Abstract
There is a paucity of data on changes in oral papilloma virus (PV) infection in people living with HIV (PLHIV) especially in low resource settings. The objective of this study was to determine the changes in oral PV infections in PLHIV from a low resource setting over a six-month follow-up period. This was a cohort study in which data was derived from a sub-sample of a parent study that examined oral human papilloma viruses, microbiota, and cancer in PLWHIV. This as a six-month follow up and a 2 mls saliva sample was collected from 541 participants on both visits. The saliva sample was used for DNA extraction, PV screening and typing using PCR methods. The DNA was subjected to Nanopore PV sequencing and subsequently analyzed using the phyloseq object, followed by a series of comparisons using the Phyloseq and Vegan packages in R to generate the alpha and beta diversity indices of the sequencing data from the sampled participants PV OTUs at the two visits. We found that 60% of participants had no detectable PVs at six-month follow-up, with a significant clearance rate of 84.47%. Oncogenic PVs were less likely to be detected as new infections compared to non-oncogenic PVs (Rate Ratio (RR) 0.42, 95% CI 0.31 to 0.56, P < 0.01). Oncogenic PV types were more likely cleared than non-oncogenic strains (RR 1.16, 95% CI 1.03 to 1.31, P = 0.02), but persistence rates did not significantly differ. This study highlights important trends in the natural course of oral PV infections, demonstrating that while most infections clear over time, there are distinct differences in the behavior of oncogenic versus non-oncogenic strains. These findings have important implications for the understanding of PV epidemiology and may guide future preventive and therapeutic strategies, particularly in the context of Human PV-related cancer prevention.