HPV16 E6 and E7 Genetic Variability in Oral and Anal Samples from HIV-Positive MSM

Persistent infection with high-risk human papillomavirus (HPV), particularly genotype 16, is the main driver of anogenital and oropharyngeal cancers. However, data on HPV16 genetic variability in anal and oral samples from people living with HIV are limited. In this study, we investigated the diversity of HPV16 E6 and E7 genes in anal and oral samples collected from HIV-positive men who have sex with men (MSM) according to different cytological outcomes and anatomical site. Among 53 MSM patients, we obtained 51 E6 and 52 E7 sequences. Lineage A predominated (96.1%), mainly represented by sublineages A1 (84.3%) and A2 (9.8%). The E6 region showed higher variability than E7: 31.4% were identical to the reference (K02718), 51.0% carried the L83V (T350G) mutation, while Q14H, D25N, and D25E were also observed. In E7, only one non-synonymous substitution was detected (N29S). No site-specific variants were detected between anal and oral samples. Overall, these findings confirm the predominance of European A1/A2 variants in Italian MSM and suggest that E6/E7 polymorphisms are not directly linked to lesion grade or anatomical localization.