Oral HPV Dynamics in MSM Living with HIV in the Nine-Valent HPV Vaccination Era

Background/Objectives: Oral human papillomavirus (HPV) infection is emerging as a key driver of HPV-associated oropharyngeal cancer, especially in high-risk groups such as men who have sex with men (MSM) living with HIV (PLWH). However, evidence on oral HPV persistence and the impact of nine-valent HPV vaccination in adults remains limited. We conducted a prospective longitudinal study including 76 MSM PLWH, of whom 64 were nine-valent HPV-vaccinated and 12 unvaccinated. Methods: Oral rinse samples were collected at baseline (T0) and after 6 months (T6). HPV DNA detection and genotyping were performed using the Allplex™ HPV28 assay. Oral HPV dynamics (persistence, clearance, and incidence) were assessed for high-risk (HR) HPV, low-risk (LR) HPV, and vaccine-type HPV genotypes. Results: Baseline oral HPV prevalence was high (59.2%), with HR HPV detected in 43.4% of participants. HPV16 was the most frequent genotype at both T0 and T6. Among participants HPV-positive at baseline, persistence of HPV DNA was high and similar regardless of vaccination status (77.8%). However, incident vaccine-type oral HPV infection was significantly lower among vaccinated individuals than unvaccinated participants (6.3% vs. 33.3%; OR 0.13, 95% CI: 0.03–0.71; p = 0.0441). Finally, reporting ≥10 sexual partners in the previous year was significantly associated with baseline oral HPV positivity (p = 0.0298). Conclusions: In MSM PLWH, oral HPV infection is highly prevalent and persistent, underscoring that it may represent a reservoir for HPV-related oropharyngeal disease. In our small observational cohort, nine-valent HPV vaccination was associated with lower incident detection of vaccine-type oral HPV, supporting targeted vaccination and oral HPV surveillance in high-risk adult populations, while highlighting the need for larger longitudinal studies to confirm these findings and better define the magnitude and durability of vaccine-associated protection at the oral site.