Cities Around the World Are Looking for Clues About Covid-19 In Human Poop

Across the globe, Covid-19 detectives are finding their research united by one thing: poop. Specifically, data that can be extracted from our sewage, which can tell us a lot about how the pandemic is spreading and mutating, and how we might rein it in. Even scientists who aren’t tracking the spread of the virus via poop alone are still using this data in their models.

People mostly spread SARS-CoV-2, the virus that causes Covid-19, through the nose and mouth, but the bug also nestles in the intestines and can spread through waste. In the early days of the Covid-19 outbreak, scientists turned to raw sewage to find traces of the virus that have been missed by other detection methods, like logging hospitalizations, contact tracing, or positive tests.

Scientists regularly deploy sewage surveillance to monitor for polioviruses, pathogens with antimicrobial resistance, and even the use of drugs like heroin and MDMA. So it didn’t take much tweaking to start looking for the new coronavirus.

Wastewater-based epidemiology (WBE), the technical term for tracking pathogens in sewage, holds a lot of promise: It can supplement the shortages, delayed results, and poor quality of testing in the United States. It can potentially tell us how the virus is evolving. Because everybody poops, it can capture the scale of the virus at a population level, which is more cost-effective than testing every single resident.

And, as an experiment in the Netherlands demonstrated, it can sometimes detect the virus before hospitals. “Better population-wide data could aid in reducing the economic damage and social burden placed on populations dealing with stay-at-home ordinances, furlough, and involuntary unemployment,” an August analysis in Science of The Total Environment found.

For these reasons, and because it involves poop, this scatological investigation strategy attracted a lot of scientific and media attention when the outbreak first began. It started with a few labs collecting samples in the Netherlands, the San Francisco Bay Area, Paris, and a few other countries. But now dozens of labs around the world are conducting experiments and collecting fecal data. Though they’ve only just begun applying it to form public health strategies, the results so far are promising.

A June letter published in Environmental Science & Technology, signed by 60 researchers, proposed a “global effort to coordinate methodologies and data-sharing” in order to harness this information from sewage surveillance in the most effective way. They built the Covid-19 WBE Collaborative, a hub for excrement spelunkers that includes a publication map, news, and other resources. They even have their own Slack channel, which they claim has more than 100 active members.

“It doesn’t matter if an infected person is asymptomatic or has full-blown symptoms — we still see traces of the virus in their waste,” Janelle Thompson, PhD, an environmental microbiologist and principal investigator at the Singapore Centre for Environmental Life Sciences Engineering (SCELSE) said in an email to OneZero. Since February 2020, SCELSE has been working with Singapore’s National Environment Agency to refine ways of sampling wastewater and detecting the virus. They started by following outbreaks in dormitories where migrant workers live.

Thompson’s project is one of the first real-world examples of how WBE could be used to help manage the Covid-19 pandemic. The agencies used WBE to help manage outbreaks in dormitories where foreign workers from places like Bangladesh and India sometimes live. These immigrants, often manual laborers or housekeepers, share a bathroom, eat together, and sleep crammed together in rooms. Social distancing is not an option. Not surprisingly, these housing units became some of the most intense hot spots for viral outbreaks in the country, although as of August 11, most workers are now virus-free, according to AP.

The SCELSE pilot program sampled sewage from the manholes of 20 large dormitories for workers. If samples came back negative for Covid-19, the residents could go to work. But in areas that came up positive, officials ordered more swab tests, which led to more detections and allowed cases to be isolated, even if they were asymptomatic. (Part of the reason Covid-19 is so deadly is because people can spread it even if they don’t have symptoms.)

“One really exciting part of this project is how eager a lot of the utilities are to give us their sewage or sludge.”

A recent study co-authored by Thompson in the journal Water Research posited that wastewater surveillance “should be a top priority of public health at the local, national and international level.”

But that was just a small study. In order to capture enough data, Singapore will need to expand the number of wastewater nodes to scan for coronavirus. “Wastewater testing for SARS-CoV-2 is still a very young science, so we are definitely still working out the details,” Thompson says. “And it doesn’t replace clinical testing.”

“The amount of work has been incredible,” Katy Graham, a PhD student at Stanford University, told OneZero. When the pandemic first started to spread in the Bay Area in February, Graham joined a dual effort between Stanford and the University of Michigan to track Covid-19 in sewage. The team is collaborating with local public health bodies and the Centers for Disease Control and Prevention to fully refine this tool.

“One really exciting part of this project is how eager a lot of the utilities are to give us their sewage or sludge,” Graham says. “They’re very happy to give us the samples that we need to make this project work… It’s amazing to see so many people from all over the world just drop everything and focus on this completely.”

One idea floated in the WBE research community includes sampling the wastewater of airlines and cruise ships before departure, so when travelers reach their destination, any passengers who are infected can be identified and isolated. This idea was tested by a team of researchers in Australia with results published in July. But although the excrement they sampled came back positive for Covid-19 and the passengers were isolated, none of their swab tests showed they were positive for the virus. Still, the test demonstrates a possible application for WBE.

The largest U.S. commercial effort to scan waste for Covid-19 comes from a MIT-borne outfit called Biobot Analytics, Inc., which claims to be working with around 400 wastewater facilities in 42 states, representing more than 10% of the U.S. population.

Biobot has been scouring through human waste for more than five years, using robots like the one they named Luigi to track the use of opioids, bacterial outbreaks, and other public health issues. When they directed their attention to Covid-19, it didn’t take long to get results.

In Massachusetts, Biobot’s home state, the company tests the water three times per week at the Deer Island Treatment Plant. They recently found a slight uptick in virus levels, the highest point since late June. On August 8, public health officials cited this data, as well as an increase in positive tests, when they recommended the state go back into a “Phase 2” lockdown, closing many businesses and limiting gatherings.

In Delaware, Biobot reported that an estimated 40,000 people were shedding the virus into the sewers of northern New Castle County, a figure six times higher than tallies from testing individuals. It prompted one county executive to remark that reopening “does not make sense.”

But it may be hard to pin exact numbers to WBE just yet. The science is extremely tricky. First, scientists are looking for tiny shreds of RNA that make up the virus. If the virus is a piñata, these are the bits of confetti left over when it bursts open. Finding the RNA is hard enough, but extrapolating the amount found to the number of people in a region who may or may not have an infection is even more difficult. That doesn’t make this tool useless, it just limits what it can tell us so far.

“Good estimates of disease prevalence in the population from sewage are not possible yet, due to significant uncertainties,” Thompson, the researcher in Singapore, says. In people who have already come down with Covid-19 symptoms, viral levels in fecal samples can span six orders of magnitude, from zero to 1 million per milliliter. That’s a lot of variance, which makes it even more difficult to use the data to estimate the rate of infection in a metropolitan area.

In spite of these limitations, Frederic Béen PhD, a Dutch researcher at KWR, the lab that first demonstrated WBE for tracking the coronavirus, tells OneZero there are still many useful applications for this tech. “Although we cannot still reliably estimate the number of people infected, trends derived from wastewater have proven to be a good diagnostic about what’s happening in a given community,” he says in an email. “Results from WBE should be combined to all other available indicators to help obtain a more precise understanding about the situation.”

Graham says her lab is still trying to develop an effective model that answers questions that will make it easier to track Covid-19 via sewage. “When a person gets infected, when do they start shedding, when is the shedding the heaviest, when do you stop shedding, and how do the concentrations look throughout that course of illness?” Graham asks. “That’s still a question that a lot of people are still working on and that’s a pretty key part of the model obviously.”

In other words, Biobot’s estimates may not be the full picture, at least probably not yet. Biobot did not respond to a request for comment.

“It is extremely important to our group [that] when we give this information to people, we want it to be accurate and we want the model to be tested,” Graham says. “There’s still just a lot of variability in what we see. We’re still working through all of the issues, and trying to have different assessments of reliability and reproducibility to make sure that it’s really sound science.”

While the Covid-19 pandemic seems never-ending, it eventually will pass. But the global wastewater surveillance infrastructure built during this crisis could easily be used to track the next pandemic, as well as other chemical biomarkers related to public health.

“Today we’re facing the Covid-19 pandemic, but this is only one of the many public health challenges WBE can be used for,” Béen says. “WBE can allow us to rapidly detect future outbreaks and, by measuring residues of chemicals… gather information about [the] health and behavior of humans in these exceptional circumstances.”