Minnesota could search sewage for all viruses, not just COVID-19

University of Minnesota researchers are studying a way to monitor wastewater for all infectious pathogens at once, not just COVID-19 and its viral variants one by one.

Wastewater surveillance emerged a year ago to provide early warnings of shifts in the COVID-19 pandemic, but a broader approach could clue Minnesotans into other viruses before they become established threats.

"Can we detect the unexpected in time to be able to sound the alarm? That's the goal," asked Dr. Timothy Schacker, the U Medical School's vice dean for research.

The U research dovetails with Thursday's report from the National Academies of Sciences that urges more U.S. investment in and broader use of wastewater surveillance — while being sensitive to privacy and ethical concerns.

Sewage sampling started early in the pandemic, when people accepted emergency measures to combat the threat of COVID-19. Tolerance for such changes over the long-term is unclear.

Although the public health value of broad wastewater surveillance outweighs privacy concerns, scientists are going to need to promote the benefits outside of the urgency of a pandemic, said Guy Palmer, an infectious disease expert at Washington State University and chair of the national committee that wrote the report.

"Looking forward, the success of a national wastewater surveillance program for infectious diseases relies on building public trust in the system, especially when 'surveillance' can be such a charged term in some communities," he wrote in a statement.

COVID-19 surveillance in Minnesota includes more than 40 plants statewide that send wastewater samples to the medical school for analysis, and urban plants in St. Paul and St. Cloud that send samples to the U's genomics center.

All of them publicize COVID-19 data in aggregate. Privacy concerns would be more of an issue if viral loads were publicized at community or neighborhood levels, Schacker said, noting that one participating plant only serves 500 to 600 people. Highly localized results could marginalize communities in which viruses emerge.

The U's scientific challenge is switching from targeted PCR testing for specific pathogens to a whole genome sequencing approach that compares genetic material from sewage against a federal database of pathogens.

One test sample produced 7,500 lines of genetic data — each representing a virus, fungus or bacteria, Schacker said. Many infectious agents harm plants and animals but not humans, so researchers would need to sort out the relevant data and determine the quantities of genetic material that matter.

A tiny amount of virus in wastewater could, for example, stem from someone who used the bathroom on a layover at the Minneapolis-St. Paul Airport — meaning there is little local threat.

The benefits of broadening samples beyond COVID-19 showed in New York, which used expanded wastewater analysis after identifying a rare case of polio and found that the underlying virus had been spreading for months.

Sewage sampling for COVID-19 proved its worth in Minnesota a year ago, when it identified a surge in the omicron variant of the coronavirus several days before Minnesota reported more illnesses. Results haven't always been easy to interpret, though.

A weekly update by the Metropolitan Wastewater Treatment Plant in St. Paul on Friday showed a 37% increase in coronavirus material over the past week, but it was influenced by one sample collected Jan. 12. Without that outlier, the increase was only 5% — matching the rolling trends in COVID-19 activity in Minnesota since the summer.

An XBB coronavirus variant made up 46% of the viral material found in metro wastewater, up from 27% the prior week. Its presence has come amid stagnant COVID-19 levels, but its growth could produce infections over the next several weeks, said Steve Balogh, a research scientist at the Metro plant.

The Minnesota Department of Health is launching its own wastewater surveillance program later this year, either working with existing plants or analyzing samples from new plants. The effort will focus on COVID-19 at first but will expand, said Sara Vetter, assistant director of the state's public health lab.

The U research will help determine whether the state lab adopts a universal approach or targets specific viruses, such as influenza. The relative cost of the different methods could be a factor, as well as other unresolved scientific questions. It appears, for example, that some viruses are easier to detect from liquid samples and others from sludge samples in sewage. But extraction of samples from sludge is more complicated and costly.

"We're all in the process of learning," Vetter said.