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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 3.

Prevalence of HPV variants of each type in samples from Costa Rica, Taiwan, China, Thailand, Rwanda and Burkina Faso.

Costa Rica Taiwan, China Thailand Rwanda Burkina Faso Total
Type/Lineage Count % within Cohort % within Lineage* Count % within Cohort % within Lineage Count % within Cohort % within Lineage Count % within Cohort % within Lineage Count % within Cohort % within Lineage Count % within Cohorts
Alpha-5, HPV26
A 19 100.0% 100.0% - - - - - - - - - - - - 19 100.0%
Total 19 100.0% 100.0% - - - - - - - - - - - - 19 100.0%
Alpha-5, HPV51
A1 80 58.0% 41.5% 1 12.5% 8.9% 18 36.0% 25.8% 9 33.3% 23.8% - - - 108 46.4%
A2 12 8.7% 8.7% 3 37.5% 37.5% 20 40.0% 40.0% 1 3.7% 3.7% 1 10.0% 10.0% 37 15.9%
A3 - - - - - - 2 4.0% 100.0% - - - - - - 2 0.9%
A4 3 2.2% 2.2% 4 50.0% 51.6% 10 20.0% 20.6% 4 14.8% 15.3% 1 10.0% 10.3% 22 9.4%
B1 43 31.2% 26.1% - - - - - - 13 48.1% 40.4% 4 40.0% 33.5% 60 25.8%
B2 - - - - - - - - - - - - 4 40.0% 100.0% 4 1.7%
Total 138 100.0% 20.0% 8 100.0% 20.0% 50 100.0% 20.0% 27 100.0% 20.0% 10 100.0% 20.0% 233 100.0%
Alpha-5, HPV69 A1 - - - - - - - - - - - - - - - - -
A2 2 9.5% 9.5% - - - - - - - - - - - - 2 9.5%
A3 7 33.3% 33.3% - - - - - - - - - - - - 7 33.3%
A4 12 57.1% 57.1% - - - - - - - - - - - - 12 57.1%
Total 21 100.0% 100.0% - - - - - - - - - - - - 21 100.0%
Alpha-5, HPV82 A1 - - - - - - - - - - - - - - - - -
A2 5 10.9% 30.3% - - - - - - 3 25.0% 69.7% - - - 8 13.8%
A3 1 2.2% 100.0% - - - - - - - - - - - - 1 1.7%
B1 - - - - - - - - - 3 25.0% 100.0% - - - 3 5.2%
B2 - - - - - - - - - - - - - - - - -
C1 38 82.6% 100.0% - - - - - - - - - - - - 38 65.5%
C2 1 2.2% 11.5% - - - - - - 2 16.7% 88.5% - - - 3 5.2%
C3 - - - - - - - - - 1 8.3% 100.0% - - - 1 1.7%
C4 - - - - - - - - - 3 25.0% 100.0% - - - 3 5.2%
C5 1 2.2% 100.0% - - - - - - - - - - - - 1 1.7%
Total 46 100.0% 50.0% - - - - - - 12 100.0% 50.0% - - - 58 100.0%
Alpha-6, HPV30
A1 1 10.0% 56.5% - - - - - - 1 7.7% 43.5% - - - 2 8.7%
A4 - - - - - - - - - 5 38.5% 100.0% - - - 5 21.7%
A5 1 10.0% 100.0% - - - - - - - - - - - - 1 4.3%
A2 1 10.0% 39.4% - - - - - - 2 15.4% 60.6% - - - 3 13.0%
A3 3 30.0% 56.5% - - - - - - 3 23.1% 43.5% - - - 6 26.1%
B 4 40.0% 72.2% - - - - - - 2 15.4% 27.8% - - - 6 26.1%
Total 10 100.0% 50.0% - - - - - - 13 100.0% 50.0% - - - 23 100.0%
Alpha-6, HPV53 - - - - - - - - - - - - - - - - -
A 65 20.2% 22.0% 2 40.0% 43.7% - - - 11 31.4% 34.3% - - - 78 21.5%
B - - - - - - - - - 8 22.9% 100.0% - - - 8 2.2%
C 32 9.9% 17.0% 2 40.0% 68.4% - - - 3 8.6% 14.6% - - - 37 10.2%
D1 221 68.6% 55.8% 1 20.0% 16.3% - - - 12 34.3% 27.9% - - - 234 64.6%
D2 2 0.6% 100.0% - - - - - - - - - - - - 2 0.6%
D3 - - - - - - - - - - - - - - - - -
D4 2 0.6% 17.9% - 10 - - - - 1 2.9% 82.1% - - - 3 0.8%
Total 322 100.0% 33.3% 5 100.0% 33.3% - - - 35 0.0% 33.3% - - - 362 100.0%
Alpha-6, HPV56 - - - - - - - - - - - - - - - - -
A1 81 38.4% 75.4% - - - 2 12.5% 24.6% - - - - - - 83 31.9%
A2 77 36.5% 12.5% 2 66.7% 22.9% 9 56.3% 19.3% 18 81.8% 28.1% 4 50.0% 17.2% 110 42.3%
B 53 25.1% 15.9% 1 33.3% 21.1% 5 31.3% 19.8% 4 18.2% 11.5% 4 50.0% 31.7% 67 25.8%
Total 211 100.0% 20.0% 3 100.0% 20.0% 16 100.0% 20.0% 22 100.0% 20.0% 8 100.0% 20.0% 260 100.0%
Alpha-6, HPV66
A 68 52.3% 45.1% - - - - - - 7 63.6% 54.9% - - - 75 51.4%
B1 11 8.5% 3.5% 1 100.0% 40.8% - - - 4 36.4% 14.9% 4 100.0% 40.8% 20 13.7%
B2 51 2% 100.0% - - - - - - - - - - - - 51 9%
Total 130 100.0% 25.0% 1 100.0% 25.0% - - - 11 100.0% 25.0% 4 100.0% 25.0% 146 100.0%
Alpha-11, HPV34
A1 11 45.8% 100.0% - - - - - - - - - - - - 11 44.0%
A2 2 8.3% 7.7% - - - - - - - - - 1 100.0% 92.3% 3 12.0%
B 1 4.2% 100.0% - - - - - - - - - - - - 1 4.0%
C1 4 16.7% 100.0% - - - - - - - - - - - - 4 16.0%
C2 6 25.0% 100.0% - - - - - - - - - - - - 6 24.0%
Total 24 100.0% 50.0% - - - - - - - - - 1 100.0% 50.0% 25 100.0%
Alpha-11, HPV73
A1 2 3.70% 100.00% - - - - - - - - - - - - 2 3.5%
A2 24 44.44% 100.00% - - - - - - - - - - - - 24 42.1%
B 28 51.85% 34.15% - - - - - - 3 100.0% 65.9% - - - 31 54.4%
Total 54 100.00% 50.00% - - - - - - 3 100.0% 50.0% - - - 57 100.0%
Alpha-13, HPV54
A1 60 50.4% 100.0% - - - - - - - - - - - - 60 49.6%
A2 43 36.1% 100.0% - - - - - - - - - - - - 43 35.5%
B 14 11.8% 100.0% - - - - - - - - - - - - 14 11.6%
C1 1 0.8% 1.7% - - - - - - - - - 1 50.0% 98.3% 2 1.7%
C2 1 0.8% 1.7% - - - - - - - - - 1 50.0% 98.3% 2 1.7%
- 11 100 50. - - - - - - - - - - 100.0 50. 12 100
Total 9 .0% 0% - - - - - - - - - 2 % 0% 1 .0%
Alpha-3, HPV61
A1 85 91.40% 100.00% - - - - - - - - - - - - 85 79.4%
A2 1 1.08% 2.45% - - - - - - 6 42.9% 97.6% - - - 7 6.5%
B 1 1.08% 2.45% - - - - - - 6 42.9% 97.6% - - - 7 6.5%
- - 6.4 31.11 - - - - - - - 14. 68. - - - - 7.5
C 6 5% 100 % 50. - - - - - - 2 3% 10 9% - - - 8 %
Total 93 .00% 00% - - - - - - 14 0.0% 50.0% - - - 107 100.0%
*

The percentage within lineage of HPV variant is taken as the proportion within cohort divided by the total proportion within cohort of variants.