Sewage test for COVID, other viruses go mainstream

Sewage testing is a go-to method for tracking COVID-19, revealing last week that the Twin Cities are in a pandemic “holding pattern” and viral levels have remained constant for a month.

But it has not always been so.

COVID-19 wastewater monitoring took more than a year to gain credibility in Minnesota — and only after scientists overcame numerous technical challenges, benefited from trial and error, and overcame the problem of image of an industry at the commercial end of the plumbing system.

“Getting people to take poo seriously as a COVID detector? It took a little while,” said Bonnie Kollodge, spokesperson for the Metropolitan Council, which reports viral levels found at the Metropolitan St. Paul sewage treatment plant.

Now, thousands of people flock to the Metro factory results every Friday. The University of Minnesota similarly reports viral load sampling from 40 plants representing 67% of Minnesota residents, while St. Cloud reports its own results.

The belated success may just be the beginning – with the Centers for Disease Control and Prevention linking sewage treatment plants to a national watchdog group capable of monitoring COVID-19, and possibly also other pathogens such as monkeypox and influenza.

“It’s really the future,” said Steve Balogh, a research scientist at the St. Paul plant, who has developed a reliable method of extracting viral material from wastewater.

Friday’s Metro plant results offer optimism: Viral loads in Twin Cities wastewater fell 1%, matching a gradual decline in COVID-19 cases in Minnesota. On the other hand, the fast-spreading BA.5 subvariant accounted for 64% of that viral material — the same variant that spawned outbreaks of COVID-19 this summer in many southern and western states.

“We are in a period of transition,” Balogh said. “We see the BA.2.12.1 variant disappearing and we see the BA.5 variant taking over. We don’t know where BA.5 will go at this time.”

Easy-to-read wastewater numbers on the treatment plant’s dashboard belie the complex process of obtaining them. Sewage flows from the homes of 1.9 million people and buildings in the Twin Cities area to the St. Paul plant, passing through screens that remove large objects thrown down the pipes before reach a sampler that collects wastewater for analysis.

Studies early in the pandemic in 2020 raised the potential for monitoring COVID-19 by looking for genetic remnants of the coronavirus in sewage.

It made sense to Balogh. Treatment plants are already responsible for removing harmful particles from wastewater that could affect water quality downstream. Phosphorus and nitrogen are special problems that are removed before the water passes through the St. Paul plant and empties into the Mississippi River.

So, analyzing the content of wastewater to address the upstream threat of COVID-19 seemed like a natural extension. The first trick was figuring out how to extract the genetic remnants of the virus suitable for analysis from this whole mess.

“That’s really the key to doing this kind of work,” Balogh said. “How do you get enough viral RNA from wastewater into cleaner water that you can analyze?”

The Metro plant researchers tried several methods from the scientific literature, but lucked out when a “fun” Balogh used a commercial chemical that surprisingly helped capture a lot more genetic material.

“Our numbers just jumped,” he said.

Purified tear-sized samples were sent to the University of Minnesota Genome Center, which separated them into thousands of tiny droplets and then counted how many contained viral material. The total was then used in a calculation at the Metro plant to determine the relative amount of viral material in the wastewater.

In the winter of 2020, the Metro plant was calculating viral loads in wastewater that rose and fell remarkably in step with the number of COVID-19 cases. More importantly, the sewage peaks came before the reported case peaks, suggesting the data could be an early warning system for emerging pandemic waves.

By spring 2021, the plant had expanded to check wastewater not only for the presence of the virus, but also for underlying variants.

Plant scientists presented the data to Minnesota Department of Health officials that summer, but it was not widely used at first. COVID-19 testing at the time provided a stable measure of coronavirus levels, and the state used genomic sequencing of infectious samples to monitor variants and epidemiological investigations to track outbreaks like the one involving youth sports. in the southwest metro.

The opportunity finally appeared in early 2022 when the rapidly spreading omicron variant was causing symptomatic and asymptomatic infections far beyond the scope of COVID-19 testing. The St. Paul plant in response began posting its results online in mid-January.

The explosion of rapid home COVID-19 tests has also reduced state oversight because those test results are not made public. By February, Minnesota had found 1.4 million infections through testing, but federal estimates based on antibody levels in blood samples suggested the true number was 3.3 million.

“We know we’re not catching the same proportion of cases as we were at the start of the pandemic,” said Stephanie Meyer, supervisor of the Minnesota Department of Health’s COVID Epidemiology Unit. “This forces us to closely monitor the impacts on the community, especially on our hospitals and healthcare systems. While these numbers are not as low as we would like, they are holding up for now.”

Hospitalizations for COVID-19 in Minnesota have hovered around 400 for the past two months — hitting 407 on Wednesday.

The late use of wastewater data was likely due to the caution of a group of plant scientists at Metro who typically work away from public scrutiny, said Kenny Beckman, director of the U.L. Genome Center. Uncertainty among public health officials about using wastewater monitoring as an alternative to COVID-19 testing has also contributed.

Science and technology may continue to evolve, but wastewater monitoring is likely to stay because it has proven to be accurate and effective, he said.

“The beauty of it is…it’s cheap compared to the infrastructure of trying to gather and aggregate all the test data,” Beckman said. “I think, for that reason, it’s going to become more common.”

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