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Table 2 Description of sequence data used in this study

From: Codon usage patterns of LT-Ag genes in polyomaviruses from different host species

No.ICTV TaxonomyNCBI Reference Sequence
Virus nameAbbr.Accession No.Host speciesIsolation sourceCountryYearbpGroup
(host)
Ref.
1bat polyomavirus 4aBatPyV4aNC_038556.1Artibeus planirostrisspleenFrench Guiana20115187M[24]
2Ateles paniscus polyomavirus 1ApanPyV1NC_019853.1Ateles paniscusNAGermanyNA5273P[25]
3bat polyomavirus 5b1BatPyV5b-1NC_026767.1Pteropus vampyrusspleenIndonesia20125047M[26]
4bat polyomavirus 5aBatPyV5aNC_026768.1Dobsonia moluccensisspleenIndonesia20125075M[26]
5Bornean orang-utan polyomavirusOraPyV-BorNC_013439.1Pongo pygmaeusbloodNANA5168P[27]
6Cardioderma polyomavirusCardiodermaPyVNC_020067.1Cardioderma correctal swabKenya20065372M[28]
7bat polyomavirus 4bBatPyV4bNC_028120.1Carollia perspicillataspleenFrench Guiana20115352M[24]
8chimpanzee polyomavirusChPyVNC_014743.1Pan troglodytes verusbloodNANA5086P[29]
9vervet monkey polyomavirus 1VmPyV1NC_019844.1Chlorocebus pygerythrusspleenZambia20095157P[30]
10vervet monkey polyomavirus 3VmPyV3NC_025898.1Chlorocebus pygerythrusspleenZambia20095055P[30]
11Eidolon polyomavirus 1EidolonPyVNC_020068.1Eidolon helvumrectal swabKenya20095294M[28]
12Gorilla gorilla gorilla polyomavirus 1GgorgPyV1NC_025380.1Gorilla gorilla gorillaNACongo Republic20085300P[31]
13Human polyomavirus 9HPyV9NC_015150.1Homo sapiensNAGermany20095026H[32]
14Human polyomavirus 12HPyV12NC_020890.1Homo sapiensNAGermany20075033H[33]
15Macaca fascicularis polyomavirus 1MfasPyV1NC_019851.1Macaca fascicularisNAGermanyNA5087P[25]
16Merkel cell polyomavirusMCPyVNC_010277.2Homo sapiensskinUSA20095387H[16]
17hamster polyomavirusHaPyVNC_001663.2Mesocricetus auratus strain Z3NAGermany19675372M[34]
18bat polyomavirus 3bBatPyV3bNC_028123.1Molossus molossusspleenFrench Guiana20114903M[24]
19mouse polyomavirusMPyVNC_001515.2Mus musculusNANANA5307MNA
20New Jersey polyomavirusNJPyVNC_024118.1Homo sapiensbicep muscleUSA20135108H[35]
21Otomops polyomavirus 2OtomopsPyVNC_020066.1Otomops martienssenirectal swabKenya20064914M[28]
22Otomops polyomavirus 1OtomopsPyV1NC_020071.1Otomops martienssenirectal swabKenya20065176M[28]
23Pan troglodytes verus polyomavirus 2aPtrovPyV2aNC_025370.1Pan troglodytes verusNACote d’Ivoire20105309P[31]
24Pan troglodytes verus polyomavirus 3PtrovPyV3NC_019855.1Pan troglodytes verusNACote d’IvoireNA5333P[25]
25Pan troglodytes verus polyomavirus 4PtrovPyV4NC_019856.1Pan troglodytes verusNACote d’IvoireNA5349P[25]
26Pan troglodytes verus polyomavirus 5PtrovPyV5NC_019857.1Pan troglodytes verusNACote d’IvoireNA4994P[25]
27Pan troglodytes schweinfurthii polyomavirus 2PtrosPyV2NC_019858.1Pan troglodytes schweinfurthiiNAUgandaNA4970P[25]
28Pan troglodytes verus polyomavirus 1aPtrovPyV1aNC_025368.1Pan troglodytes verusNACote d’Ivoire20095303P[31]
29Piliocolobus badius polyomavirus 2PbadPyV2NC_039051.1Piliocolobus badiusNACote d’Ivoire20055148P[36]
30Piliocolobus rufomitratus polyomavirus 1PrufPyV1NC_019850.1Piliocolobus rufomitratusNACote d’IvoireNA5140P[25]
31raccoon polyomavirusRacPyVNC_023845.1raccoonNAUSA20115016M[37]
32Rattus norvegicus polyomavirus 1RnorPyV1NC_027531.1Rattus norvegicusspleenGermany20055318M[38]
33bat polyomavirus 3a-B0454BatPyV3a-B0454NC_038557.1Sturnira liliumspleenFrench Guiana20115058M[24]
34Sumatran orang-utan polyomavirusOraPyV-SumNC_028127.1Pongo abeliibloodNANA5358P[27]
35Trichodysplasia spinulosa-associated polyomavirusTSPyVNC_014361.1Homo sapiensskinNetherlands20095232H[15]
36yellow baboon polyomavirus 1YbPyV1NC_025894.1Papio cynocephalusspleenZambia20095064P[30]
37African elephant polyomavirus 1AelPyV1NC_022519.1Loxodonta africanaprotruding ulcerated fibromaDenmark20115722M[39]
38BatPyV4aBatPyV2cNC_038558.1Artibeus planirostrisspleenFrench Guiana20115371M[24]
39Myodes glareolus polyomavirus 1BVPyVNC_028117.1Myodes glareolusblood serum and body fluidsGermany20135032M[40]
40bat polyomavirus 6aBatPyV6aNC_026762.1Acerodon celebensisspleenIndonesia20135019M[26]
41bat polyomavirus 6bBatPyV6bNC_026770.1Dobsonia moluccensisspleenIndonesia20125039M[26]
42bat polyomavirus 6cBatPyV6cNC_026769.1Dobsonia moluccensisspleenIndonesia20125046M[26]
43California sea lion polyomavirus 1SLPyVNC_013796.1Zalophus californianustongueUSA20065112M[41]
44Cebus albifrons polyomavirus 1CalbPyV1NC_019854.2Cebus albifronsNAGermanyNA5013P[25]
45Cercopithecus erythrotis polyomavirus 1CeryPyV1NC_025892.1Cercopithecus erythrotisNACameroonNA5189P[25]
46vervet monkey polyomavirus 2VmPyV2NC_025896.1Chlorocebus pygerythruskidneyZambia20095167P[30]
47Microtus arvalis polyomavirus 1CVPyVNC_028119.1Microtus arvalisblood serum and body fluidsGermany20135024M[40]
48bat polyomavirus 2aBatPyV2aNC_028122.1Desmodus rotundusspleenFrench Guiana20115201M[24]
49equine polyomavirusEPyVNC_017982.1Equus caballuseyeUSA20034987M[42]
50BK polyomavirusBKV; BKPyVNC_001538.1Homo sapiensNANANA5153H[43]
51KI polyomavirusKIPyVNC_009238.1Homo sapiensNANANA5040H[44]
52JC polyomavirusJCV; JCPyVNC_001699.1Homo sapiensNANANA5130H[45]
53Weddell seal polyomavirusWsPyVNC_032120.1Leptonychotes weddelliikidneyAntarctica20145186MNA
54simian virus 40SV40NC_001669.1Macaca mulattaNANANA5243P[46]
55Mastomys polyomavirusMasPyVNC_025895.1Mastomys natalensisspleenZambia20094899M[47]
56Meles meles polyomavirus 1MmelPyV1NC_026473.1Meles melessalivary glandFrance20145187M[48]
57Miniopterus polyomavirusMiniopterusPyVNC_020069.1Miniopterus africanusrectal swabKenya20065213M[28]
58mouse pneumotropic virusMPtVNC_001505.2Mus musculusNANANA4754M[49]
59Myotis polyomavirusMyPyVNC_011310.1Myotis lucifugusNACanada20075081M[50]
60Pan troglodytes verus polyomavirus 8PtrovPyV8NC_028635.1Western chimpanzeecolonNetherlands20145163P[51]
61Pteronotus polyomavirusPteronotusPyVNC_020070.1Pteronotus davyioral swabGuatemala20095136M[28]
62bat polyomavirus 2bBatPyV2bNC_028121.1Pteronotus parnelliispleenFrench Guiana20115041M[24]
63rat polyomavirus 2RatPyV2NC_032005.1Rattus norvegicusNAUSA20165108MNA
64Saimiri sciureus polyomavirus 1SsciPyV1NC_038559.1Saimiri sciureusNAGermanyNA5067PNA
65squirrel monkey polyomavirusSquiPyVNC_009951.1Saimiri boliviensisspleenNANA5075P[52]
66alpaca polyomavirusAlPyVNC_034251.1Vicugna pacosNAUSA20145052M[53]
67WU polyomavirusWUPyVNC_009539.1Homo sapiensNAAustraliaNA5229H[54]
68yellow baboon polyomavirus 2YbPyV2AB767295.2Papio cynocephalusspleen and kidneyZambia20095181P[30]
69Human polyomavirus 6HPyV6NC_014406.1Homo sapiensskinUSA20094926H[16]
70Human polyomavirus 7HPyV7NC_014407.1Homo sapiensskinUSA20094952H[16]
71MW polyomavirusMWPyVNC_018102.1Homo sapiensstoolMalawi20084927H[55]
72STL polyomavirusSTLPyVNC_020106.1Homo sapiensfecal specimenMalawiNA4776H[56]
73Adélie penguin polyomavirusADPyVNC_026141.2Pygoscelis adeliaefecal materialAntarctica20124988A[57]
74budgerigar fledgling disease virusBFDVNC_004764.2Falconiformes and Psittaciformes (wild birds)NANANA4981A[58]
75butcherbird polyomavirusButcherbird PyVNC_023008.1Cracticus torquatusperiocular skinAustralia20095084A[59]
76canary polyomavirusCaPyVNC_017085.1Serinus canarialiverNetherlands20075421A[60]
77crow polyomavirusCpyVNC_007922.1Corvus monedulaNANA20055079A[22]
78Erythrura gouldiae polyomavirus 1EgouPyV1NC_039052.1Erythrura gouldiaeliverPoland20145172A[61]
79finch polyomavirusFPyVNC_007923.1Pyrrhula pyrrhula griseiventrisNANA20055278A[22]
80goose hemorrhagic polyomavirusGHPVNC_004800.1gooseNAGermany20015256A[62]
81Hungarian finch polyomavirusHunFPyVNC_039053.1Lonchura majakidney and liverHungary20115284A[63]
82black sea bass-associated polyomavirus 1BassPyV1NC_025790.1Centropristis striataNAUSA20147369F[64]
83bovine polyomavirusBPyVNC_001442.1Bos tauruskidneyNANA4697M[65]
84dolphin polyomavirus 1DPyVNC_025899.1Delphinus delphistracheaUSA20105159M[66]
85giant guitarfish polyomavirusGfPyV1NC_026244.1Rhynchobatus djiddensisskin lesionUSA20143962F[67]
86sharp-spined notothenia polyomavirusSspPyVNC_026944.1Trematomus pennelliiNAAntarctica20136219FNA
  1. No. 1~36: Alphapolyomaviruses; No. 37~68: Betaphapolyomaviruses; No. 69~72: Deltapolyomaviruses; No. 73~81: Gammapolyomaviruses; No. 82~86: Unassigned polyomaviruses; NA Not available
  2. All 86 viruses were classified into 5 groups according to their host as follows: non-primate mammals (Group M); non-human primate (Group P); human (Group H); avian (Group A); fish (Group F)