Natural history of oral human papillomavirus among participants recruited through MSM-focused services in southwestern Kenya: an 18-month prospective cohort study

Oral human papillomavirus (HPV) DNA is associated with a subset of oropharyngeal cancers. We characterised oral HPV prevalence, incidence, same-type persistence, and first non-detection, and examined associated factors among participants recruited through MSM-focused services in Kenya. Between July and December 2023, we enrolled 398 adults through two key-population clinics in Kisumu County, Kenya, with equal numbers by HIV status. Oral-rinse specimens were collected at baseline and at months 6, 12, and 18 and tested for HPV DNA by PCR with targeted high-risk genotyping. Among 398 participants, oral HPV DNA prevalence was 7·8% at baseline, increased to 21·0% at month 12, and declined to 14·9% at month 18. The reported overall incidence rate was 82·0 per 1,000 person-months; there was no statistical evidence of a difference by HIV status (IRR 1·01, 95% CI 0·74–1·39), although the confidence interval was imprecise. Same-type high-risk HPV was detected at consecutive visits in 18 participants (4·5% of the cohort), corresponding to 35 participant-genotype combinations and 38 consecutive-interval persistence events, and more than half of genotype detections were absent at the next scheduled six-month visit. Receptive oral sex was associated with prevalent detection (aOR 2·78, 95% CI 1·17–6·42) and same-type persistence (aOR 4·14, 95% CI 1·48–11·87). Several frequently detected high-risk genotypes are included in the 9-valent HPV vaccine, whereas other detected high-risk types are not vaccine antigens. These findings motivate evaluation of inclusive HPV-vaccination strategies alongside HIV and sexual-health services, but do not alone establish vaccine effectiveness or justify a policy change.