The Key to Tracking Coronavirus Could Be Your Poo

Sewage surveillance could help scientists predict new outbreaks

WeWe won’t have to shelter from the new coronavirus forever. In fact, we may be able to briefly return to public life this summer, according to The Atlantic. But several predictors of Covid-19 outbreaks suggest the virus could be seasonal, returning with fury in the fall. It is likely that several periods of social distancing will be necessary for containing the virus until a vaccine for SARS-CoV-2, the virus that causes Covid-19, is widely available, which could take a year or more.

How will folks know when it’s safe to come out and when to go back indoors? There may be clues in our sewage.

Dozens of scientists across the globe are sampling poo to find tiny shreds of the coronavirus that can serve as an early warning of outbreaks. In theory, if viral levels reach a certain threshold, health experts can tell more people to stay home. When viral loads abate, they can tell people it’s okay to fraternize.

Last week, Dutch scientists announced a first-of-its-kind method for detecting SARS-CoV-2 in wastewater. The team, from KWR Water Research Institute, took samples of wastewater from six Dutch cities as well as Amsterdam’s airport in February 2020, weeks before the Netherlands announced its first case of Covid-19. They collected new samples and repeated the experiment in the first and third weeks of March.

After running the sewage samples through a centrifuge, the scientists looked for four genetic signatures of SARS-CoV-2. Three were from the nucleocapsid (N) gene, which builds proteins that make up the core of the virus. The remaining gene encodes the envelope (E) protein, which the virus uses to reproduce.

In the February samples, the researchers found no sign of coronavirus. But by early March, some of the results came back positive. All but one of the samples taken in the third week of March samples came back positive, with bits of the N and E genes.

In the city of Amersfoort, the team was able to detect SARS-CoV-2 before any cases had been announced locally. These results were published before peer review on MedRxiv.

Detecting the virus through sewage is only the first step toward using poo analysis as an early outbreak warning system, according to Krista Wigginton, an associate professor at the University of Michigan’s civil and environmental engineering department. She is leading a joint project between UM and Stanford University using a $200,000 grant from the National Science Foundation to study how the coronavirus worms through our pipes.

“You’re looking for a needle in the haystack,” Wigginton tells OneZero, adding that while the Dutch team has found the virus, the next stage is correlating that data in a way that corresponds with the population level.

“It’s very preliminary, but it’s a great proof of concept. We can go out and detect it, but now we need to do a lot of work to be like, ‘Okay, what level was it at and how many people in the community does that correspond to?’” Wigginton explains. “I don’t think we’re able to say yet what we can do with this tool.”

“If you could sequence the coronaviruses in wastewater, you have a much better idea of how the virus is mutating and possibly where the virus came from in your community.”

In other words, counting the pieces of a virus is one thing — but how do you know how many people might be infected when those pieces are mushed together within a smelly mess? It will take analyzing tons of wastewater to find out, which usually means waiting for it to pass through the point of the sewage treatment process in which solids separate from the liquid, which Wigginton says could still be months away.

“It’ll take some time and a lot of research to know how the levels in wastewater compare to the other indicators in a community,” Wigginton says. “But we think it’s quite possible that this could be at least as sensitive as these other indicators like using thermometer data and Google searches to figure out when communities are starting to have an uptick. This just seems like another tool.”

Wigginton has been studying ways to detect coronavirus in wastewater for several years. When Covid-19 was declared a pandemic, she says she wasn’t shocked that another virus like SARS or MERS had emerged but was stunned by how fast it spread.

Much of the focus on the novel coronavirus distribution has centered on airborne transmission. But coronaviruses, like the one that caused the 2003 SARS outbreak in Hong Kong, can also reproduce in the gastrointestinal tract. At Amoy Gardens, a housing estate in Kowloon, SARS jumped from one patient to hundreds via diarrhea that became airborne after flushing, spreading a distance of around 200 meters. According to a report in Nature, SARS-CoV-2 may be broadcast the same way.

In Palo Alto, California, Wigginton and her colleagues have been collecting local sewage samples for weeks to build accurate tools for testing. Her team is also exploring whether ultraviolet light and sunlight can disinfect the virus. The Bay Area was one of the earliest places to report a Covid-19 outbreak in the United States and still has some of the highest numbers of cases in the country, so the region will likely have a high volume of viral particles in the waste stream.

Finding new ways to track the coronavirus is especially important because many cases appear to be asymptomatic and the United States has a limited number of tests. Not everyone who gets a Covid-19 infection gets severely sick, sees a doctor, or gets tested, but they can still spread the virus. Surveilling sewage gives health experts a bigger picture of the pandemic’s scope.

“Another thing it can do is give you an idea of the diversity of the virus in the community,” Wigginton says. “If you could sequence the coronaviruses in wastewater, you have a much better idea of how the virus is mutating and possibly where the virus came from in your community because it might match with viruses that came from a certain city somewhere else. So I think there’s other valuable tools in this approach as well.”

Wigginton and the Dutch team are not the only ones monitoring our excrement for coronaviruses. Researchers at the University of Arizona Water and Energy Sustainable Technology Center and the Norwegian Institute for Water Research (NIVA) are doing similar research. “The future of public health surveillance depends on developing innovative bioanalytical approaches,” Jose Antonio Baz Lomba, a research scientist at NIVA said in a press release.

Sewage surveillance is already used to monitor public health in several ways, including monitoring for polioviruses and pathogens that have evolved to have antimicrobial resistance. Wastewater surveillance is even used to track the use of cocaine and meth. As the planet continues to be reshaped by this novel coronavirus, tracking Covid-19 by sifting through fecal matter will likely become an important, lifesaving tool.

documentary field producer, independent journalist, photo-taker. insects/drugs/vaporwave. life is a vision—enter the void. // more info at

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