As the Omicron COVID variant spreads like wildfire throughout the country, scientists are looking for ways to trace the various strains as they move throughout different communities. In addition to direct testing of individuals, one resource that scientists have for tracking large-scale COVID patterns is the wastewater system, which includes whatever goes down household drains and what is collected in sewers.
New funding will allow researchers from the U.S. Department of Energy’s (DOE) Argonne National Laboratory to build on a prototype sampling network set up in 2021 to work with the Chicago Department of Public Health to detect, and hopefully trace, how different strains of the COVID virus travel through different communities.
At the beginning of the pandemic, funding from the Walder Foundation allowed Argonne scientists to set up a network for sampling at a number of different Illinois wastewater treatment facilities. Developed with partners from the University of Illinois’s Discovery Partners Institute, the University of Illinois at Chicago and Northwestern University, this network allows researchers to detect the specific genetic information, or genome, of different strains of the SARS-CoV-2 virus responsible for causing COVID, which turns up in wastewater as individuals with the virus shed it in their waste.
“Initially, we were interested in just seeing if we could detect COVID in the wastewater,” said Argonne molecular biologist Sarah Owens. “Once we knew we could do it, it became important to look for trends. We needed to know what it meant for our public health efforts if we saw a COVID spike in a community’s wastewater — for instance, if government agencies would need to implement more controls or target a stronger vaccine or testing campaign.”
The trend analyses generated by the wastewater testing are shared with the Illinois Department of Public Health and the Chicago Department of Public Health to help inform their decisions. “Wastewater sequencing can provide a clue as to where we need more clinical testing,” said Argonne molecular biologist Rosemarie Wilton, who also helps coordinate the project.
Because the different COVID strains have such similar genomes, and because there are millions of people contributing to the wastewater stream at some of the larger wastewater treatment plants, the genomic sequencing has to be precise, Owens explained. “We take the original SARS-CoV-2 genome that was originally detected in China and compare that to the genomes that are present in our samples, because we’re looking for the differences that are characteristic of each strain,” she said.
The ability to have a detailed genomic analysis of all the COVID variants present in the wastewater means that this form of surveillance could provide researchers with the capacity to identify potential new strains, as they emerge. “If you have an asymptomatic patient, they may not pursue testing,” Owens said. “But wastewater is a reflection of the entire community, and everyone is contributing to what we are sampling. This could be the first indication we have of a dangerous new variant.”
Wastewater testing can also show how variants move from one community to another and how they respond to local efforts to combat the virus.
Although the testing and sequencing network has been created to detect COVID, Owens said that it could be used to detect a wide range of infectious diseases in the future. “We’re trying to get a handle on the pandemic, but this is a resource that could be useful for a number of different public health scenarios,” she said.
According to Owens, work on wastewater sequencing has connected researchers from different disciplines who otherwise may never have worked together. “Researchers who were previously interested in basic science are now working with public health officials to have a real impact in their communities,” she said.
