Prevalence, incidence, and dynamics of oral human papillomavirus infection among healthy individuals—A molecular epidemiology field study from India

Persistent infection with human papillomavirus (HPV) is associated with an increased risk of head and neck cancers (HNC), particularly oropharyngeal cancer. This longitudinal cohort study investigated the prevalence and dynamics of oral HPV infection among healthy adults in South India. A total of 5325 participants were enrolled, and demographic, behavioral, and oral gargle samples were collected. HPV deoxyribonucleic acid (DNA) was detected using nested PCR (PGMY/GP) and genotyped by Sanger sequencing. HPV16 messenger ribonucleic acid (mRNA) expression was analyzed by reverse transcriptase polymerase chain reaction (RT-PCR) and validated using droplet digital polymerase chain reaction (ddPCR). Logistic regression analyses were performed to estimate odds ratios. At baseline, 5011 samples were analyzed; 274 (5.5%) were HPV-positive and 4737 were negative. Among 3792 initially HPV-negative participants followed up, 126 (3.3%) acquired new infections (median 8 months; range, 6-15 months). Of 274 baseline HPV-positive individuals, 241 were followed up: 24 (10%) showed persistence, while 217 (90%) cleared infection after a median of 9 months (range, 6-20 months). Sanger sequencing of 471 samples from prevalent and incident infections yielded 290 (61.6%) high-quality sequences; 284 (98%) were HPV16, with isolated detections of HPV18, HPV66, HPV70, and HPV89. Ten novel variants were identified-nine HPV16 and one HPV89-while remaining sequences aligned with established Indian cervical HPV lineages. None of the 176 HPV16 DNA-positive samples analyzed expressed mRNA by RT-PCR, confirmed in 136 samples using ddPCR. Oral HPV infection among healthy individuals in India appears predominantly transient. Long-term monitoring may elucidate the oncogenic potential of oral HPV in this population.