{ "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 related coronavirus", "#59A3AA" ], [ "novel coronavirus", "#DC2F24" ] ], "title": "virus type", "type": "categorical" }, { "key": "host", "scale": [ [ "Bat", "#511EA8" ], [ "Badger", "#3F44C8" ], [ "Civet", "#3E5BD0" ], [ "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 (nCoV) outbreak in Wuhan. Coronaviruses from the Wuhan outbreak are colored in red, while related SARS-like coronaviruses are colored in blue. [Click here to zoom into the nCoV outbreak clade](/groups/blab/sars-like-cov?clade=nCoV).\n\nThere were 6 SNPs present in the nCoV samples in the first and last few bases of the alignment that were masked as likely sequencing artifacts. Additionally, a SNP at 18460 in BetaCoV/Wuhan/IVDC-HB-04/2020 appears directly adjacent to long stretch of ambiguous bases and so has also been masked. Additionally, sample BetaCoV/Wuhan/IVDC-HB-05/2019 may have sequencing artifacts that make it appear more diverged than it actually is. This sample has been dropped from the above analysis until resequencing occurs. Full details on bioinformatic processing can be found [here](https://github.com/blab/sars-like-cov).\n\nThe Wuhan 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*) via [GISAID](https://gisaid.org). We gratefully acknowledge the Authors, Originating and Submitting laboratories of the genetic sequence and metadata made available through GISAID on which this research is based.\n\n
\n \n \"gisaid-logo\"\n \n
\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 }, "Hong Kong": { "latitude": 22.3964, "longitude": 114.1095 }, "Taiwan": { "latitude": 23.6978, "longitude": 120.9605 } }, "key": "country" } ], "maintainers": [ { "name": "Trevor Bedford", "url": "http://bedford.io/team/trevor-bedford/" } ], "panels": [ "tree", "map", "entropy" ], "title": "Phylogeny of SARS-like betacoronaviruses including novel coronavirus from Wuhan using data generated by the Shanghai Public Health Clinical Center & School of Public Health, the National Institute for Viral Disease Control and Prevention, the Institute of Pathogen Biology, and the Wuhan Institute of Virology shared via GISAID", "updated": "2020-01-27" }, "tree": { "branch_attrs": { "mutations": {} }, "children": [ { "branch_attrs": { "labels": { "aa": "ORF1a: L6P, V8F, E44Q, N48D, L56V, L77R, S78T, T79A, N80P, K84V, V85M, F97Y, I102E, T114I, I116V, N120K, F136Y, I138A, Y143F, Y157F, E158Q, Q159E, L170T, T174M, V182Y, S211A, M212S, E223D, 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P36S, S59F, H62Q, A68P, T71V, L101V, L108I, I117F; ORF7b: N2S, T5S, I37H, E38N, P40T, N42H, V44A; ORF8a: L3F, I5V, V6F, F7L, L9I, S12T, Y14A, C15A, I16L, I19L, E21S, C23A, E24Q, N26H, L30V, I31V, E32D, K36Q; ORF8b: T1M, K4M, K12R, I13V, P15A, R20P, A23V, V25G, T27L, T29I, S30T, N31H, L33I, *34H, D35*, V36H, Q38*, I41K, S42F, E45T, P52K, V53L, I57V, Y64S, *65R; ORF9b: P10H, D29N, G34D, A38V, Q52P, S56N, R60K, N61T, D63N, A67G, R68K, V76A, A97V; envelope: T55S, V56F, G70R; membrane_protein: M1T, A2G, A29T, M32C, S39A, V51I, V75I, I86L, V96I, R124H, M133L, I144L, M150I, S154H, G187A, T188G, N196S, G211S, N213S; nucleocapsid: T22S, G32E, E64D, R66K, G80S, V95I, S121G, V132I, N153A, G193N, N194S, N206T, S213G, G214N, E217D, T377A, A380T, P382A, P391Q, M401L, R406K, N410Q; spike: L2F, A5F, F6L, V8F, T9A, K12N, A13T, G20V, I21N, I22F, S23T, R24S, K25R, P26T, P28L, K29N, M30P, Q32Y, V33T, S34N, R37Q, N43P, D45K, D63Y, L66V, Q68W, F70Y, N73H, D75S, G84N, V97I, S105T, A114L, V115F, S120A, H122N, 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"L220V", "K221E", "F224V", "S230K", "V233T", "V234L", "M235L", "M237I", "F238H", "G243R", "Q245Y", "T246P", "S248P", "S249T", "N256Y", "H259P", "T260S", "R265K", "F266Y", "S279A", "Q280L", "N281D", "A284S", "L286T", "I290L", "N292S", "N294T", "D296E", "S308Q", "E312S", "N336S", "S391F", "R426K", "I428L", "A431G", "K432E", "H433G", "D434G", "G436Y", "Y439F", "N457T", "V458E", "P459I", "F460Y", "S461Q", "S462A", "D463G", "D464S", "T468N", "P469G", "P470L", "A471D", "E518K", "S574T", "I626T", "L729I", "M770I", "A775P", "T795S", "M816I", "E821D", "S827T", "V860I", "Y1070H", "S1083H", "I1086V", "S1093E", "A1229C" ] } }, "children": [ { "branch_attrs": { "labels": { "aa": "ORF1a: I114V, M174K, K338R, F406Y, L608M, M731L, D762V, V779I, I860N, E933G, E941G, E942Q, A969S, T970S, P971S, Q972S, L973Q, D983E, D984S, E990A, E992V, E994Q, P997S, E1001Q, D1067K, S1111N, D1120E, R1148H, A1154V, K1173R, I1186V, D1203A, C1211S, A1259V, P1839S, T1922S, T1984I, V2004A, E2008G, D2020V, N2058S, L2188I, G2242V, T2574I, V2760I, A2761T, S2774F, I3029V, I3117M, I3318V, V3487L, L3589M, M3646I; ORF1b: R2049K, V2061I, E2279D, P2313L, F2314L, E2661D, I2679V, V2686I; ORF3a: L52I, V88L, A99G, P104T, Y107F, V112A, F114C, S171C, S251T; ORF3b: L30H, Q31V, Q35L, Q36R, K41R, I49T, L50R, K58R, L77H; ORF6: L44P, Y49C; ORF7a: L5F, A13V, C15G, V24I, R25K, Y75F, I88T, T121I; ORF7b: L4F, C41F; ORF8b: H6L, W26R, I29V; ORF9b: L22V, T25A, R26K, M27T, N29S, V31M, Q35L, V42A, R48H, N63R, A69V, V77L, Q78K, E86V; membrane_protein: T1S; nucleocapsid: T25S, N28S, S34N, D64N, K66T, T81K, S233N, T380L, D403E, A417T; spike: I3F, F4L, L7Q, T13S, F22L, S24G, Q27P, A31N, K45T, F47Y, V51T, H53V, T55S, D57G, T67S, F76T, N84K, V87I, K94H, F107L, T111S, F115L, N134Y, F137Y, F138L, V140G, I146S, K147I, G151A, S155F, A156Y, L169M, D171N, A173S, K175N, N178L, K180N, N181T, K188R, I190V, Y193H, Y200F, I206N, F213L, K217Q, G225S, A236T, S244G, Y245D, T247M, T249S, Y253F, S260R, F293L, E296Q, L322V, D326H, V349I, L355F, K426A, N427K, L428Q, K445S, T457S, L472E, C476R, V489L, K518Q, R553K, T555A, T559I, A609T, V621I, S623A, S673A, T750S, T827S, V1050I, V1146I, K1173R" }, "mutations": { "ORF1a": [ "I114V", "M174K", "K338R", "F406Y", "L608M", "M731L", "D762V", "V779I", "I860N", "E933G", "E941G", "E942Q", "A969S", "T970S", "P971S", "Q972S", "L973Q", "D983E", "D984S", "E990A", "E992V", "E994Q", "P997S", "E1001Q", "D1067K", "S1111N", "D1120E", "R1148H", "A1154V", "K1173R", "I1186V", "D1203A", "C1211S", "A1259V", "P1839S", "T1922S", "T1984I", "V2004A", "E2008G", "D2020V", "N2058S", "L2188I", "G2242V", "T2574I", "V2760I", "A2761T", "S2774F", "I3029V", "I3117M", "I3318V", "V3487L", "L3589M", "M3646I" ], "ORF1b": [ "R2049K", "V2061I", "E2279D", "P2313L", "F2314L", "E2661D", "I2679V", "V2686I" ], "ORF3a": [ "L52I", "V88L", "A99G", "P104T", "Y107F", "V112A", "F114C", "S171C", "S251T" ], "ORF3b": [ "L30H", "Q31V", "Q35L", "Q36R", "K41R", "I49T", "L50R", "K58R", "L77H" ], "ORF6": [ "L44P", "Y49C" ], "ORF7a": [ "L5F", "A13V", "C15G", "V24I", "R25K", "Y75F", "I88T", "T121I" ], "ORF7b": [ "L4F", "C41F" ], "ORF8b": [ "H6L", "W26R", "I29V" ], "ORF9b": [ "L22V", "T25A", "R26K", "M27T", "N29S", "V31M", "Q35L", "V42A", "R48H", "N63R", "A69V", "V77L", "Q78K", "E86V" ], "membrane_protein": [ "T1S" ], "nuc": [ "C35T", "C98T", "G99A", "A127T", "A235T", "A258G", "G370A", "G448A", "T493C", "T523C", "G526A", "C527T", "G529A", "C583T", "C601A", "A604G", "A605G", "C622T", "C715T", "C745T", "T786A", "C823A", "T826C", "T1102A", "T1237C", "C1267T", "A1278G", "T1294C", "C1300T", "T1330A", "C1441T", "T1474C", "T1482A", "A1486G", "T1561C", "T1570C", "T1606C", "C1625T", "A1900G", "A1903T", "C1973T", "T2087A", "C2137T", "C2143G", "A2456T", "A2550T", "G2600A", "T2614C", "C2695T", "A2770G", "G2785A", "T2844A", "T2875C", "A2893T", "A2896T", "T2938C", "T3001C", "G3055A", "A3063G", "A3087G", "G3089C", "A3154G", "C3163T", "G3170T", "A3173T", "C3176T", "C3179T", "A3180C", "T3183A", "T3184G", "A3202G", "T3214A", "G3215T", 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"Zhu et al", "value": "Zhu et al" }, "clade_membership": { "value": "nCoV" }, "country": { "value": "China" }, "div": 0.17029942, "host": { "value": "Bat" }, "virus_type": { "value": "SARS related coronavirus" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: A38V, D93E, T280I, P376S, Y417H, T498A, V591A, T860A, T970A, P971L, P997L, N1091H, R1102K, D1120E, V1137I, Q1201K, N1248S, M1369V, I1519T, A1606V, N1710S, L1756F, Q1772K, I1799T, T2010A, I2038V, D2059N, G2060S, T2255I, T2382N, V3120A, V3122I, T3420N, V3583L; ORF1b: D189N, I224V, K1736R, R1783L, N2165T, K2252Q, R2294S, S2309F; ORF3a: L10I, S28F, A258V; ORF3b: T5I, V8A, M14T, S54N, I70T, Q118*; ORF7a: V8A; ORF7b: S2I; ORF8a: L10I, A23T; ORF9b: T6I, N7S, E32G, H33R; nucleocapsid: P38S, Q268A; spike: S36F, L54S, P211Q, T359A, K426N, A430S, E432V, F442L, A446S, K465T, L470V, L472F, Y476F, Y479Q, T480S, Y484Q, D487N, N505H" }, "mutations": { "ORF1a": [ "A38V", "D93E", "T280I", "P376S", "Y417H", "T498A", "V591A", "T860A", "T970A", 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P3424S; envelope: L31I; membrane_protein: L92F; spike: R142I" }, "mutations": { "ORF1a": [ "P3424S" ], "envelope": [ "L31I" ], "membrane_protein": [ "L92F" ], "nuc": [ "C9892T", "C10535T", "C10741T", "G21918T", "A23758G", "C26288A", "C26753T", "C27888T" ], "spike": [ "R142I" ] } }, "name": "HKU3_8", "node_attrs": { "accession": "GQ153543", "author": { "author": "Lau et al", "journal": "J. 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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": 0.11557829000000001, "url": "https://www.ncbi.nlm.nih.gov/nuccore/GQ153539", "virus_type": { "value": "SARS related coronavirus" } } }, { "branch_attrs": { "labels": { "aa": "ORF3a: G172S" }, "mutations": { "ORF3a": [ "G172S" ], "nuc": [ "T595C", "T2533C", "T19569A", "G24643T", "G25784A" ] } }, "name": "HKU3_5", "node_attrs": { "accession": "GQ153540", "author": { "author": "Lau et al", "journal": "J. 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": 0.11551138000000001, "url": "https://www.ncbi.nlm.nih.gov/nuccore/GQ153540", "virus_type": { "value": "SARS related coronavirus" } } } ], "name": "NODE_0000013", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.11534214000000001 } } ], "name": "NODE_0000012", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.11493527 } } ], "name": "NODE_0000010", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.10314681 } }, { "branch_attrs": { "labels": { "aa": "ORF1a: V378I, E441D, F469L, E489D, V596I, M616L, K625R, R643K, T668S, I677S, L679I, A702S, I770V, P893N, 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"A8564G", "T8581A", "T8602C", "T8680A", "A8761T", "A8779G", "T8896C", "A8950G", "T8977C", "A9010G", "T9046A", "C9088T", "T9103G", "T9145C", "T9160A", "A9241T", "T9283C", "C9289T", "A9292T", "C9310G", "C9433T", "G9445T", "T9514A", "T9544C", "C9643T", "T9654G", "G9669A", "T9670C", "A9681G", "A9757G", "T9766C", "C9790G", "C9791T", "T9808C", "A9814G", "T9847C", "G9853A", "A9928T", "G9976T", "T10015A", "C10045A", "T10072A", "T10123A", "T10198C", "T10333A", "T10414A", "T10492A", "T10582C", "A10600G", "C10864A", "A10972G", "G10984A", "T11017C", "G11039A", "A11044T", "T11065A", "C11275T", "C11347T", "C11380T", "T11473G", "T11500G", "T11566C", "T11635C", "C11681T", "A11686T", "A11725G", "T11749A", "A11803T", "A11806G", "G11866A", "T11908A", "T11920C", "A11935T", "G12238A", "A12280T", "A12310G", "A12367T", "C12386T", "T12388G", "C12424T", "A12430T", "A12475T", "G12526A", "C12538T", "C12550T", "T12742G", "G12763A", "T12808A", "C12811T", "T12856A", "T12886C", "T12928C", "C12940T", "T12961A", 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"T15801C", "T15813A", "G15822A", "A15960T", "A15975C", "A15981T", "G15984A", "C15987T", "C16014T", "T16017C", "C16023T", "G16029A", "T16069C", "G16071A", "C16080T", "C16101T", "A16111C", "C16116T", "A16164G", "A16188G", "T16203C", "T16221C", "T16242G", "T16245C", "A16341T", "T16344C", "C16356A", "T16360C", "A16395G", "A16398T", "A16449G", "G16461A", "A16476C", "G16497A", "A16548T", "T16563C", "G16572A", "T16611A", "G16641C", "A16644T", "C16654T", "T16656G", "G16728A", "A16773G", "T16815A", "A16854T", "A16860T", "A16872T", "A16881T", "A16884T", "C16909A", "A16914T", "G16992A", "G17010A", "C17037T", "C17055T", "T17103A", "G17115C", "A17175G", "T17184C", "C17254T", "T17259A", "T17265A", "A17277T", "G17280A", "A17298T", "C17304T", "T17316C", "T17358C", "A17373T", "T17385A", "A17388C", "A17391T", "A17406T", "T17514C", "A17520T", "G17610A", "G17619T", "A17640T", "A17652T", "T17703C", "A17727T", "G17730A", "A17733T", "G17739A", "T17742C", "G17748A", "T17757G", "C17814T", "G17820A", "A17841T", "C17859T", "C17907T", "G17919A", "G17931A", "A17952T", "T17964A", "C18006T", "T18063A", "A18072G", "A18078G", "A18102C", "A18231T", "A18276T", "A18279T", "T18282C", "A18288T", "G18300A", "A18306T", "C18319T", "G18324A", "G18359A", "T18402C", "G18411A", "G18453A", "T18468A", "G18552A", "A18579T", "C18621T", "C18657T", "C18750T", "A18777G", "C18808T", "T18810G", "T18867A", "T18921A", "T18984C", "G18986A", "C19023T", "C19074T", "A19077T", "C19083T", "C19095T", "G19098A", "A19104T", "C19179G", "G19185T", "C19186T", "C19188G", "T19191A", "A19197G", "C19201T", "T19233G", "G19269A", "A19281C", "C19282A", "G19287A", "C19294T", "C19368A", "A19374T", "A19407G", "T19410A", "T19422C", "A19444C", "G19455A", "A19509G", "C19521T", "C19539T", "G19548A", "T19572C", "G19587A", "G19605A", "G19607C", "G19671A", "T19773C", "T19803A", "G19833A", "T19839G", "T19857C", "A19902C", "G19935A", "T20082C", "G20112A", "A20115G", "A20143C", "C20190T", "G20250A", "C20344T", "T20442C", "A20463G", "T20538C", "T20613A", "T20619A", "T20778C", "A20793T", "A20823T", "A20919T", "T21048G", "T21249C", "T21447C", "C21480T", "C21685T", "C21727T", "A21733T", "A21808C", "A21853C", "G21915C", "A22144G", "G22285T", "C22306T", "T22378C", "C22810T", "C22813T", "T22822C", "A22837T", "A22943T", "A22957C", "G22958A", "A23050T", "C23164T", "A23188G", "T23236G", "T23242A", "A23269T", "G23272A", "T23359C", "T23699C", "G23701T", "A23741T", "T23953A", "C24004T", "A24028T", "T24073C", "A24130T", "T24175C", "T24204A", "A24208C", "G24217A", "G24225A", "T24226G", "T24229G", "G24233A", "A24236C", "T24257A", "T24259A", "G24263T", "G24267C", "C24272T", "T24274G", "A24277C", "A24280G", "T24289C", "A24301G", "A24307T", "T24313A", "C24319T", "G24322A", "T24376C", "T24562C", "T24602G", "A24607T", "T24610G", "A24649T", "A24652G", "T24727A", "T24766C", "T24811A", "T24916C", "G24982A", "A25027G", "T25128C", "A25132T", "T25168C", "G25304T", "A25316C", "G25499A", "T25621C", "T25789C", "A25800C", "G26221A", "T26563C", "C26596T", "T27106C", "T27107G", "G27251A", "T27400C", "A27411T", "T27534C", "T27537C", "T27556A", "C27687T", "T27815A", "A27979C", "T28034C", "C28091T", "G28120A", "T28228C", "T28371G", "C28375A", "A28386G", "T29127C" ], "spike": [ "C141S", "N484Y", "V489I", "T750S", "L904Q", "S911K", "G914S", "K915Q", "S922T", "A924S", "S925T", "S1037A", "V1212A" ] } }, "children": [ { "branch_attrs": { "labels": { "aa": "ORF1a: V8I, N48S, L53I, L77Q, S78G, N80G, V86C, I95V, N120T, V169A, A181V, E256D, H343Q, V366L, S433A, N455H, N470T, A486V, S498T, K513R, K518Q, R527K, G542S, S546A, R564K, V585T, T609V, L617V, T619S, V621A, A633S, K634R, A637D, V639I, T654R, A667T, V682I, Q692Y, I695V, A698T, V708I, E738D, A746V, K822R, L832V, T870S, A879S, K916N, D934E, E937G, A943T, E944D, T970A, A985T, T986N, L991V, E994Q, P999L, P1002S, T1076R, K1090N, D1120E, Q1138D, K1158Q, N1159K, R1175T, A1178T, T1187I, P1190S, K1191N, E1193K, K1195E, S1196P, V1197T, V1198T, M1252V, K1257R, T1268N, V1298I, E1316D, K1319R, F1329L, I1367V, Y1492F, T1574I, V1588A, T1710A, T1740M, I1762V, T1912I, I2034V, V2061I, I2107V, I2128T, F2230L, I2323V, Y2414H, I2467V, H2497Q, V2565I, I2742V, V2743I, L2749F, H2776Y, V2798L, S2813T, R3345H, I3670V, T3752N, V4158I, V4349I, P4366S, A4371E; ORF1b: T284I, A1190V, K1385R, S1446A, F1657V, V1685I, P1851S, S2052C, V2178A, T2488I, D2666E, 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, V225A, N234S, P240A; ORF3b: P3L, L11P, I13V, H19L, L30H, Q31P, Q36M, R37C, K41R, L46*, R51K, I52T, I54T, L57*, A65V, P68L, F70S, L74S, *79C, L80R, T94A, S95N, I99M, M123T; ORF6: R23K, I31V, D61E; ORF7a: I10V, A11V, A13T, I111T, K120N, T121S; ORF7b: N2S, L34F, I37S, N42P; ORF8a: S12I, C15G, S18T, L30I; ORF8b: Y2F, L3*, T5I, H6P, T27Q, *28K, S30T, N31G, L33V, D35E, V36A, P43T, E50T, Y64H; ORF9b: Q5K, T6I, D29N; envelope: N66S; membrane_protein: N4Y, K14Q, V22L, A29P, Y46H; nucleocapsid: P8Q, T25A, G32E, Q268A, L353M; spike: L2T, I3C, A5I, F6L, L7S, V8F, T9S, V11F, K12C, A13V, H14S, E17D, G18T, G20E, I21T, I22F, S23D, R24D, K25V, P26S, Q27P, K29Q, M30Q, A31N, Q32L, R37K, N43P, F47Y, L52H, T55V, Y58L, D63N, L66V, T67V, Q68G, Y69L, F70M, L72F, V74Y, D75R, L81I, D82P, G84K, I98V, I102V, F107M, D108N, T110K, T111S, A114V, V115I, V117M, H122N, I123V, I124V, V127A, N131Q, K134D, E135N, M137F, Y138F, T139A, S141I, G145S, T146Q, K148I, S150T, W151I, V152L, Y153F, Q154E, S155N, Y161F, R163Y, E165S, K166D, Q169L, L170M, T172V, A173G, P174E, T176P, D181H, V186I, R190K, S195N, V196I, Q198S, T199G, Y200F, T201Q, A202N, V203I, N204D, L205V, P206A, R207N, T211S, V215L, I219L, F224L, I226L, S230N, V234L, M235L, A236T, M237A, L239I, K241N, T242I, S244T, Q245W, T246G, S249P, A250V, Y253F, N256Y, H259P, R265K, F266Y, N267D, E268Y, T273V, N281H, T289S, I290V, N292S, N294E, V295I, T310S, Q311K, D326G, K327E, R333T, N336S, T343K, K344R, D347N, T353S, P371A, S372I, I375N, T380S, S381N, T386S, L388V, I389V, R390K, S391G, S392D, E393D, V397I, T417M, I421L, A431T, K432S, H433S, D434G, G436F, Y439K, H443L, K445H, T446G, K449R, L455I, S462P, D464G, L472F, G474C, V475Y, C476W, T477P, S479N, T480D, D482G, P485T, N486T, V487N, P488G, E490G, A493P, T494Y, E518D, V520I, K521T, K533T, D540P, S542L, S547P, T555F, Q566K, I570V, T590I, V621I, T624A, I626V, I665L, S668N, G670D, V704I, L729Q, I754V, M770I, K1055R, Y1092F, I1096L, G1153R" }, "mutations": { "ORF1a": [ "V8I", "N48S", "L53I", "L77Q", "S78G", "N80G", "V86C", "I95V", "N120T", "V169A", "A181V", "E256D", "H343Q", "V366L", "S433A", "N455H", "N470T", "A486V", "S498T", "K513R", "K518Q", "R527K", "G542S", "S546A", "R564K", "V585T", "T609V", "L617V", "T619S", "V621A", "A633S", "K634R", "A637D", "V639I", "T654R", "A667T", "V682I", "Q692Y", "I695V", "A698T", "V708I", "E738D", "A746V", "K822R", "L832V", "T870S", "A879S", "K916N", "D934E", "E937G", "A943T", "E944D", "T970A", "A985T", "T986N", "L991V", "E994Q", "P999L", "P1002S", "T1076R", "K1090N", "D1120E", "Q1138D", "K1158Q", "N1159K", "R1175T", "A1178T", "T1187I", "P1190S", "K1191N", "E1193K", "K1195E", "S1196P", "V1197T", "V1198T", "M1252V", "K1257R", "T1268N", "V1298I", "E1316D", "K1319R", "F1329L", "I1367V", "Y1492F", "T1574I", "V1588A", "T1710A", "T1740M", "I1762V", "T1912I", "I2034V", "V2061I", "I2107V", "I2128T", "F2230L", "I2323V", "Y2414H", "I2467V", "H2497Q", "V2565I", "I2742V", "V2743I", "L2749F", "H2776Y", "V2798L", "S2813T", "R3345H", "I3670V", "T3752N", "V4158I", "V4349I", "P4366S", "A4371E" ], "ORF1b": [ "T284I", "A1190V", "K1385R", "S1446A", "F1657V", "V1685I", "P1851S", "S2052C", "V2178A", "T2488I", "D2666E", "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", "V225A", "N234S", "P240A" ], "ORF3b": [ "P3L", "L11P", "I13V", "H19L", "L30H", "Q31P", "Q36M", "R37C", "K41R", "L46*", "R51K", "I52T", 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"I1096L", "G1153R" ] } }, "name": "LYRa11", "node_attrs": { "accession": "KF569996", "author": { "author": "He et al", "journal": "J. 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": 0.14658763, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/KF569996", "virus_type": { "value": "SARS related coronavirus" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: E246D, D314N, C351S, N455S, V491I, G493S, I529V, S549A, H576Q, A620T, V627I, V631I, E673D, S677C, A746S, I785V, Q1071L, I1121T, K1141Q, H1150Q, N1159A, D1162E, Q1184P, E1213D, Q1241H, A1290S, E2189D, F2297I, A2437T, V2756L, R2823K, Y3374H, F3593L; ORF1b: E83D, A1831S, D1871E, T2070A, V2147M, V2365I; ORF3a: R6S, G18S, T40S, V97L, R134K, I169V, S171A, T175I, T176S, I203V, L219I, V225I, Y233F, D241P, H242N; ORF3b: V8A, L11Q, S29L, E34A, Q35F, R37H, *40S, *61S, *62L, N75S, R76L, L77H, N78K, *79L, I93L, Q100H, I101R; ORF6: I31M, N48K; ORF8b: S32T, D35N, P43H; ORF9b: V31M; membrane_protein: D3E, T8S, K14R, L128V; nucleocapsid: S34N, T81P, I158T, E291D; spike: E149S, E162D, G243D, R265S, D296S, C476R, E569Q, S827N, S1105A" }, "mutations": { "ORF1a": [ "E246D", "D314N", "C351S", "N455S", "V491I", "G493S", "I529V", "S549A", "H576Q", "A620T", "V627I", "V631I", "E673D", "S677C", "A746S", "I785V", "Q1071L", "I1121T", "K1141Q", "H1150Q", "N1159A", "D1162E", "Q1184P", "E1213D", "Q1241H", "A1290S", "E2189D", "F2297I", "A2437T", "V2756L", "R2823K", "Y3374H", "F3593L" ], "ORF1b": [ "E83D", "A1831S", "D1871E", "T2070A", "V2147M", "V2365I" ], "ORF3a": [ "R6S", "G18S", "T40S", "V97L", "R134K", "I169V", "S171A", "T175I", "T176S", "I203V", "L219I", "V225I", "Y233F", "D241P", "H242N" ], "ORF3b": [ "V8A", "L11Q", "S29L", "E34A", "Q35F", "R37H", "*40S", "*61S", "*62L", "N75S", "R76L", "L77H", "N78K", "*79L", "I93L", "Q100H", "I101R" ], "ORF6": [ "I31M", "N48K" ], "ORF8b": [ "S32T", 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K280T, N324S, S351V, T362I, D375N, P376K, I378V, H390Y, A412S, T439V, F480L, A501S, V517I, D571G, V681I, A698V, D829N, T870N, A879T, N893E, I896V, K916N, D933E, A936V, A943I, E944D, T968A, A985T, L991I, P997S, N1029S, I1035V, K1063R, K1158R, D1189R, D1213N, H1241R, D1299G, A1321I, A1328E, I1343V, V1371I, V1422I, L1528Q, F1596Y, V1775I, I1816V, T2024S, I2107V, I2128T, K2135R, A2184V, S2219F, T2224I, F2230L, V2267I, F2305V, A2506G, T2574I, A2577S, A2591V, V2775I, S2813A, A2971V, V3122A, I3489V, T3566M, K3816R, E3883A, N3905S, V4086I, V4327I; ORF1b: T17I, L238M, H1168Y, C2153S, A2376V, V2564A, S2658F, R2684T, N2695H; ORF3a: S24F, P25L, L41F, P42S, G44R, I77T, A103V, V118L, N152Y, D165N, K179E, Y211H, T220S, E226Q; ORF3b: M1T, Q11H, P68L, L80V, L83Q, L85F, S91L, M124T; ORF6: I16V, I33T, R38T, E56V; ORF7a: A11V, K32E, H94Q, I111L; ORF8a: F7L, G8T, L9C, L10I, T11S, S12L, V13C, Y14C, C17R, S18T, I19V, Q20V, E21Q, C22R, E24V, Q27T, L30V, D33N, K36*, Q38*; ORF8b: T1M, Y2F, T5I, K12R, I13G, G14N, P15T, R16Y, K17N, S18T, *24L, V25G, W26K, T27V, *28L, T29S, S30F, N31H, T32R, L33W, *34H, N35T, V36M, W37V, L39A, Y40C, I41T, S42P, H43N, V44I, E45T, E50D, P52V, V53G, S55A, I57V, V58A, S61W, L63F, Y64H, *65K, H67S, A71T, Y72F, Q73R, N85K; ORF9b: Q5P, P10L, Q33L, N61S, E66K, A69V; nucleocapsid: P14S, R69Q, V132I, N206T, M211I, E281D; spike: I21V, S23N, R24L, K25R, P26T, M30L, A31S, D63H, N73S, V74I, D75E, D82K, V87I, I102V, V115I, N129Y, E135D, R142A, K148I, S155N, T176S, K180I, D181A, L194F, S195T, T199D, A202P, P206L, T211A, F213L, Q245K, H259Q, T260S, E268Q, I290T, N292S, S308A, T310V, Q311T, N336S, L355F, K365N, S391F, H433Y, N435V, N437S, Y439F, K445S, T446S, D463E, V475A, Y484N, P485Q, I489L, E518S, L532F, R544T, T555A, Q566K, E593A, T608K, A609T, T616A, A618S, S623T, T624S, I626P, N627F, A644S, I665V, I687V, L729A, I754V, A775T, I776L, K777R, S792L, F805Y, G820A, E821D, D825G, E850D, V860I, S914T, S1079F, I1096T, E1177D, I1207V, A1208G, I1209L, V1210F, T1213I, C1218Y, M1219F, L1226C, A1229M, K1237R" }, "mutations": { "ORF1a": [ "R24G", "S34T", "S40T", "P62R", "Q66E", "D75E", "N80T", "L92M", "D93N", "I102T", "F136Y", "E148V", "G150N", "I154V", "N160Q", "T174I", "D203G", "F241Y", "E256D", "G268E", "K280T", "N324S", "S351V", "T362I", "D375N", "P376K", "I378V", "H390Y", "A412S", "T439V", "F480L", "A501S", "V517I", "D571G", "V681I", "A698V", "D829N", "T870N", "A879T", "N893E", "I896V", "K916N", "D933E", "A936V", "A943I", "E944D", "T968A", "A985T", "L991I", "P997S", "N1029S", "I1035V", "K1063R", "K1158R", "D1189R", "D1213N", "H1241R", "D1299G", "A1321I", "A1328E", "I1343V", "V1371I", "V1422I", "L1528Q", "F1596Y", "V1775I", "I1816V", "T2024S", "I2107V", "I2128T", "K2135R", "A2184V", "S2219F", "T2224I", "F2230L", "V2267I", "F2305V", "A2506G", "T2574I", "A2577S", "A2591V", "V2775I", "S2813A", "A2971V", "V3122A", "I3489V", "T3566M", "K3816R", "E3883A", "N3905S", "V4086I", "V4327I" ], "ORF1b": [ "T17I", "L238M", "H1168Y", "C2153S", "A2376V", "V2564A", 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"mutations": { "ORF1a": [ "L917V", "P993H", "E1541A", "Q2679P", "C4304F", "H4310Q", "I4327F", "T4331A", "L4342F" ], "ORF1b": [ "M2439R" ], "envelope": [ "T30A" ], "nuc": [ "C3014G", "C3243A", "T3604C", "A4887C", "A8301C", "G13090A", "G13176T", "C13195G", "A13207G", "A13244T", "A13256G", "C13289T", "G13378T", "T20714G", "A26285G", "G29507A" ], "nucleocapsid": [ "G414E" ] } }, "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 C" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.14409569, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/KP886809", "virus_type": { "value": "SARS related coronavirus" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: N126S, D897V, L2275R; ORF1b: A2268V; ORF6: *64L; spike: E75Q" }, "mutations": { "ORF1a": [ "N126S", "D897V", "L2275R" ], "ORF1b": [ "A2268V" ], "ORF6": [ "*64L" ], "nuc": [ "A580T", "A642G", "C1762T", "A2955T", "T7089G", "C20201T", "G21716C", "C27109T", "A27370T", "A27372T", "T29838C" ], "spike": [ "E75Q" ] } }, "name": "YNLF_31C", "node_attrs": { "accession": "KP886808", "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 C" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.14392718, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/KP886808", "virus_type": { "value": "SARS related coronavirus" } } } ], "name": "NODE_0000016", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.14355583 } }, { "branch_attrs": { "labels": { "aa": "ORF1a: F97Y, F221Y, E233D, K404R, N434G, V597I, L793I, I821T, K841R, D934C, C938Y, D955E, T970I, Q988L, L991H, P1473S, I1519V, I1560L, F2150L, K2181R, S2182G, K2185R, F2227L, F2230L, N2241S, L2246S, S3223A; ORF3a: F79L, N119S; ORF3b: I13T, T20I; ORF6: I60L; ORF7a: T14S; ORF8a: L30Q; ORF8b: Y2N, V25I, T29S; ORF9b: N7S; spike: K148Q, F185Y, H259Y, V276I, S279A, L322R, Q401E, H433Q, N435K, N437Q, T590A, I665T, T669V" }, "mutations": { "ORF1a": [ "F97Y", "F221Y", "E233D", "K404R", "N434G", "V597I", "L793I", "I821T", "K841R", "D934C", "C938Y", "D955E", "T970I", "Q988L", "L991H", "P1473S", "I1519V", "I1560L", "F2150L", "K2181R", "S2182G", "K2185R", "F2227L", "F2230L", "N2241S", "L2246S", "S3223A" ], "ORF3a": [ "F79L", "N119S" ], "ORF3b": [ "I13T", "T20I" ], "ORF6": [ "I60L" ], "ORF7a": [ "T14S" ], "ORF8a": [ "L30Q" ], "ORF8b": [ "Y2N", "V25I", "T29S" ], "ORF9b": [ "N7S" ], "nuc": [ "C421T", "T555A", "A574T", "T613C", "T772A", "T826C", "T886C", "G898A", "T927A", "A964C", 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"T6940A", "T6946A", "C6955A", "T6961C", "T6964C", "T6970A", "A6987G", "T7002C", "T7006C", "A7015C", "T7087G", "T7096C", "T7129C", "T7306C", "A7330T", "C7699T", "T7714C", "C8173T", "G9223A", "C9229T", "T9247A", "T9280A", "T9751C", "T9932G", "T10204A", "T10210C", "T10213A", "T10219C", "C10303T", "A10309T", "G10315A", "T10537A", "T10699C", "C10733T", "C10870T", "T10885C", "A10909G", "T10930C", "C11102T", "T11419C", "T12460C", "C12901T", "A13656G", "T13863C", "A14463G", "C15966T", "C16464T", "A16491G", "C16974T", "T17199C", "T17406C", "A17553G", "C17631T", "T17835C", "T18123C", "C19026T", "T20079C", "C20238T", "T20271C", "C20427T", "T20634C", "T20730C", "T20886C", "A21081T", "G21420A", "A21456G", "T21553C", "C21679T", "A21787C", "T21910A", "A21935C", "T22047A", "T22157C", "T22180A", "A22192T", "T22264A", "C22268T", "G22319A", "T22328G", "G22354A", "T22393C", "C22402T", "C22420A", "T22447C", "T22458G", "G22474A", "T22654C", "T22669A", "C22694G", "C22717T", "T22723C", "T22727C", "T22792A", "T22798G", "A22802C", "T22804G", "C22918A", "A22924T", "T22942C", "C22957T", "A22969G", "A23176C", "A23261G", "T23314A", "T23344A", "T23487C", "A23498G", "C23499T", "C23521T", "T23524C", "A23533T", "A23698T", "T23740C", "T23743G", "T23833C", "T23911C", "A23914G", "A23953C", "G24067C", "T24103C", "T24148A", "T24223C", "T24368C", "T24391A", "T24400C", "C24580T", "T24649G", "T24898C", "T25066C", "A25213G", "T25252C", "A25267C", "C25268T", "T25270A", "A25489G", "T25505C", "T25513C", "T25553C", "T25601C", "A25626G", "T25729C", "C25750T", "A26944T", "A27359T", "A27421T", "T27430C", "A27492T", "A27498T", "C27522T", "A27564T", "A27681G", "T27810C", "T27977A", "G28046A", "C28059G", "T28111A", "A28296G", "T28638C", "A29635G" ], "spike": [ "K148Q", "F185Y", "H259Y", "V276I", "S279A", "L322R", "Q401E", "H433Q", "N435K", "N437Q", "T590A", "I665T", "T669V" ] } }, "children": [ { "branch_attrs": { "labels": { "aa": "ORF1a: V8I, N48S, L53I, L64P, L77Q, S78G, N80D, K84R, V86R, I95V, V182L, E235G, S308T, H343Q, T355N, V384A, A501T, V517I, Q526H, A549S, G572S, D589N, G618D, I679V, V785I, D795A, K796N, L832V, A912S, D935E, E945R, Q958K, E969D, V971I, E976Q, T986V, L988A, T998L, P999H, F1006L, K1025E, D1067H, T1121I, V1142M, A1154V, A1159V, R1175K, E1183V, P1184L, T1187A, D1189Y, E1193D, P1201T, V1202I, A1233T, H1241Q, Q1244K, V1298I, D1299N, I1367V, V1450I, E1475D, D1508E, E1520K, F1571L, D1577E, T1758M, V1892I, S2025P, G2068D, S2113G, I2128V, V2141M, V2183I, A2184V, L2306F, T2437A, I2467V, A2614S, K2682R, L2749I, T2772I, D2777G, A2886S, T2944A, L3060P, C3130F, M3143V, G3410E, K3551R, I3598V, I3670V, D3971N, D4094E, P4097S, Y4206H; ORF1b: T17I, E268A, D734G, V1144I, V1644I, A2073T, V2089F, P2116S, Y2139H, A2145V, Q2310R, I2365V, I2525V, T2533A, V2691I; ORF3a: S12A, S18A, Y74H, K134R, N153C, Y154F, V163I, V169L, A171S, I175T, S176T, T177Q, V203I, I219L, T220S, I225A, F233Y, N234S, P240V, P241D, N242H; ORF3b: P3L, F7Y, A8V, I10T, Q11P, T13A, M14L, Q24L, I25T, L27S, L29S, L30P, A34E, F35L, Q36P, H37N, S40L, K41R, T43I, L57*, S61*, L62*, A65V, L74W, S75N, L76R, K78N, L79C, L80R, Q81L, T82I, L93I, T94A, I99M, H100*, R101I; ORF6: R20K, I24V, M31I, I32L; ORF7a: I112T; ORF8a: L31I, K36*; ORF8b: N2K, H6L, P15S, A23E, *24R, I25L, T27*, *28K, S29N, T32S, *34S, Y40H, I41T, H43L, E50A, Y64C, Y72H; ORF9b: P10L, I24T, M31V, G32V, Q33H, S37N, P40L, A58V, A67V, A69V, Q78K; membrane_protein: L26I, V128L, A210S; nucleocapsid: N30D, N34S, P81K, T158I, K238R, G239S, D291E, T363I; spike: F4L, V8A, T9S, V11A, D50N, T146A, T211I, K217R, F231Y, D274N, V314I, K435Q, N486S, I489V, E490A, E518Q, D540E, Q569E, T608A, I626T, N827S, A874S, K1055R, N1107S, A1212V" }, "mutations": { "ORF1a": [ "V8I", "N48S", "L53I", "L64P", "L77Q", "S78G", "N80D", "K84R", "V86R", "I95V", "V182L", "E235G", "S308T", "H343Q", "T355N", "V384A", "A501T", "V517I", "Q526H", "A549S", "G572S", "D589N", "G618D", "I679V", "V785I", "D795A", "K796N", "L832V", "A912S", "D935E", "E945R", "Q958K", "E969D", "V971I", "E976Q", "T986V", "L988A", "T998L", "P999H", "F1006L", "K1025E", "D1067H", "T1121I", "V1142M", "A1154V", "A1159V", "R1175K", "E1183V", "P1184L", "T1187A", "D1189Y", "E1193D", "P1201T", "V1202I", "A1233T", "H1241Q", "Q1244K", "V1298I", "D1299N", "I1367V", "V1450I", "E1475D", "D1508E", "E1520K", "F1571L", "D1577E", "T1758M", "V1892I", "S2025P", "G2068D", "S2113G", "I2128V", "V2141M", "V2183I", "A2184V", "L2306F", "T2437A", "I2467V", "A2614S", "K2682R", "L2749I", "T2772I", "D2777G", "A2886S", "T2944A", "L3060P", "C3130F", "M3143V", "G3410E", "K3551R", "I3598V", "I3670V", "D3971N", "D4094E", "P4097S", "Y4206H" ], "ORF1b": [ "T17I", "E268A", "D734G", "V1144I", "V1644I", "A2073T", "V2089F", "P2116S", "Y2139H", "A2145V", "Q2310R", "I2365V", "I2525V", "T2533A", "V2691I" ], "ORF3a": [ "S12A", "S18A", "Y74H", "K134R", "N153C", "Y154F", "V163I", "V169L", "A171S", "I175T", "S176T", "T177Q", "V203I", "I219L", "T220S", "I225A", "F233Y", "N234S", "P240V", "P241D", "N242H" ], "ORF3b": [ "P3L", "F7Y", "A8V", "I10T", "Q11P", "T13A", "M14L", "Q24L", "I25T", "L27S", "L29S", "L30P", "A34E", "F35L", "Q36P", "H37N", "S40L", "K41R", "T43I", "L57*", "S61*", "L62*", "A65V", "L74W", "S75N", "L76R", "K78N", "L79C", "L80R", "Q81L", "T82I", "L93I", "T94A", "I99M", "H100*", "R101I" ], "ORF6": [ "R20K", "I24V", "M31I", "I32L" ], "ORF7a": [ "I112T" ], "ORF8a": [ "L31I", "K36*" ], "ORF8b": [ "N2K", "H6L", "P15S", "A23E", "*24R", "I25L", "T27*", "*28K", "S29N", "T32S", "*34S", "Y40H", "I41T", "H43L", "E50A", "Y64C", "Y72H" ], "ORF9b": [ "P10L", "I24T", "M31V", "G32V", "Q33H", "S37N", "P40L", "A58V", "A67V", "A69V", "Q78K" ], "membrane_protein": [ "L26I", "V128L", "A210S" ], "nuc": [ "C98T", "T144C", "A258G", "T286A", "G287A", "G349A", "C358T", "T400C", "T403A", "A408G", "T422A", "A439G", "C446T", "T456C", "T490C", "T494C", "T495A", "A497G", "C502T", "A503G", "C508T", "C514T", "A516G", "G521C", "T522G", "G529A", "A548G", "T631C", "G809C", "C835T", "C868T", "T874C", "A898T", "C958T", "A969G", "C988T", 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"N1107S", "A1212V" ] } }, "name": "Rp3", "node_attrs": { "accession": "DQ071615", "author": { "author": "Li et al", "journal": "Science 310 (5748), 676-679 (2005)", "title": "Bats are natural reservoirs of SARS-like coronaviruses", "value": "Li et al" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.14544687, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/DQ071615", "virus_type": { "value": "SARS related coronavirus" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: E199D, L204F, S351T, E930D, T946S, E948A, I970M, D983G, P997L, M1033T, V1192I, Q1244H, V2138A, K2532R, L2759F, V2775A; ORF1b: I2136V, V2606A; ORF3a: I117V, N152H; ORF3b: Q11H, I54T; ORF6: M31V; ORF8a: F7L, Y29F; ORF8b: T1S, S42F, E50N, *65G; spike: H443P, E518G, S574T, H611R, L729Q, S750T, K1027R" }, "mutations": { "ORF1a": [ "E199D", "L204F", "S351T", "E930D", "T946S", "E948A", "I970M", "D983G", "P997L", "M1033T", "V1192I", "Q1244H", "V2138A", 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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": 0.14834986, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/FJ588686", "virus_type": { "value": "SARS related coronavirus" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: L349A, P376Q, K492R, L591I, T609I, T768A, Q1138H, A3119V; spike: A714S, E850D" }, "mutations": { "ORF1a": [ "L349A", "P376Q", "K492R", "L591I", "T609I", "T768A", "Q1138H", "A3119V" ], "nuc": [ "T967C", "T1162C", "A1192G", "C1270T", "T1309C", "T1310G", "T1311C", "C1342T", "C1392A", "A1393G", "C1645T", "T1684G", "A1740G", "A1807G", "T1873C", "C2036A", "T2071C", "C2091T", "C2245T", "A2380G", "A2567G", "A2638G", "T2662C", "A2713G", "G2716A", "C3427T", "T3523C", "G3679T", "A4150G", "A4324G", 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I2128V, A2138V, V2141M, A2552T, M3560L; ORF1b: T76A, A1428V, H1784Y; ORF3a: I77M, S119C, A143V; ORF3b: P3S, I20T; ORF8b: *28Q; ORF9b: S37N; membrane_protein: M133L; nucleocapsid: S24P, N194D; spike: C7S, V249I, S456T, G518A, T535I" }, "mutations": { "ORF1a": [ "I2128V", "A2138V", "V2141M", "A2552T", "M3560L" ], "ORF1b": [ "T76A", "A1428V", "H1784Y" ], "ORF3a": [ "I77M", "S119C", "A143V" ], "ORF3b": [ "P3S", "I20T" ], "ORF8b": [ "*28Q" ], "ORF9b": [ "S37N" ], "membrane_protein": [ "M133L" ], "nuc": [ "T202C", "G583A", "C715T", "C811T", "C892T", "T2023C", "C2644T", "T3641C", "C3736T", "T3787C", "G4810A", "A4882G", "T5023C", "A5662G", "T6616A", "A6640G", "A6647G", "T6661C", "A6676G", "C6678T", "A6679G", "A6682G", "G6686A", "T6697C", "T6706C", "T6722C", "T6727C", "T6739C", "A6745C", "A6748G", "G7003A", "G7087T", "G7417A", "C7837A", "A7867T", "G7919A", "C8032T", "T8080C", "T8122A", "T8125C", "T8299C", "A8305G", "T8536C", "T8662C", "C8788T", "T8872A", "A9121G", "T9163C", "A9169G", "C9217T", 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"T21512A", "C21910T", "T22081C", "C22231A", "G22238A", "T22468C", "C22471T", "T22504C", "A22823C", "T22859A", "G23046C", "C23097T", "C23299T", "T23584A", "T23713C", "A23728G", "C24223T", "T24535C", "T24883C", "T24937C", "T25000C", "T25039C", "T25078C", "C25099T", "C25123T", "C25216T", "A25237G", "A25297G", "C25399T", "A25441G", "G25474A", "C25487T", "T25501G", "T25517C", "C25543T", "C25553T", "A25625T", "T25690C", "C25698T", "T25750C", "T26506C", "T26576C", "C26599T", "A26876C", "C27723T", "T28055C", "T28336C", "G28386A", "C28599T", "T28614C", "C28701T", "G28791A", "T28845C", "A28846G", "T29034C" ], "nucleocapsid": [ "S24P", "N194D" ], "spike": [ "C7S", "V249I", "S456T", "G518A", "T535I" ] } }, "name": "Rs4081", "node_attrs": { "accession": "KY417143", "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": 0.14402182000000002, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/KY417143", "virus_type": { "value": "SARS related coronavirus" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: V182F, D930Y, D933N, P1185S, K1186R, S1491Y, S1933Y, Q2011R, K2062R, N2143D, L2231F, F2234Y, M2351T, D2433G, L3011F; ORF1b: D83N, R96K, D98N, T2084I, V2089I, V2136I, T2203I, A2209V; ORF3a: G44R, V117A, D192N; ORF3b: P3L, I10T, I99T, T106I; ORF9b: Q35R, K41R; membrane_protein: V87I; nucleocapsid: P8S, A36T; spike: E165G, V314I, N486T, V621I" }, "mutations": { "ORF1a": [ "V182F", "D930Y", "D933N", "P1185S", "K1186R", "S1491Y", "S1933Y", "Q2011R", "K2062R", "N2143D", "L2231F", "F2234Y", "M2351T", "D2433G", "L3011F" ], "ORF1b": [ "D83N", "R96K", "D98N", "T2084I", "V2089I", "V2136I", "T2203I", "A2209V" ], "ORF3a": [ "G44R", "V117A", "D192N" ], "ORF3b": [ "P3L", "I10T", "I99T", "T106I" ], 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"C18480T", "C18741T", "T18753C", "A18756G", "T18843C", "C18877T", "G18993A", "A19008G", "G19197A", "T19212C", "T19335C", "T19365C", "T19413C", "C19467T", "A19485G", "G19551A", "C19596T", "T19611C", "C19649T", "A19656T", "G19663A", "A19671G", "A19683G", "C19686T", "C19773T", "T19797C", "G19803A", "G19804A", "C19866T", "T19896C", "C20006T", "C20024T", "T20031C", "C20079T", "G20139A", "C20143A", "T20149C", "C20160T", "T20193C", "C20230T", "A20250G", "C20322T", "A20394G", "C20448T", "T20451C", "A20589G", "T20829A", "T20862G", "A20910G", "T20919C", "C20976T", "T20979C", "G20994A", "A21096T", "A21174T", "A21186C", "T21205C", "C21228T", "G21348A", "T21637A", "T21964C", "A21987G", "A22414G", "G22433A", "A22663G", "A22950C", "C23003T", "T23036C", "T23065C", "T23173C", "T23269C", "T23347G", "G23354A", "C24020T", "A24697G", "A24925T", "A24982G", "T25021C", "C25036T", "T25228A", "A25303C", "G25400A", "T25492C", "T25510G", "G25534A", "A25546G", "C25552T", "T25620C", "G25624C", "C25627T", "C25630T", "A25678G", "C25699T", "T25720C", "G25844A", "T25987C", "C26008T", "G26362T", "C26371T", "A26407G", "C26635T", "T26737C", "G26738A", "T26791C", "C26815T", "C26827T", "T26848C", "C26849A", "A26851G", "C26899T", "T26944G", "T27600C", "C28228T", "C28288T", "G28372A", "A28380G", "A28398G", "T28695C", "C28728T", "T29160C", "C29337T" ], "nucleocapsid": [ "P8S", "A36T" ], "spike": [ "E165G", "V314I", "N486T", "V621I" ] } }, "name": "Rs4255", "node_attrs": { "accession": "KY417149", "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": 0.14470575000000002, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/KY417149", "virus_type": { "value": "SARS related coronavirus" } } } ], "name": "NODE_0000023", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.13745898 } } ], "name": "NODE_0000022", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.13342678 } }, { "branch_attrs": { "labels": { "aa": "ORF3a: V48I; ORF3b: I10T; ORF6: V31M; spike: H14Y, G18S, G20S, K25G, A31T, N43P, Y58H, F70I, I74L, H122N, K134D, E135N, M137I, Y138F, *148T, V152I, Q154N, D162E, R163N, E165S, S167D, T172L, P174E, Y185F, S195H, S201Q, I205V, R207S, V215A, L220F, F224L, S230N, S244N, R245*, T246G, Y259H, I276V, A279S, N294D, S296G, Q311K, R322L, K327E, N336S, D347N, K435N, Q437N, K445Q, T446S, E490D, G518E, Q569E" }, "mutations": { "ORF3a": [ "V48I" ], "ORF3b": [ "I10T" ], "ORF6": [ "V31M" ], "nuc": [ "C2773T", "T3244A", "T6175C", "C6178T", "G12892A", "T13000C", "G16773A", "A16812G", "T17952C", "A18405G", "C19866T", "T20829A", "A21069G", "A21096G", "T21345C", "G21348A", "A21378G", "C21533T", "G21545A", "G21551A", "C21562T", "A21566G", "A21567G", "A21568C", "G21584A", 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"G22798T", "C22802A", "G22804T", "C22819T", "A22826C", "C22830G", "A22831C", "A22834G", "G22852A", "C22882T", "T22924A", "T22927A", "C22939T", "C22942T", "A22963C", "G22969A", "T23032A", "G23046A", "C23074T", "C23105T", "A23149T", "A23152T", "C23176A", "C23198G", "C23287T", "A23296T", "A23314T", "A23323C", "T23336C", "A23338C", "A23344T", "C23443T", "T23701C", "C23989T", "A23998G", "T24883C", "T25228A", "G25412A", "T25720C", "T26944A", "G27272A", "T27567C", "T28695C", "G29097A" ], "spike": [ "H14Y", "G18S", "G20S", "K25G", "A31T", "N43P", "Y58H", "F70I", "I74L", "H122N", "K134D", "E135N", "M137I", "Y138F", "*148T", "V152I", "Q154N", "D162E", "R163N", "E165S", "S167D", "T172L", "P174E", "Y185F", "S195H", "S201Q", "I205V", "R207S", "V215A", "L220F", "F224L", "S230N", "S244N", "R245*", "T246G", "Y259H", "I276V", "A279S", "N294D", "S296G", "Q311K", "R322L", "K327E", "N336S", "D347N", "K435N", "Q437N", "K445Q", "T446S", "E490D", "G518E", "Q569E" ] } }, "children": [ { "branch_attrs": { "labels": { "aa": "ORF1a: K141R, V182F, D233G, P305S, L349S, V350I, T351I, S455N, A501S, Q526R, V567G, V708I, T774I, K794E, V834F, D930E, E939D, Q958R, P993L, N1029S, T1033M, H1086Y, Q1138H, C1211F, H1244Q, F1329L, L1530I, K1855R, L2116F, V2195I, M2208T, V3902I, A3933T, L4108I; ORF1b: E1389D, V1806I, H1854Y, A1995V, T2537A, K2538R, A2606V, D2666E, K2674N; ORF3a: I124V, V163I, D192N, V210I; ORF3b: I12T, I20T, 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: L2F, I3F, F4L, L5I, F6G, F7Y, V8T, T9A, L10F, V11L, T12I, A13G, S20N, I22M, S23C, N24H, P26L, P28Q, K29R, M30I, 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"virus_type": { "value": "SARS related coronavirus" } } }, { "branch_attrs": { "labels": { "aa": "ORF1b: V2691I; ORF3a: S6R, R15A, S18G, E21D, L52F, S60T, V62I, H66N, I77F, L79F, V80I, L97V, I108L, I114F, V117C, V118I, S119N, F120A, F123I; ORF3b: I99T; spike: D17E, S18R, S20T, I22F, S23D, N24D, Q27P, M30N, L66V, Y69F, S71T, D75N, L81I, G84R, I102V, D108N, T110K, T111S, A114V, V117I, I123V, I124V, V127A, N131E, I137F, K149Q, W151*, Y153F, Y161F, N163Y, Q169*, T176S, R190K, A199G, P206A, S214N, V233A, V234I, M235L, M237A, K241R, T242P, *245W, V249A, N256Y, H259P, N265K, F266Y, N267D, T289S, I290V, N292S, D294E, V295I, G296D, S308A, T310S, D326G, R333T, T343K, K344R, T353S, P371A, S372T, I375N, T380S, S381N, T386S, L388V, I389V, R390K, S391G, S392D, E393D, V397I, E401Q, T417M, I421L, A431T, K432T, Q433T, D434G, G436Y, Y439K, P443L, Q445H, S446G, K449R, L455I, S462P, D464G, L472F, G474C, V475Y, R476W, T477P, S479N, T480D, D482G, P485T, N486T, V487N, P488G, D490G, A493P, T494Y, E518D, 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"T28055C", "T28336C", "C28599T", "T28614C", "C28695T", "C28701T", "C29127T", "C29133T", "A29196G" ], "nucleocapsid": [ "S24P" ] } }, "name": "RsSHC014", "node_attrs": { "accession": "KC881005", "author": { "author": "Ge et al", "journal": "Nature 503, 535-538 (2013)", "title": "Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor", "value": "Ge et al A" }, "clade_membership": { "value": "unassigned" }, "country": { "value": "China" }, "div": 0.17221626, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/KC881005", "virus_type": { "value": "SARS related coronavirus" } } }, { "branch_attrs": { "labels": { "aa": "ORF1a: K141R, S349L, V739I, R814C, A819S, A1076T, Q1138H, R1186K, I1202V, H1244Q, F1329L, V1387I, D1917A, A2126T, T2382N, T2437A, A2506T, R2532K, F2759I, V3055A, F3062V, G3269R; ORF1b: S309F, R1096K, S1159T, E1184D, S1187N, S1212N, M1765T, N1858S, H2065Y; ORF6: A25T, K48N; ORF8a: G8T, L9C, L10I, T11S, S12L, V13C, Y14S, 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], "spike": [ "V354I" ] } }, "name": "Rs4084", "node_attrs": { "accession": "KY417144", "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": 0.17765368, "host": { "value": "Bat" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/KY417144", "virus_type": { "value": "SARS related coronavirus" } } } ], "name": "NODE_0000030", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.16956069000000001 } } ], "name": "NODE_0000028", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.16441178 } } ], "name": "NODE_0000026", "node_attrs": { "clade_membership": { "value": "unassigned" }, "div": 0.16089814 } }, { "branch_attrs": { "labels": { "aa": "ORF1a: R2181K; ORF1b: V2089I, V2136I; 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