A study published in Applied and Environmental Microbiology is the first comprehensive approach to detect all known cancer-causing or oncogenic viruses concurrently by analyzing viral genomes in wastewater. The work, a collaboration between Baylor College of Medicine and the University of Texas Health Science Center at Houston, shows that it is feasible to monitor the presence and levels of cancer-causing viruses, enabling the possibility of public health interventions in the future.
"Oncogenic viruses can cause about one in five cancers worldwide," said co-corresponding author Dr. Anthony Maresso , professor of molecular virology and microbiology at Baylor. "Common examples include human papillomavirus (HPV), which can cause cervical and throat cancers, and hepatitis B and C viruses, which can lead to liver cancer. Because these infections often cause no symptoms for years or even decades, many people do not know they are infected until cancer develops. This makes prevention and early public health interventions very challenging. Our experience with viral wastewater analysis led us explore the possibility that it could be used to track oncogenic viruses."
Wastewater – a treasure trove of viral genetic data
"People shed tiny amounts of viral genetic material in urine, stool and skin cells, and that material ends up in sewage systems. By testing wastewater samples, scientists can get a snapshot of which viruses are circulating in a community, without testing individuals or identifying anyone personally," said co-corresponding author Dr. Justin Clark assistant professor of molecular virology and microbiology at Baylor.
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 pioneered the use of wastewater surveillance to track SARS-CoV-2 virus at community levels. This approach proved successful in anticipating outbreaks, predicting hospitalizations and enabling early detection of new viral variants. Since May 2022, the Texas Wastewater and Environmental Biomonitoring ( TexWEB ) group has implemented weekly-to-monthly viral sequencing of wastewater across major Texas cities.
"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 , bioinformatics analyst in the Maresso lab.
The team 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. "This approach tells us whether a virus is present or absent and which specific virus types are circulating, how common they are relative to each other, and how their prevalence changes over time," Prakash said.
The study detected all known cancer-causing viruses in wastewater across Texas. Among those detected are HPV, hepatitis B and C viruses and cancer-associated human polyomaviruses. In addition, the researchers also detected Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus, linked to several cancers such as Hodgkin lymphoma and rare blood cancers, respectively.
"Interestingly, we found that the abundance of multiple oncogenic viruses increased over the three years," Prakash said. "HPV, EBV and certain polyomaviruses stood out because they showed clear upward trends, with particularly sharp increases after 2024. It's not clear what led to this viral increase in wastewater. One possibility is that the summer spikes reflect increased travel and interpersonal contact during vacation and holiday periods in academic settings such as colleges. In addition, removal of COVID pandemic-related social distancing could also have contributed to higher transmission of sexually transmitted oncogenic viruses such as HPV."
"We took a closer look at HPV, a common virus that causes several types of cancer," Clark said. "There are hundreds of HPV types, but only some are considered high-risk for cancer. Specifically, HPV-16 and HPV-18 together cause more than 70% of cervical cancers worldwide. Our analysis 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."
Importantly, 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," Maresso said.
Ryan K. Perez, Matt Ross, Michael Tisza, Sara J. Javornik Cregeen and Joseph F. Petrosino, all at Baylor College of Medicine, and Jennifer Deegan and Eric Boerwinkle at the University of Texas Health Science Center at Houston, also contributed to this work.
This study was supported by S.B. 1780, 87th Legislature, 2021 Reg. Sess. (Texas 2021), NIH/NIAID (Grant number U19 AI157981), Baylor College of Medicine Joseph Melnick Seed and Alkek Foundation Seed.
