Scientists look to Twin Cities sewers to find COVID variants

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.

The more immediate step is developing a test that detects the presence of variants in the teardrop-sized daily sample of genetic material from wastewater supplied by the Met Council. That testing, using synthetic virus molecules spiked into the real-world sample, will be run within two weeks, Beckman said.

"Once the frequency of people with the variant is higher (based on traditional testing of people), you'll be able to say for sure if your approach is or is not working," Beckman said in an e-mail.

The latest data, from Feb. 11, say Minnesota has seen 18 cases of the U.K. variant, two cases of the Brazil variant, and no cases of the South Africa variant, according to the Centers for Disease Control and Prevention.

Researchers continue to work to understand exactly how the new strains of COVID affect vaccine effectiveness. Officials in South Africa, for example, recently stopped using a vaccine from AstraZeneca and Oxford University after initial study data showed it wasn't effective at preventing mild to moderate disease.

Only two vaccines are authorized in the U.S. today. Made by Moderna and Pfizer/BioNTech, both are mRNA vaccines requiring two doses for at least 94% effectiveness against the mainstream version of the virus. Research is ongoing to measure their effectiveness against newer strains.

Local health officials are hoping to quickly vaccinate the public before one of the mutant strains becomes the dominant form of the virus here. The Health Department said more than 661,000 Minnesotans have gotten at least one vaccine shot, and about 228,000 have gotten both.

State officials are aiming to vaccinate 80% of Minnesotans 16 or older to achieve "herd immunity" from the virus. So far, the state is about 6% of the way to that goal.

As of Sunday, 6,376 Minnesotans have died from complications of COVID since March 21, including seven newly reported deaths. Fatalities included one person in their 40s, one in their 50s, and five between 65 and 94. Two lived in long-term care or assisted-living centers.

The total number of people with confirmed cases of COVID in the state rose by 776 on Sunday, bringing the overall tally to 473,567.

Though the virus can be detected in untreated wastewater, the CDC is not aware of anyone becoming sick with COVID because of exposure to it.

Standard sewage-treatment processes kill viruses, including SARS-2, before treated wastewater is discharged back into the environment.

But the virus' genetic signature can still be detected before the treatment process — and researchers have been looking.

The Met Council was one of a number of agencies nationwide that contributed samples for the first phase of the CDC's new National Wastewater Surveillance System, and it has asked to join the project's second phase.

Separately, the Met Council is contributing samples to a statewide wastewater monitoring program run through the University of Minnesota Medical School's Duluth campus.

That program just published non-peer-reviewed data from 19 Minnesota cities showing that trends in COVID genes in wastewater last summer preceded changes in clinically confirmed cases by 15 to 17 days, on average.

"We created something that I think should be able to be leveraged for a very long time," said Glenn Simmons Jr., assistant professor of biomedical sciences at the U Medical School in Duluth.

The Met Council, which oversees the metro area's land-use planning in addition to operating mass transit and sewer systems, is running a stand-alone monitoring program for communities in its Twin Cities sewershed.

The Met Council's Environment Committee got a peek last week at nine months of preliminary data showing that seven-day averages of concentrations of the virus at the treatment facility rose and fell in sync with the November-December peak of new cases.

The readings are from samples processed daily by Met Council scientist Balogh, who uses standard lab supplies and equipment to take RNA from a 24-hour composite sample of wastewater and force it to bind to silica at the bottom of a test tube.

The RNA-rich material is then analyzed at the Genomics Center, which quantifies how much is from the COVID virus. The outputs of that process are not public.

Taking the additional step of trying to figure out how much of that COVID viral material comes from new variants of the virus is a more recent step that involves additional lab machines. But it's not an exotic idea.

Simmons said it makes sense to look for new variant strains in wastewater. The Duluth-based surveillance project he's involved with tried doing it statewide last year, but the logistics were unworkable at the time. Unfortunately, he said, the Met Council's work only helps for one place.

"What about the rest of the state?" Simmons said. "For the long term it will probably be done for a lot of different viruses and bacteria."

Staff writer Eric Roper contributed to this report.