Natural History Of Oral Human Papillomavirus In Nigerian Mothers And Youth With And Without HIV: A Prospective Cohort Study

Objectives: HPV-associated oropharyngeal cancer is rising, yet the natural history of oral-HPV, particularly persistence remains poorly characterized in sub-Saharan Africa and in people living with HIV (PLWH). We characterized oral HPV prevalence, incident detection, persistence, and clearance over four visits in a Nigerian mother-youth cohort with and without HIV and quantified the genotype distribution relative to vaccine coverage. Methods: Within the prospective HOMINY cohort, 1075 participants (404 mothers and 671 youth) were followed across four visits at 6-month intervals. Oral rinses were genotyped with the Seegene Allplex HPV28 assay (28 genotypes). Persistence was defined as detection at ≥2 visit (not necessarily consecutive), with type-specific and visit 2-4 sensitivity definitions. We used modified-Poisson models for visit-level detection, Markov multistate models for acquisition and clearance, and a permutation test for mother-youth genotype concordance. Results: Oral HPV was detected at least once in 112 participants (10.4% overall; 11.1% mothers and 10% youth); incident detection was around 6% in both groups. Persistence was uncommon (1.9%), and only 3 had oral HPV DNA detected at all four visits. Clearance predominated across every visit interval. In Markov models, clearance was slower in PLWH (HR 0.42, 95% CI 0.22-0.77) with no difference in acquisition (HR 0.77, 95% CI 0.39-1.5). Persistence concentrated among PLWH. Only 31.2% of ever-positive participants carried a Gardasil-9 preventable strain of HPV; HPV16 and HPV39 were most frequent. Mother-youth genotype concordance exceeded chance (permutation p =0.009). Conclusion: Oral HPV was common but transient; persistence was confined to a small PLWH minority and was dominated by high-risk non-vaccine genotypes, leaving most infections beyond the reach of current vaccines.