Detection of human immunodeficiency virus 1 (HIV-1) in wastewater offers a new approach to monitoring the virus in communities. Baylor College of Medicine researchers and colleagues at partner institutions report Nature communications that their method, called genetic hybrid capture sequencing, allows them to analyze viral genomes in detail and identify specific viral signals originating from community sewage. Analysis of sites with available clinical data showed that wastewater HIV signals correlated strongly with the number of people known to be living with HIV in that community, providing evidence that wastewater HIV signals can monitor HIV load.
HIV-1 is a retrovirus that has infected 90 million people and caused more than 40 million deaths. Despite advances in diagnosis, prevention and treatment, HIV-1 continues to spread – there were 1.3 million new diagnoses worldwide in 2023. HIV control is difficult because it is difficult to identify people who are undiagnosed or not receiving consistent care. these groups account for 80% of new transmissions.”
Dr. Thomas Giordano, co-corresponding author, chief of the division of infectious diseases and professor of medicine at Baylor
Current methods of HIV surveillance rely heavily on clinical diagnoses and viral load reporting, which is dependent on people accessing care. As a result, people who do not seek or delay seeking medical care remain largely invisible in public health systems.
“There is an urgent need for a complementary surveillance strategy capable of detecting undiagnosed or untreated infections,” said co-author Dr. Anthony Maresso, professor of molecular virology and microbiology at Baylor. “In the current study, we show that wastewater analysis can provide the ability to find geographic locations with untreated HIV. This would help identify communities where HIV prevention and treatment resources need to be or increased.”
Effluent analysis was first developed at Baylor for poliovirus surveillance in the mid-1920su century. During the COVID-19 pandemic, Baylor and colleagues pioneered the use of wastewater surveillance to monitor SARS-CoV-2 at the population and community level, successfully reflecting case rates, predicting hospitalizations, and enabling early detection of new viral variants.
Since May 2022, the Texas Wastewater and Environmental BiomMonitoring (TexWEB) team has implemented weekly to monthly viral sequencing of wastewater in major Texas cities. This program has now detected more than 400 human and animal viruses in wastewater, enabled monitoring and early detection of viral outbreaks, including avian influenza virus, mpox and measles, and created a sequence-based monitoring dashboard for public health reporting.
“In the current study, we used this approach to analyze wastewater collected from 40 sites in 15 cities in Texas from mid-2022 to late 2024. Instead of using tests that only look for short specific HIV genetic sequences, we used an advanced sequencing approach that allowed us to detect HIV genetic material and examine which sections of the HIV genome Dr Cl. molecular virology and microbiology at Baylor.
In more than 2,000 wastewater samples, HIV genetic material was repeatedly detected, albeit at low levels, showing that HIV can indeed be found in wastewater in a consistent and measurable manner. “It is important to note that it is highly unlikely that HIV signals in wastewater represent infectious virus,” Giordano said. “Disinfection protocols in laboratories and sewage facilities destroy any virus that ends up in sewage.”
Unexpected results
“When we looked closely at some of the HIV signals we found, the sequences appeared to come from non-circulating laboratory strains rather than viruses circulating in the community, which suggests infection,” Clark said. “But the interesting thing is that we don’t work with HIV in our lab. That meant that any ‘contamination’ had to have happened before we got the sewage samples.”
The team then looked at where these sequences came from and found them clustered near medical and research centers.
“We saw that as a sign,” Clark said. “Some HIV sequences belonging to HIV variants released in the 1980s have grown into research tools called lentiviral vectors. These are not live virus but parts of its genetic material that are used in many types of research. Our detailed analysis of sewage HIV sequences suggests that lentiviral contamination from this research activity developed. classifies the HIV sequences as circulating (community-derived) or uncirculated (carrier-derived.) Previous research has not looked for or filtered out these other signals.”
Once the researchers eliminated the confounding factor, they uncovered a significant correlation between HIV signals in wastewater and HIV diagnosis in communities.
“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 study – reaching out to focus groups, communities, individuals and advocates to make sure we’re taking people’s views into account.”
“This study lays a foundation for sequence-based monitoring of HIV wastewater and highlights lentivirus contamination as an overlooked confounder that must be addressed in future monitoring efforts for HIV-1 and other disease-causing microbes with synthetic counterparts,” said Maresso.
The following authors also contributed to this work: Dylan Chirman, Harihara Prakash, Austen Terwilliger, Matt Ross, Mike Tisza, Sara J. Javornik Cregeen, Jason T. Kimata, and Faith E. Fletcher, all at Baylor College of Medicine. Marlene McNeese and Loren Hopkins are with the Houston Department of Health. Jennifer Deegan, Catherine L. Troisi, Eric Boerwinkle, Kristina Mena, and Fuqing Wu are affiliated with the University of Texas Health Science Center at Houston, and Marc Johnson and Devon Gregory are with the University of Missouri School of Medicine.
This work was supported by NIH grants R01DA059394 and P30AI161943, from SB 1780, 87th Legislature, 2021 Reg. Sess. (Texas 2021), Baylor College of Medicine and the Alkek Foundation Seed Fund and MD Anderson Foundation Headquarters.
Source:
Journal Reference:
