LOCUS KP100794 7315 bp RNA linear VRL 09-FEB-2015 DEFINITION Enterovirus D68 strain US/CO/13-60 polyprotein gene, complete cds. ACCESSION KP100794 VERSION KP100794.1 KEYWORDS . SOURCE Enterovirus D68 (EV-D68) ORGANISM Enterovirus D68 Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Picornaviridae; Enterovirus; Enterovirus D. REFERENCE 1 (bases 1 to 7315) AUTHORS Greninger,A.L., Naccache,S.N., Yu,G., Messacar,K., Somasekar,S., Dominguez,S. and Chiu,C.Y. TITLE Genomic Analysis Uncovers a Novel Circulating Enterovirus D68 Strain in Association with Cases of Acute Flaccid Paralysis from 2012-2014 JOURNAL Unpublished REFERENCE 2 (bases 1 to 7315) AUTHORS Greninger,A.L., Naccache,S.N., Yu,G., Messacar,K., Somasekar,S., Dominguez,S. and Chiu,C.Y. TITLE Direct Submission JOURNAL Submitted (07-NOV-2014) Laboratory Medicine, UCSF, 185 Berry St, San Francisco, CA 94107, USA COMMENT ##Assembly-Data-START## Assembly Method :: Geneious v. v8.0.2 Sequencing Technology :: Illumina; Sanger dideoxy sequencing ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..7315 /organism="Enterovirus D68" /mol_type="genomic RNA" /strain="US/CO/13-60" /serotype="EV-D68" /isolation_source="nasopharyngeal swab" /host="Homo sapiens" /db_xref="taxon:42789" /country="USA" /collection_date="Nov-2013" 5'UTR 1..698 CDS 699..7265 /codon_start=1 /product="polyprotein" /protein_id="AIW58910.1" /translation="MGAQVTRQQTGTHENANIATNGSHITYNQINFYKDSYAASASKQ DFSQDPSKFTEPVVEGLKAGAPVLKSPSAEACGYSDRVLQLKLGNSAIVTQEAANYCC AYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLKSVKWETGSTGWWWKLPDALNNIGM FGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTNTSPGFDDIMKG EEGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQW TLAIIPVVPLGTRTTSSMVPITVSIAPMCCEFNGLRHAITQGVPTYLLPGSGQFLTTD DHSSAPALPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALT DVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCY TPPGGSCPTTRETAMLGTHIVWDFGLQSSVTLIIPWISGSHYRMFNNDAKSTNANVGY VTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIRQLDHLHAAEAAYQIE SIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVE NFLSRAALVSKRSFEYKDHTSSAAQADKNFFKWTINTRSFVQLRRKLELFTYLRFDAE ITILTTVAVNGSSNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKIS DPPARMTIPFMCINSAYSIFYDGFAGFEKSGLYGINPADTIGNLCVRIVNEHQPVGFT VTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGKERAPNALSAIIGNRDSVKTMPH NIVNTGPGFGGVFVGSFKIINYHLATAEERQSAIYVDWQSDVLVTPIAAHGRHQIARC KCNTGVYYCRHKNRSYPICFEGPGIQWIEQNEYYPARYQTNVLLAVGPAEAGDCGGLL VCPHGVIGLLTAGGGGIVAFTDIRNLLWLDTDAMEQGITDYIQNLGNAFGAGFTETIS NKAKEVQDMLIGESSLLEKLLKALIKIISALVIVIRNSEDLVTVTATLALLGCHDSPW SYLKQKVCSYLGIPYVPRQGESWLKKFTEACNALRGLDWLSQKIDKFINWLKTKILPE AREKYEFVQRLKQLPVIESQVSTIEHSCPTTEQQQALFNNVQYYSHYCRKYAPLYAVE AKRVVALEKKINNYIQFKSKSRIEPVCLIIHGSPGTGKSVASNLIARAITEKLGGDIY SLPPDPKYFDGYKQQTVVLMDDLMQNPDGNDISMFCQMVSTVDFIPPMASLEEKGTLY TSPFLIATTNAGSIHAPTVSDSKALSRRFKFDVDIEVTDSYKDSNKLNMSRAVEMCKS DGCAPTNYKRCCPLICGKAIQFRDRRTNARSTIDMLVTDIIKEYRTRNSTQDKLEALF QGPPQFKEIKISVTPDTPAPDAINDLLRSVDSQEVRDYCQKKGWIVIHPSNELLVEKH ISRAFITLQAIATFVSIAGVVYVIYKLFAGIQGPYTGIPNPKPKVPSLRTAKVQGPGF DFAQAIMKKNTVIARTEKGEFTMLGVYDRVAVIPTHASVGDTIYINDVETRVLDACAL RDLTDTNLEITIVKLDRNQKFRDIRHFLPRYEDDYNDAVLSVHTSKFPNMYIPVGQVT NYGFLNLGGTPTHRILMYNFPTRAGQCGGVVTTTGKVIGIHVGGNGAQGFAAMLLHSY FTDTQGEIVSSEKSGVCINAPAKTKLQPSVFHQVFEGSKEPAVLNPKDPRLKTDFEEA IFSKYTGNKIMLMDEYMEEAVDHYVGCLEPLDISVDPIPLESAMYGMDGLEALDLTTS AGFPYLLQGKKKRDIFNRHTRDTSEMTKMLEKYGVDLPFVTFVKDELRSREKVEKGKS RLIEASSLNDSVAMRVAFGNLYATFHNNPGTATGSAVGCDPDIFWSKIPILLDGEIFA FDYTGYDASLSPVWFACLKKVLIKLGYTHQTSFIDYLCHSVHLYKDKKYIVNGGMPSG SSGTSIFNTMINNIIIRTLLIRVYKGIDLDQFKMIAYGDDVIASYPHKIDPGLLAEAG KQYGLVMTPADKGTSFVDTNWENVTFLKRYFRADDQYPFLIHPVMPMKEIHESIRWTK DPRNTQDHVRSLCYLAWHNGEEAYNEFCRKIRSVPVGRALTLPAYSSLRRKWLDSF" mat_peptide 699..905 /product="VP4 peptide" mat_peptide 906..1649 /product="VP2 peptide" mat_peptide 1650..2354 /product="VP3 peptide" mat_peptide 2355..3281 /product="VP1 peptide" mat_peptide 3282..3722 /product="2A peptide" mat_peptide 3723..4019 /product="2B peptide" mat_peptide 4020..5009 /product="2C peptide" mat_peptide 5010..5276 /product="3A peptide" mat_peptide 5277..5342 /product="3B peptide" mat_peptide 5343..5891 /product="3C peptide" mat_peptide 5892..>7262 /product="3D product" 3'UTR 7266..>7315 ORIGIN 1 ttaaaacagc cttggggttg ttcccactcc aagggcccac gtggcggcta gtactctggt 61 acttcggtac ctttgtacgc ctgttttatc tcccttccca atgtaactta gaagttctta 121 aatcaatgct caataggtgg ggcgcaaacc agcgctctca tgagcaagca ctcctgtctc 181 cccggtgagg ttgtataaac tgttcccacg gttgaaaaca acctatccgt tatccgctat 241 agtacttcga gaaacctagt accacctttg gattgttgac gcgttgcgct cagcacacta 301 acccgtgtgt agcttgggtc gatgagtctg gacatacctc actggcgaca gtggtccagg 361 ctgcgttggc ggcctactca tggtgaaaac catgagacgc tagacatgaa caaggtgtga 421 agagtctatt gagctactat agagtcctcc ggcccctgaa tgcggctaat cctaaccatg 481 gagcaagtgc tcacaggcca gtgagttgct tgtcgtaatg cgcaagtccg tggcggaacc 541 gactactttg ggtgtccgtg tttcactttt tacttttatg actgcttatg gtgacaattt 601 gatattgtta ccatttagct tgtcaaatca attgcaaaag atcttaaatc ttatttatca 661 atttgcatct tgataacttt gatttgaaaa ttttaacaat gggagctcag gttactagac 721 aacaaactgg cactcatgaa aatgccaaca ttgccacaaa tggatctcat atcacataca 781 atcagataaa cttttacaag gatagttatg cggcttcagc cagcaagcag gatttttcac 841 aggacccatc aaaattcact gaaccagtag tggaaggtct aaaagcaggg gcgccagttt 901 tgaaatctcc tagtgctgag gcatgtggct acagtgatag agtattacag ctcaaattag 961 gaaattcagc tatcgtcacc caggaagcag caaactactg ttgtgcttat ggtgaatggc 1021 ccaattactt accagatcat gaagcagtag ccattgataa acctacacaa ccagaaactg 1081 ctacagatag attctacact ttgaaatcag tcaaatggga gactggaagc acaggatggt 1141 ggtggaaact acccgatgca ctaaacaaca taggcatgtt tggacagaat gtacagcatc 1201 actacctata tagatctggc ttcttgattc atgtgcagtg caatgccaca aaattccatc 1261 aaggtgcctt attagtggta gcaattccag aacatcagag gggagcgcac aacactaaca 1321 ctagcccagg gtttgatgat ataatgaaag gtgaagaagg agggaccttc aatcatccat 1381 atgtccttga tgatggaaca tcattggctt gtgcgacgat atttccacat cagtggataa 1441 atctgagaac caacaattca gcaacaattg ttcttccctg gatgaatgct gctccaatgg 1501 atttcccact tagacataat cagtggacgc tagcaataat accagtggtg ccattaggta 1561 cgcgtacaac gtcaagtatg gtcccaataa cagtttcaat cgctccaatg tgttgtgagt 1621 ttaatggact tagacacgcc attactcaag gtgtcccaac atacctttta ccaggctcgg 1681 gacaattcct aacaactgat gatcatagct ctgcaccggc tctcccgtgt ttcaacccaa 1741 ctccagaaat gcacatccca gggcaggtcc gtaacatgct agaagtggtc caagtggaat 1801 caatgatgga gattaacaac acagaaagtg cagttggcat ggagcgtctt aaggttgata 1861 tatcagcatt gacagatgtc gatcaattgt tattcaacat tccactggac atacagttgg 1921 atgggccact tagaaacact ttagtaggaa acatatctag atattacact cattggtctg 1981 gatccctaga aatgacgttt atgttttgtg gcagcttcat ggcaacggga aaattaatcc 2041 tgtgctatac tcctccaggt gggtcatgcc caacaaccag agagaccgcc atgttaggta 2101 cacatattgt ttgggatttt ggattacaat ctagtgtaac cctgataata ccttggatta 2161 gtggatccca ctacaggatg tttaacaatg atgctaagtc aactaatgcc aacgttggct 2221 atgtcacttg ttttatgcag actaatctga tagttcccag tgagtcctct gacacgtgtt 2281 ccttgatagg gttcatagca gcaaaagatg atttctctct cagactaatg agagacagcc 2341 ctgacattag acaactagac catttacatg cagcagaggc agcctaccag atcgagagca 2401 tcatcaaaac agcaaccgac actgtgaaaa gtgagattaa cgctgaactc ggtgtggtcc 2461 ctagcttaaa tgcagttgaa acaggtgcaa cttctaacac tgaaccagaa gaagccatac 2521 aaactcgcac agtgataaat cagcatggtg tgtccgagac tttagtggag aattttctca 2581 gtagagcagc tttggtatca aagagaagtt ttgaatacaa agatcatact tcgtctgcag 2641 cacaagcgga caagaacttt ttcaaatgga caattaacac cagatccttt gtacagttaa 2701 gaagaaagtt agaattattc acatacctta gatttgatgc tgagatcact atactcacaa 2761 ctgtagcagt gaatggtagt agtaataata catacgtggg tcttcctgac ttgacacttc 2821 aggcaatgtt tgtacccact ggtgctctta ccccagaaaa gcaggactca ttccactggc 2881 agtcaggtag taatgctagt gtattcttta aaatctctga ccccccagcc agaatgacca 2941 taccttttat gtgcattaac tcagcatact caatttttta tgatggcttt gccggatttg 3001 agaaaagtgg tctgtatgga ataaatccag ctgacactat tggtaactta tgtgttagaa 3061 tagtgaatga acaccaacca gttggtttca cagtgaccgt tagggtttac atgaagccta 3121 aacacataaa agcatgggca ccacgaccac cacgaaccct gccgtatatg agtattgcaa 3181 atgcaaatta caaaggcaaa gaaagagcac caaatgcgct cagtgctata attggcaata 3241 gagacagtgt caaaaccatg cctcataata tagtgaacac tggtccaggc ttcggaggag 3301 tttttgtagg gtctttcaaa ataatcaact atcacttagc cactgcagaa gagagacagt 3361 cagctatcta tgtggattgg caatcagacg tcttggttac ccccattgct gctcatggaa 3421 ggcaccaaat agcaagatgc aagtgcaata caggggttta ctattgtagg cacaaaaaca 3481 gaagttaccc aatttgcttt gaaggcccag ggattcaatg gattgaacaa aatgaatatt 3541 acccagcaag gtaccagacc aatgtacttt tggcagttgg tcctgcggaa gcaggagatt 3601 gcggtggttt actagtctgt ccacatgggg taatcggtct tcttacagca ggagggggtg 3661 gaattgtggc tttcactgat atcagaaatt tgctatggtt agatactgat gctatggaac 3721 aaggcattac tgattacatt caaaatcttg gtaatgcctt tggagcaggg tttacagaaa 3781 caatctctaa taaagccaag gaagtgcaag atatgctaat tggagagagt tcactattag 3841 aaaaattgct aaaagctcta atcaaaatca tatcagcatt agtaattgta atcagaaatt 3901 cggaagacct agtcacagtc acagctacac tagcattatt aggatgccat gattcaccat 3961 ggagctactt gaaacagaaa gtatgttcat acttaggtat tccttatgta cctagacagg 4021 gtgaatcgtg gcttaagaag ttcacagaag catgcaatgc tcttagaggt ctggattggc 4081 tatcacaaaa gatagataaa ttcatcaact ggcttaaaac caaaatatta ccagaagcta 4141 gggagaaata tgaatttgtg cagaggctca aacagttacc ggtgatagaa agccaagtta 4201 gtacgatcga gcatagctgc ccaacaacag aacaacagca ggccttattc aacaacgtcc 4261 agtactattc acactattgt agaaagtacg caccacttta cgcagtggaa gcaaagaggg 4321 tagtagctct tgaaaagaaa ataaacaact acatccagtt caagtccaaa tctcgcattg 4381 aaccggtttg tttaataata catggctctc caggaactgg caagtcagtg gcttcaaatt 4441 taattgccag ggctatcaca gaaaaattgg gaggagacat ttattccttg cctccagacc 4501 ctaaatattt tgatggatac aaacagcaaa cagtggtcct catggatgat ttaatgcaaa 4561 atccagatgg gaatgacata tctatgttct gccaaatggt ctctactgtg gatttcatac 4621 ccccaatggc tagtttggaa gaaaaaggaa ctctgtacac tagtccattt ttaatagcta 4681 ctaccaatgc tggctcaata catgcaccaa ctgtatcaga ctcaaaggct ttgtcacgca 4741 gatttaaatt tgacgtggac attgaagtca cagattcata caaggactca aataaattga 4801 atatgtcaag ggcagtcgag atgtgcaaat cagatggctg tgcccccacc aattacaaaa 4861 gatgctgccc attgatctgt ggaaaggcta ttcaattcag agatcgcaga actaatgcaa 4921 gatccactat tgatatgtta gtaactgata ttataaagga gtatagaacc agaaacagta 4981 cacaggataa gctggaagct ctgtttcagg ggcctccaca gtttaaagag atcaaaattt 5041 cagtcacccc agatacacca gctcctgatg ctataaatga tcttctcagg tcagtggatt 5101 ctcaagaagt tagggattat tgccaaaaga aaggatggat tgtaatacac ccatcaaatg 5161 aactactagt agaaaaacac atcagtagag cttttattac tctacaagcc attgccacct 5221 ttgtatcaat agctggtgta gtttatgtta tatacaaact ttttgctggc attcagggtc 5281 catacacagg aatccccaat cctaaaccta aagtaccctc tctcagaaca gctaaagtgc 5341 aaggaccagg gttcgatttt gcacaagcca taatgaagaa aaataccgtc attgcaagga 5401 ctgaaaaggg tgagttcacc atgctgggtg tatatgatag ggtagcggtc atccccacac 5461 acgcatctgt tggagatacc atttacatta atgatgtaga gactagagtt ttagatgcgt 5521 gtgcacttag agacttgact gatacaaact tagagataac catagtcaaa ttagaccgta 5581 atcaaaaatt tagagatatc agacattttc tgcccagata tgaggatgat tacaatgacg 5641 ctgtgcttag cgtacataca tcaaaattcc caaatatgta tatcccagtt ggacaagtca 5701 ccaattatgg cttcttgaac ctaggtggta caccgacgca ccgcatttta atgtataact 5761 tcccaacaag agctggccag tgtggtggtg tggtgacaac tacaggtaag gtgataggaa 5821 tacatgtagg tggaaatgga gctcaaggat ttgcagcaat gctactacac tcttacttta 5881 ccgatacaca aggtgagata gttagtagtg aaaagagtgg ggtgtgcatt aacgcaccgg 5941 caaagactaa actccaaccc agtgttttcc atcaagtttt tgaaggttca aaggaaccag 6001 cagttctcaa tccaaaagat cctaggctta aaacagattt cgaggaggcc attttctcaa 6061 aatatacagg taacaaaatc atgttaatgg atgaatacat ggaagaggca gtggatcatt 6121 atgtggggtg tctggaacca ttagatatca gtgtggatcc catacccctg gaaagtgcca 6181 tgtatggaat ggatggcctt gaggcattag acttaactac cagtgcagga ttcccttact 6241 tactacaagg gaagaagaaa agggacatat ttaatagaca tactagagac accagtgaaa 6301 tgacaaagat gttagagaaa tatggagttg acctaccttt tgtaaccttt gtaaaagatg 6361 agcttagatc aagagaaaaa gttgaaaaag ggaaatcacg cctgattgag gccagttcct 6421 tgaatgactc agttgctatg agggttgcct ttggaaacct ttacgccaca tttcacaaca 6481 atccaggtac agcaactggt agtgcagttg gttgtgatcc agatatattt tggtcgaaaa 6541 tccctatttt gttagatgga gaaatctttg cttttgacta cactggttat gatgctagtt 6601 tgtcaccagt gtggtttgcc tgtttaaaga aagttctaat taagttaggt tacacgcatc 6661 aaacatcttt tatagattat ttgtgtcatt cggtgcattt atataaggac aaaaaataca 6721 tagttaatgg tggaatgccc tctggttctt caggcaccag catattcaac actatgatca 6781 acaatataat cataagaact ttattaatta gggtttacaa aggcatagac ctggaccagt 6841 tcaaaatgat tgcctatggg gatgatgtta ttgctagcta cccacataag attgatccag 6901 gtttgctggc agaagcaggt aaacagtatg gattagtaat gacaccagca gacaaaggaa 6961 ccagttttgt cgacacaaat tgggaaaatg taactttctt aaaaagatat ttcagagcag 7021 atgatcaata cccctttctc atacatccag tgatgccaat gaaagagata catgaatcta 7081 ttagatggac taaagatccc agaaacacac aggatcatgt taggtctttg tgctacctcg 7141 catggcataa tggagaggag gcttataatg aattttgtag aaaaatcaga agtgtgcctg 7201 tgggaagggc attgacacta cctgcatact ctagtcttag acggaaatgg ttagattcgt 7261 tctagacaac tctaattgaa acccaagtta tagttatttt catttagagg taaat //