Table 2. Risk of bias within studies.

First Author	Selection of participants1	Time of exposure ascertainment2	Loss to follow- up3	Outcome ascertainment4	Confounding5,6	Selective outcome reporting7
Auvert[29]	All trial participants who provided at least one HPV result (47% of trial population). Those excluded (53%) had similar baseline characteristics Low risk	First available HPV status was used (median follow-up 2.4y/2.2y in HPV uninfected/infected). Consistent results were seen using recent HPV results. Low risk	12% loss to follow- up at 48 weeks. Unclear risk	Median follow-up 2.5 years. Low risk	Adjusted for sexual behavior at baseline, no adjustment for HSV2 High risk	No a-priori plan. No response to request for additional analyses High risk
Averbach	93% of cases included, exclusions	Repeated HPV testing, median 80 days	12% loss to follow-	Median follow-up	Adjusted for prospective	Any HPV infection was the primary
[24]	due to missing information. Controls selected from within same cohort study Low risk	between exposure and outcome Low risk	up at completion. Low risk	21.9 months Low risk	measurement of sexual behavior and HSV2 Low risk	exposure of interest. Responded to request for additional analyses Low risk
Chin-Hong [23]	No description of how subset (30% of EXPLORE study) were selected from participants in main study Unclear risk	HPV assessed at baseline only, median time to outcome between 6 and 36 months8 Unclear risk	Retention rate not documented. Unclear risk	Median follow-up 3 years Low risk	Adjusted for prospective sexual behavior, no adjustment for HSV2 High risk	Primary analysis assessed the association of HPV infection with HIV acquisition No additional analysis provided Unclear risk
Low[25]	No description of how subset (40%)of participants were selected from participants in main study Unclear risk	HPV assessed at baseline only, median time to outcome between 4 and 24 months Unclear risk	Retention rate not documented. Unclear risk	Median follow-up 1.7 years Low risk	Adjusted for HSV2, no adjustment for sexual behavior High risk	HPV analysis was not the primary aim of the publication. Additional analysis provided Low risk
Myer[27]	Cohort comprised of all HPV positives in main study and HPV negatives recruited over 1 year Unclear risk	HPV assessed at baseline only, median time to outcome between 6 and 24 months Unclear risk	25% loss to follow- up at 12months and 68% at 24 months. High risk	Median follow-up 14.3 months Low risk	Adjusted for baseline sexual behavior, no adjustment for HSV2 High risk	HPV analysis was not the primary aim of the publication. Additional analysis provided Unclear risk
Smith[30]	Cohort comprised of trial participants consenting to HPV testing (80%) Low risk	HPV assessed at baseline only, median time to outcome between 3 and 42 months Unclear risk	Retention rate not documented. Unclear risk	Median follow-up 42 months for 71% Low risk	Adjusted for HSV2, no adjustment for sexual behaviour High risk	No a-priori analysis plan. Additional analysis provided Low risk
Smith- McCune[26]	Cohort comprised of trial participants consenting to HPV sub-study (98%) Low risk	HPV assessed every 3 months. Recent infection was within 6 months excluding concurrent visit Low risk	6% loss to follow-up. Low risk	Median follow-up 21 months Low risk	Adjusted for prospective sexual behavior and HSV2 Low risk	A-priori analysis plan. Additional analysis provided Low risk
Veldhuijzen [28]	Cohort comprised of those with HPV results from main study (92%) Low risk	HPV assessed at baseline only, median time to outcome between 3 and 18 months Unclear risk	12% loss to follow- up. Low risk	Median follow-up 16.6 months Low risk	No adjustment for confounders High risk	No a-priori plan. No additional analysis provided Unclear risk

¹In case control studies here was a high risk of bias if >90% of cases were not included (and/or exclusion was related to exposure or outcome) or controls were not selected from within the cohort study. Unclear risk when this information was not available. In cohort studies, there was low risk of bias if the cohort were representative of the average individual in the population of interest, and both the exposed and unexposed were drawn from the same population. Unclear risk if this was not the case or not documented.

²Low risk if HPV was tested prospectively and/or the time between exposure and outcome was <1year. High risk if this time was ≥ 1 year and unclear risk if insufficient information was available.

³Low risk if retention was ≥80% at the end of the study. Unclear risk if information not available.

⁴High risk of bias if follow-up was not long enough for HIV to be acquired (less than 1 year). Low risk if median follow-up was at least 1 year and unclear risk if information not available.

⁵See table 1 for full list of confounders adjusted for.

⁶Low risk of bias if adjustment for prospective measurements of sexual behavior AND HSV2. Unclear risk if adjustment for sexual behavior OR HSV2 serology at baseline only. High risk if HSV2 OR sexual behavior not adjusted for.

⁷If (i)authors stated there was an a priori plan or stated which outcomes were of primary interest or (ii) authors responded to a request for further information and analysis then there was a low risk of bias. Of one of these was met this was unclear risk, if none were met this was high risk

⁸Where median time was not available in studies which tested baseline HPV only it is assumed to be between minimum follow-up HIV test frequency and total study follow-up.