Table 1.
Calculation of HPV16, 18 and 58 variations by genome region and open reading frame (ORF).
| Gene | Gene size (bp) | Point mutation (N) | Deletion (N) | Insertion (N) | Total | Variation rate | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total | Non-synonymous mutations | Synonymous mutations | ||||||||||
| Total | Ts | Tv | Total | Ts | Tv | |||||||
| HPV16 (n = 51) | ||||||||||||
| E6 | 477(83–559) | 14 | 8(57.14%) | 5 | 3 | 6(42.86%) | 3 | 3 | 0 | 0 | 14 | 2.93% |
| E7 | 297(562–858) | 9 | 2(22.22%) | 2 | 0 | 7(77.78%) | 6 | 1 | 0 | 0 | 9 | 3.03% |
| E1 | 1949(865–2813) | 45 | 17(37.78%) | 7 | 10 | 28(62.22%) | 22 | 6 | 0 | 1 | 46 | 2.36% |
| E2 | 1098(2755–3852) | 40 | 33(82.50%) | 18 | 15 | 7(17.50%) | 4 | 3 | 0 | 0 | 40 | 3.64% |
| E4 | 288(3332–3619) | 14 | 13(92.86%) | 8 | 5 | 1(7.14%) | 1 | 0 | 0 | 0 | 14 | 4.86% |
| E5 | 252(3849–4100) | 13 | 7(53.85%) | 3 | 4 | 6(46.15%) | 4 | 2 | 0 | 0 | 13 | 5.16% |
| L2 | 1422(4236–5657) | 60 | 35(58.33%) | 17 | 18 | 25(41.67%) | 17 | 8 | 3 | 0 | 63 | 4.43% |
| L1 | 1596(5560–7155) | 35 | 14(40.00%) | 5 | 9 | 21(60.00%) | 17 | 4 | 3 | 1 | 39 | 2.44% |
| LCR | 832(7156–7905 1–82) | 43 | — | — | — | — | — | — | 1 | 2 | 46 | 5.53% |
| NCR | 135(4101–4235) | 18 | — | — | — | — | — | — | 5 | 6 | 29 | 21.48% |
| HPV18 (n = 7) | ||||||||||||
| E6 | 477(105–581) | 3 | 0(0.00%) | 0 | 0 | 3(100.00%) | 1 | 2 | 0 | 0 | 3 | 0.63% |
| E7 | 318(590–907) | 2 | 1(50.00%) | 1 | 0 | 1(50.00%) | 1 | 0 | 0 | 0 | 2 | 0.63% |
| E1 | 1974(914–2887) | 11 | 3(27.27%) | 1 | 2 | 8(72.73%) | 6 | 2 | 1 | 1 | 13 | 0.66% |
| E2 | 1098(2817–3914) | 11 | 6(54.54%) | 1 | 5 | 5(45.45%) | 3 | 2 | 1 | 1 | 13 | 1.18% |
| E4 | 267(3418–3684) | 3 | 3(100.00%) | 1 | 2 | 0(0.00%) | 0 | 0 | 0 | 0 | 3 | 1.12% |
| E5 | 222(3936–4157) | 0 | 0(0.00%) | 0 | 0 | 0(0.00%) | 0 | 0 | 0 | 0 | 0 | 0.00% |
| L2 | 1389(4244–5632) | 17 | 9(52.94%) | 4 | 5 | 8(47.06%) | 2 | 6 | 0 | 0 | 17 | 1.22% |
| L1 | 1707(5430–7136) | 17 | 9(52.94%) | 3 | 6 | 8(47.06%) | 4 | 4 | 0 | 0 | 17 | 0.99% |
| LCR | 825(7137–7857 1–104) | 9 | — | — | — | — | — | — | 0 | 0 | 9 | 1.09% |
| NCR | 107(3915–3935 4158–4243) | 4 | — | — | — | — | — | — | 0 | 0 | 4 | 3.74% |
| HPV58 (n = 11) | ||||||||||||
| E6 | 450(110–559) | 3 | 2(66.67%) | 0 | 2 | 1(33.33%) | 1 | 0 | 0 | 0 | 3 | 0.67% |
| E7 | 297(574–870) | 10 | 5(50.00%) | 4 | 1 | 5(50.00%) | 4 | 1 | 0 | 0 | 10 | 3.37% |
| E1 | 1935(883–2817) | 20 | 7(35.00%) | 0 | 7 | 13(65.00%) | 11 | 2 | 1 | 0 | 21 | 1.08% |
| E2 | 1077(2753–3829) | 16 | 10(62.50%) | 3 | 7 | 6(37.50%) | 3 | 3 | 0 | 0 | 16 | 1.48% |
| E4 | 276(3330–3605) | 9 | 9(100.00%) | 3 | 6 | 0(0.00%) | 0 | 0 | 0 | 0 | 9 | 3.26% |
| E5 | 231(3892–4122) | 9 | 0(0.00%) | 0 | 0 | 9(100.00%) | 6 | 3 | 0 | 0 | 9 | 3.90% |
| L2 | 1419(4244–5662) | 31 | 7(22.58%) | 2 | 5 | 24(77.42%) | 15 | 9 | 0 | 0 | 31 | 2.18% |
| L1 | 1575(5565–7139) | 30 | 10(33.33%) | 8 | 2 | 20(66.67%) | 16 | 4 | 0 | 0 | 30 | 1.90% |
| LCR | 794(7140–7824 1–109) | 21 | — | — | — | — | — | — | 0 | 0 | 21 | 2.64% |
| NCR | 121(4123–4243) | 6 | — | — | — | — | — | — | 0 | 1 | 7 | 5.78% |
Abbreviations: Ts, Transition; Tv, Transversion.