Your Poop Might Be Key For Predicting the End of the Pandemic

On March 5, there had not yet been a clinical diagnosis of COVID-19 in Amersfoort, a Dutch city of more than 150,000 people to the east of Amsterdam. But underneath Amersfoort's streets, dotted with Medieval buildings, the sewage pipes containing people's fecal matter told another story.

In early March, researchers at KWR, an independent water research institute, detected viral fragments from SARS-CoV-2, the virus that causes COVID-19, in wastewater collected from the nearby wastewater treatment plant. Their findings, published on a preprint server without peer review, indicated that the virus had in fact arrived.

Their work also revealed the promise of wastewater sampling as a public health tool—both to monitor the spread of the current COVID-19 pandemic, as well as detect its reappearance in the future.

In Boston, a company called Biobot, in collaboration with researchers at MIT, just completed a similar study. On Tuesday, they published (also in a preprint paper) the stunning fact that the amount of virus they observed in wastewater was much higher than they expected it to be based on the number of confirmed cases in the Boston area. The amount of virus they saw would suggest that about 5 percent of all fecal samples were positive for the virus, while the reported number of infections was only at .026 percent of the population during the same period. As the researchers told STAT, this amounts to an expected 2,300 people infected around the treatment facility, when there have only been 446 confirmed cases.

Our pee and poop contain a lot of information, Mariana Matus, the CEO and co-founder of Biobot, said, and could be a critical factor—in tracking the true number of COVID-19 infections, which areas are most affected, and deciphering when the virus has actually disappeared from our communities.

“It’s an invaluable source of information about human health, because we're all using the toilet on a daily basis," she said.

Wastewater has been used to detect other viruses before. In 2013, a poliovirus outbreak in Israel was detected by surveillance of the sewage system before any cases were reported. The surveillance system was set up in 1989 by the Israeli health department, where samples were automatically collected weekly.

Epidemiologists usually detect polio, which is highly contagious, by reports of the physical symptoms in people, namely the acute flaccid paralysis (AFP) it can cause—but by that point, it's usually too late. “It’s just the tip of the iceberg – one case of AFP indicates substantial underlying polio transmission in a population,” a team of epidemiologists wrote in The Conversation in 2018.

By finding the virus early on, before any AFP cases, Israel was able to begin a polio vaccine campaign, and the virus disappeared again from the wastewater before a larger outbreak took hold. Sewage surveillance has also been shown to be a tool for early warnings of Hepatitis A and norovirus outbreaks.

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Before the COVID-19 pandemic, Matus and her colleagues at Biobot were focusing on using wastewater to track opioid use. But when studies from March found that the new coronavirus could be shed through feces, she and her team shifted gears.

KWR and Biobot both find the virus in the wastewater by looking for different genes that are specific to SARS-CoV-2. They're not alone: Nature reported that more than a dozen research groups around the world will be analyzing wastewater for SARS-CoV-2 as well.

Frederic Béen, a scientific researcher at KWR, said that his colleagues tested sewage samples from seven cities and the Amsterdam Schiphol airport. They started early: February 6—which was three weeks before the first reported clinical case of COVID-19, February 27. At that date, they didn't find any of the virus yet.

On March 5, however, they found the first viral fragment. By March 15 and 16, at least one viral fragment was found in six of the wastewater treatment plants—matching the rise of the outbreak in the country.

Matus said that in the U.S., having a system like this in place would have helped push for a faster response. “Imagine if we already had this platform at scale in the country and then when the outbreak happened in China in January?” she said. “And we started testing for SARS-CoV-2 right away. We might have had a better response, because today we only raise the alarm when we reach enough clinical cases. With technology like this, the idea is that you can respond quickly and just have that data that is naturally being generated by people's bodies.”

Even though it's too late for an early warning, this kind of data can be useful at different points in the pandemic too— it could track the progression of infection, especially since widespread COVID-19 testing has been difficult to access, and an unknown number of people have mild symptoms or are asymptomatic—but are still potentially transmitting the disease to the virus to others.

“It would be a more accurate sense of the total number of cases, and not just those confirmed through the hospital system,” Matus said. “Not to mention all of the people who lack access to healthcare. There's just many steps at which people can fall off and not be taken into account.”

Biobot hopes to use the data from the wastewater to model the actual number of infected people in a given area. Wastewater provides a large snapshot, since it can tell you about the entirety of the area that the facility services.

“The beauty of wastewater monitoring is that by collecting just a few hundred milliliters of wastewater, flowing into the wastewater treatment plant, you obtain a sample that represents thousands, like a small village, or hundreds of thousands of people, like a city the size of Amsterdam or New York,” Béen said.

About two thirds of the U.S. population is covered by wastewater infrastructure; many of the rest use septic tanks. This technology would be available only to those who are connected to wastewater facilities, for now.

To get more granular information, Matus said that Biobot has developed portable testing devices that can look at smaller neighborhoods. For now, they haven’t done that because they are too busy—it requires having people go into manholes in those communities.

Matus said that their next step is to learn more about if different people shed different amounts of the virus, and at what points in their illness, so that they can get even more accurate, detailed information from their data.

Biobot is a private company that is collaborating with researchers at MIT, Harvard, and Brigham and Women's Hospital —but is currently doing this work pro bono. It announced on Twitter that it would accept sewage samples from wastewater treatment facilities across the U.S., and they were booked up within about a week. They’re now testing wastewater from 30 different states, and their goal is to be able to test up to 10,000 samples per week by June.

As the pandemic eventually subsides, wastewater testing could provide a peace of mind that testing individuals cannot: It could help confirm that the virus isn’t present anymore in the community— critical knowledge that could inform when social distancing measures can be alleviated.

And if COVID-19 turns out to be seasonal, returning in the fall, wastewater could be an indicator to tell if the outbreaks are starting to climb back up.

“Down the line, once we start seeing a decrease in the clinical cases, getting a sense of if this is actually contained or not will be hugely invaluable,” Matus said.

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