How wastewater works to detect COVID, other viruses in Minnesota

Wastewater analysis is a prime method for tracking COVID-19, revealing last week that the Twin Cities is in a pandemic "holding pattern" and that viral levels have held constant for a month.

But it wasn't always so.

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

"Having people take poop seriously as a COVID detector? It took a little while," said Bonnie Kollodge, a spokeswoman for the Metropolitan Council, which reports viral levels found at the Metropolitan Wastewater Treatment Plant in St. Paul.

Now thousands of people flock each Friday to the Metro plant's results. The University of Minnesota similarly reports viral load sampling from 40 plants accounting for 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 wastewater plants into a national surveillance group capable of monitoring COVID-19, and perhaps other pathogens such as monkeypox and influenza too.

"This really is the future," said Steve Balogh, the research scientist at the St. Paul plant who developed a reliable method of extracting viral material from sewage.

Friday's Metro plant results offer optimism: The viral load in Twin Cities wastewater declined 1%, matching a gradual decline in Minnesota COVID-19 cases. On the other hand, the fast-spreading BA.5 subvariant made up 64% of that viral material — the same variant spawning COVID-19 surges this summer in many southern and western states.

"We're in a period of transition," Balogh said. "We're seeing the BA.2.12.1 variant disappear and we're seeing the BA.5 variant take over. We're not sure where BA.5 is going to go at the moment."

The 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 flushed down the pipes before it reaches 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 wastewater.

That made sense to Balogh. Treatment plants already are tasked with removing harmful particles from wastewater that could taint downstream water quality. Phosphorous and nitrogen are particular concerns that are removed before the water runs through the St. Paul plant and into the Mississippi River.

So analyzing wastewater's contents to address the upstream threat of COVID-19 seemed like a natural extension. The first trick was figuring out how to extract genetic remnants of the virus suitable for analysis from all that mess.

"That really is the key to doing this kind of work," Balogh said. "How do you get enough of the viral RNA out of the wastewater into cleaner water that you can analyze?"

Metro plant researchers tried multiple methods from research literature but were fortunate when a "fooling around" Balogh used a commercial chemical product that surprisingly helped to capture much more genetic material.

"Our numbers just popped," he said.

Purified samples the size of teardrops were sent to the University of Minnesota Genomics 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 back at the Metro plant to determine the relative amount of viral material in wastewater.

By winter 2020, the Metro plant was calculating viral loads in wastewater that were remarkably rising and falling in lockstep with COVID-19 case numbers. More significantly, the spikes in wastewater were coming before peaks in reported cases, suggesting the data could be an early-warning system for emerging pandemic waves.

By spring 2021, the plant had expanded to check wastewater not just for evidence of the virus but for the underlying variants.

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

Opportunity finally emerged in early 2022 when the fast-spreading omicron variant was causing both symptomatic and asymptomatic infections far beyond the lens of COVID-19 testing. The St. Paul plant in response started posting its results online in mid-January.

The explosion of at-home rapid COVID-19 tests also had reduced the state's surveillance because those test results aren't reported publicly. By February, Minnesota had found 1.4 million infections through testing, but federal estimates based on antibody levels in blood specimens suggested the actual count was 3.3 million.

"We know that we are not catching the same proportion of cases that we did earlier in the pandemic," said Stephanie Meyer, supervisor of the Minnesota Department of Health's COVID epidemiology unit. "This has us closely watching for community impacts, especially on our hospitals and health care systems. Though those figures are not as low as we would like, they are holding steady for now."

COVID-19 hospitalizations in Minnesota have hovered around 400 for the past two months — reaching 407 Wednesday.

The delayed use of wastewater data was probably due to the cautiousness of a group of Metro plant scientists who usually work far from public attention, said Kenny Beckman, director of the U genomic center. Uncertainty among public health leaders over the use of wastewater surveillance as an alternative to COVID-19 testing also contributed.

The science and technology may continue to evolve, but wastewater monitoring is likely here to stay because it is has proven accurate and efficient, he said.

"The beauty of this is ... it's cheap compared to the infrastructure of trying to gather and aggregate all of the testing data," Beckman said. "I think, for that reason, its going to become more common."