Scientists are wading through murky water to track Covid from one community to the next. The source? Wastewater.

It’s science that starts with a flush. What travels down the drain and through the pipes to the sewer system is a valuable natural resource.

Sarah Owens is a molecular biologist at Argonne Laboratories.

“These wastewater samples are a collection of viruses and bacteria,” she said. “You can imagine everything that is in the waste.”

Including covid.

“Right now we’re finding omicron,” Owens said. “For a period of time we were finding percentages of delta and omicron and a few other variants that are not listed as variants of concern.”

Unlike a nasal swab that provides a small but concentrated sample, wastewater is vast in volume. Researchers are basically fishing for the virus.

“It’s a very complex mixture that we’re looking through and that is what makes it challenging,” Owens said.

Owens said the data is worth the deep dive. It will provide a clearer picture of how much virus is circulating and where. The samples are collected from multiple treatment plants across the city of Chicago then sent to a lab, where any viral RNA, or genetic material, is extracted.

“They concentrate the wastewater for viruses, extract the RNA and then send the RNA here (to Argonne),” Owens said.

Like the technique used in PCR testing, Argonne scientists amplify the RNA in the samples and then sequence them to match for known SARS-CoV-2 genomes. Is it delta, omicron or something new? The hope is to detect new variants before they make a splash in the community.

“To potentially catch a mutation that is novel, catalog it and hopefully figure out that, ‘Oh we’ve got the makings of a new variant of concern’ ahead of time,” Owens said.

Public health officials are using the information to better understand waves of infections, even those that go undocumented.

“But then a lot of people are asymptomatic as well so people may not pursue testing,” Owens said. “And so we’re catching the virus associated with people who may be asymptomatic as well.”

Ultimately, Argonne scientists hope to improve the sequencing technique and use it to detect other infectious disease outbreaks in the future.

“That’s our hope — that we could get a good enough handle on these techniques to sense something that is novel,” Owens said.

Right now they’re looking for the latest covid variant, omicron’s sister. They’ll likely spot it soon once there’s an abundance in the water.