Wastewater-based epidemiology proved its power and worth during the COVID-19 pandemic when it played an important role in tracking movement of the virus. Right after, it was a wastewater surveillance program that caught a polio outbreak in New York, helping to ensure it did not spread beyond one neighborhood.
Since then, wastewater surveillance programs have become increasingly popular, with some cities implementing them weekly or monthly. For example, since 2022, the Texas Wastewater and Environmental Biomonitoring group has implemented weekly-to-monthly viral sequencing of wastewater across major Texas cities.
“Our experience with viral wastewater analysis led us explore the possibility that it could be used to track oncogenic (cancer-causing) viruses,” said Anthony Maresso, professor of molecular virology and microbiology at Baylor.
In a new study, Maresso and his team are the first to show a comprehensive approach can detect all known oncogenic viruses concurrently by analyzing viral genomes in wastewater.
Oncogenic viruses can cause 1 in 5 cancers worldwide. Common examples include human papillomavirus (HPV), which can cause cervical and throat cancers, as well as hepatitis B and C viruses, which can lead to liver cancer.
For their study, published in Applied and Environmental Microbiology, researchers analyzed wastewater samples that were collected between May 2022 to May 2025 from more than 40 sites in 16 cities across Texas, covering roughly a quarter of the state’s population.
The results showed all known cancer-causing viruses in wastewater across Texas, including HPV, hepatitis B and C and cancer-associated human polyomaviruses. The researchers also detected Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus, which are linked to several cancers such as Hodgkin lymphoma and rare blood cancers.
“Our method to analyze viral signals in wastewater, called hybrid-capture genetic sequencing, generates a wealth of information that allows us to identify in one test more than 3,000 known human viruses, as well as possible new mutations,” said first author Harihara Prakash, a bioinformatics analyst at Baylor.
Overall, the abundance of multiple oncogenic viruses increased in the 3-year time period studied. However, HPV, EBV and certain polyomaviruses stood out to the researchers because they showed clear upward trends, with particularly sharp increases after 2024.
While there are hundreds of HPV types, only some are considered high-risk for cancer. Specifically, HPV-16 and HPV-18 together cause more than 70% of cervical cancers worldwide. The study showed that low-risk HPV types were generally more abundant than high-risk ones, while high-risk HPV types still showed clear increases, especially from late 2024 into early 2025. HPV-16 was consistently more common than HPV-18, a pattern that mirrors clinical studies worldwide.
Critically, the study detected all nine HPV types targeted by the current HPV vaccine—Gardasil 9—showing that wastewater monitoring can track vaccine preventable viruses in real world populations. In the future, this approach could help assess whether vaccination programs are working or where they may be falling behind.
“Our study proves that cancer-causing viruses can be tracked in wastewater and opens new possibilities to better understanding the interactions of these viruses with human populations in ways we hope will lead to improved public health interventions,” said Maresso.
Viral detection in wastewater was first developed at Baylor in the mid-20th century for polio virus. During the COVID-19 pandemic, Baylor and collaborators continued to pioneer its use to track SARS-CoV-2 virus at community levels.