In April of 2020, when COVID-19 seemed to be everywhere and nowhere at the same time, Brijen Miyani, a doctoral student at Michigan State University, drove to Detroit to hunt for the virus in the sewers. 

Weeks earlier, when his adviser asked whether he wanted to drop his research on herpes and shift to more work on COVID, he did not hesitate. “I was like, ‘Hell yeah, let’s do this,’” Miyani recalled.

Within months of the first COVID cases reported in Detroit, Miyani and other scientists were regularly identifying the virus in wastewater across the state. Data from their network was used to contain COVID outbreaks on college campuses and provided warnings of new surges weeks before case numbers began to spike.

In three years, wastewater monitoring went from a niche research topic to a widely used public health tool.

Michigan, and especially the Detroit area, have collected more data from wastewater than most places in the country. Only New York and Missouri have contributed more samples than Michigan to the CDC’s national wastewater network.

Scientists are already using this same technology to screen for polio — yes, it’s back — and potentially dangerous new viruses. 

“This is a scientific leap that was a silver lining of the pandemic,” said Natasha Bagdasarian, Michigan’s chief medical executive.

But if Michigan’s wastewater network is an asset the state gained during the pandemic thanks to scientific innovation and emergency federal funds, we are at risk of losing it. Federal funds supporting sewer monitoring are expected to run out within a year, and leaders of the network say they don’t know how the money will be replaced.

In the early days of the pandemic, David Szlag, an environmental science professor at Oakland University, led an effort to test wastewater from dormitories. When COVID appeared in dorm sewage, they tested everyone in the building and quarantined infected students. Szlag said the effort reduced the number of infections on campus in the early days of the pandemic.

Testing wastewater requires “a lot of money, but if it can prevent the hospitals from being overwhelmed, that’s a huge benefit,” he said.

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How data from the sewers can keep protecting us 

Only some people go to the emergency room, a key source of public health information. Only some people will go to the doctor for tests and medical care.

But if a virus is present in poop, epidemiologists working on sewer data can be confident they’re getting information from everyone.

One of the clearest signs that COVID spread is currently at its lowest level since 2020 comes from wastewater.

This data can be unusually timely — the world got early notice that the COVID omicron variant was extremely transmissible because of wastewater monitoring in South Africa.

“The ‘Big Brother is watching you poop’ vibe is really something we’re trying to avoid right now.”

Marisa Eisenberg, a professor of epidemiology at the University of Michigan

It’s also unusually comprehensive, especially because there are plenty of people who won’t or can’t get tested for even the most serious of diseases, said Cristina Alonso, a public health professional who led a wastewater monitoring project near Boston.

“When certain people are afraid of accessing the system or cannot access the system, you’re always going to get skewed results,” she said. “Wastewater monitoring depersonalizes testing and results. It’s about monitoring the well-being of the public instead of measuring certain fluids in an individual body.”

Proponents of Michigan’s new wastewater monitoring system say it is already primed to serve as a first line of defense in the next pandemic.

“Detroit is very well positioned to be a sentinel site,” said Irene Xagoraraki, a professor of environmental engineering at Michigan State University and director of the lab that employs Miyani.

Miyani’s trip to Detroit in 2020 helped ensure that COVID was detected in the city’s wastewater system before almost anywhere else in the country. Xagoraraki has worked with other viruses in Detroit wastewater since 2017, and her relationships with officials at the Detroit area wastewater plant helped clear administrative hurdles when COVID reached Michigan.

Challenges coming down the pipes

As useful as wastewater monitoring can be, the scientists on the forefront of the method still have some challenges ahead.

Something as common as a rainstorm can throw off the results by flooding sewers with water and diluting the virus. What’s more, wastewater monitoring relies on industrial sewer systems, which means it could prove less useful in rural areas or in countries that don’t have the money to pay for modern water infrastructure.

Some viruses don’t show up in poop at all, making monitoring wastewater useless. There are also disease-specific challenges; tests for polio, for instance, can be thrown off by international visitors who have received the live polio vaccine, something that hasn’t been administered in the U.S. in decades.

COVID monitoring studies are generally conducted in large sewer systems, where separating out an individual’s data would be impossible, but ethical questions remain. For instance, when is a sewer shed small enough that scientists working on it should get consent from affected people?

Scientists are eager to stick to clear ethical guidelines around wastewater data because the process could easily be halted by political blowback.

“The ‘Big Brother is watching you poop’ vibe is really something we’re trying to avoid right now,” said Marisa Eisenberg, a professor of epidemiology at the University of Michigan, during a wastewater monitoring conference in May.

How exactly does this work?

Scientists start by collecting sewage, typically with a bucket or a pump. The material is taken back to a lab, where it is put through a complex, multi-step process that requires expensive machinery and lots of scientific expertise.

Metro Detroit samples collected at the Great Lakes Water Authority wastewater plant are processed by a team of seven people at MSU. Led by Xagoraraki, the group is a mix of doctoral students, master’s students and recently minted Ph.D.s.

“We are now combating (COVID), but we should be prepared for the next step,” said Yabing Li,  a postdoctoral researcher in the lab. “We have to think beyond this pandemic.”

Footage taken in Xagoraraki’s lab in June gives a rough sense of how scientists move from raw sewage to a tiny amount of genetic material that can be scanned for COVID or other diseases.

An ‘inflection point’ as federal funds expire

All of the spinning, freezing and data-crunching in the lab doesn’t come cheap, and pandemic funds that helped build the system are running out.

In June of 2021, Michigan sent $49 million in federal funds to wastewater monitoring sites. Those funds were expected to last through July 31. Some labs are already reducing their testing efforts, while others, such as Xagoraraki’s, have enough funding from other sources to keep testing for another year.

The latest state budget did not include new funding for wastewater monitoring.

A spokeswoman for Gov. Gretchen Whitmer declined to answer questions about funding for wastewater monitoring.

”We’re at an inflection point” for Michigan’s wastewater monitoring network, said Susan Peters, an epidemiologist for the Michigan Department of Health and Human Services who helped establish the statewide network. “We do want to try and maintain as much of that established network as we can.”

Would a slimmer, cheaper system be enough to protect public health? Xagoraraki thinks so. With less funding to go around, she envisions running weekly tests for known problems, like COVID or polio, along with monthly, more complex tests to identify dangerous new viruses.

Still, Alonso warned that if the system is allowed to shrink too much, we could lose valuable time rebooting it in the next public health emergency.

“We have the technology now,” she said, “but do local and federal governments acknowledge that there are going to be more pandemics, and that when they come, we need to activate these systems the second week of the pandemic and not the second year?”

In the face of that funding uncertainty, labs are already making the case for their continued relevance. Polio set off public health alarms in New York this spring after the virus was found in wastewater. In response, public health officials chose Michigan, along with Colorado, to pilot its own polio testing in the sewers, a process that recently began in Oakland County.

If polio arrives in Michigan, the news — and our best chance at a timely response — will likely come from the sewers. Public health officials hope funding will follow.

Koby (he/him) believes that love drives people to fight for their communities, and that curiosity is food for love. He enjoys the many moods of the Detroit River.