Wastewater could be used to track more viruses than COVID-19

Researchers have developed methods to track respiratory viruses in wastewater.


Respiratory disease is a major cause of morbidity and mortality; however, respiratory virus surveillance is passive and biased. The study aimed to use wastewater-based epidemiology to learn more about the occurrence of viral respiratory infections in communities.

SARS-CoV-2, seasonal coronavirus, parainfluenza, metapneumovirus, influenza, respiratory syncytial virus, rhinovirus, adenoviruses, bocaviruses, and non-rhinovirus enteroviruses are the leading causes of illness and mortality in children under the age of five. They result in 400,000 child hospitalizations and a $1 billion annual cost in the United States.

In cooperation with Emory University and Verily Life Sciences, researchers at Stanford University have gathered quick and precise readings of a wide range of respiratory viruses in their local Santa Clara sewer system. 

Currently, wastewater is the only source of accurate information about COVID-19 rates in communities. PCR testing is no longer widely available, and most people swab themselves at home, where the results are kept from public health agencies.

Alexandria Boehm, professor of civil and environmental engineering at Stanford Engineering and the Stanford Doerr School of Sustainability, said, “We are gathering evidence that wastewater can be useful for many infectious disease targets beyond COVID-19 and that it’s a really valuable resource for understanding community health. We found that concentrations of RNA, the building block of virus genomes, from influenza A and B, RSV, rhinovirus, parainfluenza, metapneumovirus, and seasonal coronaviruses in wastewater follow the trends also observed in the clinical data from sentinel laboratories. The possibilities seem very endless at this point.”

Boehm envisions a future in which communities could continuously test wastewater for viruses of all kinds. Calculating our risk of flu that day would be as simple as checking the local weather forecast for rain. 

Every time they use a drain in the house or at the office, sputum, mucus, feces, and urine enter the wastewater, carrying viruses and bacteria with them. When researchers collect a sample of wastewater, they collect a massive biological sample from the entire population of toilet-flushing, toothpaste-spitting, and shower-going people. That sample includes contributions from everyone, including those who are only mildly ill or asymptomatic.

Suppose the local treatment plant processes wastewater from a million people. In that case, a single sample provides scientists with information on all of them. Researchers can see which infectious diseases are circulating in the community and how the infections change over time.

Boehm and her colleagues found that the virus concentrations they measured in local wastewater matched the clinical data on the relative infection rates of the viruses collected by the state of California. 

Boehm and her colleagues decided to see if they could use wastewater to understand the circulation of other respiratory viruses because wastewater is a good resource for studying COVID-19 cases. Boehm said, “That motivated us to do this study and develop assays for all these different respiratory viruses and see if they tracked the data that was available for the state of California on circulation of these viruses in clinical samples.” 

Boehm said, “This suggests that wastewater can be used to understand the circulation of these respiratory viruses at a more local scale than at the state level with the clinical information. In addition, results on virus circulation can be real-time.”

The research team works on a regular wastewater virus surveillance program with Emory University and Verily Life Sciences. With the sampling and testing infrastructure already in place, setting up tests for new viruses in the program is simple. Researchers take the same samples and run different assays on them to learn more about respiratory viruses like influenza.

Data from wastewater can be available within 24 hours of collecting a sample, allowing public health departments to promote timely vaccinations, design education campaigns, and send warnings to vulnerable people about possible precautions. Real-time data could also assist doctors in making testing and treatment decisions. If a virus outbreak is expected, hospital directors could use more accurate virus information to help stock therapeutics in the hospital. 

Boehm said, “We envision something similar to a weather report where everybody could make their own decisions based on their levels of risk that they’re willing to take and also their health. Somebody who is undergoing chemotherapy could make their own decisions about masking or going to the grocery store, based on their understanding of what illnesses are circulating in the community.”

Boehm hopes this study will motivate more researchers to look for these infectious disease targets in wastewater across the country. Boehm said, “I think it’s really important to show that this works in more than one location, which I totally expect it will.” 

Once Boehm and her colleagues have confidence that a virus they measure can be useful and meaningful, they can incorporate it into their larger WastewaterSCAN project data.wastewaterscan.org. Marlene Wolfe, BA ’11, a co-author on the study and assistant professor of environmental health at Emory University, said, “One of the most exciting things about wastewater monitoring is how quickly we can bring our innovations into practice. Because we are already working with utilities and public health departments around the country, we can introduce new tests very quickly once we have the evidence that the wastewater data reflects community levels of disease.”

The research team is already investigating the feasibility of monitoring more infectious disease targets in wastewater, such as norovirus, adenoviruses, and enteroviruses. They are also working with public health officials to identify additional viruses, fungi, and bacteria to study. Boehm says. “We just need to keep researching and exploring how far we can take wastewater surveillance for infectious disease targets.”

Boehm is also a professor of the Oceans Department of the Stanford Doerr School of Sustainability, a senior fellow in the Stanford Woods Institute for the Environment, a member of Bio-X, a member of the Maternal & Child Health Research Institute, and a faculty fellow in the Center for Innovation in Global Health.

The research team is investigating the feasibility of monitoring more infectious disease targets in wastewater, such as norovirus, adenoviruses, and enteroviruses. Once they are confident that a virus they measure can be useful and meaningful, they can incorporate it into their larger Wastewater SCAN project data. The researchers are also working closely with public health officials to identify more viruses, fungi, and bacteria.

This study was funded by the CDC Foundation. 

Journal Reference:

  1. Alexandria B Boehm, Anna Buchman, etal. Wastewater concentrations of human influenza, metapneumovirus, parainfluenza, respiratory syncytial virus, rhinovirus, and seasonal coronavirus nucleic acids during the COVID-19 pandemic: a surveillance study. The Lancet Microbe. DOI: 10.1016/S2666-5247(22)00386-X


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