{"doi":"10.1101/2025.09.17.25335998","title":"Wastewater Sequencing Reveals Persistent Circulation and Rising Prevalence of Several Oncogenic Viruses Across Texas","abstract":"Summary Background Oncogenic viruses cause high-risk cancers in humans and are responsible for nearly 20% of all cancer cases worldwide. Currently, very limited data exists in the realm of wastewater-based viral epidemiology (WBE) of cancer-causing viruses, with existing studies using targeted approaches (i.e PCR-based approaches) which lack scalability. Our study aims to carry out WBE with hybrid-capture probes to detect and track multiple oncogenic viruses simultaneously in wastewater across Texas, USA, overcoming the drawbacks associated with targeted approaches. Methods Here, we used a hybrid-capture approach to detect, filter and sequence oncogenic virus signals from wastewater samples collected over a duration of three years, from May 2022 to May 2025. Once viral reads were sequenced, we utilized established computational tools to characterize reads into their respective virus of origin. Next, viral abundances of each characterized oncogenic virus were tracked over time and read coverage across their genomes was measured using read mapping techniques. Findings We detected six known oncogenic viruses, along with three suspected oncogenic viruses across all sampling locations within Texas. Over three years, viral abundance gradually increased, with distinct peaks and dips over the summer and winter months. The prevalence of high-risk viruses such as HPV and EBV rose sharply, with increases in abundance observed post-2024. We also obtained nearly 100% genome coverage with viral reads captured using a hybrid-capture technique for almost all oncogenic viruses and their types.] Interpretations Our study shows that a hybrid-capture method can efficiently overcome the challenges faced with using targeted approaches for WBE. Using this method, we get broader read coverage, coupled with concurrent and consistent real-time tracking dynamics of multiple oncogenic viruses. Our findings also emphasize the persistent circulation and rising prevalence of high-risk cancer-causing viruses, underscoring the need for sustained public health interventions to protect communities and assess viral prevalence in high-risk populations. Funding This work was supported by S.B. 1780, 87th Legislature, 2021 Reg. Sess. (Texas 2021), the Baylor College of Medicine and the Alkek Foundation Seed Funds. Research in context Evidence before this study Cancer-causing viruses are of major clinical significance, responsible for nearly 20% of all recorded cancer incidences in humans worldwide. With some of these viruses causing high-risk cancers such as cervical cancer, there is a need for improved detection, tracking and control of oncogenic viruses across the globe. During the SARS-CoV-2 pandemic, wastewater-based viral epidemiology (WBE) rose to the forefront of virus tracking, utilizing non-invasive methods to detect and monitor the prevalence of medically relevant viruses of concern. Today, WBE has been utilized to accelerate the surveillance of numerous viruses such as SARS-CoV-2, mpox, influenza and more. To reinforce our prior knowledge on current trends in WBE of oncogenic viruses, we searched for research articles in PubMed and Google Scholar containing keywords “wastewater” and “oncogenic viruses” or “tumor viruses”. Further, to look specifically at oncogenic viruses of clinical concern, we searched for studies containing the keywords “wastewater” along with each of the 9 oncogenic viruses—Human papillomavirus, Hepatitis B virus, Hepatitis C virus, BK virus, Epstein-Barr virus, Merkel cell polyomavirus, Human polyomavirus, Kaposi Sarcoma-associated virus and Human T-cell lymphotropic virus type 1. On assessment of the search results, we found that specific oncogenic viruses had been detected in the wastewater of numerous countries including Egypt, Uruguay, Canada, Catalonia, Italy, India and Australia. These studies primarily focused on using PCR-based techniques to sequence and obtain viral read sequences from wastewater, measuring viral RNA concent","journal":"medRxiv","year":2025,"id":559088,"datarank":0.16479184330021646,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.0,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9152,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1460306,"name":"Ryan K. Perez","orcid":null,"position":1,"is_corresponding":false},{"id":1460307,"name":"Matt Ross","orcid":null,"position":2,"is_corresponding":false},{"id":619143,"name":"Michael J. Tisza","orcid":"0000-0003-1168-1617","position":3,"is_corresponding":false},{"id":551100,"name":"Sara Javornik Cregeen","orcid":null,"position":4,"is_corresponding":false},{"id":1167101,"name":"Jennifer Deegan","orcid":"0009-0004-9988-966X","position":5,"is_corresponding":false},{"id":19859,"name":"Joseph F. Petrosino","orcid":"0000-0002-4046-6898","position":6,"is_corresponding":false},{"id":245381,"name":"Eric Boerwinkle","orcid":"0000-0001-8813-0544","position":7,"is_corresponding":false},{"id":465023,"name":"Justin R. Clark","orcid":"0000-0003-1590-6828","position":8,"is_corresponding":false},{"id":363659,"name":"Anthony W. Maresso","orcid":"0000-0002-4452-3490","position":9,"is_corresponding":false},{"id":1460305,"name":"Harihara Prakash","orcid":null,"position":0,"is_corresponding":true}],"reference_count":26,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:55:30.312295Z","pmid":"41001489","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}