{ "meta": { "build_url": "https://github.com/blab/sars-like-cov", "colorings": [ { "key": "clade_membership", "title": "Clade", "type": "categorical" }, { "key": "gt", "title": "Genotype", "type": "categorical" }, { "key": "virus_type", "scale": [ [ "SARS-like CoV", "#4274CE" ], [ "SARS-CoV", "#CEB541" ], [ "SARS-CoV-2", "#DC2F24" ] ], "title": "virus type", "type": "categorical" }, { "key": "host", "scale": [ [ "Bat", "#4274CE" ], [ "Civet", "#69B091" ], [ "Pangolin", "#ADBD51" ], [ "Human", "#DC2F24" ] ], "title": "host", "type": "categorical" }, { "key": "country", "title": "country", "type": "categorical" }, { "key": "author", "title": "authors", "type": "categorical" } ], "description": "This phylogeny shows evolution of SARS-like betacoronaviruses including samples from the novel coronavirus SARS-CoV-2 causing the COVID-19 epidemic in Hubei and in China. SARS-CoV-2 coronaviruses from the COVID-19 epidemic are colored in red, SARS-CoV-1 coronaviruses from the 2002-03 SARS outbreak are colored in yellow, while related SARS-like coronaviruses are colored in blue.\n\nFull details on bioinformatic processing can be found [here](https://github.com/blab/sars-like-cov).\n\nWe gratefully acknowledge the Authors, Originating and Submitting laboratories of the genetic sequence and metadata made available through [GISAID](https://gisaid.org) on which this research is based.\n\nThe SARS-CoV-2 coronavirus genomes were generously shared by scientists at the Shanghai Public Health Clinical Center & School of Public Health, Fudan University (*WH-Human_1*), at the National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China (*Wuhan/IVDC-HB-01/2019*, *Wuhan/IVDC-HB-05/2019*, *IVDC-HB-04/2020*) at the Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China (*Wuhan/IPBCAMS-WH-01/2019*), and at the Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China (*Wuhan/WIV04/2019*, *bat/Yunnan/RaTG13/2013*).\n\nRelated SARS-like bat virus was shared by Zhu et al at the Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China (*bat/Yunnan/RaTG13/2013*). Related SARS-like pangolin viruses were shared by Lam, Cao et al at the State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China and at the State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, University of Hong Kong, Hong Kong (*pangolin/Guangdong/P2S/2019*, *pangolin/Guangxi/P1E/2017*, *pangolin/Guangxi/P2V/2017*, *pangolin/Guangxi/P3B/2017*, *pangolin/Guangxi/P4L/2017*, *pangolin/Guangxi/P5E/2017*, *pangolin/Guangxi/P5L/2017*). Other related SARS-like pangolin viruses were shared by Shen, Xiao et al at the South China Agricultural University (*pangolin/Guandong/1/2020*).\n", "display_defaults": { "color_by": "virus_type", "map_triplicate": true }, "filters": [ "virus_type", "host", "country", "author" ], "genome_annotations": { "ORF1a": { "end": 13414, "seqid": "config/sars-like-cov_reference.gb", "start": 266, "strand": "+", "type": "CDS" }, "ORF1b": { "end": 21486, "seqid": "config/sars-like-cov_reference.gb", "start": 13399, "strand": "+", "type": "CDS" }, "ORF3a": { "end": 26095, "seqid": "config/sars-like-cov_reference.gb", "start": 25271, "strand": "+", "type": "CDS" }, "ORF3b": { "end": 26156, "seqid": "config/sars-like-cov_reference.gb", "start": 25692, "strand": "+", "type": "CDS" }, "ORF6": { "end": 27373, "seqid": "config/sars-like-cov_reference.gb", "start": 27182, "strand": "+", "type": "CDS" }, "ORF7a": { "end": 27750, "seqid": "config/sars-like-cov_reference.gb", "start": 27382, "strand": "+", "type": "CDS" }, "ORF7b": { "end": 27881, "seqid": "config/sars-like-cov_reference.gb", "start": 27747, "strand": "+", "type": "CDS" }, "ORF8a": { "end": 28008, "seqid": "config/sars-like-cov_reference.gb", "start": 27889, "strand": "+", "type": "CDS" }, "ORF8b": { "end": 28228, "seqid": "config/sars-like-cov_reference.gb", "start": 27974, "strand": "+", "type": "CDS" }, "ORF9b": { "end": 28573, "seqid": "config/sars-like-cov_reference.gb", "start": 28277, "strand": "+", "type": "CDS" }, "envelope": { "end": 26428, "seqid": "config/sars-like-cov_reference.gb", "start": 26198, "strand": "+", "type": "CDS" }, "membrane_protein": { "end": 27145, "seqid": "config/sars-like-cov_reference.gb", "start": 26480, "strand": "+", "type": "CDS" }, "nuc": { "end": 29874, "seqid": "config/sars-like-cov_reference.gb", "start": 1, "strand": "+", "type": "source" }, "nucleocapsid": { "end": 29535, "seqid": "config/sars-like-cov_reference.gb", "start": 28267, "strand": "+", "type": "CDS" }, "spike": { "end": 25261, "seqid": "config/sars-like-cov_reference.gb", "start": 21494, "strand": "+", "type": "CDS" } }, "geo_resolutions": [ { "demes": { "China": { "latitude": 35.000074, "longitude": 104.999927 }, "Japan": { "latitude": 35.68536, "longitude": 139.75309 }, "Nepal": { "latitude": 28.0, "longitude": 84.0 }, "Singapore": { "latitude": 1.2904527, "longitude": 103.852038 }, "Sweden": { "latitude": 59.6749712, "longitude": 14.5208584 }, "Taiwan": { "latitude": 23.6978, "longitude": 120.9605 }, "USA": { "latitude": 39.7837304, "longitude": -100.4458824 } }, "key": "country" } ], "maintainers": [ { "name": "Trevor Bedford", "url": "http://bedford.io/team/trevor-bedford/" }, { "name": "Emma Hodcroft", "url": "https://neherlab.org/emma-hodcroft.html" } ], "panels": [ "tree", "map", "entropy" ], "title": "Phylogeny of SARS-like betacoronaviruses including novel coronavirus SARS-CoV-2", "updated": "2020-06-04" }, "tree": { "branch_attrs": { "mutations": {} }, "children": [ { "branch_attrs": 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M3560L, F3564I, I3570V, L3593M, M3596I, I3598M, A3599S, C3601F, L3604M, L3605F, E3645D, L3646M, A3647V, Y3654F, R3655K, L3666V, A3681G, I3692L, V3714I, I3728V, A3734G, V3738M, Y3743C, F3745I, L3746F, C3766F, C3768T; ORF1b: Q2274E, M2302L, I2365V, A2376T, A2398S, E2429D, N2430S, V2432T, I2433L, H2535N, L2550I, K2555Q, S2585A, V2606C, K2613R, T2620V, N2662G, Y2669L, E2673S, V2687I; ORF3a: I13V, R15L, P17Q, K19E, E21K, N22D, S24T, A26S, S27D, T28S, H30R, L37I, V62I, A64T, H66K, Y74S, Q78H, I90V, M101L, Q104P, I108L, I112V, I114F, I117T, C121V, F123I, C127F, V147L, N153C, D165S, T166S, K177N, K179I, L180S, K181E, E182D, S190T, D192K, H194E, Y200C, I203L, G205S, E209S, V210D, E215Y, T220S, A225V, N227H, A228V, S234N, L236I, K238D, D239E, D241E, D260E; ORF3b: L6F, I13V, T16I, T21I, S23*, Q24L, I25L, S37I, Q38P, N39F, *40Q, K42M, R51K, I52S, T54N, Q55L, M60V, *61L, *62Y, M64I, A65V, K69Q, F70I, L74C, N75T, R76Q, R80A, K86N, H89L, I93T, A94I, S95K, K98M, I99S, I101N, C103S, Y105F, A110V, L111H, *115L, I120N, S125N, K138L, V139M; ORF6: I16L, R23K, A25S, I31Y, S34N, S35L, V37I, R38K, Q39N, F41S, K46E, K47N, E51Q, D54E, E56Q; ORF7a: T8A, A11T, P36S, S59F, H62Q, A68P, T71V, L108I, I117F; ORF7b: N2S, T5S, I37H, E38N, P40T, N42H, K43N, V44A; ORF8a: L3F, I5V, V6F, L9I, S12T, Y14T, C15A, I16L, I19L, E21S, C23A, E24Q, N26H, L30V, I31V, E32D, K36*; ORF8b: T1M, K4M, K12R, I13V, P15A, R20P, A23V, V25G, T27F, K28*, T29I, S30T, N31H, L33I, *34H, D35*, V36H, Q38*, I41K, S42F, E45T, A50E, P52K, V53L, I57V, Y64F, *65R; ORF9b: P10H, D29N, G34D, A38V, Q52P, S56N, R60K, N61T, A67D, R68K, S72L, V76A, A97V; envelope: T55S, V56F, G70R; membrane_protein: M1S, A2G, E3D, S8T, R14K, A29T, M32C, S39A, V51I, V75I, I86L, V96I, R124H, M133L, I144L, M150I, S154H, G187A, T188G, N196S, G211S, N213S; nucleocapsid: T22S, G32E, E64D, G80S, V95I, S121G, V132I, N153A, G193N, N194S, N206T, S213G, G214N, E217D, V235I, T377A, A380T, P382A, P391Q, M401L, R406K, K410Q; spike: L2F, I3V, V5F, F6L, V8F, S9A, K12N, A13T, G18V, G20D, I21N, I22F, N23T, P26T, P28L, K29N, L30P, Q32Y, I33T, S34N, R37Q, N43P, D45K, D50T, Y58F, D63I, L66V, Q68W, F70Y, F72L, N73T, I74T, D75N, G84N, V97I, V98I, S105T, A114L, I115F, S120A, H122N, I123V, R126K, N131D, K134N, E135D, M137F, Y138F, T139S, R142Y, P143H, Q147*, Q148E, W151P, Q154S, F157T, Y161F, D162E, R163Y, E165S, Q169L, T172I, P174G, T176D, D181N, S190I, F193Y, L194F, S195K, V196I, H198S, T199K, P206I, A211T, K217E, I219L, L220V, K221E, F224I, S230K, V233T, V234F, M235L, M237I, F238H, P242S, D243R, Q245Y, T246P, S248P, S249A, N256Y, H259P, T260S, F266Y, S279A, Q280L, N281D, A284S, L286T, I290L, N292S, N294T, D296E, S308Q, E312S, V313I, E401Q, R426N, I428L, A431E, K432I, H433G, D434G, G436Y, Y439F, N457T, V458E, P459I, F460Y, S461Q, S462A, D463G, D464S, K465T, T468N, P469Q, P470A, A471G, S574T, A590T, R611H, V626A, L729I, M770I, A775P, T795S, M816I, E821D, S827A, V860I, L986F, R1055K, Y1070H, S1083H, I1086V, S1093E, A1229C" }, "mutations": { "ORF1a": [ "L6P", 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E941G, E942Q, A969S, T970S, P971S, Q972S, H973Q, D983E, D984S, Q988H, A991T, E992Q, P995S, V1000T, V1003Q, D1067K, K1102R, S1111N, E1135D, R1148H, A1154V, I1186V, D1192E, I1198F, C1211S, A1259V, D1269E, D1271A, D1370E, Y1416N, D1683E, V1765M, E1790Q, F1799V, P1839S, A1882S, T1922S, T1984I, V2004A, E2008G, D2020V, N2058S, V2061L, L2188I, G2242V, T2574I, V2760I, A2761T, S2774F, I3029V, L3033I, I3117M, I3318V, V3487L, I3564V, L3589M, M3646I; ORF1b: F1086L, N1654S, K1863R, N1962H, R2049K, V2061I, E2279D, P2313L, E2661D, I2679V, V2686I; ORF3a: L52I, V88L, A99G, P104T, Y107F, V112A, F114C, S171C, S251T; ORF3b: L24P, Q31V, A34V, Q35L, Q36R, Q40L, K41R, I49T, L50R, N54S, K58R, L77H, Q112L; ORF6: L44P, K48N, Y49C; ORF7a: L5F, A8V, A13V, C15G, V24I, R25K, Y75F, I88T, L101V, T121I; ORF7b: L4F, C41F; ORF8a: T14A, *36Q; ORF8b: H6L, W26R, F27L, I29V, F64S; ORF9b: L22V, T25A, R26K, M27T, N29S, V31M, Q35L, V42A, R48H, D63R, D67G, V77L, E86V; nucleocapsid: T25S, N28S, S34N, D64N, R66T, S233N, T380L, 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E868D, E1001K, V1041I, K1067*, A1134V, E1179G, Y1301H, A1328V, I1336L, H1522Y, L1536I, T1544S, V1560I, A1606V, P1617S, K1645R, K1906R, T1912I, S1929L, E2006K, S2058I, N2088S, N2164T, T2255I, Q2679H, K2738R, V2770A, S2799P, V2831I, A2902S, T2929I, V3238I, G3681S, I3904L, E3924K, A3946V, A3985T, A4171S; ORF1b: T15S, T17I, T76N, D145G, R458T, V464I, G669S, P976L, S997L, H1087Y, A1443T, A1643T, N2070S, V2089I, Y2139H, K2160E, S2165N, V2182A, D2183N, Q2400H, H2583Y; ORF3a: T14S, V29I, L139V; ORF3b: L27S, I70T; ORF7b: F41S; ORF8b: *24R; ORF9b: N7R, V94A; nucleocapsid: R11S; spike: L52*, A55V, I98V, N144T, P248S, T294S, A430T, N437H, T624I, N627S, Q1190H, S1234F" }, "mutations": { "ORF1a": [ "R24C", "P80H", "D203N", "L251S", "P537A", "H557Y", "K564Q", "C667R", "I671V", "N860S", "E868D", "E1001K", "V1041I", "K1067*", "A1134V", "E1179G", "Y1301H", "A1328V", "I1336L", "H1522Y", "L1536I", "T1544S", "V1560I", "A1606V", "P1617S", "K1645R", "K1906R", "T1912I", "S1929L", "E2006K", "S2058I", "N2088S", 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"C3666T", "C3745T", "A3801G", "T4166C", "T4168C", "C4248T", "A4271C", "T4444C", "T4699C", "C4829T", "C4831T", "C4871A", "A4885G", "A4895T", "C4921T", "C4930T", "G4939T", "G4943A", "A4969G", "T4981C", "C5082T", "A5083G", "T5113C", "C5114T", "G5125T", "A5199G", "T5209C", "C5737T", "T5755C", "A5803G", "T5905C", "A5982G", "C6000T", "C6051T", "G6281A", "G6438T", "A6528G", "A6756C", "T7006C", "T7021C", "C7029T", "T7702C", "T7894C", "T8110C", "T8140C", "T8257C", "T8260C", "G8302T", "A8311G", "A8478G", "T8574C", "A8590G", "T8660C", "T8728C", "G8756A", "T8839C", "G8842A", "T8959C", "G8969T", "C9051T", "T9097C", "G9977A", "A10213G", "T10648C", "A10660G", "G11116A", "G11306A", "A11686T", "C11719T", "G11728A", "A11746G", "T11749A", "T11752C", "A11803T", "A11806G", "A11818T", "T11821A", "T11890C", "G11902A", "T11908A", "A11935T", "G11962A", "A11975C", "C12016T", "G12022A", "G12035A", "T12061C", "C12070A", "T12073A", "T12076C", "C12102T", "T12193C", "G12218A", "C12418G", "T12580C", "C12595T", "A12646G", "T12742G", "G12776T", "C12784T", "T12799C", "T12814C", "A12820G", "T12877C", "T12985C", "T13009C", "T13012C", "A13018T", "A13030G", "T13033C", "C13046T", "A13048G", "A13126G", "T13147C", "A13150G", "A13153G", "T13204C", "T13222C", "C13228T", "C13315T", "A13441T", "C13448T", "T13467C", "A13542G", "C13625A", "T13641C", "A13644G", "A13722G", "C13726T", "A13734G", "A13832G", "T13860C", "T13866C", "A13872G", "T13884C", "T13971C", "G13986C", "G14043A", "A14049G", "G14073T", "T14076C", "A14079G", "C14092T", "T14100C", "A14109T", "C14145T", "C14154T", "G14160A", "C14196T", "A14211T", "T14217C", "C14283T", "G14316C", "A14337G", "A14361T", "C14415T", "T14452C", "T14466C", "C14580T", "G14771C", "G14788A", "T14889C", "T14892C", "T14940C", "T15000C", "T15087C", "C15147T", "C15327T", "G15403A", "A15411G", "A15483G", "T15495C", "T15528C", "A15582G", "T15645C", "T15648A", "T15654C", "C15657A", "C15681T", "C15694T", "T15732C", "T15741C", "C15783T", "T15801C", "T15912C", "A15918G", "T16059C", "T16134C", "A16158G", "A16173G", "C16191T", "T16224C", "A16287G", "T16320C", "C16325T", "T16359C", "C16380T", "C16388T", "T16434C", "C16446T", "C16527T", "C16602T", "T16620A", "A16653G", "C16657T", "T16704C", "T16725C", "T16815A", "T16818C", "T16833C", "T17169C", "G17253T", "T17367C", "T17574G", "C17595T", "C17631A", "T17697C", "T17724C", "G17725A", "A17808G", "T17862C", "A17952T", "C18051T", "G18111A", "T18210C", "A18225G", "G18325A", "A18531G", "T18546C", "T18642C", "T18690C", "T18744C", "A18747G", "T18888C", "A18894G", "C19044T", "T19113C", "C19443T", "A19607G", "G19663A", "T19813C", "A19876G", "G19892A", "T19943C", "A19944G", "G19945A", "C19962T", "A20043G", "T20235C", "T20595C", "A20598C", "T20718C", "T20778C", "T20796C", "G20850A", "G21108A", "T21123C", "C21145T", "T21192C", "T21222C", "T21648A", "C21657T", "A21785G", "C21850T", "T21895C", "A21924C", "T21955C", "G21988A", "T22039C", "T22105C", "A22147G", "C22235T", "C22374G", "T22507C", "T22546C", "T22585C", "T22606C", "C22627T", "A22672G", "A22696G", "T22717C", "T22759C", "T22768A", "C22771A", "T22780C", "G22781A", "A22802C", "T22825C", "T22855C", "A22957G", "C22966T", "T22987C", "C23077T", "C23119T", "C23336T", "T23353C", "C23364T", "A23373G", "T23599C", "T23605C", "T23653C", "T23668C", "T23794C", "T23860C", "A23866T", "C23941A", "T24013C", "G24154A", "C24622T", "T24769C", "T24775C", "T24808C", "C24841T", "A25063C", "C25194T", "C25216T", "A25258G", "C25311G", "T25315G", "A25333G", "G25355A", "T25501C", "G25573A", "C25588T", "T25672C", "T25685G", "T25771C", "T25900C", "T27868C", "C27888T", "T28043C", "A28296G", "C28297A", "T28557C", "A28608G", "A28968G", "T29127C", "A29223T", "T29313C", "A29433G", "C29712T", "T29732C" ], "nucleocapsid": [ "R11S" ], "spike": [ "L52*", "A55V", "I98V", "N144T", "P248S", "T294S", "A430T", "N437H", "T624I", "N627S", "Q1190H", "S1234F" ] } }, "name": "bat_SL_CoVZXC21", "node_attrs": { "accession": "MG772934", "author": { "author": "Hu et al", "journal": "Unpublished", "title": "Genomic Characterization and Infectivity of A Novel SARS-like coronavirus in Chinese Bats", "value": "Hu et al A" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.13055305, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/MG772934", "virus_type": { "value": "SARS-like CoV" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: V14G, Q15P, F204L, C213Y, T214A, T319I, I368L, T484I, K527S, E539D, R542H, Q556H, R560H, T568I, V639I, L891I, T892I, F943C, S1080G, I1252T, P1337S, E1339A, E1498Q, I1519T, V1527T, T1544N, T1574I, L1660I, E2065K, A2119V, L3215I, A4334V; ORF1b: E83G, N141K, D146N, I162V, S354N, H730Q, T1511M, N1653H, A1868S, I2078V, V2086L, T2432I, D2511H; ORF3a: D22G, S26T, D27N, A31T, V97L, L219V; ORF3b: M42T, N78K, A80V, S103F; ORF7a: T57A; ORF9b: L72S; nucleocapsid: Q29K, I235V; spike: L54S, F155S, I313V, A430V, S592L, G670S, D825G, Q1095K" }, "mutations": { "ORF1a": [ "V14G", "Q15P", "F204L", "C213Y", "T214A", "T319I", "I368L", "T484I", "K527S", "E539D", "R542H", "Q556H", "R560H", "T568I", "V639I", "L891I", "T892I", "F943C", "S1080G", "I1252T", "P1337S", "E1339A", "E1498Q", "I1519T", "V1527T", "T1544N", "T1574I", "L1660I", "E2065K", "A2119V", "L3215I", "A4334V" ], "ORF1b": [ "E83G", "N141K", "D146N", "I162V", "S354N", "H730Q", "T1511M", "N1653H", "A1868S", "I2078V", "V2086L", "T2432I", "D2511H" ], "ORF3a": [ "D22G", "S26T", "D27N", "A31T", "V97L", "L219V" ], "ORF3b": [ "M42T", "N78K", "A80V", "S103F" ], "ORF7a": [ "T57A" ], "ORF9b": [ "L72S" ], "nuc": [ "T306G", "C307T", "A309C", "G376A", "C556T", "G598A", "T875C", "A880G", "G903A", "C904T", "A905G", "C920T", "T967C", "C1221T", "A1367C", "T1711C", "C1716T", "T1801G", "A1804G", "T1813A", "T1834A", "G1843A", "A1845G", "A1846T", "T1861G", "T1864C", "A1870G", "T1873C", "A1876T", "G1882T", "G1890A", "T1906C", "T1912A", "T1918A", "T1921A", "A1933C", "G1944A", "C1960T", "C1968T", "A1969T", "C1997T", "G2173A", "G2180A", "T2242A", "T2308C", "C2936A", "C2940T", "T3093G", "T3313C", "A3503G", "T3895C", "T4020C", "C4045A", "T4075C", "T4123C", "C4274T", "A4281C", "T4468C", "G4582T", "C4708T", "G4757C", "T4765C", "T4819C", "T4821C", "C4822T", "C4828T", "G4844A", "T4845C", "C4896A", "C4986T", "T5026C", "C5071T", "T5074C", "A5143T", "A5236G", "C5243A", "T5245C", "T5287C", "A5341G", "T5482C", "A5587G", "A5626G", "T5746C", "C5773T", "T6049C", "T6152C", "T6205C", "G6458A", "C6621T", "C6667T", "C7540T", "C7555T", "T8293C", "T8513C", "T8719C", "A8776G", "A8803G", "C8836T", "T8935C", "G8986A", "C9001T", "T9808C", "C9908A", "C10270T", "T11293C", "T11662C", "A11677G", "T11680C", "T11704C", "T11734C", "A11809G", "G11812T", "A11827G", "C11878T", "T11899C", "A11923G", "C11939T", "A11953G", "T12040C", "A12052T", "T12103A", "A12253G", "C12400A", "T12760C", "A12763G", "T12811C", "C12821T", "T12835C", "A12856T", "A12934G", "T12940C", "C13003T", "T13108A", "T13120C", "G13171A", "C13266T", "T13282G", "T13291C", "C13381T", "A13419G", "C13533T", "T13632C", "A13646G", "T13656C", "T13776C", "C13791T", "A13800G", "T13821A", "T13833C", "G13834A", "T13836C", "C13881T", "A13882G", "T13885C", "T13899G", "A13926C", "A13932G", "G13935A", "A13941G", "T13974C", "T13995C", "T14007G", "C14016T", "T14025C", "T14031A", "T14055C", "T14064C", "T14082C", "A14088T", "T14106G", "G14112C", "A14121T", "A14124G", "A14157G", "T14182C", "T14244C", "A14250G", "C14259T", "C14271T", "A14343G", "G14459A", "T14526C", "T14541C", "C14808T", "T14823C", "A14865G", "A14895G", "T14922C", "C15039T", "A15132G", "T15555C", "T15588G", "A15624G", "A15642T", "G15747A", "T15750C", "C15768T", "C15810T", "G15822C", "A15837G", "T15876C", "C15972T", "A16110G", "A16137G", "A16164G", "A16185G", "T16248C", "T16266C", "T16272C", "A16326C", "T16344C", "G16347A", "A16362G", "T16413G", "T16473C", "T16503C", "T16674A", "C16938T", "T16986C", "A17010G", "T17073C", "A17124G", "T17139C", "T17199C", "T17247C", "T17334C", "A17373G", "A17484G", "T17502C", "T17583C", "A17670G", "C17676T", "T17679A", "C17700T", "C17703T", "A17754T", "A17874G", "G17922T", "C17930T", "A18045G", "A18072G", "T18147C", "A18355C", "T18357C", "C18369T", "C18486T", "C18561T", "C18567T", "T18636C", "A18687G", "T18771C", "T18837C", "A18861G", "C18963T", "G19000T", "A19245G", "C19338T", "T19581C", "A19630G", "G19654T", "T19746G", "T19827G", "C19908T", "T20127C", "A20313G", "T20439C", "T20631C", "C20667T", "C20693T", "T20730C", "A20805G", "T20913C", "G20929C", "T21556C", "T21565C", "T21571C", "T21640A", "T21654C", "C21685T", "T21703C", "C21724T", "C21727T", "T21757C", "C21886T", "T21957C", "C21985T", "T22054C", "A22090G", "A22120G", "T22132C", "A22138G", "A22144G", "T22186C", "T22378C", "T22387C", "T22408C", "A22430G", "A22489G", "T22501C", "T22504C", "T22666C", "A22681G", "T22705C", "C22782T", "T22813C", "A22837G", "T22861C", "T22906C", "T22942C", "T23036C", "C23268T", "T23494C", "G23501A", "T23554C", "A23746G", "A23758G", "T23773C", "C23839T", "T23855C", "T23863C", "T23899C", "T23932C", "A23967G", "T24376C", "T24685C", "C24776A", "A25297T", "A25309T", "T25330C", "A25335G", "T25346A", "G25349A", "G25361A", "C25504T", "C25543T", "A25546T", "C25550T", "A25552G", "G25559C", "T25690C", "T25816C", "T25925G", "C25930T", "C25999T", "G27377T", "A27550G", "T27869C", "A27960G", "C28351A", "T28491C", "A28695G", "A28969G", "A28995G", "C29061T", "T29448C", "A29542G", "C29670T", "A29704G", "T29769C", "G29770C" ], "nucleocapsid": [ "Q29K", "I235V" ], "spike": [ "L54S", "F155S", "I313V", "A430V", "S592L", "G670S", "D825G", "Q1095K" ] } }, "name": "bat_SL_CoVZC45", "node_attrs": { "accession": "MG772933", "author": { "author": "Hu et al", "journal": "Unpublished", "title": "Genomic Characterization and Infectivity of A Novel SARS-like coronavirus in Chinese Bats", "value": "Hu et al A" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.12944725999999998, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/MG772933", "virus_type": { "value": "SARS-like CoV" } } } ], "name": "NODE_0000003", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.11697294999999999 } }, { "branch_attrs": { "labels": { "aa": "ORF1a: A412S, Y417H, R722K, S902G, T1070A, I1076K, K1185N, N1189I, V1481I, L2007S, I2107V, L2149F, R2168K, V2207I, I2430V, A2588T, R2718K, V2762A, S3810N, Y3934F, G4055N, N4151T, H4165L, P4253A, R4343K, M4368L, S4374Q, T4375S; ORF1b: E53D, L57I, M68F, V81L, E83D, V214I, V216T, A217T, C220S, A253T, L256Y, C272N, I290V, S602N, S634T, N638S, H730T, E731D, D734N, Y757F, N760T, A763S, A775S, F1086L, E1389D, I1538V, D1623E, E1652P, N1661S, G1700N, S1744A, N1752H, H1784Y, S1817T, S1843A, E1869D, H1898S, T1961V, Q2017L, Y2058F, N2070Q, A2081T, I2093L, I2120V, S2169P, T2203Q, K2206V, A2209K, V2213L, S2222A, F2230Y, I2236V, I2237V, D2250N, E2252Q, D2253E, T2262I, Q2310K, K2315E, V2566I; ORF3a: L15F, V47I, T117S, F127L, D182H; ORF3b: S29L, K41N, I66T, P68L; ORF7a: R72K, I112T, F117L; ORF8b: *35R, Y62F; ORF9b: T6I, V8E, D39G, Q71R; nucleocapsid: E104D, T218A, I235M, H335T, Q346N, G414R; spike: F8L, A9P, N12S, T13S, S24T, N29P, Q37T, I46V, T50S, I63F, Y70H, S71V, L72S, I80V, H82P, A91S, N109T, T110K, F115L, I124V, N129E, D131Q, F138L, S139G, T146S, *147K, E148V, N149S, P151A, T157N, K166Q, S167P, L170M, I172L, A173E, D176Q, Y200H, V203I, I206V, G208D, V215A, E221D, K230R, R232Q, F234L, I237L, P246L, K258Q, S260R, M263L, Q311E, D326G, K327E, P335A, E341N, T343K, K344R, D347N, T353S, S372T, I375N, S381N, T386S, L388V, F391G, S392D, V397I, T425S, E431K, S442F, H443F, T446S, L455I, G474C, V475Y, R476Y, T477P, S479N, D482G, N484H, N486T, P488G, E490D, A493P, T494S, Q518K, Q523K, K533T, D540E, S542N, R544K, Q546L, S547P, T555I, F558T, S561A, S592N, E593Q, D605E, T608I, Q632R, A644N, T669V, K672Q, V675I, I687V, S701T, V708I, M709L, A714T, A854Q, A857S, I860L, S861A, A864I, A866S, T921S, N1107S, I1115V, V1198I, V1210I, L1215M" }, "mutations": { "ORF1a": [ "A412S", "Y417H", "R722K", "S902G", "T1070A", "I1076K", "K1185N", "N1189I", "V1481I", "L2007S", "I2107V", "L2149F", "R2168K", "V2207I", "I2430V", "A2588T", "R2718K", "V2762A", "S3810N", "Y3934F", "G4055N", "N4151T", "H4165L", "P4253A", "R4343K", "M4368L", "S4374Q", "T4375S" ], "ORF1b": [ "E53D", "L57I", "M68F", "V81L", "E83D", "V214I", "V216T", "A217T", "C220S", "A253T", "L256Y", "C272N", "I290V", "S602N", "S634T", "N638S", "H730T", "E731D", "D734N", "Y757F", "N760T", "A763S", "A775S", "F1086L", "E1389D", "I1538V", "D1623E", "E1652P", "N1661S", "G1700N", "S1744A", "N1752H", "H1784Y", "S1817T", "S1843A", "E1869D", "H1898S", "T1961V", "Q2017L", "Y2058F", "N2070Q", "A2081T", "I2093L", "I2120V", "S2169P", "T2203Q", "K2206V", "A2209K", "V2213L", "S2222A", "F2230Y", "I2236V", "I2237V", "D2250N", "E2252Q", "D2253E", "T2262I", "Q2310K", "K2315E", "V2566I" ], "ORF3a": [ "L15F", "V47I", "T117S", "F127L", "D182H" ], "ORF3b": [ "S29L", "K41N", "I66T", "P68L" ], "ORF7a": [ "R72K", "I112T", "F117L" ], "ORF8b": [ "*35R", "Y62F" ], "ORF9b": [ "T6I", "V8E", "D39G", "Q71R" ], "nuc": [ "T337C", "T805C", "A844T", "T913C", "T925C", "G1039A", "T1093C", "C1153T", "T1426C", "T1498C", "G1499T", "T1514C", "A1603T", "G1627T", "T1714C", "A1729G", "A1738G", "C1831T", "T1912C", "G2281A", "T2314C", "G2430A", "T2845C", "C2933T", "A2969G", "G3127A", "C3133T", "G3226A", "G3235A", "A3268G", "T3328A", "G3451A", "A3473G", "T3492A", "C3526T", "T3538C", "A3811T", "A3820T", "T3823C", "A3831T", "T3859A", "C3970T", "C3985T", "C4117T", "A4297T", "A4414G", "C4693T", "G4706A", "T4951C", "C5380T", "C5704T", "A5839T", "T6022C", "A6025G", "A6163T", "T6285C", "T6496A", "A6505T", "C6565T", "A6584G", "C6631T", "G6712C", "G6768A", "G6884A", "C6913T", "A7102T", "T7162C", "C7163T", "T7435C", "A7553G", "T7606A", "G7963A", "T8008G", "G8027A", "C8209T", "T8357C", "G8418A", "A8419G", "A8467G", "T8550C", "C8770A", "T8782G", "T8848C", "C8849T", "C9163T", "G9604A", "G9724A", "G9727A", "G9769A", "G9898C", "A9964T", "C10057A", "A10186G", "T10189A", "C10372T", "A10417T", "G10483A", "G10651A", "A10666T", "T10678C", "C10897T", "C11278T", "C11515T", "C11641T", "C11668T", "T11671A", "G11694A", "T11698C", "T11701A", "T11707C", "G11713A", "G11758A", "T11761A", "T11764C", "T11785A", "C11788T", "A11809C", "G11812A", "C11822T", "T11824G", "C11876T", "C11878A", "T11917C", "G11926A", "T11938A", "T11977A", "T11984C", "G11986T", "C11989T", "G11992A", "C12008A", "T12010G", "T12013A", "C12017T", "T12019A", "A12066T", "C12070T", "G12082A", "G12166A", "T12181A", "A12211T", "G12217A", "A12271T", "C12353A", "T12355A", "C12373G", "C12379A", "C12406A", "C12418A", "G12428A", "G12429A", "A12430C", "C12436T", "C12457T", "A12466T", "C12541T", "A12556T", "G12562A", "T12580A", "A12634T", "C12655A", "G12661T", "T12664C", "T12703A", "A12717C", "T12718A", "G12739A", "A12754T", "C12757T", "A12759T", "A12802T", "C12896T", "T12952A", "G12955A", "G12967A", "C13021T", "C13022G", "G13081T", "A13111T", "T13120A", "G13123A", "C13174T", "T13183C", "T13198A", "T13246A", "G13293A", "A13318T", 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"A20217T", "G20229A", "A20280T", "C20289T", "C20293T", "T20295A", "C20326A", "A20341G", "T20367C", "C20370T", "G20376T", "C20427T", "C20440T", "T20442A", "C20454T", "G20472A", "A20496T", "T20511G", "A20514T", "T20571A", "C20758T", "T20760A", "A20859T", "T20862G", "C20976T", "T20985C", "G21015A", "A21069G", "A21090G", "G21094A", "A21162T", "T21186C", "C21288T", "C21459T", "C21517G", "G21518C", "A21527T", "A21528C", "C21531G", "G21564C", "C21575T", "A21578C", "A21579C", "C21602A", "A21603C", "A21629G", "A21641T", "C21652T", "T21664C", "A21680T", "T21701C", "T21704G", "C21705T", "T21708C", "A21731G", "A21733T", "A21738C", "T21739A", "G21764T", "A21819C", "C21822A", "T21823G", "T21836C", "A21856T", "A21863G", "T21874C", "A21878G", "T21880A", "G21884C", "C21886A", "C21901A", "T21907G", "A21908G", "A21929T", "A21931G", "T21932A", "A21936T", "A21939G", "C21944G", "C21963A", "G21988T", "A21989C", "T21992C", "C21994T", "G22000T", "T22001A", "A22007C", "C22011A", "T22012A", "T22015A", "G22019C", "T22021G", "T22051G", "T22091C", "G22100A", "A22109G", "T22111G", "G22116A", "T22118C", "A22120T", "T22123C", "T22137C", "T22153A", "A22156T", "T22165A", "A22182G", "A22187C", "G22188A", "C22195A", "A22202T", "C22230T", "A22265C", "T22273G", "C22276T", "A22280C", "G22282A", "G22285A", "C22303A", "T22369C", "T22372C", "C22420A", "C22424G", "A22470G", "C22471T", "A22472G", "G22474A", "C22496G", "T22498A", "G22514A", "A22516C", "C22521A", "A22524G", "T22529A", "C22530G", "G22532A", "A22550T", "C22558T", "A22567C", "T22573A", "T22579C", "T22607A", "G22615A", "T22617A", "T22622C", "G22624C", "A22633T", "G22635A", "T22645A", "T22648C", "A22649T", "C22655G", "A22660T", "T22664G", "T22665G", "T22667G", "C22668A", "G22682A", "T22732A", "A22744T", "C22753T", "A22766T", "G22784A", "C22818T", "C22820T", "A22821T", "A22829T", "C22856A", "G22913T", "G22916T", "T22917A", "C22919T", "G22920A", "A22922C", "G22929A", "A22938G", "A22943C", "A22950C", "C22955G", "C22956G", "A22957T", "A22963T", "G22970C", "A22973T", "G22978A", "T22981A", "A23020T", "A23032T", "A23038G", "C23041T", "C23045A", "C23060A", "G23062A", "A23086T", "C23089A", "A23091C", "T23098A", "T23105C", "G23107T", "T23110A", "T23113G", "T23117A", "C23118A", "G23124A", "A23130T", "T23132C", "A23134T", "C23157T", "A23158T", "T23165A", "T23166C", "T23174G", "A23176T", "A23179C", "T23267A", "C23268A", "A23269C", "G23270C", "T23308A", "C23316T", "A23323T", "T23365A", "A23388G", "C23399T", "T23401A", "G23423A", "C23424A", "T23461A", "A23479T", "T23482G", "A23498G", "C23499T", "A23507C", "G23516A", "G23518T", "T23524C", "T23542A", "T23551A", "A23552G", "T23594A", "G23615A", "A23618C", "G23620A", "A23626G", "G23633A", "T23677A", "G23779A", "T23860A", "T23920A", "T23938C", "A23962T", "T23995A", "C24019T", "G24053C", "C24054A", "A24061T", "G24062T", "A24071C", "A24074G", "G24075C", "T24082A", "G24083A", "C24084T", "G24089T", "C24119T", "T24121A", "A24208T", "A24254T", "G24283T", "G24409A", "A24628G", "G24649A", "A24670T", "T24694A", "A24813G", "A24836G", "T24973C", "G25085A", "C25096T", "G25121A", "C25136A", "C25147T", "T25159C", "T25195C", "C25313T", "G25409A", "G25480A", "A25495G", "T25571C", "G25573T", "C25620G", "A25648G", "T25649C", "C25651T", "C25777T", "G25814C", "T25888C", "C25894T", "A26578T", "T26788G", "C26815T", "T26845A", "T26848C", "T27097C", "T27265C", "T27274C", "C27396T", "A27492T", "G27596A", "T27702A", "T27716C", "T27730C", "T28076C", "A28158T", "C28293T", "T28299A", "A28392G", "A28488G", "G28578T", "C28584T", "C28587A", "A28617G", "C28689T", "C28701T", "A28918G", "A28941T", "A28971G", "A29031T", "A29037G", "G29040A", "G29070A", "C29076T", "G29094C", "A29196T", "T29199C", "C29202T", "A29223G", "C29269A", "A29270C", "T29271A", "A29274T", "T29280C", "C29302A", "A29304T", "T29505C", "G29506A", "A29692G" ], "nucleocapsid": [ "E104D", "T218A", "I235M", "H335T", "Q346N", "G414R" ], "spike": [ "F8L", "A9P", "N12S", "T13S", "S24T", "N29P", "Q37T", "I46V", "T50S", "I63F", "Y70H", "S71V", "L72S", "I80V", "H82P", "A91S", "N109T", "T110K", "F115L", "I124V", "N129E", "D131Q", "F138L", "S139G", "T146S", "*147K", "E148V", "N149S", "P151A", "T157N", "K166Q", "S167P", "L170M", "I172L", "A173E", "D176Q", "Y200H", "V203I", "I206V", "G208D", "V215A", "E221D", "K230R", "R232Q", "F234L", "I237L", "P246L", "K258Q", "S260R", "M263L", "Q311E", "D326G", "K327E", "P335A", "E341N", "T343K", "K344R", "D347N", "T353S", "S372T", "I375N", "S381N", "T386S", "L388V", "F391G", "S392D", "V397I", "T425S", "E431K", "S442F", "H443F", "T446S", "L455I", "G474C", "V475Y", "R476Y", "T477P", "S479N", "D482G", "N484H", "N486T", "P488G", "E490D", "A493P", "T494S", "Q518K", "Q523K", "K533T", "D540E", "S542N", "R544K", "Q546L", "S547P", "T555I", "F558T", "S561A", "S592N", "E593Q", "D605E", "T608I", "Q632R", "A644N", "T669V", "K672Q", "V675I", "I687V", "S701T", "V708I", "M709L", "A714T", "A854Q", "A857S", "I860L", "S861A", "A864I", "A866S", "T921S", "N1107S", "I1115V", "V1198I", "V1210I", "L1215M" ] } }, "children": [ { "branch_attrs": { "labels": { "aa": "ORF1a: K47L, L53I, V54I, E55D, I71V, I95V, V121I, Y136F, A138I, E155D, E159V, F204L, A211S, T214S, A239V, E246D, T265N, N267T, D294E, Q314P, C316H, D324E, G327S, V337L, L349Q, T350V, A354P, Y369F, V378M, L393I, I396T, I404K, S428A, I431V, Q455T, N470T, T498S, A516F, G519N, Q526P, M585L, D589E, V591T, N593D, N594S, L595I, I601V, S610T, V627I, V639I, R643K, S653T, A656S, V660I, I664L, T666A, C667F, A668T, K669T, I671L, E673D, Q676K, T677K, I694V, K714R, R718K, E725G, E726D, T727S, I739V, E743D, T753S, V757I, D762E, Q768E, N771A, E772Q, A776V, S839N, I850V, E868N, V869I, N870D, F872L, D878E, M903V, F915Y, K916T, H920R, E932Y, D935E, D937Y, C938S, E942Q, F943P, P945Q, S946P, D955S, Q958K, K960L, T967S, P971V, H973Q, E974Q, D983E, D984T, D985E, S986A, Q987E, A991V, E992A, P995Q, P997T, V999I, T1002L, V1003C, N1004D, F1017S, A1021V, E1025S, K1029N, V1034I, Y1042H, V1063I, T1071R, K1076N, V1082L, S1084N, V1100L, S1111V, Q1118H, I1121K, E1135Q, V1137I, H1138Q, R1141K, V1144I, N1150Q, Y1152F, N1159D, D1162E, K1163E, S1166A, K1180T, Q1181K, N1185D, I1186H, A1187F, E1188D, I1189V, P1190V, K1191E, D1192T, E1193K, K1195E, F1197I, I1198T, N1199Q, K1200S, P1201A, V1203S, Q1205K, R1206P, I1208V, A1210P, I1233A, H1240Y, A1244T, T1245S, K1248E, D1249N, I1250V, I1252V, V1266I, K1268T, D1269S, D1271N, A1274T, N1300H, L1310C, N1311V, V1315I, V1321A, C1325S, F1329Y, I1331V, E1339K, Q1341E, A1356T, V1367I, V1375M, I1378V, A1396V, T1406P, S1409T, N1412A, Y1416S, N1418G, S1496A, S1510V, Y1513H, N1517K, L1523M, T1529N, F1530I, N1532S, S1538A, R1543K, N1588A, E1591D, G1592S, A1606S, P1617E, Y1635F, N1710S, Y1711H, K1758R, Q1761T, I1762V, K1768R, P1780S, E1792K, F1799L, C1824V, T1831S, S1833T, I1840V, V1857I, T1858V, N1894T, A1900S, S1901N, L1921M, T1922S, V1934I, A1974T, T1975I, Y1980F, I1987L, S2001I, E2006Q, D2014E, N2015T, L2021T, P2023L, S2025T, N2031T, L2039V, N2042D, I2052V, N2058Q, T2070E, S2080T, R2092V, V2093M, A2100K, A2116V, N2117T, V2127T, T2129V, T2130A, T2131A, N2132S, I2133G, T2135A, V2141I, T2143V, F2149V, F2150L, L2156F, K2161R, N2205T, I2208V, T2224S, G2242S, E2245D, A2256T, T2257A, L2272M, T2277A, S2280A, I2286V, L2300I, V2301I, F2305C, S2329G, V2375I, I2467V, T2472A, I2478L, L2513I, E2527D, K2532R, S2533A, E2584D, V2590I, A2595T, E2624D, L2634I, A2687S, V2692I, I2742F, N2744T, L2747F, Q2749Y, I2751L, V2753A, F2757C, L2758V, F2759V, V2760I, A2762C, I2763V, L2766F, M2773L, S2774T, N2777G, S2780A, S2781D, D2790E, G2791D, A2798S, T2800N, T2802N, A2809V, D2810G, A2827T, L2830I, E2838D, L2851F, I2854L, N2855S, S2903A, A2921P, R2968K, A3000S, I3029L, L3033F, F3063L, I3085F, I3103V, F3130C, K3139R, V3147T, D3173E, V3174T, S3286A, Q3314H, T3333A, T3439V, V3442I, F3463Y, Y3477F, L3526I, V3549I, I3553V, M3593L, F3654Y, V3660I, V3666I, V3667I, F3746L, I3819V, D4062E, N4064S, N4092T, L4099I, T4141N, D4142E, A4254S, K4258R, F4319Y, D4321E; ORF1b: V62I, T76A, D144T, M248L, I257V, D275N, L352I, H590N, A707G, V711I, N902S, P976T, S997A, H1087Y, V1116T, K1385R, A1392Q, A1428T, S1446A, H1550Y, R1605K, I1611V, P1652S, N1654A, T1658S, V1685I, S1742C, V1818I, V1870T, T1902K, V2061I, A2073T, I2078V, P2162S, S2165T, V2172I, S2198N, T2376A, S2379A, E2420D, D2429E, S2430A, N2535H, K2538R, R2684K, I2687V; ORF3a: T12S, Q17P, E19K, K21E, V29I, T40S, L71F, V80A, P104Q, F120A, V121C, V163I, T176P, N177S, S180T, E181D, V202T, S205G, D210E, Y211C, V228T, N234S, K235R, E241D, E260D; ORF3b: T4I, V8A, V13A, T20I, V22A, Q35L, I37V, P38L, F39L, N41T, L50R, Y62H, I64M, S67L, L68H, I70N, T71A, Q76L, L77H, *79L, A80V, T82I, M87I, L89P, S92F, I94V, K95E, L97W, S99N, N101T, S103F, V110A, L115*, N120I, Q121L, F122S, N125S; ORF6: I17V, V24I; ORF7a: F6L, I10V, L12F, L17R, L31I, T57A, F59S, T61Q, V71T, Y75F, V105I, I108L; ORF7b: L4I, S5T, I26M, S31A, E33T, H37D, N38D, T40C, N43K, A44V; ORF8a: F6L, T14H, A15T, A23Q, Q24F, H26N, Q27S; ORF8b: T5I, G25S, W26R, *28K, I29N, H31Y, S32*, *38Q, K41M, P43L, F64C, R65*, G66C; ORF9b: Q21R, N29T, V32E, H33Q, D34G, V38E, K41R, V42D, A58V, A76V, V77P; membrane_protein: G2A, S211N; nucleocapsid: E32D, S80T, I95V, A153N, T167A, M211I, Q230A, Q240S, G244S, D298E, N346S, A377T, T380S, A382P; spike: M1L, F5L, L6F, L7V, V18M, F22L, Q27G, L28I, A31G, V51I, F58L, Y69F, H70N, V71I, S72*, T73I, T74I, N75K, F107L, T109A, K110R, N134T, S146L, V148M, S150L, V164I, I190V, N204D, T211R, S214A, P259Q, K265S, E268Q, A279S, F293L, E311I, T332S, R333K, I389V, R390K, N426V, N427K, L428Q, K431L, I432T, N437G, F439L, F442L, A470V, N479E, T480R, V487T, D490N, S494F, A506G, K518T, N522D, E540T, N542K, K544Q, I608M, D613E, T624A, I637V, I652V, T662S, A663M, I665S, G670N, Q672R, A690S, F986L, S1052A, V1086I" }, "mutations": { "ORF1a": [ "K47L", "L53I", "V54I", "E55D", "I71V", "I95V", "V121I", "Y136F", "A138I", "E155D", "E159V", "F204L", "A211S", "T214S", "A239V", "E246D", "T265N", "N267T", "D294E", "Q314P", "C316H", "D324E", "G327S", "V337L", "L349Q", "T350V", "A354P", "Y369F", "V378M", "L393I", "I396T", "I404K", "S428A", "I431V", "Q455T", "N470T", "T498S", "A516F", "G519N", "Q526P", "M585L", "D589E", "V591T", "N593D", "N594S", "L595I", "I601V", "S610T", "V627I", "V639I", "R643K", "S653T", "A656S", "V660I", "I664L", "T666A", "C667F", "A668T", "K669T", "I671L", "E673D", "Q676K", "T677K", "I694V", "K714R", "R718K", "E725G", "E726D", "T727S", "I739V", "E743D", "T753S", "V757I", "D762E", "Q768E", "N771A", "E772Q", "A776V", "S839N", "I850V", "E868N", "V869I", "N870D", "F872L", "D878E", "M903V", "F915Y", "K916T", "H920R", "E932Y", "D935E", "D937Y", "C938S", "E942Q", "F943P", "P945Q", "S946P", "D955S", "Q958K", "K960L", "T967S", "P971V", "H973Q", "E974Q", "D983E", "D984T", "D985E", "S986A", "Q987E", "A991V", "E992A", "P995Q", "P997T", "V999I", "T1002L", "V1003C", "N1004D", "F1017S", "A1021V", "E1025S", "K1029N", "V1034I", "Y1042H", "V1063I", "T1071R", "K1076N", "V1082L", "S1084N", "V1100L", "S1111V", "Q1118H", "I1121K", "E1135Q", "V1137I", "H1138Q", "R1141K", "V1144I", "N1150Q", "Y1152F", "N1159D", "D1162E", "K1163E", "S1166A", "K1180T", "Q1181K", "N1185D", "I1186H", "A1187F", "E1188D", "I1189V", "P1190V", "K1191E", "D1192T", "E1193K", "K1195E", "F1197I", "I1198T", "N1199Q", "K1200S", "P1201A", "V1203S", "Q1205K", "R1206P", "I1208V", "A1210P", "I1233A", "H1240Y", "A1244T", "T1245S", "K1248E", "D1249N", "I1250V", "I1252V", "V1266I", "K1268T", "D1269S", "D1271N", "A1274T", "N1300H", "L1310C", "N1311V", "V1315I", "V1321A", "C1325S", "F1329Y", "I1331V", "E1339K", "Q1341E", "A1356T", "V1367I", "V1375M", "I1378V", "A1396V", "T1406P", "S1409T", "N1412A", "Y1416S", "N1418G", "S1496A", "S1510V", "Y1513H", "N1517K", "L1523M", "T1529N", "F1530I", "N1532S", "S1538A", "R1543K", "N1588A", "E1591D", "G1592S", "A1606S", "P1617E", "Y1635F", "N1710S", "Y1711H", "K1758R", "Q1761T", "I1762V", "K1768R", "P1780S", "E1792K", "F1799L", "C1824V", "T1831S", "S1833T", "I1840V", "V1857I", "T1858V", "N1894T", "A1900S", "S1901N", "L1921M", "T1922S", "V1934I", "A1974T", "T1975I", "Y1980F", "I1987L", "S2001I", "E2006Q", "D2014E", "N2015T", "L2021T", "P2023L", "S2025T", "N2031T", "L2039V", "N2042D", "I2052V", "N2058Q", "T2070E", "S2080T", "R2092V", "V2093M", "A2100K", "A2116V", "N2117T", "V2127T", "T2129V", "T2130A", "T2131A", "N2132S", "I2133G", "T2135A", "V2141I", "T2143V", "F2149V", "F2150L", "L2156F", "K2161R", "N2205T", "I2208V", "T2224S", "G2242S", "E2245D", "A2256T", "T2257A", "L2272M", "T2277A", "S2280A", "I2286V", "L2300I", "V2301I", "F2305C", "S2329G", "V2375I", "I2467V", "T2472A", "I2478L", "L2513I", "E2527D", "K2532R", "S2533A", "E2584D", "V2590I", "A2595T", "E2624D", "L2634I", "A2687S", "V2692I", "I2742F", "N2744T", "L2747F", "Q2749Y", "I2751L", "V2753A", "F2757C", "L2758V", "F2759V", "V2760I", "A2762C", "I2763V", "L2766F", "M2773L", "S2774T", "N2777G", "S2780A", "S2781D", "D2790E", "G2791D", "A2798S", "T2800N", "T2802N", "A2809V", "D2810G", "A2827T", "L2830I", "E2838D", "L2851F", "I2854L", "N2855S", "S2903A", "A2921P", "R2968K", "A3000S", "I3029L", "L3033F", "F3063L", "I3085F", "I3103V", "F3130C", "K3139R", "V3147T", "D3173E", "V3174T", "S3286A", "Q3314H", "T3333A", "T3439V", "V3442I", "F3463Y", "Y3477F", "L3526I", "V3549I", "I3553V", "M3593L", "F3654Y", "V3660I", "V3666I", "V3667I", "F3746L", "I3819V", "D4062E", "N4064S", "N4092T", "L4099I", "T4141N", "D4142E", "A4254S", "K4258R", "F4319Y", "D4321E" ], "ORF1b": [ "V62I", "T76A", "D144T", "M248L", "I257V", "D275N", "L352I", "H590N", "A707G", "V711I", "N902S", "P976T", "S997A", "H1087Y", "V1116T", "K1385R", "A1392Q", "A1428T", "S1446A", "H1550Y", "R1605K", "I1611V", "P1652S", "N1654A", "T1658S", "V1685I", "S1742C", "V1818I", "V1870T", "T1902K", "V2061I", "A2073T", "I2078V", "P2162S", "S2165T", "V2172I", "S2198N", "T2376A", "S2379A", "E2420D", "D2429E", "S2430A", "N2535H", "K2538R", "R2684K", "I2687V" ], "ORF3a": [ "T12S", "Q17P", "E19K", "K21E", "V29I", "T40S", "L71F", "V80A", "P104Q", "F120A", "V121C", "V163I", "T176P", "N177S", "S180T", "E181D", "V202T", "S205G", "D210E", "Y211C", "V228T", "N234S", 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"EPI_ISL_410544", "author": { "author": "Jiang et al", "value": "Jiang et al" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.18019083, "host": { "value": "Pangolin" }, "virus_type": { "value": "SARS-like CoV" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: Y143F, G166S, F204L, S445G, P537A, H557N, M608L, A711T, N771S, N860T, S918A, D935G, H973P, Q988H, A991D, V993M, E1001Q, N1005S, T1007S, F1017Y, I1121V, E1135D, E1145D, N1185K, D1192E, N1199S, I1212V, K1248N, I1267V, K1268Q, D1269E, D1271V, P1337S, Y1416D, D1683E, V1765T, E1790Q, F1799I, A1882S, E2006K, V2061L, K2161R, V2831I, I2973V, L3033V, S4152T; ORF1b: E31D, G54D, T1658S, V1755I, V1818I, D1871E, A1920S, A2073V, E2142D, V2147I, T2154S, S2165N, V2166I, D2311E; ORF3a: T40S, N177S; ORF3b: H19L, I37V, P38L, Q40L, K45R, T71I, L89P; ORF6: P43S; ORF7a: I74V; ORF8b: H6R, W37R, H40Y; ORF9b: V32E, D63N; membrane_protein: S1A, G2D, D3S; nucleocapsid: R66K, E129D; spike: F5L, L6V, F22L, F58L, Y69F, T73G, F107L, T109S, N144I, S146W, T211P, L515K, H661Q, A663Q, S664T, I665N, L666S, A690S, I729T, S1052A, E1066D" }, "mutations": { "ORF1a": [ "Y143F", "G166S", "F204L", "S445G", "P537A", "H557N", "M608L", "A711T", "N771S", "N860T", "S918A", "D935G", "H973P", "Q988H", "A991D", "V993M", "E1001Q", "N1005S", "T1007S", "F1017Y", "I1121V", "E1135D", "E1145D", "N1185K", "D1192E", "N1199S", "I1212V", "K1248N", "I1267V", "K1268Q", "D1269E", "D1271V", "P1337S", "Y1416D", "D1683E", "V1765T", "E1790Q", "F1799I", "A1882S", "E2006K", "V2061L", "K2161R", "V2831I", "I2973V", "L3033V", "S4152T" ], "ORF1b": [ "E31D", "G54D", "T1658S", "V1755I", "V1818I", "D1871E", "A1920S", "A2073V", "E2142D", "V2147I", "T2154S", "S2165N", "V2166I", "D2311E" ], "ORF3a": [ "T40S", "N177S" ], "ORF3b": [ "H19L", "I37V", "P38L", "Q40L", "K45R", "T71I", "L89P" ], "ORF6": [ "P43S" ], "ORF7a": [ "I74V" ], "ORF8b": [ "H6R", "W37R", "H40Y" ], "ORF9b": [ "V32E", "D63N" ], "membrane_protein": [ "S1A", "G2D", "D3S" ], "nuc": 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"Y436F", "F442L", "S446A", "T465K", "A470T", "H479Y", "T480R", "H484Y", "Y491H", "T590A" ] } }, "name": "bat/Yunnan/RaTG13/2013", "node_attrs": { "accession": "EPI_ISL_402131", "author": { "author": "Zhu et al", "value": "Zhu et al" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.17877437999999998, "host": { "value": "Bat" }, "virus_type": { "value": "SARS-like CoV" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: T114I, T498A, V591A, T970A, N1248S, I1519T, G2060S, T2255I, V3122I; ORF1b: D189N, K1736R, N2165T; ORF3b: V8A; spike: S36F" }, "mutations": { "ORF1a": [ "T114I", "T498A", "V591A", "T970A", "N1248S", "I1519T", "G2060S", "T2255I", "V3122I" ], "ORF1b": [ "D189N", "K1736R", "N2165T" ], "ORF3b": [ "V8A" ], "nuc": [ "T487G", "C606T", "A943G", "T1186G", "T1288C", "A1306G", "C1343T", "C1363T", "T1387C", "T1480C", "C1516T", "T1594C", "T1627C", "A1757G", "C1789T", "G1816A", "T2037C", "T2146C", "C2170T", "C2314T", "A2893G", "A3173G", "T3421C", "C3478T", "T3517C", "T3553C", "T3937C", "A4008G", "T4468C", "A4489G", "T4723C", "T4821C", "C4876T", "T4891G", "T5323C", "T5476A", "T5875C", "T5953A", "T5962C", "C5980T", "T6217C", "T6268G", "G6443A", "T6469C", "T6913C", "C7029T", "T7093C", "T7234C", "T7402C", "T7666C", "T7774C", "T7775C", "T7876C", "T8251C", "C8357T", "G8410A", "C8554T", "T9004C", "T9043C", "T9157C", "T9217C", "T9250C", "C9289T", "T9337A", "T9355A", "G9629A", "T9734C", "A9772G", "A9787G", "T9790A", "C9791T", "T9817C", "T9916C", "T10045A", "A10213G", "T10417A", "C10528T", "A10549G", "T10939C", "T11083C", "C11101T", "C11113T", "A12253G", "T12502A", "T12746C", "T12940C", "C12995T", "A13132G", "G13963A", "A14121T", "A15720G", "T17334C", "A17385T", "T17664C", "T17865C", "T18279C", "C18300T", "A18393G", "T18414C", "G18516A", "A18546G", "A18605G", "A18804G", "C18858T", "C19521T", "A19677G", "A19892C", "T19893G", "T20022C", "T20109C", "C20116T", "A20139G", "C20230T", "C20385T", "A20475C", "A20559C", "T20565A", "T20754C", "T20763A", "T20829A", "A20868G", "A20871G", "C21075T", "G21108A", "C21600T", "A21709T", "C22075T", "T22378A", "C22549T", "A22588G", "C22648T", "T22750C", "A22825G", "A22924T", "C22925T", "A23110T", "C23359T", "C23503T", "T23512C", "T23584C", "G23683A", "C23719T", "T23731C", "C23839T", "T23983C", "T24259C", "T24592C", "T24721C", "C24724T", "T24781C", "C24805G", "A24868T", "T24946C", "C24970A", "C25129G", "A25441G", "A25582T", "T25714C", "T26861C", "T26890C", "T28048C", "C28596T", "T28599C", "C28857T", "C29064T", "A29136G" ], "spike": [ "S36F" ] } }, "children": [ { "branch_attrs": { "labels": { "aa": "ORF1a: D335N, T350I, Q501R, N557S, A591T, D629E, V757I, E767A, L865F, D937E, Q958R, P961S, D985A, A1027V, P1201S, K1319R, M1369I, K1381N, D1457E, I1481T, S1486F, H1522Y, E1526K, R1543K, K1740T, E1778D, S1882A, D2003G, K2006R, T2070I, T2114I, L2156F, R2161K, S2165F, T2277I, S2477F, A2506V, L2586I, I3029V, P3348S, S3363C, A3602V, V3630I, K3655R, N3810S; ORF1b: I192V, E1514V, L1551I, A1995S, R2009K, K2538Q, L2672I, I2679V, V2686I, S2688P; ORF3a: T12I, V77I, V80T, V201I, V202A, N234S; ORF3b: I21T, K51R, T59I, Y62H, L77P, I94V, L97*; ORF6: V9F, S43P; ORF7a: T39I, V71I, V93I, V105I, T121I; ORF7b: H37C, N38S, E39D, T40A, N43K, A44V; ORF8a: F3L, V5I, F6G, T14L, A15V, L16Y, C17S, L19T, Q20K, S21V, A23V, Q24*, Y29H, V31L, D32E, D33N; ORF8b: *2Y, M4K, R6L, V13Y, G14D, A15T, R16K, K17G, S18N, A19T, P20*, L21W, *24L, W26K, F27V, *28L, I29L, T30F, S32Q, H34A, R35Q, R37G, K41N, F42Y, P43L, V44A, N47S, Q49I, E50D, K52T, L53G, S55A, V57I, V58A, R59C, C60W, S61Y, F62L, L63P; ORF9b: P3T, I6V, H10R, G39V, Q78E; membrane_protein: A1V, H154Y; nucleocapsid: P6H, N9S, P81R, T206I; spike: V3I, F4L, V6L, L7I, L8G, P9Y, L10T, V11A, S12A, S13T, H14T, V18M, N21G, L22P, T24I, R25E, T26N, Q27K, A31E, Y32N, T33V, N34S, F36L, T37M, K45D, V46I, F47Y, S50L, V51M, L52F, H53F, Q56L, D57Y, P61G, F62L, F63I, N65T, V66L, F69Y, H70N, S72F, N75K, P79L, L81M, P82E, N84G, V87I, A90S, S91T, T92V, E93D, I97A, I98V, S109N, K110T, L114A, I116L, V117I, A120G, T121S, N122L, V124T, K126Q, E129Y, N134A, D135N, F137A, Y141*, Y142*, H143R, I144V, V148A, S150A, S154I, A156S, N157H, F161Y, E162S, Y163E, S165L, Q166S, P167H, F168I, L169S, M170L, L172F, E173T, G174E, K175D, Q176T, N178S, N181R, I190N, Y193F, F194L, K195H, H200Q, T201V, P202L, V206M, R207Y, L209I, P211S, G212T, S214K, A215P, E217I, V220W, D221K, I224L, I226L, R230N, Q232K, T233V, L234V, A236T, L237F, H238R, R243N, Y245Q, L246P, T247L, P248H, Y256S, Q258K, P259L, R260T, F262I, L263M, K265S, Y266F, N267D, E268V, T273D, D274K, A279S, L280S, T286L, T294N, E296S, Q301P, V307I, Q308L, T310S, E311T, S312E, I313V, L322F, G326D, E327K, A335P, S336N, N341Q, K343T, R344K, N347D, V349I, S353T, T372S, N375I, N381S, S386T, V388L, G391F, D392S, Q401E, K404V, I421L, S425T, N426A, N427Q, L428Q, A430I, K431G, N437S, L439F, F442S, F443H, K445A, S446V, N447K, I455L, T457S, L472E, C474G, Y475V, Y476R, P477T, H479S, G482D, H484N, T486N, D487V, G488P, V489L, G490D, P493A, Y494T, K515L, N518Q, K523R, T533R, E540D, N542D, K544R, L546Q, P547S, I555S, T558F, A561S, E569Q, T574S, N589Q, N592S, Q593K, E605D, V608T, I610L, H611G, A612L, L615I, T616S, P617A, T618A, S623A, T624I, S626N, N627D, R632Q, I637V, V642T, N644I, I656V, R667A, S668R, A670G, S671T, Q672N, T678A, L681I, N685S, V687I, T701S, S703Q, I708V, M713V, T714S, T729Q, S732N, N733K, T743A, T750S, I752V, Q761E, E762A, T773A, P775V, F779L, I787L, S792T, K796Q, N806D, A811S, Q854A, L860V, A861S, I864A, S866A, A872I, I878V, H1065Y" }, "mutations": { "ORF1a": [ "D335N", "T350I", "Q501R", "N557S", "A591T", "D629E", "V757I", "E767A", "L865F", "D937E", "Q958R", "P961S", "D985A", "A1027V", "P1201S", "K1319R", "M1369I", "K1381N", "D1457E", "I1481T", "S1486F", "H1522Y", "E1526K", "R1543K", "K1740T", "E1778D", "S1882A", "D2003G", "K2006R", "T2070I", "T2114I", "L2156F", "R2161K", "S2165F", "T2277I", "S2477F", "A2506V", "L2586I", "I3029V", "P3348S", "S3363C", "A3602V", "V3630I", "K3655R", "N3810S" ], "ORF1b": [ "I192V", "E1514V", "L1551I", "A1995S", "R2009K", "K2538Q", "L2672I", "I2679V", "V2686I", "S2688P" ], "ORF3a": [ "T12I", "V77I", "V80T", "V201I", "V202A", "N234S" ], "ORF3b": [ "I21T", "K51R", "T59I", "Y62H", "L77P", "I94V", "L97*" ], "ORF6": [ "V9F", "S43P" ], "ORF7a": [ "T39I", "V71I", "V93I", "V105I", "T121I" ], "ORF7b": [ "H37C", "N38S", "E39D", "T40A", "N43K", "A44V" ], "ORF8a": [ "F3L", "V5I", "F6G", "T14L", "A15V", "L16Y", "C17S", "L19T", "Q20K", "S21V", "A23V", "Q24*", "Y29H", "V31L", "D32E", "D33N" ], "ORF8b": [ "*2Y", "M4K", "R6L", "V13Y", "G14D", "A15T", "R16K", "K17G", "S18N", "A19T", "P20*", "L21W", "*24L", "W26K", "F27V", "*28L", "I29L", "T30F", "S32Q", "H34A", "R35Q", "R37G", "K41N", "F42Y", "P43L", "V44A", "N47S", "Q49I", "E50D", "K52T", "L53G", "S55A", "V57I", "V58A", "R59C", "C60W", "S61Y", "F62L", "L63P" ], "ORF9b": [ "P3T", "I6V", "H10R", "G39V", "Q78E" ], "membrane_protein": [ "A1V", "H154Y" ], "nuc": [ "C35T", "C421T", "T517C", 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N1029S, I1041T, D1067E, K1070R, K1090E, I1106V, E1120D, I1121V, V1142M, T1149A, H1150Q, N1159S, V1164I, V1165I, R1175K, T1178S, K1180N, Q1181K, Q1184E, T1187L, D1189E, V1192A, K1195Q, K1199E, E1213D, M1262I, V1276I, T1279A, E1287D, D1299A, I1343V, M1369L, I1387V, A1438T, V1481I, Q1559H, I1663V, K1755E, D1769N, T1797A, I1825V, T1853A, L1897M, A1954T, V1968L, A1974T, T1984I, E2003G, A2006V, K2022T, P2023T, I2034V, D2058E, N2079E, I2104A, A2126T, I2128V, T2129I, V2134I, R2136K, N2143S, F2150I, R2168K, A2190V, I2215T, I2221T, L2230C, N2233S, N2241D, L2248I, E2260Q, I2297F, F2305L, T2424A, S2465A, A2613T, I2689V, V2763F, I2766V, T2772S, D2825N, S2827N, I2854L, A2886S, Y2945H, I2973V, V3084I, S3223A, E3295D, I3598V, A3703S, F3745L, A3946S, P4097S, S4152A; ORF1b: V81I, D146N, I162V, R240K, I257V, T284I, F1086L, H1087Y, F1398Y, V1515I, N1654S, K1699R, G1756S, V1818I, K1863R, S1881I, N1962H, R2049K, N2070S, V2089I, R2141K, H2146Y, A2209I, S2359A, D2386N, V2691I; ORF3a: R6S, T12A, K16N, G18A, 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Virol. 84 (6), 2808-2819 (2010)", "title": "Ecoepidemiology and complete genome comparison of different strains of severe acute respiratory syndrome-related Rhinolophus bat coronavirus in China reveal bats as a reservoir for acute, self-limiting infection that allows recombination events", "value": "Lau et al A" }, "clade_membership": { "value": "unassigned" }, "div": 0.11409760999999999, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/GQ153542", "virus_type": { "value": "SARS-like CoV" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: V378I, E441D, I473V, E489D, V596I, M616L, K625R, R643K, T668S, I677S, F679I, A702S, I770V, I774T, P893N, P971V, A991V, I998T, K1031N, N1063K, R1111A, I1121T, E1145Q, L1153I, L1166M, V1194E, K1199Q, T1279S, E1339A, L1433F, A1461T, T1515L, G1516E, I1615L, K1740T, K1755N, K1925T, T1933S, N1976T, Y1980F, K2022Q, I2038V, L2099I, V2134A, C2137L, C2191G, V2207A, L2234F, V2236A, V2370I, V2407M, T2472A, E2527D, M2611V, I2640L, L2750M, V2753A, V2756L, I2767V, F3130C, S3135N, K3139R, Y3374H, A3592T, F3745L; ORF1b: S602T, F1086L, N2070A, V2147M; ORF3a: T12S, K16Q, V77I, K177T; ORF3b: M33T, S37R; ORF6: V24I; ORF7a: S59T; ORF8a: I31L; ORF8b: *2Y, H40Y, A50T; ORF9b: V32G, H33Q, N37S, V69A, K78Q; membrane_protein: S210A; nucleocapsid: K81T, K410N; spike: S24N, I33F, F107L, Y141S, T199A, N204D, Q311K, N484Y, V489I, Q518*, E569Q, L729Q, L904Q, S911K, G914S, K915Q, D918E, S922T, A924S, S925T, S1037A, V1212A" }, "mutations": { "ORF1a": [ "V378I", "E441D", "I473V", "E489D", "V596I", "M616L", "K625R", "R643K", "T668S", "I677S", "F679I", "A702S", "I770V", "I774T", "P893N", "P971V", "A991V", "I998T", "K1031N", "N1063K", "R1111A", "I1121T", "E1145Q", "L1153I", "L1166M", "V1194E", "K1199Q", "T1279S", "E1339A", "L1433F", "A1461T", "T1515L", "G1516E", "I1615L", "K1740T", "K1755N", "K1925T", "T1933S", "N1976T", "Y1980F", "K2022Q", "I2038V", "L2099I", "V2134A", "C2137L", "C2191G", "V2207A", "L2234F", "V2236A", "V2370I", "V2407M", 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V1198T, M1252V, K1257R, T1268N, E1316D, T1710A, I1762V, T1912I, H2497Q, V2743I, V2798L, S2813T, I3670V; ORF1b: V1685I, I2365V, T2488I, D2666E; ORF6: I31V, K48N; ORF7b: N2S, L34F, I37S, N42P; ORF8a: L7F, S12I, C15G, S18T, L30I; ORF8b: Y2F, L3*, T5I, H6P, T27Q, S30T, N31G, L33V, D35E, V36A, P43T; spike: L2F, I3F, V5I, F6L, V8F, K12*, G18A, I22F, R37K, D63N, F72L, L107M, T110N, Y138F, N144K, Q147H, Q148H, N149S, L205I, P206T, A211V, A236T, T273A, T310S, V397I, H443L, N486T, V520I, T624A, I665L, S668N, T750S, Y1092F" }, "mutations": { "ORF1a": [ "N48S", "L53I", "L77Q", "S78G", "N80G", "V86C", "I95V", "N120T", "A181V", "F204L", "S351C", "V366L", "N455H", "S498T", "K518Q", "R527K", "G542S", "R564K", "V585T", "T609V", "L617V", "T619S", "V621A", "A633S", "K634R", "A637D", "V639I", "T654R", "A667T", "V682I", "Q692Y", "I695V", "A698T", "V708I", "E738D", "A746V", "L832V", "T870S", "A879S", "K916N", "A943T", "E944D", "A985T", "T1076R", "K1090N", "Q1138D", "K1158Q", "N1159K", "R1175T", "T1187I", "P1190S", "K1191N", "E1193K", "K1195E", "V1197T", "V1198T", "M1252V", "K1257R", "T1268N", "E1316D", "T1710A", "I1762V", "T1912I", "H2497Q", "V2743I", "V2798L", "S2813T", "I3670V" ], "ORF1b": [ "V1685I", "I2365V", "T2488I", "D2666E" ], "ORF6": [ "I31V", "K48N" ], "ORF7b": [ "N2S", "L34F", "I37S", "N42P" ], "ORF8a": [ "L7F", "S12I", "C15G", "S18T", "L30I" ], "ORF8b": [ "Y2F", "L3*", "T5I", "H6P", "T27Q", "S30T", "N31G", "L33V", "D35E", "V36A", "P43T" ], "nuc": [ "G349A", "A408G", "T422A", "T490C", "T495A", "A496G", "A497G", "C502T", "A503G", "A504G", "C508T", "G521T", "T522G", "G529A", "A535T", "A548G", "T583A", "A624C", "C643T", "G757A", "T772C", "C775T", "T805A", "C807T", "G850C", "T856C", "T874C", "T875C", "C958T", "C988T", "C1060T", "T1189C", "G1198A", "C1243T", "A1316T", "G1361C", "A1363T", "C1381T", "C1390T", "A1486T", "C1489G", "T1585A", "G1609A", "A1628C", "C1645T", "C1687T", "G1696A", "A1717T", "T1744C", "T1750C", "T1757A", "T1759C", "G1777A", "C1783T", "T1786A", "C1813T", 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"Y1092F" ] } }, "children": [ { "branch_attrs": { "labels": { "aa": "ORF1a: V8I, E256D, N470T, A486V, K513R, S546A, K822R, D934E, E937G, T970A, E994Q, P999L, P1002S, T1033M, T1121I, V1298I, K1319R, F1329L, I1367V, Y1492F, T1574I, V1588A, T1740M, I2034V, V2061I, I2107V, I2128T, D2189E, L2227F, I2297F, I2323V, Y2414H, V2565I, L2749F, L2756V, H2776Y, R3345H, H3374Y, L3593F, T3752N, V4158I, V4349I, P4366S, A4371E; ORF1b: T284I, A1190V, K1385R, S1446A, F1657V, P1851S, S2052C, A2070T, M2147V, V2178A, L2672I, V2691I; ORF3a: R15A, E21D, V48I, L52F, S60T, V62I, H66N, I77F, V80I, I108L, I114F, I117C, V118I, F120A, F123I, N153C, I169L, G172S, T176N, T177V, V210I, T220S, P240A; ORF3b: P3L, L11P, I13V, H19L, Q31P, A34E, Q36M, R37C, K41R, L46*, R51K, I52T, L57*, A65V, P68L, F70S, L74S, *79C, S95N, I99M, M123T; ORF6: R23K, D61E; ORF7a: I10V, A11V, A13T, I111T, K120N, T121S; ORF8b: Y64H; ORF9b: Q5K, T6I, D29N; envelope: N66S; membrane_protein: E3D, N4Y, S8T, R14Q, V22L, A29P, Y46H; nucleocapsid: P8Q, T25A, G32E, Q268A, L353M; spike: F2T, F3C, L7S, V11F, *12C, A13V, H14S, D15G, E17D, A18T, G20E, I21T, N23D, N24D, R25V, P28Q, K29N, N43P, F47Y, L52H, T55V, Y58L, T67L, Q68D, Y69S, F70C, S71P, L72S, N73T, L81I, H82P, G84K, I102V, D108N, N110K, T111S, A114V, V117M, H122N, I123V, I124V, V127A, N131Q, F132L, K134D, E135N, M137F, T139A, S141I, G145D, T146P, H147L, H148R, S150R, W151*, V152I, Y153F, Q154E, S155N, Y161F, D162E, R163Y, E165S, K166D, Q169L, L170M, T172V, A173G, P174E, T176P, D181H, V186I, S190K, S195N, V196I, H198S, A199G, Y200F, T201Q, P202N, V203I, I205V, T206A, R207N, V211S, V215L, I219L, F224L, I226L, S230N, V234L, M235L, M237A, S244I, Q245P, T246N, T247I, S248G, S249P, A250V, Y253F, N256Y, H259P, F266Y, N267D, E268Y, A273V, N281H, T289S, I290V, N292S, N294E, V295I, D326G, K327E, R333T, T343K, K344R, D347N, T353S, P371A, S372I, I375N, T380S, S381N, T386S, L388V, I389V, R390K, F391G, S392D, E393D, E401Q, T417M, I421L, A431T, K432S, H433S, D434G, G436F, Y439K, K445H, T446G, K449R, L455I, S462P, D464G, L472F, G474C, V475Y, R476W, T477P, S479N, T480D, D482G, P485T, V487N, P488G, E490G, A493P, T494Y, *518D, K521T, K533T, D540P, S542L, S547P, T555F, Q566K, Q569E, I570V, A590I, R611H, V621I, G670D, V704I, M770I, I1096L, G1153R" }, "mutations": { "ORF1a": [ "V8I", "E256D", "N470T", "A486V", "K513R", "S546A", "K822R", "D934E", "E937G", "T970A", "E994Q", "P999L", "P1002S", "T1033M", "T1121I", "V1298I", "K1319R", "F1329L", "I1367V", "Y1492F", "T1574I", "V1588A", "T1740M", "I2034V", "V2061I", "I2107V", "I2128T", "D2189E", "L2227F", "I2297F", "I2323V", "Y2414H", "V2565I", "L2749F", "L2756V", "H2776Y", "R3345H", "H3374Y", "L3593F", "T3752N", "V4158I", "V4349I", "P4366S", "A4371E" ], "ORF1b": [ "T284I", "A1190V", "K1385R", "S1446A", "F1657V", "P1851S", "S2052C", "A2070T", "M2147V", "V2178A", "L2672I", "V2691I" ], "ORF3a": [ "R15A", "E21D", "V48I", "L52F", "S60T", "V62I", "H66N", "I77F", "V80I", "I108L", "I114F", "I117C", "V118I", "F120A", "F123I", "N153C", "I169L", "G172S", "T176N", "T177V", "V210I", "T220S", "P240A" ], "ORF3b": [ "P3L", "L11P", "I13V", "H19L", "Q31P", "A34E", "Q36M", "R37C", "K41R", "L46*", "R51K", "I52T", "L57*", "A65V", "P68L", "F70S", "L74S", "*79C", "S95N", "I99M", "M123T" ], "ORF6": [ "R23K", "D61E" ], "ORF7a": [ "I10V", "A11V", "A13T", "I111T", "K120N", "T121S" ], "ORF8b": [ "Y64H" ], "ORF9b": [ "Q5K", "T6I", "D29N" ], "envelope": [ "N66S" ], "membrane_protein": [ "E3D", "N4Y", "S8T", "R14Q", "V22L", "A29P", "Y46H" ], "nuc": [ "T179C", "A196G", "T240C", "T286A", "G287A", "T328C", "T403G", "A445C", "C493T", "T550G", "C575T", "C601T", "C826T", "C835T", "A898G", "A1003G", "C1009T", "A1033T", "T1201C", "C1213T", "T1223C", "T1426C", "C1429T", "T1483C", "G1522A", "C1552A", "C1588T", "T1601C", "G1618A", "A1674C", "T1711C", "C1722T", "A1803G", "A1807C", "T1885C", "T1901G", "T1972C", "T1975C", "A1990G", "G2104A", "T2113C", "C2212T", "A2233G", "C2323T", "C2338T", "T2518A", "T2575C", "T2590C", "G2683A", "A2730G", "T2929C", "T3067A", 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"A29427G", "T29682C" ], "nucleocapsid": [ "P8Q", "T25A", "G32E", "Q268A", "L353M" ], "spike": [ "F2T", "F3C", "L7S", "V11F", "*12C", "A13V", "H14S", "D15G", "E17D", "A18T", "G20E", "I21T", "N23D", "N24D", "R25V", "P28Q", "K29N", "N43P", "F47Y", "L52H", "T55V", "Y58L", "T67L", "Q68D", "Y69S", "F70C", "S71P", "L72S", "N73T", "L81I", "H82P", "G84K", "I102V", "D108N", "N110K", "T111S", "A114V", "V117M", "H122N", "I123V", "I124V", "V127A", "N131Q", "F132L", "K134D", "E135N", "M137F", "T139A", "S141I", "G145D", "T146P", "H147L", "H148R", "S150R", "W151*", "V152I", "Y153F", "Q154E", "S155N", "Y161F", "D162E", "R163Y", "E165S", "K166D", "Q169L", "L170M", "T172V", "A173G", "P174E", "T176P", "D181H", "V186I", "S190K", "S195N", "V196I", "H198S", "A199G", "Y200F", "T201Q", "P202N", "V203I", "I205V", "T206A", "R207N", "V211S", "V215L", "I219L", "F224L", "I226L", "S230N", "V234L", "M235L", "M237A", "S244I", "Q245P", "T246N", "T247I", "S248G", "S249P", "A250V", "Y253F", "N256Y", "H259P", "F266Y", 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Virol. 88 (12), 7070-7082 (2014)", "title": "Identification of Diverse Alphacoronaviruses and Genomic Characterization of a Novel Severe Acute Respiratory Syndrome-Like Coronavirus from Bats in China", "value": "He et al" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.14961593, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/KF569996", "virus_type": { "value": "SARS-like CoV" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: K280R, Q310G, E311D, I461V, V581I, S614F, R814C, A966S, P993L, N1236S, T1336S, P1473S, I1519V, E1520K, Q1559H, I1560L, T1614A, K1961R, K1981R, Q2022R, K2120R, Q2125R, A2126T, F2150L, S2182G, N2241S, L2246S, F2364V, N2475S, A2588T, D2825G, I2854T, V3025I, V3084I, A3286V, T3520A, F3564L, T4179S; ORF1b: T76A, I192V, T1747N, E1888K, T1902I, I2077V, A2081V, T2203I, M2322T; ORF7a: A11S, T14F, T59I, V93F; ORF7b: F34I; ORF8b: N47S; spike: F3L, I5S, L10V, V11A, *12L, H14Q, I16V, C19H, G20*, I21V, F22P, N63H, I74V, I80T, H82N, V98I, N110S, F132L, T146V, H148F, F185Y, S190R, A199S, T206I, L209I, F224I, R232K, F238Y, H259Y, T260V, L264F, K265Q, I290L, D296S, K311T, V314I, L322R, K327R, T332S, D415E, R426K, N427T, I428R, N437Q, L443S, P470S, A471D, L472E, T486S, I489L, *518S, R544K, T555A, E1066Q, Y1070H" }, "mutations": { "ORF1a": [ "K280R", "Q310G", "E311D", "I461V", "V581I", "S614F", "R814C", "A966S", "P993L", "N1236S", "T1336S", "P1473S", "I1519V", "E1520K", "Q1559H", "I1560L", "T1614A", "K1961R", "K1981R", "Q2022R", "K2120R", "Q2125R", "A2126T", "F2150L", "S2182G", "N2241S", "L2246S", "F2364V", "N2475S", "A2588T", "D2825G", "I2854T", "V3025I", "V3084I", "A3286V", "T3520A", "F3564L", "T4179S" ], "ORF1b": [ "T76A", "I192V", "T1747N", "E1888K", "T1902I", "I2077V", "A2081V", "T2203I", "M2322T" ], "ORF7a": [ "A11S", "T14F", "T59I", "V93F" ], "ORF7b": [ "F34I" ], "ORF8b": [ "N47S" ], "nuc": [ "C451T", "T484A", "T595C", "G598T", "A604G", "T691A", "C811T", "C832T", "C868T", "C928T", 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"bat/Yunnan/RmYN01/2019", "node_attrs": { "accession": "EPI_ISL_412976", "author": { "author": "Zhou et al", "value": "Zhou et al" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.13800263999999998, "host": { "value": "Bat" }, "virus_type": { "value": "SARS-like CoV" } } } ], "name": "NODE_0000021", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.11259744 } }, { "branch_attrs": { "labels": { "aa": "ORF1a: E246D, D314N, Q343H, S351T, A433S, N455S, V491I, G493S, I529V, S549A, H576Q, A620T, V627I, V631I, E673D, S677C, A746S, I785V, N986T, Q1071L, E1120D, K1141Q, H1150Q, N1159A, D1162E, T1178A, Q1184P, P1196S, E1213D, Q1241H, A1290S, A2437T, V2467I, V2742I, R2823K; ORF1b: E83D, A1831S, D1871E; ORF3a: R6S, G18S, T40S, V97L, R134K, N152H, I169V, S171A, T175I, T176S, I203V, L219I, A225I, Y233F, S234N, D241P, H242N; ORF3b: V8A, L11H, S29L, H30L, Q35F, R37H, *40S, *61S, *62L, N75S, R76L, L77H, N78K, *79L, R80L, I93L, A94T, Q100H, I101R; ORF6: I31M; ORF8b: K28*, S32T, D35N, P43H, T50N, *65G; ORF9b: V31M; membrane_protein: L128V; nucleocapsid: S34N, T81P, I158T, E291D; spike: S9T, R142K, S155N, K265N, K311N, S827N, E850D, R1055K, S1105A" }, "mutations": { "ORF1a": [ "E246D", "D314N", "Q343H", "S351T", "A433S", "N455S", "V491I", "G493S", "I529V", "S549A", "H576Q", "A620T", "V627I", "V631I", "E673D", "S677C", "A746S", "I785V", "N986T", "Q1071L", "E1120D", "K1141Q", "H1150Q", "N1159A", "D1162E", "T1178A", "Q1184P", "P1196S", "E1213D", "Q1241H", "A1290S", "A2437T", "V2467I", "V2742I", "R2823K" ], "ORF1b": [ "E83D", "A1831S", "D1871E" ], "ORF3a": [ "R6S", "G18S", "T40S", "V97L", "R134K", "N152H", "I169V", "S171A", "T175I", "T176S", "I203V", "L219I", "A225I", "Y233F", "S234N", "D241P", "H242N" ], "ORF3b": [ "V8A", "L11H", "S29L", "H30L", "Q35F", "R37H", "*40S", "*61S", "*62L", "N75S", "R76L", "L77H", "N78K", "*79L", "R80L", "I93L", "A94T", "Q100H", "I101R" ], "ORF6": [ "I31M" ], "ORF8b": [ "K28*", "S32T", 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D93N, I102T, F136Y, E148V, G150N, I154V, N160Q, A169V, T174I, D203G, F204L, F241Y, E256D, G268E, K280T, N324S, T351V, T362I, D375N, P376K, I378V, H390Y, A412S, T439V, F480L, A501S, V517I, D571G, V681I, A698V, D829N, T870N, A879T, N893E, I896V, K916N, L917V, D933E, A936V, A943I, E944D, T968A, A985T, V991I, P993H, P997S, N1029S, T1033M, I1035V, K1063R, K1158R, D1189R, D1213N, H1241R, D1299G, A1321I, A1328E, I1343V, V1371I, V1422I, L1528Q, E1541A, F1596Y, V1775I, I1816V, T2024S, I2107V, I2128T, K2135R, A2184V, S2219F, T2224I, L2227F, V2267I, F2305V, A2506G, T2574I, A2577S, A2591V, Q2679P, V2775I, S2813A, A2971V, V3122A, I3489V, T3566M, K3816R, E3883A, N3905S, V4086I, C4304F, H4310Q, V4327F, T4331A, L4342F; ORF1b: T17I, L238M, H1168Y, C2153S, A2376V, M2439R, V2564A, S2658F, R2684T, N2695H; ORF3a: S24F, P25L, L41F, P42S, G44R, I77T, A103V, V118L, H152Y, D165N, K179E, Y211H, T220S, E226Q; ORF3b: M1T, T54I, P68L, L80V, L83Q, L85F, S91L, M124T; ORF6: I16V, I33T, R38T, E56V; ORF7a: A11V, K32E, 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"A1208G", "I1209L", "V1210F", "T1213I", "C1218Y", "M1219F", "L1226C", "A1229M", "K1237R" ] } }, "name": "YNLF_34C", "node_attrs": { "accession": "KP886809", "author": { "author": "Lau et al", "journal": "Submitted (04-MAR-2015) Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong, Hong Kong", "title": "Direct Submission", "value": "Lau et al B" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.14644851, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/KP886809", "virus_type": { "value": "SARS-like CoV" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: F97Y, E199D, F221Y, E233D, K404R, N434G, V597I, L793I, I821T, K841R, E930D, D934C, C938Y, T946S, E948A, D955E, T970M, D983G, Q988L, V991H, P997L, V1192I, P1473S, I1519V, I1560L, V2138A, F2150L, K2181R, S2182G, K2185R, N2241S, L2246S, K2532R, L2759F, V2775A, S3223A; ORF1b: I2136V; ORF3a: F79L, I117V, N119S; 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"T23608G", "G23753A", "T23995A", "A24010C", "G24031A", "T24043C", "C24055A", "A24142G", "A25228T", "A25297G", "T25483C", "T25690C", "A26876C", "A26944T", "A27272G", "T27531C", "C27567T", "A29097G" ], "spike": [ "N23S", "R25K", "L30M", "N149K", "F185Y", "S190R", "H259Y", "V276I", "S279A", "G296S", "N311H", "L322R", "T332S", "F391S", "H433Q", "N435K", "N437Q", "H443S", "E518G", "V754I" ] } }, "children": [ { "branch_attrs": { "labels": { "aa": "ORF1a: A2552T; ORF8b: *28Q; ORF9b: S37N; spike: F4V, V5L, F6L, L7R, V8L, T9G, N12T, E17D, I21H, N24T, K29L, A31D, Q32K, S64T, F70L, I74M, I80T, V87I, L107M, N129Y, V140I, G145E, T146Q, Q147H, Q148Y, F157Y, K166Q, K175Q, R190K, H198N, T201S, L205I, A211V, F224I, R232K, A236S, Q245R, S249I, T260S, A284S, K435Q, S456T" }, "mutations": { "ORF1a": [ "A2552T" ], "ORF8b": [ "*28Q" ], "ORF9b": [ "S37N" ], "nuc": [ "G583A", "T1906C", "A7867T", "G7919A", "A8101C", "T8104A", "T8122A", "C11788T", "G11842A", "G11923A", "C11980T", "T12514C", "C12598T", 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"T201S", "L205I", "A211V", "F224I", "R232K", "A236S", "Q245R", "S249I", "T260S", "A284S", "K435Q", "S456T" ] } }, "children": [ { "branch_attrs": { "labels": { "aa": "ORF1a: L92K, D93E, F136Y, F190L, T346I, V350I, A501S, A629V, T774K, K816R, V876I, A879T, E932D, D933E, G983D, P993L, L997P, P999S, Q1141E, D1189H, E1437D, D1508E, K1532E, R2181K, S2246L, N2249S, F2305V, P2457S, R2532K, T2552S, H2636Y, F2759L, L2762F, I2783V, L3063F, P3372S, I3392V; ORF1b: I958V, M991V, K1385R, F1657C, K1736R, I2077V, V2089I, V2136I, K2140N, M2147V, T2243A, D2253N; ORF3a: S24L, Y141H, T268M; ORF3b: T20I, T59I, I99T, R128*; ORF8b: T5I, H43R; ORF9b: M31V, G32V, Q33H, N36S, M57T, Q78K; membrane_protein: L133M; nucleocapsid: N30D, N34S, P81K, E129Q, T158I; spike: R7C, G225S, I249V, V314I, I752V, I754L, N827S, D850E, L1016P" }, "mutations": { "ORF1a": [ "L92K", "D93E", "F136Y", "F190L", "T346I", "V350I", "A501S", "A629V", "T774K", "K816R", "V876I", "A879T", "E932D", "D933E", "G983D", "P993L", "L997P", "P999S", 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Gen. Virol. 91 (PT 4), 1058-1062 (2010)", "title": "Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans", "value": "Yuan et al" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.14475973, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/FJ588686", "virus_type": { "value": "SARS-like CoV" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: A169V, L349A, P376Q, K492R, L591I, T609I, T768A, Q1138H, Q1244H, G2068D, I2128V, A2138V, V2141M, A3119V, M3560L; ORF1b: T76A, A1428V, H1784Y; ORF3a: I77M, S119C, A143V; ORF3b: P3S; nucleocapsid: S24P, N194D; spike: R7S, G518A, T535I, V626I, A714S" }, "mutations": { "ORF1a": [ "A169V", "L349A", "P376Q", "K492R", "L591I", "T609I", "T768A", "Q1138H", "Q1244H", "G2068D", "I2128V", "A2138V", "V2141M", "A3119V", "M3560L" ], "ORF1b": [ "T76A", "A1428V", "H1784Y" ], "ORF3a": [ "I77M", "S119C", "A143V" ], 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"P8S", "Q268A" ], "spike": [ "I21L", "K435Q", "N486T", "T555M" ] } }, "name": "Rs4237", "node_attrs": { "accession": "KY417147", "author": { "author": "Hu et al", "journal": "PLoS Pathog. 13 (11), e1006698 (2017)", "title": "Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus", "value": "Hu et al B" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.13923396, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/KY417147", "virus_type": { "value": "SARS-like CoV" } } } ], "name": "NODE_0000027", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.13223104 } } ], "name": "NODE_0000026", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.12786555 } } ], "name": "NODE_0000024", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.12354268 } }, { "branch_attrs": { "labels": { "aa": "ORF1a: A169V, V182F; 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"Q569E" ] } }, "children": [ { "branch_attrs": { "labels": { "aa": "ORF1a: K141R, D233G, P305S, L349S, V350I, T351I, S455N, A501S, Q526R, V567G, V708I, T774I, K794E, V834F, D930E, E939D, Q958R, P993L, N1029S, T1033M, H1086Y, Q1138H, C1211F, F1329L, L1530I, K1855R, L2116F, V2195I, M2208T, V3902I, A3933T, L4108I; ORF1b: E1389D, V1806I, H1854Y, A1995V, T2537A, K2538R, D2666E, K2674N; ORF3a: I124V, V163I, D192N, V210I; ORF3b: I12T, V22A, V47A, Q118R; ORF6: K48N; ORF7b: L34F; ORF8a: G8T, L9C, L10I, T11S, S12L, V13C, Y14S, C17R, S18T, I19V, Q20V, E21Q, C22R, E24A, Q27K, F29H, Q30V; ORF8b: S1M, N2C, T5I, H6L, K12R, I13G, G14N, P15T, R16Y, K17S, S18T, R20W, *24L, I25G, W26K, T27V, *28L, S29P, S30F, N31H, T32R, L33W, *34H, N35T, V36M, W37V, L39T, Y40C, I41T, F42P, H43N, E45T, N50D, P52V, V53G, S55A, V58A, S61W, Y64H, G65E, Y72F, Q73R, N85K; ORF9b: Q35R, K41R; nucleocapsid: P8S, P38S, P123L, N410S; spike: I3F, F4L, V5I, F6G, F7Y, V8T, T9A, L10F, V11L, N12I, A13G, D15T, I16N, E17N, R18M, R20H, 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"url": "https://www.ncbi.nlm.nih.gov/nuccore/KY417145", "virus_type": { "value": "SARS-like CoV" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: N470T; ORF1b: V2691I; ORF3a: S6R, R15A, S18G, E21D, L52F, S60T, V62I, H66N, I77F, L79F, V80I, L97V, I108L, I114F, V117C, V118I, S119N, F120A, F123I; ORF3b: T20I, I99T; spike: V5L, N12S, R20P, I21T, I22F, N23D, N24D, R25G, Q27P, *30Y, A31T, L66V, Y69F, S71T, D75N, L81I, G84R, I102V, L107M, D108N, T110K, T111S, A114V, V117I, I123V, I124V, V127A, N131E, I137F, N149H, W151*, Y153F, Y161F, D162E, N163Y, *165S, Q169*, D174E, T176S, S190K, H198Y, A199G, P206A, A211T, S214N, V233A, V234I, M235L, M237A, *245W, S249A, N256Y, H259P, N265K, F266Y, N267D, T289S, I290V, N292S, D294E, V295I, G296D, S308A, T310S, N311K, D326G, R333T, T343K, K344R, T353S, P371A, S372T, I375N, T380S, S381N, T386S, L388V, I389V, R390K, F391G, S392D, E393D, V397I, E401Q, T417M, I421L, A431T, K432T, H433T, D434G, G436Y, Y439K, H443L, K445Q, S446G, K449R, L455I, S462P, D464G, 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P241Q; ORF3b: T10I, L27S, T99I; ORF6: S50P; ORF8a: L31P; ORF8b: *28Q; ORF9b: T6I, E86D; envelope: S68A; membrane_protein: I47V, T188I; nucleocapsid: V132I; spike: R18S, T31P, K75R, A167S, T215I, S239L, T260A, M417L, R426N, N427S, I428K, A430S, T431S, T433S, K439L, C442W, L443V, Q445R, G446S, R449N, F451Y, I455L, V458D, P459I, F460Y, D463G, K465Q, P466S, T468S, P469A, P470I, A471G, L472P, W476N, S479R, A480P, I489V, Y491H, I826V, Y1049C, N1107S" }, "mutations": { "ORF1a": [ "I238V", "E289D", "H343Q", "A819S", "Q1138H", "K1323R", "I2039L", "R2140C", "A2588V", "M2903K", "A3072T", "P4097S" ], "ORF1b": [ "V728I", "T2203I", "A2209V", "I2465M", "K2538R" ], "ORF3a": [ "P17S", "A59V", "P241Q" ], "ORF3b": [ "T10I", "L27S", "T99I" ], "ORF6": [ "S50P" ], "ORF8a": [ "L31P" ], "ORF8b": [ "*28Q" ], "ORF9b": [ "T6I", "E86D" ], "envelope": [ "S68A" ], "membrane_protein": [ "I47V", "T188I" ], "nuc": [ "C446T", "C556T", "T736C", "A871G", "C931T", "A977G", "G1069A", "A1132C", "C1168T", "T1294G", "C1381T", "C1801T", "T1906C", "C2008T", "T2023C", "G2035A", "C2041T", "C2137T", "T2263C", "A2380G", "C2650T", "T2719C", "G2720T", "T2752C", "G3679T", "T3787C", "G3997A", "A4233G", "A4324G", "C4435T", "G4480A", "C4505T", "C4585T", "A4630G", "A4681G", "G4810A", "T5023C", "T5143G", "T5476C", "T5497C", "C5659T", "T6007C", "T6016C", "A6380C", "A6640G", "C6664T", "C6683T", "A6775G", "T6814A", "T6841C", "C7084T", "C8028T", "C8602T", "T8973A", "A9121G", "C9421T", "T9475C", "G9479A", "A9577G", "C9980T", "A10126G", "T10138C", "C10171T", "T10321C", "C10328T", "A10918G", "A10999G", "C11515T", "C11557T", "T12064C", "A12472C", "C12554T", "G12628A", "C12749T", "C12814T", "C12883T", "A12892G", "C13000T", "A13018G", "T13042C", "T13078C", "T13093C", "A13108G", "A13189G", "G13545A", "A13800G", "C13863T", "C14016T", "T14193C", "C14220T", "A14565G", "G14661A", "A14664G", "T15324C", "A15354G", "A15357G", "C15417A", "G15580A", "T15870C", "T16218C", "C16263T", "C16764T", "A16773G", "T16782C", "T16788C", "G16812A", "G16848A", "T16872C", "G16908T", "T16974C", "C17007T", "T17019A", "C17046T", "T17097C", "C17145T", "A17163G", "C17166T", "T17232C", "T17307C", "T17325C", "C17355T", "T17361C", "C17367T", "T17380C", "C17388T", "A17397G", "G17403A", "A17409G", "C17634T", "T17676C", "T17712C", "C17772T", "A17775C", "T17898C", "C17952T", "C18249T", "C18444T", "C18480T", "G18597A", "T18636C", "T18843C", "G18993A", "G19197A", "T19212C", "T19278C", "T19362C", "A19398G", "C19452T", "T19464C", "A19485G", "T19515C", "G19551A", "T19555C", "T19575C", "A19683G", "C20006T", "C20024T", "T20031C", "G20139A", "T20149C", "G20154A", "C20230T", "A20250G", "C20322T", "T20340C", "A20394G", "T20451C", "A20589G", "C20628T", "C20634T", "C20748T", "T20793G", "T20862G", "A20910G", "T20919C", "C20964T", "C20976T", "T20979C", "G20994A", "A21011G", "A21054G", "A21174T", "A21186G", "G21213A", "C21228T", "T21342C", "G21378A", "T21393C", "T21408C", "T21511C", "T21517C", "G21547T", "C21550T", "A21584C", "T21592C", "T21601C", "T21631C", "T21679C", "A21717G", "T21805C", "T21844C", "C21847T", "C21928A", "T21940C", "T21955C", "T21988A", "T21991C", "G21992T", "A22063G", "T22084C", "T22105C", "T22129C", "C22137T", "T22204A", "C22209T", "A22243T", "A22271G", "A22339C", "C22357T", "C22381T", "A22471G", "T22621C", "T22636C", "T22723C", "G22729A", "T22738C", "A22742T", "T22756A", "T22759A", "T22768C", "G22770A", "G22771T", "A22772T", "A22773C", "C22774T", "T22776A", "T22777A", "G22781T", "A22784T", "T22786C", "A22789T", "A22790T", "T22792C", "A22808T", "A22809T", "T22819G", "C22820G", "C22826A", "A22827G", "G22829T", "G22830C", "C22831T", "G22839A", "G22840C", "T22845A", "A22850C", "A22852C", "A22856T", "T22864C", "T22866A", "G22867C", "C22868A", "C22869T", "T22870C", "T22872A", "C22873T", "C22876A", "A22881G", "T22882A", "C22885T", "A22886C", "A22888G", "C22889T", "A22895T", "C22897A", "C22898G", "A22900T", "C22901A", "C22902T", "T22903A", "C22905G", "T22908C", "T22919A", "G22920A", "G22921C", "A22924C", "A22928C", "G22931C", "T22933A", "T22939C", "C22945T", "T22948A", "T22951A", "C22957T", "A22958G", "C22963A", "T22964C", "T23014C", "T23116C", "A23191G", "C23299T", "T23476C", "C23590T", "A23671C", "C23726T", "T23749C", "T23755C", "A23773G", "C23794G", "A23800G", "T23830C", "G23884A", "A23969G", "C24223T", "T24235C", "A24259T", "A24265C", "A24355T", "C24368T", "T24451G", "G24574A", "T24586C", "A24598G", "A24639G", "G24652A", "A24670T", "T24688C", "G24727T", "A24811G", "A24813G", "T24937C", "T24964C", "C24973T", "A24979G", "T25144C", "G25204A", "A25228G", "C25319T", "A25384G", "C25446T", "A25567G", "T25690C", "C25720T", "T25771C", "C25987T", "C25992A", "C26275T", "T26383C", "T26399G", "A26477G", "C26503T", "A26618G", "C26635T", "T26737C", "T26791C", "C26815T", "C26827T", "C26849A", "A26944G", "A26971G", "C27013T", "C27042T", "C27085T", "T27259A", "T27329C", "T27498C", "T27564C", "A27666G", "T27980C", "T28055C", "C28293T", "A28534C", "G28660A", "C28695G", "C28701T", "T28707C", "A28830G", "C29163T", "C29331T" ], "nucleocapsid": [ "V132I" ], "spike": [ "R18S", "T31P", "K75R", "A167S", "T215I", "S239L", "T260A", "M417L", "R426N", "N427S", "I428K", "A430S", "T431S", "T433S", "K439L", "C442W", "L443V", "Q445R", "G446S", "R449N", "F451Y", "I455L", "V458D", "P459I", "F460Y", "D463G", "K465Q", "P466S", "T468S", "P469A", "P470I", "A471G", "L472P", "W476N", "S479R", "A480P", "I489V", "Y491H", "I826V", "Y1049C", "N1107S" ] } }, "name": "Rs4231", "node_attrs": { "accession": "KY417146", "author": { "author": "Hu et al", "journal": "PLoS Pathog. 13 (11), e1006698 (2017)", "title": "Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus", "value": "Hu et al B" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.16056874000000002, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/KY417146", "virus_type": { "value": "SARS-like CoV" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: L92M, F136Y, V169A, F182V, T351I, Q468H, T470N, A501T, A629E, V778I, K916N, L917F, D930E, D933E, C934D, Y938C, A943I, E944D, S946T, A948E, E955D, T968A, M970T, Q972R, G983D, A985T, L988Q, H991I, L997P, N1029S, T1033M, S1171N, K1186N, P1190S, I1192T, T1336A, P1529S, L2150F, G2182S, R2185K, Y2222C, L2227F, S2241N, S2246L, V2267I, F2305V, A2531S, R2532K, F2759L, A2775I, V2798I, S2813A, P2992S, K3906R, M4367L; ORF1b: A176S, S634N, V1515I, T1555I, K1828R, I1829V, Q2069H, M2147V, K2532R, V2564I; ORF3a: G18V, A171E, W193R, V255A; ORF3b: Q31K, *115L; ORF6: M31V; ORF7a: A11V, L12F, A13T, H94Q, I111L; ORF7b: L34I, I37L, N42T; ORF8a: G8T, L9C, L10I, T11S, S12L, V13C, Y14S, C17R, S18T, I19V, Q20V, E21Q, C22R, E24A, Q27K, F29H, Q30V; ORF8b: S1M, N2C, T5I, H6L, K12R, I13G, G14N, P15T, R16Y, K17S, S18T, R20W, *24L, I25G, W26K, T27V, *28L, S29P, S30F, N31H, T32R, L33W, *34H, N35T, V36M, W37V, L39T, Y40C, I41T, F42P, H43N, E45T, N50D, P52A, V53G, S55A, V58A, S61W, Y64H, G65E, Y72F, Q73R, N85K; ORF9b: S7N; nucleocapsid: P8S; spike: F6L, E17D, S34T, R37M, K75T, V87I, T144M, A173S, A308V, K311G, E312D, T333K, T432S, C442Y, Q445H, S479N, A480D, F484Y, A487T, S540P, T590A, P607S, V608T, V754A, A775T", "clade": "SARS-CoV" }, "mutations": { "ORF1a": [ "L92M", "F136Y", "V169A", "F182V", "T351I", "Q468H", "T470N", "A501T", "A629E", "V778I", "K916N", "L917F", "D930E", "D933E", "C934D", "Y938C", "A943I", "E944D", "S946T", "A948E", "E955D", "T968A", "M970T", "Q972R", "G983D", "A985T", "L988Q", "H991I", "L997P", "N1029S", "T1033M", "S1171N", "K1186N", "P1190S", "I1192T", "T1336A", "P1529S", "L2150F", "G2182S", "R2185K", "Y2222C", "L2227F", "S2241N", "S2246L", "V2267I", "F2305V", "A2531S", "R2532K", "F2759L", "A2775I", "V2798I", "S2813A", "P2992S", "K3906R", "M4367L" ], "ORF1b": [ "A176S", "S634N", "V1515I", "T1555I", "K1828R", "I1829V", "Q2069H", "M2147V", "K2532R", "V2564I" ], "ORF3a": [ "G18V", "A171E", "W193R", "V255A" ], "ORF3b": [ "Q31K", "*115L" ], "ORF6": [ "M31V" ], "ORF7a": [ "A11V", "L12F", "A13T", "H94Q", "I111L" ], "ORF7b": [ "L34I", "I37L", "N42T" ], "ORF8a": [ "G8T", "L9C", "L10I", "T11S", "S12L", "V13C", "Y14S", "C17R", "S18T", "I19V", "Q20V", "E21Q", "C22R", "E24A", "Q27K", "F29H", "Q30V" ], "ORF8b": [ "S1M", "N2C", "T5I", "H6L", "K12R", "I13G", "G14N", "P15T", "R16Y", "K17S", "S18T", "R20W", "*24L", "I25G", "W26K", "T27V", "*28L", "S29P", "S30F", "N31H", "T32R", "L33W", "*34H", "N35T", "V36M", "W37V", "L39T", "Y40C", "I41T", "F42P", "H43N", "E45T", "N50D", "P52A", "V53G", "S55A", "V58A", "S61W", "Y64H", "G65E", "Y72F", "Q73R", "N85K" ], "ORF9b": [ "S7N" ], "nuc": [ "T325C", "T400C", "T403C", "T422C", "T539A", "T574A", "G583A", "C613T", "C664T", "T672A", "T771C", "T809G", "C832T", "T883A", "T913C", "T1012C", "T1018C", "C1060T", "A1087G", "C1096T", "T1099C", "A1147G", "C1315T", "C1317T", "G1393A", "C1507T", "C1516T", "C1519T", "T1561C", "C1591T", "G1669T", "C1674A", "T1705C", "C1708T", "G1766A", "C1792T", "C1798T", "A1912G", "C1948T", "G1999A", "T2011C", "C2026T", "C2143T", "C2151A", "A2317G", "C2338T", "A2440G", "C2482A", "T2572C", "G2597A", "C2644T", "T2665C", "C2708T", "A2815T", "T2935C", "T2944C", "A2965G", "G2974A", "T2986C", "G2989A", "A3013C", "C3014T", "T3019A", "C3031T", "C3040T", "T3043C", "T3049A", "T3055G", "G3058A", "G3061A", "T3064G", "T3065G", "G3066A", "T3067C", "A3078G", "G3091A", "G3092A", "C3093T", "G3094T", "A3097T", "T3101A", "C3108A", "G3109A", "A3115G", "A3127G", "A3130T", "C3133T", "C3136T", "T3145C", "A3148T", "A3167G", "T3174C", "G3175A", "A3180G", "A3187G", "A3199G", "G3202A", "T3211G", "G3213A", "G3218A", "A3226G", "T3227C", "T3228A", "G3232A", "C3236A", "A3237T", "A3241G", "T3255C", "A3256T", "C3277T", "G3322A", "G3328T", "G3337T", "G3346A", "A3351G", "C3352T", "C3358T", "C3361T", "C3363T", "T3391C", "C3439T", "A3454G", "C3460T", "C3490T", "G3496A", "T3502G", "A3505T", "A3703G", "C3769T", "G3777A", "G3823C", "C3833T", "T3835C", "T3840C", "T3895C", "C3967T", "A4123T", "A4177G", "C4255T", "G4258A", "T4259C", "A4271G", "C4366A", "C4393A", "C4405T", "C4411T", "A4432G", "T4438C", "A4450T", "C4495T", "A4525G", "G4699A", "T4808C", "C4850T", "T4873C", "C5104T", "C5371T", "C5425T", "C5461T", "A5635G", "T5743C", "T5800C", "A5839G", "C5954T", "C5974T", "T5998C", "T6181C", "T6205C", "C6713T", "C6719T", "T6727C", "A6745T", "A6754C", "G6784A", "G6809A", "G6819A", "T6835C", "A6850G", "T6880A", "T6883C", "A6886T", "A6898G", "C6907T", "A6922T", "A6930G", "A6940T", "A6946T", "T6953C", "A6955C", "G6958A", "C6961T", "C6964T", "A6970T", "G6987A", "C7002T", "C7006T", "C7009T", "C7015G", "T7021C", "T7063C", "G7064A", "G7087C", "C7096T", "C7129T", "T7168C", "T7178G", "T7198C", "C7217T", "C7306T", "T7366C", "T7396C", "T7408C", "T7639C", "A7696G", "T7732C", "C7744T", "A7747G", "A7804G", "C7822T", "G7856T", "G7860A", "A7867T", "A7888G", "C7924T", "T7933C", "T7957C", "C8032T", "T8047C", "C8054T", "G8056A", "T8095C", "T8107C", "T8110A", "T8128C", "C8149T", "C8179T", "G8185A", "C8212T", "C8230T", "A8233G", "T8251C", "T8275C", "T8293C", "T8299C", "T8350C", "T8395C", "T8540C", "C8554T", "T8587A", "G8588A", "C8589T", "T8590C", "G8657A", "C8683T", "T8702G", "A8806G", "T8816C", "C8860T", "C9061G", "T9178A", "T9188C", "A9223G", "T9229C", "C9239T", "T9241A", "A9247T", "A9265G", "T9274C", "A9280T", "C9295T", "T9490C", "T9497C", "A9502G", "T9547C", "T9754C", "T9781C", "C9808T", "T9925C", "A10012G", "A10081G", "C10183T", "A10204T", "C10210T", "A10213T", "C10219T", "C10264T", "T10303C", "C10384T", "C10477T", "T10765C", "C10981T", "T10990A", "T11185C", "C11228A", "C11239T", "C11440T", "C11980T", "A11982G", "C12004T", "A12079G", "T12295C", "T12406C", "A12508G", "T12514C", "T12547C", "C12607T", "G12634A", "T12901C", "C13138T", "C13174T", "T13222C", "T13348C", "A13364T", "G13384A", "C13452T", "C13533T", "T13665C", "T13824C", "G13924T", "C14110T", "T14430C", "C14508T", "C14619T", "T14712C", "C14868T", "A15150G", "C15171T", "G15299A", "G15315A", "T15342C", "C15510T", "T15552C", "G15942A", "T15948C", 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