Background
Methods
Sample collection
Viral metagenomic sequencing
Viral detection and genomic sequencing
Sequence analysis
Results
PV and PyV in Chinese tree shrew
Samples | Virus infection and co-infection rates in swabs and tissues | ||||||
---|---|---|---|---|---|---|---|
PyV1a | PV1b | PV2c | PyV1/PV1 | PyV1/PV2 | PV1/PV2 | PyV1/PV1/PV2 | |
Oral swab | 21/56 (37.5%) | 14/56 (25%) | 17/56 (30.4%) | 7/56 (12.5%) | 9/56 (16.1%) | 4/56 (7.1%) | 2/56 (3.6%) |
Rectal swab | 0/56 | 0/56 | 0/56 | – | – | – | – |
Heart | 0/15 | 0/15 | 0/15 | – | – | – | – |
Liver | 0/15 | 0/15 | 0/15 | – | – | – | – |
Spleen | 7/15 (46.7%) | 0/15 | 0/15 | – | – | – | – |
Lung | 0/15 | 0/15 | 0/15 | – | – | – | – |
kidney | 0/15 | 0/15 | 0/15 | – | – | – | – |
Characterization of TbelPV1, TbelPV2, and TbelPyV1 genomes
Analysis of genomes of TbelPV1 and TbelPV2
Papillomavirus | GenBank number | Genome size(nt) | G + C content (%) | pairwise identities of nucleotide and amino acid sequence(nt/aa%) | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Tupaia belangeri chinensis papillomavirus 1 | Tupaia belangeri chinensis papillomavirus 2 | |||||||||||||||
L1 | L2 | E1 | E2 | E4 | E6 | E7 | L1 | L2 | E1 | E2 | E6 | E7 | ||||
TbelPV1 | MK443496 | 7410 | 48.3 | / | / | / | / | / | / | / | / | / | / | / | / | / |
TbelPV2 | MK443497 | 7568 | 54.3 | 58/54 | 49/35 | 56/45 | 45/31 | / | 42/27 | 50/36 | / | / | / | / | / | / |
Alphapapillomavirus
| ||||||||||||||||
Human papillomavirus 2 | NC_001352 | 7860 | 48.4 | 55/48 | 32/28 | 46/41 | 39/30 | 32/13 | 37/26 | 39/27 | 53/50 | 31/27 | 47/39 | 35/25 | 35/22 | 39/35 |
Human papillomavirus 18 | NC_001357 | 7857 | 40.4 | 52/46 | 35/27 | 46/37 | 41/31 | 23/12 | 36/26 | 40/31 | 52/48 | 33/27 | 45/36 | 32/24 | 29/18 | 40/31 |
Rhesus monkey papillomavirus | NC_001678 | 8028 | 48.0 | 54/48 | 33/25 | 49/41 | 40/30 | – | 29/24 | 37/31 | 54/49 | 34/25 | 49/39 | 33/26 | 29/26 | 40/34 |
Betapapillomavirus
| ||||||||||||||||
Human papillomoavirus type 5 | NC_001531 | 7746 | 42.4 | 53/49 | 40/35 | 52/44 | 38/29 | 19/8 | 34/25 | 38/35 | 53/50 | 38/35 | 50/44 | 33/23 | 36/27 | 36/36 |
Chipapillomavirus
| ||||||||||||||||
Canine papillomavirus 3 | NC_008297 | 7801 | 51.5 | 55/50 | 35/31 | 51/44 | 38/27 | – | 35/24 | 40/29 | 57/56 | 36/30 | 52/44 | 38/26 | 37/22 | 42/32 |
Canine papillomavirus 4 | NC_010226 | 7742 | 53.3 | 54/52 | 35/30 | 50/43 | 38/29 | – | 33/24 | 41/29 | 56/54 | 35/30 | 50/44 | 37/28 | 39/27 | 43/35 |
Deltapapillomavirus
| ||||||||||||||||
Bos grunniens papillomavirus type 1 | JX174437 | 7946 | 44.4 | 54/48 | 30/24 | 47/38 | 39/27 | 34/8 | 28/18 | 27/19 | 52/48 | 28/22 | 46/39 | 32/23 | 32/18 | 31/19 |
Dyodeltapapillomavirus
| ||||||||||||||||
Ursus maritimus papillomavirus 1 | NC_010739 | 7582 | 48.4 | 56/54 | 31/26 | 51/44 | 39/26 | – | 39/27 | – | 59/54 | 32/26 | 50/42 | 37/26 | 39/28 | – |
Feline papillomavirus type 2 | EU796884 | 7899 | 53.0 | 55/54 | 35/27 | 51/44 | 34/23 | – | 38/27 | 40/34 | 57/58 | 36/29 | 52/47 | 36/25 | 38/28 | 44/32 |
Dyomupapillomavirus
| ||||||||||||||||
Morelia spilota papillomavirus 1 | HQ262535 | 7048 | 40.9 | 54/50 | 31/26 | 51/43 | 44/33 | 34/14 | 29/21 | 33/25 | 53/54 | 30/25 | 48/44 | 36/27 | 32/26 | 34/24 |
Dyorhopapillomavirus
| ||||||||||||||||
Equine papillomavirus 2 | NC_012123 | 7802 | 56.1 | 56/49 | 32/27 | 39/49 | 38/28 | – | 25/15 | 33/19 | 54/49 | 31/27 | 40/48 | 36/26 | 26/23 | 35/22 |
Gammapapillomavirus
| ||||||||||||||||
Human papillomavirus type 4 | NC_001457 | 7353 | 38.5 | 53/48 | 33/25 | 51/43 | 43/36 | 41/17 | 37/25 | 37/23 | 52/53 | 34/29 | 48/42 | 36/27 | 36/26 | 36/23 |
Iotapapillomavirus
| ||||||||||||||||
Mastomys natalensis papillomavirus | NC_001605 | 7687 | 50.2 | 55/53 | 36/31 | 50/44 | 32/25 | – | 33/24 | 37/24 | 58/59 | 33/38 | 50/48 | 34/29 | 39/32 | 33/29 |
Kappapapillomavirus
| ||||||||||||||||
Cottontail rabbit papillomavirus | NC_001541 | 7868 | 46.4 | 58/56 | 32/26 | 49/44 | 44/36 | 44/12 | 23/12 | 39/31 | 54/51 | 32/28 | 49/43 | 35/29 | 21/10 | 37/28 |
Rabbit oral papillomavirus | NC_002232 | 7565 | 44.4 | 59/57 | 34/31 | 49/44 | 43/37 | 38/10 | 22/22 | 43/34 | 54/53 | 36/30 | 48/42 | 34/29 | 24/23 | 42/29 |
Lambdapapillomavirus
| ||||||||||||||||
Crocuta crocutapapillomavirus 1 | NC_018575 | 8344 | 38.4 | 55/54 | 36/34 | 52/43 | 45/31 | 34/14 | 29/20 | 40/26 | 52/50 | 32/27 | 48/41 | 35/25 | 34/25 | 38/33 |
Procyon lotor papillomavirus 1 | NC_007150 | 8170 | 45.9 | 59/59 | 38/37 | 52/46 | 45/38 | 39/15 | 32/20 | 38/26 | 55/53 | 36/30 | 52/46 | 36/28 | 33/25 | 38/38 |
Puma concolor papillomavirus type 1 | AY904723 | 8321 | 47.2 | 56/55 | 39/37 | 53/47 | 44/31 | 32/21 | 39/23 | 35/26 | 54/50 | 37/31 | 51/44 | 37/27 | 38/27 | 37/30 |
Mupapillomavirus
| ||||||||||||||||
Human papillomavirus 1 | NC_001356 | 7815 | 40.3 | 56/55 | 39/37 | 51/45 | 42/32 | – | 41/27 | 41/27 | 55/54 | 36/31 | 49/45 | 35/28 | 37/28 | 42/37 |
Human papillomavirus type 63 | NC_001458 | 7348 | 40.4 | 60/59 | 38/36 | 51/44 | 44/34 | 34/12 | 39/29 | 36/28 | 55/56 | 35/32 | 49/43 | 36/26 | 36/25 | 41/34 |
Zetapapillomavirus
| ||||||||||||||||
Equus caballus papillomavirus type 1 | NC_003748 | 7610 | 53.0 | 53/50 | 32/26 | 50/41 | 43/34 | 28/10 | 27/21 | 39/26 | 54/52 | 32/24 | 51/48 | 37/28 | 33/23 | 39/32 |
virus | ORFs | position | length | MW kDa | pI | |
---|---|---|---|---|---|---|
nt | aa | |||||
TbelPV1 | E1 | 1–1824 | 1824 | 607 | 69.94 | 5.14 |
E2 | 1775–2950 | 1176 | 391 | 43.64 | 9.83 | |
E4 | 2136–2678 | 543 | 160 | 20.22 | 6.54 | |
L2 | 2994–4628 | 1635 | 544 | 58.16 | 4.63 | |
L1 | 4639–6156 | 1518 | 505 | 57.07 | 6.55 | |
LCRa | 6157-6701 | 545 | – | – | – | |
E6 | 6702–7121 | 420 | 139 | 16.26 | 8.07 | |
E7 | 7106–7408 | 303 | 100 | 11.25 | 3.48 | |
TbelPV2 | E1 | 1–1818 | 1818 | 605 | 68.08 | 6.14 |
E2 | 1757–3148 | 1392 | 463 | 50.43 | 7.00 | |
L2 | 3261–4796 | 1536 | 511 | 53.81 | 5.53 | |
L1 | 4827–6329 | 1503 | 500 | 56.85 | 6.13 | |
LCRa | 6330-6792 | 463 | – | – | – | |
E6 | 6793–7239 | 447 | 148 | 16.33 | 8.61 | |
E7 | 7214–7522 | 309 | 102 | 11.55 | 4.11 |
Gene similarities and phylogenetics of TbelPV1 and TbelPV2
Analysis of TbelPyV1 genome
Polyomaviruses | GenBank numbers | Genome size(nt) | G + C content (%) | Nucleotide and amino acid sequence pairwise identities(nt/aa, %) | |||
---|---|---|---|---|---|---|---|
Large T antigen | Small T antigen | VP1 | VP2 | ||||
Alphapolyomavirus
| |||||||
TbelPyV1 | MK443498 | 4982 | 42.6 | – | – | – | – |
Human polyomavirus 9 | NC_015150 | 5026 | 39.2 | 60.8/64 | 64.9/67.7 | 72/77.5 | 64.6/67.6 |
African green monkey polyomavirus | NC_004763 | 5270 | 40.9 | 59.6/61.5 | 64/63 | 69.4/76.4 | 62.7/67 |
Pan troglodytes polyomavirus 3 | HQ385748 | 5309 | 40.9 | 42.4/36.9 | 48/39.9 | 52.9/55 | 34.7/27.7 |
Pan troglodytes verus polyomavirus 2c | HQ385749 | 5315 | 41.1 | 42.6/37.1 | 48.1/40.4 | 52.4/55.2 | 35.3/27.7 |
Gorilla gorilla gorilla polyomavirus 1 | HQ385752 | 5300 | 42.2 | 43.2/38.2 | 48.9/39.4 | 52/54.7 | 35.4/28 |
Pan troglodytes verus polyomavirus 1 | HQ385746 | 5303 | 40.4 | 43.7/38.7 | 49.7/41.5 | 53.1/56.7 | 36.2/28.6 |
Artibeus planirostris polyomavirus 1 | JQ958887 | 5371 | 39.5 | 44.4/37.3 | 49.6/39.9 | 46/52.3 | 33.4/25.5 |
Carollia perspicillata polyomavirus 1 | JQ958889 | 5352 | 42.4 | 44.9/37.9 | 48.3/39.4 | 42.8/49.9 | 32.6/25.8 |
Sumatran orang-utan polyomavirus | FN356901 | 5358 | 38.7 | 46.9/41.9 | 45.1/37 | 59.3/62.6 | 53.9/47.8 |
Chimpanzee polyomavirus | FR692334 | 5086 | 38.2 | 46.5/41.5 | 46.2/36.3 | 43.2/51.4 | 33.5/29.1 |
Tupaia glis polyomavirus | MG721015 | 5234 | 42.1 | 45.5/39.1 | 48.3/40.1 | 43/50.6 | 31.3/26.1 |
Molossus molossus polyomavirus 1 | JQ958893 | 4903 | 40.9 | 46.1/40.4 | 44.9/32.3 | 52.8/50.6 | 33.1/27.1 |
Artibeus planirostris polyomavirus 2 | JQ958886 | 5019 | 41.2 | 44.5/40.2 | 45.6/37 | 55.8/51.5 | 32.7/27 |
Sturnira lilium polyomavirus 1 | JQ958888 | 5058 | 42.2 | 44.9/40.1 | 44.7/34.9 | 53.8/51.2 | 32.7/27.6 |
Bornean orang-utan polyomavirus | FN356900 | 5168 | 40.2 | 52.7/47.5 | 49.2/37.8 | 58.9/56.6 | 51.7/44.6 |
Murine polyomavirus strain A3 | J02289 | 5296 | 47.2 | 42.7/37.8 | 42/30.9 | 57.2/56.9 | 45.6/37.6 |
Hamster polyomavirus | M26281 | 5366 | 41.5 | 43.5/37.3 | 39.9/31.8 | 55.6/55.9 | 46.2/37 |
Betapolyomavirus
| |||||||
Human polyomavirus 3 | EF127906 | 5040 | 39.4 | 49.3/41.5 | 42.4/32 | 36.1/24 | 27.8/15.1 |
Murine polyomavirus 2 | EF186666 | 5001 | 40.3 | 48/37.7 | 37.4/29.3 | 56.8/55.4 | 44.6/35.4 |
Mastomys natalensis polyomavirus 1 | AB588640 | 4899 | 39.9 | 47.6/37.7 | 38.3/28.4 | 58.2/58.4 | 46.6/39.1 |
Myotis polyomavirus VM-2008 | NC_011310 | 5081 | 41.7 | 45.8/36.4 | 39/27.9 | 57.1/57.9 | 43/36.5 |
Artibeus planirostris polyomavirus 3 | JQ958890 | 5187 | 44.2 | 44.4/39.8 | 45.9/33.7 | 59.5/59.1 | 45.1/38.4 |
Pteronotus parnellii polyomavirus 1 | JQ958891 | 5041 | 38.6 | 45.6/38.8 | 43.4/34.8 | 57.2/57.8 | 43.9/37.2 |
Desmodus rotundus polyomavirus 1 | JQ958892 | 5201 | 43.3 | 47.2/40.5 | 41.8/33.2 | 58.7/57.7 | 43.6/39.3 |
Equus caballus polyomavirus 1 | NC_017982 | 4987 | 44.6 | 46.7/39.7 | 39/33.9 | 55.3/56.3 | 45/42.3 |
Simian polyomavirus 1 | J02400 | 5243 | 40.8 | 44.2/41 | 42.9/32.8 | 55.5/51.8 | 40.5/29.5 |
Human polyomavirus 1 | V01108 | 5153 | 39.5 | 46.1/40.6 | 42.6/33.3 | 54.8/51.5 | 38.4/28 |
Simian polyomavirus 12 | AY614708 | 5230 | 41.2 | 46.2/41.6 | 43.1/32.8 | 56.4/53.1 | 39.8/28.9 |
Deltapolyomavirus
| |||||||
Human polyomavirus 7 | NC_014407 | 4952 | 42.9 | 47.5/40.8 | 48/40.9 | 36.2/27.2 | 31/15.6 |
Human polyomavirus 6 | NC_014406 | 4926 | 42.7 | 46.9/39 | 46.3/36.8 | 36.3/25.7 | 29.3/15.1 |
Human polyomavirus 10 | JX262162 | 4939 | 36.7 | 50.8/42.3 | 50.4/42.1 | 49.8/44.9 | 46.1/33.8 |
Gammapolymavirus
| |||||||
Pyrrhula pyrrhula polyomavirus 1 | DQ192571 | 5278 | 51.2 | 36.6/28 | 30.4/16.8 | 53.3/54.3 | 38.9/31.2 |
Corvus monedula polyomavirus 1 | DQ192570 | 5079 | 45.7 | 36.7/26.9 | 29.6/21.6 | 56.5/58.3 | 42.4/36.4 |
ORFs | position | length | MW kDa | pI | |
---|---|---|---|---|---|
nt | aa | ||||
URRa | 1-463 | – | – | – | – |
VP2 | 464–1438 | 975 | 324 | 35.82 | 5.02 |
VP3 | 821–1438 | 618 | 205 | 23.96 | 6.71 |
VP1 | 1395–2501 | 1107 | 388 | 40.1 | 6.07 |
NCRb | 2502-2567 | – | – | – | – |
LT | 2568–4385 | 2058 | 685 | 78.34 | 6.67 |
4743–4982 | |||||
ST | 4413–4982 | 570 | 189 | 22.37 | 8.31 |