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

Cho, Myeongji; Kim, Hayeon; Son, Hyeon S.

doi:10.1186/s12985-019-1245-2

Virology Journal

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
No.	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

No. 1~36: Alphapolyomaviruses; No. 37~68: Betaphapolyomaviruses; No. 69~72: Deltapolyomaviruses; No. 73~81: Gammapolyomaviruses; No. 82~86: Unassigned polyomaviruses; NA Not available
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)

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ISSN: 1743-422X

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