Future Tense

We’re Flushing Some of Our Best COVID Data Down the Toilet

But don’t worry, we can test it there, too.

A hand holds a magnifying glass over a toilet bowl containing coronaviruses.
Photo illustration by Slate. Photos by Getty Images Plus.

COVID-19 cases are relatively low across the country, with even fewer people being hospitalized and dying. But the situation remains uncertain. In the past, new variants have caused sharp surges in the U.S. with little warning, and case numbers usually lag behind when a person was actually infected by one or two weeks. With the popularity of at-home tests, many cases are never even reported to public health officials. The Centers for Disease Control and Prevention has also loosened many guidelines related to COVID-19, including no longer urging most people to wear masks. Instead, its new color-based Community Levels system is focused on determining whether the virus is overwhelming hospitals. That’s useful information, but it’s a poor indicator of community spread, as hospitalizations tend to lag even further behind transmission trends than case data. So how can we know a surge is coming before it tears through communities?

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The answer may lie in testing wastewater—what goes down the sink and bathtub drain, comes out of dishwashers and washing machines, and is flushed down the toilet. The wastewater from your toilet includes sewage, which can contain bacteria and viruses. Wastewater testing has been used to track COVID-19 since nearly the beginning of the pandemic, but the idea goes back decades: In the 1940s, U.S. scientists started using it to track and contain polio and other viral disease like typhoid, and it continues to be used to track polio.

It may seem that wastewater is a strange place to look for SARS-CoV-2, since we think of COVID as mainly a respiratory virus. However, most people infected with COVID-19 shed virus in their stools, no matter the severity of infection. It happens even if they don’t have gastrointestinal symptoms, or even any symptoms at all, said Shangxin Yang, the assistant medical director of the clinical microbiology laboratory at the University of California Los Angeles.

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Wastewater can be tested in a number of different ways. According to the CDC, water collected from a wastewater treatment plant or from other wastewater sources like manholes can be used. Because of how wastewater is pooled, sampling collects data from an entire area or community, much more so than even regular periodic rapid or PCR testing. After all, you aren’t likely to opt out of using your toilet.

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With more people testing themselves at home and not reporting cases to public health authorities (even if they wanted to, there’s rarely a way), wastewater testing can provide the broad, population-based data the clinical testing could be missing. Though not without its limitations, wastewater testing is invaluable in helping to show virus transmission in real time, say experts, and will likely be an increasingly important part of monitoring the pandemic going forward.

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Although it may be increasingly useful as other COVID monitoring falls by the wayside, wastewater testing been used since the very beginning of the pandemic. Cambridge-based wastewater epidemiology company Biobot started testing wastewater for SARS-CoV-2 in March 2020. In May 2020, Rolf Halden, the founding director of the Biodesign Center for Environmental Health Engineering at Arizona State University, led the ASU team that, together with the city of Tempe, Arizona, created the world’s first open access online dashboard that displayed data on SARS-CoV-2 informed by analysis of city wastewater. (Disclosure: ASU is a partner with Slate and New America in Future Tense.) The Centers for Disease Control and Prevention launched its National Wastewater Surveillance System in September 2020.

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Wastewater testing’s ability to provide effective early warnings has already been used to guide public health practice and policy. For instance, the early testing of the city of Clemson’s wastewater in summer 2020 was so influential in convincing the city council to impose a mask mandate that it is specifically referenced in the official mandate ordinance, said David Freedman, professor and department chair in the department of environmental engineering and earth sciences at Clemson University. According to Halden, wastewater testing in Tempe and surrounding areas led to identifying a previously undocumented virus hotspot in the neighboring town of Guadalupe, which is home to a large number of Native American and Latino residents who often did not have access to tests. Tempe partnered with Guadalupe to mount an effective public health response that caused cases to fall sharply. “I think that that is a strategy that becomes more and more prevalent, and rightly so,” said Halden.

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“Wastewater’s going to provide us information about what’s actually happening on the ground,” said Freedman. If used effectively, wastewater testing data could influence future policy in similar ways. Freedman imagines that an increasing viral concentration in wastewater could trigger public health measures, like increased testing and masking. Recently, some places, like the city of Philadelphia and several universities, have even reinstated mask mandates in response to rising case numbers (though Philadelphia quickly dropped its mandate again). Wastewater testing could allow for these changes even earlier in a surge.

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According to the CDC, 80 percent of households in the United States have their wastewater go to a municipal treatment plant, which it can reach in a matter of hours. Testing wastewater can therefore track the virus in almost real time. Infected people often start shedding virus days before they have any symptoms, if they develop symptoms at all. Collected wastewater can carry COVID before the person who shed it even knows they are sick. That means that wastewater testing can serve as a very effective early warning system, said Freedman, helping to alert public health officials of future surges or ascendant variants.

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That early shedding is “the biological characteristic of COVID [that] actually makes wastewater testing effectively a good way of solving how the virus evolves and how the virus spreads in the community,” he said.

Another advantage to wastewater testing is that it’s passive, said Katelyn Jetelina, an epidemiologist at the University of Texas Health Science Center School of Public Health who writes the newsletter Your Local Epidemiologist. “You’re captured irrespective of your testing behavior,” she said. With wastewater testing, said Jetelina, as long as you flush your toilet, your data is picked up.

But like any technology, wastewater testing has its limitations. Depending on the wastewater collection method, samples can be diluted by different amounts by stormwater, or street runoff. That makes it difficult to judge what different virus concentrations in wastewater really mean, though following trends is still useful. Scientists have also been surprised to find variants in wastewater that have never been found in clinical testing samples, said Yang, leaving some to suspect that the virus data comes from infected animals in the area. Wastewater also can’t tell scientists anything about the potential severity of an upcoming surge, whether a new variant is particularly harsh or mild, only that people are becoming infected, said Yang.

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Wastewater testing still has a ways to go before it could serve as a robust early warning system for COVID-19 in the U.S., not to mention other parts of the world. Many places don’t have a system in place to test wastewater, and some don’t have municipal wastewater treatment systems at all. But as we move into what some people hope might be a new stage of the pandemic, wastewater testing might help us stay ahead of COVID-19. It could even help us address other challenges in public health, from the opioid crisis to future disease outbreaks, said Halden. Testing wastewater is a relatively simple technical project, and it’s been scaled up for COVID.

“It is clear that wastewater testing is here to stay and probably will outlive the pandemic,” he said.

Future Tense is a partnership of Slate, New America, and Arizona State University that examines emerging technologies, public policy, and society.

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