein which shows its high affinity to humans. The homologous model of M proteins showed that the viruses had obtained the ability of anti-amantadine due to the mutation at the drug-sensitive site, while sequence analysis of NA proteins indicated that the viruses are still susceptible to the neuraminidase inhibitor drug (i.e. oseltamivir and zanamivir) because no mutations have been observed. Our results strongly suggested that the viruses responsible for the 2009 outbreaks of influenza A (H1N1) virus have the ability to cross species barriers to infect human and mammalian animals based on molecular analysis. These findings may further facilitate the therapy and prevention of possible transmission from North America to other countries.",influenza A viruses;H1N1 subtype;molecular characterization;North;America;NEURAMINIDASE INHIBITOR;RECEPTOR-BINDING;SIALIC-ACID;B VIRUS;RESISTANCE;HEMAGGLUTININ;DETERMINANT;AMANTADINE;ZANAMIVIR;PROTEIN,"Wu, B.;Wang, C. M.;Dong, G. Y.;Luo, J.;Zhao, B. H.;He, H. X.",2009,Jul,,0
2277,"Genetic and molecular characterization of H9N2 and H5 avian influenza viruses from live poultry markets in Zhejiang Province, eastern China","Live poultry markets (LPMs) are a key source of reassorted avian influenza viruses (AIVs) because of the density of terrestrial and aquatic poultry and the frequency of AIV infection. H9N2 viruses are prevalent in terrestrial poultry throughout Asia and have been isolated from poultry outbreaks worldwide. They infect both avian and mammalian species and may be significant donors of genetic material to emerging human pathogens. LPMs in Zhejiang Province were surveyed from 2013-2014 for AIVs. Three hundred seventy-four (374) AIV strains were isolated from 3,328 samples. Whole-genome sequencing and phylogenetic analyses were performed. We identified a novel H9N2 virus genotype that had undergone reassortment with gene segments from Qa/HK/G1/97-like, Ck/BJ/1/94-like, and Dk/HK/Y439/97-like viruses. Phylogenetic analyses suggested the H9N2 viruses had undergone reassortments with other AIV subtypes. The results also suggested that two different clades (2.3.2 and 2.3.4.6) of H5 viruses were co-circulating in Zhejiang Province. Given that reassorted H5 AIVs were detected in geese and ducks, it is possible that apparently healthy birds contribute to emerging H5 AIVs. Continued surveillance is required in poultry in eastern China.",animal;China;genetics;genotype;human;Influenza A virus (H9N2);avian influenza;isolation and purification;phylogeny;poultry;virology;virus genome,"Wu, H.;Peng, X.;Peng, X.;Cheng, L.;Lu, X.;Jin, C.;Xie, T.;Yao, H.;Wu, N.",2015,,10.1038/srep17508,0
2278,Specific microRNA library of IFN-t on bovine endometrial epithelial cells,"IFN-t is specifically secreted by the conceptus in ruminants during early pregnancy, and it plays a vital role in the immunological function of pregnancy. However, its mechanism involving microRNA (miRNA) is still not well understood. Deep sequencing was used to explore the specific miRNA library of IFN-t on bovine endometrial epithelial cells (bEECs). The results showed that 574 known bovine miRNAs and 109 novel miRNAs were identified. We found 74 differentially expressed miRNAs, including 30 commonly expressed miRNAs in the experiment. Then, qPCR verification of six selected miRNAs showed that they corresponded with the sequencing data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed significant enrichment of predicted target genes of differentially expressed miRNAs, including influenza A, herpes simplex infection, antigen processing and presentation, viral myocarditis, TNF signaling pathway, graftversus- host disease, and allograft rejection. These results may provide important contributions to the immune response during early pregnancy in ruminants, but further studies are need to verify the proposed cellular/immunological effects and role of specific miRNA as biomarkers in vivo.",biological marker;microRNA;tau interferon;animal cell;antigen presentation;article;bovine;controlled study;endometrium cell;first trimester pregnancy;gene expression regulation;gene library;gene targeting;graft rejection;graft versus host reaction;herpes simplex;high throughput sequencing;immune response;in vivo study;influenza A;MTT assay;nonhuman;ontology;prediction;quantitative analysis;reverse transcription polymerase chain reaction;sequence analysis;signal transduction;virus myocarditis,"Wu, H.;Zhang, T.;Ma, X.;Jiang, K.;Zhao, G.;Qiu, C.;Deng, G.",2017,,10.18632/oncotarget.18470,0
2279,Common RNA replication signals exist among group 2 coronaviruses: Evidence for in vivo recombination between animal and human coronavius molecules,"5′ and 3′ UTR sequences on the coronavirus genome are known to carry cis-acting elements for DI RNA replication and presumably also virus genome replication. 5′ UTR-adjacent coding sequences are also thought to harbor cis-acting elements. Here we have determined the 5′ UTR and adjacent 289-nt sequences, and 3′ UTR sequences, for six group 2 coronaviruses and have compared them to each other and to three previously reported group 2 members. Extensive regions of highly similar UTR sequences were found but small regions of divergence were also found indicating group 2 coronaviruses could be subdivided into those that are bovine coronavirus (BCoV)-like (BCoV, human respiratory coronavirus-OC43, human enteric coronavirus, porcine hemagglutinating encephalomyelitis virus, and equine coronavirus) and those that are murine hepatitis virus (MHV)-like (A59, 2, and JHM strains of MHV, puffinosis virus, and rat sialodacryoadenitis virus). The 3′ UTRs of BCoV and MHV have been previously shown to be interchangeable. Here, a reporter-containing BCoV DI RNA was shown to be replicated by all five BCoV-like helper viruses and by MHV-H2 (a human cell-adapted MHV strain), a representative of the MHV-like subgroup, demonstrating group 2 common 5′ and 3′ replication signaling elements. BCoV DI RNA, furthermore, acquired the leader of HCoV-OC43 by leader switching, demonstrating for the first time in vivo recombination between animal and human coronavirus molecules. These results indicate that common replication signaling elements exist among group 2 coronaviruses despite a two-cluster pattern within the group and imply there could exist a high potential for recombination among group members. © 2003 Elsevier Inc. All rights reserved.",virus RNA;3' untranslated region;5' untranslated region;animal cell;article;controlled study;Coronavirinae;helper virus;hepatitis virus;human;human cell;in vivo study;mouse;nonhuman;nucleotide sequence;priority journal;RNA analysis;RNA replication;RNA sequence;sequence analysis;signal transduction;virus classification;virus recombination;virus strain,"Wu, H. Y.;Guy, J. S.;Yoo, D.;Vlasak, R.;Urbach, E.;Brian, D. A.",2003,,10.1016/s0042-6822(03)00511-7,0
2280,"Effect of Live Poultry Market Interventions on Influenza A(H7N9) Virus, Guangdong, China","Since March 2013, three waves of human infection with avian influenza A(H7N9) virus have been detected in China. To investigate virus transmission within and across epidemic waves, we used surveillance data and whole-genome analysis of viruses sampled in Guangdong during 2013-2015. We observed a geographic shift of human A(H7N9) infections from the second to the third waves. Live poultry market interventions were undertaken in epicenter cities; however, spatial phylogenetic analysis indicated that the third-wave outbreaks in central Guangdong most likely resulted from local virus persistence rather than introduction from elsewhere. Although the number of clinical cases in humans declined by 35% from the second to the third waves, the genetic diversity of third-wave viruses in Guangdong increased. Our results highlight the epidemic risk to a region reporting comparatively few A(H7N9) cases. Moreover, our results suggest that live-poultry market interventions cannot completely halt A(H7N9) virus persistence and dissemination.","Animals;Bayes Theorem;China/ep [Epidemiology];Disease Outbreaks;Genetic Variation;Genotype;Humans;Incidence;*Influenza A Virus, H7N9 Subtype/cl [Classification];*Influenza A Virus, H7N9 Subtype/ge [Genetics];Influenza A Virus, H7N9 Subtype/ip [Isolation & Purification];Influenza, Human/ep [Epidemiology];*Influenza, Human/pc [Prevention & Control];*Influenza, Human/tm [Transmission];Phylogeny;Population Surveillance;*Poultry/vi [Virology];RNA, Viral;Spatio-Temporal Analysis;0 (RNA, Viral)","Wu, J.;Lu, J.;Faria, N. R.;Zeng, X.;Song, Y.;Zou, L.;Yi, L.;Liang, L.;Ni, H.;Kang, M.;Zhang, X.;Huang, G.;Zhong, H.;Bowden, T. A.;Raghwani, J.;He, J.;He, X.;Lin, J.;Koopmans, M.;Pybus, O. G.;Ke, C.",2016,12,,0
2281,"Molecular detection of hepatitis E virus in sheep from southern Xinjiang, China","Hepatitis E virus (HEV) is a causative agent of infectious hepatitis in animals and humans both in developing and developed countries. Here, we collected 500 sheep sera and 75 raw sheep liver samples from a slaughterhouse in the southern part of the Xinjiang region, China, along with 26 sera of butchers from the same slaughterhouse. All serum samples were tested for anti-HEV antibody by enzyme-linked immunosorbent assay. Both serum and liver samples were evaluated for the presence of HEV RNA by nested polymerase chain reaction targeting partial nucleotide sequences of open reading frame 2 (ORF2). The results indicate that sheep seroprevalence was 35.20 % (176/500) and that four of the 75 (5.3 %) sheep livers showed detectable amounts of HEV RNA. The seroprevalence of the butchers was 57.7 % (15/26). The four amplicons shared 97.8–100 % nucleotide sequence identity and had pairwise sequence identities of 81.6–85.3 %, 84.2–85.3 %, 82.1–85.3 % and 84.7–97.9 % with the corresponding regions of genotypes 1, 2, 3 and 4 of HEV, respectively. A phylogenetic tree was constructed based on alignments of an amplified 186-bp ORF2 sequence and corresponding reference strains. The analysis showed that the four sheep strains detected in our study formed a lineage within a genotype 4 cluster that contains hb-3, bjsw1, T1, swCH189 and swCH25, all of which belong to genotype 4, subtype 4d. The results indicated a high level of seroconversion in sheep and suggested that sheep liver may be a source of foodborne HEV infection in humans.",hepatitis E antibody;virus RNA;amplicon;animal tissue;antibody blood level;article;China;enzyme linked immunosorbent assay;Hepatitis E virus;Hepatitis E virus genotype 1;Hepatitis E virus genotype 2;Hepatitis E virus genotype 3;Hepatitis E virus genotype 4;liver;nonhuman;nucleotide sequence;open reading frame;phylogenetic tree;polymerase chain reaction;priority journal;sequence alignment;sequence homology;seroconversion;seroprevalence;sheep;virus detection,"Wu, J.;Si, F.;Jiang, C.;Li, T.;Jin, M.",2015,,10.1007/s11262-015-1194-9,0
2282,High-throughput sequencing of pituitary and hypothalamic microRNA transcriptome associated with high rate of egg production,"Background: MicroRNAs exist widely in viruses, plants and animals. As endogenous small non-coding RNAs, miRNAs regulate a variety of biological processes. Tissue miRNA expression studies have discovered numerous functions for miRNAs in various tissues of chicken, but the regulation of miRNAs in chicken pituitary and hypothalamic development related to high and low egg-laying performance has remained unclear. Results: In this study, using high-throughput sequencing technology, we sequenced two tissues (pituitary and hypothalamus) in 3 high-and 3 low-rate egg production Luhua chickens at the age of 300 days. By comparing low-and high-rate egg production chickens, 46 known miRNAs and 27 novel miRNAs were identified as differentially expressed (P < 0.05). Six differentially expressed known miRNAs, which are expressed in both tissues, were used in RT-qPCR validation and SNP detection. Among them, seven SNPs in two miRNA precursors (gga-miR1684a and gga-miR-1434) were found that might enhance or reduce the production of the mature miRNAs. In addition, 124 and 30 reciprocally expressed miRNA-target pairs were identified by RNA-seq in pituitary and hypothalamic tissues, respectively and randomly selected candidate miRNA and miRNA-target pairs were validated by RT-qPCR in Jiuyuan black fowl. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation illustrated that a large number of egg laying-related pathways were enriched in the high-rate egg production chickens, including ovarian steroidogenesis and steroid hormone biosynthesis. Conclusions: These differentially expressed miRNAs and their predicted target genes, especially identified reciprocally expressed miRNA-target pairs, advance the study of miRNA function and egg production associated miRNA identification. The analysis of the miRNA-related SNPs and their effects provided insights into the effects of SNPs on miRNA biogenesis and function. The data generated in this study will further our understanding of miRNA regulation mechanisms in the chicken egg-laying process.",Luhua chicken;Egg-laying;qRT-PCR;SNPs;Reproduction regulation;DIFFERENTIAL EXPRESSION ANALYSIS;DOWN-REGULATION;BREAST-CANCER;CHICKEN MICRORNAS;TUMOR-GROWTH;GENES;CELLS;IDENTIFICATION;BIOGENESIS;MIRNA,"Wu, N.;Zhu, Q.;Chen, B. L.;Gao, J.;Xu, Z. X.;Li, D. Y.",2017,Mar,,0
2283,Genetic diversity of Newcastle disease viruses isolated from domestic poultry species in Eastern China during 2005-2008,"Seventy-nine Newcastle disease viruses (NDV) isolated from clinical specimens of different poultry species including chickens, pigeons (Columba livia), geese and ostriches in Eastern China during 2005-2008 were characterized biologically and phylogenetically. The results showed genetic diversity of these viruses: three class I viruses and one genotype I and 12 genotype II viruses of class II circulating in chickens were avirulent; four genotype VIb viruses isolated from pigeons were moderately virulent; and two genotype III viruses and 57 genotype VIId viruses were highly virulent. The three class I viruses were further classified as genotypes 2 and 3. The very high F protein sequence identity of one genotype I virus with strain Queensland V4 and 12 genotype II viruses with strain La Sota indicated that these viruses originated from the two vaccine strains. Two genotype III viruses shared greater than 99% sequence identity with the moderately virulent vaccine strain Mukteswar but exhibited significantly higher virulence, suggesting that they evolved from the vaccine virus and that the Mukteswar vaccine should be banned in China. Fifty-seven of the 63 virulent NDVs in this study belonged to genotype VIId, indicating its predominance in Eastern China. Genotype VIId viruses could be further classified into two subgroups. Four of the five NDVs isolated from pigeons belonged to genotype VIb, indicating its host-specific preference. Both the genotype VIb and VIId NDVs showed low amino acid similarity to the vaccine strains currently used in China, implying the urgent need to develop better vaccines against the most prevalent NDVs in China.",animal;bird disease;chicken;China;classification;domestic animal;genetic variability;genetics;goose;isolation and purification;molecular genetics;Newcastle disease;Newcastle disease virus;ostrich;phylogeny;Columbidae;virology,"Wu, S.;Wang, W.;Yao, C.;Wang, X.;Hu, S.;Cao, J.;Wu, Y.;Liu, W.;Liu, X.",2011,,10.1007/s00705-010-0851-5,0
2284,Molecular and antigenic characteristics of newcastle disease virus isolates from domestic ducks in China,"Newcastle disease (ND) is one of the most devastating diseases to the poultry industry. The causative agents of ND are virulent strains of Newcastle disease virus (NDV), which are members of the genus Avulavirus within the family Paramyxoviridae. Waterfowl, such as ducks and geese, are generally considered potential reservoirs of NDV and may show few or no clinical signs when infected with viruses that are obviously virulent in chickens. However, ND outbreaks in domestic waterfowl have been frequently reported in many countries in the past decade. In this study, 18 NDV strains isolated from domestic ducks in southern and eastern China, between 2005 and 2013, were genetically and phylogenetically characterized. The complete genomes of these strains were sequenced, and they exhibited genome sizes of 15,186 nucleotides (nt), 15,192. nt, and 15,198. nt, which follow the ""rule of six"" that is required for the replication of NDV strains. Based on the cleavage site of the F protein and pathogenicity tests in chickens, 17 of our NDV isolates were categorized as lentogenic viruses, and one was characterized as a velogenic virus. Phylogenetic analysis based on the partial sequences of the F gene and the complete genome sequences showed that there are at least four genotypes of NDV circulating in domestic ducks; GD1, AH224, and AH209 belong to genotypes VIId, Ib, and II of class II NDVs, respectively, and the remaining 15 isolates belong to genotype 1b of class I NDVs. Cross-reactive hemagglutination inhibition tests demonstrated that the antigenic relatedness between NDV strains may be associated with their genotypes, rather than their hosts. These results suggest that though those NDV isolates were from duck, they still don't form a phylogenetic group because they came from the same species; however, they may play an important role in promoting the evolution of NDVs.",F protein;nucleotide;unclassified drug;virus antigen;viral protein;AH209 gene;AH224 gene;Anas platyrhynchos;article;chicken;China;controlled study;cross reaction;embryo;F gene;GD1 gene;gene sequence;genome size;genotype;hemagglutination inhibition test;molecular evolution;molecular genetics;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;priority journal;protein cleavage;viral genetics;virus cell interaction;virus characterization;virus gene;virus genome;virus isolation;virus replication;virus strain;virus virulence,"Wu, W.;Liu, H.;Zhang, T.;Han, Z.;Jiang, Y.;Xu, Q.;Shao, Y.;Li, H.;Kong, X.;Chen, H.;Liu, S.",2015,,10.1016/j.meegid.2015.02.016,0
2285,Virulent duck enteritis virus infected DEF cells generate a unique pattern of viral microRNAs and a novel set of host microRNAs,"Background: Duck enteritis virus (DEV) belongs to the family Herpesviridae and is an important epornitic agent that causes economic losses in the waterfowl industry. The Chinese virulent (CHv) and attenuate vaccines (VAC) are two different pathogenic DEV strains. MicroRNAs (miRNAs) are a class of non-coding RNAs that regulate gene expression in viral infection. Nonetheless, there is little information on virulent duck enteritis virus (DEV)-encoded miRNAs. Results: Using high-throughput sequencing, we identified 39 mature viral miRNAs from CHv-infected duck embryo fibroblasts cells. Compared with the reported 33 VAC-encoded miRNAs, only 13 miRNA sequences and 22 ""seed sequences"" of miRNA were identical, and 8 novel viral miRNAs were detected and confirmed by stem-loop RT-qPCR in this study. Using RNAhybrid and PITA software, 38 CHv-encoded miRNAs were predicted to target 41 viral genes and formed a complex regulatory network. Dual luciferase reporter assay (DLRA) confirmed that viral dev-miR-D8-3p can directly target the 3'-UTR of CHv US1 gene (p < 0.05). Gene Ontology analysis on host target genes of viral miRNAs were mainly involved in biological regulation, cellular and metabolic processes. In addition, 598 novel duck-encoded miRNAs were detected in this study. Thirty-eight host miRNAs showed significant differential expression after CHv infection: 13 miRNAs were up-regulated, and 25 miRNAs were down-regulated, which may affect viral replication in the host cell. Conclusions: These data suggested that CHv encoded a different set of microRNAs and formed a unique regulatory network compared with VAC. This is the first report of DEF miRNAs expression profile and an analysis of these miRNAs regulatory mechanisms during DEV infection. These data provide a basis for further exploring miRNA regulatory roles in the pathogenesis of DEV infection and contribute to the understanding of the CHv-host interaction at the miRNA level.",microRNA;microRNA d8 3p;transcriptome;unclassified drug;virus RNA;animal cell;apoptosis;article;controlled study;down regulation;Duck enteritis virus;enteritis;fibroblast culture;gene expression;gene ontology;genetic transfection;herpes virus infection;Herpesviridae;high throughput sequencing;host cell;luciferase assay;nonhuman;real time polymerase chain reaction;reverse transcription polymerase chain reaction;signal transduction;upregulation;virus cell interaction;virus replication,"Wu, X.;Jia, R.;Zhou, J.;Wang, M.;Chen, S.;Liu, M.;Zhu, D.;Zhao, X.;Sun, K.;Yang, Q.;Wu, Y.;Yin, Z.;Chen, X.;Wang, J.;Cheng, A.",2018,,10.1186/s12917-018-1468-2,0
2286,"Peste des Petits Ruminants Viruses Re-emerging in China, 2013-2014","Re-emergence of peste des petits ruminants (PPR) was officially reported in Xinjiang Uygur Autonomous Region in north-western China in November 2013, and then along with the movements of goats and sheep, this disease rapidly spread to other provinces, autonomous regions and municipalities (P/A/M) of China. A total of 256 PPR-affected counties in 22 P/A/M were identified up to September 2014. Phylogenetic analysis revealed that the current circulating strains and Tibet strains isolated previously in 2007, both belonged to lineage IV but in different sub-branches. Nevertheless, compared with the Tibet strains, the current circulating strains shared high degree of genetic homology with those from Pakistan and Tajikistan.",animal;China;communicable disease;genetics;goat;peste des petits ruminants;Peste-des-petits-ruminants virus;phylogeny;sheep;virology,"Wu, X.;Li, L.;Li, J.;Liu, C.;Wang, Q.;Bao, J. Y.;Zou, Y.;Ren, W.;Wang, H.;Zhang, Y.;Lv, Y.;Liu, F.;Wang, S.;Ma, H.;Wang, Z.",2016,,10.1111/tbed.12308,0
2287,A Novel Capillary Electrophoresis-Based High-Throughput Multiplex Polymerase Chain Reaction System for the Simultaneous Detection of Nine Pathogens in Swine,"Here we aimed to develop a capillary electrophoresis-based high-throughput multiplex polymerase chain reaction (PCR) system for the simultaneous detection of nine pathogens in swine. Nine pairs of specific primers and a set of universal primers were designed; the multiplex PCR was established. The specificity and cross-reactivity of this assay were examined, and the detection limit was determined using serial 10-fold dilutions of plasmids containing the target sequences. The assay was further tested using 144 clinical samples. We found that the nine specific amplification peaks were observed, and the assay had a high degree of specificity, without nonspecific amplification. The simultaneous detection limit for the nine viruses reached 10000 copies μL-1 when all of the premixed viral targets were present. Seventy-seven of the clinical samples tested positive for at least one of the viruses; the principal viral infections in the clinical samples were porcine circovirus type 2 and porcine reproductive and respiratory syndrome virus. This approach has much potential for further development of high-throughput detection tools for the diagnosis of diseases in animals.",animal tissue;article;capillary electrophoresis;controlled study;cross reaction;dilution;female;high throughput sequencing;limit of detection;male;multiplex polymerase chain reaction;nonhuman;pig;plasmid;Porcine circovirus 2;Porcine reproductive and respiratory syndrome virus;virus detection;virus isolation;virus strain,"Wu, X. L.;Xiao, L.;Lin, H.;Yang, M.;Chen, S. J.;An, W.;Wang, Y.;Yao, X. P.;Yang, Z. X.;Tang, Z. Z.",2017,,10.1155/2017/7243909,0
2288,The molecular characteristics of avian influenza viruses (H9N2) derived from air samples in live poultry markets,"Objective: To study the molecular characteristics of H9N2-subtype avian influenza viruses (AIVs) isolated from air samples collected in live poultry markets (LPMs) and explore their sequence identities with AIVs that caused human infection. Methods: Weekly surveillance of H9N2-subtype AIVs in the air of LPMs was conducted from 2015 to 2016. H9-positive samples were isolated from chicken embryos. Whole genome sequences of the isolated AIVs were obtained through high-throughput sequencing. Phylogenetic analysis and key loci variations of the sequences were further analyzed. Results: A total of 327 aerosol samples were collected from LPMs. Nine samples were positive for H9-subtype AIVs based on quantitative real-time reverse transcription polymerase chain reaction (qRRT-PCR). According to the whole genome sequence analysis and phylogenetic analysis, except for the A/Environment/Zhongshan/ZS201505/2015 (ZS201505) strain, 8 gene segments of 8 aerosol H9N2 isolates and 2 H9N2 human isolates in 2015 were located in the same clade. Among key loci variations, except for the ZS201505 strain, H9N2-subtype AIVs had no mutations in eight receptor binding sites of hemagglutinin (HA), and stalks of neuraminidase (NA) proteins exhibited a deletion site of three bases. The PA gene of ZS201503 and ZS201602 exhibited an L336M mutation. The N30D and T215A mutations in the M1 gene and amino acid residues L89V in PB2, P42S in NS1 and S31N in M2 were retained in these 9 strains of H9N2 isolates, which could enhance the virus's virulence. Conclusion: Live H9N2 AIVs survived in the aerosol of LPMs in Zhongshan City. The aerosol viruses had a close evolutionary relationship with human epidemic strains, indicating that there might be a risk of AIV transmission from polluted aerosols in LPMs to humans. Mutations in H9N2-subtype AIVs isolated from air samples collected from LPMs suggested their pathogenicity was enhanced to infect humans.",sialidase;air sampling;animal tissue;article;binding site;cladistics;controlled study;embryo;gene locus;genetic variability;high throughput sequencing;Influenza A virus (H9N2);molecular evolution;nonhuman;nucleotide sequence;phylogeny;poultry farming;priority journal;quantitative analysis;real time polymerase chain reaction;virus identification;virus isolation;virus strain;virus virulence;whole genome sequencing,"Wu, Y.;Lin, J.;Yang, S.;Xie, Y.;Wang, M.;Chen, X.;Zhu, Y.;Luo, L.;Shi, W.",2018,,10.1016/j.meegid.2018.01.009,0
2289,Pseudorabies virus infected porcine epithelial cell line generates a diverse set of host microRNAs and a special cluster of viral microRNAs,"Pseudorabies virus (PRV) belongs to Alphaherpesvirinae subfamily that causes huge economic loss in pig industry worldwide. It has been recently demonstrated that many herpesviruses encode microRNAs (miRNAs), which play crucial roles in viral life cycle. However, the knowledge about PRV-encoded miRNAs is still limited. Here, we report a comprehensive analysis of both viral and host miRNA expression profiles in PRV-infected porcine epithelial cell line (PK-15). Deep sequencing data showed that the ~4.6 kb intron of the large latency transcript (LLT) functions as a primary microRNA precursor (pri-miRNA) that encodes a cluster of 11 distinct miRNAs in the PRV genome, and 209 known and 39 novel porcine miRNAs were detected. Viral miRNAs were further confirmed by stem-loop RT-PCR and northern blot analysis. Intriguingly, all of these viral miRNAs exhibited terminal heterogeneity both at the 5' and 3' ends. Seven miRNA genes produced mature miRNAs from both arms and two of the viral miRNA genes showed partially overlapped in their precursor regions. Unexpectedly, a terminal loop-derived small RNA with high abundance and one special miRNA offset RNA (moRNA) were processed from a same viral miRNA precursor. The polymorphisms of viral miRNAs shed light on the complexity of host miRNA-processing machinery and viral miRNA-regulatory mechanism. The swine genes and PRV genes were collected for target prediction of the viral miRNAs, revealing a complex network formed by both host and viral genes. GO enrichment analysis of host target genes suggests that PRV miRNAs are involved in complex cellular pathways including cell death, immune system process, metabolic pathway, indicating that these miRNAs play significant roles in virus-cells interaction of PRV and its hosts. Collectively, these data suggest that PRV infected epithelial cell line generates a diverse set of host miRNAs and a special cluster of viral miRNAs, which might facilitate PRV replication in cells.","Animals;Base Sequence;Cell Line;*Epithelial Cells/me [Metabolism];*Epithelial Cells/vi [Virology];Gene Expression Profiling;Gene Expression Regulation, Viral;Herpesvirus 1, Suid/ge [Genetics];*Herpesvirus 1, Suid/ph [Physiology];High-Throughput Nucleotide Sequencing;Host-Pathogen Interactions/ge [Genetics];*MicroRNAs/ge [Genetics];MicroRNAs/me [Metabolism];Models, Theoretical;Molecular Sequence Data;*Pseudorabies/ge [Genetics];Pseudorabies/pa [Pathology];RNA, Viral/ge [Genetics];Swine;Swine Diseases/ge [Genetics];Swine Diseases/pa [Pathology];0 (MicroRNAs);0 (RNA, Viral)","Wu, Y. Q.;Chen, D. J.;He, H. B.;Chen, D. S.;Chen, L. L.;Chen, H. C.;Liu, Z. F.",2012,,,0
2290,Discovery of diverse rodent and bat pestiviruses with distinct genomic and phylogenetic characteristics in several Chinese provinces,"Bats and rodents are widely distributed worldwide and can be native or intermediate reservoirs of many important zoonotic viruses. Pestiviruses are a group of virus species of the genus Pestivirus under the family Flaviviridae that can infect a wide variety of artiodactylous hosts, including swine and ruminants. Two classic types of pestiviruses, bovine viral diarrhea virus and classical swine fever virus, are important causative agents of mild-to-severe disease in bovine and swine hosts, respectively, and cause tremendous economic losses in these industries. Recent reports revealed that bats and rodents could also act as natural hosts of pestiviruses and an atypical porcine pestivirus, which cause disease in piglets, showed a close genetic relationship with a specific bat pestivirus, RaPestV-1. This study aimed to describe the detection and characterization of novel pestiviruses from bats and rodents in different locations by analyzing the available bat and rodent virome data from throughout China. Two bat pestivirus species and four rodent pestivirus species that are distinct from other known viruses were identified and sequenced. These viruses were identified from two bat species and four rodent species in different Chinese provinces. There were two distinct lineages present in these viruses, that differ from artiodactylous pestivirus. These findings expand our understanding of the genetic diversity of pestiviruses in bats and rodents and suggest the presence of a diverse set of pestiviruses in non-artiodactylous hosts. This study may provide new insight for the prevention of future viral disease outbreaks originating from bats and rodents.",polyprotein;article;bat;Bovine viral diarrhea virus 1;Classical swine fever virus;controlled study;DNA library;genetic variability;genome analysis;genomics;geographic distribution;molecular phylogeny;next generation sequencing;nonhuman;nucleotide sequence;Pestivirus;polymerase chain reaction;prevalence;rodent;sampling;screening;taxonomy;virus characterization;virus detection,"Wu, Z.;Liu, B.;Du, J.;Zhang, J.;Lu, L.;Zhu, G.;Han, Y.;Su, H.;Yang, L.;Zhang, S.;Liu, Q.;Jin, Q.",2018,,10.3389/fmicb.2018.02562,0
2291,Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases,"Studies have demonstrated that ~60%-80% of emerging infectious diseases (EIDs) in humans originated from wild life. Bats are natural reservoirs of a large variety of viruses, including many important zoonotic viruses that cause severe diseases in humans and domestic animals. However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. The purpose of this study was to survey the ecological and biological diversities of viruses residing in these bat species, to investigate the presence of potential bat-borne zoonotic viruses and to evaluate the impacts of these viruses on public health. The data obtained in this study revealed an overview of the viral community present in these bat samples. Many novel bat viruses were reported for the first time and some bat viruses closely related to known human or animal pathogens were identified. This genetic evidence provides new clues in the search for the origin or evolution pattern of certain viruses, such as coronaviruses and noroviruses. These data offer meaningful ecological information for predicting and tracing wildlife-originated EIDs.",animal;bat;biodiversity;China;classification;communicable disease;disease carrier;genetics;human;isolation and purification;phylogeny;public health;transmission;virology;virus;virus infection,"Wu, Z.;Yang, L.;Ren, X.;He, G.;Zhang, J.;Yang, J.;Qian, Z.;Dong, J.;Sun, L.;Zhu, Y.;Du, J.;Yang, F.;Zhang, S.;Jin, Q.",2016,,10.1038/ismej.2015.138,0
2292,Virome Analysis for Identification of Novel Mammalian Viruses in Bat Species from Chinese Provinces,"Bats are natural hosts for a large variety of zoonotic viruses. This study aimed to describe the range of bat viromes, including viruses from mammals, insects, fungi, plants, and phages, in 11 insectivorous bat species (216 bats in total) common in six provinces of China. To analyze viromes, we used sequence-independent PCR amplification and next-generation sequencing technology (Solexa Genome Analyzer II; Illumina). The viromes were identified by sequence similarity comparisons to known viruses. The mammalian viruses included those of the Adenoviridae, Herpesviridae, Papillomaviridae, Retroviridae, Circoviridae, Rhabdoviridae, Astroviridae, Flaviridae, Coronaviridae, Picornaviridae, and Parvovirinae; insect viruses included those of the Baculoviridae, Iflaviridae, Dicistroviridae, Tetraviridae, and Densovirinae; fungal viruses included those of the Chrysoviridae, Hypoviridae, Partitiviridae, and Totiviridae; and phages included those of the Caudovirales, Inoviridae, and Microviridae and unclassified phages. In addition to the viruses and phages associated with the insects, plants, and bacterial flora related to the diet and habitation of bats, we identified the complete or partial genome sequences of 13 novel mammalian viruses. These included herpesviruses, papillomaviruses, a circovirus, a bocavirus, picornaviruses, a pestivirus, and a foamy virus. Pairwise alignments and phylogenetic analyses indicated that these novel viruses showed little genetic similarity with previously reported viruses. This study also revealed a high prevalence and diversity of bat astroviruses and coronaviruses in some provinces. These findings have expanded our understanding of the viromes of bats in China and hinted at the presence of a large variety of unknown mammalian viruses in many common bat species of mainland China.",PAPILLOMAVIRUS TYPE-1;PORCINE CIRCOVIRUS;GENETIC DIVERSITY;MOLECULAR;CHARACTERIZATION;METAGENOMIC ANALYSIS;INSECTIVOROUS BATS;RESERVOIR;HOSTS;SAFFOLD VIRUS;SAMPLES;CHILDREN,"Wu, Z. Q.;Ren, X. W.;Yang, L.;Hu, Y. F.;Yang, J.;He, G. M.;Zhang, J. P.;Dong, J.;Sun, L. L.;Du, J.;Liu, L. G.;Xue, Y.;Wang, J. M.;Yang, F.;Zhang, S. Y.;Jin, Q.",2012,Oct,,0
2293,Exploring the virome of cattle with non-suppurative encephalitis of unknown etiology by metagenomics,"Non-suppurative encephalitis is one of the most frequent pathological diagnosis in cattle with neurological disease, but there is a gap in the knowledge on disease-associated pathogens. In order to identify viruses that are associated with non-suppurative encephalitis in cattle, we used a viral metagenomics approach on a sample set of 16 neurologically-diseased cows. We detected six virus candidates: parainfluenza virus 5 (PIV-5), bovine astrovirus CH13/NeuroS1 (BoAstV-CH13/NeuroS1), bovine polyomavirus 2 (BPyV-2 SF), ovine herpesvirus 2 (OvHV-2), bovine herpesvirus 6 (BHV-6) and a novel bovine betaretrovirus termed BoRV-CH15. In a case-control study using PCR, BoAstV-CH13 (p=0.046), BoPV-2 SF (p=0.005) and BoHV-6 (p=4.3E-05) were statistically associated with the disease. These data expand our knowledge on encephalitis-associated pathogens in cattle and point to the value of NGS in resolving complex infection scenarios in a clinical disease setting.",animal tissue;article;Astroviridae;Betaretrovirus;bovine;bovine astrovirus;bovine betaretrovirus;bovine herpesvirus 6;bovine polyomavirus 2;case control study;controlled study;encephalitis;Herpesviridae;metagenomics;next generation sequencing;nonhuman;nonsuppurativeencephalitis;Ovine herpesvirus 2;Parainfluenza virus 5;polymerase chain reaction;Polyomavirus;priority journal;virus detection;virus identification,"Wüthrich, D.;Boujon, C. L.;Truchet, L.;Selimovic-Hamza, S.;Oevermann, A.;Bouzalas, I. G.;Bruggmann, R.;Seuberlich, T.",2016,,10.1016/j.virol.2016.03.009,1
2294,Equine rhinovirus serotypes 1 and 2: Relationship to each other and to aphthoviruses and cardioviruses,"Equine rhinoviruses (ERVs) are picornaviruses which cause a mild respiratory infection in horses. The illness resembles the common cold brought about by rhinoviruses in humans; however, the presence of a viraemia during ERV-1 infection, the occurrence of persistent infections and the physical properties are all more reminiscent of foot-and-mouth disease virus (FMDV). cDNA cloning and sequencing of the genomes of ERV-1 and ERV-2 between the poly(C) and poly(A) tracts showed that the serotypes are heterogeneous. Nevertheless, the genomic architecture of both serotypes is most similar to that of FMDV. Indeed, a comparison of the derived protein sequences of ERV-1 shows that their identity is greatest to FMDV. In contrast, most ERV-2 proteins are more related to encephalomyocarditis virus (EMCV) proteins than they are to FMDV or ERV-1. These results place ERV-1 alongside FMDV in the aphthovirus genus of the picornavirus family and indicate that this virus may serve as a model system for examining the biology of FMDV.",complementary DNA;viral protein;amino acid sequence;article;Cardiovirus;Encephalomyocarditis virus;Foot and mouth disease virus;molecular cloning;nonhuman;nucleotide sequence;priority journal;Rhinovirus;sequence homology;serotype;virus classification;virus genome,"Wutz, G.;Auer, H.;Nowotny, N.;Grosse, B.;Skern, T.;Kuechler, E.",1996,,,0
2295,Sequence analysis of the human virome in febrile and afebrile children,,,"Wylie, K. M.;Mihindukulasuriya, K. A.;Sodergren, E.",2012,,,0
2296,Virome genomics: a tool for defining the human virome,,,"Wylie, K. M.;Weinstock, G. M.;Storch, G. A.",2013,,,0
2297,Enhanced virome sequencing using targeted sequence capture,,,"Wylie, T. N.;Wylie, K. M.;Herter, B. N.;Storch, G. A.",2015,,,0
2298,Comparative Transcriptomics Highlights the Role of the Activator Protein 1 Transcription Factor in the Host Response to Ebolavirus,"Ebolavirus and Marburgvirus comprise two genera of negative-sense single-stranded RNA viruses that cause severe hemorrhagic fevers in humans. Despite considerable research efforts, the molecular events following Ebola virus (EBOV) infection are poorly understood. With the view of identifying host factors that underpin EBOV pathogenesis, we compared the transcriptomes of EBOV-infected human, pig, and bat kidney cells using a transcriptome sequencing (RNA-seq) approach. Despite a significant difference in viral transcription/replication between the cell lines, all cells responded to EBOV infection through a robust induction of extracellular growth factors. Furthermore, a significant upregulation of activator protein 1 (AP1) transcription factor complex members FOS and JUN was observed in permissive cell lines. Functional studies focusing on human cells showed that EBOV infection induces protein expression, phosphorylation, and nuclear accumulation of JUN and, to a lesser degree, FOS. Using a luciferase-based reporter, we show that EBOV infection induces AP1 transactivation activity within human cells at 48 and 72 h postinfection. Finally, we show that JUN knockdown decreases the expression of EBOV-induced host gene expression. Taken together, our study highlights the role of AP1 in promoting the host gene expression profile that defines EBOV pathogenesis.<b>IMPORTANCE</b> Many questions remain about the molecular events that underpin filovirus pathophysiology. The rational design of new intervention strategies, such as postexposure therapeutics, will be significantly enhanced through an in-depth understanding of these molecular events. We believe that new insights into the molecular pathogenesis of EBOV may be possible by examining the transcriptomic response of taxonomically diverse cell lines (derived from human, pig, and bat). We first identified the responsive pathways using an RNA-seq-based transcriptomics approach. Further functional and computational analysis focusing on human cells highlighted an important role for the AP1 transcription factor in mediating the transcriptional response to EBOV infection. Our study sheds new light on how host transcription factors respond to and promote the transcriptional landscape that follows viral infection.","Animals;Cell Line;Chiroptera;Ebolavirus/py [Pathogenicity];*Gene Expression Profiling;Genes, fos;Genes, jun;*Hemorrhagic Fever, Ebola/vi [Virology];High-Throughput Nucleotide Sequencing;*Host-Pathogen Interactions;Humans;Kidney/cy [Cytology];Kidney/vi [Virology];Phosphorylation;Swine;Transcription Factor AP-1/ge [Genetics];*Transcription Factor AP-1/me [Metabolism];Viral Proteins;Virus Replication;0 (Transcription Factor AP-1);0 (Viral Proteins)","Wynne, J. W.;Todd, S.;Boyd, V.;Tachedjian, M.;Klein, R.;Shiell, B.;Dearnley, M.;McAuley, A. J.;Woon, A. P.;Purcell, A. W.;Marsh, G. A.;Baker, M. L.",2017,12 01,,0
2299,Microbiological safety of the first clinical pig islet xenotransplantation trial in New Zealand,,,"Wynyard, S.;Nathu, D.;Garkavenko, O.",2014,,,0
2300,Molecular phylogenetic analysis of bovine viral diarrhoea virus: A Bayesian approach,"Genetic typing of bovine viral diarrhoea virus (BVDV) is important for precise classification of viruses. Traditionally, inferring BVDV phylogeny has been performed by distance-based method, i.e. neighbor-joining for single genes. In this study, a Bayesian approach was exploited to analyze five genetic regions of BVDV genome (5′ UTR, Npro, E2a, E2b, and NS3) for 68 taxa retrieved from GenBank. The results showed that all taxa in the consensus tree of E2a have been assigned correctly to corresponding groups, i.e. type-2 BVDV, and BVDV-1a, -1b, -1c, -1e, and -1g, supported by a high posterior probability. In contrast, subgroup 1a formed polytomies in the consensus trees of 5′ UTR and NS3. Polytomies also appeared among the subgroup 1b in the consensus trees of Npro and E2b. Analysis of a combined dataset produced an unambiguous, well-supported phylogenetic hypothesis. The topologies found for each genetic region separately and combined were different, but the differences were mainly weakly supported by the data. Combining the data allowed the identification of well-supported clades of strains that correspond to some of the previously defined subgroups. Only a combined approach will allow the confident placement of new strains in the current classification of viruses into genotype and subgenotype. © 2007 Elsevier B.V. All rights reserved.",article;Bovine viral diarrhea virus 1;controlled study;genotype;nonhuman;nucleotide sequence;phylogeny;priority journal;virus genome;virus strain,"Xia, H.;Liu, L.;Wahlberg, N.;Baule, C.;Belák, S.",2007,,10.1016/j.virusres.2007.05.017,0
2301,"Sequence analysis of peste des petits ruminants virus from ibexes in Xinjiang, China","Peste des petits ruminants (PPR) is an infectious disease caused by peste des petits ruminants virus (PPRV). While PPR mainly affects domestic goats and sheep, it also affects wild ungulates such as ibex, blue sheep, and gazelle, although there are few reports regarding PPRV infection in wild animals. Between January 2015 and February 2015, it was found for the first time that wild ibexes died from PPRV infection in Bazhou, Xinjiang, China, where a total of 38 ibexes (including young and adult ibexes) were found to have died abnormally from PPR-related issues. First, we tested for the presence of the F gene of PPRV by RT-PCR. Then, we compared the sequence of the isolated F gene from the ibex strain, termed PPRV Xinjiang/Ibex/2015, with those previously identified from small domestic ruminants from local areas near where the reported isolate was collected as well as those from other regions. The current sequence was phylogenetically classified as a lineage IV virus, and shared a high level of sequence identity (99.7%) with a previously described Xinjiang PPRV isolate.",article;China;gene identification;gene sequence;ibex;nonhuman;Peste-des-petits-ruminants virus;phylogeny;reverse transcription polymerase chain reaction;sequence homology;virus classification;virus gene;virus isolation;virus strain,"Xia, J.;Zheng, X. G.;Adili, G. Z.;Wei, Y. R.;Ma, W. G.;Xue, X. M.;Mi, X. Y.;Yi, Z.;Chen, S. J.;Du, W.;Muhan, M.;Duhaxi, C.;Han, T.;Gudai, B.;Huang, J.",2016,,10.4238/gmr.15027783,0
2302,"Spillover of Newcastle disease viruses from poultry to wild birds in Guangdong province, southern China","Despite intensive vaccination programs in many countries, including China, Newcastle disease has been reported sporadically and is still a significant threat to the poultry industry in China. Newcastle disease virus (NDV) is infectious for at least 250 bird species, but the role of wild birds in virus epidemiology remains largely unknown. Fourteen NDV isolates were obtained from 2040 samples collected from wild birds or the environment in Guangdong province, southern China, from 2013 to 2015. The isolation rate was the highest in the period of wintering and lowest during the periods of spring migration, nesting, and postnesting. A maximum clade credibility phylogenetic analysis revealed that at least four genotypes circulate in southern China: three class II genotypes (II, VI, and IX) and one class I (1b). We also demonstrated that most isolates from wild birds were highly similar to isolates from poultry, and two isolates were linked to viruses from wild birds in northern China. These data suggested that wild birds could disseminate NDV and poultry-derived viruses may spillover to wild birds. Accordingly, vaccine development and poultry management strategies should be considered to prevent future NDV outbreaks, particularly given the strength of the poultry industry in developing countries, such as China.",article;bird;China;controlled study;epidemiology;human;nesting;Newcastle disease virus;nonhuman;overwintering;phylogeny;population migration;poultry;priority journal;real time polymerase chain reaction;RNA extraction;spring;vaccine production;virus isolation;virus transmission;virus virulence,"Xiang, B.;Han, L.;Gao, P.;You, R.;Wang, F.;Xiao, J.;Liao, M.;Kang, Y.;Ren, T.",2017,,10.1016/j.meegid.2017.09.020,0
2303,Cloning and structural analysis of mouse genomic nucleophosmin gene Chinese,"Nucleophosmin (NPM) is an abundant nucleolar phosphoprotein. NPM gene involved chromosomal translocations were found in the patients with anaplastic large cell lymphomas (ALCL), myelodysplastic syndrome (MDS), acute myeloid leukemia (AML) and acute promyelocytic leukemia (APL). To generate NPM gene knockout mice and study its biological function in vivo, we screened the lambda phage genomic library derived from 129S1 mice with mouse NPM cDNA probe. A positive phage clone which contained the full-length NPM genomic DNA was obtained and the insert of 15.3 kb genomic DNA in this clone was sequenced with shotgun method. BLAST analysis showed that the sequence of insert are 99.8% identity to that of NPM gene of C57BL/6 mouse strain. Based on the sequence, bioinformatics analysis on genomic structure of NPM and the transcription factor binding sites in the NPM 5' flanking region were performed.","*5' Flanking Region/ge [Genetics];Amino Acid Sequence;Animals;Bacteriophage lambda/ge [Genetics];Base Sequence;Binding Sites;Cloning, Molecular;*Genomic Library;Humans;Mice;Mice, Inbred C57BL;Mice, Inbred Strains;Mice, Knockout;Molecular Sequence Data;*Nuclear Proteins/ge [Genetics];Rats;Sequence Alignment;Sequence Analysis, DNA;Sequence Homology, Amino Acid;0 (Nuclear Proteins);117896-08-9 (nucleophosmin)","Xiang, Y. G.;Lu, S. Y.;Gu, M. M.;Wang, S. Y.;Ren, S. X.;Fu, G.;Wang, Z. G.",2005,Jun,,0
2304,Characterization of porcine parvovirus type 2 (PPV2) which is highly prevalent in the USA,"A novel porcine parvovirus designated as porcine parvovirus 2 (PPV2) was initially identified in Myanmar in 2001, in China during 2006-2007, and in Hungary in 2012. To investigate the presence and prevalence of PPV2 in the USA, a novel TaqMan® real-time PCR method was developed and used for a PPV2 survey using 483 lung samples, 185 fecal samples and 122 sera collected from pigs on 295 farms in 18 U.S. states. The overall prevalence of PPV2 was 20.7% (100/483) in lung samples and 7.6% (14/185) in fecal samples obtained from pigs of different age groups, and 1.6% (2/122) in sera or thoracic fluids obtained from neonatal pigs. Further genomic sequence comparison demonstrated that the 2011 U.S. PPV2 sequences have nucleotide identities of 95.4-97.7% with the 2006-2007 strains detected in China while the nucleotide identity was 94.7% with the 2001 strain detected in Myanmar, indicating persistent evolution of the virus. Phylogenetic and sequence homology analyses demonstrated a close relationship of PPV2 with members of the proposed genus PARV4-like virus, and the classification of PPV2 into this proposed genus is suggested. © 2012 Elsevier B.V.",nucleotide;animal experiment;animal tissue;article;blood analysis;controlled study;feces analysis;gene sequence;genome;groups by age;lung;newborn;nonhuman;nucleotide sequence;phylogenetic tree;Porcine parvovirus;porcine parvovirus 2;prevalence;real time polymerase chain reaction;sequence homology;United States;virus characterization;virus classification;TaqMan,"Xiao, C. T.;Gerber, P. F.;Giménez-Lirola, L. G.;Halbur, P. G.;Opriessnig, T.",2013,,10.1016/j.vetmic.2012.07.038,0
2305,Molecular evolutionary genetic analysis of emerging parvoviruses identified in pigs,"Parvoviruses infect a wide variety of vertebrates and arthropods and are associated with various clinical manifestations. Due to the advent of new sequence-independent PCR methods and high-throughput sequencing, several novel members of parvoviruses within the subfamily Parvovirinae were recently described. Several of these viruses do not fit in the current classification and others now have confusing or contradictory nomenclature because two or more names were used for similar or identical groups of parvoviruses or identical names were used for distinct virus groups. In this study, recently described vertebrate parvoviruses with emphasis on those identified in pigs were classified through phylogenetic analyses based on the sequences of their complete or near complete genomes, open reading frame (ORF) 1 (non-structural protein, NS1), ORF2 (capsid protein, VP1), and ORF3 (nuclear phosphoprotein, NP1) genes by using Bayesian Markov chain Monte Carlo (MCMC), Maximum Likelihood (ML) and Neighbor-Joining (NJ) methods. Among all available vertebrate parvovirus sequences, eight distinct clades were identified, corresponding to the five well established genera Parvovirus, Erythrovirus, Denpendovirus, Amdovirus and Bocavirus. Moreover, three novel clades were identified and tentatively designated as PARV4-like virus, novel clade 1 and novel clade 2. Parvoviruses in pigs were found to be distributed across four different clades including Parvovirus, Bocavirus, PARV4-like virus and the novel clade 2. All pig parvoviruses identified to date were organized based on the current analysis. The present analysis will assist to clarify the nomenclature of parvoviruses in pigs and facilitate future uniform assignment of names for new parvoviruses within the subfamily Parvovirinae. © 2013 Elsevier B.V.",nonstructural protein 1;protein VP1;Adeno associated virus;Aleutian mink disease virus;article;Bocaparvovirus;cladistics;gene sequence;genetic analysis;genome analysis;Human parvovirus B19;molecular evolution;molecular phylogeny;nonhuman;nonstructural protein 1 gene;nuclear phosphoprotein gene;nucleotide sequence;open reading frame;Parvoviridae;Porcine bocavirus group 1;Porcine bocavirus group 2;Porcine bocavirus group 3;Porcine parvovirus;Porcine parvovirus type 1;Porcine parvovirus type 2;Porcine parvovirus type 3;Porcine parvovirus type 4;Porcine parvovirus type 5;priority journal;pig;unindexed sequence;virus gene;virus identification;VP1 gene,"Xiao, C. T.;Halbur, P. G.;Opriessnig, T.",2013,,10.1016/j.meegid.2013.03.017,0
2306,Identification and classification of endogenous retroviruses in cattle,"The aim of this study was to identify the endogenous retrovirus (ERV) sequences in a bovine genome. We subjected bovine genomic DNA to PCR with degenerate or ovine ERV (OERV) family-specific primers that aimed to amplify the retroviral pro/pol region. Sequence analysis of 113 clones obtained by PCR revealed that 69 were of retroviral origin. On the basis of the OERV classification system, these clones from degenerate PCR could be divided into the β3, γ4, and γ9 families. PCR with OERV family-specific primers revealed an additional ERV that was classified into the bovine endogenous retrovirus (BERV) γ7 family. In conclusion, here we report the results of a genome scale study of the BERV. Our study shows that the ERV family expansion in cattle may be somewhat limited, while more diverse family members of ERVs have been reported from other artiodactyls, such as pigs and sheep. Copyright © 2008, American Society for Microbiology. All Rights Reserved.",virus DNA;animal cell;article;bovine endogenous retrovirus gamma7;cattle disease;gene sequence;molecular cloning;multigene family;nonhuman;nucleotide sequence;polymerase chain reaction;priority journal;pro gene;Retroviridae;sequence analysis;sheep;structural gene;pig;virus classification;virus gene;virus identification;virus typing,"Xiao, R.;Park, K.;Lee, H.;Kim, J.;Park, C.",2008,,10.1128/jvi.01451-07,0
2307,Understanding PRRSV infection in porcine lung based on genome-wide transcriptome response identified by deep sequencing,"Porcine reproductive and respiratory syndrome (PRRS) has been one of the most economically important diseases affecting swine industry worldwide and causes great economic losses each year. PRRS virus (PRRSV) replicates mainly in porcine alveolar macrophages (PAMs) and dendritic cells (DCs) and develops persistent infections, antibody-dependent enhancement (ADE), interstitial pneumonia and immunosuppression. But the molecular mechanisms of PRRSV infection still are poorly understood. Here we report on the first genome-wide host transcriptional responses to classical North American type PRRSV (N-PRRSV) strain CH 1a infection using Solexa/Illumina's digital gene expression (DGE) system, a tag-based high-throughput transcriptome sequencing method, and analyse systematically the relationship between pulmonary gene expression profiles after N-PRRSV infection and infection pathology. Our results suggest that N-PRRSV appeared to utilize multiple strategies for its replication and spread in infected pigs, including subverting host innate immune response, inducing an anti-apoptotic and anti-inflammatory state as well as developing ADE. Upregulation expression of virus-induced pro-inflammatory cytokines, chemokines, adhesion molecules and inflammatory enzymes and inflammatory cells, antibodies, complement activation were likely to result in the development of inflammatory responses during N-PRRSV infection processes. N-PRRSV-induced immunosuppression might be mediated by apoptosis of infected cells, which caused depletion of immune cells and induced an anti-inflammatory cytokine response in which they were unable to eradicate the primary infection. Our systems analysis will benefit for better understanding the molecular pathogenesis of N-PRRSV infection, developing novel antiviral therapies and identifying genetic components for swine resistance/susceptibility to PRRS. © 2010 Xiao et al.",antibody;cell adhesion molecule;chemokine;cytokine;transcriptome;animal experiment;animal tissue;antibody dependent enhancement;antiinflammatory activity;apoptosis;Arterivirus;article;controlled study;gene expression profiling;gene sequence;genetic transcription;genome analysis;immune deficiency;immune response;immunocompetent cell;infection control;infection resistance;infection sensitivity;inflammatory cell;innate immunity;lung infection;nonhuman;North America;pathogenesis;porcine reproductive and respiratory syndrome;sequence analysis;upregulation;virus replication,"Xiao, S.;Jia, J.;Mo, D.;Wang, Q.;Qin, L.;He, Z.;Zhao, X.;Huang, Y.;Li, A.;Yu, J.;Niu, Y.;Liu, X.;Chen, Y.",2010,,10.1371/journal.pone.0011377,0
2308,Aberrant host immune response induced by highly virulent PRRSV identified by digital gene expression tag profiling,"Background: There was a large scale outbreak of the highly pathogenic porcine reproductive and respiratory syndrome (PRRS) in China and Vietnam during 2006 and 2007 that resulted in unusually high morbidity and mortality among pigs of all ages. The mechanisms underlying the molecular pathogenesis of the highly virulent PRRS virus (H-PRRSV) remains unknown. Therefore, the relationship between pulmonary gene expression profiles after H-PRRSV infection and infection pathology were analyzed in this study using high-throughput deep sequencing and histopathology.Results: H-PRRSV infection resulted in severe lung pathology. The results indicate that aberrant host innate immune responses to H-PRRSV and induction of an anti-apoptotic state could be responsible for the aggressive replication and dissemination of H-PRRSV. Prolific rapid replication of H-PRRSV could have triggered aberrant sustained expression of pro-inflammatory cytokines and chemokines leading to a markedly robust inflammatory response compounded by significant cell death and increased oxidative damage. The end result was severe tissue damage and high pathogenicity.Conclusions: The systems analysis utilized in this study provides a comprehensive basis for better understanding the pathogenesis of H-PRRSV. Furthermore, it allows the genetic components involved in H-PRRSV resistance/susceptibility in swine populations to be identified. © 2010 Xiao et al; licensee BioMed Central Ltd.",animal experiment;animal model;animal tissue;apoptosis;Arterivirus;article;cell death;controlled study;disease severity;gene expression profiling;histopathology;host resistance;inflammation;innate immunity;lung disease;nonhuman;oxidative stress;porcine reproductive and respiratory syndrome;tissue injury;virus pathogenesis;virus replication;virus transmission;virus virulence,"Xiao, S.;Mo, D.;Wang, Q.;Jia, J.;Qin, L.;Yu, X.;Niu, Y.;Zhao, X.;Liu, X.;Chen, Y.",2010,,10.1186/1471-2164-11-544,0
2309,"Generation by Reverse Genetics of an Effective, Stable, Live-Attenuated Newcastle Disease Virus Vaccine Based on a Currently Circulating, Highly Virulent Indonesian Strain","Newcastle disease virus (NDV) can cause severe disease in chickens. Although NDV vaccines exist, there are frequent reports of outbreaks in vaccinated chickens. During 2009-2010, despite intense vaccination, NDV caused major outbreaks among commercial poultry farms in Indonesia. These outbreaks raised concern regarding the protective immunity of current vaccines against circulating virulent strains in Indonesia. In this study, we investigated whether a recombinant attenuated Indonesian NDV strain could provide better protection against prevalent Indonesian viruses. A reverse genetics system for the highly virulent NDV strain Banjarmasin/010/10 (Ban/010) isolated in Indonesia in 2010 was constructed. The Ban/010 virus is classified in genotype VII of class II NDV, which is genetically distinct from the commercial vaccine strains B1 and LaSota, which belong to genotype II, and shares only 89 and 87% amino acid identity for the protective antigens F and HN, respectively. A mutant virus, named Ban/AF, was developed in which the virulent F protein cleavage site motif ""RRQKR↓F"" was modified to an avirulent motif ""GRQGR↓L"" by three amino acid substitutions (underlined). The Ban/AF vaccine virus did not produce syncytia or plaques in cell culture, even in the presence of added protease. Pathogenicity tests showed that Ban/AF was completely avirulent. Ban/AF replicated efficiently during 10 consecutive passages in chickens and remained genetically stable. Serological analysis showed that Ban/AF induced higher neutralization and hemagglutination inhibition antibody titers against the prevalent viruses than the commercial vaccines B1 or LaSota. Both Ban/AF and commercial vaccines provided protection against clinical disease and mortality after challenge with virulent NDV strain Ban/010 (genotype VII) or GB Texas (genotype II). However, Ban/AF significantly reduced challenge virus shedding from the vaccinated birds compared to B1 vaccine. These results suggest that Ban/AF can provide better protection than commercial vaccines and is a promising vaccine candidate against NDV strains circulating in Indonesia.",Newcastle disease vaccine;protein f;proteinase;recombinant vaccine;unclassified drug;viral protein;amino acid sequence;amino acid substitution;animal cell;animal experiment;animal model;antibody titer;article;cell culture;chicken;comparative effectiveness;controlled study;drug cross reactivity;drug efficacy;drug stability;embryo;genetic stability;genotype;hemagglutination inhibition;human;human cell;in vitro study;in vivo study;Newcastle disease;nonhuman;protein cleavage;protein motif;provocation test;reverse genetics;serology;viral genetics;virogenesis;virus classification;virus isolation;virus shedding;virus strain;virus virulence;wild type,"Xiao, S.;Nayak, B.;Samuel, A.;Paldurai, A.;Kanabagattebasavarajappa, M.;Prajitno, T. Y.;Bharoto, E. E.;Collins, P. L.;Samal, S. K.",2012,,10.1371/journal.pone.0052751,0
2310,Design and validation of a universal influenza virus enrichment probe set and its utility in deep sequence analysis of primary cloacal swab surveillance samples of wild birds,"Influenza virus infections in humans and animals are major public health concerns. In the current study, a set of universal influenza enrichment probes was developed to increase the sensitivity of sequence-based virus detection and characterization for all influenza viruses. This universal influenza enrichment probe set contains 46,953 120nt RNA biotin-labeled probes designed based on all available influenza viral sequences and it can be used to enrich for influenza sequences without prior knowledge of type or subtype. Marked enrichment was demonstrated in influenza A/H1N1, influenza B, and H1-to-H16 hemagglutinin plasmids spiked into human DNA and in cultured influenza A/H2N1 virus. Furthermore, enrichment effects and mixed influenza A virus infections were revealed in wild bird cloacal swab samples. Therefore, this universal influenza virus enrichment probe system can capture and enrich influenza viral sequences selectively and effectively in different samples, especially ones with degraded RNA or containing low amount of influenza RNA.","Animals;Birds;Cloaca/vi [Virology];*DNA Probes/ge [Genetics];Epidemiological Monitoring;High-Throughput Nucleotide Sequencing/ve [Veterinary];Influenza A virus/ge [Genetics];*Influenza A virus/ip [Isolation & Purification];*Influenza in Birds/ep [Epidemiology];Influenza in Birds/vi [Virology];RNA, Viral/an [Analysis];RNA, Viral/ip [Isolation & Purification];Sequence Analysis, DNA/ve [Veterinary];0 (DNA Probes);0 (RNA, Viral)","Xiao, Y.;Nolting, J. M.;Sheng, Z. M.;Bristol, T.;Qi, L.;Bowman, A. S.;Taubenberger, J. K.",2018,11,,0
2311,Characterization of the Fecal Virome and Fecal Virus Shedding Patterns of Commercial Mink (Neovison vison),,,"Xie, X. T.",2017,,,0
2312,Analysis of the miRNA expression profile in an Aedes albopictus cell line in response to bluetongue virus infection,"Cellular microRNAs (miRNAs) have been reported to be key regulators of virus-host interactions. Bluetongue virus (BTV) is an insect-borne virus that causes huge economic losses in the livestock industry worldwide. Aedes albopictus cell lines have become powerful and convenient tools for studying BTV-vector interactions. However, the role of miRNAs in A. albopictus cells during BTV infection is not well understood. In this study, we performed a deep sequencing analysis of small RNA libraries of BTV-infected and mock-infected A. albopictus cells, and a total of 11,206,854 and 12,125,274 clean reads were identified, respectively. A differential expression analysis showed that 140 miRNAs, including 15 known and 125 novel miRNAs, were significantly dysregulated after infection, and a total of 414 and 2307 target genes were annotated, respectively. Real-time quantitative reverse transcription-polymerase chain reaction validated the expression patterns of 11 selected miRNAs and their mRNA targets. Functional annotation of the target genes suggested that these target genes were mainly involved in metabolic pathways, oxidative phosphorylation, endocytosis, RNA transport, as well as the FoxO, Hippo, Jak-STAT, and MAPK signaling pathways. This is the first systematic study on the effect of BTV infection on miRNA expression in A. albopictus cells. This investigation provides information concerning the cellular miRNA expression profile in response to BTV infection, and it offers clues for identifying potential candidates for vector-based antiviral strategies.","*Aedes/ge [Genetics];Aedes/vi [Virology];Animals;*Bluetongue virus/py [Pathogenicity];Cell Line;*Gene Expression Profiling/mt [Methods];Gene Expression Regulation;High-Throughput Nucleotide Sequencing/mt [Methods];*MicroRNAs/ge [Genetics];Sequence Analysis, RNA/mt [Methods];Signal Transduction;0 (MicroRNAs)","Xing, S.;Du, J.;Gao, S.;Tian, Z.;Zheng, Y.;Liu, G.;Luo, J.;Yin, H.",2016,Apr,,0
2313,First identification of porcine parvovirus 7 in China,"Porcine parvovirus (PPV) are small, non-enveloped and single-stranded DNA viruses, taxonomically classifiable within the family Parvoviridae. Seven PPV genotypes (PPV1 to PPV7) have been identified to date. PPV7, the most recently discovered PPV genotype, was first reported in US pigs in 2016. To explore PPV7 status in Chinese pig populations a total of 64 serum samples collected from two commercial farms in Guangdong province in 2014 were analyzed. PPV7 DNA was detected in 32.8% (21/64) of tested samples. On the porcine circovirus type 2 (PCV2) positive farm, the prevalence rate of PPV7 was 65.5% (19/29) which was significantly higher than that on the PCV2 negative farm (2/35, 5.7%), indicating a possible association between PCV2 and PPV7 infections. The sequences of three PPV7 strains were determined. Phylogenetic analysis revealed that the identified PPV7 strains circulating in China shared 98.7%-99.7% nucleotide homology with the US strain. Further sequence comparison analysis indicated that GD-2014-2 and GD-2014-3 possess a consecutive 9-nt deletion in the VP gene. This is the first report of the existence of PPV7 in China and this finding will strengthen understanding of the epidemiology of porcine parvovirus in Chinese pigs.",viral protein;animal;China;classification;gene expression regulation;genetics;isolation and purification;metabolism;nucleotide sequence;parvovirus infection;phylogeny;pig;Porcine parvovirus;swine disease;veterinary medicine;virology,"Xing, X.;Zhou, H.;Tong, L.;Chen, Y.;Sun, Y.;Wang, H.;Zhang, G.",2018,,10.1007/s00705-017-3585-9,0
2314,Investigation of Porcine Endogenous Retrovirus in the Conservation Population of Ningxiang Pig,"Porcine endogenous retrovirus (PERV) varies between pig breeds. Screening and analysis of PERV in putative pig breeds may provide basic parameters to evaluate the biological safety of xenotransplantation from pigs to humans. In this study, PERV was investigated among the conservation population of the Ningxiang pig. The result revealed that the genotype of PERV distribution was subtype A, 100%; subtype B, 100%; and subtype C, 100%. The env sequences of PERV-A and -B showed 11 clones detected by KpnI and MboI digestion, indicating that there existed multiple variants of PERV-A and -B in the Ningxiang pig. Reverse transcriptase polymerase chain reaction results showed that PERV had transcriptional activity in these individuals. In addition, PERV A/C recombinant was detected in most individuals of Ningxiang pig. Because PERV A/C recombinants increase the potential infectious risk, the breed may not be a proper donor for xenotransplantation. Crown Copyright © 2009.",genomic DNA;RNA;analysis;article;blood sampling;breeding;gene sequence;genetic transcription;genetic variability;genotype;infection risk;molecular cloning;nonhuman;Porcine endogenous retrovirus;priority journal;Retroviridae;reverse transcription polymerase chain reaction;RNA isolation;screening;virus classification;virus recombinant;wildlife conservation;xenotransplantation,"Xing, X. W.;Hawthorne, W. J.;Yi, S.;Simond, D. M.;Dong, Q.;Ye, B.;Tong, Q. J.;Ye, Z.;Wang, W.",2009,,10.1016/j.transproceed.2009.09.051,0
2315,Detection and phylogenetic analysis of porcine bocaviruses carried by murine rodents and house shrews in China,"Bocaparvovirus infections of humans and both wild and domestic animals have been widely reported around the world. In this study, we detected and genetically characterized porcine bocavirus (PBoV) carried by murine rodents (Rattus norvegicus, Rattus tanezumi, and Rattus losea) and house shrews (Suncus murinus) in China. Between May 2015 and May 2017, 496 murine rodents and 23 house shrews were captured in four Chinese provinces. Nested polymerase chain reaction was used to investigate the prevalence of PBoV in throat swab, faecal and serum samples. A total of 7.5% (39/519) throat swab samples, 60.5% (309/511) faecal samples, and 22.9% (52/227) serum samples were PBoV-positive. The prevalence among R. norvegicus and R. tanezumi was higher than that among R. losea and house shrews. PBoV-positive samples were found in all four provinces. Phylogenetic analysis based on partial viral capsid protein 1/2 (VP1/VP2) showed that sequences obtained in this study formed a novel group (PBoV G4). In addition, five near full-length PBoV genomes (4,715–4,798 nt) were acquired. These genomes encoded two non-structural proteins, NS1 (1,908 nt in four genomes and 1,923 nt in the remaining genome) and NP1 (600 nt), and the structural proteins, VP1/VP2 (1,851 nt). Phylogenetic analysis showed that PBoV G4 is distinct from rodent, human, and other bocaviruses. In conclusion, PBoV G4 prevalence was high among two common murine rodents in China, and the pathogenecity of PBoV G4 need to be further clarified.",nonstructural protein 1;nucleic acid;animal experiment;animal model;article;Bocaparvovirus;controlled study;DNA extraction;feces analysis;metagenomics;mouse;nested polymerase chain reaction;nonhuman;phylogeny;pig;prevalence;rat;Rattus norvegicus;Suncus murinus;throat culture;virus capsid;virus characterization;virus detection;virus infection,"Xiong, Y. Q.;You, F. F.;Chen, X. J.;Chen, Y. X.;Wen, Y. Q.;Chen, Q.",2019,,10.1111/tbed.13011,0
2316,Metagenomic analysis of the Rhinopithecus bieti fecal microbiome reveals a broad diversity of bacterial and glycoside hydrolase profiles related to lignocellulose degradation,"BACKGROUND: The animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host and the diet adopted by the host. Although the importance of gut microbiota of humans has been well demonstrated, there is a paucity of research regarding non-human primates (NHPs), especially herbivorous NHPs. RESULTS: In this study, an analysis of 97,942 pyrosequencing reads generated from Rhinopithecus bieti fecal DNA extracts was performed to help better understanding of the microbial diversity and functional capacity of the R. bieti gut microbiome. The taxonomic analysis of the metagenomic reads indicated that R. bieti fecal microbiomes were dominated by Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria phyla. The comparative analysis of taxonomic classification revealed that the metagenome of R. bieti was characterized by an overrepresentation of bacteria of phylum Fibrobacteres and Spirochaetes as compared with other animals. Primary functional categories were associated mainly with protein, carbohydrates, amino acids, DNA and RNA metabolism, cofactors, cell wall and capsule and membrane transport. Comparing glycoside hydrolase profiles of R. bieti with those of other animal revealed that the R. bieti microbiome was most closely related to cow rumen. CONCLUSIONS: Metagenomic and functional analysis demonstrated that R. bieti possesses a broad diversity of bacteria and numerous glycoside hydrolases responsible for lignocellulosic biomass degradation which might reflect the adaptations associated with a diet rich in fibrous matter. These results would contribute to the limited body of NHPs metagenome studies and provide a unique genetic resource of plant cell wall degrading microbial enzymes. However, future studies on the metagenome sequencing of R. bieti regarding the effects of age, genetics, diet and environment on the composition and activity of the metagenomes are required.",glycosidase;lignin;lignocellulose;animal;archaeon;bacterium;biodiversity;bovine;classification;Colobinae;dog;eukaryote;feces;genetics;human;isolation and purification;metabolism;metagenome;metagenomics;microbiology;microflora;mouse;phylogeny;virology;virus,"Xu, B.;Xu, W.;Li, J.;Dai, L.;Xiong, C.;Tang, X.;Yang, Y.;Mu, Y.;Zhou, J.;Ding, J.;Wu, Q.;Huang, Z.",2015,,10.1186/s12864-015-1378-7,0
2317,Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing,"Seronegative hepatitis--non-A, non-B, non-C, non-D, non-E hepatitis--is poorly characterized but strongly associated with serious complications. We collected 92 sera specimens from patients with non-A-E hepatitis in Chongqing, China between 1999 and 2007. Ten sera pools were screened by Solexa deep sequencing. We discovered a 3,780-bp contig present in all 10 pools that yielded BLASTx E scores of 7e-05-0.008 against parvoviruses. The complete sequence of the in silico-assembled 3,780-bp contig was confirmed by gene amplification of overlapping regions over almost the entire genome, and the virus was provisionally designated NIH-CQV. Further analysis revealed that the contig was composed of two major ORFs. By protein BLAST, ORF1 and ORF2 were most homologous to the replication-associated protein of bat circovirus and the capsid protein of porcine parvovirus, respectively. Phylogenetic analysis indicated that NIH-CQV is located at the interface of Parvoviridae and Circoviridae. Prevalence of NIH-CQV in patients was determined by quantitative PCR. Sixty-three of 90 patient samples (70%) were positive, but all those from 45 healthy controls were negative. Average virus titer in the patient specimens was 1.05 e4 copies/micro L. Specific antibodies against NIH-CQV were sought by immunoblotting. Eighty-four percent of patients were positive for IgG, and 31% were positive for IgM; in contrast, 78% of healthy controls were positive for IgG, but all were negative for IgM. Although more work is needed to determine the etiologic role of NIH-CQV in human disease, our data indicate that a parvovirus-like virus is highly prevalent in a cohort of patients with non-A-E hepatitis.","Adolescent;Adult;Aged;*Anemia, Aplastic/ep [Epidemiology];*Anemia, Aplastic/vi [Virology];*Asian Continental Ancestry Group/sn [Statistics & Numerical Data];Child;China/ep [Epidemiology];Circoviridae/ge [Genetics];*DNA, Viral/ge [Genetics];Evolution, Molecular;Female;Hepatitis Antibodies/bl [Blood];*Hepatitis, Viral, Human/ep [Epidemiology];*Hepatitis, Viral, Human/vi [Virology];High-Throughput Nucleotide Sequencing;Humans;Male;Middle Aged;Molecular Sequence Data;Parvoviridae/ge [Genetics];Phylogeny;Prevalence;Risk Factors;Seroepidemiologic Studies;Young Adult;0 (DNA, Viral);0 (Hepatitis Antibodies)","Xu, B.;Zhi, N.;Hu, G.;Wan, Z.;Zheng, X.;Liu, X.;Wong, S.;Kajigaya, S.;Zhao, K.;Mao, Q.;Young, N. S.",2013,Jun 18,,0
2318,Comprehensive serological profiling of human populations using a synthetic human virome,,,"Xu, G. J.;Kula, T.;Xu, Q.;Li, M. Z.;Vernon, S. D.",2015,,,0
2319,Transcriptome analysis of HepG2 cells expressing orf3 from swine hepatitis e virus to determine the effects of ORF3 on host cells,"Hepatitis E virus- (HEV-) mediated hepatitis has become a global public health problem. An important regulatory protein of HEV, ORF3, influences multiple signal pathways in host cells. In this study, to investigate the function of ORF3 from the swine form of HEV (SHEV), high-throughput RNA-Seq-based screening was performed to identify the differentially expressed genes in ORF3-expressing HepG2 cells. The results were validated with quantitative real-time PCR and gene ontology was employed to assign differentially expressed genes to functional categories. The results indicated that, in the established ORF3-expressing HepG2 cells, the mRNA levels of CLDN6, YLPM1, APOC3, NLRP1, SCARA3, FGA, FGG, FGB, and FREM1 were upregulated, whereas the mRNA levels of SLC2A3, DKK1, BPIFB2, and PTGR1 were downregulated. The deregulated expression of CLDN6 and FREM1 might contribute to changes in integral membrane protein and basement membrane protein expression, expression changes for NLRP1 might affect the apoptosis of HepG2 cells, and the altered expression of APOC3, SCARA3, and DKK1 may affect lipid metabolism in HepG2 cells. In conclusion, ORF3 plays a functional role in virus-cell interactions by affecting the expression of integral membrane protein and basement membrane proteins and by altering the process of apoptosis and lipid metabolism in host cells. These findings provide important insight into the pathogenic mechanism of HEV.",apolipoprotein C3;claudin 6;dickkopf related protein 1;enhanced green fluorescent protein;fibrinogen;fibrinogen beta;fras1 related extracellular matrix 1;lipid;membrane protein;messenger RNA;nucleotide binding oligomerization domain like receptor;nucleotide binding oligomerization domain like receptor 1;open reading frame 3 protein;regulator protein;RNA;scavenger receptor A;scavenger receptor class a member 3;solute carrier family 22 member 3;transcriptome;unclassified drug;viral protein;ylp motif containing protein 1;apoptosis;article;basement membrane;controlled study;gene expression profiling;gene ontology;hepatitis E;Hepatitis E virus;Hep-G2 cell line;high throughput sequencing;human;human cell;lipid metabolism;nonhuman;protein expression;protein function;quantitative analysis;RNA sequence;transcriptomics;upregulation;virus cell interaction;virus pathogenesis,"Xu, K.;Guo, S.;Zhao, T.;Zhu, H.;Jiao, H.;Shi, Q.;Pang, F.;Li, Y.;Li, G.;Peng, D.;Nie, X.;Cheng, Y.;Wu, K.;Du, L.;Cui, K.;Zhang, W.;Wang, F.",2016,,10.1155/2016/1648030,0
2320,Isolation and genetic analysis of a novel triple-reassortant H1N1 influenza virus from a pig in China,"Influenza A viruses of subtype H1N1 have been reported widely in pigs in China, associated with clinical disease. These mainly include classical swine H1N1, avian-like H1N1, and human-like H1N1 viruses. In this study, we reported a novel triple-reassortant H1N1 virus (A/swine/Guangdong/1/2010) containing genes from the classical swine (NP, NS), human (PB1) and avian (HA, NA, M, PB2, PA) lineages, which was for the first time reported in China. Also, phylogenetic analysis further confirmed that five genes segments (NS, NP, PB2, PB1, PA) of the isolate were closely related to the novel reassortant H1N2 viruses isolated in China in 2006, while the other three (HA, NA, M) were closely related to avian-like H1N1 viruses in China. The isolation of triple-reassortant H1N1 influenza virus provides further evidence that pigs serve as emergence hosts or ""mixing vessels"", and swine influenza virus (SIV) surveillance in China should be given a high priority. © 2010 Elsevier B.V.",article;gene isolation;genetic analysis;Influenza A virus (H1N1);nonhuman;nucleotide sequence;phylogeny;pig;virus isolation,"Xu, M.;Huang, Y.;Chen, J.;Huang, Z.;Zhang, J.;Zhu, Y.;Xie, S.;Chen, Q.;Wei, W.;Yang, D.;Huang, X.;Xuan, H.;Xiang, H.",2011,,10.1016/j.vetmic.2010.07.012,0
2321,Characteristics of very virulent infectious bursal disease viruses isolated from Chinese broiler chickens (2012-2013),"The objective of this study was to characterize the infectious bursal disease viruses (IBDVs) circulating in broiler chicken farms in China between 2012 and 2013. The VP2 gene sequences of nine newly isolated IBDVs, obtained using reverse transcriptase polymerase chain reaction, were determined and compared with worldwide reference isolates, which have been previously well characterized. Phylogenetic analysis revealed that the nine broiler IBDV isolates are closely related to very virulent IBDV (vvIBDV) strains. Analysis of the predicted amino acid sequences of VP2 from the nine vvIBDVs isolated from the broilers revealed that they share 99.2 to 100% sequence similarity. Additionally, amino acids A222, I242, I256, I294 and S299 of VP2 that are conserved among previously characterized vvIBDV strains are also encoded by the nine isolates. This study confirms the circulation of vvIBDVs in Chinese broiler chicken farms experienced slow evolution and was relatively stable in China.",amino acid;amino acid sequence;article;chicken;China;controlled study;evolution;genetic conservation;genetic similarity;hydrophilicity;infectious bursal disease virus;nonhuman;nucleotide sequence;phylogeny;prediction;reverse transcription polymerase chain reaction;sequence analysis;virus characterization;virus gene;virus isolation;virus strain;VP2 gene,"Xu, M. Y.;Lin, S. Y.;Zhao, Y.;Jin, J. H.;Tang, N.;Zhang, G. Z.",2015,,10.1016/j.actatropica.2014.10.003,0
2322,"Epidemiological and Evolutionary Inference of the Transmission Network of the 2014 Highly Pathogenic Avian Influenza H5N2 Outbreak in British Columbia, Canada","The first North American outbreak of highly pathogenic avian influenza (HPAI) involving a virus of Eurasian A/goose/Guangdong/1/1996 (H5N1) lineage began in the Fraser Valley of British Columbia, Canada in late November 2014. A total of 11 commercial and 1 non-commercial (backyard) operations were infected before the outbreak was terminated. Control measures included movement restrictions that were placed on a total of 404 individual premises, 150 of which were located within a 3 km radius of an infected premise(s) (IP). A complete epidemiological investigation revealed that the source of this HPAI H5N2 virus for 4 of the commercial IPs and the single non-commercial IP likely involved indirect contact with wild birds. Three IPs were associated with the movement of birds or service providers and localized/environmental spread was suspected as the source of infection for the remaining 4 IPs. Viral phylogenies, as determined by Bayesian Inference and Maximum Likelihood methods, were used to validate the epidemiologically inferred transmission network. The phylogenetic clustering of concatenated viral genomes and the median-joining phylogenetic network of the viruses supported, for the most part, the transmission network that was inferred by the epidemiologic analysis.",agricultural land;animal;avian influenza;bird disease;British Columbia;chicken;epidemic;female;genetics;Influenza A virus (H5N2);male;pathogenicity;phylogeny;population migration;transmission;turkey (bird);veterinary medicine;virology;virus genome;wild animal,"Xu, W.;Berhane, Y.;Dubé, C.;Liang, B.;Pasick, J.;VanDomselaar, G.;Alexandersen, S.",2016,,10.1038/srep30858,0
2323,"A novel Enterovirus 96 circulating in China causes hand, foot, and mouth disease","Enterovirus 96 (EV-96) is a recently described member of the species Enterovirus C and is associated with paralysis and myelitis. In this study, using metagenomic sequencing, we identified a new enterovirus 96 strain (EV-96-SZ/GD/CHN/2014) as the sole pathogen causing hand, foot, and mouth disease (HFMD). A genomic comparison showed that EV-96-SZ/GD/CHN/2014 is most similar to the EV-96-05517 strain (85% identity), which has also been detected in Guangdong Province. This is the first time that metagenomic sequencing has been used to identify an EV-96 strain shown to be associated with HFMD.",article;case report;child;China;Enterovirus;Enterovirus 96;fever;hand foot and mouth disease;human;male;metagenomics;molecular phylogeny;next generation sequencing;nonhuman;preschool child;reverse transcription polymerase chain reaction;Sanger sequencing;vesicular rash;virus genome,"Xu, Y.;Sun, Y.;Ma, J.;Zhou, S.;Fang, W.;Ye, J.;Tan, L.;Ji, J.;Luo, D.;Li, L.;Li, J.;Fang, C.;Pei, N.;Shi, S.;Liu, X.;Jiang, H.;Gong, S.;Xu, X.",2017,,10.1007/s11262-017-1431-5,0
2324,H9N2 influenza virus isolated from minks has enhanced virulence in mice,"H9N2 is one of the major subtypes of influenza virus circulating in poultry in China, which has a wide host range from bird to mammals. Two H9N2 viruses were isolated from one mink farm in 2014. Phylogenetic analysis showed that internal genes of the H9N2 viruses have close relationship with those of H7N9 viruses. Interestingly, two H9N2 were separated in phylogenetic trees, indicating that they are introduced to this mink farm in two independent events. And further mice studies showed that one H9N2 caused obvious weight loss and 20% mortality in infected mice, while another virus did not cause any clinical sign in mice infected at the same dose. Genetic analysis indicated that the virulent H9N2 contain a natural mutation at 701N in PB2 protein, which was reported to contribute to mammalian adaptation. However, such substitution is absent in the H9N2 avirulent to mice. Circulation of H9N2 in mink may drive the virus to adapt mammals; continual surveillance of influenza virus in mink was warranted.",animal experiment;animal model;article;body weight loss;China;gene mutation;genetic analysis;host range;Influenza A virus (H7N9);Influenza A virus (H9N2);mortality;mouse;Neovison vison;nonhuman;phylogenetic tree;poultry;virulence,"Xue, R.;Tian, Y.;Hou, T.;Bao, D.;Chen, H.;Teng, Q.;Yang, J.;Li, X.;Wang, G.;Li, Z.;Liu, Q.",2018,,10.1111/tbed.12805,0
2325,Sequence and phylogenetic analysis of surface protein genes of emerging H9N2 influenza viruses isolated from poultry in two geographical regions of China,"Subtype H9N2 avian influenza viruses (AIVs) circulating in China have aroused increasing concerns for their impact on poultry and risk to public health. The present study was an attempt to elucidate the phylogenetic relationship of H9N2 AIVs in two geographically distinct regions of China where vaccination is routinely practiced. A total of 18 emerging H9N2 isolates were identified and genetically characterized. Phylogenetic analysis of hemagglutinin (HA) and neuraminidase (NA) genes confirmed that the isolates belonged to the Y280 lineage. Based on the HA genes, the isolates were subdivided into two subgroups. The viruses from Zhejiang Province were clustered together in Group I, while the isolates from Guangdong Province were clustered together in Group II. Antigenic characterization showed that the tested viruses were antigenically different when compared to the current used vaccine strain. It was notable that 14 out of total 18 isolates had an amino acid exchange (Q?L) at position 216 (226 by H3 Numbering) in the receptor-binding site, which indicated that the virus had potential affinity of binding to human like receptor. These results suggest that the emerging viruses have potential risk to public health than previously thought. Therefore, continuous surveillance studies of H9N2 influenza virus are very important to the prognosis and control of future influenza pandemics. © Springer Science+Business Media 2014.",Influenza virus hemagglutinin;virus sialidase;amino acid substitution;article;binding affinity;binding site;China;controlled study;Influenza A virus (H9N2);Influenza virus hemagglutinin gene;molecular phylogeny;nonhuman;nucleotide sequence;phylogenetic tree;priority journal;sequence analysis;sequence homology;strain difference;virus attachment;virus identification;virus isolation;virus sialidase gene,"Xue, Y.;Wang, J. L.;Yan, Z. Q.;Li, G. W.;Chen, S. Y.;Zhang, X. B.;Qin, J. P.;Li, H. Y.;Chang, S.;Chen, F.;Bee, Y. Z.;Xie, Q. M.",2014,,10.1007/s11262-014-1060-1,0
2326,"Isolation and characterization of Oya virus a member of Simbu serogroup, family Bunyaviridae, isolated from Karnataka, India","During a study on Japanese encephalitis (JE) from Kolar district of Karnataka state, India in 1986; two virus isolates were obtained in infant Swiss albino mouse from a pig and a human serum sample. For characterization of these virus isolates, they were propagated in Vero CCL-81 cells. These virus isolates were screened for flaviviruses (Japanese encephalitis, West Nile, Dengue, Kyasanur forest disease) and Alphavirus (Chikungunya) by RT-PCR and found to be negative. Further these they were screened for bunyaviruses using genus-specific primers. A virus isolate from a human sample was sequenced using next generation sequencing; which identified it as Oya virus, Simbu group of the genus Orthobunyavirus of the family Bunyaviridae. Phylogenetic analysis of L, M, S (N and NSs) revealed its close association with Chinese strain of Oya virus in Simbu serogroup with the distance of 6.5>4.2>3.2% for nucleotides and 2.4>0.8>0.0% for the amino acid of L>M>S segments respectively. Based on the PCR results; an isolate from pig sample was also confirmed as Oya virus. This study was strengthened by findings of IgG antibody positivity against Oya virus in retrospective serum samples of suspected febrile illness cases from this area by an indigenously developed ELISA. Oya virus positivity was also recorded in human samples collected from Karnataka using nested RT-PCR. This is the first report of the presence of Oya virus in human samples. Further studies are needed to determine disease-causing potential in humans.","Animals;Antibodies, Viral/bl [Blood];*Bunyaviridae Infections/vi [Virology];Cercopithecus aethiops;High-Throughput Nucleotide Sequencing;Humans;India;Serogroup;*Simbu virus/ge [Genetics];Simbu virus/ip [Isolation & Purification];*Simbu virus/py [Pathogenicity];Swine;Vero Cells/vi [Virology];0 (Antibodies, Viral)","Yadav, P.;Shete, A.;Bondre, V.;Patil, D.;Kokate, P.;Chaudhari, S.;Srivastava, S.;Jadhav, S.;Mourya, D.",2016,10,,0
2327,"Molecular analysis of the genome of Chuzan virus, a member of the Palyam serogroup viruses, and its phylogenetic relationships to other orbiviruses","The nucleotide sequence of the entire genome of Chuzan virus, which belongs to the Palyam serogroup orbiviruses and causes congenital abnormalities of cattle, has been completed by analysis of the genes encoding minor core proteins (VP1, VP4 and VP6) and non-structural proteins (NS1, NS2 and NS3). The genome of Chuzan virus is 18,915 bp in length and the coding capacity of its open reading frames is 6071 aa. Comparative sequence analysis with other serogroups of the genus Orbivirus indicated that the outer capsid protein VP2, which is the neutralizing antigen, appears to be the most variable and the major core protein VP3 is the most conserved. Overall, the structural proteins, with the exception of VP2, are more conserved than the non-structural proteins among orbiviruses. Chuzan virus is phylogenetically most related to African horsesickness virus.",core protein;viral protein;article;molecular genetics;nucleotide sequence;open reading frame;Orbivirus;phylogeny;priority journal;sequence analysis;virus genome,"Yamakawa, M.;Kubo, M.;Furuuchi, S.",1999,,,0
2328,Genomic analyses of bovine viral diarrhea viruses isolated from cattle imported into Japan between 1991 and 2005,"Thirty-one isolates of bovine viral diarrhea virus (BVDV) isolated within the past 15 years from imported cattle by the Japanese Animal Quarantine Service (AQS) were used in this study in which a 5′-untranslated region of each isolate was genetically analyzed. Twenty-six of the 31 isolates were classified as BVDV1 and the remainder as BVDV2. Phylogenetic analysis of the RT-PCR fragments amplified from the isolates showed the presence of viruses belonging to the BVDV1a, BVDV1b, BVDV1c, unclassified BVDV1 genotypes, and BVDV2. From the cattle of Australian origin, 16 of 17 isolates were classified as BVDV1c. This result was in agreement with a report showing that BVDV1c was a predominant subgenotype in Australia. From the cattle of North American origin, BVDV1 and BVDV2 species were both found. BVDV2 from the North American cattle was identified as the same cluster as the BVDV 890 strain, which is the prototype of BVDV2. These results suggest that the BVDVs isolated from exported cattle at the AQS reflect the predominant genotypes of BVDVs found in the exporting countries. The unclassified BVDV1 genotype of Chinese origin was in the same cluster as the ZM-95 strain, which was isolated from pigs in China. In this study, the genomic properties of 31 isolates of BVDV collected in the AQS were investigated. We concluded that isolates are genetically heterogeneous but geographically restricted. The information obtained from this report will be useful when carrying out epidemiological surveys of BVDV isolated in Japan. © 2007 Elsevier B.V. All rights reserved.",5' untranslated region;article;bacterial genetics;bacterial genome;bovine;Rinderpest virus;gene cluster;genotype;geographic distribution;infection control;Japan;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;strain difference;virus classification;virus identification;virus isolation;virus strain,"Yamamoto, T.;Kozasa, T.;Aoki, H.;Sekiguchi, H.;Morino, S.;Nakamura, S.",2008,,10.1016/j.vetmic.2007.08.020,0
2329,"Three male patients with sporadic acute hepatitis E in Sendai, Japan, who were domestically infected with hepatitis E virus of genotype III or IV","Recent studies indicate that hepatitis E virus (HEV) infection occurs not only in developing countries but also in industrialized nations. However, the characteristics of domestic infections of hepatitis E in Japan are not fully understood. We analyzed serum samples from 34 patients who were seen at a city hospital in Sendai, Japan, between January 1997 and December 2002, and who had been given the diagnosis of sporadic acute hepatitis of non-A, non-B, non-C etiology. Among these 34 patients, 3 (9%; all men; aged 54, 59, and 61 years) were positive for both IgG and IgM anti-HEV antibodies and for HEV RNA. The HEV isolates (HE-JAS1 and HE-JAS3) obtained from case 1 and case 3, respectively, segregated into genotype III; they had the highest nucleotide sequence identity, of 99.5% and 99.0%, with HE-JA7 and HE-JA8, respectively, both of which had been isolated in Iwate, a neighboring prefecture of Sendai. In contrast, the remaining HEV isolate (HE-JAS2), obtained from case 2, segregated into genotype IV; it had the highest nucleotide sequence identity, of 99.8% and 99.3%, with JKK-Sap and HE-JA3, respectively, both of which had been isolated in Hokkaido, Japan, although case 2 had never been to Hokkaido. Our three patients with hepatitis E had not traveled abroad in the preceding 1 year, had had no contact with pigs, and no history of blood transfusion. These results indicate that HEV should be considered as an etiological agent of acute hepatitis of non-A, non-B, non-C etiology in Japan. The risk factor(s) for acquiring domestic HEV infection in Japan needs to be clarified in future studies. © Springer-Verlag 2004.",alanine aminotransferase;alkaline phosphatase;aspartate aminotransferase;bilirubin;gamma glutamyltransferase;immunoglobulin G;immunoglobulin M;virus RNA;adult;alcohol consumption;article;blood analysis;blood sampling;blood transfusion;case report;convalescence;developing country;genotype;hepatitis E;Hepatitis E virus;hepatitis non A non B non C;hospital discharge;human;industrialization;Japan;laboratory test;laparoscopy;liver biopsy;male;neighbor joining method;nonhuman;nucleotide sequence;phylogenetic tree;priority journal;risk factor;sequence analysis;pig;travel;virus isolation,"Yamamoto, T.;Suzuki, H.;Toyota, T.;Takahashi, M.;Okamoto, H.",2004,,10.1007/s00535-003-1292-7,0
2330,Characterization of variant infectious bursal disease virus from a broiler farm in Japan using immunized sentinel chickens,"We attempted the isolation of variant infectious bursal disease (IBD) viruses by using sentinel chickens immunized with inactivated classical-type IBD vaccine. Immunized sentinel chickens with high levels of neutralizing antibodies and non-immunized sentinel chickens were raised together with broiler chickens in a commercial farm. Severe atrophy of the bursa of Fabricius was observed from the second week after cohabitation in non-immunized sentinel chickens. However, in immunized sentinel chickens and broiler chickens, atrophy was observed from the third week after cohabitation. The IBD virus (IBDV) isolated from the bursa of Fabricius of immunized sentinel chickens, designated as strain IBDV TY2, showed severe atrophy of the bursa in infected SPF chickens. Antiserum to the IBDV TY2 strain showed higher neutralizing activity to heterologous IBDV strains than did antiserum to the K strain vaccine virus. Phylogenetic analysis revealed that the nucleotide sequences encoding the hypervariable region of virus protein 2 of the IBDV TY2 strain did not cluster with the classical, variant or very virulent IBDV groups. Based on these results, we suggest that the IBDV TY2 strain may constitute a novel variant type of IBDV.",virus vaccine;animal;atrophy;bird disease;birnavirus infection;bursa Fabricii;chicken;genetics;immunology;infectious bursal disease virus;isolation and purification;Japan;pathology;restriction fragment length polymorphism;reverse transcription polymerase chain reaction;veterinary medicine;virology,"Yamazaki, K.;Ohta, H.;Kawai, T.;Yamaguchi, T.;Obi, T.;Takase, K.",2017,,10.1292/jvms.16-0301,0
2331,"Hepatitis E Virus in Yellow Cattle, Shandong, Eastern China",,Animals;Cattle;*Cattle Diseases/ep [Epidemiology];*Cattle Diseases/vi [Virology];China/ep [Epidemiology];*Hepatitis E/ve [Veterinary];Hepatitis E virus/cl [Classification];Hepatitis E virus/ge [Genetics];Hepatitis E virus/im [Immunology];*Hepatitis E virus,"Yan, B.;Zhang, L.;Gong, L.;Lv, J.;Feng, Y.;Liu, J.;Song, L.;Xu, Q.;Jiang, M.;Xu, A.",2016,12,,0
2332,Phylogenetic analysis of S1 gene of infectious bronchitis virus isolates from China,"Between 2006 and 2009, seven strains of infectious bronchitis (IB) virus (IBV) were isolated from vaccinated chicken flocks on different chicken farms in China. The pathogenic characters of seven IBV strains were assessed. Each of the seven strains was infective to the test chickens and could induce an immune response. The results from chicken embryo cross-neutralization assays showed that these strains were antigenically distinct from classic IBV strains of H120, M41, Conn, and Gray. Compared to H120 vaccine strain, point mutation, short insertion, and deletion occurred at many positions in the S1 protein of the seven strains. Five of the seven strains had the motif (HRRRR), which was identical to that of the epidemic IBV strains in China. Two new motifs (HRLRR and RRIRR) emerged in the isolated strains. The homology of the nucleotide and amino acid sequences of the S1 gene among the seven isolates was 81.7%-99.7% and 79.0%-99.4%, respectively. These seven strains were also genetically different from the vaccine strains and non-China IBV strains but closely related to large numbers of Chinese strains. The seven isolates and 36 reference IBV strains were clustered into six distinct groups (IVI). The seven strains were categorized into groups I, II, and III, forming a big phylogenetic branch, which is closely related to Chinese IBVs, whereas the vaccine strains belonging to group VI are genetically distant from groups I, II, and III. The results from this study indicate that different IBV strains cocirculate in the chicken population in China. © American Association of Avian Pathologists.",membrane protein;coronavirus spike glycoprotein;virus envelope protein;virus vaccine;animal;animal disease;article;Avian infectious bronchitis virus;bird disease;chick embryo;chicken;China;classification;Coronavirus infection;genetics;immunology;isolation and purification;molecular cloning;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;sequence alignment;sequence analysis;virology,"Yan, F.;Zhao, Y.;Yue, W.;Yao, J.;Lv, L.;Ji, W.;Li, X.;Liu, F.;Wu, Q.",2011,,10.1637/9446-070510-ResNote.1,0
2333,Failed detection of Bovine viral diarrhea virus 2 subgenotype a (BVDV-2a) by direct fluorescent antibody test on tissue samples due to reduced reactivity of field isolates to raw anti-BVDV antibody,"Bovine viral diarrhea virus 1 (BVDV-1) is associated with mild or subclinical infections, whereas BVDV-2 is frequently implicated in outbreaks of severe thrombocytopenia and acute fatal disease. In the present study, the carcass of a beef breed cow and tissue samples of a beef calf were received for laboratory diagnosis. Both animals exhibited severe clinical signs compatible with thrombocytopenia or hemorrhagic syndrome. Direct fluorescent antibody test (DFAT) failed to detect BVDV antigen in the tissue specimens of both cases. However, immunohistochemistry (IHC) revealed the presence of BVDV antigen in oral and esophageal mucosa and Peyer patches of the beef breed cow. Real-time reverse transcription polymerase chain reaction (real-time RT-PCR) detected BVDV-2 in selected tissues of both animals. Subsequently, BVDV was isolated from both cases and subjected to genetic and serologic characterizations. Mutations in the 5'-untranslated genomic region (5'-UTR) primer and probe binding sites and the E2 gene were associated with reduced efficiency of an established real-time RT-PCR assay and amino acid alterations in the E2 glycoprotein, respectively. Both viral isolates were classified by real-time RT-PCR and phylogenetic analysis as BVDV-2 subgenotype a. Unlike BVDV reference strains Singer and 125c, the isolates cross-reacted with anti-BVDV-1 and anti-BVDV-2 reference sera, indicating antigenic variations in field isolates. The isolates also showed reduced reactivity to porcine anti-BVDV antiserum (the raw serum used to produce BVDV DFA conjugate). In summary, data from the present investigation indicated that genetic and antigenic variations affected the performance of detection assays, especially DFAT, highlighting the need for regular evaluation and modification of BVDV tests.",primer DNA;animal;bovine;Bovine viral diarrhea virus 2;bovine viral diarrhea;case report;diagnostic error;differential diagnosis;direct fluorescent antibody technique;genetics;immunohistochemistry;immunology;isolation and purification;meat;phylogeny;polymerase chain reaction;veterinary medicine;virology,"Yan, L.;Pace, L. W.;Baughman, B.;Wilson, F. D.;Zhang, S.;Zhang, M. Z.",2016,,10.1177/1040638715626483,0
2334,Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek's disease,"BACKGROUND: Copy number variation (CNV) is a major source of genome polymorphism that directly contributes to phenotypic variation such as resistance to infectious diseases. Lines 63 and 72 are two highly inbred experimental chicken lines that differ greatly in susceptibility to Marek's disease (MD), and have been used extensively in efforts to identify the genetic and molecular basis for genetic resistance to MD. Using next generation sequencing, we present a genome-wide assessment of CNVs that are potentially associated with genetic resistance to MD. METHODS: Three chickens randomly selected from each line were sequenced to an average depth of 20x. Two popular software, CNVnator and Pindel, were used to call genomic CNVs separately. The results were combined to obtain a union set of genomic CNVs in the two chicken lines. RESULTS: A total of 5,680 CNV regions (CNVRs) were identified after merging the two datasets, of which 1,546 and 1,866 were specific to the MD resistant or susceptible line, respectively. Over half of the line-specific CNVRs were shared by 2 or more chickens, reflecting the reduced diversity in both inbred lines. The CNVRs fixed in the susceptible lines were significantly enriched in genes involved in MAPK signaling pathway. We also found 67 CNVRs overlapping with 62 genes previously shown to be strong candidates of the underlying genes responsible for the susceptibility to MD. CONCLUSIONS: Our findings provide new insights into the genetic architecture of the two chicken lines and additional evidence that MAPK signaling pathway may play an important role in host response to MD virus infection. The rich source of line-specific CNVs is valuable for future disease-related association studies in the two chicken lines.",Animals;*Chickens/ge [Genetics];Chickens/vi [Virology];*DNA Copy Number Variations/ge [Genetics];*Disease Resistance/ge [Genetics];Disease Susceptibility;Genome;High-Throughput Nucleotide Sequencing;*Marek Disease/ge [Genetics];Marek Disease/vi [Virology],"Yan, Y.;Yang, N.;Cheng, H. H.;Song, J.;Qu, L.",2015,Oct 23,,0
2335,Isolation and Characterization of a Novel Tembusu Virus Circulating in Muscovy Ducks in South China,"Duck Tembusu virus (DTMUV) is an infectious pathogen that can cause epidemics in egg-laying ducks. Here, we isolated and characterized a DTMUV, designated GDLH01, thought to be responsible for the noticeable egg drop in Muscovy duck flocks in South China since 2011. The genome sequence of GDLH01 shared 97-99% homology with other avian-origin Tembusu viruses, and 99.5% homology with the mosquito-borne strain SDMS recently reported in China. Phylogenetic analysis based on the nucleotide sequence of the entire open reading frame confirmed that the isolate was of avian origin and closely related to a mosquito-borne strain. Our findings characterize a novel Tembusu virus circulating in Muscovy ducks in South China and emphasize the importance of reinforcing biosecurity measures and developing vaccines to prevent the spread of this viral pathogen.",animal;bird disease;China;DNA sequence;duck;female;Flavivirus;Flavivirus infection;genetics;isolation and purification;open reading frame;ovum;phylogeny;veterinary medicine;virology;virus genome,"Yan, Z.;Shen, H.;Wang, Z.;Lin, W.;Xie, Q.;Bi, Y.;Chen, F.",2017,,10.1111/tbed.12525,0
2336,"Sequence analysis of the medium RNA segment of three Simbu serogroup viruses, Akabane, Aino, and Peaton viruses","The sequence analysis was carried out for the medium (M) RNA segment of the Akabane virus (AKAV), Aino virus (AINV), and Peaton virus (PEAV) of the Simbu serogroup of the genus Orthobunyavirus of the family Bunyaviridae. The complementary sequences of the M RNA segments of AKAV, AINV, and PEAV contain a single large open reading frame (ORF), like other orthobunyaviruses. The ORFs potentially encode 1401 amino acids (aa), 1404 aa, and 1400 aa polypeptides, respectively. The identity of the M segment among these viruses is remarkably low, although previous researchers reported that the small RNA segments are highly conserved. Because the M segment codes for the viral surface glycoproteins G1 and G2, the variability of the M segment may affect the antigenicity of these viruses. Phylogenetic studies based on the M and S segment sequences suggested that genetic reassortment has been occurring among ancestral viruses of the three Simbu serogroup viruses throughout their evolution. (C) 2003 Elsevier Science B.V. All rights reserved.",arbovirus;orthobunyavirus;reassortment;vector-borne;Culicoides;NEUTRALIZING MONOCLONAL-ANTIBODIES;ARTHROPOD-BORNE VIRUSES;BUNYAVIRUS;GENOME;GLYCOPROTEINS;REASSORTMENT;JAPANESE;CATTLE,"Yanase, T.;Yoshida, K.;Ohashi, S.;Kato, T.;Tsuda, T.",2003,May,,0
2337,Detection and genetic characterization of porcine pegivirus in pigs in the United States,"Using next-generation sequencing on vesicular swab and serum from swine from the USA exhibiting lameness and vesicles, porcine pegivirus (PPgV) was first identified and genetically characterized in the United States. Further screening using RT-PCR revealed that 24 of 159 (15.1%) serum samples were positive for PPgV. Future studies are needed to understand clinical impacts of the virus.",Animals;*Flaviviridae/ge [Genetics];*Flaviviridae/ip [Isolation & Purification];*Flavivirus Infections/ge [Genetics];*High-Throughput Nucleotide Sequencing;Phylogeny;Swine;*Swine Diseases/vi [Virology];United States,"Yang, C.;Wang, L.;Shen, H.;Zheng, Y.;Bade, S. A.;Gauger, P. C.;Chen, Q.;Zhang, J.;Guo, B.;Yoon, K. J.;Harmon, K. M.;Main, R. G.;Li, G.",2018,Jun,,1
2338,Newcastle disease virus isolated from recent outbreaks in Taiwan phylogenetically related to viruses (genotype VII) from recent outbreaks in western Europe,"Three major outbreaks of Newcastle disease (ND) occurred in Taiwan in the last three decades (in 1969, 1984, and 1995). Newcastle disease viruses (NDVs) isolated in the three outbreaks, together with those isolated in 1998, were sequenced between nucleotides 47 and 435 of the fusion gene. A phylogenetic tree based on sequences obtained showed that the NDV isolated in 1969 was similar to the genotype III viruses. In contrast, all isolates in 1984 and seven of the eight isolates in 1995, together with all isolates in 1998, fell into the genotype VII. These results suggest that the 1969 outbreak of ND in Taiwan was caused by the genotype III virus, whereas the 1984 and 1995 outbreaks were caused by the genotype VII viruses. To date, the genotype VII viruses have caused many outbreaks in east Asia and western Europe. We suspect that these outbreaks have constituted the fourth panzootic of ND, which is distinct from the third panzootic caused by the ""pigeon PMV-1 viruses."" NDV isolated in Taiwan in 1984 was the earliest isolation of the genotype VII virus.","Amino Acid Sequence;Animals;Base Sequence;Columbidae;DNA, Viral/ch [Chemistry];*Disease Outbreaks/ve [Veterinary];Europe/ep [Epidemiology];Genotype;Molecular Sequence Data;*Newcastle Disease/ep [Epidemiology];*Newcastle disease virus/ip [Isolation & Purification];Phylogeny;Sequence Alignment;Taiwan/ep [Epidemiology];Viral Proteins/ch [Chemistry];0 (DNA, Viral);0 (Viral Proteins)","Yang, C. Y.;Shieh, H. K.;Lin, Y. L.;Chang, P. C.",1999,Jan-Mar,,0
2339,"Genetic analysis of H3N2 avian influenza viruses isolated from live poultry markets and poultry slaughterhouses in Shanghai, China in 2013","Five H3N2 avian influenza viruses (AIVs) were isolated from live poultry markets (LPMs) and poultry slaughterhouses in Shanghai, China in 2013. All viruses were characterized by whole-genome sequencing with subsequent genetic comparison and phylogenetic analysis. The hemagglutinin cleavage site of all viruses indicated that the five strains were low-pathogenic AIVs. Phylogenetic analysis of all eight viral genes showed that the five H3N2 viruses clustered in the Eurasian lineage of influenza viruses. The eight genes showed evidence of reassortment events between these H3 subtype viruses and other subtype viruses, especially H5 and H7 subtypes, probably in pigeons, domestic ducks, and wild birds. These findings emphasized the importance of AIV surveillance in LPMs and poultry slaughterhouses for understanding the genesis and emergence of novel reassortants with pandemic potential.",hemagglutinin;Anas platyrhynchos;article;avian influenza;bird;China;controlled study;gene cluster;gene sequence;genetic analysis;Influenza A virus (H3N2);nonhuman;nucleotide sequence;phylogeny;Columbidae;poultry;priority journal;sequence analysis;slaughterhouse;virus gene;virus isolation,"Yang, D.;Liu, J.;Ju, H.;Ge, F.;Wang, J.;Li, X.;Zhou, J.;Liu, P.",2015,,10.1007/s11262-015-1198-5,0
2340,"Phylogenetic Characterization Genome Segment 2 of Bluetongue Virus Strains Belonging to Serotypes 5, 7 and 24 Isolated for the First Time in China During 2012 to 2014","Bluetongue is endemic in China, and Bluetongue virus (BTV) strains belonging to eight different serotypes (BTV-1, BTV-2, BTV-3, BTV-4, BTV-9, BTV-12, BTV-15 and BTV-16) had been isolated between 1996 and 1997. However, there has been a long pause in investigating the epidemiology of BTV infection since then. During 2012-2014, eight BTV strains belonging to serotypes 5, 7 and 24 were isolated for the first time in Yunnan and Guangdong provinces from the blood of sentinel animals. Phylogenetic analyses of genome segment 2 of these Chinese BTV strains grouped them into nucleotypes E, F and A, respectively, along with the reference strains of the same serotype. For each serotype, Chinese strains cluster together closely to form a China's sublineage. In addition, these strains were most closely related to strains from Africa, indicating that they may share a recent common ancestry with African strains. To our knowledge, this is the first time that BTV-5, BTV-7 and BTV-24 strains have been isolated in South-East Asia. These data will be beneficial for understanding the BTV epidemiology and improving diagnostic assays and control measures against bluetongue in China and its neighbouring countries in the Asia-Pacific region.",virus RNA;animal;bluetongue;Bluetongue orbivirus;China;classification;genetics;isolation and purification;phylogeny;sequence analysis;serotype;sheep;sheep disease;veterinary medicine;virology;virus genome,"Yang, H.;Xiao, L.;Wang, J.;Meng, J.;Lv, M.;Liao, D.;Song, J.;Gao, L.;Xiong, H.;He, Y.;Niu, B.;Chuang, X.;Li, H.",2017,,10.1111/tbed.12479,0
2341,Isolation and genomic characterization of a novel chicken-orign orthoreovirus causing goslings hepatitis,"A severe infectious disease characterized by nephritis, hepatitis and splenitis has attacked goslings around Shandong province in China since 2016. A novel chicken-origin avian orthoreovirus (ARV) was isolated with LMH cells from affected goslings named Reo/Goose/SDPY/1116/17 (SDPY-ARV) strain, and the infection was successfully reproduced experimentally. The ARV-SDPY full genome sequencing was conducted using Next-Generation Sequencing (NGS) technique on Illumina HiSeq platform. The complete genome of SDPY-ARV was 23,427 bp in length and consist of 10 dsRNA segments ranged from 1192 bp (S4) to 3958 bp (L1) which encoding 12 viral proteins. Genomic sequence analysis showed that the SDPY-ARV strain is in the same branch with broiler, pheasant-origin ARV isolates, and shares 51.8-96.2% of nucleotide identity of sigmaC gene with them; while only 49.3-50.3% with waterfowl isolates. In addition, the occurrence of 10 segments genetic reassortment of SDPY strain is confirmed among the PA15511, the 1733 and the PA13649 strains from America. In conclusion, the causative agent of gosling hemorrhagic necrotic hepatitis and nephritis occurring in China is a novel chicken-origin goose orthoreovirus.","Age Factors;Animals;Chickens;China/ep [Epidemiology];*Geese/vi [Virology];*Genome, Viral;Genomics;Hepatitis, Viral, Animal/ep [Epidemiology];*Hepatitis, Viral, Animal/et [Etiology];Hepatitis, Viral, Animal/vi [Virology];High-Throughput Nucleotide Sequencing/mt [Methods];Liver/pa [Pathology];Liver/vi [Virology];Necrosis/ve [Veterinary];Necrosis/vi [Virology];Open Reading Frames;*Orthoreovirus, Avian/ge [Genetics];*Orthoreovirus, Avian/ip [Isolation & Purification];Orthoreovirus, Avian/ph [Physiology];Phylogeny;Poultry Diseases/ep [Epidemiology];Poultry Diseases/tm [Transmission];*Poultry Diseases/vi [Virology];Reoviridae Infections/ep [Epidemiology];Reoviridae Infections/tm [Transmission];*Reoviridae Infections/ve [Veterinary];Reoviridae Infections/vi [Virology];Sequence Analysis, DNA;Viral Proteins/ge [Genetics];0 (Viral Proteins)","Yang, J.;Tian, J.;Chen, L.;Tang, Y.;Diao, Y.",2018,Dec,,0
2342,Isolation and genomic characterization of gosling gout caused by a novel goose astrovirus,"A severe infectious disease characterized with gout, haemorrhage and swellings of kidneys has affected goslings around the major goose-producing regions in China since November 2016. A Novel goose-origin astrovirus (AStV), designated as AStV/SDPY/Goose/1116/17 (AStV-SDPY) strain, was isolated from diseased goslings, and experimental reproduction of gout was successful using the AStV-SDPY strain. Additionally, the AStV-SDPY was conducted for its full genome sequencing characterization using next-generation sequencing (NGS) technique on Illumina HiSeq platform. A complete genome of the AStV-SDPY was 7,252 nt in length and encoded three viral proteins. Phylogenetic analysis revealed that AStV-SDPY strain belongs to an independent branch of avian astroviruses, and the nucleotide homology among AStV-SDPY and other classic avian astrovirus strains was only 48.8%-68.2%.","Animals;*Astroviridae/ge [Genetics];*Astroviridae/ip [Isolation & Purification];Astroviridae Infections/ep [Epidemiology];*Astroviridae Infections/ve [Veterinary];Astroviridae Infections/vi [Virology];Base Sequence;China/ep [Epidemiology];*Geese/vi [Virology];*Genome, Viral/ge [Genetics];Genomics;*Gout/ve [Veterinary];Gout/vi [Virology];High-Throughput Nucleotide Sequencing/ve [Veterinary];Phylogeny;Poultry Diseases/ep [Epidemiology];*Poultry Diseases/vi [Virology]","Yang, J.;Tian, J.;Tang, Y.;Diao, Y.",2018,Dec,,0
2343,Molecular characterization of avian influenza virus (H7N8) isolated from poultry in Central China in the mid-1980s,"The molecular and pathogenic properties of avian influenza virus (A/duck/Hubei/216/1985/H7N8) isolated from Hubei Province of China in 1985 were characterized. The hemagglutinin gene (HA) of Dk/Hb/216/85/H7N8 had the multiple amino acid sequences (-PEIPKGRG-) at the connecting peptide between HA1 and HA2, which is considered to be a distinguishing molecular characteristic of low pathogenicity. The key sites of host markers among the genes (M, NP, NS, PA and PB2) of Dk/Hb/216/85/H7N8 were similar to those of H5N1 viruses. Phylogenetic analysis showed that the genes (M, NS and PB2) of Dk/Hb/216/85/H7N8 clustered closely with those of Gs/Guangdong/1996/H5N1 (Gs/GD/96), implying that three ancient genes of Gs/GD/96-like viruses had been circulating in Central China during the 1980s. In experimental infection, Dk/Hb/216/85/H7N8 was lowly pathogenic to chickens and mice, consistent with the molecular feature of HA gene.",avian influenza virus;low pathogenicity;H7N8;H5N1;A VIRUSES;H5N1 VIRUSES;HONG-KONG;HEMAGGLUTININ;TRANSMISSION;ORIGIN,"Yang, J. L.;Xia, H.;Zhao, J. R.;He, X. B.;Pan, L. M.;Tang, S. A.;Zhang, Z.;Kou, Z.;Li, T. X.",2010,Jun,,0
2344,"Genomes and seroprevalence of severe fever with thrombocytopenia syndrome virus and Nairobi sheep disease virus in Haemaphysalis longicornis ticks and goats in Hubei, China","Ticks are medically-important arthropods that maintain and transmit numerous emerging viruses. China suffers severely from tick-borne viral diseases such as tick-borne encephalitis and severe fever with thrombocytopenia syndrome (SFTS), but the background of tick-borne viruses is very limited. Here we report the virome profiling of ticks and goat sera from SFTS-epidemic areas, and serological investigation of SFTS virus (SFTSV) and Nairobi sheep disease virus (NSDV). Results revealed divergent viruses in ticks and goat sera, including SFTSV and NSDV. Sequence and phylogenetic analyses showed that the SFTSV identified here was most closely related to human SFTSV in sampling and surrounding areas, and the NSDV to the previously identified NSDV from northeast China. Serological investigation of SFTSV infection in goats revealed intensive activity in those areas. Surprisingly, two different methods of NSDV serological investigation showed no sera positive for this virus.",animal experiment;animal model;animal tissue;article;China;epidemic;genome;goat;Haemaphysalis longicornis;Nairobi sheep disease virus;nonhuman;phylogeny;sampling;seroprevalence;severe fever with thrombocytopenia syndrome;tick borne encephalitis,"Yang, L. E.;Zhao, Z.;Hou, G.;Zhang, C.;Liu, J.;Xu, L.;Li, W.;Tan, Z.;Tu, C.;He, B.",2019,,10.1016/j.virol.2019.01.026,1
2345,"Westward Spread of Highly Pathogenic Avian Influenza A(H7N9) Virus among Humans, China","We report infection of humans with highly pathogenic avian influenza A(H7N9) virus in Shaanxi, China, in May 2017. We obtained complete genomes for samples from 5 patients and from live poultry markets or farms in 4 cities.",,"Yang, Q.;Shi, W.;Zhang, L.;Xu, Y.;Xu, J.;Li, S.;Zhang, J.;Hu, K.;Ma, C.;Zhao, X.;Li, X.;Liu, F.;Tong, X.;Zhang, G.;Yu, P.;Pybus, O. G.;Tian, H.",2018,06,,0
2346,A novel rodent Chapparvovirus in feces of wild rats,"Chapparvovirus, a recently determined new genus in the family Parvoviridae, can infect many species of animals including bats, chickens, and pigs. Here, using viral metagenomics method, we identified a novel Chapparvovirus from feces of wild rats and designated it as rat parvovirus 2 (RPV2). The nearly complete genome of RPV2 is 4222-nt long and includes two ORFs encoding a 654-aa nonstructural protein 1 (NS1) and a 472-aa capsid protein (VP), respectively. Phylogenetic analysis over the amino acid sequence of the NS1 showed that RPV2 clustered with Eidolon helvum parvovirus 2 (EHPV2), porcine parvovirus 7 (PPV7), and Turkey parvovirus 1 (TP1), forming a separate clade. Sequence analysis indicated that the NS1 protein of RPV2 shared the highest amino acid sequence identity (51 %) with that of EHPV2. According to the genetic distance-based criteria, RPV2 identified here belongs to a novel species of Chapparvovirus.",capsid protein;nonstructural protein 1;amino acid sequence;article;cladistics;DNA virus;Eidolon helvum parvovirus 2;feces;genetic distance;metagenomics;molecular phylogeny;nonhuman;nucleotide sequence;Parvoviridae;Porcine parvovirus 7;protein expression;rat parvovirus 2;sequence analysis;turkey parvovirus 1;virus genome;virus identification;wild animal;wild rat,"Yang, S.;Liu, Z.;Wang, Y.;Li, W.;Fu, X.;Lin, Y.;Shen, Q.;Wang, X.;Wang, H.;Zhang, W.",2016,,10.1186/s12985-016-0589-0,0
2347,"A novel bocavirus from domestic mink, China","Bocaviruses have been found in the feces of humans and a variety of animals, including pigs, cattle, dogs, gorillas, cats, and sea lions. Here, we have characterized the almost complete genome (5224 nt) of a novel bocavirus from feces of domestic minks, which has been provisionally named mink bocavirus. The NS1 protein of mink bocavirus shared 36.9–52 % amino acid sequence identities with those of other known bocaviruses and phylogenetically clustered with bocaviruses from other carnivores. According to the genetic distance-based criteria, mink bocavirus qualifies as a novel species of bocavirus. PCR of feces from a group of domestic minks, which included both healthy animals and animals suffering from diarrhea, revealed that 30 % (9/30) shed virus. However, no association between viral shedding and the presence of diarrhea could be determined.",amino acid sequence;article;Bocaparvovirus;carnivore;China;diarrhea;disease association;domestic animal;feces analysis;genetic distance;Neovison vison;mink bocavirus;nonhuman;phylogeny;polymerase chain reaction;priority journal;virus characterization;virus genome;virus shedding,"Yang, S.;Wang, Y.;Li, W.;Fan, Z.;Jiang, L.;Lin, Y.;Fu, X.;Shen, Q.;Sun, Z.;Wang, X.;Deng, X.;Zhang, W.;Delwart, E.",2016,,10.1007/s11262-016-1380-4,0
2348,High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses,"The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses) and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gene sequences in the leachate was the highest at 6 weeks, in contrast to those at 2 and 14 weeks. The relative abundance of Firmicutes was reduced, while the proportion of Bacteroidetes and Proteobacteria increased from 3-6 weeks. The representation of phyla was restored after 14 weeks. However, the community structures between the samples taken at 1-2 and 14 weeks differed at the bacterial classification level. The trend in pH was similar to the changes seen in bacterial communities, indicating that the pH of the leachate could be related to the shift in the microbial community. The results indicate that the composition of bacterial communities in leachates of decomposing pig carcasses shifted continuously during the study period and might be influenced by the burial site.",pig;decomposition;leachate;bacterial community;pyrosequencing;MOUTH-DISEASE VIRUS;MICROBIAL COMMUNITY;POLLUTED AQUIFER;FOREST;SOILS;HUMAN-BODY;SP-NOV;PEPTOSTREPTOCOCCUS;CADAVERS;DEATH;ACIDS,"Yang, S. H.;Lim, J. S.;Khan, M. A.;Kim, B. S.;Choi, D. Y.;Lee, E. Y.;Ahn, H. K.",2015,,,0
2349,Next-generation sequencing enables the discovery of more diverse positive clones from a phage-displayed antibody library,"Phage display technology provides a powerful tool to screen a library for a binding molecule via an enrichment process. It has been adopted as a critical technology in the development of therapeutic antibodies. However, a major drawback of phage display technology is that because the degree of the enrichment cannot be controlled during the bio-panning process, it frequently results in a limited number of clones. In this study, we applied next-generation sequencing (NGS) to screen clones from a library and determine whether a greater number of clones can be identified using NGS than using conventional methods. Three chicken immune single-chain variable fragment (scFv) libraries were subjected to bio-panning on prostate-specific antigen (PSA). Phagemid DNA prepared from the original libraries as well as from the Escherichia coli pool after each round of bio-panning was analyzed using NGS, and the heavy chain complementarity-determining region 3 (HCDR3) sequences of the scFv clones were determined. Subsequently, through two-step linker PCR and cloning, the entire scFv gene was retrieved and analyzed for its reactivity to PSA in a phage enzyme immunoassay. After four rounds of bio-panning, the conventional colony screening method was performed for comparison. The scFv clones retrieved from NGS analysis included all clones identified by the conventional colony screening method as well as many additional clones. The enrichment of the HCDR3 sequence throughout the bio-panning process was a positive predictive factor for the selection of PSA-reactive scFv clones.","Bacteriophages/ge [Genetics];*Cloning, Molecular/mt [Methods];*High-Throughput Nucleotide Sequencing/mt [Methods];Humans;*Peptide Library;*Sequence Analysis, DNA/mt [Methods];*Single-Chain Antibodies/ge [Genetics];0 (Peptide Library);0 (Single-Chain Antibodies)","Yang, W.;Yoon, A.;Lee, S.;Kim, S.;Han, J.;Chung, J.",2017,03 24,,0
2350,Genetic characterization of a densovirus isolated from great tit (Parus major) in China,"During a study of ornithophilous viruses in China, a new densovirus (DNV) was isolated from the lung tissue of Parus major (PmDNV-JL). The complete genome of PmDNV-JL was cloned and sequenced. Five open reading frames (ORFs) were identified in the 5166nt sequence, on the basis of deduced amino acids. It was further shown that this virus caused cytopathic effects (CPE) in Feline kidney cells. The NS1 gene sequence of PmDNV-JL shares 70-99% nucleotide sequence identity with isolates of the Blattella germanica densovirus (BgDNV) and BgDNV-like virus. Phylogenetic analysis indicated that the predicted amino acid sequences of capsid (VP) and non-structural domain (NS1) of PmDNV-JL clustered with the BgDNV and were similar to BgDNV-HB within the genus Densovirus.","Animals;*Bird Diseases/ep [Epidemiology];Bird Diseases/tm [Transmission];Bird Diseases/vi [Virology];Capsid Proteins/ge [Genetics];Cats;China/ep [Epidemiology];DNA, Viral/ge [Genetics];Densovirus/cl [Classification];*Densovirus/ge [Genetics];Densovirus/ip [Isolation & Purification];Epithelial Cells/vi [Virology];*Genome, Viral;Kidney/vi [Virology];Lung/vi [Virology];Open Reading Frames;Parvoviridae Infections/ep [Epidemiology];Parvoviridae Infections/tm [Transmission];*Parvoviridae Infections/ve [Veterinary];Parvoviridae Infections/vi [Virology];*Passeriformes/vi [Virology];*Phylogeny;Sequence Analysis, DNA;Viral Nonstructural Proteins/ge [Genetics];0 (Capsid Proteins);0 (DNA, Viral);0 (Viral Nonstructural Proteins)","Yang, W. T.;Shi, S. H.;Jiang, Y. L.;Zhao, L.;Chen, H. L.;Huang, K. Y.;Yang, G. L.;Wang, C. F.",2016,07,,0
2351,Genome characterization of a novel porcine bocavirus,"Using a high-throughput DNA sequencing method, one DNA sequence (contig01006), suspected to belong to a novel porcine bocavirus (PBoV), was found with a high rate of detection (19. 6 %) in fecal samples from healthy piglets. Moreover, a novel PBoV (tentatively named PBoV3C) with a nearly complete genome sequence (5235 bp) was identified. PBoV3C exhibits typical genome characteristics of bocaviruses and shows the highest genomic sequence identity (78 % to 81 %) to PBoV3A/B (PBoV3/4-UK) and PBoV3D/E (PBoV3/4-HK), respectively. Phylogenetic and recombination analysis indicated high diversity, prevalence and complexity among the PBoVs. The phospholipase A2 (PLA2) site of VP1 and the secondary structure of VP2 of PBoV3C were also analyzed. Additionally, we propose a uniform method of PBoV nomenclature based on the VP1 gene. © 2012 Springer-Verlag.",virus DNA;viral protein;animal;article;Bocaparvovirus;chemistry;cluster analysis;DNA sequence;genetics;isolation and purification;molecular genetics;nomenclature;nucleotide sequence;phylogeny;protein secondary structure;sequence homology;pig;virus genome,"Yang, W. Z.;Yu, J. M.;Li, J. S.;Cheng, W. X.;Huang, C. P.;Duan, Z. J.",2012,,10.1007/s00705-012-1407-7,1
2352,MicroRNA transcriptome analysis in chicken kidneys in response to differing virulent infectious bronchitis virus infections,"Infectious bronchitis virus (IBV) can cause a highly contagious and acute respiratory disease in poultry. MicroRNAs (miRNAs) have emerged as a class of crucial regulators for gene expression and are involved in the regulation of virus defence and immunological processes. To understand miRNA regulation in chickens in response to IBV infection, high-throughput sequencing was performed to compare the small RNA libraries from the kidneys of chicken infected with SCK2, SCDY2 and LDT3-A. By comparing these data to healthy chickens, a total of 58 differentially expressed (DE) miRNAs were identified. The DE miRNAs were further classified into five miRNA expression patterns (up or down regulation compared to control). Using Gene Ontology (GO) enrichment prediction, the DE miRNAs were shown to be mostly associated with metabolic processes, catalytic activities, gene expression, binding activities and immune responses. Seven highly expressed miRNAs (gga-miR-30d, gga-miR-1454, gga-miR-7b, gga-miR-215-5p, gga-miR-1a-3p, gga-miR-3538 and gga-miR-2954) were selected for miRNA-mRNA conjoint analysis. Furthermore, the miRNAs inversely correlated with the corresponding target gene mRNAs. These seven miRNAs were considered to play an important role in IBV-host interactions and the differing virulence of IBV strains. This is the first demonstration that infection with different virulent IBVs elicits different expression of miRNAs in chicken kidneys; this expression also seems to be associated with the virulence of IBV. These results are significant for the study of immune responses to infection with different virulent IBVs mediated by miRNAs as well as the interaction between the chicken host and IBV.",microRNA;transcriptome;animal;Avian infectious bronchitis virus;bird disease;chicken;Coronavirus infection;genetics;germfree animal;kidney;metabolism;pathogenicity;reverse transcription polymerase chain reaction;veterinary medicine;virology;virulence,"Yang, X.;Gao, W.;Liu, H.;Li, J.;Chen, D.;Yuan, F.;Zhang, Z.;Wang, H.",2017,,10.1007/s00705-017-3502-2,0
2353,Novel characteristics of the avian gyrovirus 2 genome,"Avian gyrovirus 2 (AGV2) was the second member of the viral genus Cyclovirus to be discovered. This virus poses a significant potential threat to humans and poultry due to its global dissemination and infectiousness. We used three overlapping polymerase chain reactions (PCRs) to map the whole genome of AGV2. We then modelled the evolutionary history of these novel sequence data in the context of related sequences from GenBank. We analysed the viral protein characteristics of the different phylogenetic groups and explored differences in evolutionary trends between Chinese strains and strains from other countries. We obtained 17 avian-sourced AGV2 whole genomes from different regions of China from 2015 to 2016. Phylogenetic analyses of these Chinese AGV2 sequences and related sequences produced four distinct groups (A-D) with significant bootstrap values. We also built phylogenies using predicted viral protein sequences. We found a potential hypervariable region in VP1 at sites 288-314, and we identified the amino acid changes responsible for the distinct VP2 and VP3 groups. Three new motifs in the AGV2 5'-UTR direct repeat (DR) region were discovered and grouped. The novel characteristics and diverse research on the AGV2 genome provide a valuable framework for additional research.",capsid protein;virus DNA;5' untranslated region;amino acid sequence;animal;bird disease;chemistry;chicken;classification;DNA sequence;evolution;genetics;Gyrovirus;isolation and purification;metabolism;nucleotide motif;phylogeny;polymerase chain reaction;sequence alignment;virology;virus genome,"Yao, S.;Gao, X.;Tuo, T.;Han, C.;Gao, Y.;Qi, X.;Zhang, Y.;Liu, C.;Gao, H.;Wang, Y.;Wang, X.",2017,,10.1038/srep41068,0
2354,Isolation of a novel serotype strain of infectious bronchitis virus ZZ2004 from ducks in China,"In chickens, the infectious bronchitis virus (IBV) often causes respiratory distress, a decrease in egg production, poor egg quality, and occasional nephritis. However, ZZ2004, a Chinese isolate of IBV, was obtained from ducks with clinical growth suppression and mild respiratory symptoms that had been reared with chickens in the central region of China. Virus isolation, virus neutralization testing, and RT-PCR were employed to identify the causative pathogen, while sequence alignment was used to analyze gene variations of the S1 subunit and M genes. The results showed that the ducks were infected with IBV due to the emergence of a dwarfing phenotype and the death of embryos between 48 and 144 h post-inoculation. RT-PCR also confirmed the presence of the expected fragment sizes of the S1 subunit and M genes by RT-PCR. Meanwhile, the results of the virus neutralization test indicated that the strains of JX/99/01, GD, SAIBK, LDT3 showed cross-reactivity with the ZZ2004 isolate, and hardly any cross-neutralization of IBV ZZ2004 was observed with the strains of M41, H120, Gray, Holte, or Aust-T. Phylogenetic analysis suggested that there were large differences between ZZ2004 and other IBV reference strains on the S1 subunit. Meanwhile, homologies in the nucleotide and amino acid sequences of the M gene of IBV ZZ2004 were 86.9–92.0 % and 91.1–93.9 %, respectively, compared with 35 other IBV reference strains derived from different regions. This result revealed that there were conspicuous variations among the selected strains. Furthermore, the results showed that the prevalent strains of IBV in ducks had no antigen homology with the vaccine strains widely used in China except the LDT3-strain, making it urgent to explore and develop new IBV vaccines.",amino acid sequence;article;Avian infectious bronchitis virus;China;cross reaction;duck;embryo death;genetic variation;M gene;nonhuman;nucleotide sequence;phenotype;phylogeny;priority journal;reverse transcription polymerase chain reaction;sequence alignment;virus gene;virus isolation;virus neutralization;virus strain,"Yao, S.;Ou, C.;Liu, X.;Wang, X.;Yao, Z.;Liu, J.",2016,,10.1007/s11262-016-1352-8,0
2355,Isolation and characterization of a native avirulent strain of Streptococcus suis serotype 2: a perspective for vaccine development,"Streptococcus suis, an emerging infectious pathogen, is the cause of two large-scale outbreaks of human streptococcal toxic shock syndrome in China, and has attracted much attention from the scientific community. The genetic basis of its pathogenesis remains enigmatic, and no effective prevention measures have been established. To better understand the virulence differentiation of S. suis and develop a promising vaccine, we isolated and sequenced a native avirulent S. suis strain (05HAS68). Animal experiments revealed that 05HAS68 is an avirulent strain and could protect piglets from the attack of virulent strains. Comparative genomics analyses demonstrated the genetic basis for the lack of virulence in 05HAS68, which is characterized by the absence of some important virulence-associated factors and the intact 89K pathogenicity island. Lack of virulence was also illustrated by reduced survival of 05HAS68 compared to a virulent strain in pig whole blood. Further investigations revealed a large-scale genomic rearrangement in 05HAS68, which was proposed to be mediated by transposase genes and/or prophages. This genomic rearrangement may have caused the genomic diversity of S. suis, and resulted in biological discrepancies between 05HAS68 and highly virulent S. suis strains.",bacterial DNA;bacterial vaccine;virulence factor;animal;bacterial genome;classification;clustered regularly interspaced short palindromic repeat;comparative genomic hybridization;disease model;DNA sequence;genetics;high throughput sequencing;human;immunology;microbiology;multigene family;phylogeny;pig;prophage;prospective study;serotype;Streptococcus infection;Streptococcus suis;virus gene,"Yao, X.;Li, M.;Wang, J.;Wang, C.;Hu, D.;Zheng, F.;Pan, X.;Tan, Y.;Zhao, Y.;Hu, L.;Tang, J.;Hu, F.",2015,,10.1038/srep09835,0
2356,Novel microRNAs encoded by duck enteritis virus,"Duck enteritis virus (DEV) is an important herpesvirus pathogen associated with acute, highly contagious lethal disease in waterfowls. Using a deep sequencing approach on RNA from infected chicken embryo fibroblast cultures, we identified several novel DEV-encoded micro (mi)RNAs. Unlike most mardivirus-encoded miRNAs, DEV-encoded miRNAs mapped mostly to the unique long region of the genome. The precursors of DEV miR-D18 and miR-D19 overlapped with each other, suggesting similarities to miRNA-offset RNAs, although only the DEV-miR-D18-3p was functional in reporter assays. Identification of these novel miRNAs will add to the growing list of virus-encoded miRNAs enabling the exploration of their roles in pathogenesis.","Animals;Cells, Cultured;Chickens;Fibroblasts/vi [Virology];High-Throughput Nucleotide Sequencing;*Mardivirus/ge [Genetics];*MicroRNAs/ge [Genetics];*RNA, Viral/ge [Genetics];0 (MicroRNAs);0 (RNA, Viral)","Yao, Y.;Smith, L. P.;Petherbridge, L.;Watson, M.;Nair, V.",2012,Jul,,0
2357,Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling,"BACKGROUND: The exact origin of the cause of the Severe Acute Respiratory Syndrome (SARS) is still an open question. The genomic sequence relationship of SARS-CoV with 30 different single-stranded RNA (ssRNA) viruses of various families was studied using two non-standard approaches. Both approaches began with the vectorial profiling of the tetra-nucleotide usage pattern V for each virus. In approach one, a distance measure of a vector V, based on correlation coefficient was devised to construct a relationship tree by the neighbor-joining algorithm. In approach two, a multivariate factor analysis was performed to derive the embedded tetra-nucleotide usage patterns. These patterns were subsequently used to classify the selected viruses. RESULTS: Both approaches yielded relationship outcomes that are consistent with the known virus classification. They also indicated that the genome of RNA viruses from the same family conform to a specific pattern of word usage. Based on the correlation of the overall tetra-nucleotide usage patterns, the Transmissible Gastroenteritis Virus (TGV) and the Feline CoronaVirus (FCoV) are closest to SARS-CoV. Surprisingly also, the RNA viruses that do not go through a DNA stage displayed a remarkable discrimination against the CpG and UpA di-nucleotide (z = -77.31, -52.48 respectively) and selection for UpG and CpA (z = 65.79,49.99 respectively). Potential factors influencing these biases are discussed. CONCLUSION: The study of genomic word usage is a powerful method to classify RNA viruses. The congruence of the relationship outcomes with the known classification indicates that there exist phylogenetic signals in the tetra-nucleotide usage patterns, that is most prominent in the replicase open reading frames.","Algorithms;Animals;Cattle;Coronavirus 229E, Human/ge [Genetics];Coronavirus, Bovine/ge [Genetics];Dinucleotide Repeats/ge [Genetics];*Gene Expression Profiling/mt [Methods];Gene Expression Profiling/sn [Statistics & Numerical Data];*Gene Expression Regulation, Viral/ge [Genetics];Genome, Viral;Hemorrhagic Disease Virus, Rabbit/ge [Genetics];Humans;*Microsatellite Repeats/ge [Genetics];Multivariate Analysis;Open Reading Frames/ge [Genetics];Phylogeny;*RNA Viruses/ge [Genetics];*RNA Viruses/py [Pathogenicity];RNA, Viral/bi [Biosynthesis];RNA, Viral/ge [Genetics];Rabbits;*SARS Virus/ge [Genetics];*SARS Virus/py [Pathogenicity];0 (RNA, Viral)","Yap, Y. L.;Zhang, X. W.;Danchin, A.",2003,Sep 20,,0
2358,Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010,"Background: In April 2009, a novel swine-derived influenza A virus (H1N1pdm) emerged and rapidly spread around the world, including Japan. It has been suggested that the virus can bind to both 2,3- and 2,6-linked sialic acid receptors in infected mammals, in contrast to contemporary seasonal H1N1 viruses, which have a predilection for 2,6-linked sialic acid. Methods/Results: To elucidate the existence and transmissibility of α2,3 sialic acid-specific viruses in H1N1pdm, amino acid substitutions within viral hemagglutinin molecules were investigated, especially D187E, D222G, and Q223R, which are related to a shift from human to avian receptor specificity. Samples from individuals infected during the first and second waves of the outbreak in Japan were examined using a high-throughput sequencing approach. In May 2009, three specimens from mild cases showed D222G and/or Q223R substitutions in a minor subpopulation of viruses infecting these individuals. However, the substitutions almost disappeared in the samples from five mild cases in December 2010. The D187E substitution was not widespread in specimens, even in May 2009. Conclusions: These results suggest that α2,3 sialic acid-specific viruses, including G222 and R223, existed in humans as a minor population in the early phase of the pandemic, and that D222 and Q223 became more dominant through human-to-human transmission during the first and second waves of the epidemic. These results are consistent with the low substitution rates identified in seasonal H1N1 viruses in 2008. © 2012 Yasugi et al.","alpha2,3 sialic acid;arginine;aspartic acid;glutamic acid;glutamine;glycine;hemagglutinin;hemagglutinin receptor;sialic acid;unclassified drug;virus hemagglutinin;2009 H1N1 influenza;amino acid substitution;article;binding site;controlled study;disease severity;epidemic;high throughput screening;human;Influenza A virus (H1N1);Japan;nonhuman;nose smear;receptor binding;seasonal influenza;sequence alignment;sequence analysis;virus replication;virus transmission","Yasugi, M.;Nakamura, S.;Daidoji, T.;Kawashita, N.;Ramadhany, R.;Yang, C. S.;Yasunaga, T.;Iida, T.;Horii, T.;Ikuta, K.;Takahashi, K.;Nakaya, T.",2012,,10.1371/journal.pone.0030946,0
2359,Isolation and molecular characterization of the influenza A/H5N1 viruses isolated during the outbreaks of avian influenza among birds in the European part of Russia in 2005: A virus strain with ozeltamivir-resistance mutation was found,"The isolation and characterization of the influenza A/H5NI viruses isolated from hens that died during the outbreak of avian influenza in autumn 2005 in the Yandovka village (Tula oblast) and from a wild swan that died near the orifice of the Volga River in the zone of the Karalat Furrow were carried out. Molecular-biologic and phylogenetic analyses were performed with a view of determining possible geographical origin of strains, phylogenetic similarity of viruses and also estimating their pathogenicity, epidemic danger for people, and possible resistance to antiviral drugs. It was shown that the virus belonged to the high pathogenic variants that arose in China as a result of the reassortment of the viruses of the genotypes Z and V that circulated among poultry and wild birds. A number of molecular markers characterizing the high pathogenicity of the virus for gallinaceous birds and mammals were revealed, but the specific mutations in the hemagglutinin gene that promote the high rate of virus replication in a human organism and also the mutations of adaptation to it were not found. It was shown that the variants of the influenza A/H5N1 virus that circulated in this epizootic were sensitive to remantadine. The strain isolated from the wild swan had the mutation causing resistance to Tamiflu/ozeltamivir.",H5N1 INFLUENZA;A VIRUSES;OSELTAMIVIR RESISTANCE;RECEPTOR SPECIFICITY;HEMAGGLUTININ;ASIA;CELL;GLYCOSYLATION;NEURAMINIDASE;CHICKENS,"Yatsyshina, S. B.;Shestopalov, A. M.;Evseyenko, V. A.;Astakhova, T. S.;Braslavskaya, S. I.;Ternovoi, V. A.;Kondratieva, T. Y.;Alekseev, A. Y.;Zolotykh, S. I.;Rassadkin, Y. N.;Zaikovskaya, A. V.;Durymanov, A. G.;Netesov, S. V.;Shipulin, G. A.",2008,Mar,,0
2360,ISOLATION AND CHARACTERIZATION OF A SMALL ROUND VIRUS ABOUT 15 NM IN DIAMETER FROM THE FECES OF THE PIGLET WITH DIARRHEA,,,"Yawei, N.;Huishen, Q.;Guoan, L.",1989,,,0
2361,Phylogenetic analysis and pathogenicity assessment of two strains of avian influenza virus subtype H9N2 isolated from migratory birds: High homology of internal genes with human H10N8 virus,"Two human-infecting avian influenza viruses (AIVs), H7N9 and H10N8, have emerged in China, which further indicate that the H9N2 subtype of AIVs, as an internal gene donor, may have an important role in the generation of new viruses with cross-species transmissibility and pathogenicity. H9N2 viruses that contain such internal genes widely exist in poultry but are rarely reported in migratory birds. In this study, two strains of the H9N2 virus were isolated from fecal samples of migratory birds in 2014: one strain from Caizi Lake in Anhui Province and one from Chen Lake in Hubei Province of China. Nucleotide sequence analysis revealed high homology of all six internal genes of these two strains with the internal genes of the human H10N8 virus in Jiangxi Province, as well as with the human H7N9 virus. Phylogenetic analysis indicated a possible origin of these two strains from poultry in South China. Both of the two viruses tested could replicated in respiratory organs of infective mice without adaption, by both strains of the H9N2 AIVs from wild birds, suggesting their potential capacity for directly infecting mammals. Our findings indicate the existence of H9N2 viruses that contain internal genes highly homologous with human H10N8 or H7N9 viruses. Wild birds can contribute to the spread of the H9N2 virus that contains the ""harmful"" internal gene complex, leading to gene rearrangement with other influenza viruses and to the generation of new pathogenic viruses. Therefore, strengthening AIV surveillance in wild birds can promote an understanding of the presence and prevalence of viruses and provide scientific evidence for the prevention and control of AIVs and human-infecting AIVs.",avian influenza virus;bird;China;clinical article;gene rearrangement;human;Influenza A virus (H10N8);Influenza A virus (H7N9);Influenza A virus (H9N2);mammal;nucleotide sequence;organ;pathogenicity;phylogeny;poultry;prevalence;virus,"Ye, G.;Liang, C. H.;Hua, D. G.;Song, L. Y.;Xiang, Y. G.;Guang, C.;Lan, C. H.;Ping, H. Y.",2016,,10.3389/fmicb.2016.00057,0
2362,"Full sequence analysis of hemagglutinin and neuraminidase genes and proteins of highly pathogenic avian influenza H5N1 virus detected in Iran, 2015","Over the last two decades, the highly pathogenic avian influenza H5N1 virus has gained a lot of attention due to its zoonotic and mutative nature. Iran is among the countries significantly affected by the virus as it hosts migratory birds during seasonal migration. In this study, the molecular characterizations of hemagglutinin (HA) and neuraminidase (NA) genes and proteins of H5N1 strain A/chicken/Iran/8/2015 detected in backyard poultry, Mazandaran province, were investigated. Phylogenetic analysis classified this virus as a member of subclade 2.3.2.1c, with the cleavage site motif of ""PQRERRRK-R/GLF"". HA carried a few mutations altering affinity to mammalian cells; however, the virus was categorized as avian. NA protein had the 20-amino acid deletion at aa position 49-69 similar to those isolated since 2000. Mutations of H253Y and H274Y contributing to antiviral resistance were present in NA. From this analysis, it can be concluded that the wild migratory birds flying from Western Asia to Eastern Africa are probably the main carriers of seasonal H5N1 in the country.",,"Yegani, S.;Shoushtari, A. H.;Eshratabadi, F.;Molouki, A.",2018,Oct 27,,0
2363,"Molecular characterization of low pathogenic avian influenza viruses, isolated from food products imported into Singapore","We have completed the genetic characterization of all eight gene segments for four low pathogenic avian influenza (LPAI) viruses. The objective of this study was to detect the presence of novel signatures that may serve as early warning indicators of the conversion of LPAI viruses to high pathogenic avian influenza (HPAI) viruses. This study included three H5N2 and one H5N3 viruses that were isolated from live poultry imported into Singapore as part of the national avian influenza virus (AIV) surveillance program. Based on the molecular criterion of the World Organisation for Animal Health (OIE), sequence analysis with the translated amino acid (aa) sequence of the hemagglutinin (HA) gene revealed the absence of multibasic aa at the HA cleavage site, identifying all four virus isolates as LPAI. Detailed phylogenetic tree analyses using the HA and neuraminidase (NA) genes clustered these isolates in the Eurasian H5 lineage, but away from the HPAI H5 subtypes. This analysis further revealed that the internal genes clustered to different avian and swine subtypes, suggesting that the four isolates may possibly share their ancestry with these different influenza subtypes. Our results suggest that the four LPAI isolates in this study contained mainly avian signatures, and the phylogenetic tree for the internal genes further suggests the potential for reassortment with other different circulating avian subtypes. This is the first comprehensive report on the genetic characterization of LPAI H5N2/3 viruses isolated in South-East Asia. © 2009 Elsevier B.V. All rights reserved.",hemagglutinin;virus RNA;virus sialidase;amino acid sequence;article;avian influenza virus;controlled study;food contamination;gene cluster;genetic reassortment;Influenza virus;Influenza A virus (H5N2);Influenza A virus (H5N3);molecular genetics;molecular phylogeny;nonhuman;nucleotide sequence;phylogenetic tree;poultry;protein degradation;sequence analysis;Singapore;Southeast Asia;virus characterization;virus classification;virus isolation;virus virulence,"Yeo, D. S. Y.;Ng, S. H.;Liaw, C. W.;Ng, L. M.;Wee, E. J. H.;Lim, E. A. S.;Seah, S. L. K.;Wong, W. K.;Lim, C. W.;Sugrue, R. J.;Tan, B. H.",2009,,10.1016/j.vetmic.2009.04.025,0
2364,Presence of bovine hepacivirus in Turkish cattle,"Hepatitis C virus (HCV), a worldwide distributed human pathogen, causes one of the most important viral infections in human being. HCV is the type species of the genus Hepacivirus (Flaviviridae) in which recently discovered animal viruses i.e. from horses, bats, rodents and cattle are allocated. After preliminary reports in 2015 from German and African cattle, a wide distribution of bovine hepacivirus (BovHepV, Hepacivirus N) was proposed. We investigated the possible presence of BovHepV in serum samples from cattle in different locations of Turkey. Analyzing a total of 120 samples from 98 female (dairy) and 22 male (beef) cattle by real-time RT-PCR resulted in 15 (12.5%) positives. BovHepV infection was detected in 6 out of 10 locations included in the study. There were positive samples both from eastern and western parts of the country indicating possible wide distribution in the Turkish cattle population. Phylogenetic analysis of 9 selected positive samples clearly assigned 8 sequences to a separate cluster on the basis of NS3 gene region, while one of the sequences obtained from an imported animal from north of Italy grouped with sequences obtained from cattle in Germany. The latter finding may indicate possible occurrence of this genetic group of BovHepV not only in Germany but in other European countries. Results of the present study demonstrate the presence of BovHepV infections in Turkey and in The Middle East region.",Bovine hepacivirus;Hepaci N;Cattle;Turkey;HEPATITIS-C VIRUS;IDENTIFICATION;VIROME,"Yesilbag, K.;Baechlein, C.;Kadiroglu, B.;Toker, E. B.;Alpay, G.;Becher, P.",2018,Nov,,0
2365,Detection and genetic characterization of feline bocavirus in Northeast China,"Background: Bocaviruses have been reported to cause respiratory tract infection and gastroenteritis in most animal species. In cats, different genotype bocaviruses have been identified in USA, Japan, Hong Kong and Portugal. However, the clear relationship between the clinical symptoms and FBoV infection is unknown, and the prevalence of FBoV and the distribution of FBoV genotypes in China are still unclear. Results: In this study, 197 fecal samples from cats with diarrhea (n = 105) and normal cats (n = 92) were collected in different regions between January 2016 and November 2017 and investigated using PCR targeting different FBoV genotypes. Screening results showed that 51 of 197 samples (25.9%) were positive for FBoV, and a higher positive rate was observed in cats with diarrhea (33.3%, 35/105) than in normal cats (17.4%, 16/92). Of these FBoV-positive samples, 35 were identified as FBoV-1, 12 as FBoV-2 and 4 as coinfection of FBoV-1 and FBoV-2. A phylogenetic analysis based on partial NS1 gene indicated that 24 sequences from randomly selected FBoV-positive samples were divided into 2 different FBoV groups: FBoV-1 and FBoV-2. Furthermore, 6 strains were randomly selected, and the complete genome was sequenced and analyzed. These strains exhibited the typical genome organization of bocavirus and were closely related to FBoV. Two FBoV-2 identified strains shared high homologies with FBoV-2 reference strains based on the complete genome and entire encoding gene, but lower identities were exhibited in the NP1 and VP1 regions for the other 4 FBoV-1 identified strains compared with FBoV-1 reference strains. Conclusion: These findings demonstrate that genetically diverse FBoV-1 and FBoV-2 widely circulate in cats in Northeast China and that FBoV-1 is more prevalent. The high prevalence of FBoV in cats with diarrhea symptoms suggests that FBoV infection may be associated with diarrhea in cats.",Feline bocavirus;Genotype;Genetic characterization;Complete genome;NONSTRUCTURAL PROTEIN NP1;CANINE BOCAVIRUSES;PORCINE BOCAVIRUS;MINUTE;VIRUS;FECAL VIROME;REVEALS;CATS;DOGS,"Yi, S. S.;Niu, J. T.;Wang, H. L.;Dong, G. Y.;Zhao, Y. L.;Dong, H.;Guo, Y. B.;Wang, K.;Hu, G. X.",2018,Aug,,0
2366,Novel highly divergent sapoviruses detected by metagenomics analysis in straw-colored fruit bats in Cameroon,"Sapoviruses (SaVs) belong to the Sapovirus genus, in the family Caliciviridae. They have been associated with gastroenteritis in humans and in pigs but not in other animals. In addition, some strains from pigs, chimpanzees and rodents show close sequence identity with human SaVs thereby suggesting the possibility of interspecies transmissions. Bats are known to be a major reservoir of zoonotic viruses, however, very little is known about the genetic diversity of SaVs in bats. To explore the genetic diversity of bat SaVs, fecal samples of Eidolon helvum and Epomophorus gambianus were treated according to the NetoVIR protocol and sequenced by Illumina technology. Nearly complete genome sequences of six highly divergent SaVs and one partial SaV (only VP1 region) were identified in Eidolon helvum and based on sequence identities and phylogenetic analysis, they potentially represent two novel genogroups, only distantly related to known SaVs. Furthermore, comparing these sequences with currently used screening primers and probes indicated that the novel SaVs would not be detected in routine epidemiological screening studies in humans in case an interspecies transmission would occur. Therefore, we designed and validated new primers that can detect both human and bat SaVs. In this study, we identified multiple novel bat SaVs, however, further epidemiological studies in humans are needed to unravel their potential role in gastroenteritis.",adult;article;bat;Cameroon;feces analysis;female;gastroenteritis;gene sequence;genetic variability;genome;human;male;metagenomics;nonhuman;phylogeny;priority journal;Sapovirus,"Yinda, C. K.;Conceição-Neto, N.;Zeller, M.;Heylen, E.;Maes, P.;Ghogomu, S. M.;Van Ranst, M.;Matthijnssens, J.",2017,,10.1038/emi.2017.20,0
2367,"Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code","Most human emerging infectious diseases originate from wildlife and bats are a major reservoir of viruses, a few of which have been highly pathogenic to humans. In some regions of Cameroon, bats are hunted and eaten as a delicacy. This close proximity between human and bats provides ample opportunity for zoonotic events. To elucidate the viral diversity of Cameroonian fruit bats, we collected and metagenomically screened eighty-seven fecal samples of Eidolon helvum and Epomophorus gambianus fruit bats. The results showed a plethora of known and novel viruses. Phylogenetic analyses of the eleven gene segments of the first complete bat rotavirus H genome, showed clearly separated clusters of human, porcine, and bat rotavirus H strains, not indicating any recent interspecies transmission events. Additionally, we identified and analyzed a bat bastrovirus genome (a novel group of recently described viruses, related to astroviruses and hepatitis E viruses), confirming their recombinant nature, and provide further evidence of additional recombination events among bat bastroviruses. Interestingly, picobirnavirus-like RNA-dependent RNA polymerase gene segments were identified using an alternative mitochondrial genetic code, and further principal component analyses suggested that they may have a similar lifestyle to mitoviruses, a group of virus-like elements known to infect the mitochondria of fungi. Although identified bat coronavirus, parvovirus, and cyclovirus strains belong to established genera, most of the identified partitiviruses and densoviruses constitute putative novel genera in their respective families. Finally, the results of the phage community analyses of these bats indicate a very diverse geographically distinct bat phage population, probably reflecting different diets and gut bacterial ecosystems.",,"Yinda, C. K.;Ghogomu, S. M.;Conceicao-Neto, N.;Beller, L.;Deboutte, W.;Vanhulle, E.;Maes, P.;Van Ranst, M.;Matthijnssens, J.",2018,Jan,,0
2368,Phylogenetic evidence for inter-typic recombination in the emergence of human enterovirus 71 subgenotypes,"Background: Human enterovirus 71 (EV-71) is a common causative agent of hand, foot and mouth disease (HFMD). In recent years, the virus has caused several outbreaks with high numbers of deaths and severe neurological complications. Several new EV-71 subgenotypes were identified from these outbreaks. The mechanisms that contributed to the emergence of these subgenotypes are unknown. Results: Six EV-71 isolates from an outbreak in Malaysia, in 1997, were sequenced completely. These isolates were identified as EV-71 subgenotypes, B3, B4 and C2. A phylogenetic tree that correlated well with the present enterovirus classification scheme was established using these full genome sequences and all other available full genome sequences of EV-71 and human enterovirus A (HEV-A). Using the 5′ UTR, P2 and P3 genomic regions, however, isolates of EV-71 subgenotypes B3 and C4 segregated away from other EV-71 subgenotypes into a cluster together with coxsackievirus A16 (CV-A16/G10) and EV-71 subgenotype C2 clustered with CV-A8. Results from the similarity plot analyses supported the clustering of these isolates with other HEV-A. In contrast, at the same genomic regions, a CV-A16 isolate, Tainan5079, clustered with EV-71. This suggests that amongst EV-71 and CV-A16, only the structural genes were conserved. The 3′ end of the virus genome varied and consisted of sequences highly similar to various HEV-A viruses. Numerous recombination crossover breakpoints were identified within the non-structural genes of some of these newer EV-71 subgenotypes. Conclusion: Phylogenetic evidence obtained from analyses of the full genome sequence supports the possible occurrence of inter-typic recombination involving EV-71 and various HEV-A, including CV-A16, the most common causal agent of HFMD. It is suggested that these recombination events played important roles in the emergence of the various EV-71 subgenotypes. © 2006 Yoke-Fun and AbuBakar; licensee BioMed Central Ltd.",5' untranslated region;article;controlled study;Enterovirus;Coxsackievirus A16;coxsackie virus a8;Enterovirus A71;gene sequence;gene structure;genetic recombination;genotype;nonhuman;phylogenetic tree;phylogeny;viral genetics;virus classification;virus gene;virus identification;virus isolation;virus recombination,"Yoke-Fun, C.;AbuBakar, S.",2006,,10.1186/1471-2180-6-74,0
2369,Tracing the genetic history of porcine reproductive and respiratory syndrome viruses derived from the complete ORF 5-7 sequences: A Bayesian coalescent approach,"To trace the genetic history of porcine reproductive and respiratory syndrome virus (PRRSV), we determined the complete sequences of ORFs 5 to 7 of four PRRSV isolates. These sequences were analyzed together with published sequences from 146 isolates from various parts of the world using a Bayesian coalescent approach as well as Bayesian inference and maximum-likelihood methods. All of the European-type (EU-type) viruses were classified into one of two groups or unclassified (4 isolates), while all North American-type (NA-type) viruses belonged to one of three major groups or were unclassified (5 isolates). Within each genotype, no apparent periodic and/or geographic influence on the evolution of PRRSVs was observed. The evolutionary rate of PRRSV isolates was estimated to be 1. 55 × 10-3 substitutions/site/year, and the time of the most recent common ancestor (TMRCA) was 491. 2 years ago. Here, the TMRCA for the EU- and NA-type viruses was 58. 7 and 62. 6 years ago, respectively. A Bayesian skyline plot revealed that the viruses evolved at an almost constant population size until the late 1970s, when they experienced a population expansion that continued until the late 1980s. The population size then remained constant again until the early 2000s, when a rapid, sharp decline in the effective number of infections occurred. © 2012 Springer-Verlag.",virus RNA;animal;Arterivirus;article;classification;cluster analysis;DNA sequence;genetics;genotype;isolation and purification;molecular evolution;molecular genetics;mutation rate;nucleotide sequence;open reading frame;phylogeography;porcine reproductive and respiratory syndrome;pig;virology,"Yoon, S. H.;Kim, H.;Park, B.;Kim, H.",2012,,10.1007/s00705-012-1408-6,0
2370,Phylogenomics and molecular evolution of foot-and-mouth disease virus,"This report describes the use of Bayesian methods to analyze polyprotein coding region sequences (n = 217) obtained from GenBank to define the genome-wide phylogeny of foot and mouth disease virus (FMDV). The results strongly supported the monophyly of five FMDV serotypes, O, A, Asia 1, C, and SAT 3, while sequences for the two remaining FMDV serotypes, SAT 1 and SAT 2 did not separate into entirely distinct clades. The phylogenomic tree revealed three sister-group relationships, serotype O + Asia 1, A + C, and SAT 1 + 3 + 2, with a new branching pattern: {[(O, Asia 1), (A, C)], (SAT 1, 2, 3)}. Within each serotype, there was no apparent periodic, geographic, or host species influence on the evolution of global FMDVs. Analysis of the polyprotein coding region of these sequences provided evidence for the influence of purifying selection on the evolution of FMDV. Using a Bayesian coalescent approach, the evolutionary rate of FMDV isolates that circulated during the years 1932-2007 was estimated to be 1.46 × 10-3 substitutions/site/year, and the most recent common ancestor of the virus existed approximately 481 years ago. Bayesian skyline plot revealed a population expansion in the early 20th century that was followed by a rapid decline in population size from the late 20th century to the present day. These findings provide new insights into the mechanisms that impact on the evolution of this important livestock pathogen. © 2011 KSMCB.",polyprotein;article;Bayes theorem;cladistics;Foot and mouth disease virus;molecular evolution;nonhuman;nucleotide sequence;phylogenomics;serotype;unindexed sequence;virus isolation,"Yoon, S. H.;Park, W.;King, D. P.;Kim, H.",2011,,10.1007/s10059-011-0249-6,0
2371,Polymerase chain reaction-based genetic typing of Japanese porcine reproductive and respiratory syndrome viruses,"Porcine reproductive and respiratory syndrome viruses (PRRSVs) are classified into 2 distinct genotypes: the North American type and the European type. The Japanese PRRSVs were genotyped by reverse transcriptase-polymerase chain reaction using the reported primer pairs that were either reactive to both types, specific to the North American type or specific to the European type. All the PRRSV genomes from 66 tissue homogenates or sera and 55 infectious viruses were of the North American type, whereas no European-type viral genome was detected. Two PCR primers specific to the North American type showed different detection efficiency. Half of the tissue samples and 15% of the infectious viruses were not detected with one primer pair, although all of them were detected with the other primer pair. Nucleotide sequencing analysis of the forward- and reverse primer-binding sites of the nonreactive viruses indicated that all these viruses had nucleotide mismatches within the 4 bases corresponding to the 3′ end of the reverse primer. These mismatches appeared to be responsible for the nonreactivity of the former primers to these viruses.",animal;animal disease;Arterivirus;article;DNA sequence;genetics;genotype;Japan;molecular genetics;North America;nucleotide sequence;reverse transcription polymerase chain reaction;pig;virus infection,"Yoshii, M.;Kaku, Y.;Murakami, Y.;Shimizu, M.;Kato, K.;Ikeda, H.",2004,,,0
2372,Molecular and serological epidemiology of Japanese encephalitis virus (JEV) in a remote Island of Western Japan: An implication of JEV migration over the East China Sea,"Background: Japanese encephalitis (JE) is a mosquito-borne infectious disease caused by Japanese encephalitis virus (JEV). About 1-10 cases with severe central nervous system symptoms have been constantly reported every year in Japan. To clarify the mechanism of maintenance of JEV, the present study surveyed pigs for serological evidence of JEV infection and isolated JEV strains from pigs and mosquitoes in Isahaya City (Isahaya) and Goto City (Goto) in the islets of Goto in Nagasaki Prefecture from 2008 to 2014. Results: The serological survey of pigs showed the increase of IgM sero-positivity against JEV in July or August, and it was maintained until October or November in both Isahaya and Goto every year. There were 47 JEV strains isolated in Nagasaki from 2001 to 2014 including the isolates in this study, and they belonged to genotype 1. Thirty four of the isolated strains were from pigs in Isahaya and were classified under six subclusters (1-A-1, 1-A-2, 1-A-3, 1-A-4, 1-A-5, and 1-A-9). Thirteen strains were isolated from pigs and mosquitoes in Goto and were classified into three subclusters (1-A-5 (2008); 1-A-1 (2009); and 1-A-2). In the subcluster 1-A-2, three different monophyletic subgroups, 1-A-2-2 (2010), 1-A-2-3 (2011), and 1-A-2-1 (2013, 2014), appeared in Goto. Conclusions: These data strongly suggested that JEV appearance in Goto seems to depend on the frequent introduction of JEV from outside of the island and this pattern is different from what has been observed in subtropical islands in the East China Sea such as Okinawa and Taiwan, where the same populations of JEV (1-A-7 (1998-2008) in Okinawa; genotype 3 (until 2012) in Taiwan) have been maintained for a long period.",article;controlled study;enzyme linked immunosorbent assay;gene cluster;Japan;Japanese encephalitis virus;molecular genetics;nonhuman;phylogenetic tree;phylogeny;reverse transcription polymerase chain reaction;sea;sequence analysis;serology;virus isolation,"Yoshikawa, A.;Nabeshima, T.;Inoue, S.;Agoh, M.;Morita, K.",2016,,10.1186/s41182-016-0010-0,0
2373,"Molecular epidemiology of coxsackievirus A6 derived from hand, foot, and mouth disease in Fukuoka between 2013 and 2017","Coxsackievirus (CV)-A6 has been the primary causative agent of hand, foot, and mouth disease (HFMD) in Japan since 2011. In Fukuoka, CV-A6-associated HFMD caused epidemics in 2013, 2015, and 2017. This paper reports the genetic characteristics of the CV-A6 entire viral protein 1 (VP1) derived from patients with HFMD in Fukuoka between 2013 and 2017. CV-A6 was detected in 105 of 280 clinical specimens, and the entire VP1 sequences could be analyzed for 90 of the 105 specimens. Phylogenetic analysis revealed that the CV-A6 strains were classified into clade A and subgrouped into subclade A3 or subclade A4. Each subclade strain carried amino acid substitutions in the presumed DE and GH loops of the VP1, and no amino acid substitutions were identified as deleterious to the protein function. No significant difference was found in the clinical symptoms between the genetic subclades using statistical analyses. In conclusion, this study clarified the genetic diversity of CV-A6 in Fukuoka from 2013 to 2017. The emergence of the CV-A6 strains was classified into derived new subclades based on phylogenetic analysis of the VP1 gene that may cause CV-A6-associated HFMD epidemics approximately every 2 years.",protein VP1;adolescent;adult;amino acid sequence;amino acid substitution;article;child;cladistics;clinical feature;controlled study;Coxsackievirus A6;Enterovirus;female;genetic analysis;genetic trait;genetic variability;hand foot and mouth disease;human;infant;Japan;major clinical study;male;molecular epidemiology;nonhuman;nucleotide sequence;phylogeny;preschool child;protein function;school child;symptom;viral genetics;virus detection;virus gene;virus strain;VP1 gene,"Yoshitomi, H.;Ashizuka, Y.;Ichihara, S.;Nakamura, T.;Nakamura, A.;Kobayashi, T.;Kajiwara, J.",2018,,10.1002/jmv.25250,0
2374,VIRAL INFECTIONS OF DOMESTIC ANIMALS Review,,"*Allergy and Immunology;Animals;*Animals, Domestic;*Classification;*Communicable Disease Control;Female;Pregnancy;*Veterinary Medicine;*Virus Diseases","Young, G. A.",1964,,,0
2375,Isolation and genetic characterization of avian-like H1N1 and novel ressortant H1N2 influenza viruses from pigs in China,"As pigs are susceptible to both human and avian influenza viruses, they have been proposed to be intermediate hosts or mixing vessels for the generation of pandemic influenza viruses through reassortment or adaptation to the mammalian host. In this study, we reported avian-like H1N1 and novel ressortant H1N2 influenza viruses from pigs in China. Homology and phylogenetic analyses showed that the H1N1 virus (A/swine/Zhejiang/1/07) was closely to avian-like H1N1 viruses and seemed to be derived from the European swine H1N1 viruses, which was for the first time reported in China; and the two H1N2 viruses (A/swine/Shanghai/1/07 and A/swine/Guangxi/13/06) were novel ressortant H1N2 influenza viruses containing genes from the classical swine (HA, NP, M and NS), human (NA and PB1) and avian (PB2 and PA) lineages, which indicted that the reassortment among human, avian, and swine influenza viruses had taken place in pigs in China and resulted in the generation of new viruses. The isolation of avian-like H1N1 influenza virus originated from the European swine H1N1 viruses, especially the emergence of two novel ressortant H1N2 influenza viruses provides further evidence that pigs serve as intermediate hosts or ""mixing vessels"", and swine influenza virus surveillance in China should be given a high priority. © 2009.",avian influenza;China;controlled study;genetic analysis;Influenza virus;Influenza A virus;Influenza A virus (H1N1);Influenza A virus (H1N2);nonhuman;phylogeny;priority journal;sequence homology;short survey;pig;swine influenza virus;virus isolation,"Yu, H.;Zhang, P. C.;Zhou, Y. J.;Li, G. X.;Pan, J.;Yan, L. P.;Shi, X. X.;Liu, H. L.;Tong, G. Z.",2009,,10.1016/j.bbrc.2009.05.056,0
2376,Genetic diversity of H9N2 influenza viruses from pigs in China: A potential threat to human health?,"Pandemic strains of influenza A virus might arise by genetic reassortment between viruses from different hosts. Pigs are susceptible to both human and avian influenza viruses and have been proposed to be intermediate hosts or mixing vessels, for the generation of pandemic influenza viruses through reassortment or adaptation to the mammalian host. In this study, we summarize and report for the first time the coexistence of 10 (A-J) genotypes in pigs in China by analyzing the eight genes of 28 swine H9N2 viruses isolated in China from 1998 to 2007. Swine H9N2 viruses in genotype A and B were completely derived from Y280-like and Shanghai/F/98-like viruses, respectively, which indicated avian-to-pig interspecies transmission of H9N2 viruses did exist in China. The other eight genotype (C-J) viruses might be double-reassortant viruses, in which six genotype (E-J) viruses possessed 1-4 H5-like gene segments indicating they were reassortants of H9 and H5 viruses. In conclusion, genetic diversity of H9N2 influenza viruses from pigs in China provides further evidence that avian to pig interspecies transmission of H9N2 viruses did occur and might result in the generation of new reassortant viruses by genetic reassortment with swine H1N1, H1N2 and H3N2 influenza viruses, therefore, these swine H9N2 influenza viruses might be a potential threat to human health and continuing to carry out swine influenza virus surveillance in China is of great significance. © 2010 Elsevier B.V.",article;China;gene sequence;genetic variability;genotype;health hazard;Influenza A virus (H9N2);nonhuman;nucleotide sequence;swine influenza;virus gene;virus isolation;virus transmission,"Yu, H.;Zhou, Y. J.;Li, G. X.;Ma, J. H.;Yan, L. P.;Wang, B.;Yang, F. R.;Huang, M.;Tong, G. Z.",2011,,10.1016/j.vetmic.2010.11.008,0
2377,Further evidence for infection of pigs with human-like H1N1 influenza viruses in China,"Classical swine and avian-like H1N1 influenza viruses were reported widely in swine population worldwide, but human-like H1N1 swine viruses were reported occasionally. In 2006, a human-like H1N1 swine virus (A/swine/Guangdong/96/06) was isolated from pigs in Guangdong province, which was reported in China for the first time. To get further evidence for infection of pigs with human-like H1N1 influenza viruses, we analyzed eight gene segments of three human-like swine H1N1 viruses (A/swine/Guangdong/96/06, A/swine/Tianjin/01/04 and A/swine/Henan/01/06) isolated in China. All the eight genes of the three viruses are highly homologous to recent (about 2000) and early (1980s) human H1N1 influenza viruses, respectively. Phylogenetic analyses revealed that A/Swine/Guangdong/96/06 was directly derived from about 2000 human H1N1 influenza viruses, while A/swine/Tianjin/01/04 and A/swine/Henan/01/06 seemed to be descendants of human H1N1 viruses circulating in 1980s. Seroprevalence of our isolate (A/swine/Guangdong/96/06) confirmed the presence of human-like H1N1 virus in pigs in China. Existence of these influenza viruses, especially older viruses (A/swine/Tianjin/01/04 and A/swine/Henan/01/06), indicates that human-like H1N1 influenza viruses may remain invariant for long periods in pigs and provides the evidence that pigs serve as reservoirs of older influenza viruses for human pandemics. © 2008 Elsevier B.V. All rights reserved.",animal experiment;animal model;article;gene isolation;influenza;Influenza A virus (H1N1);nonhuman;nucleotide sequence;phylogeny;priority journal;swine influenza virus,"Yu, H.;Zhou, Y. J.;Li, G. X.;Zhang, G. H.;Liu, H. L.;Yan, L. P.;Liao, M.;Tong, G. Z.",2009,,10.1016/j.virusres.2008.11.008,0
2378,Detection of novel viruses in porcine fecal samples from China,"Background: Pigs are well known source of human infectious disease. To better understand the spectrum of viruses present in pigs, we utilized the 454 Life Sciences GS-FLX high-throughput sequencing platform to sequence stool samples from healthy pigs. Findings. Total nucleic acid was extracted from stool samples of healthy piglets and randomly amplified. The amplified materials were pooled and processed using a high-throughput pyrosequencing technique. The raw sequences were deconvoluted on the basis of the barcode and then processed through a standardized bioinformatics pipeline. The unique reads (348, 70 and 13) had limited similarity to known astroviruses, bocaviruses and parechoviruses. Specific primers were synthesized to assess the prevalence of the viruses in healthy piglets. Our results indicate extremely high rates of positivity. Conclusions: Several novel astroviruses, bocaviruses and Ljungan-like viruses were identified in stool samples from healthy pigs. The rates of isolation for the new viruses were high. The high detection rate, diverse sequences and categories indicate that pigs are well-established reservoirs for and likely sources of different enteric viruses. © 2013 Yu et al; licensee BioMed Central Ltd.",article;Astroviridae;bioinformatics;biomedicine;Bocaparvovirus;feces analysis;high throughput sequencing;nonhuman;nucleotide sequence;open reading frame;Parechovirus;pyrosequencing;virus detection,"Yu, J. M.;Li, J. S.;Ao, Y. Y.;Duan, Z. J.",2013,,10.1186/1743-422x-10-39,1
2379,Identification of a Novel Picornavirus in Healthy Piglets and Seroepidemiological Evidence of Its Presence in Humans,"In this study, we describe a novel porcine parechovirus-like virus (tentatively named PLV-CHN) from healthy piglets in China using 454 high-throughput sequencing. The complete genome of the virus comprises 6832 bp, encoding a predicted polyprotein of 2132 amino acids that is most similar to Ljungan virus (32% identity). A similar virus that belongs to a novel Picornaviridae genus, named swine pasivirus 1 (SPaV-1), was reported during the preparation of this paper. Sequence analysis revealed that PLV-CHN and SPaV1 shared 82% nucleotide identity and 89% amino acid identity. Further genomic and phylogenetic analyses suggested that both SPaV1 and PLV-CHN shared similar genomic characteristics and belong to the same novel Picornaviridae genus. A total of 36 (20.0%) fecal samples from 180 healthy piglets were positive for PLV-CHN by RT-PCR, while no fecal samples from 100 healthy children and 100 children with diarrhea, and no cerebrospinal fluid samples from 196 children with suspected viral encephalitis, was positive for the virus. However, Western blot and enzyme-linked immunosorbent assays using recombinant PLV-CHN VP1 polypeptide as an antigen showed a high seroprevalence of 63.5% in the healthy population. When grouped by age, the antibody-positivity rates showed that the majority of children under 12 years of age have been infected by the virus. It was suggested that PLV-CHN, SPaV1, or an as-yet-uncharacterized virus can infect humans early in life. Thus, investigation of the role of this novel virus is vital. © 2013 Yu et al.",acute gastroenteritis;age distribution;animal cell;article;child;China;controlled study;diarrhea;enzyme linked immunosorbent assay;feces analysis;high throughput sequencing;human;human cell;Ljungan virus;major clinical study;nonhuman;nucleotide sequence;phylogeny;Picornaviridae;piglet;porcine parechovirus like virus;reverse transcription polymerase chain reaction;school child;sequence analysis;seroepidemiology;seroprevalence;swine pasivirus 1;virus encephalitis;virus genome;virus identification;Western blotting,"Yu, J. M.;Li, X. Y.;Ao, Y. Y.;Li, L. L.;Liu, N.;Li, J. S.;Duan, Z. J.",2013,,10.1371/journal.pone.0070137,0
2380,Molecular characteristics of full-length genomic segment A of three infectious bursal disease viruses in China: two attenuated strains and one virulent field strain,"The full-length cDNA of genomic segment A of three infectious bursal disease viruses, two attenuated strains (HZ2 and JD1) and one virulent field strain (ZJ2000), was amplified in a single step by reverse transcription-polymerase chain reaction, cloned into pGEM-T Easy Vector, and sequenced. The full length of cloned segment A contains 3259 nucleotides, which includes two partially overlapping open reading fragments (ORFs) ORF1 and ORF2, flanked by 5' and 3' noncoding regions. These strains shared high sequence identity with each other either at the nucleotide or deduced amino acid level. Strains HZ2 and JD1 were highly related to two attenuated strains, CEF94 and P2, whereas ZJ2000 was closely related to two other virulent strains, Cu-1 and Harbin. Substitutions of four amino acids at positions 253, 279, 284, and 330, a common feature of attenuated and most virulent strains, were also observed in these three strains. Two major hydrophilic peaks were conserved in the three strains; however, there are two amino acid substitutions at positions 280 (N to S) and 290 (M to L) in the second minor hydrophilic peak for all three strains, which might have a critical influence on antigenicity. Two amino acid substitutions near the VP2-VP4 cleavage site were identified in virulent strain JZ2000, which might be involved in increasing the virulence of the virus. Phylogenetic analyses indicated that these three Chinese strains are most closely related to some European virulent strains but are distinct from very virulent infectious bursal disease virus and variant strains.",complementary DNA;virus RNA;animal;animal disease;article;bird disease;chicken;China;classification;gene amplification;genetics;infectious bursal disease virus;molecular genetics;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;sequence analysis;virology;virulence;virus infection,"Yu, L.;Li, J. R.;Huang, Y. W.;Dikki, J.;Deng, R.",2001,,,0
2381,Growth characteristics and complete genomic sequence analysis of a novel pseudorabies virus in China,"Swine pseudorabies (PR) re-emerged in Bartha-vaccinated pig herds and caused death of millions of piglets in China since the later part of 2011. We isolated a novel pseudorabies virus (PRV), named HNX strain, from the brain of abortion fetuses to diagnose the disease. To reveal the genomic organization and characterize the HNX strain, the complete genomes of HNX and Fa strain, an isolate in the 1960s, were sequenced and analyzed. The genomic size of HNX and Fa strains were 142,294 and 141,930 nt, respectively, with corresponding G + C contents of 73.56 and 73.70 %. The two strains consistently possessed 70 open reading frames. In addition, comparative genomic analysis between HNX and Bartha strains was performed to understand the possible reason of immune failure. The major virulence-associated genes of HNX strain had slight changes, whereas glycoprotein B and glycoprotein C genes of HNX strain had 73 mutations; the homology at the whole genomic level between HNX and Bartha strains was 90.6 %. Genome-wide comparison between HNX and Fa strains indicated that the strains shared about 96.4 % of homology and clustered in a separate Chinese isolate group; the two strains are also distant from the isolates from other countries. Similarity plot and bootscanning analysis of complete genome sequences of nine PRV strains, including HNX and Fa, four newly Chinese strains, and three traditional reference strains, revealed that non-recombination events occurred in the HNX strain. The PRV HNX strain with genomic variations might contribute to the PR outbreak in China since the later part of 2011.",glycoprotein B;protein C;animal cell;article;China;controlled study;fetus;gene cluster;gene mapping;gene mutation;gene structure;genetic analysis;genetic variability;human;human tissue;nonhuman;nucleotide sequence;open reading frame;phylogeny;priority journal;Pseudorabies virus;sequence analysis;virogenesis;virus gene;virus identification;virus isolation;virus strain;virus virulence,"Yu, T.;Chen, F.;Ku, X.;Fan, J.;Zhu, Y.;Ma, H.;Li, S.;Wu, B.;He, Q.",2016,,10.1007/s11262-016-1324-z,0
2382,Influenza H7N9 and H9N2 viruses: Coexistence in poultry linked to human H7N9 infection and genome characteristics,"Avian influenza virus A of the novel H7N9 reassortant subtype was recently found to cause severe human respiratory infections in China. Live poultry markets were suspected locations of the human H7N9 infection sources, based on the cases' exposure histories and sequence similarities between viral isolates. To explore the role of live poultry markets in the origin of the novel H7N9 virus, we systematically examined poultry and environmental specimens from local markets and farms in Hangzhou, using realtime reverse transcription-PCR (RT-PCR) as well as high-throughput next-generation sequencing (NGS). RT-PCR identified specimens positive for the H7 and N9 genomic segments in all of the 12 poultry markets epidemiologically linked to 10 human H7N9 cases. Chickens, ducks, and environmental specimens from the markets contained heavily mixed subtypes, including H7, N9, H9, and N2 and sometimes H5 and N1. The idea of the coexistence of H7N9 and H9N2 subtypes in chickens was further supported by metagenomic sequencing. In contrast, human H7N9 infection cases (n=31) were all negative for H9N2 virus according to real-time RT-PCR. The six internal segments were indistinguishable for the H7N9 and H9N2 viruses. The H9, N2, and internal- segment sequences were very close to the sequence of the H9N2 virus circulating in chickens in China recently. Our results provide direct evidence that H9N2 strains coexisted with the novel human-pathogenic H7N9 influenza virus in epidemiologically linked live poultry markets. Avian influenza A virus of the H9N2 subtype likely made a recent contribution to the evolution of the H7N9 virus and continues to do so. © 2014, American Society for Microbiology.",amino acid;animal experiment;article;avian influenza;chicken;China;controlled study;genome analysis;high throughput sequencing;Influenza A virus (H7N9);Influenza A virus (H9N2);metagenomics;molecular phylogeny;next generation sequencing;nonhuman;nucleotide sequence;poultry;priority journal;quantitative analysis;real time polymerase chain reaction;reverse transcription polymerase chain reaction;RNA sequence;sequence analysis;social marketing;unindexed sequence;virus genome;virus identification,"Yu, X.;Jin, T.;Cui, Y.;Pu, X.;Li, J.;Xu, J.;Liu, G.;Jia, H.;Liu, D.;Song, S.;Yu, Y.;Xie, L.;Huang, R.;Ding, H.;Kou, Y.;Zhou, Y.;Wang, Y.;Xu, X.;Yin, Y.;Wang, J.;Guo, C.;Yang, X.;Hu, L.;Wu, X.;Wang, H.;Liu, J.;Zhao, G.;Zhou, J.;Pan, J.;Gao, G. F.;Yang, R.;Wang, J.",2014,,10.1128/jvi.02059-13,1
2383,Newly emergent highly pathogenic H5N9 subtype avian influenza A virus,"The novel H7N9 avian influenza virus (AIV) was demonstrated to cause severe human respiratory infections in China. Here, we examined poultry specimens from live bird markets linked to human H7N9 infection in Hangzhou, China. Metagenomic sequencing revealed mixed subtypes (H5, H7, H9, N1, N2, and N9). Subsequently, AIV subtypes H5N9, H7N9, and H9N2 were isolated. Evolutionary analysis showed that the hemagglutinin gene of the novel H5N9 virus originated from A/Muscovy duck/Vietnam/ LBM227/2012 (H5N1), which belongs to clade 2.3.2.1. The neuraminidase gene of the novel H5N9 virus originated from human-infective A/Hangzhou/1/2013 (H7N9). The six internal genes were similar to those of other H5N1, H7N9, and H9N2 virus strains. The virus harbored the PQRERRRKR/GL motif characteristic of highly pathogenic AIVs at the HA cleavage site. Receptor- binding experiments demonstrated that the virus binds α-2,3 sialic acid but not α-2,6 sialic acid. Identically, pathogenicity experiments also showed that the virus caused low mortality rates in mice. This newly isolated H5N9 virus is a highly pathogenic reassortant virus originating from H5N1, H7N9, and H9N2 subtypes. Live bird markets represent a potential transmission risk to public health and the poultry industry.","alpha 2,3 sialic acid;apha 2,6 sialic acid;hemagglutinin;sialic acid;sialidase;unclassified drug;animal experiment;animal tissue;article;avian influenza;avian influenza virus;chicken;China;controlled study;disease transmission;duck;hemagglutinin gene;Influenza A virus (H5N1);Influenza virus A H5N9;Influenza A virus (H7N9);Influenza A virus (H9N2);mortality;mouse;neuraminidase gene;next generation sequencing;nonhuman;nucleotide sequence;priority journal;quail;receptor binding;virus attachment;virus gene;virus infection;virus isolation;virus virulence","Yu, Y.;Wang, X.;Jin, T.;Wang, H.;Si, W.;Yang, H.;Wu, J.;Yan, Y.;Liu, G.;Sang, X.;Wu, X.;Gao, Y.;Xia, X.;Yu, X.;Pan, J.;Gao, G. F.;Zhou, J.",2015,,10.1128/jvi.00653-15,0
2384,Analysis of microRNA expression profile in specific pathogen-free chickens in response to reticuloendotheliosis virus infection,"Reticuloendotheliosis virus (REV) is an avian retrovirus that causes immunosuppression, growth retardation, and oncogenesis in a variety of birds. REV infection is epidemic in many countries. In this study, we used high-throughput sequencing to identify microRNAs (miRNAs) associated with REV infection. A total of 88 differentially expressed miRNAs were identified in samples collected on days 21 and 28 post-REV infection. Possible target genes of the differentially expressed miRNAs were analyzed. We observed that expression of proapoptotic, proto-oncogene, and carcinogenic cytokine mRNAs was highly upregulated, whereas expression of antiapoptotic cytokine mRNAs was significantly downregulated. Our findings provide a potential link between miRNA expression and the pathogenesis of REV infection.",microRNA;animal experiment;animal model;article;avian reticuloendotheliosis;down regulation;germfree chicken;high throughput sequencing;nonhuman;protein expression;Reticuloendotheliosis virus;RNA analysis;RNA sequence;upregulation;virus pathogenesis,"Yu, Z.;Gao, X.;Liu, C.;Lv, X.;Zheng, S.",2017,,10.1007/s00253-016-8060-0,0
2385,Isolation and molecular analysis of porcine encephalomyocarditis virus strain BD2 from northern china,"Encephalomyocarditis virus (EMCV) can cause acute myocarditis in young pigs or reproductive failure in sows. In this study, an EMCV strain (BD2) was isolated from the suspected piglets with EMCV in China. It was identified by an indirect immunofluorescence assay and reverse-transcription polymerase chain reaction. The virus could reproduce on BHK-21 cells and reach a peak titer by 16hpi with maximum titers of 108.22TCID50/0.1ml. Phylogenetic analyses of open reading frame and the VP3/VP1 genes using neighbor-joining method revealed that EMCV isolates fell into two clusters: groups I and II. The BD2 isolate belonged to group I, along with strains NJ08, HB1, BJC3, CBNU, K3, K11, BEL-2887A, GX0601, GXLC, pEC9, and PV21, whereas four strains (D variant, EMCV-B, EMCV-D, and PV2) belonged to group II. © 2013.",antibody titer;article;BHK cell line;China;Encephalomyocarditis virus;gene cluster;gene sequence;genetic analysis;immunofluorescence;nucleotide sequence;open reading frame;phylogeny;priority journal;reverse transcription polymerase chain reaction;virus examination;virus isolation;virus strain,"Yuan, W.;Song, Q.;Zhang, X.;Zhang, L.;Sun, J.",2014,,10.1016/j.meegid.2013.11.014,0
2386,"Hepatitis E virus: Foodborne, waterborne and zoonotic transmission","Hepatitis E virus (HEV) is responsible for epidemics and endemics of acute hepatitis in humans, mainly through waterborne, foodborne, and zoonotic transmission routes. HEV is a single-stranded, positive-sense RNA virus classified in the family Hepeviridae and encompasses four known Genotypes (1-4), at least two new putative genotypes of mammalian HEV, and one floating genus of avian HEV. Genotypes 1 and 2 HEVs only affect humans, while Genotypes 3 and 4 are zoonotic and responsible for sporadic and autochthonous infections in both humans and several other animal species worldwide. HEV has an ever-expanding host range and has been identified in numerous animal species. Swine serve as a reservoir species for HEV transmission to humans; however, it is likely that other animal species may also act as reservoirs. HEV poses an important public health concern with cases of the disease definitively linked to handling of infected pigs, consumption of raw and undercooked animal meats, and animal manure contamination of drinking or irrigation water. Infectious HEV has been identified in numerous sources of concern including animal feces, sewage water, inadequately-treated water, contaminated shellfish and produce, as well as animal meats. Many aspects of HEV pathogenesis, replication, and immunological responses remain unknown, as HEV is an extremely understudied but important human pathogen. This article reviews the current understanding of HEV transmission routes with emphasis on food and environmental sources and the prevalence of HEV in animal species with zoonotic potential in humans. © 2013 by the authors; licensee MDPI, Basel, Switzerland.",virus RNA;animal disease;bird;bloodstream infection;bovid;coastal waters;deer;disease carrier;domestic animal;environmental protection;food contamination;food poisoning;food safety;genotype;hepatitis E;human;incubation time;infection prevention;infection risk;manure;Muridae;nonhuman;Leporidae;review;sewage;pig;virus classification;virus genome;virus infectivity;virus morphology;virus transmission;water contamination;wild animal;zoonosis,"Yugo, D. M.;Meng, X. J.",2013,,10.3390/ijerph10104507,0
2387,A new family of hybrid virophages from an animal gut metagenome,"Search of metagenomics sequence databases for homologs of virophage capsid proteins resulted in the discovery of a new family of virophages in the sheep rumen metagenome. The genomes of the rumen virophages (RVP) encode a typical virophage major capsid protein, ATPase and protease combined with a Polinton-type, protein primed family B DNA polymerase. The RVP genomes appear to be linear molecules, with terminal inverted repeats. Thus, the RVP seem to represent virophage-Polinton hybrids that are likely capable of formation of infectious virions. Virion proteins of mimiviruses were detected in the same metagenomes as the RVP suggesting that the virophages of the new family parasitize on giant viruses that infect protist inhabitants of the rumen.",adenosine triphosphatase;peptide hydrolase;single stranded DNA;virus DNA;animal;bacteriophage;classification;genetics;genome;metabolism;metagenome;open reading frame;phylogeny;physiology;rumen;sheep;virology;virus capsid;virus genome,"Yutin, N.;Kapitonov, V. V.;Koonin, E. V.",2015,,10.1186/s13062-015-0054-9,0
2388,Genetic and antigenic characterization of Indian foot-and-mouth disease virus serotype O isolates collected during the period 2001 to 2012,"The phylogenetic analysis of VP1 sequences of the 39 type O foot and mouth virus (FMDV) isolates collected from different regions of India during the year of 2001-12 revealed that all isolates belonged to the Middle East - South Asia (ME-SA) topotype. Based on the amount of divergence among the isolates, the viruses were further classified into three distinct lineages namely Ind 2001, PanAsia and PanAsia-2 as well as a minor, unnamed group. Ind 2001 lineage viruses accounted for most of the current type O outbreaks. At the nucleotide level these isolates showed a divergence of 2% to 14% with an average sequence variation of ∼9.9%. The serological spectrum of the current vaccine strain was studied by using bovine vaccinate serum (BVS) raised against O/IND/R2/75. All the current field isolates (n= 24) were homologous ('. r' value 0.4 to 1.0) to the vaccine strain. Examination of the amino acid sequences for selection pressure revealed the positive selection at amino acid sites 13 and 45. © 2012 Elsevier B.V..",protein VP1;amino acid sequence;antigenic variation;article;Foot and mouth disease virus;India;nonhuman;nucleotide sequence;phylogeny;priority journal;serotype;virus genome;virus strain,"Yuvaraj, S.;Madhanmohan, M.;Nagendrakumar, S. B.;Kumar, R.;Mohana Subramanian, B.;Mohapatra, J. K.;Sanyal, A.;Pattnaik, B.;Srinivasan, V. A.",2013,,10.1016/j.meegid.2012.10.004,0
2389,Mapping the virome in wild-caught Aedes aegypti from Cairns and Bangkok,,,"Zakrzewski, M.;Rašić, G.;Darbro, J.;Krause, L.;Poo, Y. S.",2018,,,0
2390,The Vampire Bat Virome: Evolutionary Implications in an Immunological Context,,,"Zamudio, M. Escalera",2016,,,0
2391,The trans-activating C-type retroviruses share a distinct epitope(s) that induces antibodies in certain infected hosts,"Using sera from hosts infected with bovine leukaemia virus (BLV), human T cell lymphoma virus types I and II (HTLV-I and -II), or simian T cell lymphoma virus type I (STLV-I), we found that the major gag proteins of these viruses cross-react immunologically. The specificity of this cross-reactivity was demonstrated by absorption using purified viral proteins, virus lysates and extracts of infected cells. The data strongly suggested that the cross-reacting epitope(s), referred to as CE, differs from those responsible for crossreactions between the major gag proteins of HTLV-I, HTLV-II and STLV-I, and between those of BLV and HTLV-I reported previously. The prevalence of antibodies to CE was low, even amongst infected hosts with high titres to other epitopes present in the major gag proteins of the homologous viruses. CE was not detected in any of the other C- or D-type retroviruses, or lentiviruses examined. Therefore, it is likely that CE can be used to define serologically a subgroup of C-type retroviruses, the genomes of which display unique features and functional activities.",cross reacting antigen;Gag protein;viral protein;antibody titer;article;Bovine leukemia virus;Human T-lymphotropic virus 1;Human T-lymphotropic virus 2;immunoblotting;leukemia virus;nonhuman;priority journal;serology;serum;transactivation;virus classification;virus typing,"Zandomeni, R.;Carrera-Zandomeni, M.;Esteban, E.;Ferrer, J. F.",1991,,,0
2392,Matrix protein gene sequence analysis of avian paramyxovirus 1 isolates obtained from pigeons,"The matrix protein gene was cloned and sequenced for several recent isolates of avian paramyxovirus type 1 (APMV-1). Specifically, isolates from pigeons and doves, members of the Columbidae family were examined. APMV-1 is the causative agent of Newcastle disease and the virus is associated with disease among a diverse number of avian species. Newcastle disease virus (NDV) isolates from pigeons have also been classified as pigeon paramyxovirus type 1 (PPMV-1). Matrix protein gene sequences for PPMV-1 isolates clustered together as a group relative to isolates from other species phylogenetically. However, there were also isolates from pigeons or doves that grouped with APMV-1 isolates from other species. This indicates that PPMV-1 may be circulating among Columbidae members as a distinct lineage, but that these avian species may also harbor other NDV strains as well. Of particular interest was a dove isolate from Europe that had an aberrant fusion protein cleavage site and was an outlying member phylogenetically between the two major groups of APMV-1 isolates.",M protein;matrix protein;virus RNA;amino acid sequence;article;avian paramyxovirus type 1;bird disease;controlled study;Columbidae;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;priority journal;reverse transcription polymerase chain reaction;virus isolation;virus replication;virus strain,"Zanetti, F.;Rodríguez, M.;King, D. J.;Capua, I.;Carrillo, E.;Seal, B. S.;Berinstein, A.",2003,,10.1023/a:1023495615729,0
2393,Genomic heterogeneity of small ruminant lentiviruses detected by PCR,"In order to detect a large spectrum of small ruminant lentiviruses, primers for PCR were chosen in conserved parts of the LTR and GAG genes of Icelandic Visna virus 1514 and of the POL gene of caprine arthritis-encephalitis virus. This set of primers was tested in six different caprine arthritis-encephalitis virus (CAEV)- and Maedi-Visna virus isolates of Dutch, American and Swiss origin. The LTR primers allowed the detection of the corresponding fragments of all isolates. The GAG primers allowed amplification of the corresponding fragments of all but the Swiss Maedi-Visna virus strain OLV. Using the POL primers, one Maedi-Visna- and two caprine arthritis-encephalitis virus strains were detected after one round of amplification. Sequencing of the GAG and POL amplification products and comparison to Icelandic Visna virus and CAEV strain CO revealed total heterogeneity of 38% for the GAG- and 28% for the POL fragment. The virus strains studied fall into two groups which are more closely related to one another than to Icelandic Visna virus.",animal cell;animal model;bovine;conference paper;genetic variability;goat;Lentivirus;nonhuman;polymerase chain reaction;sheep;veterinary medicine;virus characterization;virus classification;virus detection;virus infection;virus strain,"Zanoni, R. G.;Nauta, I. M.;Kuhnert, P.;Pauli, U.;Pohl, B.;Peterhans, E.",1992,,10.1016/0378-1135(92)90061-w,0
2394,"Influenza A(H9N2) Virus, Burkina Faso",We identified influenza A(H9N2) virus G1 lineage in poultry in Burkina Faso. Urgent actions are needed to raise awareness about the risk associated with spread of this zoonotic virus subtype in the area and to construct a strategy for effective prevention and control of influenza caused by this virus.,"Animals;Burkina Faso/ep [Epidemiology];*Chickens/vi [Virology];Gene Expression;Genotype;*Hemagglutinin Glycoproteins, Influenza Virus/ge [Genetics];Humans;Influenza A Virus, H9N2 Subtype/cl [Classification];*Influenza A Virus, H9N2 Subtype/ge [Genetics];Influenza A Virus, H9N2 Subtype/ip [Isolation & Purification];*Influenza in Birds/ep [Epidemiology];Influenza in Birds/tm [Transmission];Influenza in Birds/vi [Virology];Phylogeny;*Poultry Diseases/ep [Epidemiology];Poultry Diseases/tm [Transmission];Poultry Diseases/vi [Virology];0 (Hemagglutinin Glycoproteins, Influenza Virus);0 (hemagglutinin, avian influenza A virus)","Zecchin, B.;Minoungou, G.;Fusaro, A.;Moctar, S.;Ouedraogo-Kabore, A.;Schivo, A.;Salviato, A.;Marciano, S.;Monne, I.",2017,12,,0
2395,Phylogeography and phylodynamics of European genotype 3 hepatitis E virus,"Hepatitis E virus is classified into four genotypes that have different geographical and host distributions. The main cause of sporadic autochthonous type E acute hepatitis in developed countries is genotype 3, which has a worldwide distribution and widely infects pigs. The aim of this study was to make hypotheses concerning the origin and global dispersion routes of this genotype by reconstructing the spatial and temporal dynamics of 208 HEV genotype 3 ORF-2 sequences (retrieved from public databases) isolated in different geographical areas.The evolutionary rates, time of the most recent common ancestors (tMRCAs), epidemic growth and phylogeography of HEV-3 were co-estimated using a MCMC Bayesian method.The maximum clade credibility tree showed the existence of two distinct main clades: clade A, which consists of only European subtypes (HEV-3e and 3f), and clade B, which consists of European subtype 3c and all of the Asian subtypes (3a, 3b and 3d) sharing a common ancestor, which most probably existed in Asia in 1920s. All of the North American isolates belonged to Asian subtype 3a.On the basis of our time-scaled phylogeographical reconstruction, we hypothesise that after originating in the early 1800s in Europe, HEV reached Asia in the first decades of 1900, and then moved to America probably in the 1970s-1980s.Analysis of the skyline plot showed a sharp increase of the number of infections between the 1980s and 2005, thus suggesting the intervention of new and highly efficient routes of transmission possibly related to changes in the pig industry. © 2014 Elsevier B.V.",Africa;article;Asia;Bayes theorem;cladistics;controlled study;dispersion;Europe;evolutionary rate;genotype;hepatitis E;Hepatitis E virus;Hepatitis E virus genotype 3;human;Markov Chain Monte Carlo;nonhuman;North America;open reading frame;phylogeny;phylogeography;population dynamics;priority journal;virus classification;virus isolation,"Zehender, G.;Ebranati, E.;Lai, A.;Luzzago, C.;Paladini, S.;Tagliacarne, C.;Galli, C.;Galli, M.;Ciccozzi, M.;Zanetti, A. R.;Romanò, L.",2014,,10.1016/j.meegid.2014.04.016,0
2396,New ecological aspects of hantavirus infection: A change of a paradigm and a challenge of prevention - A review,"In the last decades a significant number of so far unknown or underestimated pathogens have emerged as fundamental health hazards of the human population despite intensive research and exceptional efforts of modern medicine to embank and eradicate infectious diseases. Almost all incidents caused by such emerging pathogens could be ascribed to agents that are zoonotic or expanded their host range and crossed species barriers. Many different factors influence the status of a pathogen to remain unnoticed or evolves into a worldwide threat. The ability of an infectious agent to adapt to changing environmental conditions and variations in human behavior, population development, nutrition, education, social, and health status are relevant factors affecting the correlation between pathogen and host. Hantaviruses belong to the emerging pathogens having gained more and more attention in the last decades. These viruses are members of the family Bunyaviridae and are grouped into a separate genus known as Hantavirus. The serotypes Hantaan (HTN), Seoul (SEO), Puumala (PUU), and Dobrava (DOB) virus predominantly cause hemorrhagic fever with renal syndrome (HFRS), a disease characterized by renal failure, hemorrhages, and shock. In the recent past, many hantavirus isolates have been identified and classified in hitherto unaffected geographic regions in the New World (North, Middle, and South America) with characteristic features affecting the lungs of infected individuals and causing an acute pulmonary syndrome. Hantavirus outbreaks in the United States of America at the beginning of the 10th decade of the last century fundamentally changed our knowledge about the appearance of the hantavirus specific clinical picture, mortality, origin, and transmission route in human beings. The hantavirus pulmonary syndrome (HPS) was first recognized in 1993 in the Four Corners Region of the United States and had a lethality of more than 50%. Although the causative virus was first termed in connection with the geographic name of its outbreak region the analysis of the individual viruses indicate that the causing virus of HPS was a genetically distinct hantavirus and consequently termed as Sin Nombre virus. Hantaviruses are distributed worldwide and are assumed to share a long time period of co-evolution with specific rodent species as their natural reservoir. The degree of relatedness between virus serotypes normally coincides with the relatedness between their respective hosts. There are no known diseases that are associated with hantavirus infections in rodents underlining the amicable relationship between virus and host developed by mutual interaction in hundreds of thousands of years. Although rodents are the major reservoir, antibodies against hantaviruses are also present in domestic and wild animals like cats, dogs, pigs, cattle, and deer. Domestic animals and rodents live jointly in a similar habitat. Therefore the transmission of hantaviruses from rodents to domestic animals seems to be possible, if the target organs, tissues, and cell parenchyma of the co-habitat domestic animals possess adequate virus receptors and are suitable for hantavirus entry and replication. The most likely incidental infection of species other than rodents as for example humans turns hantaviruses from harmless to life-threatening pathogenic agents focusing the attention on this virus group, their ecology and evolution in order to prevent the human population from a serious health risk. Much more studies on the influence of non-natural hosts on the ecology of hantaviruses are needed to understand the directions that the hantavirus evolution could pursue. At least, domestic animals that share their environmental habitat with rodents and humans particularly in areas known as high endemic hantavirus regions have to be copiously screened. Each transfer of hantaviruses from their original natural hosts to other often incidental hosts is accompanied by a change of ecology, a change of environment, a modulation of numerous factors probably influencing the pathogenic ty and virulence of the virus. The new environment exerts a modified evolutionary pressure on the virus forcing it to adapt and probably to adopt a form that is much more dangerous for other host species compared to the original one. © 2005 Springer Science+Business Media, Inc.",ribavirin;virus receptor;virus vaccine;virus vector;behavior;bleeding;Bunyaviridae;correlation analysis;crush syndrome;domestic animal;ecology;education;environmental factor;geographic distribution;Hantavirus;Hantavirus pulmonary syndrome;health hazard;health status;hemorrhagic fever;history of medicine;human;incidence;infection prevention;kidney failure;lethality;mortality;nonhuman;nucleotide sequence;nutrition;pathogenicity;priority journal;Puumala virus;review;Seoul virus;serotype;shock;Sin Nombre virus;social aspect;unindexed sequence;United States;vaccination;viral genetics;virus cell interaction;virus classification;virus identification;virus infection;virus replication;virus transmission;virus virulence,"Zeier, M.;Handermann, M.;Bahr, U.;Rensch, B.;Müller, S.;Kehm, R.;Muranyi, W.;Darai, G.",2005,,10.1007/s11262-004-5625-2,0
2397,ICTV Virus Taxonomy Profile: Picornaviridae,"The family Picornaviridae comprises small non-enveloped viruses with RNA genomes of 6.7 to 10.1 kb, and contains > 30 genera and > 75 species. Most of the known picornaviruses infect mammals and birds, but some have also been detected in reptiles, amphibians and fish. Many picornaviruses are important human and veterinary pathogens and may cause diseases of the central nervous system, heart, liver, skin, gastrointestinal tract or upper respiratory tract. Most picornaviruses are transmitted by the faecal-oral or respiratory routes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Picornaviridae, which is available at www. ictv. global/report/picornaviridae.",Picornaviridae;ICTV;taxonomy;poliovirus;foot-and-mouth disease;virus;rhinovirus;enterovirus;REPLICATION ORGANELLES,"Zell, R.;Delwart, E.;Gorbalenya, A. E.;Hovi, T.;King, A. M. Q.;Knowles, N. J.;Lindberg, A. M.;Pallansch, M. A.;Palmenberg, A. C.;Reuter, G.;Simmonds, P.;Skern, T.;Stanway, G.;Yamashita, T.",2017,Oct,,0
2398,Molecular-based reclassification of the bovine enteroviruses,"Bovine enteroviruses are currently classified into two serotypes within the species Bovine enterovirus (BEV). Comparison of the sequences of six American and eleven German BEV isolates with published BEV sequences revealed the necessity to revise the taxonomy of these viruses. Molecular data indicate that the bovine enteroviruses are composed of two clusters (designated BEV-A and -B) each with two and three geno-/ serotypes, respectively. Whereas low amino acid identity of the capsid proteins 1C (VP3) and 1 D (VP1) is the main criterion for the discrimination of geno-/serotypes, the BEV clusters, presumably representing species, differ in sequence identity of all viral proteins. In addition, characteristic lengths of (i) the capsid proteins 1B, 1C and 1D, (ii) the 2C protein, and (iii) the 3′-non-translated region are observed. The BEVs can be distinguished from the other enteroviruses by sequence identity and unique features of the 5′-non-translated region, i.e. a conserved second cloverleaf and characteristic RNA structures of the internal ribosome entry site. Phylogenetically, the closest relatives of the bovine enteroviruses are the porcine enteroviruses. Incongruent phylogenies; of the 5′-non-translated region, the capsid proteins and the 3D polymerase indicate frequent intraserotypic and interserotypic recombination within the non-capsid and the capsid region of the BEV genome. © 2006 SGM.",amino acid;capsid protein;protein VP1;RNA polymerase;viral protein;virus RNA;3' untranslated region;5' untranslated region;animal cell;article;Bovine enterovirus;controlled study;data analysis;Enterovirus;gene cluster;genetic conservation;genetic recombination;genotype;Germany;internal ribosome entry site;nonhuman;nucleotide sequence;phylogeny;priority journal;RNA structure;sequence analysis;serotype;species difference;taxonomy;United States;virus capsid;virus classification;virus genome;virus isolation,"Zell, R.;Krumbholz, A.;Dauber, M.;Hoey, E.;Wutzler, P.",2006,,10.1099/vir.0.81298-0,0
2399,Application of genome sequence information to the classification of bovine enteroviruses: The importance of 5'- and 3'-nontranslated regions,"Comparative genomics of viruses in evolutionary and phylogenetic studies is well established. Previous nucleic acid sequence analyses have demonstrated that enteroviruses and rhinoviruses of the family Picornaviridae exhibit a similar structure of the 5'-nontranslated region (NTR) differing significantly from the 5'-NTR of cardiovirus, aphthovirus, hepatovirus, and echovirus 22 (provisionally parechovirus 1). Available nucleotide sequence information of the 5'- and 3'-nontranslated regions of more than 70 serotypes of enteroviruses, bovine enteroviruses and rhinoviruses has been compared and correlated with previous findings obtained after analysis of the coding and noncoding genome regions. As a result, the 5'- and 3'-NTRs of all three virus groups are characterized by group-specific nucleotide sequences. Focusing on bovine enterovirus (BEV) serotypes, unique characteristics in all secondary structures of the NTRs were observed. These features clearly separate the BEVs from the human enteroviruses and rhinoviruses. Concerning the 5'-NTR, the most remarkable property is an insertion of about 110 nucleotides between the putative cloverleaf structure at the very 5'-end of the viral genome and the IRES element. This insertion was demonstrated for BEV I and :! and has a predicted folding pattern which is very similar to the 5'-cloverleaf structure. One stem-loop of this second cloverleaf is almost identical to the 3CD(pro)-binding domain of rhinoviral 5'-cloverleafs. It was also demonstrated that the IRES elements and the 3'-NTRs of both, enteroviruses and rhinoviruses, have group-specific Features which differ significantly from the corresponding genome regions of BEV. These results suggest that bovine enteroviruses hold an exceptional taxonomic position besides the established genera Enterovirus and Rhinovirus. Within the Enterovirus and Rhinovirus genera, the existence of virus clusters representing subgenera was previously proposed. Whereas the 5'-NTRs of the four human enterovirus clusters fall into two groups, all four clusters have characteristic secondary structures at the 3'-NTR supporting the concept of enterovirus clusters. For rhinoviruses, the existence of two virus clusters was confirmed.",article;bovine;Enterovirus;evolution;genetic procedures;nucleotide sequence;phylogeny;priority journal;RNA structure;serotype;taxonomy;virus classification,"Zell, R.;Stelzner, A.",1997,,10.1016/s0168-1702(97)00096-8,0
2400,"… Novel Human-Like H3N2 Influenza A Viruses, A/swine/Oklahoma/65980/2017 (H3N2) and A/Swine/Oklahoma/65260/2017 (H3N2), Detected in Swine in the United …",,,"Zeller, M. A.;Li, G.;Harmon, K. M.;Zhang, J.",2018,,,0
2401,Complete genome sequence analysis of goatpox virus isolated from china shows high variation,"Goatpox virus (GTPV), a member of the Capripoxvirus genus of the Poxviridae family, is the causative agent of variolo caprina (goatpox). GTPV can cause significant economic losses of domestic ruminants in endemic regions and can threaten breeding stocks. In this study, we report on the compilation of the complete genomic sequence of an isolated GTPV field strain FZ (GTPV_FZ). The 150,194. bp GTPV genome consists of a central coding region bounded by two identical 2301. bp inverted terminal repeats and contains 151 putative genes. Comparative genomic analysis reveals the apparent genetic relationships among Capripoxviruses are close, but sufficient genomic variants in the field isolate strain FZ have been identified to distinguish it from other GTPV strains and other Capripoxvirus species. Phylogenetic analysis based on the p32 and complete GTPV genome can be used to differentiate SPPVs, GTPVs and LSDVs. These data may contribute to the epidemiological study of the Chinese capripoxvirus and help to develop more specific detection methods to distinguish GTPVs, SPPVs and LSDVs. © 2014 Elsevier B.V.",genomic DNA;article;Capripoxvirus;China;comparative genomic hybridization;DNA sequence;genetic variability;inverted terminal repeat;molecular phylogeny;nonhuman;nucleotide sequence;open reading frame;phylogeny;sequence analysis;virus genome;virus isolation;virus strain,"Zeng, X.;Chi, X.;Li, W.;Hao, W.;Li, M.;Huang, X.;Huang, Y.;Rock, D. L.;Luo, S.;Wang, S.",2014,,10.1016/j.vetmic.2014.07.013,0
2402,Integrative analyses of transcriptome sequencing identify functional mirnas in the chicken embryo fibroblasts cells infected with reticuloendotheliosis virus,"In this study, we found a much higher proportion of reticuloendotheliosis virus (REV) infected chicken embryo fibroblasts (CEF) were in active cell division phase than that of control cells which indicated that REV can affect the fate of CEF. So, we performed high-throughput sequencing and transcriptomic analysis to identify functional miRNAs, in order to figure out the possible mechanism in the interaction of REV with CEF. In total, 50 differentially expressed miRNAs (DEmiRNAs) were identified. Then target genes of DEmiRNAs were predicted and identified by transcriptome profile results. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were conducted to analyze the identified target genes of miRNAs which showed that metabolism, cell cycle, and apoptosis were the most related pathways involved in infection of REV. We analyzed the genes related to cell cycle which indicated that CyclinD1-CDK6 complex played an important role in regulating the transition of the cell cycle from G1 phase to S phase during REV infection. Fluorescence microscope identification showed that REV inhibited the apoptosis of CEF which was in accordance with transcriptome results. A novel miRNA, named novel-72 was found, KEGG analysis was conducted to predict the biological function of its target genes which showed that those target genes were significantly enriched in mTOR signaling pathway and functioned to promote cell cycle and cell growth during the REV infection. In conclusion, REV could induce the up-regulation of cell metabolism, cell cycle and mTOR signaling pathway while inhibit apoptosis of the cell.",cyclin D1;cyclin dependent kinase 6;cyclin dependent kinase inhibitor 1B;cycline;microRNA;microRNA 106;microRNA 10a;microRNA 10b;microRNA 140;microRNA 142;microRNA 146a;microRNA 147;microRNA 155;microRNA 1559;microRNA 184;microRNA 187;microRNA 199;microRNA 1a;microRNA 203a;microRNA 21;microRNA 218;microRNA 22;microRNA 221;microRNA 30a;microRNA 3536;microRNA 3538;microRNA 3607;microRNA 9;protein MDM2;transcriptome;unclassified drug;animal cell;apoptosis;article;carcinogenesis;cell cycle;cell growth;cell metabolism;controlled study;embryo;fibroblast;flow cytometry;gene expression;mTOR signaling;nonhuman;real time polymerase chain reaction;reticuloendotheliosis;RNA extraction;RNA sequence;upregulation,"Zhai, J.;Ga, C.;Fu, L.;Jing, L.;Dang, S.;Zheng, S.",2018,,10.3389/fgene.2018.00340,0
2403,Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China,"To investigate the diversity of viral flora, we used metagenomics to study the viral communities in a pooled faecal sample of 27 diarrhoeic piglets from intensive commercial farms in China. The 15 distinct mammalian viruses identified in the pooled diarrhoeic sample were, in order of abundance of nucleic acid sequence, Porcine epidemic diarrhea virus (PEDV), sapovirus, porcine bocavirus- 4 (PBoV-4), sapelovirus, torovirus, coronavirus, PBoV-2, stool-associated single-stranded DNA virus (poSCV), astrovirus (AstV), kobuvirus, posavirus-1, porcine enterovirus-9 (PEV-9), porcine circovirus-like (po-circo-like) virus, picobirnavirus (PBV) and Torque teno sus virus 2 (TTSuV-2). The prevalence rate of each virus was verified from diarrhoeic and healthy piglets by PCR assay. A mean of 5.5 different viruses were shed in diarrhoeic piglets, and one piglet was in fact coinfected with 11 different viruses. By contrast, healthy piglets shed a mean of 3.2 different viruses. Compared with samples from healthy piglets, the co-infection of PEDV and PBoV had a high prevalence rate in diarrhoea samples, suggesting a correlation with the appearance of diarrhoea in piglets. Furthermore, we report here for the first time the presence of several recently described viruses in China, and the identification of novel genotypes. Therefore, our investigation results provide an unbiased survey of viral communities and prevalence in faecal samples of piglets.",capsid protein;article;Astroviridae;China;Coronavirinae;diarrhea;DNA virus;feces;feces microflora;Kobuvirus;metagenomics;mixed infection;nonhuman;nucleotide sequence;Picobirnavirus;piglet;porcine bocavirus 4;porcine circovirus like virus;porcine enterovirus 9;Porcine epidemic diarrhea virus;priority journal;Sapelovirus;Sapovirus;Torovirus;Torque teno sus virus 2;virus;virus genome;virus infection,"Zhang, B.;Tang, C.;Yue, H.;Ren, Y.;Song, Z.",2014,,10.1099/vir.0.063743-0,1
2404,Identification and characterization of a novel rodent bocavirus from different rodent species in China,"Members in the genus Bocaparvovirus are closely related to human health and have a wide host range. The diverse hosts raise the possibility of crossing species barrier, which is a feature of emerging viruses. Among the mammalian hosts, rodents are generally acknowledged to be important reservoirs of emerging viruses. Here, rodent samples collected from six provinces and autonomous regions of China (Liaoning, Inner Mongolia, Tibet, Xinjiang, Guangxi and Yunnan) were used to investigate the prevalence and distribution of bocaparvoviruses. By using next-generation sequencing first, a partial non-structural protein 1 (NS1) gene belonging to a possible novel bocaparvovirus was discovered. Following this, PCR-based screening of NS1 gene was conducted in 485 rodent samples, with 106 positive results found in seven rodent species (Rattus norvegicus, Mus musculus, Apodemus agrarius, Cricetulus barabensis, Rattus flavipectus, Rattus rattus and Rhombomys opimus). Finally, six nearly full-length genomes and three complete CDS were obtained and the newly identified bocaparvovirus was tentatively named rodent bocavirus (RoBoV). RoBoV has three ORFs: NS1, NP1, and VP, which are characteristics of bocaparvoviruses. Phylogenetic analyses revealed that porcine bocavirus isolate PBoV-KU14, a member of Ungulate bocaparvovirus 4, was the most related virus to RoBoV, with 92.1-92.9% amino acid identities in NS1 protein. Alignments of RoBoV-related sequences showed RoBoV isolates could be classified into two clades, demonstrating an inter-host genetic diversity. The results indicate a potential interspecies transmission of RoBoV between rodents and swine and expand our knowledge on bocaparvoviruses in rodent populations.","Animals;Bocavirus/cl [Classification];*Bocavirus/ge [Genetics];*Bocavirus/ip [Isolation & Purification];China/ep [Epidemiology];Disease Reservoirs/vi [Virology];Genetic Variation;Genome, Viral/ge [Genetics];High-Throughput Nucleotide Sequencing;Mice;Open Reading Frames;Parvoviridae Infections/ep [Epidemiology];Parvoviridae Infections/tm [Transmission];*Parvoviridae Infections/vi [Virology];Phylogeny;Prevalence;Rats;*Rodentia/vi [Virology];Viral Proteins/ge [Genetics];0 (Viral Proteins)","Zhang, C.;Song, F.;Xiu, L.;Liu, Y.;Yang, J.;Yao, L.;Peng, J.",2018,Mar 29,,0
2405,[Phylogenetic analysis of 2009 H1N1 (A) influenza virus based on genomic sequence features],"From April 2009 onward, a new strain of human H1N1 influenza virus has swept over the world. The genome of influenza virus consists of 8 segments, encoding 10 proteins, respectively. The reassortments among the 8 segments cause the variation of influenza virus. Therefore, phylogenetic analysis of the 8 genes is very important. In this paper, we choose neighboring word frequency as the genomic features, using VC++ programming to analyze evolution of the 8 segments of H1N1 virus. As a result, we found that PB2 genes and PA genes of these three isolated virus were originated from North American avian influenza virus, that PB1 genes were originated from the seasonal influenza virus of human, and that HA genes, NS genes and NP genes came from the North American classical swine influenza A virus. The NA segments and M segments were originated from the European swine influenza virus.",article;genetic reassortment;genetics;human;influenza;Influenza A virus (H1N1);Mexico;molecular cloning;phylogeny;United States;virology;virus gene;virus genome,"Zhang, F.;Guo, X.;Cheng, W.;Wang, Y.;Zhang, S.",2010,,,0
2406,Complete nucleotide sequence of a coxsackie B5 virus and its relationship to swine vesicular disease virus,"We report the first complete nucleotide sequence of the picornavirus coxsackievirus B5 (CB5), strain 1954/ UK/85, an isolate from a case of hand-foot-and-mouth disease. We have compared the sequence with those of other coxsackie B viruses, coxsackievirus A9, poliovirus and swine vesicular disease virus (SVDV). The genes encoding the three major capsid proteins are most closely related to those of SVDV but the 5' and 3' non-coding regions and the P3 gene are more similar to the corresponding regions in the other coxsackie B viruses than to those of SVDV. These observations are considered in the light of the antigenic and biochemical relationships between SVDV and CB5.",capsid protein;antigenicity;article;comparative study;Enterovirus;Enterovirus B;hand foot and mouth disease;molecular genetics;nonhuman;nucleotide sequence;Poliomyelitis virus;priority journal;virus classification;virus gene,"Zhang, G.;Wilsden, L. G.;Knowles, L. N. J.;McCauley, J. W.",1993,,,0
2407,Characterization of an Enterovirus species E isolated from naturally infected bovine in China,"Bovine enteroviruses, which belong to the Picornaviridae family, can cause clinical symptoms in cattle and are excreted in feces. In this study, a cytolytic virus was isolated from Madin-Darby bovine kidney (MDBK) cells from fecal samples of bovine with severe diarrhea and hemorrhagic intestinal mucosa that had been originally diagnosed with bovine viral diarrhea (BVD) by a bovine viral diarrhea virus Ag point-of-care test (IDEXX, American). Random priming PCR was used to amplify underlying viral sequences and identify the isolated virus. Phylogenetic analysis indicated that the isolated virus closely matches the EV-E2 species, which is different from other Chinese strains previously isolated. The newly identified virus was named HLJ-3531/2013. We infected the sulking mice with the isolated virus. Reverse-transcription PCR, hematoxylin and eosin (HE) staining, serum neutralization (SN) test, and virus isolation from various tissues revealed that HLJ-3531/2013 can infect the intestine, liver, and lung of suckling mice. The present work is the first to report the reproduction of clinical symptoms by an isolated virus in an experimental infection model of animals and lays a solid foundation for the development of the pathogenesis of bovine enteroviruses.",protein VP1;virus RNA;5' untranslated region;animal cell;animal experiment;animal model;animal tissue;article;Bovine enterovirus;bovine viral diarrhea;China;controlled study;Enterovirus infection;Enterovirus species e;erythrocyte;feces analysis;gel electrophoresis;histopathology;hyperemia;immunoelectron microscopy;intestinal bleeding;intestine;liver;lung;lung emphysema;lymphocyte;molecular weight;mouse;nonhuman;nucleotide sequence;pathogenesis;phylogenetic tree;priority journal;reverse transcription polymerase chain reaction;virus isolation;virus particle;virus purification;virus strain,"Zhang, H.;Liu, H.;Bao, J.;Guo, Y.;Peng, T.;Zhou, P.;Zhang, W.;Ma, B.;Wang, J.;Gao, M.",2014,,10.1016/j.virusres.2014.07.032,0
2408,Genome-wide analysis of differentially expressed genes and the modulation of PEDV infection in Vero E6 cells,"PEDV remains one of the most important swine diseases that infects pigs of all ages. It causes devastating viral enteric disease in piglets with a high mortality rate, leading to significant threats and huge economic loss to the pork industry. In this study, a transcriptomic shotgun sequencing (RNA-Seq) procedure was used to study gene responses against PEDV infection. Genome-wide analysis of differentially expressed genes (DEGs) was performed in Vero E6 cells post-PEDV infection. mTOR signaling pathway activator-MHY1485, and inhibitor-PP242 were used to study the antiviral function. Results revealed that the IRF3 was significantly up-regulated post-PEDV infection. Although most of the IFN-regulatory and –related genes evaluated in this study were either down-regulated or remained unchanged, IL11 behaved significantly up-regulated, with the peak at 16 hpi. Nearly 90% of PEDV infections were suppressed in the PP242 pretreated cells whereas the reverse effect was observed in the MYH1485 pretreated cells. Results indicated that the mTOR signaling pathway played a vital role in the PEDV antiviral regulation in the Vero E6 cells. Future studies will contribute to better understand the cellular antiviral mechanism against PEDV.","2 (4 amino 1 isopropyl 1h pyrazolo[3,4 d]pyrimidin 3 yl) 1h indol 5 ol;interferon;interferon consensus sequence binding protein;interferon regulatory factor 1;interferon regulatory factor 2;interferon regulatory factor 3;interferon regulatory factor 4;interferon regulatory factor 5;interferon regulatory factor 6;interferon regulatory factor 7;interferon regulatory factor 9;interleukin 11;interleukin 4 receptor;interleukin 5;mammalian target of rapamycin;mammalian target of rapamycin complex 1;mammalian target of rapamycin complex 2;mammalian target of rapamycin inhibitor;mhy 1485;unclassified drug;animal cell;article;controlled study;Coronaviridae infection;down regulation;gene expression;IFNAR1 gene;IFNAR2 gene;IFNGR1 gene;IFNGR2 gene;IL11 gene;IL4R gene;IL5 gene;IRF 1 gene;IRF 2 gene;IRF 3 gene;IRF 4 gene;IRF 5 gene;IRF 6 gene;IRF 7 gene;IRF 8 gene;IRF 9 gene;mTOR signaling;nonhuman;Porcine epidemic diarrhea virus infection;priority journal;RNA sequence;upregulation;Vero C1008 cell line;virus gene","Zhang, H.;Liu, Q.;Su, W.;Wang, J.;Sun, Y.;Zhang, J.;Shang, K.;Chen, Z.;Cheng, S.;Wu, H.",2018,,10.1016/j.micpath.2018.02.004,0
2409,Porcine bocaviruses: Genetic analysis and prevalence in Chinese swine population,"In members of the Bocavirus genus, that contain three open reading frames (ORFs) of the Parvovirinae subfamily, porcine bocaviruses (PoBoVs) exhibit the most genetic diversity. Based on the ORF2-encoded viral protein (VP1) classification, the six reported porcine bocaviruses were grouped into four species: PoBoV1 (porcine boca-like virus or PBoLV), PoBoV2 (porcine parvovirus 4 or PPV4), PoBoV3 (PBoV1/PBoV2) and PoBoV4 (6V/7V), with PoBoV3 and PoBoV4 each having two genotype viruses. All four PoBoV species were detected in the 166 samples collected in 2010 from swine herds located in ten provinces of China. The detection rates for PoBoV1-4 were 28·9%, 6·6%, 19·3% and 39·7%, respectively. The co-infection combinations involving these six porcine bocaviruses in the collected samples were very complex. Furthermore, mixed infections with viruses from other families (porcine reproductive and respiratory syndrome virus, classic swine fever virus and porcine circovirus type 2) were also detected. © Cambridge University Press 2011.",protein VP1;amino acid sequence;Arterivirus;article;Bocaparvovirus;China;Chinese swine;Circovirus;Circovirus type 2;genetic analysis;genetic variability;genotype;herd;mixed infection;nonhuman;nucleotide sequence;open reading frame;Pestivirus;phylogeny;porcine boca like virus;Porcine bocavirus;Porcine parvovirus 4;prevalence;pig;virus classification;virus detection,"Zhang, H. B.;Huang, L.;Liu, Y. J.;Lin, T.;Sun, C. Q.;Deng, Y.;Wei, Z. Z.;Cheung, A. K.;Long, J. X.;Yuan, S. S.",2011,,10.1017/s0950268811000847,0
2410,"Reply to ""classification of emergent U.S. strains of porcine epidemic diarrhea virus by phylogenetic analysis of nucleocapsid and ORF3 genes""",,cell receptor;epitope;guanine nucleotide binding protein;hemagglutinin;M protein;membrane protein;neutralizing antibody;nucleocapsid protein;RNA;virus envelope protein;virus spike protein;Arterivirus;envelope gene;evolutionary adaptation;gene;gene sequence;genetic variability;genotype;letter;membrane gene;nonhuman;nucleocapsid gene;nucleotide sequence;ORF3 gene;phylogenetic tree;phylogeny;Porcine epidemic diarrhea virus;priority journal;reverse transcription polymerase chain reaction;spike gene;swine influenza virus;virion;virogenesis;virus assembly;virus attachment;virus attenuation;virus detection;virus envelope;virus genome;virus neutralization;virus nucleocapsid;virus particle;virus strain,"Zhang, J.;Chen, Q.;Gauger, P. C.;Harmon, K. M.;Yoon, K. J.",2014,,10.1128/jcm.01747-14,0
2411,"Molecular Characterization and Seroprevalence in Pigs of SC0806, a Cat Que Virus Isolated from Mosquitoes in Sichuan Province, China","The Simbu serogroup currently consists of a highly diverse group of related arboviruses that infect both humans and economically important livestock species. Cat Que virus (CQV), a Simbu serogroup virus of the genus Orthobunyavirus (family Bunyaviridae), was first isolated in 2004 from mosquitoes during surveillance of arbovirus activity in acute pediatric encephalitis in northern Vietnam. We report here the complete genome sequence of SC0806 isolated from mosquitoes (Culex tritaeniorhynchus) in Sichuan Province, China. Consistent with the genomic organization of Simbu serogroup viruses, the SC0806 genome comprises three RNA segments - a large (L) segment (6928 nucleotides) that encodes the 2261-amino-acid RNA-dependent RNA polymerase, a medium (M) segment (4481 nucleotides) that encodes the 1433-amino-acid polyprotein, and a small (S) segment (984 nucleotides) that encodes a 234-amino-acid nucleocapsid protein and a 95-amino-acid nonstructural protein. The respective lengths of the 5′-untranslated region (UTR) and 3′-UTR of L, M, and S are 56 and 86, 43 and 136, and 44 and 238 nucleotides. Sequence (nucleotide and deduced amino acid) comparison and phylogenetic analysis revealed that SC0806 was closely related to the reported Vietnam isolate CQV. This is the first time that CQV has been isolated in Sichuan Province, China. Anti-SC0806 immunoglobulin M (IgM) and IgG antibodies were found in pigs reared locally, indicating that CQV has formed a natural cycle in the local area. Surveillance of the distribution and pathogenicity of SC0806 should be strengthened.",amino acid;immunoglobulin G antibody;immunoglobulin M antibody;article;Cat Que virus;China;Culex tritaeniorhynchus;disease surveillance;nonhuman;Orthobunyavirus;phylogeny;pig;priority journal;seroprevalence;virus isolation,"Zhang, J.;Wang, J.;Wang, L.;Fu, S.;Li, M.;Zhao, G.;Zhu, W.;Wang, D.;Liang, G.",2015,,10.1089/vbz.2014.1767,0
2412,High-throughput whole genome sequencing of Porcine reproductive and respiratory syndrome virus from cell culture materials and clinical specimens using next-generation sequencing technology,"Next-generation sequencing (NGS) technologies have increasingly played crucial roles in biological and medical research, but are not yet in routine use in veterinary diagnostic laboratories. We developed and applied a procedure for high-throughput RNA sequencing of Porcine reproductive and respiratory syndrome virus (PRRSV) from cell culture-derived isolates and clinical specimens. Ten PRRSV isolates with known sequence information, 2 mixtures each with 2 different PRRSV isolates, and 51 clinical specimens (19 sera, 16 lungs, and 16 oral fluids) with various PCR threshold cycle (Ct) values were subjected to nucleic acid extraction, cDNA library preparation (24-plexed), and sequencing. Whole genome sequences were obtained from 10 reference isolates with expected sequences and from sera with a PRRSV real-time reverse transcription PCR Ct ≤ 23.6, lung tissues with Ct ≤ 21, and oral fluids with Ct ≤ 20.6. For mixtures with PRRSV-1 and -2 isolates (57.8% nucleotide identity), NGS was able to distinguish them as well as obtain their respective genome sequences. For mixtures with 2 PRRSV-2 isolates (92.4% nucleotide identity), sequence reads with nucleotide ambiguity at numerous sites were observed, indicating mixed infection; however, individual virus sequences could only be separated when 1 isolate identity and sequence in the mixture is known. The NGS approach described herein offers the prospect of high-throughput sequencing and could be adapted to routine workflows in veterinary diagnostic laboratories, although further improvement of sequencing outcomes from clinical specimens with higher Ct values remains to be investigated.",virus RNA;animal;blood;evaluation study;genetics;high throughput sequencing;isolation and purification;pig;polymerase chain reaction;porcine reproductive and respiratory syndrome;Porcine reproductive and respiratory syndrome virus;predictive value;veterinary medicine;virology;virus genome,"Zhang, J.;Zheng, Y.;Xia, X. Q.;Chen, Q.;Bade, S. A.;Yoon, K. J.;Harmon, K. M.;Gauger, P. C.;Main, R. G.;Li, G.",2017,,10.1177/1040638716673404,1
2413,Insights into leghorn male hepatocellular cells response to fowl adenovirus serotype 4 infection by transcriptome analysis,"Fowl adenovirus serotype 4 (FAdV-4), a member of the Aviadenovirus genus of the Adenoviridae family, causes hepatitis–hydropericardium syndrome (HHS) in chickens. It causes mortality of up to 80% in 3–6-week-old broilers, posing a substantial threat to the poultry industry. However, the specific host responses to the virus are not well understood. To better understand the interactions between the host and FAdV-4 and to explore the pathogenesis of this virus, a high-throughput RNA-seq technology was utilized with leghorn male hepatocellular (LMH) cells at 12, 24, and 48 h after FAdV-4 infection. We identified a total of 7000 differentially expressed genes (DEGs), which were enriched in a variety of biological processes and pathways using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Several immune related pathways, including Toll-like receptor (TLR) signaling pathway and cytokine–cytokine receptor interaction pathway, were activated after the FAdV-4 infection. The transcriptional data were validated by quantitative real-time PCR. The expression profiles of 10 genes involved in FAdV-4-infected chicken livers, including TLR2A, TLR3, TLR5, MyD88, IL12B, IL15, IL18, CCL20, TNFRSF21, and CD30, were consistent with RNA-seq profiles. By transfecting small interfering RNA into LMH cells, our results confirmed that MyD88 mediated FAdV-4-induced inflammation. To our knowledge, this was the first study to use transcriptome analysis to investigate host responses to FAdV-4 infection. These findings provide insights into the mechanisms of FAdV-4 pathogenesis and host-FAdV-4 interaction.",tumor necrosis factor receptor superfamily member 8;cytokine receptor;interleukin 12p40;interleukin 18;macrophage inflammatory protein 3alpha;myeloid differentiation factor 88;protein derivative;protein TNFRSF21;toll like receptor;toll like receptor 2;toll like receptor 3;toll like receptor 5;transcriptome;unclassified drug;animal cell;animal model;article;Chick embryo lethal orphan virus;controlled study;Fowl adenovirus serotype 4;genetic transcription;high throughput sequencing;innate immunity;Leghorn chicken;liver cell;male;molecular interaction;nonhuman;pathogenesis;RNA sequence;serotype;signal transduction;virus infection;virus pathogenesis,"Zhang, J.;Zou, Z.;Huang, K.;Lin, X.;Chen, H.;Jin, M.",2018,,10.1016/j.vetmic.2017.12.007,0
2414,"Human infection with Orf virus from goats in China, 2012","Orf virus, which belongs to the Parapoxvirus genus, induces a zoonotic infectious disease characterized by acute, highly vascularized cutaneous pustular lesions in sheep and goats. A number of Orf outbreaks have been reported in sheep and goats in recent years, but no reports have described an Orf virus strain from humans in China. In this study, we diagnosed Orf virus infection in two people, a mother and son, in the Gansu province of China. The human Orf virus was isolated and its phylogenetic characterization was analyzed based on a complete B2L gene. The results are useful for developing prospective programs to control Orf virus infections in both goats and humans © Copyright 2014, Mary Ann Liebert, Inc. 2014.",adult;article;B2L gene;case report;China;female;goat;human;male;middle aged;nonhuman;nucleotide sequence;Parapoxvirus;phylogeny;Poxviridae;poxvirus infection;priority journal;sheep;virus gene;virus isolation;virus strain;zoonosis,"Zhang, K.;Liu, Y.;Kong, H.;Shang, Y.;Liu, X.",2014,,10.1089/vbz.2013.1445,0
2415,Identification and analysis of differential miRNAs in PK-15 cells after foot-and-mouth disease virus infection,"The alterations of MicroRNAs(miRNAs) in host cell after foot-and-mouth disease virus (FMDV) infection is still obscure. To increase our understanding of the pathogenesis of FMDV at the post-transcriptional regulation level, Solexa high-throu MicroRNAs (miRNAs) play an important role both in the post-transcriptional regulation of gene expression and host-virus interactions. Despite investigations of miRNA expression ghput sequencing and bioinformatic tools were used to identify differentially expressed miRNAs and analyze their functions during FMDV infection of PK-15cells. Results indicated that 9,165,674 and 9,230,378 clean reads were obtained, with 172 known and 72 novel miRNAs differently expressed in infected and uninfected groups respectively. Some of differently expressed miRNAs were validated using stem-loop real-time quantitative RT-PCR. The GO annotation and KEGG pathway analysis for target genes revealed that differently expressed miRNAs were involved in immune response and cell death pathways. © 2014 Zhang et al.",microRNA;microrna 142 5p;microRNA 146b;microRNA 20a;microRNA 22 5p;microRNA 221 3p;microRNA 23b;microRNA 320;microRNA 365 3p;microRNA 451;unclassified drug;article;cell death;controlled study;down regulation;foot and mouth disease;gene expression regulation;genetic transcription;high throughput sequencing;immune response;nonhuman;pathogenesis;RNA analysis;RNA sequence;single nucleotide polymorphism;pig;virus cell interaction,"Zhang, K. S.;Liu, Y. J.;Kong, H. J.;Cheng, W. W.;Shang, Y. J.;Tian, H.;Zheng, H. X.;Guo, J. H.;Liu, X. T.",2014,,10.1371/journal.pone.0090865,0
2416,"Molecular Detection of Indigenous Hepatitis E Virus (HEV) from Tibetan Pigs in Tibet, China","Hepatitis E is an important public health concern throughout the world. Many molecular and serological surveys have reported the prevalence and genotypic characteristics of HEV in humans and animals worldwide. However, the genotypic characterization of this virus is very limited in Tibetan pigs. Hence, we aimed to explore the genotype of HEV, prevailing among Tibetan pigs in China. For this purpose, 253 bile samples of Tibetan pigs (free-range animals) were collected from different slaughterhouses during 2017–2018 and subsequently tested for HEV RNA by RT-nPCR. A total of 11 out of 253 (4.35%) samples tested were positive for HEV RNA. Based on the sequence alignment and phylogenetic analysis, all the isolated HEV strains belonged to genotype 4 and clustered into subtype 4b by sharing more than 84.8–95.2% identities with other reported strains. Our results concluded that HEV genotype 4 is prevailing among Tibetan pigs in Tibet, China.",article;Hepatitis E virus;nested polymerase chain reaction;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;pig;priority journal;reverse transcription polymerase chain reaction;sequence alignment;slaughterhouse;Tibet;virus detection;virus strain,"Zhang, L.;Huang, S.;Li, K.;Rehman, M. U.;Jiang, X.;Tong, X.;Zhang, H.;Iqbal, M. K.;Mehmood, K.;Liu, S.;Shen, Y.;Li, J.",2018,,10.1007/s12560-018-9352-6,0
2417,Identification and characterization of microRNA in the lung tissue of pigs with different susceptibilities to PCV2 infection,"Porcine circovirus type 2 (PCV2) is the primary cause of post-weaning multisystemic wasting syndrome (PMWS) and other PCV-associated diseases. According to our previous RNA-sequencing analysis, the differences in the susceptibility to PCV2 infection depended on the genetic differences between the Laiwu (LW) and Yorkshire × Landrace crossbred (YL) pigs, but the cellular microRNA (miRNA) that are differentially expressed between the LW and YL pigs before and after PCV2 infection remain to be determined. In this study, high-throughput sequencing was performed to determine the abundance and differential expression of miRNA in lung tissues from PCV2-infected and PCV2-uninfected LW and YL pigs. In total, 295 known and 95 novel miRNA were identified, and 23 known and 25 novel miRNA were significantly differentially expressed in the PCV2-infected vs. PCV2-uninfected LW pigs and/or the PCV2-infected vs. PCV2-uninfected YL pigs. The expression levels of ssc-miR-122, ssc-miR-192, ssc-miR-451, ssc-miR-486, and ssc-miR-504 were confirmed by quantitative real-time PCR (qRT-PCR). Analysis of the potential targets of the four up-regulated miRNA (i.e., ssc-miR-122, ssc-miR-192, ssc-miR-451 and ssc-miR-486) identified pathways and genes that may be important for disease resistance. Among the up-regulated miRNA, ssc-miR-122 can repress the protein expression and viral DNA replication of PCV2 and down-regulate the expression of the nuclear factor of activated T-cells 5 (NFAT5) and aminopeptidase puromycin sensitive (NPEPPS) by binding to their 3′ untranslated region (3′UTR) in PK15 cells. Therefore, ssc-miR-122 may indirectly suppress PCV2 infection by targeting genes related to the host immune system, such as NFAT5 and NPEPPS.",aminopeptidase puromycin sensitive;membrane protein;microRNA;microRNA 122;nuclear factor of activated T cells 5;transfer RNA;unclassified drug;virus DNA;3' untranslated region;animal cell;animal experiment;animal tissue;article;Circoviridae infection;controlled study;disease resistance;down regulation;gene expression;high throughput sequencing;luciferase assay;lung parenchyma;non small cell lung cancer;nonhuman;phylogeny;pig;PK-15 cell line;polyacrylamide gel electrophoresis;Porcine circovirus 2;protein binding;protein expression;real time polymerase chain reaction;sequence alignment;sequence analysis;upregulation;virus replication,"Zhang, P.;Wang, L.;Li, Y.;Jiang, P.;Wang, Y.;Wang, P.;Kang, L.;Wang, Y.;Sun, Y.;Jiang, Y.",2018,,10.1186/s13567-018-0512-3,0
2418,"Characterization and complete genome sequence analysis of a novel virulent Siphoviridae phage against Staphylococcus aureus isolated from bovine mastitis in Xinjiang, China","Bovine mastitis is one of the most costly diseases in dairy cows worldwide. It can be caused by over 150 different microorganisms, where Staphylococcus aureus is the most frequently isolated and a major pathogen responsible for heavy economic losses in dairy industry. Although antibiotic therapy is most widely used, alternative treatments are necessary due to the increasing antibiotic resistance. Using phage for pathogen control is a promising tool in the fight against antibiotic resistance. Mainly using high-throughput sequencing, bioinformatics and our proposed phage termini identification method, we have isolated and characterized a novel virulent phage, designated as vB_SauS_IMEP5, from manure collected from dairy farms in Shihezi, Xinjiang, China, for use as a biocontrol agent against Staphylococcus aureus infections. Its latent period was about 30 min and its burst size was approximately 272PFU/cell. Phage vB_SauS_IMEP5 survives in a wide pH range between 3 and 12. A treatment at 70 °C for 20 min can inactive the phage. Morphological analysis of vB_SauS_IMEP5 revealed that phage vB_SauS_IMEP5 morphologically resembles phages in the family Siphoviridae. Among our tested multiplicity of infections (MOIs), the optimal multiplicity of infection (MOI) of this phage was determined to be 0.001, suggesting that phage vB_SauS_IMEP5 has high bacteriolytic potential and good efficiency for reducing bacterial growth. The complete genome of IME-P5 is a 44,677-bp, linear, double-stranded DNA, with a G+C content of 34.26%, containing 69 putative ORFs. The termini of genome were determined with next-generation sequencing data using our previously proposed termini identification method, which suggests that this phage has non-redundant termini with 9nt 3′ protruding cohesive ends. The genomic and proteomic characteristics of IMEP5 demonstrate that this phage does not belong to any of the previously recognized Siphoviridae Staphylococcus phage groups, suggesting the creation of a new lineage, thus adding to the knowledge on the diversity of Staphylococcus phages. An N-acetylmuramoyl-l-alanine amidase gene and several conserved genes were predicted, while no virulence or antibiotic resistance genes were identified. This study isolated and characterized a novel S. aureus phage vB_SauS_IMEP5, and our findings suggest that this phage may be potentially utilized as a therapeutic or prophylactic candidate against S.aureus infections.",double stranded DNA;n acetylmuramoylalanine amidase;article;bacteriolysis;bacteriophage;bovine mastitis;China;controlled study;DNA base composition;N acetylmuramoyl L alanine amidase gene;next generation sequencing;nonhuman;open reading frame;Siphoviridae;Staphylococcus aureus;virus gene;virus genome,"Zhang, Q.;Xing, S.;Sun, Q.;Pei, G.;Cheng, S.;Liu, Y.;An, X.;Zhang, X.;Qu, Y.;Tong, Y.",2017,,10.1007/s11262-017-1445-z,0
2419,Phylogenetic and pathotypical analysis of two virulent Newcastle disease viruses isolated from domestic ducks in China,"Two velogenic Newcastle disease viruses (NDV) obtained from outbreaks in domestic ducks in China were characterized in this study. Phylogenetic analysis revealed that both strains clustered with the class II viruses, with one phylogenetically close to the genotype VII NDVs and the other closer to genotype IX. The deduced amino acid sequence of the cleavage site of the fusion (F) protein confirmed that both isolates contained the virulent motif 112RRQK/RRF117 at the cleavage site. The two NDVs had severe pathogenicity in fully susceptible chickens, resulting in 100% mortality. One of the isolates also demonstrated some pathogenicity in domestic ducks. The present study suggests that more than one genotype of NDV circulates in domestic ducks in China and viral transmission may occur among chickens and domestic ducks. © 2011 Zhang et al.",amino acid sequence;article;China;domestic animal;duck;genotype;mortality;Newcastle disease virus;nonhuman;nucleotide sequence;pathogenicity;pathotype;phylogeny;reverse transcription polymerase chain reaction;unindexed sequence;virus isolation;virus strain;virus transmission;virus virulence,"Zhang, S.;Wang, X.;Zhao, C.;Liu, D.;Hu, Y.;Zhao, J.;Zhang, G.",2011,,10.1371/journal.pone.0025000,0
2420,Serologic and virologic survey for evidence of infection with velogenic newcastle disease virus in Chinese duck farms,"A serologic and virologic survey was performed to determine the prevalence and distribution of Newcastle disease virus (NDV) infection in Chinese duck flocks. NDV infection was detected in nine of the 12 sampled farms throughout the two geographic regions covered by the survey. The percentage antibody positivity among the 406 serum samples was 35.7%. Three velogenic NDVs were obtained from different duck flocks identified by hemagglutination and hemagglutination-inhibition tests, a pathogenicity test, and reverse transcriptionpolymerase chain reaction on the fusion (F) genes. Phylogenetic analysis revealed that all three isolates clustered with the class II viruses; two were phylogenetically close to genotype VII NDVs, and the other was more closely related to genotype IX NDVs. These findings suggest that NDV infections were prevalent, and at least two distinct virulent genotypes may be responsible for recent epidemics in Chinese duck flocks. © American Association of Avian Pathologists.",virus antibody;virus RNA;animal;animal disease;bird disease;blood;China;duck;epidemiology;hemagglutination inhibition test;isolation and purification;molecular genetics;Newcastle disease;Newcastle disease virus;nucleotide sequence;pathogenicity;review;virology;virulence,"Zhang, S.;Zhao, L.;Wang, X.;Zhang, D.;Zhao, J.;Zhang, G.",2011,,10.1637/9649-010611-ResNote.1,0
2421,Transcript Profiling Identifies Early Response Genes against FMDV Infection in PK-15 Cells,"Foot-and-mouth disease (FMD) is a highly contagious disease that results in enormous economic loses worldwide. Although the protection provided by vaccination is limited during early infection, it is recognized as the best method to prevent FMD outbreaks. Furthermore, the mechanism of host early responses against foot-and-mouth disease virus (FMDV) infection remains unclear. In our study, a pig kidney cell line (PK-15) was used as a cell model to reveal the mechanism of early pig responses to FMDV infection. Four non-treated control and four FMDV-treated PK-15 cells were sequenced with RNA-seq technology, and the differentially expressed genes (DEGs) were analyzed. The results showed that 1212 DEGs were in the FMDV-infected PK-15 cells, including 914 up-regulated and 298 down-regulated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly enriched in the tumor necrosis factor (TNF), cytokine-cytokine receptor interaction, NOD-like receptor, toll-like receptor, NF-kappaB, and the chemokine signaling pathways. To verify the results of the DEGs, 30 immune-related DEGs (19 up-regulated and 11 down-regulated) were selected for Quantitative Reverse Transcriptase polymerase chain reaction (RT-qPCR) verification. The results showed that RT-qPCR-measured genes exhibited a similar pattern as the RNA-seq analyses. Based on bioinformatics analysis, during FMDV early infection, we found that a series of cytokines, such as interleukins (IL6), chemokines (CXCL2, CCL20 and CCL4), and transcription factors (ZFP36, FOS, NFKBIA, ZBTB3, ZNF503, ZNF283, dymeclin (DYM), and orthodenticle homeobox 1 (OTX1)) were involved in the battle between FMDV and the host. Combined with their features and functions, we propose inflammation as the main early mechanism by which the host responds to FMDV infection. These data provide an additional panel of candidate genes for deciphering the mechanisms of a host's early response against FMDV infection.",Animals;Cell Line;Computational Biology/mt [Methods];*Foot-and-Mouth Disease/ge [Genetics];*Foot-and-Mouth Disease/vi [Virology];*Foot-and-Mouth Disease Virus/ph [Physiology];*Gene Expression Profiling;*Gene Expression Regulation;Gene Ontology;High-Throughput Nucleotide Sequencing;Molecular Sequence Annotation;Reproducibility of Results;Swine;*Transcriptome,"Zhang, T.;Chen, H.;Qi, L.;Zhang, J.;Wu, R.;Zhang, Y.;Sun, Y.",2018,07 11,,0
2422,Effects of PrPC on DF-1 cells' biological processes and RNA-seq-based analysis of differential genes,"To reveal the effects of PrPC on cells' biological processes and on gene expression. We established stable DF-1 (PrPC-knockdown (KD)) cells, and combined with DF-1 (wt) and DF-1 (PrPC-overexpression (OE)) cells that we previously established we studied the effects of chicken PrPC (PrPC) on DF-1 cells' processes. Then by using high throughput sequencing technology (HTS) and bioinformatics, we analyzed the differentially expressed genes (DEGs) between these cells. The results show that compared with DF-1 (wt) and DF-1 (PrPC-scramble), DF-1 (PrPC-KD) are significantly decreased in adhesion, proliferation, formation rate of colony and cells number of colony, scratch wound healing rate, cells number of invasion and migration, S phase cell populations, but the apoptosis rate and G1 phase cell populations are significantly increased. Conversely, all of these features in DF-1 (PrPC-OE) are opposite. In addition, compared with DF-1 (wt), we found that there are totally 1055 DE genes between DF-1 (PrPC-KD) and DF-1 (PrPC-OE) cells. After Go and pathway enrichment analysis, we know that these DEGs are significantly enriched in cell, cell part, cellular process, and metabolic pathway. In short, we found that PrPC can promote DF-1 cells' processes except apoptosis. Furthermore, PrPC involves in the focal adhesion, cancer, ribosome, metabolic pathways, and so forth, and the overexpression of PrPC can promote the pathway of amoebiasis, but its down-regulation can promote the pathway of serotonergic synapse. However, the details are keeping unknown and that would be our next research.",biological processes;DF-1 cells;effects;PrPC;RNA-seq;CELLULAR PRION PROTEIN;ALZHEIMERS-DISEASE;ENDOTHELIAL-CELLS;BRAIN;RECEPTOR;VIRUSES;BINDING;LINE,"Zhang, T. L.;Wan, X. R.;Wu, R.;Wang, C.",2018,Oct,,0
2423,Evolution and variation of the H3 gene of influenza A virus and interaction among hosts,"Objective: Continual mutations to the hemagglutinin (HA) gene of influenza A virus generate novel antigenic strains that cause annual epidemics. The aim of this study was to evaluate evolution tendency of the H3 gene in a long period of time. Methods: 1842 H3 HA1 nucleotide strains of different hosts were collected for analysis. A two-step clustering method was used to divide strains into groups, and then a phylogenetic tree was constructed based on cluster results. Evolution rate in lineages were future estimated. Results: Tree structure showed three lineages: horse/canine, human/swine and avian. As a single trunk, the human/swine lineage was mainly composed of human strains, and more big branches appeared in recent years. Tree topology showed no evidence that swine affected the main evolution tendency of human H3 strains. The evolution rate of H3 strains varied between lineages. We observed that the rate in the human lineage decreased from 3.2 substitutions/year before 1980 to 1.8 after 1997. Conclusion: We concluded that the variation of human H3 gene was associated with swine strains but independent of others, including bird strains. The evolution rate of human H3 strains seems to have decreased in recent years, while the reasons for the rate change need to be further explored. Copyright © 2007 S. Karger AG.",h3 protein;nucleotide;protein derivative;unclassified drug;article;bird;cluster analysis;fowl;genetic variability;horse;host;human;Influenza A virus;molecular evolution;nonhuman;phylogenetic tree;priority journal;pig;virus gene;virus strain,"Zhang, W.;Jiang, Q.;Chen, Y.",2007,,10.1159/000104788,0
2424,Faecal virome of cats in an animal shelter,,,"Zhang, W.;Li, L.;Deng, X.;Kapusinszky, B.",2014,,,0
2425,"What is for dinner? Viral metagenomics of US store bought beef, pork, and chicken","We describe here the metagenomics-derived viral sequences detected in beef, pork, and chicken purchased from stores in San Francisco. In beef we detected four previously reported viruses (two parvoviruses belonging to different genera, an anellovirus, and one circovirus-like virus) and one novel bovine polyomavirus species (BPyV2-SF) whose closest relatives infect primates. Detection of porcine hokovirus in beef indicated that this parvovirus can infect both ungulate species. In pork we detected four known parvoviruses from three genera, an anellovirus, and pig circovirus 2. Chicken meat contained numerous gyrovirus sequences including those of chicken anemia virus and of a novel gyrovirus species (GyV7-SF). Our results provide an initial characterization of some of the viruses commonly found in US store-bought meats which included a diverse group of parvoviruses and viral families with small circular DNA genomes. Whether any of these viruses can infect humans will require testing human sera for specific antibodies.",amino acid sequence;Anelloviridae;antibody specificity;article;beef;binding site;chicken;Circovirus;Copiparvovirus;Gyrovirus;Gyrovirus 1;Gyrovirus 2;Gyrovirus 3;Gyrovirus 4;metagenomics;nonhuman;nucleotide sequence;open reading frame;Parvoviridae;polymerase chain reaction;Polyomavirus;Porcine cirvovirus 2;pork;protein database;protein motif;sequence alignment;Torque teno virus 1;Ungulate copiparvovirus 2;Ungulate erythroparvovirus 1;Ungulate protoparvovirus 1;Ungulate tetraparvovirus 2;United States;virus genome;virus identification;virus strain,"Zhang, W.;Li, L.;Deng, X.;Kapusinszky, B.;Delwart, E.",2014,,10.1016/j.virol.2014.08.025,0
2426,Hepatitis E virus infection among domestic animals in eastern China,"Hepatitis E virus (HEV) is a zoonotic pathogen of which several species of animal were reported as reservoirs. Antibodies to HEV and HEV RNA have been detected in some Chinese population and swine groups but few other domestic animals. In this study, to investigate the HEV prevalence, we tested sera from 788 pigs, 100 cows, 50 goats, 49 horses, 101 pet dogs, 105 chickens, 47 duck and 45 pigeons in eastern China for anti-HEV immunoglobulin G (IgG). We also tested 50% of the swine sera, all of sera from the other domestic animals and 13 Shanghai human sera which were positive for anti-HEV immunoglobulin M (IgM) for HEV RNA using reverse transcriptase-polymerase chain reaction. Our results indicated that 82.5% (222/269) of the sows, 53.9% (104/193) of the 4- to 6-month-old swine, 63.4% (168/265) of the 1- to 3-month-old swine, 55.7% (34/61) of the slaughterhouse swine, 24% (12/50) of the goats, 16.3% (8/49) of the horses, 17.8% (21/101) of the pet dogs, 6% (6/100) of the cows, 12.8% (6/47) of the ducks, 4.4% (2/45) of the pigeons and 1.9% (2/105) of the chickens exhibited positive for anti-HEV IgG. Inhibition assay confirmed the infection with HEV or HEV-like viruses in these domestic animals except pigeons and chickens. From the sera, we isolated 18 swine HEV strains, one horse HEV strain and two human HEV strains. Sequence analysis showed that the horse HEV isolate and one swine isolate belonged to genotype 3. The other isolates belonged to genotype 4. The two human isolates were phylogenetically closely related to eight of the swine isolates. In short, the presence of anti-HEV antibody had been confirmed in several species of domestic animals in eastern China and HEV RNA has been identified in swine, human and horse. This suggested that the authorities should pay more attention to the prevalence of HEV in eastern China. © 2008 The Authors.",immunoglobulin G;immunoglobulin M;RNA;article;China;controlled study;domestic animal;genotype;hepatitis E;Hepatitis E virus;nonhuman;nucleotide sequence;open reading frame;phylogeny;prevalence;priority journal;reverse transcription polymerase chain reaction;sequence analysis;unindexed sequence,"Zhang, W.;Shen, Q.;Mou, J.;Gong, G.;Yang, Z.;Cui, L.;Zhu, J.;Ju, G.;Hua, X.",2008,,10.1111/j.1863-2378.2008.01136.x,0
2427,Identification and genomic characterization of a novel species of feline anellovirus,"Here, a novel feline anellovirus strain (named FelineAV621 and GenBank no. KX262893) was detected in two cats with diarrhea. The complete genome of FelineAV621 is 2409 nt long with a G+C content of 56.67 %, including three open reading frames (ORFs). Phylogenetic analysis based on the amino acid sequence of the putative capsid protein (ORF1) indicated that FelineAV621 belonged to a novel anellovirus species inside a clade containing the seal anellovirus, canine TTVs, and porcine TTVs, but was distant from all the previous feline anelloviruses.",capsid protein;Anelloviridae;article;cladistics;Feline anellovirus;gene amplification;gene identification;gene structure;genetic analysis;nonhuman;open reading frame;phylogeny;polymerase chain reaction;sequence analysis;strain identification;virus detection;virus strain,"Zhang, W.;Wang, H.;Wang, Y.;Liu, Z.;Li, J.;Guo, L.;Yang, S.;Shen, Q.;Zhao, X.;Cui, L.;Hua, X.",2016,,10.1186/s12985-016-0601-8,0
2428,Virome comparisons in wild-diseased and healthy captive giant pandas,"Background: The giant panda (Ailuropoda melanoleuca) is a vulnerable mammal herbivore living wild in central China. Viral infections have become a potential threat to the health of these endangered animals, but limited information related to these infections is available. Methods: Using a viral metagenomic approach, we surveyed viruses in the feces, nasopharyngeal secretions, blood, and different tissues from a wild giant panda that died from an unknown disease, a healthy wild giant panda, and 46 healthy captive animals. Results: The previously uncharacterized complete or near complete genomes of four viruses from three genera in Papillomaviridae family, six viruses in a proposed new Picornaviridae genus (Aimelvirus), two unclassified viruses related to posaviruses in Picornavirales order, 19 anelloviruses in four different clades of Anelloviridae family, four putative circoviruses, and 15 viruses belonging to the recently described Genomoviridae family were sequenced. Reflecting the diet of giant pandas, numerous insect virus sequences related to the families Iflaviridae, Dicistroviridae, Iridoviridae, Baculoviridae, Polydnaviridae, and subfamily Densovirinae and plant viruses sequences related to the families Tombusviridae, Partitiviridae, Secoviridae, Geminiviridae, Luteoviridae, Virgaviridae, and Rhabdoviridae; genus Umbravirus, Alphaflexiviridae, and Phycodnaviridae were also detected in fecal samples. A small number of insect virus sequences were also detected in the nasopharyngeal secretions of healthy giant pandas and lung tissues from the dead wild giant panda. Although the viral families present in the sick giant panda were also detected in the healthy ones, a higher proportion of papillomaviruses, picornaviruses, and anelloviruses reads were detected in the diseased panda. Conclusion: This viral survey increases our understanding of eukaryotic viruses in giant pandas and provides a baseline for comparison to viruses detected in future infectious disease outbreaks. The similar viral families detected in sick and healthy giant pandas indicate that these viruses result in commensal infections in most immuno-competent animals.",Giant panda;Viral metagenomics;Virome;Papillomavirus;Picornavirus;Anellovirus;Gemycircularvirus;Putative circovirus;CHICKEN ANEMIA VIRUS;STRANDED-DNA VIRUSES;AILUROPODA-MELANOLEUCA;PAPILLOMAVIRUS TYPE-1;GENOMIC CHARACTERIZATION;METAGENOMIC ANALYSIS;HUMAN ANELLOVIRUSES;VIRAL METAGENOMICS;GUT MICROBIOME;FECAL VIROME,"Zhang, W.;Yang, S. X.;Shan, T. L.;Hou, R.;Liu, Z. J.;Li, W.;Guo, L. H.;Wang, Y.;Chen, P.;Wang, X. C.;Feng, F. F.;Wang, H.;Chen, C.;Shen, Q.;Zhou, C. L.;Hua, X. G.;Cui, L.;Deng, X. T.;Zhang, Z. H.;Qi, D. W.;Delwart, E.",2017,Aug,,0
2429,The hemagglutinin/esterase gene of human coronavirus strain OC43: Phylogenetic relationships to bovine and murine coronaviruses and influenza C virus,"The complete nucleotide sequences of the hemagglutinin/esterase (HE) genes of human coronavirus (HCV) strain OC43 and bovine respiratory coronavirus (BRCV) strain G95 were determined from single-stranded cDNA fragments generated by reverse transcription of virus-specific mRNAs and amplified by polymerase chain reaction. An open reading frame of 1272 nucleotides was identified as the putative HE gene by homology to the bovine coronavirus HE gene. This open reading frame encodes a protein of 424 amino acids with an estimated molecular weight of 47.7 kDa. Ten potential N-linked glycosylation sites were predicted in the HE protein of HCV-OC43 while nine of them were present in BRCV-G95. Fourteen cysteine residues were conserved in the HE proteins of both viruses. Two hydrophobic sequences at the N-terminus and the C-terminus may serve as signal peptide and transmembrane anchoring domain, respectively. The predicted HE protein of HCV-OC43 was 95% identical to the HEs of BRCV-G95 and other bovine coronaviruses, and 60% identical to the HEs of mouse hepatitis viruses. Phylogenetic analysis suggests that the HE genes of coronaviruses and influenza C virus have a common ancestral origin, and that bovine coronaviruses and HCV-OC43 are closely related.",esterase;hemagglutinin;article;Coronavirinae;Influenza C virus;nonhuman;phylogeny;priority journal;virus gene,"Zhang, X.;Kousoulas, K. G.;Storz, J.",1992,,10.1016/0042-6822(92)90089-8,0
2430,Deciphering the Sharp Decrease in H7N9 Human Infections,"The H7N9 virus has caused five waves of human infections since 2013. However, human infections have almost disappeared in the past year. In a recent study, Shi et al. revealed that the usage of a bivalent H5/H7 vaccine successfully prevented chicken infections, and thus prevented, and nearly eliminated, human infections.",influenza vaccine;China;epidemic;evolution;host range;human;infection control;influenza A (H7N9);Influenza A virus (H7N9);influenza vaccination;nonhuman;pathogenicity;poultry;prevalence;priority journal;risk assessment;short survey;vaccination coverage;vaccine failure;virus classification,"Zhang, X.;Luo, T.;Shen, Y.",2018,,10.1016/j.tim.2018.10.002,0
2431,Complete Genome Sequence of an H9N2 Influenza Virus Lethal to Chickens,An H9N2 virus lethal to chickens was isolated from an acutely ill chicken flock in 2012. Phylogenetic analyses indicated that this virus was phylogenetically related to the Y280 lineage. Sequence analysis showed 1 amino acid deletion in HA1 and 3 amino acid deletions in the NA stalk region.,,"Zhang, Y.;Guo, X.;Qi, J.;Liu, L.;Wang, J.;Xu, S.;Wang, J.;Yin, Y.",2014,Nov 26,,0
2432,Integration analysis of miRNA and mRNA expression profiles in swine testis cells infected with Japanese encephalitis virus,"To elucidate the role of microRNAs (miRNA) in the regulation of gene expression in Japanese encephalitis virus (JEV) infected swine testis (ST) cells, we analyzed miRNA and mRNA expression profiles of JEV infected ST cells by high-throughput sequencing technology as compared to uninfected controls. The results showed that 104 known miRNAs and 9 new miRNA candidates were differentially expressed in ST cells after JEV infection. We identified 396 differentially expressed mRNAs. Bioinformatics analysis identified 435 known miRNA-mRNA interaction pairs and 94 novel miRNA-mRNA interaction pairs involving miRNAs inversely correlated with the expression of their predicted target mRNAs. The known miRNAs inversely correlated with their target genes were involved in the biological processes of immunity, cytokine production, inflammation, and apoptosis. Selected miRNA-mRNA interactions were validated by luciferase reporter assay. Overall, our findings indicate that miRNAs may play critical roles in the pathogenesis of JEV infection.",messenger RNA;microRNA;animal cell;apoptosis;article;bioinformatics;controlled study;cytokine production;gene expression profiling;gene expression regulation;gene identification;high throughput sequencing;inflammation;integration;Japanese encephalitis virus;male;nonhuman;priority journal;protein secondary structure;quantitative analysis;real time polymerase chain reaction;RNA analysis;RNA sequence;signal transduction;testis cell,"Zhang, Y.;Jing, J.;Li, X.;Wang, J.;Feng, X.;Cao, R.;Chen, P.",2015,,10.1016/j.meegid.2015.03.037,0
2433,Characterization of the σC-encoding gene from Musocvy duck reovirus,"The σC-encoding gene of two muscovy duck reovirus (DRV) S14 and C4 strains were cloned and completely sequenced. The open reading frame (ORF) comprised 810 bp and encoded 269 amino acids with a predicated molecular mass of 29.5 kDa. Expressed σC fusion protein in Escherichia coli BL21 strain could be detected by Western blotting under duck anti-reovirus polyclonal serum. There are two large gap insertions at the N-terminal part of the DRV σC when necessary to optimize the alignment of the amino acid sequences of the DRV σC had a heptapeptide repeat and leucine zipper patterns structurally related to ARV σC. All DRVs grouped into one specified genogroup within Orthoreoviruses genus subgroup II. The degree of differences between the S14/C4 and ARV was only 23-24%, and 21-22%, respectively, at both the nucleotide and deduced amino acid levels, suggested that DRVs are quite different from ARVs and should give a precise classification for DRVs in Orthoreovirus genus. © Springer Science+Business Media, Inc. 2006.",heptapeptide;fusion protein;leucine;amino acid sequence;amino terminal sequence;article;Escherichia coli;gene expression;gene insertion;gene sequence;gene structure;genetic analysis;genetic code;molecular cloning;molecular weight;nonhuman;open reading frame;Orthoreovirus;priority journal;Reoviridae;virus classification;virus strain;Western blotting,"Zhang, Y.;Liu, M.;Hu, Q.;Ouyang, S.;Tong, G.",2006,,10.1007/s11262-005-6872-6,0
2434,"Isolation and characterization of H7N9 avian influenza A virus from humans with respiratory diseases in Zhejiang, China","In 2013, the novel reassortant avian-origin influenza A (H7N9) virus was reported in China. Through enhanced surveillance, infection by the H7N9 virus in humans was first identified in Zhejiang Province. Real-time reverse-transcriptase-polymerase-chain-reaction (RT-PCR) was used to confirm the infection. Embryonated chicken eggs were used for virus isolation from pharyngeal swabs taken from infected human patients. The H7N9 isolates were first identified by the hemagglutination test and electron microscopy, then used for whole genome sequencing. Bioinformatics software was used to construct the phylogenetic tree and for computing the mean rate of evolution of the HA gene in H7Nx and NA in HxN9. Two novel H7N9 avian influenza A viruses (A/Zhejiang/1/2013 and A/Zhejiang/2/2013) were isolated from the positive infection cases. Substitutions were found in both Zhejiang isolates and were identified as human-type viruses. All phylogenetic results indicated that the novel reassortant in H7N9 originated in viruses that infected birds. The sequencing and phylogenetic analysis of the whole genome revealed the mean rate of evolution of the HA gene in H7NX to be 5.74E-3 (95% Highest posterior density: 3.8218E-3 to 7.7873E-3) while the NA gene showed 2.243E-3 (4.378E-4 to 3.79E-3) substitutions per nucleotide site per year. The novel reassortant H7N9 virus was confirmed by molecular methods to have originated in poultry, with the mutations occurring during the spread of the H7N9 virus infection. Live poultry markets played an important role in whole H7N9 circulation. © 2014 Elsevier B.V.",adult;article;avian influenza;bioinformatics;case report;chicken;China;controlled study;egg;genome analysis;hemagglutination test;human;influenza A;Influenza A virus (H7N9);male;molecular evolution;nonhuman;nucleic acid base substitution;nucleotide sequence;phylogenetic tree;phylogeny;poultry;priority journal;real time polymerase chain reaction;reverse transcription polymerase chain reaction;throat culture;transmission electron microscopy;virus characterization;virus genome;virus isolation;virus mutation,"Zhang, Y.;Mao, H.;Yan, J.;Zhang, L.;Sun, Y.;Wang, X.;Chen, Y.;Lu, Y.;Chen, E.;Lv, H.;Gong, L.;Li, Z.;Gao, J.;Xu, C.;Feng, Y.;Ge, Q.;Xu, B.;Xu, F.;Yang, Z.;Zhao, G.;Han, J.;Guus, K.;Li, H.;Shu, Y.;Chen, Z.;Xia, S.",2014,,10.1016/j.virusres.2014.05.002,0
2435,"The epidemiologic and virological analysis of an outbreak of hand, foot, and mouth disease in Inner Mongolia in 2007","In 2007, an outbreak of hand, foot, and mouth disease (HFMD) occurred in Jungar Banner, Erdos city, Inner Mongolia Autonomous Region, China Fever, vesicular exanthema on the hands, feet, mouth, and buttocks were presented in most of the patients. Most of the patients were infants less than 5 years old, and an obvious peak period appeared in the disease outbreak. From 28 hospitalized patients, 23 stool specimens and 6 throat swab specimens were collected for enterovirus isolation, and 15 enteroviruses were isolated, 9 were identified as Human Enterovirus 71 (HEV71, the isolation rate is 31.03%) and 1 was identified as Coxsackievirus A16 (CVA16). According to the comprehensive analysis of clinical manifestation, epidemiology data and laboratory results, this outbreak was probably mainly caused by HEV71. The variability at nucleotide acid level and amino acid level among 9 HEV71 was relatively low, and the homology was more than 99.4% and 99.0% respectively, showing that this outbreak was caused by only one viral transmission chain. Phylogenetic analysis of 9 HEV71 strains isolated during this outbreak revealed that they all belonged to subgenotype C4, which has been continuously circulating in mainland China since its first reported occurrence in Shenzhen City in 1998. It was also suggested that subgenotype C4 HEV71 had a widely distribution and transmission in mainland China.",article;China;classification;DNA sequence;Enterovirus;genetics;hand foot and mouth disease;human;molecular genetics;phylogeny;physiology;polymerase chain reaction;virology,"Zhang, Y.;Nan, L. J.;Wu, G. S.;Tan, X. J.;Xu, D. D.;Gu, S. Y.;Zhu, S. L.;Yan, D. M.;An, H. Q.;Xu, W. B.",2009,,,0
2436,The potential of the human immune system to develop broadly neutralizing HIV-1 antibodies: Implications for vaccine development,"OBJECTIVES AND DESIGN: Developing an effective HIV-1 vaccine that elicits broadly neutralizing HIV-1 human antibodies (bnAbs) remains a challenging goal. Extensive studies on HIV-1 have revealed various strategies employed by the virus to escape host immune surveillance. Here, we investigated the human antibody gene repertoires of uninfected and HIV-1-infected individuals at genomic DNA (gDNA) and cDNA levels by deep sequencing followed by high-throughput sequence analysis to determine the frequencies of putative germline antibody genes of known HIV-1 monoclonal bnAbs (bnmAbs). METHODS: Combinatorial gDNA and cDNA antibody libraries were constructed using the gDNAs and mRNAs isolated from uninfected and HIV-1-infected human peripheral blood mononuclear cells (PBMCs). All libraries were deep sequenced and sequences analysed using IMGT/HighV-QUEST software (http://imgt.org/HighV-QUEST/index. action). The frequencies of putative germline antibodies of known bnmAbs in the gDNA and cDNA libraries were determined. RESULTS AND CONCLUSION: The human gDNA antibody libraries were more diverse in heavy and light chain V-gene lineage usage than the cDNA libraries, indicating that the human gDNA antibody gene repertoires may have more potential than the cDNA repertoires to develop HIV-1 bnAbs. The frequencies of the heavy and kappa and lambda light chain variable regions with identical V(D)J recombinations to known HIV-1 bnmAbs were extremely low in human antibody gene repertoires. However, we found relatively high frequencies of the heavy and kappa and lambda light chain variable regions that used the same V-genes and had the same CDR3 lengths as known HIV-1 bnmAbs regardless of (D)J-gene usage. B-cells bearing B-cell receptors of such heavy and kappa and lambda light chain variable regions may be stimulated to induce HIV-1 bnAbs. © 2013 Wolters Kluwer Health | Lippincott Williams & Wilkins.",B lymphocyte receptor;complementary DNA;genomic DNA;Human immunodeficiency virus antibody;Human immunodeficiency virus vaccine;immunoglobulin kappa chain;immunoglobulin lambda chain;article;B lymphocyte;combinatorial library;DNA library;DNA sequence;heavy chain;high throughput sequencing;human;human cell;Human immunodeficiency virus 1 infection;immune system;light chain;peripheral blood mononuclear cell;priority journal;VDJ recombination,"Zhang, Y.;Yuan, T.;Li, J.;Zhang, Y.;Xu, J.;Shao, Y.;Chen, Z.;Zhang, M. Y.",2013,,10.1097/qad.0000000000000015,0
2437,Complete genome sequence of a subgenotype VIId newcastle disease virus circulating predominantly in chickens in China,"At least 11 genotypes of class II viruses have been identified since the discovery of Newcastle disease virus (NDV)in 1926. Here,we reported the complete genome sequence of a prevalent NDV variant from China, belonging to subgenotype VIId in class II.The similar viruses have been the predominant strains circulating in China for the past decade, which occupied over 80% of Chinese prevalent strains and were phylogenetically different from currently available vaccines. © 2012, American Society for Microbiology.",F protein;unclassified drug;viral protein;chicken;China;gene amplification;genome analysis;genotype;Newcastle disease virus;nonhuman;note;nucleotide sequence;phylogeny;priority journal;reverse transcription polymerase chain reaction;sequence alignment;sequence analysis;sequence homology;virus classification;virus genome;virus isolation;virus strain;virus virulence,"Zhang, Y.;Zhang, S.;Wang, X.;Zhang, G.",2012,,10.1128/jvi.02663-12,0
2438,[Research on construction of sheep lung adenomas virus pEGFP-C1/exJSRV-env and induction of malignant transformation in NIH3T3],"This study aims to construct a eukaryotic expression system for envelope gene of Jaagsiekte sheep retrovirus, observes its localization in 293T cells, and investigates the potential in inducing malignant transformation of NIH3T3 cells. By RT-PCR, the full-length cDNA of envelope gene of Jaagsiekte sheep retrovirus (exJSRV-env) was amplified from the extract of naturally infected sheep lung. The clone of target gene was sub-cloned into eukaryotic expression system pEGFP-C1, and validated by PCR, restriction endonuclease, and sequencing. Bioinformatic analysis concerning biological function and cellular localiza tion of exJSRV-env was also performed. The recombinant clone of exJSRV-env was transfected into 293T cells and NIH3T3 cells by Lipofectamine LTX. The expression and celluar localization in 293T cells were validated by confocal microscopy. Soft agar colony formation assay was employed to test the anchorage-independent growth of NIH3T3. DNA sequencing and restriction enzyme digestion with Kpn I and Hind III indicated the correct construction of the recombinant plasmid, which was named pEGFP-C1/exJSRV-env. Amino acid sequence alignment of exJSRV-env with reference sequences found 85%-100% homogeneity. A YRNM motif was discovered at the cytoplasmic tail of envelope gene, which is exclusively found in exogenous viruses. Phylogenetic tree analysis showed that our clone of exJSRV-env clustered closely with pathogenic exogenous Jaagsiekte sheep retroviruses. Fluorescence microscopy indicated typical membrane localization of exJSRV-env protein. NIH3T3 cells transfected with exJSRV-env lost contact inhibition, and acquired colony forming ability in soft agar. This study indicated that envelope protein of Jaagsiekte sheep retrovirus can induce malignant transformation of mouse fibroblast cell NIH3T3. Discoveries of this study provide a basis for further structural and functional research on Jaagsiekte sheep retrovirus envelope protein.",enhanced green fluorescent protein;green fluorescent protein;virus envelope protein;3T3 cell line;amino acid sequence;animal;animal disease;article;chemistry;classification;genetic transformation;genetics;metabolism;molecular genetics;mouse;phylogeny;physiology;Retroviridae;retrovirus infection;sequence alignment;sheep;sheep disease;virology;virus cell transformation;virus infection,"Zhang, Y. F.;Liu, Y.;Wang, Z. J.;Sun, X. L.;Liu, S. Y.",2014,,,0
2439,Molecular characterization of chicken-derived genotype VIId Newcastle disease virus isolates in China during 2005-2012 reveals a new length in hemagglutinin-neuraminidase,"Newcastle disease (ND) is one of the most important diseases of poultry, and causes severe economic losses in the global poultry industry. Although all Newcastle disease virus (NDV) isolates belong to a single serotype, significant genetic diversity has been described between different NDV isolates. Here, we report the molecular characterization of 23 virulent genotype VIId NDV isolates of class II circulating in China. Phylogenetic construction and analysis revealed the existence of distinctly genomic and amino acid differences that clearly distinguished these isolates from other typical NDV genotypes and vaccine strains. We also report a new 582-amino-acid hemagglutinin-neuraminidase in genotype VII NDV strains. This is believed to be the first study to investigate systematically the most predominant NDV strains, and provides more information on the genetic nature of genotype VIId NDV of class II circulating in China. © 2013 Elsevier B.V.",amino acid;virus hemagglutinin;virus sialidase;virus vaccine;article;chicken;China;genetic difference;genotype;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;priority journal;virus genome;virus isolation;virus strain,"Zhang, Y. Y.;Shao, M. Y.;Yu, X. H.;Zhao, J.;Zhang, G. Z.",2014,,10.1016/j.meegid.2013.12.003,0
2440,A simple method for high-throughput quantification of genome-wide DNA methylation by fluorescence polarization,"To rapidly determine DNA methylation levels from a large number of biological or clinical samples, we have developed an accurate and sensitive method for high-throughput quantification of global methylation of 5'-Cm ( 5) CGG-3' sites in the genome, visualized by fluorescence polarization (FP) based measurement of DNA methylation (FPDM). In FPDM, the methyl-sensitive HpaII and methyl-insensitive MspI restriction enzymes were employed to achieve DNA cleavage, followed by incorporation of fluorescent dCMP into the enzyme-cleavage products through polymerase chain extension, yielding an FP-ratio between the HpaII- and MspI-restricted preparations as a measure of methylation. FPDM provided stable estimates of methylation level of submicrograms of lambda or human DNA, and of a 255-bp DNA segment containing a single HpaII/MspI restriction site in accord with, and more accurate than, determination by gel electrophoresis. FPDM was also applied to measure dose-dependent DNA hypomethylation in human embryonic kidney 293T cells treated with the DNA-methyltransferase inhibitor 5-aza-dC.","Azacitidine/aa [Analogs & Derivatives];Azacitidine/pd [Pharmacology];*Bacteriophage lambda/ge [Genetics];Bacteriophage lambda/me [Metabolism];Base Sequence;CpG Islands;*DNA Methylation;DNA, Viral/ge [Genetics];*DNA, Viral/me [Metabolism];Decitabine;Deoxyribonuclease HpaII/ge [Genetics];Deoxyribonuclease HpaII/me [Metabolism];*Fluorescence Polarization/mt [Methods];Genome, Human;HEK293 Cells;*High-Throughput Nucleotide Sequencing/mt [Methods];Humans;Receptors, GABA-A/ge [Genetics];Receptors, GABA-A/me [Metabolism];Restriction Mapping/mt [Methods];Sensitivity and Specificity;0 (DNA, Viral);0 (GABRB2 protein, human);0 (Receptors, GABA-A);776B62CQ27 (Decitabine)","Zhao, C.;Xue, H.",2012,Apr,,0
2441,The unfolded protein response induced by Tembusu virus infection,"BACKGROUND: Tembusu virus (TMUV), classified in the genus Flavivirus, causes reduced egg production and neurological problems in poultry. Flavivirus replication depends on the host endoplasmic reticulum (ER) and induces ER stress that leads to activation of the cellular unfolded protein response (UPR), an important signalling pathway that regulates many biological functions involved in viral pathogenesis and innate immunity. However, the mechanism of TMUV-induced UPR activation remains unclear. RESULTS: In this study, we systematically investigated the three UPR pathways in TMUV-infected BHK-21 cells. Our results showed that expression of glucose-related protein 78 (GRP78) and GRP94 was upregulated during the course of TMUV infection. We then demonstrated that TMUV activated the PERK pathway in the early stage of infection, resulting in upregulation of ATF4, GADD34 and CHOP, with CHOP induction leading to caspase-3 activation. We also found the IRE1 pathway to be activated, leading to splicing of X box binding protein 1 (XBP1) mRNA and enhanced expression of p58IPK. Finally, we observed increased expression of ATF6 and activity of ER stress-response elements, suggesting stimulation of the ATF6 pathway. In addition, ATF6 pathway activation correlated with the induction of downstream chaperones calnexin, calreticulin, ERp57 and PDI. UPR activity was also observed by the marked elevation in GRP78 and sXBP1 levels in TMUV-infected DF-1 cells. CONCLUSIONS: This is the first report that TMUV infection-induced ER stress activates three branches of the UPR, and these results lay the foundation for elucidating the pathogenesis of TMUV and understanding the inherent mechanism of TMUV infection as well as the host response.",interleukin 1beta converting enzyme;PERK kinase;protein kinase R;animal;cell line;chicken;endoplasmic reticulum;Flavivirus;Flavivirus infection;hamster;metabolism;real time polymerase chain reaction;signal transduction;unfolded protein response;virology;Western blotting,"Zhao, D.;Yang, J.;Han, K.;Liu, Q.;Wang, H.;Liu, Y.;Huang, X.;Zhang, L.;Li, Y.",2019,,10.1186/s12917-019-1781-4,0
2442,Transcriptomic analysis of porcine PBMCs in response to FMDV infection,"Foot-and-mouth disease (FMD) is a significant zoonotic infectious disease. It has an important economic impact throughout the world. As well, it is a considerable threat to food security. At present, the molecular mechanism of FMDV infection is not clear to a large extent. Innate immune response is the first line of defense against infectious diseases. The systematic analysis of the host immune response to infection has an important role in understanding the pathogenesis of infection. However, there are few reports about effect of immune regulation on virus replication in the interaction of virus and host cellular. High-throughput RNA-seq technology as a powerful and efficient means for transcript analysis provides a new insight into FMDV study. In this study, RNA extracted from pig PBMCs infected with O subtype FMDV at 4 dpi. A total of 29942658 and 31452917 Illumina read pairs were obtained from the non-infected (NI) group and infected (I) group, respectively. The clean bases for all samples are 3.61G (NI group) and 3.79G (I group), respectively. The clean reads of the NI and I group that mapped to pig genome data were 47195073 (81.82%) and 46556714 (76.85%), respectively. Most of the clean reads were distributed in the exon region, followed by intron region and intergenic region. Differently expressed (DE) genes were analyzed using edgeR software. 451 genes were differentially expressed between the infected and the non-infected groups. According to the comparison analysis, more genes were down-regulated in the non-infected samples than in those infected with FMDV.66 out of 451 genes were down-regulated, 385 out of 451 genes were up-regulated following FMDV infection. For function classification and pathway analysis, among 17741 assembled unigenes, there are 349 genes which are different genes of GO notes. Moreover, 49 genes were down-regulated, 300 genes were up-regulated associate with GO term. 1621 were successfully annotated by GO assignments, belonging to one or more of the three categories: biological process, cellular component, and molecular function. According to KEGG analysis,the main pathway was represented including protein processing in endoplasmic reticulum, phagosome, cell cycle and cytokine-cytokine receptor interaction. Some key DE genes related to immune process and signaling pathways were analyzed and quantified by RT-PCR. This is the first systematical transcriptome analysis of pig PBMCs infected by FMDV. These findings will help us better understand the host Cell-FMDV interaction and its relationship to pathogenesis, as well as contribute to the prevention and control of FMDV.",cytokine;cytokine receptor;animal cell;animal experiment;article;cell cycle;cell interaction;controlled study;down regulation;endoplasmic reticulum;exon;foot and mouth disease;Foot and mouth disease virus;gene expression regulation;gene sequence;genetic association;high throughput sequencing;immune response;immunoregulation;innate immunity;intron;nonhuman;peripheral blood mononuclear cell;phagosome;pig;protein processing;real time polymerase chain reaction;sequence alignment;signal transduction;transcriptomics;upregulation;virus replication,"Zhao, F. R.;Xie, Y. L.;Liu, Z. Z.;Shao, J. J.;Li, S. F.;Zhang, Y. G.;Chang, H. Y.",2017,,10.1016/j.actatropica.2017.05.009,0
2443,Characterisation of one H6N6 influenza virus isolated from swine in China,"There is multiple evidence that swine may act as a vessel for the generation of novel influenza A viruses. In this study, we have analyzed the evolution and pathogenicity of one strain of H6N6 influenza virus isolated from swine with clinical signs of infection in China. Although phylogenetic analysis revealed that this virus might originate from domestic ducks, pathogenicity experiments indicated that the virus replicated in mice without prior adaptation. These findings suggest that the virus has transmitted from ducks to swine in China, and replicated in mammalian hosts without prior adaptation, which may pose a threat to both veterinary and public health. © 2013 Elsevier Ltd.",adaptation;animal experiment;animal model;animal tissue;article;China;Circovirus;Circovirus 2;controlled study;duck;female;genome analysis;host pathogen interaction;influenza A;influenza A (H6N6);Influenza A virus;Influenza virus A H6N6;molecular evolution;mouse;nonhuman;nose smear;nucleotide sequence;phylogeny;public health;sequence alignment;sequence homology;pig;swine influenza;swine influenza virus;virus characterization;virus genome;virus isolation;virus replication;virus strain;virus transmission;virus virulence,"Zhao, G.;Chen, C.;Huang, J.;Wang, Y.;Peng, D.;Liu, X.",2013,,10.1016/j.rvsc.2013.06.013,0
2444,Isolation and phylogenetic analysis of pandemic H1N1/09 influenza virus from swine in Jiangsu province of China,"To investigate whether the 2009 pandemic H1N1 influenza A virus was still being transmitted in swine, a total of 1029 nasal swab samples from healthy swine were collected from January to May 2010 in Jiangsu province of China. Eight H1N1 influenza viruses were isolated and identified, and their full length genomes were sequenced. We found that all eight of the H1N1 viruses shared higher than 98.0% sequence identity with the 2009 pandemic virus A/Jiangsu/1/2009 (JS1). In addition, some of these viruses had D225G (3/8) mutations in the receptor binding sites of the hemagglutinin (HA) protein, indicating enhancement of their binding affinity to the sialic α2, 3Gal receptor. In conclusion, the 2009 pandemic H1N1 influenza A virus has retro-infected swine from humans in mainland China, and significant viral evolution is still ongoing in this species. © 2011 Elsevier Ltd.",Influenza virus hemagglutinin;sialic alpha2 3Gal receptor;unclassified drug;virus receptor;amino acid substitution;article;binding affinity;binding site;China;Influenza A virus (H1N1);nonhuman;nose smear;nucleotide sequence;phylogeny;sequence homology;pig;virus gene;virus genome;virus identification;virus isolation;virus mutation,"Zhao, G.;Fan, Q.;Zhong, L.;Li, Y.;Liu, W.;Liu, X.;Gao, S.;Peng, D.;Liu, X.",2012,,10.1016/j.rvsc.2011.06.009,0
2445,Molecular evolution of the H6 subtype influenza a viruses from poultry in eastern China from 2002 to 2010,"Background: Although extensive data demonstrates that the majority of H6 duck isolates belonged to a single H6N2 virus lineage with a single gene constellation in southern China from 2000 to 2005, the prevalence of H6N2 virus in poultry in Eastern China is largely unknown. Results: Epidemiology revealed that H6N2 viruses were the most frequently detected influenza subtypes in live bird markets from 2002 to 2008 in Eastern China, but from 2009 onwards, they were replaced with novel H6N6 viruses. We phylogenetically and antigenically analyzed 42 H6 viruses isolated mainly in domestic ducks from 2002 to 2010 in Eastern China. Surprisingly, none of these isolates grouped with the previously described H6N2 viruses which belonged to a single H6N2 virus lineage with a single gene constellation in domestic ducks in southern China from 2000 to 2005. Two distinct hemagglutinin lineages were identified and they all underwent frequent reassortment with multiple virus subtypes from the natural gene pool, but few reassortants were persistent or prevalent. Conclusions: Five subtypes of H6 influenza viruses (H6N1, H6N2, H6N5, H6N6 and H6N8) cocirculated in Eastern China, which form a significant part of the natural influenza virus reservoir in domestic ducks, and significant viral reassortment is still ongoing in this species. © 2011Zhao et al; licensee BioMed Central Ltd.",hemagglutinin;antigenicity;article;chicken;China;domestic animal;duck;gene pool;genetic reassortment;genetic variability;goose;Influenza A virus;influenza virus A H6;molecular phylogeny;nonhuman;nucleotide sequence;poultry;virus isolation,"Zhao, G.;Lu, X.;Gu, X.;Zhao, K.;Song, Q.;Pan, J.;Xu, Q.;Duan, Z.;Peng, D.;Hu, S.;Wang, X.;Liu, X.",2011,,10.1186/1743-422x-8-470,0
2446,Characterization of VP1 sequence of Coxsackievirus A16 isolates by Bayesian evolutionary method,"Background: Coxsackievirus A16 (CV-A16), a major etiopathologic cause of pediatric hand, foot, and mouth disease (HFMD) worldwide, has been reported to have caused several fatalities. Revealing the evolutionary and epidemiologic dynamics of CV-A16 across time and space is central to understanding its outbreak potential. Methods: In this study, we isolated six CV-A16 strains in China's Jilin province and construct a maximum clade credibility (MCC) tree for CV-A16 VP1 gene by the Bayesian Markov Chain Monte Carlo method using 708 strains from GenBank with epidemiological information. The evolution characteristics of CV-A16 VP1 gene was also analysed dynamicly through Bayesian skyline plot. Results: All CV-A16 strains identified could be classified into five major genogroups, denoted by GI-GV. GIV and GV have co-circulated in China since 2007, and the CV-A16 epidemic strain isolated in the Jilin province, China, can be classified as GIV-3. The CV-A16 genogroups circulating recently in China have the same ancestor since 2007. The genetic diversity of the CV-A16 VP1 gene shows a continuous increase since the mid-1990s, with sharp increases in genetic diversity in 1997 and 2007 and reached peak in 2007. Very low genetic diversity existed after 2010. The CV-A16 VP1 gene evolutionary rate was 6.656E-3 substitutions per site per year. Conclusions: We predicted the dynamic phylogenetic trends, which indicate outbreak trends of CV-A16, and provide theoretical foundations for clinical prevention and treatment of HFMD which caused by a CV-A16.",protein VP1;article;Bayes theorem;Bayesian evolutionary method;China;codon;controlled study;Coxsackievirus A16;evolutionary rate;genetic variability;Japan;Malaysia;Markov Chain Monte Carlo;maximum clade credibility;Monte Carlo method;nonhuman;nucleotide sequence;phylogenetic tree;phylogeny;virus classification;virus gene;virus isolation;virus strain;VP1 gene,"Zhao, G.;Zhang, X.;Wang, C.;Wang, G.;Li, F.",2016,,10.1186/s12985-016-0578-3,0
2447,Metagenomic Analysis of the Jinding Duck Fecal Virome,"Ducks play an important role in transmitting and maintaining mammalian viruses in nature, and are a reservoir host of many animal viruses. We analyzed the fecal virome of four strains (A, B, C, and D) of ducks living in isolation by using metagenomic analysis. The feces of the ducks tested contained 18 animal virus families. The percentage values of RNA virus reads, compared to the total animal virus reads in each of the four strains were 96.96% (A), 97.30% (B), 98.01 (C), and 67.49% (D), and were mainly from Orthomyxoviridae, Mimiviridae, Bunyaviridae, Picobirnaviridae, and Reoviridae. Meanwhile, the minority of DNA virus reads were related to Herpesviridae, Adenoviridae, Iridoviridae, and other, low abundance viral families. The percentage values of Orthomyxoviridae, Mimiviridae, Bunyaviridae, Picobirnaviridae, and Herpesviridae reads were not significantly different among strains A, B, and C; however, there were marked differences in the abundance of these reads in strain D. In summary, this study provides an unbiased examination of the viral diversity in the feces of four strains of ducks in specific-pathogen-free periods, and highlights the variation in the percentage of viral families present. These results can be used as a reference for detecting duck viral pathogens and predicting zoonotic potential.",Anas platyrhynchos;animal virus;article;Bunyaviridae;feces;feces analysis;germfree animal;metagenomics;Mimiviridae;nonhuman;Orthomyxoviridae;Picobirnaviridae;priority journal;Reoviridae;RNA virus;virus detection,"Zhao, L.;Niu, Y.;Lu, T.;Yin, H.;Zhang, Y.;Xu, L.;Wang, Y.;Chen, H.",2018,,10.1007/s00284-018-1430-3,1
2448,Sequence analyses of the representative Chinese-prevalent strain of avian nephritis virus in healthy chicken flocks,"Avian nephritis virus (ANV), which belongs to the Astroviridae family, has been associated with acute nephritis in chickens. Cases of ANV infection have been recorded in Japan and in several European countries. However, related studies have never been performed in China. Thus, this study isolated ANV in Chinese chicken flocks. ANV RNA was detected by reverse transcription-PCR in stool samples collected from healthy layer chickens in the Sichuan Province of China in 2009. Of the 192 stool specimens collected, 32.3% (62/192) were positive for ANV infection. The whole genome of ANV-Sichuan54, the first representative Chinese strain, was 6941 nucleotides in length, including the 5′ untranslated region, three open reading frames (ORFs), a 3′ UTR, and a poly-(A) tail. Comparative and phylogenetic analyses based on partial RNA-dependent RNA polymerase (ORF1b) demonstrated that the majority of ANV investigations were more closely related to the U.S. ANV strain (DQ324827-324836) than to the G-4260 (AB033998). © 2011 American Association of Avian Pathologists.",complementary DNA;animal;animal disease;article;Astroviridae;astrovirus infection;bird disease;chicken;China;feces;phylogeny;virology;virus genome,"Zhao, W.;Hua, X. G.;Yuan, C. L.;Cui, L.;Shan, T. L.;Dai, X. Q.;Zhu, A. L.;Yu, Y.;Zhu, C. X.;Yang, Z. B.",2011,,10.1637/9506-081810-Reg.1,0
2449,"Confirmed diagnosis by RT-PCR and phylogenetic analysis of peste des petits ruminants viruses in Tibet, China","This paper reports the confirmed diagnosis by nested RT-PCR of PPR cases in Tibet, China in 2007, and results of phylogenetic analysis. Results showed that the 11 tested samples were PPRV positive by nested RT-PCR, of which 2 samples were genetically close to the X7443 strain (Nigeria 75/1) of lineage I, and 3 samples close to the strain AY560591 (Sungri96) of linage IV with 96.6%, 97.3%, 97.6% and 98% nucleotide sequence homogeneity respectively, based on partial sequencing of the F gene from 5 samples and complete sequencing of the N/M/F/H genes from one sample. This study suggested that there are at least 2 origins of PPRV in China. © 2009 Wuhan Institute of Virology, CAS and Springer Berlin Heidelberg.",animal experiment;article;controlled study;female;gene sequence;genomic fragment;male;Measles virus;nonhuman;nucleotide sequence;phylogeny;reverse transcription polymerase chain reaction;sequence alignment;sequence analysis;virus strain,"Zhao, W. H.;Yang, S. B.;Han, J. Q.;Jiang, M.;Li, H. C.;Zhang, N. Z.;Li, Q. H.",2009,,10.1007/s12250-009-3064-x,0
2450,[Detection of an NA gene molecular marker in H7N9 subtype avian influenza viruses by pyrosequencing],"This study aimed to establish a method for the detection and identification of H7N9 avian influenza viruses based on the NA gene by pyrosequencing. According to the published NA gene sequences of the avian influenza A (H7N9) virus, a 15-nt deletion was found in the NA gene of H7N9 avian influenza viruses. The 15-nt deletion of the NA gene was targeted as the molecular marker for the rapid detection and identification of H7N9 avian influenza viruses by pyrosequencing. Three H7N9 avian influenza virus isolates underwent pyrosequencing using the same assay, and were proven to have the same 15-nt deletion. Pyrosequencing technology based on the NA gene molecular marker can be used to identify H7N9 avian influenza viruses.","NA protein, influenza A virus;sialidase;viral protein;animal;article;avian influenza;bird;bird disease;chicken;classification;enzymology;evaluation study;genetics;high throughput sequencing;Influenza A virus (H7N9);isolation and purification;methodology;molecular genetics;nucleotide sequence;phylogeny;virology","Zhao, Y. G.;Liu, H. L.;Wang, J. J.;Zheng, D. X.;Zhao, Y. L.;Ge, S. Q.;Wang, Z. L.",2014,,,0
2451,Genomes and seroprevalence of severe fever with thrombocytopenia syndrome virus and Nairobi sheep disease virus in Haemaphysalis longicornis ticks and …,,,"Zhao, Z.;Hou, G.;Zhang, C.;Liu, J.;Xu, L.;Li, W.;Tan, Z.;Tu, C.",2019,,,0
2452,Molecular characterization of Japanese encephalitis virus strains prevalent in Chinese swine herds,"Japanese encephalitis virus (JEV) is the leading cause of viral encephalitis in Asia and domestic pigs serve as the amplifying hosts. In the present study, the full genomic sequences of two JEV strains (HEN0701 and SH0601) isolated from pigs in China were determined and compared with other 12 JEV strains deposited in GenBank. These two strains had an 88.8% nucleotide sequence similarity and 97.9% deduced amino acid sequence homology. HEN0701 had high nucleotide sequence and high amino acid sequence identity with genotype I (GI) strains, while SH0601 had high nucleotide sequence and high amino acid sequence identity with GIII strains at both the gene and full genome levels. Further phylogenetic analysis showed that HEN0701 belonged to the JEV GI group and SH0601 was classified as a GIII strain. Analysis of codon usage showed there were a few differences between the GI and GIII strains in nucleotide composition and codon usage for the open reading frames. © 2013 The Korean Society of Veterinary Science.",animal;animal disease;article;cell line;classification;gene expression regulation;genetics;genotype;hamster;Japanese encephalitis;Japanese encephalitis virus;molecular epidemiology;phylogeny;physiology;pig;swine disease;virology;virus genome,"Zheng, H.;Shan, T.;Den, Y.;Sun, C.;Yuan, S.;Yin, Y.;Tong, G.",2013,,10.4142/jvs.2013.14.1.27,0
2453,The occurrence of porcine circovirus 3 without clinical infection signs in Shandong Province,"Porcine circovirus type 3 (PCV3) was detected in Shandong, China. One hundred and thirty-two of 222 (59.46%) samples were PCV3 positive, while 52 of 132 (39.39%) samples were co-infected with PCV2. There were no clinical signs of infection in either multiparous sows or live-born infants. Two strains of PCV3 were indentified from natural stillborn foetuses. Phylogenetic analysis showed the two strains of PCV3 are 96% identical to the known PCV3/Pig/USA (KX778720.1, KX966193.1 and KX898030.1) and closely related to Barbel Circovirus. Further studies of the epidemiology of PCV3 and the co-infection with PCV2 are needed.",animal experiment;animal tissue;article;China;Circoviridae infection;Circovirus;genetic analysis;metagenomics;mixed infection;nonhuman;nucleotide sequence;phylogeny;polymerase chain reaction;Porcine circovirus 3;Sanger sequencing;stillbirth;tissue microarray,"Zheng, S.;Wu, X.;Zhang, L.;Xin, C.;Liu, Y.;Shi, J.;Peng, Z.;Xu, S.;Fu, F.;Yu, J.;Sun, W.;Xu, S.;Li, J.;Wang, J.",2017,,10.1111/tbed.12667,1
2454,Genetic typing and epidemiologic observation of bovine viral diarrhea virus in Western China,"Whole blood samples (472) were collected during the period of 2006-2008 from 15 cattle farms in seven districts of the Xinjiang Uygur Autonomous Region, which is a major pastoral area and represents 1/6 of Chinese territory. Bovine viral diarrhea virus (BVDV) was detected by nested reverse transcription polymerase chain reaction assay (RT-nPCR) and sequenced within the 5′-untranslated region of the genome. Approximately 43% (202 samples) were BVDV-positive. Of the positive samples, 24 were chosen for further sequencing, sequence comparisons, and phylogenetic reconstructions. The phylogenetic reconstructions demonstrated that these isolates clustered into either BVDV1b (18 samples) or BVDV1c (six samples) subgenotypes. None of the isolates sequenced showed any cytopathic effect in culture. Unlike previously published studies in Chinese cattle, no BVDV2 genotypes were detected. These results indicate that the predominant subgenotypes in Xinjiang are BVDV1b and BVDV1c. This finding can be useful for further BVDV epidemiological study in China. © 2010 Springer Science+Business Media, LLC.",5' untranslated region;article;Bovine viral diarrhea virus 1;bovine viral diarrhea;bovine;China;gene amplification;gene sequence;genetic variability;genotype;nonhuman;nucleotide sequence;phylogeny;prevalence;priority journal;RNA sequence;vertical transmission;virus genome;virus transmission,"Zhong, F.;Li, N.;Huang, X.;Guo, Y.;Chen, H.;Wang, X.;Shi, C.;Zhang, X.",2011,,10.1007/s11262-010-0558-4,0
2455,Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and swine origin human influenza A viruses,"Pandemic influenza A viruses that emerge from animal reservoirs are inevitable. Therefore, rapid genomic analysis and creation of vaccines are vital. We developed a multisegment reverse transcription-PCR (M-RTPCR) approach that simultaneously amplifies eight genomic RNA segments, irrespective of virus subtype. M-RTPCR amplicons can be used for high-throughput sequencing and/or cloned into modified reverse-genetics plasmids via regions of sequence identity. We used these procedures to rescue a contemporary H3N2 virus and a swine origin H1N1 virus directly from human swab specimens. Together, M-RTPCR and the modified reverse-genetics plasmids that we designed streamline the creation of vaccine seed stocks (9 to 12 days). Copyright © 2009, American Society for Microbiology. All Rights Reserved.",genomic RNA;influenza vaccine;amplicon;article;clone;controlled study;gene amplification;high throughput screening;human;Influenza A virus (H3N2);nonhuman;nucleotide sequence;plasmid;priority journal;reverse transcription polymerase chain reaction;RNA sequence;swine influenza virus;vaccine production,"Zhou, B.;Donnelly, M. E.;Scholes, D. T.;St. George, K.;Hatta, M.;Kawaoka, Y.;Wentworth, D. E.",2009,,10.1128/jvi.01109-09,0
2456,Reticuloendotheliosis virus and avian leukosis virus subgroup J synergistically increase the accumulation of exosomal miRNAs,"BACKGROUND: Co-infection with avian leukosis virus subgroup J and reticuloendotheliosis virus induces synergistic pathogenic effects and increases mortality. However, the role of exosomal miRNAs in the molecular mechanism of the synergistic infection of the two viruses remains unknown. RESULTS: In this study, exosomal RNAs from CEF cells infected with ALV-J, REV or both at the optimal synergistic infection time were analysed by Illumina RNA deep sequencing. A total of 54 (23 upregulated and 31 downregulated) and 16 (7 upregulated and 9 downregulated) miRNAs were identified by comparing co-infection with two viruses, single-infected ALV-J and REV, respectively. Moreover, five key miRNAs, including miR-184-3p, miR-146a-3p, miR-146a-5p, miR-3538 and miR-155, were validated in both exosomes and CEF cells by qRT-PCR. GO annotation and KEGG pathway analysis of the miRNA target genes showed that the five differentially expressed miRNAs participated in virus-vector interaction, oxidative phosphorylation, energy metabolism and cell growth. CONCLUSIONS: We demonstrated that REV and ALV-J synergistically increased the accumulation of exosomal miRNAs, which sheds light on the synergistic molecular mechanism of ALV-J and REV.",Animals;Avian Leukosis/ge [Genetics];Avian Leukosis/me [Metabolism];Avian Leukosis/vi [Virology];*Avian Leukosis Virus/ph [Physiology];Cell Line;*Coinfection;*Exosomes/ge [Genetics];Exosomes/me [Metabolism];Exosomes/ul [Ultrastructure];Gene Expression Regulation;High-Throughput Nucleotide Sequencing;Host-Pathogen Interactions;*MicroRNAs/ge [Genetics];*Microbial Interactions;RNA Interference;Reproducibility of Results;*Reticuloendotheliosis virus/ph [Physiology];*Retroviridae Infections/ge [Genetics];Retroviridae Infections/me [Metabolism];*Retroviridae Infections/vi [Virology];Virus Replication;0 (MicroRNAs),"Zhou, D.;Xue, J.;He, S.;Du, X.;Zhou, J.;Li, C.;Huang, L.;Nair, V.;Yao, Y.;Cheng, Z.",2018,07 03,,0
2457,Identification and genome characterization of the first sicinivirus isolate from chickens in mainland China by using viral metagenomics,"Unlike traditional virus isolation and sequencing approaches, sequence-independent amplification based viral metagenomics technique allows one to discover unexpected or novel viruses efficiently while bypassing culturing step. Here we report the discovery of the first Sicinivirus isolate (designated as strain JSY) of picornaviruses from commercial layer chickens in mainland China by using a viral metagenomics technique. This Sicinivirus isolate, which contains a whole genome of 9,797 nucleotides (nt) excluding the poly(A) tail, possesses one of the largest picornavirus genome so far reported, but only shares 88.83% and 82.78% of amino acid sequence identity to that of ChPV1 100C (KF979332) and Sicinivirus 1 strain UCC001 (NC-023861), respectively. The complete 939 nt 50UTR of the isolate strain contains at least twelve stem-loop domains (A-L), representing the highest set of loops reported within Sicinivirus genus. The conserved 'barbell-like' structure was also present in the 272 nt 30UTR of the isolate as that in the 30 UTR of Sicinivirus 1 strain UCC001. The 8,586 nt large open reading frame encodes a 2,862 amino acids polyprotein precursor. Moreover, Sicinivirus infection might be widely present in commercial chicken farms in Yancheng region of the Jiangsu Province as evidenced by all the tested stool samples from three different farms being positive (17/17) for Sicinivirus detection. This is the first report on identification of Sicinivirus in commercial layer chickens with a severe clinical disease in mainland China, however, further studies are needed to evaluate the pathogenic potential of this picornavirus in chickens.",protein precursor;3' untranslated region;5' untranslated region;amino acid sequence;article;chicken;China;controlled study;feces analysis;genetic code;metagenomics;nonhuman;nucleotide sequence;open reading frame;phylogeny;Picornaviridae;picornavirus infection;poultry;protein domain;Sicinivirus;Sicinivirus infection;virus gene;virus identification;virus isolation;virus strain,"Zhou, H.;Zhu, S.;Quan, R.;Wang, J.;Wei, L.;Yang, B.;Xu, F.;Wang, J.;Chen, F.;Liu, J.",2015,,10.1371/journal.pone.0139668,0
2458,Characteristics of codon usage bias in two regions downstream of the initiation codons of foot-and-mouth disease virus,"The mechanism of utilization of alternative two AUGs in foot-and-mouth disease virus (FMDV) is still unknown to date. In this study, the characteristics of codon usage bias (CUB) of the region between the two AUGs (the region-La) and of the same-sized region behind the second AUG (the region-Lb) in 94 different FMDV RNA sequences were analyzed using relative synonymous codon usage (RSCU) values. The results indicated that many codons with negative CUB were preferentially used in the region-La. There were two conserved residues (Thr and Cys) on the 4th and 6th residue positions of the region-La. The conserved residues had a general tendency to choose synonymous codons with negative CUB. Although most positions in the region-La did not contain conserved residues, many positions tended to use codons with negative CUB in this region. Among these codons, the majority belonged to the amino acids containing synonymous codons with clearly positive and negative CUB, including Asp, Val, Ile, Leu, Thr, Ala, Ser, Asn and Arg. The presence of many codons with negative CUB in the region-La might impair the efficiency of the first AUG selection. The phylogenetic incongruence of the region-La and the region-Lb implied that intertypic recombination played an important role in the evolution of FMDV. Furthermore, due to the existence of more positions with positive CUB and more widespread phylogenetic incongruence in the region-Lb than the region-La, a probable relationship between the degree of CUB and the evolution of the two target regions was revealed. © 2010 Elsevier Ireland Ltd.",cysteine;threonine;article;codon usage;codon usage bias;Foot and mouth disease virus;gene expression regulation;gene mutation;nonhuman;open reading frame;phylogenetic tree;RNA sequence;transcription initiation,"Zhou, J. H.;Zhang, J.;Ding, Y. Z.;Chen, H. T.;Ma, L. N.;Liu, Y. S.",2010,,10.1016/j.biosystems.2010.04.001,0
2459,Global pairwise RNA interaction landscapes reveal core features of protein recognition,"RNA-protein interactions permeate biology. Transcription, translation, and splicing all hinge on the recognition of structured RNA elements by RNA-binding proteins. Models of RNA-protein interactions are generally limited to short linear motifs and structures because of the vast sequence sampling required to access longer elements. Here, we develop an integrated approach that calculates global pairwise interaction scores from in vitro selection and high-throughput sequencing. We examine four RNA-binding proteins of phage, viral, and human origin. Our approach reveals regulatory motifs, discriminates between regulated and non-regulated RNAs within their native genomic context, and correctly predicts the consequence of mutational events on binding activity. We design binding elements that improve binding activity in cells and infer mutational pathways that reveal permissive versus disruptive evolutionary trajectories between regulated motifs. These coupling landscapes are broadly applicable for the discovery and characterization of protein-RNA recognition at single nucleotide resolution.",DIRECT-COUPLING ANALYSIS;BOVINE IMMUNODEFICIENCY VIRUS;IN-VITRO;SELECTION;BINDING-SPECIFICITY;SECONDARY STRUCTURE;GENOME-WIDE;STRUCTURE PREDICTION;COMPLEX;TAT;ANTITERMINATION,"Zhou, Q.;Kunder, N.;De la Paz, J. A.;Lasley, A. E.;Bhat, V. D.;Morcos, F.;Campbell, Z. T.",2018,Jun,,0
2460,Rovac is the possible ancestor of the Russian lapinized vaccines LK-VNIVViM and CS strains but not the Chinese strain (C-strain) vaccine against classical swine fever,"Classical swine fever (CSF), or hog cholera, is a highly contagious disease that emerged in the first half of the nineteenth century. To fight against the disease and protect pigs, different vaccines were developed, including early generation of lapinized Rovac strain and the later development of the ""Chinese"" strain (C-strain). However, details of the development of these vaccines are lost in history. In order to investigate the phylogenetic relationship between the Rovac and other lapinized vaccines, this study determined the genome sequence of the Rovac, which comprised 12,304 nucleotides, notably with the 3'untranslated region (3'UTR) containing a 13-nucleotide insertion. The near-complete genome of Russian vaccine strain LK-VNIVViM was determined by next-generation sequencing on Illumina MiSeq platform. Whole genome phylogenetic analysis revealed a closer relationship of the Rovac strain with the Russian LK-VNIVViM, CS strain and its derivative RUCSFPLUM (genotype 1.2), rather than with the C-strain (genotype 1.1). In addition, it demonstrated an ancestry role of the LK-VNIVViM in relation to the CS strain and RUCSFPLUM. The study suggested that the Rovac vaccine is the possible ancestor of the Russian vaccine strains but not the C-strain vaccine.","Animals;Classical Swine Fever/im [Immunology];*Classical Swine Fever/pc [Prevention & Control];Classical Swine Fever Virus/ge [Genetics];*Classical Swine Fever Virus/im [Immunology];Genome, Viral;High-Throughput Nucleotide Sequencing;Molecular Sequence Data;Phylogeny;RNA, Viral/ge [Genetics];Sequence Analysis, DNA;Sequence Homology;Swine;*Viral Vaccines/im [Immunology];0 (RNA, Viral);0 (Viral Vaccines)","Zhou, W.;Gao, S.;Podgorska, K.;Stadejek, T.;Qiu, H. J.;Yin, H.;Drew, T.;Liu, L.",2014,Nov 20,,0
2461,Molecular investigations on the prevalence and viral load of enteric viruses in pigs from five European countries,"Enteric viral infections in pigs may cause diarrhea resulting in ill-thrift and substantial economic losses. This study reports the enteric infections with porcine astrovirus type 4 (PAstV4), porcine group A rotavirus (GARV), porcine group C rotavirus (GCRV), porcine circovirus type 2 (PCV2) and porcine kobuvirus (PKoV) in 419 pigs, comprising both healthy and diarrheic animals, from 49 farms in five European countries (Austria, Germany, Hungary, Spain and Sweden). Real-time RT-PCR assays were developed to test fecal samples and to compare the prevalence and viral load in relation to health status, farms of origin and age groups. The results showed that PAstV4 (70.4%) was the dominant virus species, followed by PKoV (56.7%), PCV2 (42.2%), GCRV (3%) and GARV (0.9%). Diarrheic pigs had a higher viral load of PAstV4 in the nursery and growing-finishing groups. Rotaviruses were mainly detected in diarrheic pigs, whereas PCV2 was more often detected in clinically healthy than in diarrheic pigs, suggesting that most PCV2 infections were subclinical. PAstV4, PCV2 and PKoV were considered ubiquitous in the European pig livestock and co-infections among them were frequent, independently of the disease status, in contrast to a low prevalence of classical rotavirus infections.",article;Astroviridae;Austria;enteric virus;European;feces;Germany;groups by age;health status;Hungary;Kobuvirus;livestock;nonhuman;pig;Porcine circovirus 2;real time polymerase chain reaction;reverse transcription polymerase chain reaction;Rotavirus;Spain;Sweden;virus infection;virus load,"Zhou, W.;Ullman, K.;Chowdry, V.;Reining, M.;Benyeda, Z.;Baule, C.;Juremalm, M.;Wallgren, P.;Schwarz, L.;Zhou, E.;Pedrero, S. P.;Hennig-Pauka, I.;Segales, J.;Liu, L.",2016,,10.1016/j.vetmic.2015.10.019,0
2462,MicroRNA expression profiling in alveolar macrophages of indigenous Chinese Tongcheng pigs infected with PRRSV in vivo,"Porcine respiratory and reproductive syndrome (PRRS), caused by PRRS virus (PRRSV), is one of the most serious infectious diseases in the swine industry worldwide. Indigenous Chinese Tongcheng (TC) pigs reportedly show strong resistance to PRRSV infection. The miRNA expression profiles of porcine alveolar macrophages (PAMs) of control TC pigs and those infected with PRRSV in vivo were analyzed by high-throughput sequencing to explore changes induced by infection. A total of 182 known miRNAs including 101 miRNA-5p and 81 miRNA-3p were identified with 23 up-regulated differentially expressed miRNAs (DEmiRNAs) and 25 down-regulated DEmiRNAs. Gene Ontology analysis showed that predicted target genes for the DEmiRNAs were enriched in immune response, transcription regulation, and cell death. The integrative analysis of mRNA and miRNA expression revealed that down-regulated methylation-related genes (DNMT1 and DNMT3b) were targeted by five up-regulated DEmiRNAs. Furthermore, 35 pairs of miRNAs (70 miRNAs) were co-expressed after PRRSV infection and six pairs were co-expressed differently. Our results describe miRNA expression profiles of TC pigs in response to PRRSV infection and lay a strong foundation for developing novel therapies to control PRRS in pigs.",DNA (cytosine 5) methyltransferase 1;DNA methyltransferase 3B;microRNA;animal cell;article;cell death;cell differentiation;controlled study;down regulation;gene expression;gene ontology;high throughput sequencing;histone methylation;immune response;lung alveolus macrophage;native species;nonhuman;Porcine reproductive and respiratory syndrome virus;protein expression;reverse transcription polymerase chain reaction;RNA analysis;swine disease;transcription regulation;upregulation,"Zhou, X.;Michal, J. J.;Jiang, Z.;Liu, B.",2017,,10.1007/s13353-017-0410-9,0
2463,"Complete Genome Sequence of a Genotype III Japanese Encephalitis Virus, Isolated from Pigs in Sichuan, China","A complete genomic sequence of Japanese encephalitis virus (JEV) was detected by viral metagenome analysis on aborted piglets. A phylogenetic analysis of this genome reveals that it is highly similar to previously reported India JEV genomes. The complete JEV sequence is 10,718 nucleotides long.",,"Zhou, Y.;Zhuo, X.;Ye, J.;Cai, Y.",2016,Dec 08,,0
2464,Molecular characterization of a novel bat-associated circovirus with a poly-T tract in the 3′ intergenic region,"The family Circoviridae comprises a large group of small circular single-stranded DNA viruses with several members causing severe pig and poultry diseases. In recent years the number of new viruses within the family has had an explosive increase showing a high level of genetic diversity and a broad host range. In this report we describe two more circoviruses identified from bats in Yunnan and Heilongjiang provinces in China. Full genome sequencing has revealed that these bat associated circoviruses (bat ACV) should be classified as new species within the genus Circovirus based on the demarcation criteria of the International Committee on the Taxonomy of Viruses (ICTV). The most striking result is the novel finding of a 21–28 nt polythymidine (poly-T) tract in the 3′ terminal intergenic region of bat ACV isolates from Heilongjiang province. To understand its role in viral replication, a wild type bat ACV and a mutated version with the entire poly-T deleted were rescued through construction of infectious clones. Replication comparison in vitro showed that the poly-T is not essential for viral replication. Identification of additional bat ACV isolates and study of their biological characteristics will be the main task in future to understand the potential roles of bats in transmission of circoviruses to terrestrial mammals and humans.",polythymidine;spacer DNA;unclassified drug;adult;article;bat;Circovirus;nonhuman;phylogeny;priority journal;virus genome;virus identification;virus isolation;virus replication;whole genome sequencing;wild type,"Zhu, A.;Jiang, T.;Hu, T.;Mi, S.;Zhao, Z.;Zhang, F.;Feng, J.;Fan, Q.;He, B.;Tu, C.",2018,,10.1016/j.virusres.2018.04.012,0
2465,Comparative genomic analysis identifies structural features of CRISPR-Cas systems in Riemerella anatipestifer,"Background: Riemerella anatipestifer infection is a contagious disease that has resulted in major economic losses in the duck industry worldwide. This study attempted to characterize CRISPR-Cas systems in the disease-causing agent, Riemerella anatipestifer (R. anatipestifer). The CRISPR-Cas system provides adaptive immunity against foreign genetic elements in prokaryotes and CRISPR-cas loci extensively exist in the genomes of archaea and bacteria. However, the structure characteristics of R. anatipestifer CRISPR-Cas systems remains to be elucidated due to the limited availability of genomic data. Results: To identify the structure and components associated with CRISPR-Cas systems in R. anatipestifer, we performed comparative genomic analysis of CRISPR-Cas systems in 25 R. anatipestifer strains using high-throughput sequencing. The results showed that most of the R. anatipestifer strains (20/25) that were analyzed have two CRISPR loci (CRISPR1 and CRISPR2). CRISPR1 was shown to be flanked on one side by cas genes, while CRISPR2 was designated as an orphan. The other analyzed strains harbored only one locus, either CRISPR1 or CRISPR2. The length and content of consensus direct repeat sequences, as well as the length of spacer sequences associated with the two loci, differed from each other. Only three cas genes (cas1, cas2 and cas9) were located upstream of CRISPR1. CRISPR1 was also shown to be flanked by a 107 bp-long putative leader sequence and a 16 nt-long anti-repeat sequence. Combined with analysis of spacer organization similarity and phylogenetic tree of the R. anatipestifer strains, CRISPR arrays can be divided into different subgroups. The diversity of spacer organization was observed in the same subgroup. In general, spacer organization in CRISPR1 was more divergent than that in CRISPR2. Additionally, only 8 % of spacers (13/153) were homologous with phage or plasmid sequences. The cas operon flanking CRISPR1 was observed to be relatively conserved based on multiple sequence alignments of Cas amino acid sequences. The phylogenetic analysis associated with Cas9 showed Cas9 sequence from R. anatipestifer was closely related to that of Bacteroides fragilis and formed part of the subtype II-C subcluster. Conclusions: Our data revealed for the first time the structural features of R. anatipestifer CRISPR-Cas systems. The illumination of structural features of CRISPR-Cas system may assist in studying the specific mechanism associated with CRISPR-mediated adaptive immunity and other biological functions in R. anatipestifer.",adaptive immunity;amino acid sequence;article;bacterial genetics;bacteriophage;cas1 gene;cas2 gene;cas9 gene;comparative study;CRISPR Cas system;DNA flanking region;gene;gene location;gene locus;gene structure;genetic analysis;high throughput sequencing;nonhuman;operon;phylogeny;prokaryote;Riemerella anatipestifer;sequence alignment,"Zhu, D. K.;Yang, X. Q.;He, Y.;Zhou, W. S.;Song, X. H.;Wang, J. B.;Zhang, Y.;Liu, M. F.;Wang, M. S.;Jia, R. Y.;Chen, S.;Sun, K. F.;Yang, Q.;Wu, Y.;Chen, X. Y.;Cheng, A. C.",2016,,10.1186/s12864-016-3040-4,0
2466,"Prevalence of hepatitis E virus in animals in Changchun area, China","Objective: To analyze the prevalence of hepatitis E virus(HEV) in animals in Changchun Area, China, as well as the phylogenetics of the virus. Methods: The sera of pig, cattle, sheep, deer, chicken and horse were tested for antibody against HEV by anti-HEV antibody kit, a part of which for HEV RNA by RT-PCR, and the positive ones were subject to gene cloning and sequencing. Results: Of 493 pig, 266 cattle, 93 sheep, 798 deer, 369 chicken and 197 horse sera, 427(86.61%), 122(45.86%), 7 (7.53%), 348(43.61%), 18(4.88%) and 31(15.74%) were positive for anti-HEV antibody respectively, and 5 of the 493 pig sera were positive for HEV RNA. The homology of the 5 HEV RNA positive clones was 91.2%-99.1%, and those of 348 hp at ORF2 domain to HEV genotype 1,2,3 and 4 were 77.8%-82.3%,77.2%-78.1%,77.2%-99.1% and 85.2%-95.2% respectively. Conclusion: The prevalence of HEV was observed in various animals in Changchun Area. The prevalent in pigs was much higher than those in other animals. The HEV gene sequence prevalent in pigs showed high homology to that of HEV -4 isolated from sporadic HE case in humans. The analysis of phylogenetics proved that the HEV in pigs and humans in Changchun Area belonged to the same branch.",article;bovine;chicken;China;controlled study;deer;gene sequence;genetic analysis;genotype;Hepatitis E virus;horse;immunoassay;molecular cloning;nonhuman;nucleotide sequence;open reading frame;phylogeny;reverse transcription polymerase chain reaction;sequence homology;seroprevalence;sheep;pig;virus isolation;zoonosis,"Zhu, G. Z.;Liu, T. M.;Sun, Z. F.",2007,,,0
2467,Origins and Evolutionary Dynamics of H3N2 Canine Influenza Virus,"UNLABELLED: Influenza A viruses (IAVs) are maintained mainly in wild birds, and despite frequent spillover infections of avian IAVs into mammals, only a small number of viruses have become established in mammalian hosts. A new H3N2 canine influenza virus (CIV) of avian origin emerged in Asia in the mid-2000s and is now circulating in dog populations of China and South Korea, and possibly in Thailand. The emergence of CIV provides new opportunities for zoonotic infections and interspecies transmission. We examined 14,764 complete IAV genomes together with all CIV genomes publicly available since its first isolation until 2013. We show that CIV may have originated as early as 1999 as a result of segment reassortment among Eurasian and North American avian IAV lineages. We also identified amino acid changes that might have played a role in CIV emergence, some of which have not been previously identified in other cross-species jumps. CIV evolves at a lower rate than H3N2 human influenza viruses do, and viral phylogenies exhibit geographical structure compatible with high levels of local transmission. We detected multiple intrasubtypic and heterosubtypic reassortment events, including the acquisition of the NS segment of an H5N1 avian influenza virus that had previously been overlooked. In sum, our results provide insight into the adaptive changes required by avian viruses to establish themselves in mammals and also highlight the potential role of dogs to act as intermediate hosts in which viruses with zoonotic and/or pandemic potential could originate, particularly with an estimated dog population of ~ 700 million. IMPORTANCE: Influenza A viruses circulate in humans and animals. This multihost ecology has important implications, as past pandemics were caused by IAVs carrying gene segments of both human and animal origin. Adaptive evolution is central to cross-species jumps, and this is why understanding the evolutionary processes that shape influenza A virus genomes is key to elucidating the mechanisms underpinning viral emergence. An avian-origin canine influenza virus (CIV) has recently emerged in dogs and is spreading in Asia. We reconstructed the evolutionary history of CIV and show that it originated from both Eurasian and North American avian lineages. We also identified the mutations that might have been responsible for the cross-species jump. Finally, we provide evidence of multiple reassortment events between CIV and other influenza viruses (including an H5N1 avian virus). This is a cause for concern, as there is a large global dog population to which humans are highly exposed.","Animals;Birds;Databases, Genetic;*Dog Diseases/vi [Virology];Dogs;Evolution, Molecular;Genome, Viral;Host Specificity;Humans;*Influenza A Virus, H3N2 Subtype/ge [Genetics];Influenza A Virus, H3N2 Subtype/ip [Isolation & Purification];Influenza A Virus, H3N2 Subtype/py [Pathogenicity];Influenza A Virus, H5N1 Subtype/ge [Genetics];Influenza A Virus, H5N1 Subtype/ip [Isolation & Purification];Influenza A Virus, H5N1 Subtype/py [Pathogenicity];*Influenza in Birds/vi [Virology];Influenza, Human/vi [Virology];Mutation;*Orthomyxoviridae Infections/ve [Veterinary];Orthomyxoviridae Infections/vi [Virology];Phylogeny;Reassortant Viruses/ge [Genetics];Reassortant Viruses/ip [Isolation & Purification];Reassortant Viruses/py [Pathogenicity];Selection, Genetic;Time Factors;Viral Proteins/ge [Genetics];0 (Viral Proteins)","Zhu, H.;Hughes, J.;Murcia, P. R.",2015,May,,0
2468,"Phylogenetic and pathotypic characterization of newcastle disease virus in Tibetan chickens, China","Chickens are considered to be potential reservoirs of Newcastle disease virus (NDV). In this study, six Newcastle disease virus strains were isolated and characterized in Tibetan chickens. The HN gene was sequenced, and phylogenetic relationship to reference strains was studied. The phylogenetic analysis demonstrated that these six isolated strains were closely related to NDV isolates of the reference strains GQ245823, KT002186, KU527561, KJ563939, AY225110, EU305607, KM056357, Y18898, GQ245832, AF077761 and lasota strain. Among them, EU305607, KJ563939 and KM056357 were isolated from India, while lasota strain came from attenuated vaccine widely used in China. Then, mean death time (MDT) and intracerebral pathogenicity index (ICPI) were used to estimate the pathogenicity of the isolates. Pathogenicity experiment showed HNH1 and HN17 to be virulent. Our results indicated that genetically diverse viruses circulate in Tibetan chickens, and based upon the phlogeographic analysis, we estimated the origin of ancestral viruses of the isolates and its sister strains located in India and China (lasota strain). It indicates the importance of continuous surveillance to enhance current understanding of the genetic evolution of the NDV strains.",HN protein;amino acid sequence;article;chicken;controlled study;gene sequence;genetic distance;genetic variability;Newcastle disease virus;nonhuman;phylogenetic tree;polymerase chain reaction;sequence alignment;sequence homology;time of death;virus characterization;virus identification;virus isolation;virus virulence,"Zhu, H.;Zhang, H.;Wang, Y.;Ciren, D.;Dong, H.;Wu, Q.;Rehman, M. U.;Nabi, F.;Mehmood, K.;Li, J.",2018,,10.1590/1678-5150-pvb-5039,0
2469,"Molecular characterization of H3N2 and H4N6 subtypes avian influenza viruses isolated from mallards in Poyang Lake, China in 2010","Poyang Lake is the largest inland freshwater lake in China and contains many species of wild birds and waterfowls. We conducted a survey of avian influenza viruses in nine semi-artificial waterfowl farms in Poyang Lake during January to March of 2010. Out of 1036 cloacal swabs collected, three H3N2 and one H4N6 influenza viruses were isolated from healthy mallards. All the isolates were genetically and phylogenetically characterized. The analysis of putative HA cleavage sites showed that all the four isolates possessed the molecular characteristics (QTRGL for H3N2 viruses, PEKASR for H4N6 virus) of lowly pathogenic avian influenza (LPAI) virus. The phylogenetic analysis of the viral genomes showed that all four virus isolates clustered in the Eurasian clade of influenza viruses. The M gene of the viruses possessed the highest homology with highly pathogenic H5N1 influenza viruses. In addition, co-infection of H3N2 and H4N6 in the same farm was observed. And interestingly, we isolated two subtypes viruses (H3N2 and H4N6) and their progeny virus (H3N2) with evidence of genome reassortment from the same farm, in which the PB1 and PB2 gene segments of H4N6 replaced those of the H3N2 strain. The results of animal infection experiments showed that all the four isolated viruses were lowly pathogenic to chickens and not pathogenic to mice, which was consistent with the results of genetic analysis.",influenza A virus;Poyang Lake;epidemic survey;evolution;WILD BIRDS;MIGRATORY BIRDS;A VIRUSES;H5N1;POULTRY;ESTABLISHMENT;HUMANS;ASIA,"Zhu, N.;Zhao, J. R.;Li, Y. D.;Ding, C. Q.;Xia, H.;Tang, S.;Zhang, Z.;Yu, J. F.;Chen, J.;Fan, Z. J.;Kou, Z.;Li, T. X.",2012,Sep,,0
2470,Phylogenetic and pathogenic analysis of Newcastle disease virus isolated from house sparrow (Passer domesticus) living around poultry farm in southern China,"House sparrow (Passer domesticus) is one of the most widely distributed wild birds in China. Five Newcastle disease virus (NDV) strains were isolated from house sparrows living around the poultry farms in southern China. These isolates were characterized by pathogenic assays and phylogenetic analysis. The results showed that all NDV isolates except one were velogenic and virulent for chickens. These four virulent strains for chickens possess the amino acid sequence 112R/K-R-Q-K/R-R-F117 in the F0 cleavage site which is typical of velogenic NDV. Phylogenetic analysis indicated that these isolates belong to genotype VII and were closely related to the strains which were isolated from NDV outbreaks in chickens since 2000. One isolate of NDV from house sparrow belong to genotype II and was proved to be vaccine strain (Chicken/ U.S./LaSota/46). The result of this study proved that house sparrow can carry the virulent NDV strains and the same genotype of viruses that are circulating in poultry are existing in house sparrows living around poultry farm in southern China. © Springer Science+Business Media, LLC 2009.",arginine;glutamine;lysine;phenylalanine;amino acid sequence;article;China;embryo;genotype;Newcastle disease virus;nonhuman;nucleotide sequence;phylogeny;poultry;priority journal;protein cleavage;sparrow;virus carrier;virus characterization;virus isolation;virus strain;virus virulence,"Zhu, W.;Dong, J.;Xie, Z.;Liu, Q.;Khan, M. I.",2010,,10.1007/s11262-009-0436-0,0
2471,Human monoclonal antibodies as candidate therapeutics against emerging viruses and HIV-1,"More than 40 monoclonal antibodies (mAbs) have been approved for a number of disease indications with only one of these (Synagis) - for a viral disease, and not for therapy but for prevention. However, in the last decade novel potent mAbs have been discovered and characterized with potential as therapeutics against viruses of major importance for public health and biosecurity including Hendra virus (HeV), Nipah virus (NiV), severe acute respiratory syndrome coronavirus (SARS-CoV), Ebola virus (EBOV), West Nile virus (WNV), influenza virus (IFV) and human immunodeficiency virus type 1 (HIV-1). Here, we review such mAbs with an emphasis on antibodies of human origin, and highlight recent results as well as technologies and mechanisms related to their potential as therapeutics. © Wuhan Institute of Virology, CAS and Springer-Verlag Berlin Heidelberg 2013.",bispecific antibody;fusion protein;monoclonal antibody;neutralizing antibody;absence of side effects;clinical effectiveness;disease association;drug design;drug determination;drug efficacy;drug half life;drug isolation;drug potency;drug safety;drug structure;drug targeting;drug tolerability;Ebola hemorrhagic fever;Ebolavirus;food and drug administration;Hendra virus;Hendra virus infection;high throughput sequencing;human;Human immunodeficiency virus 1;Human immunodeficiency virus 1 infection;immune response;influenza;Influenza virus;molecular dynamics;Nipah virus;Nipah virus infection;nonhuman;outcome assessment;review;SARS coronavirus;sequence analysis;severe acute respiratory syndrome;virus identification;virus infection;virus neutralization;West Nile fever;West Nile virus,"Zhu, Z.;Prabakaran, P.;Chen, W.;Broder, C. C.;Gong, R.;Dimitrov, D. S.",2013,,10.1007/s12250-013-3313-x,0
2472,First detection of foot-and-mouth disease virus O/ME-SA/Ind2001 in China,"Foot-and-mouth disease (FMD) is endemic in China and is predominantly due to foot-and-mouth disease virus (FMDV) serotype O Mya-98 lineage. In recent years, FMDV O/ME-SA/Ind2001 lineage has spread from the Indian subcontinent to South-East Asia, Middle East and Africa, which may pose potential threats for future trans-regional livestock movements. In this study, we identified the appearance of FMDV O/ME-SA/Ind2001 in China; the first time that this virus lineage has been found there. Sequencing and phylogenetic analysis of VP1 sequences revealed that this newly determined strain belongs to O/ME-SA/Ind2001 sublineage d and is closely related to strains that have caused recent outbreaks of FMD in Nepal, Myanmar, Russia and South Korea. The results suggest extensive movements of the current O/ME-SA/Ind2001 sublineage d viruses and provide essential information for an effective national FMDV control programme in China.",foot and mouth disease vaccine;protein VP1;article;bioinformatics;disease transmission;foot and mouth disease;Foot and mouth disease virus;gene amplification;gene sequence;livestock;maximum likelihood method;nonhuman;phylogeny;real time polymerase chain reaction;reverse transcription polymerase chain reaction;sequence alignment;virus detection;virus isolation,"Zhu, Z.;Yang, F.;He, J.;Li, J.;Cao, W.;Li, J.;Xia, Y.;Guo, J.;Jin, Y.;Zhang, K.;Zheng, H.;Liu, X.",2018,,10.1111/tbed.12895,0
2473,Selected microRNA-192 mutant indicates association with several function genes in bovine cells,"MicroRNAs are implicated in many cellular processes such as cell differentiation and development, tumorigenesis, and immune regulation. In this study, miR192 was detected using quantitative real-time polymerase chain reaction (qRT-PCR) when MDBK cells were exposed to Escherichia coli. Cells with malfunction of bta-miR-192 were established using transcription activator-like effector nuclease (TALEN) technology. Finally, bta-miR-192 mutant cells were screened for differentially expressed genes using RNA-sequencing (RNA-seq). The results showed that miR192 significantly decreased in cells exposed to E. coli F18ac and E. coli K88ac. The RNA-seq results showed that 1673 differentially expressed transcripts were identified; 890 genes were upregulated and 775 genes were downregulated. With the gene ontology enrichment analysis, 431 differentially expressed genes (DEGs) were classified into 937 gene ontology terms. The pathway enrichment analysis showed that 535 genes were involved in 254 pathway terms. Interestingly, most of these DEGs were associated with the pathways in cancers or infectious diseases. When the selected DEGs (n = 162) in these pathways were intersected with 120 differential transcripts, 11 DEGs were identified. Subsequently, several genes associated with regulation, cancers, or viral infections, such as LEF1, AXIN2, MX1, and FCGR2B, were identified among the DEGs using functional analysis. Furthermore, associations between bta-miR-192 and DEGs were detected by intersecting the bta-miR-192’s target genes with the DEGs, indicating that three genes including CBL, DICER1 and TRERF1 were involved in this relationship. These findings provided useful guidance for investigating the role played by bta-miR-192 in cellular functionality in bovine cells.","2',5' oligoadenylate synthetase;Adenosine deaminase acting on RNA;axin;axin 2;glyceraldehyde 3 phosphate dehydrogenase;guanosine triphosphatase;interferon regulatory factor 9;Janus kinase;lymphoid enhancer factor 1;microRNA 192;MX dynamin like GTPase 1;STAT1 protein;STAT2 protein;transcription activator like effector nuclease;transcriptome;unclassified drug;animal cell;article;bacterium culture;biological phenomena and functions concerning the entire organism;bovine;controlled study;DNA sequence;down regulation;Escherichia coli;gene expression;gene function;gene ontology;genetic association;genetic transcription;high throughput sequencing;infection;lysogenization;malignant neoplasm;MDBK cell line;nonhuman;quality control;real time polymerase chain reaction;RNA sequence;transcriptomics;upregulation;validation study;virus infection","Zi, C.;Zeng, D.;Zhou, J.;Dai, J.;Jiang, L.;Xue, F.;Jiang, Y.;Li, B.",2018,,10.1007/s13258-017-0635-3,0
2474,Evidence for an independent third Usutu virus introduction into Germany,"Usutu virus (USUV) is an arbovirus within the genus flavivirus, which was first introduced to Southern Europe approximately twenty years ago causing epizootics among wild and captive birds. In Germany USUV was initially discovered in wild birds, mainly Common blackbirds (Turdus merula), in the Upper Rhine valley in southwest of the country in 2011 and has not spread much northwards since. Phylogenetic analyses revealed that the still ongoing USUV epidemic is caused by two different USUV strains, USUV-Germany belonging to the USUV Europe 3 lineage and USUV-Bonn belonging to the USUV Africa 3 lineage. The two strains were introduced independently. In August 2015 a new USUV strain, named USUV-Berlin, was isolated in Vero cells from two carcasses of juvenile Great grey owls (Strix nebulosa) kept in the Zoological Garden Berlin, which had suffered from a hyperacute fatal systemic infection. Both owls carried high USUV genome loads. Full-length USUV genomes sequences were determined and phylogenetic analysis demonstrated a close relationship with a Spanish mosquito-derived sequence from 2006. Immunohistochemical antigen detection in organ samples of the owls showed the typical USUV infection patterns. According to the phylogenetic analysis, USUV-Berlin belongs to the Africa 2 lineage, and can thus be distinguished from the other strains circulating in Germany. Repeated findings of different USUV strains suggest more frequent introductions into Central Europe and a higher mobility of this virus than assumed to date.","Animals;Animals, Zoo;Bird Diseases/ep [Epidemiology];*Bird Diseases/vi [Virology];Disease Outbreaks/ve [Veterinary];*Flavivirus/cl [Classification];Flavivirus/ge [Genetics];Flavivirus Infections/ep [Epidemiology];*Flavivirus Infections/ve [Veterinary];Flavivirus Infections/vi [Virology];Germany/ep [Epidemiology];Phylogeny;*Strigiformes","Ziegler, U.;Fast, C.;Eiden, M.;Bock, S.;Schulze, C.;Hoeper, D.;Ochs, A.;Schlieben, P.;Keller, M.;Zielke, D. E.;Luehken, R.;Cadar, D.;Walther, D.;Schmidt-Chanasit, J.;Groschup, M. H.",2016,Aug 30,,0
2475,Phylogenetic Analysis of the Rabies Virus N-coding Region in Lithuanian Rabies Isolates,"Rabies infection among wild and domestic animals constitutes a well-known problem in Lithuania, but only one dog rabies virus isolate sequence (1992) from Lithuania was used in the European rabies virus phylogenetic analysis. The objective of this work was to determine nucleoprotein (N) gene sequences and genetically characterize the rabies virus isolates in order to learn which virus group (biotype) is circulating in reservoir species in Lithuania. Classical rabies virus isolate nucleoprotein (N) gene sequences from different parts of Lithuania were found to be closely related to each other and demonstrated nucleotide identity from 97.7 to 100% and could be placed in one lineage with 100% bootstrap support. All 12 sequences of raccoon dogs, red foxes, dogs and marten rabies viruses exhibited 97.7 - 99.0% identity to previously published sequences from Eastern parts of Poland, Estonia, Finland, and the North-Eastern part of Russia. Phylogenetic analysis revealed that all Lithuanian strains belong to the North East Europe (NEE) group of rabies virus.",Rabies;nucleoprotein gene;sequencing;group determination;MOLECULAR EPIDEMIOLOGY;LYSSAVIRUSES;DIAGNOSIS;DIVERSITY;EVOLUTION;STRAINS;EUROPE;GENUS,"Zienius, D.;Sajute, K.;Zilinskas, H.;Stankevicius, A.",2009,Jun,,0
2476,"Genetic analysis revealed LX4 genotype strains of avian infectious bronchitis virus became predominant in recent years in Sichuan area, China","Between 2008 and 2010, 19 strains of infectious bronchitis virus (IBV) were isolated from the vaccinated chicken flocks in Sichuan province, China. The S1 genes of the isolates were amplified and sequenced. Phylogenetic analysis revealed that the 19 isolates and 37 reference IBV strains can be grouped into eight genotypes. Although IBVs of Taiwan-I type, massachusetts type, and proventriculitis type were isolated, but most isolates were LX4 genotype. Homology analysis of the sequences of S1 genes of the 19 isolates and 37 reference IBV strains revealed that the identity of the nucleotides and amino acid sequences of the S1 genes between the 15 LX4-type isolates and other IBV strains were 71.9-99.3% and 72.1-99.1%, respectively, while those of the analyzed IBV of LX4 type were 96.0-99.9% and 94.3-99.8%, respectively. The results from this study and other published results in the GenBank database showed that isolates circulating in Sichuan province in recent years were mainly LX4 genotype, which is the predominant genotype circulated in China in recent years. © 2010 Springer Science+Business Media, LLC.",protein s 1;unclassified drug;viral protein;amino acid sequence;animal tissue;article;Avian infectious bronchitis virus;chicken;China;controlled study;embryo;genetic analysis;genotype;molecular phylogeny;nonhuman;nucleotide sequence;priority journal;sequence homology;viral genetics;virus gene;virus isolation;virus strain;virus virulence,"Zou, N. L.;Zhao, F. F.;Wang, Y. P.;Liu, P.;Cao, S. J.;Wen, X. T.;Huang, Y.",2010,,10.1007/s11262-010-0500-9,0
2477,Molecular characterization and receptor binding specificity of H9N2 avian influenza viruses based on poultry-related environmental surveillance in China between 2013 and 2016,"H9N2 avian influenza viruses (AIVs) have become panzootic and caused sporadic human cases since 1998. Based on the poultry-related environmental surveillance data in mainland China from 2013 to 2016, a total of 68 representative environment isolates were selected and further investigated systematically. Phylogenetic analysis indicated that Y280-like H9N2 viruses have been predominant during 2013–2016 and acquired multiple specific amino acid substitutions that might favor viral transmission from avian to mammalians. Additionally, the viruses have undergone dramatic evolution and reassortment, resulting in an increased genetic diversity or acting as the gene contributors to new avian viruses. Receptor-binding tests indicated that most of the H9N2 isolates bound to human-type receptor, making them easily cross the species barrier and infect human efficiently. Our results suggested that the H9N2 AIVs prevalent in poultry may pose severe public health threat.",article;avian influenza virus;China;genetic reassortment;genetic variability;human;Influenza A virus (H9N2);nonhuman;phylogeny;poultry;public health;receptor binding,"Zou, S.;Zhang, Y.;Li, X.;Bo, H.;Wei, H.;Dong, L.;Yang, L.;Dong, J.;Liu, J.;Shu, Y.;Wang, D.",2019,,10.1016/j.virol.2019.01.002,0
2478,Insights into the increasing virulence of the swine-origin pandemic H1N1/2009 influenza virus,"Pandemic H1N1/2009 viruses have been stabilized in swine herds, and some strains display higher pathogenicity than the human-origin isolates. In this study, high-throughput RNA sequencing (RNA-seq) is applied to explore the systemic transcriptome responses of the mouse lungs infected by swine (Jia6/10) and human (LN/09) H1N1/2009 viruses. The transcriptome data show that Jia6/10 activates stronger virus-sensing signals, such as the toll-like receptor, RIG-I like receptor and NOD-like receptor signalings, as well as a stronger NF-κB and JAK-STAT signals, which play significant roles in inducing innate immunity. Most cytokines and interferon-stimulated genes show higher expression lever in Jia/06 infected groups. Meanwhile, virus Jia6/10 activates stronger production of reactive oxygen species, which might further promote higher mutation rate of the virus genome. Collectively, our data reveal that the swine-origin pandemic H1N1/2009 virus elicits a stronger innate immune reaction and pro-oxidation stimulation, which might relate closely to the increasing pathogenicity.",transcriptome;virulence factor;animal;article;human;immunology;influenza;Influenza A virus (H1N1);lung;molecular genetics;mouse;pandemic;pathogenicity;statistics;pig;virology;virulence,"Zou, W.;Chen, D.;Xiong, M.;Zhu, J.;Lin, X.;Wang, L.;Zhang, J.;Chen, L.;Zhang, H.;Chen, H.;Chen, M.;Jin, M.",2013,,,0
2479,Genetic analysis of old Hungarian avian influenza viruses,"Certain genes of 13 avian influenza viruses (AIV) isolated in the 1970s were subjected to phylogenetic analysis. The viruses derived from the eastern part of Hungary from ducks and guinea fowls with relatively severe respiratory signs. In addition to the hemagglutinin (HA) subtypes (H4, H5, H6, H7 and H10) identified at the time by serological methods, neuraminidase (NA) subtypes have been identified with genetic analysis (table). Based on the amino acid pattern at the proteolytic cleavage site of the HA, it was ascertained that all H5 and H7 strains belonged to the low pathogenicity (LP) category. Phylogenetic analysis of the HA, NA and NS genes allowed the following epidemiological conclusions to be drawn. (1) All Hungarian strains belonged to the Eurasian lineage of AIV. (2) H5 strains were the members of an old European group (Figure 1). The H4 strains (Figure 2) originated from three different sources (two from the Far East while one from Europe). (3) The fact that most viruses in H4 and H5 subtypes were reassortants (some even multiple ones; Figure 3) suggested that their reservoirs were unlikely to be wild aquatic birds but rather domestic ducks. Further studies of old viruses would be needed for a more detailed knowledge on the role of these ""artificial"" reservoirs in the maintenance and epidemiology of AIV.",NEWCASTLE-DISEASE VIRUS;A VIRUSES;EVOLUTION;DUCKS,"Zsofia, S.;Sandor, K.;Istvan, K.;Bela, L.",2008,Mar,,0
2480,Molecular epidemiology of rabies: Focus on domestic dogs (Canis familiaris) and black-backed jackals (Canis mesomelas) from northern South Africa,"Phylogenetic relationships of rabies viruses recovered from black-backed jackals (Canis mesomelas) and domestic dogs (Canis familiaris) in northern South Africa were investigated to determine whether the black-backed jackal is an emerging maintenance host species for rabies in this region. A panel of 123 rabies viruses obtained from the two host species between 1980 and 2006 were characterised by nucleotide sequencing of the cytoplasmic domain of the glycoprotein gene and the non-coding G-L intergenic region. Through phylogenetic analysis a viral cluster specific to black-backed jackals and spanning a 5-year period was delineated in western Limpopo. Virus strains associated with domestic dogs prevail in densely populated communal areas in north-eastern Limpopo and in south and eastern Mpumalanga. The data presented in this study indicated the likelihood that black-backed jackals are capable of sustaining rabies cycles independent of domestic dogs. It is proposed that wildlife rabies control strategies, in synergy with domestic animal vaccination should be considered for effective control of rabies in South Africa. © 2008 Elsevier B.V. All rights reserved.",spacer DNA;article;cytoplasm;dog;gene cluster;glycoprotein gene;host;jackal;molecular epidemiology;nonhuman;nucleotide sequence;phylogeny;priority journal;rabies;Rabies virus;South Africa;virus characterization;virus gene;virus strain,"Zulu, G. C.;Sabeta, C. T.;Nel, L. H.",2009,,10.1016/j.virusres.2008.11.004,0
2481,Novel Picornavirus Associated with Avian Keratin Disorder in Alaskan Birds,"UNLABELLED: Avian keratin disorder (AKD), characterized by debilitating overgrowth of the avian beak, was first documented in black-capped chickadees (Poecile atricapillus) in Alaska. Subsequently, similar deformities have appeared in numerous species across continents. Despite the widespread distribution of this emerging pathology, the cause of AKD remains elusive. As a result, it is unknown whether suspected cases of AKD in the afflicted species are causally linked, and the impacts of this pathology at the population and community levels are difficult to evaluate. We applied unbiased, metagenomic next-generation sequencing to search for candidate pathogens in birds affected with AKD. We identified and sequenced the complete coding region of a novel picornavirus, which we are calling poecivirus. Subsequent screening of 19 AKD-affected black-capped chickadees and 9 control individuals for the presence of poecivirus revealed that 19/19 (100%) AKD-affected individuals were positive, while only 2/9 (22%) control individuals were infected with poecivirus. Two northwestern crows (Corvus caurinus) and two red-breasted nuthatches (Sitta canadensis) with AKD-consistent pathology also tested positive for poecivirus. We suggest that poecivirus is a candidate etiological agent of AKD. IMPORTANCE: Avian keratin disorder (AKD) is an increasingly common disease of wild birds. This disease, characterized by beak overgrowth, was first described in the late 1990s and has been spreading rapidly both geographically and in terms of host species affected. AKD decreases host fitness and can be fatal. However, the cause of the disease has remained elusive, and its impact on host populations is poorly understood. We found a novel and divergent picornavirus in 19/19 AKD-affected black-capped chickadees that we examined but in only 2/9 control cases. We also found this virus in 4 individuals of 2 other passerine species that exhibited symptoms consistent with AKD. Our data suggest that this novel picornavirus warrants further investigation as the causative agent of AKD.",Alaska;Animals;*Beak/pa [Pathology];*Bird Diseases/vi [Virology];Birds;Computational Biology;Gene Order;High-Throughput Nucleotide Sequencing;*Keratins/me [Metabolism];Metagenomics;Phylogeny;Picornaviridae/cl [Classification];Picornaviridae/ge [Genetics];*Picornaviridae/ip [Isolation & Purification];Picornaviridae Infections/pa [Pathology];*Picornaviridae Infections/ve [Veterinary];Picornaviridae Infections/vi [Virology];Sequence Homology;68238-35-7 (Keratins),"Zylberberg, M.;Van Hemert, C.;Dumbacher, J. P.;Handel, C. M.;Tihan, T.;DeRisi, J. L.",2016,07 26,,0