Identification of circulating human papillomavirus types through high-throughput sequencing of Canadian municipal and institutional wastewater samples.

Abstract

Human papillomaviruses (HPVs) are a diverse group of viruses that infect human mucosal and cutaneous tissues, with a ubiquitous global distribution. Several types are classified as high-risk due to their association with cervical, anal, penile, and oropharyngeal cancers. Given its widespread prevalence and the limitations of clinical surveillance, HPV is an ideal candidate for wastewater-based testing (WBT), as a way to characterize circulating HPV types. Toward this goal, we utilized high-throughput Illumina-based amplicon sequencing targeting the conserved GP5+/GP6+ sites of HPV in wastewater samples collected from two urban treatment plants, two town sites, and three correctional facilities. Larger population catchments displayed greater diversity of HPV types in wastewater compared to institutional settings, reflecting differences in community composition and exposure. A total of 24 distinct HPV types were detected, all belonging to the alpha-papillomavirus genus, encompassing high- and low-risk types, types of unknown risk, and both cutaneous and mucosal types. Among these were six vaccine-preventable types, including HPV-16 and HPV-18, as well as probably carcinogenic types not routinely monitored in clinical settings, such as HPV-67, HPV-69, and HPV-73. These findings demonstrate the utility of WBT as a complementary tool to clinical testing, providing critical insights to inform cancer prevention strategies and evaluate the impact of vaccination programs.

Importance: Human papillomavirus (HPV)-related cancers, including cervical, anal, penile, and oropharyngeal cancers, impose a significant economic burden on healthcare systems, with billions spent annually on treatment and management. This study reports the detection of HPV in Canadian wastewater, providing new insights into HPV circulation within communities. The findings highlight the ongoing prevalence of high-risk HPV types targeted by vaccines and the circulation of probable carcinogenic types, such as HPV-67, HPV-69, and HPV-73, which are not included in current clinical testing algorithms. Wastewater-based surveillance of HPV could complement clinical testing by capturing data on populations typically underrepresented in clinical settings. A clearer understanding of circulating HPV types can support public health efforts to promote cancer screening, monitor vaccination campaigns, and address gaps in prevention strategies. The continued development of wastewater-based testing systems hints toward a promising future for unbiased monitoring of community health.