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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 Taxonomy NCBI Reference Sequence
Virus name Abbr. Accession No. Host species Isolation source Country Year bp Group
(host)
Ref.
1 bat polyomavirus 4a BatPyV4a NC_038556.1 Artibeus planirostris spleen French Guiana 2011 5187 M [24]
2 Ateles paniscus polyomavirus 1 ApanPyV1 NC_019853.1 Ateles paniscus NA Germany NA 5273 P [25]
3 bat polyomavirus 5b1 BatPyV5b-1 NC_026767.1 Pteropus vampyrus spleen Indonesia 2012 5047 M [26]
4 bat polyomavirus 5a BatPyV5a NC_026768.1 Dobsonia moluccensis spleen Indonesia 2012 5075 M [26]
5 Bornean orang-utan polyomavirus OraPyV-Bor NC_013439.1 Pongo pygmaeus blood NA NA 5168 P [27]
6 Cardioderma polyomavirus CardiodermaPyV NC_020067.1 Cardioderma cor rectal swab Kenya 2006 5372 M [28]
7 bat polyomavirus 4b BatPyV4b NC_028120.1 Carollia perspicillata spleen French Guiana 2011 5352 M [24]
8 chimpanzee polyomavirus ChPyV NC_014743.1 Pan troglodytes verus blood NA NA 5086 P [29]
9 vervet monkey polyomavirus 1 VmPyV1 NC_019844.1 Chlorocebus pygerythrus spleen Zambia 2009 5157 P [30]
10 vervet monkey polyomavirus 3 VmPyV3 NC_025898.1 Chlorocebus pygerythrus spleen Zambia 2009 5055 P [30]
11 Eidolon polyomavirus 1 EidolonPyV NC_020068.1 Eidolon helvum rectal swab Kenya 2009 5294 M [28]
12 Gorilla gorilla gorilla polyomavirus 1 GgorgPyV1 NC_025380.1 Gorilla gorilla gorilla NA Congo Republic 2008 5300 P [31]
13 Human polyomavirus 9 HPyV9 NC_015150.1 Homo sapiens NA Germany 2009 5026 H [32]
14 Human polyomavirus 12 HPyV12 NC_020890.1 Homo sapiens NA Germany 2007 5033 H [33]
15 Macaca fascicularis polyomavirus 1 MfasPyV1 NC_019851.1 Macaca fascicularis NA Germany NA 5087 P [25]
16 Merkel cell polyomavirus MCPyV NC_010277.2 Homo sapiens skin USA 2009 5387 H [16]
17 hamster polyomavirus HaPyV NC_001663.2 Mesocricetus auratus strain Z3 NA Germany 1967 5372 M [34]
18 bat polyomavirus 3b BatPyV3b NC_028123.1 Molossus molossus spleen French Guiana 2011 4903 M [24]
19 mouse polyomavirus MPyV NC_001515.2 Mus musculus NA NA NA 5307 M NA
20 New Jersey polyomavirus NJPyV NC_024118.1 Homo sapiens bicep muscle USA 2013 5108 H [35]
21 Otomops polyomavirus 2 OtomopsPyV NC_020066.1 Otomops martiensseni rectal swab Kenya 2006 4914 M [28]
22 Otomops polyomavirus 1 OtomopsPyV1 NC_020071.1 Otomops martiensseni rectal swab Kenya 2006 5176 M [28]
23 Pan troglodytes verus polyomavirus 2a PtrovPyV2a NC_025370.1 Pan troglodytes verus NA Cote d’Ivoire 2010 5309 P [31]
24 Pan troglodytes verus polyomavirus 3 PtrovPyV3 NC_019855.1 Pan troglodytes verus NA Cote d’Ivoire NA 5333 P [25]
25 Pan troglodytes verus polyomavirus 4 PtrovPyV4 NC_019856.1 Pan troglodytes verus NA Cote d’Ivoire NA 5349 P [25]
26 Pan troglodytes verus polyomavirus 5 PtrovPyV5 NC_019857.1 Pan troglodytes verus NA Cote d’Ivoire NA 4994 P [25]
27 Pan troglodytes schweinfurthii polyomavirus 2 PtrosPyV2 NC_019858.1 Pan troglodytes schweinfurthii NA Uganda NA 4970 P [25]
28 Pan troglodytes verus polyomavirus 1a PtrovPyV1a NC_025368.1 Pan troglodytes verus NA Cote d’Ivoire 2009 5303 P [31]
29 Piliocolobus badius polyomavirus 2 PbadPyV2 NC_039051.1 Piliocolobus badius NA Cote d’Ivoire 2005 5148 P [36]
30 Piliocolobus rufomitratus polyomavirus 1 PrufPyV1 NC_019850.1 Piliocolobus rufomitratus NA Cote d’Ivoire NA 5140 P [25]
31 raccoon polyomavirus RacPyV NC_023845.1 raccoon NA USA 2011 5016 M [37]
32 Rattus norvegicus polyomavirus 1 RnorPyV1 NC_027531.1 Rattus norvegicus spleen Germany 2005 5318 M [38]
33 bat polyomavirus 3a-B0454 BatPyV3a-B0454 NC_038557.1 Sturnira lilium spleen French Guiana 2011 5058 M [24]
34 Sumatran orang-utan polyomavirus OraPyV-Sum NC_028127.1 Pongo abelii blood NA NA 5358 P [27]
35 Trichodysplasia spinulosa-associated polyomavirus TSPyV NC_014361.1 Homo sapiens skin Netherlands 2009 5232 H [15]
36 yellow baboon polyomavirus 1 YbPyV1 NC_025894.1 Papio cynocephalus spleen Zambia 2009 5064 P [30]
37 African elephant polyomavirus 1 AelPyV1 NC_022519.1 Loxodonta africana protruding ulcerated fibroma Denmark 2011 5722 M [39]
38 BatPyV4a BatPyV2c NC_038558.1 Artibeus planirostris spleen French Guiana 2011 5371 M [24]
39 Myodes glareolus polyomavirus 1 BVPyV NC_028117.1 Myodes glareolus blood serum and body fluids Germany 2013 5032 M [40]
40 bat polyomavirus 6a BatPyV6a NC_026762.1 Acerodon celebensis spleen Indonesia 2013 5019 M [26]
41 bat polyomavirus 6b BatPyV6b NC_026770.1 Dobsonia moluccensis spleen Indonesia 2012 5039 M [26]
42 bat polyomavirus 6c BatPyV6c NC_026769.1 Dobsonia moluccensis spleen Indonesia 2012 5046 M [26]
43 California sea lion polyomavirus 1 SLPyV NC_013796.1 Zalophus californianus tongue USA 2006 5112 M [41]
44 Cebus albifrons polyomavirus 1 CalbPyV1 NC_019854.2 Cebus albifrons NA Germany NA 5013 P [25]
45 Cercopithecus erythrotis polyomavirus 1 CeryPyV1 NC_025892.1 Cercopithecus erythrotis NA Cameroon NA 5189 P [25]
46 vervet monkey polyomavirus 2 VmPyV2 NC_025896.1 Chlorocebus pygerythrus kidney Zambia 2009 5167 P [30]
47 Microtus arvalis polyomavirus 1 CVPyV NC_028119.1 Microtus arvalis blood serum and body fluids Germany 2013 5024 M [40]
48 bat polyomavirus 2a BatPyV2a NC_028122.1 Desmodus rotundus spleen French Guiana 2011 5201 M [24]
49 equine polyomavirus EPyV NC_017982.1 Equus caballus eye USA 2003 4987 M [42]
50 BK polyomavirus BKV; BKPyV NC_001538.1 Homo sapiens NA NA NA 5153 H [43]
51 KI polyomavirus KIPyV NC_009238.1 Homo sapiens NA NA NA 5040 H [44]
52 JC polyomavirus JCV; JCPyV NC_001699.1 Homo sapiens NA NA NA 5130 H [45]
53 Weddell seal polyomavirus WsPyV NC_032120.1 Leptonychotes weddellii kidney Antarctica 2014 5186 M NA
54 simian virus 40 SV40 NC_001669.1 Macaca mulatta NA NA NA 5243 P [46]
55 Mastomys polyomavirus MasPyV NC_025895.1 Mastomys natalensis spleen Zambia 2009 4899 M [47]
56 Meles meles polyomavirus 1 MmelPyV1 NC_026473.1 Meles meles salivary gland France 2014 5187 M [48]
57 Miniopterus polyomavirus MiniopterusPyV NC_020069.1 Miniopterus africanus rectal swab Kenya 2006 5213 M [28]
58 mouse pneumotropic virus MPtV NC_001505.2 Mus musculus NA NA NA 4754 M [49]
59 Myotis polyomavirus MyPyV NC_011310.1 Myotis lucifugus NA Canada 2007 5081 M [50]
60 Pan troglodytes verus polyomavirus 8 PtrovPyV8 NC_028635.1 Western chimpanzee colon Netherlands 2014 5163 P [51]
61 Pteronotus polyomavirus PteronotusPyV NC_020070.1 Pteronotus davyi oral swab Guatemala 2009 5136 M [28]
62 bat polyomavirus 2b BatPyV2b NC_028121.1 Pteronotus parnellii spleen French Guiana 2011 5041 M [24]
63 rat polyomavirus 2 RatPyV2 NC_032005.1 Rattus norvegicus NA USA 2016 5108 M NA
64 Saimiri sciureus polyomavirus 1 SsciPyV1 NC_038559.1 Saimiri sciureus NA Germany NA 5067 P NA
65 squirrel monkey polyomavirus SquiPyV NC_009951.1 Saimiri boliviensis spleen NA NA 5075 P [52]
66 alpaca polyomavirus AlPyV NC_034251.1 Vicugna pacos NA USA 2014 5052 M [53]
67 WU polyomavirus WUPyV NC_009539.1 Homo sapiens NA Australia NA 5229 H [54]
68 yellow baboon polyomavirus 2 YbPyV2 AB767295.2 Papio cynocephalus spleen and kidney Zambia 2009 5181 P [30]
69 Human polyomavirus 6 HPyV6 NC_014406.1 Homo sapiens skin USA 2009 4926 H [16]
70 Human polyomavirus 7 HPyV7 NC_014407.1 Homo sapiens skin USA 2009 4952 H [16]
71 MW polyomavirus MWPyV NC_018102.1 Homo sapiens stool Malawi 2008 4927 H [55]
72 STL polyomavirus STLPyV NC_020106.1 Homo sapiens fecal specimen Malawi NA 4776 H [56]
73 Adélie penguin polyomavirus ADPyV NC_026141.2 Pygoscelis adeliae fecal material Antarctica 2012 4988 A [57]
74 budgerigar fledgling disease virus BFDV NC_004764.2 Falconiformes and Psittaciformes (wild birds) NA NA NA 4981 A [58]
75 butcherbird polyomavirus Butcherbird PyV NC_023008.1 Cracticus torquatus periocular skin Australia 2009 5084 A [59]
76 canary polyomavirus CaPyV NC_017085.1 Serinus canaria liver Netherlands 2007 5421 A [60]
77 crow polyomavirus CpyV NC_007922.1 Corvus monedula NA NA 2005 5079 A [22]
78 Erythrura gouldiae polyomavirus 1 EgouPyV1 NC_039052.1 Erythrura gouldiae liver Poland 2014 5172 A [61]
79 finch polyomavirus FPyV NC_007923.1 Pyrrhula pyrrhula griseiventris NA NA 2005 5278 A [22]
80 goose hemorrhagic polyomavirus GHPV NC_004800.1 goose NA Germany 2001 5256 A [62]
81 Hungarian finch polyomavirus HunFPyV NC_039053.1 Lonchura maja kidney and liver Hungary 2011 5284 A [63]
82 black sea bass-associated polyomavirus 1 BassPyV1 NC_025790.1 Centropristis striata NA USA 2014 7369 F [64]
83 bovine polyomavirus BPyV NC_001442.1 Bos taurus kidney NA NA 4697 M [65]
84 dolphin polyomavirus 1 DPyV NC_025899.1 Delphinus delphis trachea USA 2010 5159 M [66]
85 giant guitarfish polyomavirus GfPyV1 NC_026244.1 Rhynchobatus djiddensis skin lesion USA 2014 3962 F [67]
86 sharp-spined notothenia polyomavirus SspPyV NC_026944.1 Trematomus pennellii NA Antarctica 2013 6219 F NA
  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)