Table 1.

Variant lineages of HPV types in the high-risk clade and outcome of infection in the prospective Guanacaste, Costa Rica, cohort study

SpeciesHPV typeTest variantn%Referencen%Case statusORP
α-952A, B, C166.78%D00.00%CIN3+0.78
208.47%00.00%CIN20.42
166.78%216.67%Persistent0.430.17
18477.97%1083.33%Control1.00
236100.00%12100.00%Total
67A18.33%B15.88%CIN3+1.36
00.00%15.88%CIN20.00
1191.67%1588.24%Control1.00
12100.00%17100.00%Total
33A, B99.78%C00.00%CIN3+0.80
1111.96%19.09%CIN21.240.80
1010.87%327.27%Persistent0.380.12
6267.39%763.64%Control1.00
92100.00%11100.00%Total
58A217.87%B, C, D00.00%CIN3+0.47
3613.48%00.00%CIN20.16
2810.49%529.41%Persistent0.370.050
18268.16%1270.59%Control1.00
267100.00%17100.00%Total
16Non-E2129.58%E6815.74%CIN3+2.430.004
57.04%6314.58%CIN20.630.45
1115.49%337.64%Persistent2.630.010
3447.89%26862.04%Control1.00
71100.00%432100.00%Total
31A,B1810.23%C45.71%CIN3+1.810.38
2011.36%68.57%CIN21.340.56
169.09%1115.71%Persistent0.580.22
12269.32%4970.00%Control1.00
176100.00%70100.00%Total
35A1413.33%A222.99%CIN3+6.35
26.67%57.46%CIN21.27
723.33%68.96%Persistent3.71
1756.67%5480.60%Control1.00
30100.00%67100.00%Total
α-1173A14.00%B00.00%CIN3+
14.00%27.69%CIN20.50
14.00%27.69%Persistent0.50
2288.00%2284.62%Control1.00
25100.00%26100.00%Total
α-718AA,E179.94%Af48.00%CIN3+1.230.89
127.02%00.00%CIN20.05
1810.53%1020.00%Persistent0.520.12
12472.51%3672.00%Control1.00
171100.00%50100.00%Total
45B56.41%A23.17%CIN3+2.250.35
33.85%46.35%CIN20.680.58
1012.82%34.76%Persistent3.000.11
6076.92%5485.71%Control1.00
78100.00%63100.00%Total
70B33.33%A31.81%CIN3+1.77
55.56%74.22%CIN21.26
1314.44%3420.48%Persistent0.68
6976.67%12273.49%Control1.00
90100.00%166100.00%total
39A212.86%A122.94%CIN3+1.09
38.57%34.41%CIN22.19
411.43%45.88%Persistent2.19
2777.14%5986.76%Control1.00
35100.00%68100.00%Total
68A15.00%B24.26%CIN3+1.33
315.00%00.00%CIN2
15.00%510.64%Persistent0.53
1575.00%4085.11%Control1.00
20100.00%47100.00%Total
α-569A111.11%B19.09%CIN21.50
222.22%19.09%Persistent3.00
666.67%981.82%Control1.00
9100.00%11100.00%Total
51B716.28%A33.19%CIN3+5.190.02
12.33%1313.83%CIN20.170.09
49.30%99.57%Persistent0.990.88
3172.09%6973.40%Control1.00
43100.00%94100.00%Total
α-653A23.57%B73.11%CIN3+1.070.84
23.57%83.56%CIN20.940.85
47.14%3013.33%Persistent0.500.21
4885.71%18080.00%Control1.00
56100.00%225100.00%Total
56A, B64.38%C00.00%CIN3+0.12
107.30%12.04%CIN24.170.13
1813.14%510.20%Persistent1.500.54
10375.18%4387.76%Control1.00
137100.00%49100.00%Total
66A46.56%B11.85%CIN3+3.450.27
46.56%35.56%CIN21.150.85
23.28%611.11%Persistent0.290.11
5183.61%4481.48%Control1.00
61100.00%54100.00%Total

NOTE: The order of the species groups and the types parallel Fig. 1 to highlight phylogenetic relationships. For ease of interpretation, the choices of “test” and “reference” variant lineage for each type were made to produce OR values for CIN3+ versus control of >1. This does not affect the P value for each type or the combined P values. P values were computed only when the number of cases of CIN3+ for test and reference lineages combined was 5 or more.

For HPV types including HPV16, the combined mid-P value was 0.07 for CIN3+ versus controls, 0.27 for CIN2 versus controls, and <0.01 for long-term persistence. When we excluded HPV16, the combined mid-P values were 0.37, 0.25, and 0.04, respectively.