Poop could be the key to tracking COVID-19 outbreaks

Searching wastewater for the coronavirus is fast, cheap, and anonymous.

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Your poop might soon be pressed into service in the fight against COVID-19.

When we flush the toilet, our effluvia are whisked out of sight and mind and in most cases wind up at a wastewater treatment plant. All this waste represents a golden (so to speak) opportunity to track the spread of the coronavirus that causes COVID-19.

Around the world, scientists are detecting remnants of the virus in municipal sewage. Sampling our stool could offer a faster and cheaper way to pinpoint where outbreaks of COVID-19 are brewing before scores of people become seriously ill, they argue. This technique also picks up virus bits that were “shed” by people whose mild or asymptomatic infections often go unnoticed.

“We can actually measure hundreds of thousands of people with a single sample,” says Rolf Halden, the director of the Biodesign Center for Environmental Health Engineering at Arizona State University in Tempe, who discussed the feasibility of this technique on April 22 in the journal Science of the Total Environment. “You get information that cannot be produced by any other means.”

In the United States, aggressive social distancing is beginning to slow the spread of COVID-19 in some places. However, most of the population is still susceptible, including folks in hard hit regions. This means that the virus that causes COVID-19—officially known as SARS-CoV-2—will continue to infect people for the foreseeable future.

To prevent an immediate spike in COVID-19 cases as we ease social distancing and stay-at-home orders, we’ll need to know exactly where the virus is circulating. That means doing widespread testing for COVID-19, then swiftly isolating people who test positive and identifying everybody else they might have infected.

This will be no easy feat. The United States has lagged behind many other nations in testing people for COVID-19. Testing efforts have ramped up in recent weeks and since late March the U.S. has been averaging 150,000 tests per day. However, researchers at Harvard University recently estimated that the country would have to perform up to 20 million diagnostic tests daily to fully reopen the economy.

The novel coronavirus is also a tricky germ to track. It can spread through communities undetected because many people who catch it have mild symptoms, or none at all. COVID-19 also may be most contagious early in the disease, before people are even aware that they are sick. And it can take more than a week before some people start feeling ill, which means there is a lag between when somebody gets infected and when they receive an official diagnosis.

Enter the poop. Halden and other scientists have been inspecting sewage for years to find clues to the overall health and behavior of a community’s residents, a practice known as wastewater-based epidemiology. Our sewage offers a crude—but anonymous—picture of what people are consuming, from caffeine to opioids. Scientists can also detect remnants of medicines or hormones that might indicate that people are ill or stressed, pesticides and other harmful chemicals, and disease-causing viruses such as polio.

Researchers are now turning their focus to the COVID-19 pandemic. Regular sewage sampling could give public health officials an early warning that the coronavirus is on the rise in their communities, Halden says. Depending on where in the sewer system researchers collect these samples, they could potentially identify clusters of infections in a city, neighborhood, or apartment complex. Once they’ve zeroed in on a hotspot, experts can step up their efforts to test people in that community for COVID-19 and trace their contacts.

“We can take a sample at the wastewater treatment plant and then bring it to the lab and within typically 24 hours we have the results,” Halden says. “We’ll be able to do more testing faster and then put our resources exactly where they’re needed.”

fridge of poop
Our sewage offers a crude—but anonymous—picture of what people are consuming, from caffeine to opioids. Researchers are now turning their focus to the COVID-19 pandemic. Regular sewage sampling could give public health officials an early warning that the coronavirus is on the rise in their communities. ASU, Media Relations

He and his colleagues have begun testing the wastewater around Tempe for SARS-CoV-2. They use the same kind of tests that diagnose individuals with COVID-19 by detecting fragments of RNA from the virus. The more genetic material that appears in a sample, the more people in the area are likely infected.

Other teams have also reported finding the novel coronavirus in sewage from Massachusetts, the Netherlands, Australia, and France. Together, the findings demonstrate that enough virus is excreted in stool—and that at least some of its genetic material persists long enough—for scientists to measure after it has traveled through a community’s sewers.

In their new study, Halden and his ASU colleague Olga Hart ran computer models that predicted how sensitive these tests might be in different cities. Depending on temperature and other local conditions, it should in theory be possible to detect the novel coronavirus even if it was excreted by a single infected person and then mixed in with the poop of between 100 and 2 million other people.

The researchers also crunched some numbers to find out how much money sewage sampling could save in the U.S. They calculated that it should be possible to collect fecal data from the nation’s 15,014 wastewater treatment plants within several days. This screen would cover about 70 percent of the U.S. population; because septic systems do not convey their waste to treatment plants, people who use them would not be represented. The whole venture would cost about $225,000. By contrast, the team estimated, diagnostic tests for all 330 million or so Americans would cost around $3.5 billion. Sewage testing could never fully replace traditional diagnostic tests. Importantly, wastewater sampling can’t identify which individuals are infected. But sewage sampling would make diagnostic testing more efficient by signaling where officials should be testing people more aggressively.

Halden believes that sewage can answer a few other questions about the pandemic as well. He and his colleagues had already been examining the traces of alcohol, nicotine, and caffeine that show up in wastewater. Before COVID-19 struck, the team also collected samples of wastewater across the city of Tempe. They hope to use these samples to trace how the city’s health changes before, during, and after the pandemic.

“With everything changing right now and every normalcy being gone from our lives, we are interested in measuring in communities like Tempe how the virus impacts our health irrespective of the direct infection, but just our ability to carry on normally,” Halden says.

Meanwhile, researchers in Paris have tracked the presence of SARS-CoV-2 in stool over the course of a month, from March 5th to April 7th. They saw that the concentration of genetic material from SARS-CoV-2 rose ahead of the city’s surge in fatal cases of COVID-19. While findings are preliminary and have not yet undergone the peer-review process, they add to the evidence that sewage could provide an early warning that an outbreak is imminent. The team has previously tracked waterborne viruses in the Seine River.

“Wastewater-based epidemiology is a powerful tool [during] epidemic events,” Laurent Moulin, a microbiologist at the city’s public water company, Eau de Paris, said in an email to Popular Science. He and his colleagues described their results on April 17 on the preprint server medRxiv. “The concentration of viral RNA in wastewater correlates with the epidemic status of the population linked to the wastewater network.”

He and his colleagues were able to detect the virus flowing from parts of the city where fewer than 100 people had tested positive for COVID-19. However, in samples with sparse RNA, it was hard to get an accurate count of exactly how much virus was floating around.

Scientists in Brisbane, Australia have also found it difficult to analyze samples where the virus is present at low concentrations.

“If we know the level of SARS-CoV-2 in wastewater, we would be able to roughly estimate how many are infected,” said Warish Ahmed, a senior research scientist in the contaminants and biotechnologies program at CSIRO Land and Water, a subunit of Australia’s national science agency. He and his colleagues made the first report of SARS-CoV-2 in Australian wastewater on April 18 in Science of the Total Environment. “The next step is to refine methods for the sensitive detection of SARS-CoV-2 in wastewater and build the capacity to deliver a program for surveillance of COVID-19 in the community.”

There are other challenges to using wastewater-based epidemiology to track COVID-19. Weather and even a city’s geographical layout can influence the amount of RNA that researchers can detect in a sample.

“There’s a lot of celebration right now that the virus can be measured in wastewater and we are equally proud to do so in our laboratories,” Halden says. “But it is also important to understand what the limitations are with respect to the data that we have.”

When it is flowing through the sewers, the virus will have more time to break down before it can be sampled if it’s coming from a neighborhood far from the treatment plant. This also means that infected people who live near the treatment plant will create a stronger signal than those using restrooms at the edge of town. So it might be easy to over or underestimate how many people are sick, depending on how far from the plant the hotspot is located.

Viruses also degrade more quickly at higher temperatures. This means that in hot climates or during typical summer days, viruses excreted by people farther from the site where sewage is collected will be more likely to break down before reaching it. “Depending on the season you can look farther—or not so far—down the pipe into your community,” Halden says.

It might seem troubling that SARS-CoV-2 can persist in wastewater long enough to be detected. However, these fragments of genetic material don’t necessarily indicate the presence of a live or active virus.

“It means that we can measure the ‘license plate’ of the virus,” Halden says. “The genetic information is still floating by, but it doesn’t imply that the car that was previously attached to that license plate is intact.”

Future studies will be needed to determine whether the virus is still capable of growing after passing through wastewater treatment plants. The team in Paris is currently investigating whether the viruses showing up in sewage are still infectious, Sebastien Wurtzer, a virologist at Eau de Paris and coauthor of the recent findings, said in an email.

He and his colleagues are now working on a national system to monitor SARS-CoV-2 in wastewater. Halden and Ahmed too are hoping to expand the search for the novel coronavirus in their nation’s sewer pipes and beyond.

“We should be bringing this technology to other cities as quickly as possible,” Halden says. “I think we just have to get organized.”