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. Author manuscript; available in PMC: 2019 Mar 1.
Published in final edited form as: Virology. 2018 Jan 11;516:86–101. doi: 10.1016/j.virol.2018.01.002

Table 2.

Genomic diversity of HPV complete genome variants.

Number of variable nt positionsb Variable nt codon positionsc Max aa pairwise difference Number of aa sequences Number of variable aa positionsd
no. % 1st 2nd 3rd no. %
1 0.2% 0 0 1 0.0% 150 0 0.0%
1 0.3% 1 0 0 0.0% 104 0 0.0%
1 0.1% 0 0 1 0.2% 638 1 0.2%
3 0.3% 1 0 2 0.3% 375 1 0.3%
0 0.0% 0 0 0 0.0% 106 0 0.0%
0 0.0% - - - - - - -
0 0.0% 0 0 0 0.0% 85 0 0.0%
0 0.0% - - - - - - -
0 0.0% 0 0 0 0.0% 472 0 0.0%
5 0.3% 2 0 3 0.4% 503 2 0.4%
7 0.8% - - - - - - -
18 0.2% - - - - 2433 4 0.2%
6 1.3% 0 3 3 2.0% 151 3 2.0%
15 4.9% 5 4 6 6.9% 101 10 9.9%
33 1.7% 7 4 22 0.8% 634 10 1.6%
33 3.1% 7 11 15 3.1% 358 20 5.6%
7 2.7% 1 4 2 4.6% 87 4 4.6%
4 6.7% - - - - - - -
9 3.5% 5 2 2 7.1% 84 8 9.5%
4 16.0% - - - - - - -
46 3.3% 14 3 29 1.7% 469 19 4.1%
52 3.4% 7 9 36 1.4% 504 15 3.0%
34 3.9% - - - - - - -
235 3.0% - - - - 2388 85 3.6%
7 1.5% 2 3 2 2.0% 151 5 3.3%
2 0.6% 0 1 1 1.9% 104 2 1.9%
18 0.9% 4 2 12 1.0% 634 8 1.3%
23 2.1% 6 2 15 1.9% 368 9 2.4%
8 2.6% 2 3 3 5.0% 101 7 6.9%
2 28.6% - - - - - - -
9 3.0% 4 4 1 8.2% 98 8 8.2%
0 0.0% - - - - - - -
22 1.6% 4 5 13 2.0% 467 9 1.9%
20 1.3% 5 4 11 1.2% 508 8 1.6%
17 2.3% - - - - - - -
119 1.5% - - - - 2431 56 2.3%
16 3.5% 5 4 7 5.3% 151 8 5.3%
24 7.9% 9 4 11 11.7% 100 13 13.0%
172 8.9% 32 24 116 6.6% 642 55 8.6%
87 8.1% 20 17 50 10.0% 359 39 10.9%
25 9.4% 8 8 9 15.9% 88 15 17.0%
10 14.7% - - - - - - -
21 8.2% 7 3 11 9.8% 84 9 10.7%
3 10.7% - - - - - - -
124 8.7% 24 13 87 5.7% 473 30 6.3%
149 9.9% 25 11 113 5.0% 503 29 5.8%
120 12.7% - - - - - - -
719 9.1% - - - - 2384 201 8.4%
6 1.3% 2 1 3 1.3% 153 4 2.6%
5 1.6% 2 0 3 1.9% 105 2 1.9%
67 3.5% 15 7 45 2.6% 631 20 3.2%
31 2.7% 7 4 20 2.7% 380 15 3.9%
13 3.5% 2 6 5 5.2% 154 10 6.5%
6 7.4% - - - - - - -
9 3.1% 5 1 3 3.1% 96 4 4.2%
1 2.1% - - - - - - -
46 3.3% 3 6 37 2.2% 463 12 2.6%
50 3.3% 7 9 34 2.0% 501 15 3.0%
32 3.9% - - - - - - -
254 3.2% - - - - 2471 81 3.3%
27 5.8% 8 7 12 5.3% 154 11 7.1%
3 0.9% 1 0 1 1.9% 105 2 1.9%
55 2.9% 16 11 28 2.6% 636 28 4.4%
44 3.8% 13 10 21 3.6% 384 27 7.0%
17 3.8% 1 9 7 4.0% 150 12 8.0%
4 3.8% - - - - - - -
13 5.0% 3 5 5 5.9% 85 8 9.4%
3 7.0% - - - - - - -
54 3.9% 2 8 44 1.5% 463 12 2.6%
58 3.9% 12 3 43 1.6% 499 15 3.0%
39 4.8% - - - - - - -
295 3.7% - - - - 2476 116 4.7%
6 1.3% 2 1 3 2.6% 155 4 2.6%
7 2.2% 2 0 5 2.9% 105 4 3.8%
23 1.2% 11 3 9 1.6% 636 13 2.0%
21 1.9% 7 5 8 2.7% 371 12 3.2%
6 1.5% 1 1 4 3.0% 135 4 3.0%
4 1.1% 0 2 2 2.7% 120 2 1.7%
24 1.7% 3 2 19 0.9% 464 6 1.3%
26 1.6% 3 3 20 0.9% 534 7 1.3%
24 2.6% - - - - - - -
134 1.7% - - - - 2520 51 2.0%
6 1.3% 4 0 2 1.3% 155 2 1.3%
9 2.8% 4 2 3 4.8% 105 5 4.8%
48 2.5% 10 11 26 1.7% 630 21 3.3%
25 2.3% 6 5 14 2.2% 369 11 3.0%
12 2.3% 3 5 4 3.4% 170 7 4.1%
8 5.2% - - - - - - -
11 4.3% 2 4 5 5.9% 85 6 7.1%
3 14.3% - - - - - - -
40 2.9% 5 10 25 1.5% 464 14 3.0%
49 3.2% 7 15 27 1.9% 503 18 3.6%
21 2.7% - - - - - - -
218 2.8% - - - - 2519 82 3.3%
23 5.1% 7 7 9 5.4% 148 11 7.4%
9 3.1% 5 1 3 3.1% 96 4 4.2%
1 2.1% - - - - - - -
46 3.3% 3 6 37 2.2% 463 12 2.6%
50 3.3% 7 9 34 2.0% 501 15 3.0%
32 3.9% - - - - - - -
254 3.2% - - - - 2471 81 3.3%
27 5.8% 8 7 12 5.3% 154 11 7.1%
3 0.9% 1 0 1 1.9% 105 2 1.9%
55 2.9% 16 11 28 2.6% 636 28 4.4%
44 3.8% 13 10 21 3.6% 384 27 7.0%
17 3.8% 1 9 7 4.0% 150 12 8.0%
4 3.8% - - - - - - -
13 5.0% 3 5 5 5.9% 85 8 9.4%
3 7.0% - - - - - - -
54 3.9% 2 8 44 1.5% 463 12 2.6%
58 3.9% 12 3 43 1.6% 499 15 3.0%
39 4.8% - - - - - - -
295 3.7% - - - - 2476 116 4.7%
6 1.3% 2 1 3 2.6% 155 4 2.6%
7 2.2% 2 0 5 2.9% 105 4 3.8%
23 1.2% 11 3 9 1.6% 636 13 2.0%
21 1.9% 7 5 8 2.7% 371 12 3.2%
6 1.5% 1 1 4 3.0% 135 4 3.0%
4 1.1% 0 2 2 2.7% 120 2 1.7%
24 1.7% 3 2 19 0.9% 464 6 1.3%
26 1.6% 3 3 20 0.9% 534 7 1.3%
24 2.6% - - - - - - -
134 1.7% - - - - 2520 51 2.0%
6 1.3% 4 0 2 1.3% 155 2 1.3%
9 2.8% 4 2 3 4.8% 105 5 4.8%
48 2.5% 10 11 26 1.7% 630 21 3.3%
25 2.3% 6 5 14 2.2% 369 11 3.0%
12 2.3% 3 5 4 3.4% 170 7 4.1%
8 5.2% - - - - - - -
11 4.3% 2 4 5 5.9% 85 6 7.1%
3 14.3% - - - - - - -
40 2.9% 5 10 25 1.5% 464 14 3.0%
49 3.2% 7 15 27 1.9% 503 18 3.6%
21 2.7% - - - - - - -
218 2.8% - - - - 2519 82 3.3%
23 5.1% 7 7 9 5.4% 148 11 7.4%
8 2.7% 2 4 2 5.2% 97 6 6.2%
88 4.5% 21 11 56 3.9% 647 27 4.2%
44 4.2% 13 6 25 4.9% 345 18 5.2%
9 3.8% 3 2 4 5.1% 78 4 5.1%
15 12.5% - - - - - - -
21 9.3% 7 1 13 6.8% 74 5 6.8%
5 8.6% - - - - - - -
99 7.0% 27 13 59 6.8% 473 37 7.8%
96 6.4% 13 8 75 3.4% 502 18 3.6%
66 8.1% - - - - - - -
466 6.0% - - - - 2364 126 5.3%
8 1.8% 3 2 3 3.4% 148 6 4.1%
5 1.7% 2 1 2 3.1% 97 3 3.1%
36 1.8% 11 7 18 1.5% 650 18 2.8%
24 2.3% 8 3 13 2.9% 350 14 4.0%
7 3.0% 0 5 2 3.9% 78 5 6.4%
2 0.9% 1 0 1 1.4% 74 1 1.4%
2 4.4% - - - - - - -
25 1.8% 5 1 19 1.7% 475 9 1.9%
25 1.7% 2 1 22 0.6% 503 4 0.8%
33 4.0% - - - - - - -
159 2.1% - - - - 2375 59 2.5%
27 6.2% 9 6 12 9.7% 144 15 10.4%
18 6.3% 5 7 6 7.7% 95 10 10.5%
111 5.8% 25 12 73 4.9% 635 36 5.7%
74 6.7% 27 16 31 8.9% 367 44 12.0%
30 7.4% 4 14 12 14.7% 134 18 13.4%
24 16.7% - - - - - - -
10 4.9% 3 1 6 7.6% 67 6 9.0%
7 8.0% - - - - - - -
113 8.0% 22 12 79 6.8% 470 34 7.2%
85 5.4% 21 12 52 4.6% 525 26 5.0%
57 7.3% - - - - - - -
520 6.7% - - - - 2372 186 7.8%
16 3.6% 4 2 10 3.5% 146 6 4.1%
7 2.4% 2 0 5 4.3% 95 4 4.2%
59 3.0% 16 7 36 2.2% 654 21 3.2%
30 2.6% 14 7 9 4.0% 382 19 5.0%
11 3.5% 2 1 8 2.9% 104 3 2.9%
5 3.9% - - - - - - -
7 3.1% 1 4 2 3.6% 75 4 5.3%
10 5.1% - - - - - - -
48 3.5% 10 5 33 3.1% 459 15 3.3%
42 2.8% 15 2 25 2.4% 505 13 2.6%
33 3.9% - - - - - - -
259 3.2% - - - - 2345 81 3.5%
Type/Genea Max nt pairwise difference Number of nt sequences Number of variable nt positionsb Variable nt codon positionsc Max aa pairwise difference Number of aa sequences Number of variable aa positionsd
no. % 1st 2nd 3rd no. %
Alpha-6, HPV30 (N=16)
E6 0.7% 462 6 1.3% 2 1 3 1.3% 153 4 2.6%
E7 1.3% 318 5 1.6% 2 0 3 1.9% 105 2 1.9%
El 2.2% 1896 67 3.5% 15 7 45 2.6% 631 20 3.2%
E2 1.6% 1143 31 2.7% 7 4 20 2.7% 380 15 3.9%
E4 2.2% 375 13 3.5% 2 6 5 5.2% 154 10 6.5%
NCR1 5.1% 81 6 7.4% - - - - - - -
E5 2.4% 291 9 3.1% 5 1 3 3.1% 96 4 4.2%
NCR2 2.1% 47 1 2.1% - - - - - - -
L2 2.4% 1392 46 3.3% 3 6 37 2.2% 463 12 2.6%
L1 2.3% 1506 50 3.3% 7 9 34 2.0% 501 15 3.0%
URR 2.4% 828 32 3.9% - - - - - - -
CG 1.9% 7890 254 3.2% - - - - 2471 81 3.3%
Alpha-6, HPV53 (N=27)
E6 3.2% 465 27 5.8% 8 7 12 5.3% 154 11 7.1%
E7 0.9% 318 3 0.9% 1 0 1 1.9% 105 2 1.9%
E1 1.7% 1911 55 2.9% 16 11 28 2.6% 636 28 4.4%
E2 1.7% 1155 44 3.8% 13 10 21 3.6% 384 27 7.0%
E4 2.2% 453 17 3.8% 1 9 7 4.0% 150 12 8.0%
NCR1 3.5% 104 4 3.8% - - - - - - -
E5 3.1% 258 13 5.0% 3 5 5 5.9% 85 8 9.4%
NCR2 7.0% 43 3 7.0% - - - - - - -
L2 2.3% 1392 54 3.9% 2 8 44 1.5% 463 12 2.6%
L1 2.1% 1500 58 3.9% 12 3 43 1.6% 499 15 3.0%
URR 2.9% 818 39 4.8% - - - - - - -
CG 1.8% 7892 295 3.7% - - - - 2476 116 4.7%
Alpha-6, HPV56 (N=12)
E6 1.1% 468 6 1.3% 2 1 3 2.6% 155 4 2.6%
E7 1.9% 318 7 2.2% 2 0 5 2.9% 105 4 3.8%
E1 0.8% 1911 23 1.2% 11 3 9 1.6% 636 13 2.0%
E2 1.4% 1116 21 1.9% 7 5 8 2.7% 371 12 3.2%
E4 1.5% 408 6 1.5% 1 1 4 3.0% 135 4 3.0%
E5 0.8% 363 4 1.1% 0 2 2 2.7% 120 2 1.7%
L2 0.9% 1395 24 1.7% 3 2 19 0.9% 464 6 1.3%
L1 1.1% 1605 26 1.6% 3 3 20 0.9% 534 7 1.3%
URR 2.0% 926 24 2.6% - - - - - - -
CG 1.0% 7922 134 1.7% - - - - 2520 51 2.0%
Alpha-6, HPV66 (N=14)
E6 1.1% 468 6 1.3% 4 0 2 1.3% 155 2 1.3%
E7 2.5% 318 9 2.8% 4 2 3 4.8% 105 5 4.8%
E1 1.7% 1893 48 2.5% 10 11 26 1.7% 630 21 3.3%
E2 1.6% 1110 25 2.3% 6 5 14 2.2% 369 11 3.0%
E4 1.9% 513 12 2.3% 3 5 4 3.4% 170 7 4.1%
NCR1 5.2% 155 8 5.2% - - - - - - -
E5 3.9% 258 11 4.3% 2 4 5 5.9% 85 6 7.1%
NCR2 10.0% 21 3 14.3% - - - - - - -
L2 1.9% 1395 40 2.9% 5 10 25 1.5% 464 14 3.0%
L1 2.0% 1512 49 3.2% 7 15 27 1.9% 503 18 3.6%
URR 1.5% 769 21 2.7% - - - - - - -
CG 1.8% 7827 218 2.8% - - - - 2519 82 3.3%
Alpha-11, HPV34 (N=15)
E6 4.0% 447 23 5.1% 7 7 9 5.4% 148 11 7.4%
E7 2.0% 294 8 2.7% 2 4 2 5.2% 97 6 6.2%
El 4.0% 1944 88 4.5% 21 11 56 3.9% 647 27 4.2%
E2 3.5% 1038 44 4.2% 13 6 25 4.9% 345 18 5.2%
E4 4.1% 237 9 3.8% 3 2 4 5.1% 78 4 5.1%
NCR1 17.8% 120 15 12.5% - - - - - - -
E5 8.9% 225 21 9.3% 7 1 13 6.8% 74 5 6.8%
NCR2 14.3% 58 5 8.6% - - - - - - -
L2 5.6% 1422 99 7.0% 27 13 59 6.8% 473 37 7.8%
L1 5.4% 1509 96 6.4% 13 8 75 3.4% 502 18 3.6%
URR 6.4% 819 66 8.1% - - - - - - -
CG 4.7% 7828 466 6.0% - - - - 2364 126 5.3%
Alpha-11, HPV73 (N=16)
E6 1.6% 447 8 1.8% 3 2 3 3.4% 148 6 4.1%
E7 1.4% 294 5 1.7% 2 1 2 3.1% 97 3 3.1%
E1 1.2% 1953 36 1.8% 11 7 18 1.5% 650 18 2.8%
E2 1.7% 1053 24 2.3% 8 3 13 2.9% 350 14 4.0%
E4 2.1% 237 7 3.0% 0 5 2 3.9% 78 5 6.4%
E5 0.9% 225 2 0.9% 1 0 1 1.4% 74 1 1.4%
NCR2 4.4% 45 2 4.4% - - - - - - -
L2 1.3% 1428 25 1.8% 5 1 19 1.7% 475 9 1.9%
L1 1.2% 1512 25 1.7% 2 1 22 0.6% 503 4 0.8%
URR 2.8% 829 33 4.0% - - - - - - -
CG 1.4% 7733 159 2.1% - - - - 2375 59 2.5%
Alpha-13, HPV54 (N=11)
E6 5.1% 435 27 6.2% 9 6 12 9.7% 144 15 10.4%
E7 4.5% 288 18 6.3% 5 7 6 7.7% 95 10 10.5%
E1 4.8% 1908 111 5.8% 25 12 73 4.9% 635 36 5.7%
E2 5.0% 1104 74 6.7% 27 16 31 8.9% 367 44 12.0%
E4 6.2% 405 30 7.4% 4 14 12 14.7% 134 18 13.4%
NCR1 16.7% 144 24 16.7% - - - - - - -
E5 3.5% 204 10 4.9% 3 1 6 7.6% 67 6 9.0%
NCR2 8.0% 87 7 8.0% - - - - - - -
L2 7.4% 1413 113 8.0% 22 12 79 6.8% 470 34 7.2%
L1 5.0% 1578 85 5.4% 21 12 52 4.6% 525 26 5.0%
URR 7.0% 111 57 7.3% - - - - - - -
CG 5.6% 7799 520 6.7% - - - - 2372 186 7.8%
Alpha-3, HPV61 (N=10)
E6 2.3% 441 16 3.6% 4 2 10 3.5% 146 6 4.1%
E7 2.4% 288 7 2.4% 2 0 5 4.3% 95 4 4.2%
E1 2.3% 1965 59 3.0% 16 7 36 2.2% 654 21 3.2%
E2 1.8% 1149 30 2.6% 14 7 9 4.0% 382 19 5.0%
E4 2.5% 315 11 3.5% 2 1 8 2.9% 104 3 2.9%
NCR1 1.6% 129 5 3.9% - - - - - - -
E5 2.9% 228 7 3.1% 1 4 2 3.6% 75 4 5.3%
NCR2 4.6% 196 10 5.1% - - - - - - -
L2 2.8% 1380 48 3.5% 10 5 33 3.1% 459 15 3.3%
L1 2.0% 1518 42 2.8% 15 2 25 2.4% 505 13 2.6%
URR 2.4% 851 33 3.9% - - - - - - -
CG 2.3% 8037 259 3.2% - - - - 2345 81 3.5%
Alpha-11, HPV34 (N=15)
E6 4.0% 447 23 5.1% 7 7 9 5.4% 148 11 7.4%
E7 2.0% 294 8 2.7% 2 4 2 5.2% 97 6 6.2%
E1 4.0% 1944 88 4.5% 21 11 56 3.9% 647 27 4.2%
E2 3.5% 1038 44 4.2% 13 6 25 4.9% 345 18 5.2%
E4 4.1% 237 9 3.8% 3 2 4 5.1% 78 4 5.1%
NCR1 17.8% 120 15 12.5% - - - - - - -
E5 8.9% 225 21 9.3% 7 1 13 6.8% 74 5 6.8%
NCR2 14.3% 58 5 8.6% - - - - - - -
L2 5.6% 1422 99 7.0% 27 13 59 6.8% 473 37 7.8%
L1 5.4% 1509 96 6.4% 13 8 75 3.4% 502 18 3.6%
URR 6.4% 819 66 8.1% - - - - - - -
CG 4.7% 7828 466 6.0% - - - - 2364 126 5.3%
Alpha-11, HPV73 (N=16)
E6 1.6% 447 8 1.8% 3 2 3 3.4% 148 6 4.1%
E7 1.4% 294 5 1.7% 2 1 2 3.1% 97 3 3.1%
E1 1.2% 1953 36 1.8% 11 7 18 1.5% 650 18 2.8%
E2 1.7% 1053 24 2.3% 8 3 13 2.9% 350 14 4.0%
E4 2.1% 237 7 3.0% 0 5 2 3.9% 78 5 6.4%
E5 0.9% 225 2 0.9% 1 0 1 1.4% 74 1 1.4%
NCR2 4.4% 45 2 4.4% - - - - - - -
L2 1.3% 1428 25 1.8% 5 1 19 1.7% 475 9 1.9%
L1 1.2% 1512 25 1.7% 2 1 22 0.6% 503 4 0.8%
URR 2.8% 829 33 4.0% - - - - - - -
CG 1.4% 7733 159 2.1% - - - - 2375 59 2.5%
Alpha-13, HPV54 (N=11)
E6 5.1% 435 27 6.2% 9 6 12 9.7% 144 15 10.4%
E7 4.5% 288 18 6.3% 5 7 6 7.7% 95 10 10.5%
E1 4.8% 1908 111 5.8% 25 12 73 4.9% 635 36 5.7%
E2 5.0% 1104 74 6.7% 27 16 31 8.9% 367 44 12.0%
E4 6.2% 405 30 7.4% 4 14 12 14.7% 134 18 13.4%
NCR1 16.7% 144 24 16.7% - - - - - - -
E5 3.5% 204 10 4.9% 3 1 6 7.6% 67 6 9.0%
NCR2 8.0% 87 7 8.0% - - - - - - -
L2 7.4% 1413 113 8.0% 22 12 79 6.8% 470 34 7.2%
L1 5.0% 1578 85 5.4% 21 12 52 4.6% 525 26 5.0%
URR 7.0% 111 57 7.3% - - - - - - -
CG 5.6% 7799 520 6.7% - - - - 2372 186 7.8%
Alpha-3, HPV61 (N=10)
E6 2.3% 441 16 3.6% 4 2 10 3.5% 146 6 4.1%
E7 2.4% 288 7 2.4% 2 0 5 4.3% 95 4 4.2%
E1 2.3% 1965 59 3.0% 16 7 36 2.2% 654 21 3.2%
E2 1.8% 1149 30 2.6% 14 7 9 4.0% 382 19 5.0%
E4 2.5% 315 11 3.5% 2 1 8 2.9% 104 3 2.9%
NCR1 1.6% 129 5 3.9% - - - - - - -
E5 2.9% 228 7 3.1% 1 4 2 3.6% 75 4 5.3%
NCR2 4.6% 196 10 5.1% - - - - - - -
L2 2.8% 1380 48 3.5% 10 5 33 3.1% 459 15 3.3%
LI 2.0% 1518 42 2.8% 15 2 25 2.4% 505 13 2.6%
URR 2.4% 851 33 3.9% - - - - - - -
CG 2.3% 8037 259 3.2% - - - - 2345 81 3.5%
a

CG, complete genome; NCR1, noncoding region 1 between the E2 and E5 ORFs; NCR2, noncoding region 2 between the E5 and L2 ORFs; URR, upstream regulatory region.

b

Each insert or deletion event was counted as one variation.

c

The first, second, and third nucleotide positions in a codon.

d

Amino acid changes (nonsynonymous changes). Each insert or deletion event was counted as one variation.