Wastewater-Based Surveillance of Human Papillomavirus Genotype Diversity

Importance Human papillomaviruses (HPVs) account for more than 30% of infection-related cancers worldwide. Surveillance of circulating HPV genotypes at the population level remains limited because clinical monitoring primarily relies on cervical screening and does not capture infections in men or individuals outside screening programs. Objective To assess whether wastewater-based epidemiology can monitor the diversity and temporal circulation of HPV genotypes at the population level. Design, Setting, and Participants This is a cross-sectional study of raw wastewater collected twice weekly from January 24, 2024, to January 29, 2025, at a large wastewater treatment plant serving approximately 1 million population equivalents in the Paris, France, metropolitan area. Exposure Population-level shedding of HPV DNA into wastewater. Main Outcomes and Measures The primary outcomes were detection frequency, diversity, and temporal patterns of HPV genotypes in wastewater. HPVs of the genus Alphapapillomavirus were quantified using a broad-spectrum quantitative polymerase chain reaction assay and normalized using human-associated excretion markers (crAssphage and mitochondrial DNA). Twenty-eight HPV genotypes were screened using a multiplex polymerase chain reaction assay. Detection reproducibility was evaluated with McNemar tests (mid-P method); quantification reproducibility was evaluated using Wilcoxon signed-rank tests for censored data. Results HPVs were detected in all 100 wastewater samples analyzed, with a mean concentration of 7.3 × 10 3 genome equivalents/L (range, 7.3 × 10 1 to 3.0 × 10 5 genome equivalents/L), showing moderate temporal variability over the study period. Twenty-seven HPV genotypes were identified, with a median of 6 genotypes per sample (range, 1-12). The most frequently detected genotypes were HPV-66 (97%; 95% CI, 93%-100%), HPV-6 (93%; 95% CI, 88%-97%), and HPV-53 (89%; 95% CI, 83%-95%). High-risk HPV-39 and HPV-56, which are not covered by current vaccines, were detected in 72% (95% CI, 63%-81%) and 58% (95% CI, 48%-68%) of samples, respectively, vs 21% (95% CI, 13%-29%) for HPV-16 and 5% (95% CI, 1%-10%) for HPV-18, both of which are vaccine targeted. Temporal modeling showed relatively stable viral circulation over the study period. Conclusions and Relevance In this cross-sectional study of wastewater collected from a large urban population, wastewater-based epidemiology enabled population-level monitoring of HPV genotype circulation and complemented clinical surveillance by capturing infections across sexes and age groups. These findings suggested that this approach may facilitate evaluation of the effectiveness of HPV vaccination programs and serve as a scalable tool for monitoring HPV genotype diversity within the population.