Scientists look to Twin Cities sewers to find COVID variants

The hunt for new strains locally is piggybacking on long-running COVID wastewater surveillance

Joe Carlson - Star Tribune, February 15th, 2021

Some of the best evidence for detecting early signs of new COVID strains in Minnesota is being flushed right down the toilet.

But scientists at the Metropolitan Council and the University of Minnesota's Genomics Center have started work to detect new strains of COVID in the wastewater flowing into the Twin Cities' primary sewage treatment plant in St. Paul.

The project is an outgrowth of ongoing epidemiological work with Minnesota's wastewater. Genetic traces of the virus that causes COVID are detectable in wastewater, which is why researchers are analyzing it for early warnings about COVID hot spots.

In addition to running its own program for the Twin Cities since last spring, the Met Council is providing wastewater samples to statewide and national wastewater surveillance projects.

In December, as the more contagious U.K. strain of the virus started making international headlines, Met Council officials asked the U's Genomics Center in Minneapolis to find out how to spot it and track its growth through sewage.

"We asked, 'Can we see that in wastewater? And what kind of samples could we give you that would give the best chance of seeing it?'" said Steve Balogh, a Met Council principal research scientist.

"They said, 'We need a lot of RNA in there because we are looking for very small amounts of these particular variants.'"

Researchers elsewhere have shown it's possible to find new COVID variants in wastewater with the same genetic-sequencing systems used in standard clinical labs.

A team in California analyzed viral gene fragments in raw sewage in the Bay Area and last month reported evidence of COVID variants that doctors had not yet found through clinical testing of individual patients.

"This approach ... has the potential to reveal patterns of virus distribution within communities," the California researchers wrote. "Perhaps most significantly, the results indicate that wastewater sequencing can detect recent introductions of SARS-CoV-2 [viruses] and other disease-causing viruses at a population scale."

Minnesota officials are trying to use essentially the same methods to detect the SARS-CoV-2 strains first discovered in the United Kingdom, South Africa and Brazil (known as the B.1.1.7, B.1.351 and P.1 strains, respectively).

Kenny Beckman, director of the U Genomics Center, said a long-term goal is to develop a way to rule out the presence of newer strains. That will be difficult at first because of the low prevalence of the variants right in Minnesota. Read the full Star Tribune article here.