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Anal infection by cutaneous Human Papillomaviruses (HPV) has been rarely investigated. We aimed to assess the prevalence, genotype diversity, and determinants of mucosal (alpha) and cutaneous (beta and gamma) anal HPV infection in men who have sex with men (MSM).Anal samples were collected with a Dacron swab. Alpha HPVs were detected using the Linear Array HPV genotyping test, while beta and gamma HPVs using a PCR combined with Luminex technology.A total of 609 MSM (437 HIV-uninfected and 172 HIV-infected, most of which were undergoing cART) were enrolled. Alpha, beta, and gamma HPVs were detected in 78.0%, 27.6% and 29.3% of the participants. Only alpha HPV prevalence was significantly higher among HIV-infected compared to uninfected MSM (93.0% vs. 72.1%, p 0.0001). Beta2 and gamma10 represented the most frequent cutaneous HPV species, with no significant differences between HIV-infected and uninfected individuals. The most common alpha, beta, and gamma genotypes were HPV16, HPV111, HPV121, respectively. Alpha HPV infection was significantly associated with lifetime number of partners, receptive anal sex, and HIV status. Beta and/or gamma HPV infection showed no significant association with HIV status, socio-demographic or sexual behavioral factors.A wide spectrum of mucosal and cutaneous HPV types is present in the anal canal. Only mucosal HPV prevalence increased significantly in cases of concomitant HIV infection.

Background Mucosal high-risk human papillomavirus (HPV) types benefit differently from the immunocompromised status of the host. So far it is not known whether a similar scenario holds for the large group of the β and γ cutaneous HPV types that appear to be present at several anatomical sites. Methods The presence of β ( n = 43) and γ ( n = 30) HPVs in the anal samples of 66 HIV-positive and 153 HIV-negative anonymized men who have sex with men (MSM) was determined by multiplex PCR, using type-specific primers and bead-based hybridization (Luminex technology). Results The prevalence of β and γ HPV infection was 65.6% and 68.2%, respectively, among HIV-positive MSM and 59.1% and 57.7%, respectively, among HIV-negative MSM. β-2 and γ-10 were found to be the most prevalent species in both groups. The prevalence of infection with HPV types of the species β-1 ( P = 0.02), β-3 ( P = 0.002), γ-6 ( P = 0.002), and γ-7 ( P = 0.02) was higher in HIV-positive than HIV-negative men. In contrast, the β-2 species was equally distributed in the two groups, while the γ-10 species was slightly affected by HIV status. Conclusions These findings provide evidence that impairment of the host’s immune surveillance impacts β and γ HPV infections differently.