Table 5. Similarity between novel HPV type ORFs and other representative PVs.
Putative ORFs (E6, E7, E1, E2, E4, L1, and L2) of novel HPV types (HPV 171, 172, and 173) are compared to each other, as well as representative γ-HPV types (HPV 4, 60, 103, 156, 163, 169), β-HPV (HPV 5) and α-HPV (HPV 16). The most similar HPV type for each novel HPV type is highlighted in bold.
| (A) HPV 171 | Genome length | E6 | E7 | E1 | E2 | E4 | L2 | L1 |
|---|---|---|---|---|---|---|---|---|
| Number of nucleotides (nt)* | 7261 | 432 | 300 | 1815 | 1173 | 519 | 1491 | 1578 |
| Position of ORF in genome | - | 19–450 | 453–752 | 736–2550 | 2486–3658 | 2913–3431 | 3660–5152 | 5159–6736 |
| Number of amino acids (aa) | - | 143 | 99 | 604 | 390 | 172 | 496 | 525 |
| Sequence similarity percentage nt (percentage aa) |
γ1-HPV 4 | 52.7 (43.6) | 48.6 (40.0) | 64.6 (58.8) | 53.8 (44.5) | 51.6 (30.3) | 50.5 (43.9) | 63.2 (58.2) |
| γ4-HPV 60 | 57.3 (49.6) | 54.0 (44.8) | 64.3 (53.9) | 57.6 (48.0) | 53.3 (32.7) | 51.5 (44.6) | 62.5 (58.5) | |
| γ6-HPV 103 | - | 45.6 (36.1) | 59.9 (48.0) | 54.2 (42.8) | 49.9 (24.3) | 46.1 (37.4) | 57.8 (52.4) | |
| γ23-HPV 156 | 56.3 (42.9) | 57.6 (54.7) | 62.6 (52.9) | 59.5 (49.2) | 56.7 (35.9) | 49.5 (38.8) | 62.0 (57.7) | |
| γ22-HPV 163 | 54.1 (46.0) | 49.5 (42.7) | 62.6 (54.4) | 53.7 (45.0) | 49.9 (24.1) | 52.2 (44.1) | 61.5 (59.0) | |
| γ11-HPV 169 | 92.4 (94.4) | 96.0 (98.0) | 92.4 (97.4) | 93.2 (94.9) | 95.6 (93.6) | 89.8 (92.3) | 88.3 (97.0) | |
| γ23-HPV 172 | 54.9 (46.2) | 51.9 (47.9) | 60.4 (47.7) | 56.7 (44.1) | 54.3 (35.2) | 50.1 (36.5) | 60.1 (54.2) | |
| γ1-HPV 173 | 50.1 (45.0) | 47.9 (40.4) | 63.4 (52.9) | 53.9 (43.5) | 49.8 (27.5) | 53.7 (43.2) | 62.0 (56.2) | |
| β-HPV 5 | 43.6 (30.3) | 44.1 (35.1) | 56.8 (46.4) | 46.6 (42.1) | 46.0 (23.5) | 45.1 (34.8) | 59.1 (54.7) | |
| α-HPV 16 | 41.7 (23.1) | 40.5 (28.4) | 54.8 (42.4) | 48.5 (30.7) | 42.2 (13.5) | 45.1 (29.7) | 40.5 (48.1) | |
| (B) HPV 172 | Genome length | E6 | E7 | E1 | E2 | E4 | L2 | L1 |
| Number of nucleotides (nt)* |
7203 | 552 | 297 | 1803 | 1188 | 420 | 1554 | 1551 |
| Position of ORF in genome | - | 106–657 | 638–934 | 921–2723 | 2659–3846 | 3191–3610 | 3846–5152 | 5410–6960 |
| Number of amino acids (aa) | - | 183 | 98 | 600 | 395 | 139 | 517 | 516 |
| Sequence similarity percentage nt (percentage aa) |
γl-HPV 4 | 53.9 (42.9) | 53.1 (46.4) | 60.9 (50.2) | 56.3 (44.0) | 53.8 (27.1) | 50.1 (39.9) | 60.3 (52.6) |
| γ4-HPV 60 | 52.4 (43.7) | 54.0 (46.9) | 63.6 (53.2) | 60.6 (49.4) | 51.7 (34.4) | 53.0 (42.0) | 63.2 (55.0) | |
| y6-HPV 103 | - | 50.2 (48.0) | 55.9 (45.0) | 52.2 (40.5) | 47.0 (23.4) | 44.0 (37.3) | 54.9 (47.0) | |
| γ23-HPV 156 | 62.4 (52.9) | 65.3 (58.8) | 68.2 (61.3) | 67.6 (60.2) | 66.7 (48.1) | 58.2 (48.7) | 68.2 (66.2) | |
| γ22-HPV 163 | 60.1 (47.1) | 56.9 (49.0) | 61.7 (48.6) | 54.3 (41.4) | 47.9 (21.1) | 52.0 (41.0) | 59.5 (53.0) | |
| γll-HPV 169 | 53.9 (45.5) | 51.6 (49.0) | 60.1 (47.8) | 56.9 (43.9) | 55.3 (35.2) | 50.1 (36.0) | 59.8 (55.0) | |
| γ11-HPV 171 | 54.9 (46.2) | 51.9 (47.9) | 60.4 (47.7) | 56.7 (44.1) | 54.3 (35.2) | 50.1 (36.5) | 60.1 (54.2) | |
| γ1-HPV 173 | 59.3 (48.6) | 55.6 (45.8) | 59.6 (48.8) | 56.1 (41.3) | 48.9 (22.6) | 49.7 (40.3) | 60.1 (51.9) | |
| β-HPV 5 | 46.2 (30.1) | 44.9 (36.1) | 55.2 (43.4) | 47.1 (40.8) | 43.7 (28.7) | 42.6 (33.7) | 57.4 (48.9) | |
| γ-HPV 16 | 45.9 (25.8) | 44.3 (32.2) | 53.9 (41.3) | 47.8 (30.2) | 36.3 (18.0) | 43.3 (31.8) | 37.2 (44.2) | |
| (C) HPV 173 | Genome length | E6 | E7 | E1 | E2 | E4 | L2 | L1 |
| Number of nucleotides (nt)* | 7297 | 423 | 294 | 1812 | 1176 | 357 | 1584 | 1542 |
| Position of ORF in genome | - | 31–453 | 450–743 | 730–2541 | 2483–3658 | 3066–3422 | 3689–5272 | 5287–6828 |
| Number of amino acids (aa) | - | 140 | 97 | 603 | 391 | 118 | 527 | 513 |
| Sequence similarity percentage nt (percentage aa) |
γ1-HPV 4 | 61.0 (52.9) | 67.7 (57.3) | 71.6 (66.7) | 70.2 (67.8) | 66.1 (44.6) | 64.4 (60.4) | 71.0 (73.6) |
| γ4-HPV 60 | 54.6 (46.8) | 54.4 (41.5) | 63.6 (52.7) | 57.5 (46.6) | 51.5 (32.7) | 55.0 (46.8) | 63.6 (59.9) | |
| γ6-HPV 103 | - | 53.2 (45.8) | 59.9 (47.2) | 53.2 (40.0) | 50.7 (27.9) | 48.2 (47.3) | 61.0 (58.6) | |
| γ23-HPV 156 | 64.8 (52.1) | 58.4 (53.7) | 61.0 (49.6) | 57.3 (42.6) | 50.9 (25.2) | 53.6 (43.1) | 62.3 (55.2) | |
| γ22-HPV 163 | 61.0 (48.9) | 64.0 (57.7) | 68.3 (58.0) | 67.3 (61.1) | 65.8 (51.7) | 64.2 (58.8) | 67.6 (69.8) | |
| γ11-HPV 169 | 49.9 (44.3) | 47.9 (39.4) | 63.6 (53.0) | 54.4 (43.2) | 48.3 (26.5) | 52.2 (42.1) | 60.8 (55.8) | |
| γ11-HPV 171 | 50.1 (45.0) | 47.9 (40.4) | 63.4 (52.9) | 53.9 (43.5) | 49.8 (27.5) | 53.7 (43.2) | 62.0 (56.2) | |
| γ23-HPV 172 | 59.3 (48.6) | 55.6 (45.8) | 59.6 (48.8) | 56.1 (41.3) | 48.9 (22.6) | 49.7 (40.3) | 60.1 (51.9) | |
| β-HPV 5 | 47.3 (34.3) | 44.8 (32.6) | 56.7 (44.8) | 46.5 (35.9) | 40.0 (19.5) | 45.0 (41.3) | 60.8 (57.7) | |
| α-HPV 16 | 46.3 (27.9) | 41.6 (35.2) | 54.5 (42.0) | 48.8 (32.6) | 38.6 (15.0) | 45.8 (34.6) | 37.4 (49.9) |
*
Including STOP codon