Argonne Scientists Track Community Spread Of COVID-19 In Wastewater

Wastewater provides a clue to virus transmission.

In the ongoing COVID-19 pandemic, finding ways to improve testing has been key to addressing the spread of disease. While much effort has focused on testing individual people, scientists have begun to explore large-scale sampling of wastewater to understand patterns of viral transmission over larger areas.

Researchers from the U.S. Department of Energy’s (DOE) Argonne National Laboratory are participating in a pilot study to sample wastewater at some of the Chicago area’s wastewater treatment plants.

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“The idea is that some people might contract the virus and be asymptomatic, but they’d still be shedding the virus,” said Argonne ecologist Mark Grippo, who is leading Argonne’s effort in wastewater-based epidemiology. “Wastewater monitoring would give us a window into how the virus spreads throughout a community in the early stages of an outbreak — you can follow not only the initial outbreak, but also the overall trends over time. Plus, once doctors start administering the vaccine, you can see how viral loads change in wastewater.”

This project, known as the Chicago Prototype Coronavirus Assessment Network Node, or PCANN, looks to create a Chicago-based wastewater surveillance system for SARS-CoV-2, the virus that causes COVID-19. The system would provide a noninvasive and cost-effective way to examine community spread of the virus. By giving advance warning of emerging viral hotspots up to a week earlier than traditional tests, wastewater surveillance could give public health workers valuable time to mobilize and protect communities from uncontrolled outbreaks.

This idea is generally called wastewater-based epidemiology and has been used to trace polio outbreaks in communities, including in Israel in 2013.

One potential advantage of doing wastewater-based epidemiology is that it can help cities focus where they may want to deploy further testing efforts, Grippo said. To get a neighborhood-by-neighborhood view of the COVID-19 epidemic, they hope to sample multiple locations within the Chicago sewer system to get trends in specific neighborhoods that can inform city public health officials about testing. This neighborhood-scale sampling could also help determine where more resources might be needed for vaccination, if the virus remains detectable after broader vaccination has occurred.

“This is by no means meant to be a substitute for testing, but it’s meant to further reinforce the data collection on how the virus is being transmitted in certain communities and help out testing efforts,” Grippo said. However, he indicated that it may not be fully useful in justifying restrictions or other interventions given how people travel between different regions.

At Argonne, researchers will be performing genomic sequencing of the virus from wastewater to look at variation in strains present in different communities, said Argonne sequencing laboratory manager Sarah Owens.

Live virus is not studied at Argonne. Studies have found evidence for tracking introduction events of the virus based on the mutations present in the genome and have used this evidence to understand transmission patterns.

Sequencing can also detect new mutations as they arise. While this project is focused on targeting the SARS-CoV-2 genome specifically, future projects could focus on sequencing the wastewater more broadly to monitor for novel pathogens. “This is a genetic-based test, so you can test for pretty much any kind of pathogen that may come along in the future,” Grippo said. Genomic sequencing, paired with other pathogen detection methods, is also complemented by work in data analytics and integration as part of PCANN.

One additional use of wastewater-based epidemiology is to look for opioids in wastewater as an indicator of opioid addiction. “This technique is very versatile,” Grippo said. “It’s not going to stop COVID-19, but it is going to give us another tool in our toolkit to grapple with it.”

Additional wastewater-based epidemiology projects are underway in Arizona, Ohio, Utah and Virginia.

This work is funded by the Walder Foundation and is being led by the University of Illinois-directed Discovery Partners Institute and includes researchers from Argonne, the University of Illinois at Chicago, Northwestern University and the Chicago Department of Public Health.

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