Detection of human immunodeficiency virus 1 (HIV-1) in wastewater provides a new approach for monitoring the virus in communities. Researchers at Baylor College of Medicine and colleagues at collaborating institutions report. nature communications Their method, called hybrid-capture gene sequencing, allows them to dissect the viral genome and specifically identify viral signals coming from local sewage. Analysis of facilities with available clinical data showed that the sewage HIV signal strongly matched the number of people known to be living with HIV in the community, providing evidence that the sewage HIV signal can track HIV burden.
HIV-1 is a retrovirus that has infected 90 million people and killed more than 40 million. Despite advances in diagnosis, prevention, and treatment, HIV-1 continues to spread, with 1.3 million new cases diagnosed worldwide in 2023. Managing HIV is difficult because it is difficult to identify people who are undiagnosed or who do not receive consistent care. These groups account for 80% of new infections. ”
Dr. Thomas Giordano, Co-corresponding author, Chief of the Division of Infectious Diseases and Professor, Baylor University School of Medicine
Current HIV surveillance methods rely heavily on clinical diagnosis and viral load reporting, which in turn is dependent on the individual receiving care. As a result, people who do not seek medical care or delay seeking care remain largely invisible to public health systems.
“Complementary surveillance strategies that can detect undiagnosed or untreated infections are urgently needed,” said co-author Dr. Anthony Maresso, professor of molecular virology and microbiology at Baylor University. “This study shows that wastewater analysis has the potential to identify geographic locations where untreated HIV exists. This could help identify communities where resources for HIV prevention and treatment exist or need to be increased.”
Wastewater analysis was first developed at Baylor in the mid-20th century for poliovirus surveillance. During the COVID-19 pandemic, Baylor and colleagues pioneered the use of wastewater surveillance to track the SARS-CoV-2 virus at the population and community level, successfully reflecting case rates, predicting hospitalizations, and enabling early detection of emerging virus variants.
Since May 2022, the Texas Wastewater Environmental Biomonitoring (TexWEB) group has been conducting weekly to monthly viral sequencing of wastewater across major Texas cities. The program has now detected over 400 human and animal viruses in sewage, enabled surveillance and early detection of viral outbreaks such as avian influenza virus, mpox, and measles, and generated a sequence-based tracking dashboard for public health reporting.
“In this study, we used this approach to analyze wastewater collected from 40 sites in 15 cities in Texas from mid-2022 to the end of 2024. Instead of using a test that only looks for short, specific genetic sequences of HIV, we used an advanced sequencing approach that can detect HIV genetic material and see what parts of the HIV genome are present,” said lead author Dr. Justin Clark, assistant professor of molecular virology and microbiology. Baylor.
More than 2,000 wastewater samples repeatedly detected HIV genetic material, albeit at low levels, indicating that HIV can indeed be detected in wastewater in a consistent and measurable manner. “It is important to point out that it is very unlikely that the HIV signal in wastewater represents infectious virus,” Giordano said. “Decontamination protocols in laboratories and wastewater facilities will destroy any viruses that enter the wastewater.”
unexpected results
“When we looked closely at some of the HIV signals, we found that the sequences appeared to come from a non-circulating laboratory strain rather than from a virus circulating in the community, suggesting contamination,” Clark said. “But what’s interesting is that our lab doesn’t work with HIV, so some ‘contamination’ must have happened before we received the wastewater sample.”
The team then looked at where these sequences came from and found that they were concentrated near medical and research centers.
“We took this as a clue,” Clark said. “Certain HIV sequences belonging to HIV variants that were prevalent in the 1980s were developed into research tools called lentiviral vectors. These are not live viruses, but pieces of their genetic material used in various types of research. Our detailed analysis of wastewater HIV sequences suggested that lentiviral contamination from research activities was confounding the data. To remove this confounding factor, we developed an approach to classify HIV sequences as circulating.” (community derived) or non-circulating (vector derived). Previous studies did not look for or exclude these other signals. ”
Once researchers eliminated confounding factors, they found a significant association between HIV signals in wastewater and HIV diagnoses in the community.
“Our study also addresses the need to maintain site anonymity, which is important for HIV surveillance given ongoing stigma and criminalization,” Giordano said. “We have another element of this research, which is to engage with focus groups, communities, individuals, and advocates to ensure that people’s perspectives are considered.”
“This study establishes the basis for sequencing-based HIV wastewater surveillance and highlights lentiviral vector contamination as an overlooked confounding factor that must be addressed in future efforts to monitor HIV-1 and other pathogenic microorganisms with synthetic equivalents,” said Professor Mareso.
The following authors also contributed to this study: Dylan Chirman, Harihara Prakash, Austen Terwilliger, Matt Ross, Mike Tisza, Sara J. Javornik Cregeen, Jason T. Kimata, and Faith E. Fletcher (all Baylor College of Medicine). Marlene McNeese and Lauren Hopkins are with the Houston Health Department. Jennifer Deegan, Katherine L. Troisi, Eric Boerwinkle, Christina Mena, and Fu-Ching Wu are at the University of Texas Health Science Center at Houston, and Mark Johnson and Devon Gregory are at the University of Missouri School of Medicine.
This research was supported by NIH grants R01DA059394 and P30AI161943, SB 1780, 87th Congress, 2021 Reg. Seth. (Texas 2021), Baylor College of Medicine, Alkek Foundation Seed Fund, MD Anderson Foundation Chair.
sauce:
Baylor College of Medicine
Reference magazines:
Clark, J.R. Others. (2026). Multiyear sequencing of wastewater across the state reveals dual origins of HIV-1 signals. nature communications. DOI: 10.1038/s41467-026-74140-7. https://www.nature.com/articles/s41467-026-74140-7
