Introduction Persistent infection with high-risk human papillomavirus (hrHPV) is a necessary step in anal cancer’s pathogenesis. With no universally-accepted guidelines on screening, and given the suboptimal performance of cytology, anal HPV testing is increasingly recognised as an important, adjunctive screening tool for anal cancer precursors. mRNA-based HPV assays targeting the E6/7 oncogenes are emerging as more specific tests for persistent HPV than the traditionally-used DNA-based tests. No data exists on serial monitoring of anal hrHPV in MSM using this novel assay. The objectives of this study are to describe HPV prevalence/persistence rates in a sample of high-risk, HIV-negative MSM enrolled in a PrEP demonstration project.

Methods Participants were drawn from PREPARATORY-5, which recruited HIV-negative MSM with high HIV risk as determined by a score of ≥10 on the HIV Incidence Risk Index for MSM (HIRI-MSM) and a history of condomless receptive anal sex in the prior 6 months. Anal samples were tested for hrHPV via the mRNA-based Aptima HPV Assay at baseline, months 6 and 12. Logistic regression was used to assess characteristics associated with hrHPV infection.

Results 43 participants were recruited, with median age 33 years (IQR 28–37). 10 (23%) were current smokers, and median HIRI-MSM score was 28 (IQR 19.5–35.5). 24 (56%) participants had hrHPV at any timepoint, and 15 (35%) had persistent hrHPV, defined as hrHPV isolated at two different timepoints. In multivariable logistic regression, current smoking status (OR=9.2, 95%CI=1.16–72.59, p=0.03) and HIRI-MSM score (OR: 1.2 per 1-point increase, 95%CI=1.03–1.33, p=0.01) were associated with hrHPV infection.

Conclusion Using a novel HPV E6/E7 mRNA assay with higher specificity for persistent infection, this study demonstrated a high burden of overall and persistent hrHPV infection in high-risk, HIV-negative MSM. These findings support the inclusion of MSM at high risk of sexual HIV acquisition when considering interventions related to the prevention and screening of anal cancer precursors.