Sewers Are Now a COVID-19 Early-Warning System

Wastewater samples can give communities a near-immediate snapshot of how the pandemic is spreading.

Officials collect a wastewater sample from a Montana State University sewage line.
Officials collect a wastewater sample from a Montana State University sewage line. (Mike Greener / High Country News)

The sewer is the last stop for Bozeman, Montana’s waste, but lately it’s been the first one for Blake Wiedenheft’s work. An associate professor of microbiology and immunology at Montana State University, Wiedenheft has joined other virologists, epidemiologists, and immunologists as a member of the university’s COVID-19 task force.

Back in March, a colleague mentioned testing wastewater for evidence of COVID-19 in human waste. The next day, Wiedenheft drove down to Bozeman’s wastewater-treatment plant to see if he could grab a sample. Given how few cases there were in the area at the time, and that 6 million gallons of water flow through the plant daily, he wasn’t sure if the virus would be detectable. But Wiedenheft immediately found evidence of it—and it kept appearing in the four samples he analyzed over the next 10 days. Wiedenheft worked with local officials to continue regular testing as Bozeman became one of the world’s first cities to look to sewage for answers.

Now municipalities across the western United States are sampling wastewater for evidence of SARS-CoV-2, the virus that causes COVID-19, as a potential early-warning system for outbreaks. Scientists estimate that up to 45 percent of people infected with the virus show no symptoms. Given that asymptomatic people are less likely to get tested, many cases may go undetected. With several areas in the U.S. experiencing substantial delays in swab-test results, daily wastewater testing can give scientists an idea of community infection nearly immediately, Wiedenheft says.

To capture such a snapshot of community spread, Josh French, the operations foreman at the Bozeman Water Reclamation Facility, and his colleagues take regular samples from the city’s wastewater, which flows from showers, laundry machines, greasy sinks, and, of course, toilets. All that liquid—a cloudy, hay-colored mixture with only a mild stench—arrives at the wastewater plant, where a machine called an autosampler takes small samples.

The autosampler looks like two mini-fridges stacked vertically. The top compartment houses a tube and pump, which sucks up half-cup samples and deposits them into a plastic jug in the cool bottom compartment. Every 24 hours, a sample from this jug is taken to Wiedenheft’s lab, where it’s tested with the same methods used to analyze COVID-19 nose-swab tests. Researchers take RNA—whether floating in a liter of wastewater or smeared on a swab—and perform a procedure that amplifies the genetic signature of the SARS-CoV-2 virus. That lets researchers identify the virus.

The challenge of analyzing wastewater, as opposed to a swab, is that RNA samples are a tiny part of each overall jug of wastewater. “Imagine you’ve got a jar full of jelly beans, and you’re dipping into the jar to see if you can find a red jelly bean,” Wiedenheft says. “If your jar is small, it’s more likely you’re going to scoop up that red jelly bean—but if your jar is big, it’s less likely, and you’re going to have to collect more of the sample to find it.” The virus is like the red jelly bean; to get an accurate glimpse into how much virus is in a city’s water, scientists must make sure the samples they collect are representative of its overall water flow. That means taking more frequent samples at peak times—in the mornings, when people are starting their routines, or in the evenings, when they’re doing chores—as well as less frequent samples when the water flow is lower, as it is very early in the morning. Bozeman’s autosampler collects about three dozen samples daily.

The upshot of Wiedenheft’s lab analyses—whether the samples are positive or negative for the virus—is posted on the county’s public-health website. In the 26 samples tested from June to mid-August, the coronavirus was detected every time.

French says they’re now experimenting with sampling from specific areas of town, such as the hospital and Montana State’s campus. Engineers have identified their main sewer-flow lines and placed mobile samplers just beneath manhole covers, where they collect samples one day a week. As the school year kicks off, MSU’s data could track viral spread on campus, while the hospital data could help scientists better understand how their results map onto community spread. “We know how much viral protein [Wiedenheft] is detecting in his lab, but how many individuals is that reflective of?” French asks.

Researchers don’t yet have a definitive answer. Converting wastewater data into an estimate of positive cases requires a key metric scientists are still learning about: how much virus an infected person sheds. That can depend on whether the person is sick—and, if so, the stage of illness the person is in and how severe the illness is. Because those variables are hard to nail down, Wiedenheft has intentionally avoided reporting such estimates. “We don’t feel confident enough to make that translation,” he says.

But in some cities, officials have released estimates using wastewater data to indicate how many community members are infected. For instance, analyses by Biobot, a wastewater-testing startup, estimated that levels of SARS-CoV-2 found at one point in Moscow, Idaho’s sewage corresponded to 1,800 cases. At the time of that estimate, Latah County, where Moscow is located, had only 46 known cases. (Biobot declined to be interviewed, and its hired communications firm didn’t answer questions about how the company calculates case estimates. A recent study published by Biobot’s co-founders and colleagues reported that assumptions about individuals’ viral load can massively affect these estimates. According to their calculations, the assumption that infected people have a low viral load leads to an estimate that 5 percent of the population is infected; assuming a high viral load will lower that estimate to 0.1 percent.)

So far, many local officials have looked to wastewater analyses more as a way to corroborate their knowledge about community viral spread than as a way to estimate case numbers. “We won’t know how many people in the community have COVID-19 from the methodology, but this data will tell us if trends are going up or down,” says Nicole Rowan, the clean-water program manager at the Colorado Department of Public Health and Environment, which has launched a statewide wastewater-testing effort.

Matt Kelley, a health officer at the Gallatin City-County Health Department in Bozeman, says that when Gallatin County went through a period of few cases in May, the sewage data gave additional confirmation that spread had slowed. “It was somewhat reassuring to have another backstop indicator of what was happening,” he says—and when positive COVID-19 swab tests rose again, so did levels of SARS-CoV-2 in the water. Kelley notes that once cases fall again, it will be helpful to track wastewater as an indicator of undetected community spread. “If we’re not seeing tests in the traditional medical testing, and also not seeing them in the wastewater, that’s a validating factor for us.”

As more areas launch wastewater-tracking programs, Wiedenheft says one thing is still needed: a central repository for this data, which could provide a bigger-picture view of viral spread. Over the last few months, Montana has developed several monitoring sites, and some states, like California, Colorado, and Wyoming, have created their own networks. It’s difficult to compile a list of cities conducting testing, since some key data are private; Biobot says it’s working with 400 facilities, but declined to provide additional information, including how many cities that corresponds to. Wiedenheft points to Johns Hopkins’ popular coronavirus tracker as an example of a well-organized health surveillance tool. “It would be nice to have a wastewater-surveillance website that does the same thing,” he says, “where you could look at a geographic map and look at what’s happening.”

In mid-August, the U.S. Centers for Disease Control and Prevention and the Department of Health and Human Services announced plans for a National Wastewater Surveillance System, a portal to which health departments can submit their wastewater data. After the federal government’s changes to a portal tracking hospital data led to widespread reporting delays and data inconsistencies, it’s unclear how this database will fare—and whether this new initiative provides funding to areas that are conducting testing. Wiedenheft’s funding went through August, and he’s unsure where the money will come from now. “If wastewater sampling is important—and I think it is, since there’s plenty of evidence to suggest it’s really the only real-time indicator in the community—then it seems important to have funding to support this ongoing effort,” he says. “That’s imperative to be able to manage a pandemic.”

This post appears courtesy of  High Country News.