Cities are using poop to look for early Covid-19 outbreaks

So far, Covid-19 testing has failed miserably to track the progress of the pandemic in the US. Not everyone who has the virus can access swab-based diagnostic tests, and once they do, their results are often massively delayed by scheduling bottlenecks or short-stocked supplies.

But scientists are hoping that a simple fact of life will complement swab testing: Everybody poops.

In cities across the US — ranging from Boston, Massachusetts in the northeast to Las Vegas, Nevada in the southwest — scientists are working with public health officials to conduct wastewater-based epidemiology. Research early in the pandemic showed that people infected with SARS-CoV-2 shed bits of the virus’ genetic material in their feces. So by measuring the viral load in sewage, public health officials can get an idea of how prevalent the coronavirus is within a community.

In combination with other data, sewage samples can even be an economical way to help determine whether a community is safe to open up or should consider restricting activities.

“Wastewater is convenient in that you get a population level understanding of transmission in a single sample,” says David Larsen, an environmental epidemiologist at Syracuse University who’s been working with his local health department in Syracuse, New York to monitor wastewater. “It’s extremely cost effective.” The tests employ the same kind of analysis as an individual swab — scanning a sample for viral genetic material using a technique called polymerase chain reaction — but instead of conducting dozens of individual tests, a single sewage sample provides a picture of all the Covid-19 activity in an area.

In small enough settings, wastewater monitoring could even predict outbreaks. In one study conducted by researchers at Yale, fecal matter contained viral signatures about a week before cases popped up. Already, wastewater monitoring has been used to catch outbreaks among students at the University of Arizona and Utah State University before they displayed symptoms — potentially saving the universities hundreds of cases as they implemented quarantining strategies for the affected dorms.

At universities, wastewater monitoring can show early spikes of Covid-19 down to specific dorms. Cities are much larger, and sewage lines serve hundreds of families, so it’s impossible to trace the presence of viral genetic material down to a single residence based on one sample. But conceivably, the sewage samples municipalities collect could give snapshots of how entire zip codes will be doing soon, says Larsen. Eventually, wastewater monitoring could clear certain areas for reopening, or indicate that lockdowns need to remain in place for longer.

Wastewater trends in community spread can be complemented by individual clinical testing, says Ted Smith, an environmental engineer at the University of Louisville in Kentucky who is working with his local public health department to carry out wastewater monitoring. “We can compare what they’re seeing with our test data,” he says. These comparisons can indicate the number of cases the jurisdiction can expect in the coming weeks.

In countries like Finland, Germany, and the Netherlands, national wastewater monitoring initiatives are already cluing authorities in as to where they need to provide mass testing. But the US isn’t ready to scale up wastewater monitoring just yet.

For one thing, there’s no standardized method. Some cities open up manholes and skim off the wastewater over a period of 24 hours; this method reflects Covid-19 activity in a smaller geographic location. Others collect the solid sludge from wastewater treatment plants, which provides larger amounts of potential genetic material. But those results are less actionable, because they represent the composite of several sewage lines.

Scientists also aren’t sure how much viral genetic material in stool corresponds to individuals who may be sick. A large concentration of viral genetic material from one testing site could come from one super shedder, or several infected individuals, Smith says.

The US Centers for Disease Control and Prevention has created a National Wastewater Surveillance System, and is working with the nonprofit Water Research Foundation to compare the different testing methods and establish standards.

But sewage monitoring will never be a one-size-fits-all solution: Only about 80% of the US’ population is connected to sewage lines. The remaining 20% have private septic tanks and are in more rural areas. Everybody poops — we just can’t sample it all.

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