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These scientists are fighting the pandemic with sewage

caption: A researcher siphons up wastewater from a sewer near the University of Washingon campus in 2021.
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A researcher siphons up wastewater from a sewer near the University of Washingon campus in 2021.
University of Washington/Kiyomi Taguchi

Sewage stinks, and it’s often laden with disease. But it can also be of tremendous value to public health.

Cutting-edge biomedical research sometimes begins with prying a heavy steel lid off a sewer hole, to gain access to the data gushing below.

Studies of wastewater have helped scientists pinpoint where Covid-19 variants have popped up, even before people know they’re infected.

In Washington state, sewage hasn’t turned into the public-health tool experts hoped it would. But here’s how researchers have been doing it near the University of Washington campus in Seattle.

After a technician lowers a long hose into the sewer beneath the Northeast 45th Street viaduct, small samples of frothy brown liquid are siphoned off and taken to a laboratory. There, the foul liquid will be concentrated and its chunks of genetic material copied until there’s enough RNA to know whether people living in the sewershed — the area upstream of that sewer line — are infected with the coronavirus.

“Wastewater testing is a very powerful tool, because it is inherently inclusive, unbiased, and cost effective,” said Tanisha Jain, a University of Washington urban planner and sewer expert.

Jain calls wastewater monitoring inclusive because it includes people who might not have access to health care or Covid tests.

On the other hand, to quote a classic children’s book: Everyone poops.

“When you are infected, even if you're asymptomatic, you shed the viral matter when you use the toilet, when you're brushing your teeth, or you're pooping or peeing,” Jain said.

Since the virus can lurk in the body for days before any symptoms develop, wastewater monitoring can detect an outbreak faster than relying on nasal-swab tests.

That’s the promise, at least.

It’s been a long, slow road trying to work out the science and produce results fast enough and accurate enough to be useful to the control the pandemic.

Researchers in Washington have backed away from their early hopes that they could measure the pace of the pandemic with sewage. They say wastewater can reveal when a virus first shows up or when cases skyrocket or plummet, but not more subtle trends.

The technique known as wastewater-based epidemiology or environmental surveillance is nothing new. Virologists began tracking polio — another viral disease that often spreads silently from people with no symptoms — in wastewater in the 1930s.

In March 2020, scientists around the world, including in Seattle, started spotting particles of the new coronavirus in sewage.

“We had a lot of folks get out of the gate very early,” University of Washington microbiologist Scott Meschke said. “The methods that they were using were untested, but they were getting positive results.”

Meschke said the field is still a “Wild West” of incompatible methods and techniques, hindering comparisons of results from different places.

Logistical challenges have stymied efforts in Washington as well.

On the University of Washington campus, finding out which dorms might be harboring silent outbreaks proved impossible.

“The way the pipes are plumbed doesn't really allow you to do it," said Scott Meschke. “Many of our buildings, you can't isolate an individual building because I'll capture everything from 50th Street on down.”

At a much larger level, Meschke said his team found Covid in the wastewater at Seattle’s three main wastewater plants back in March 2020. But they stopped looking for Covid at the plants last October. The big plants handle so much sewage and stormwater runoff from such wide areas that the signal of the virus is too dilute to measure reliably.

Now, University of Washington researchers are looking for Covid variants in the sewers of six Seattle neighborhoods, but they don’t have results yet.

caption: Six sewer sites and their "sewersheds" being monitored for the presence of Covid-19 variants by University of Washington researchers
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Six sewer sites and their "sewersheds" being monitored for the presence of Covid-19 variants by University of Washington researchers
University of Washington/Mari Winkler Lab

In other parts of the country, researchers have accomplished more with data dredged up from the sewers.

San Diego has online dashboards that show how many cases of Covid variants the city has, based on wastewater studies.

A Massachusetts company called Biobot is testing sewage across the country for the virus.

“We saw when delta completely started spreading everywhere because concentrations in wastewater completely skyrocketed,” said Nour Sharara, a public health scientist with Biobot.

The company also spied when Boston’s omicron spike peaked and began to descend in January.

Some Washington researchers say they’re dubious of the for-profit firm’s results. They question the methods Biobot uses to correct for the ever-changing volumes of water flowing through sewers that can alter the concentrations of viral particles detected.

“To leap from 'oh, here's a virus load' to 'here's the number of cases' is way ahead of its time, if we ever get there,” said microbiologist Ken Oostra with Exact Scientific Services in Ferndale. “Everybody can shed [the virus] differently. I mean, that's why some people end up in the hospital and some don't.”

“Wastewater is a great indicator for trends,” Sharara said. “It can show you how much viral infections are spreading in a community.”

Sharara said sewage testing is becoming more important to tracking the pandemic as more people rely on at-home tests to find out if they’re infected.

“Everyone who takes an at-home test, this positive result is not reported in official statistics,” she said.

Sharara said wastewater data has also proved useful to schools, nursing centers, and other institutions.

“Hospital systems also have used it, especially when the trend is going upwards,” Sharara said. “For resource allocation, how many nurses are we going to need? How many beds are we going to need? Should we cancel procedures or not?”

Here in Washington, sewage has been put to good use in some places.

In the town of Lynden, churches shut down and Lynden Christian High School stopped after-school activities after finding Covid in wastewater in 2020.

“We see these big trends in sewage data prior to that big increase in caseload,” said Oostra, whose firm tested Lynden’s wastewater.

In 2021, a spike in sewage coronavirus led Lynden officials and the chamber of commerce in the conservative town to encourage more voluntary safety precautions. Oostra said learning of the virus in their local wastewater made the pandemic more real to a lot of people in Lynden.

Lynden stopped sewage testing in October after federal funding ran out. Now, the Food and Drug Administration has launched sewage testing in agricultural areas, including Lynden and Shelton.

State and federal agencies are tracking outbreaks of Covid variants in 21 states, with the aim of protecting farmworkers and the food-supply chain.

“We did see early on in the pandemic that our agricultural workers were really disproportionately affected by the virus and that really did impact the food supply,” said Amber Betts with the Washington state Department of Agriculture.

Microbiologist Scott Meschke is part of the new effort to spot Covid variants in Lynden.

“We're trying to identify them sooner rather than later,” Meschke said.

Unfortunately, he said, researchers weren’t able to catch the initial onset of the omicron variant there because of problems with shipping.

“We all think of FedEx as giving us that overnight delivery,” Meschke said. “But for the last three weeks of sampling, we've had delayed shipments, both ingoing and outgoing, which has confounded our sampling.”

Cascadia Daily News reports hundreds of customers complaining of lost and delayed packages at FedEx’s Northwest Washington hub in Burlington.

In Whatcom and Mason counties, farmworker advocates say they’ve never heard of the sewage monitoring effort that’s supposed to benefit their communities.

“I think it's great that they're testing the sewage water,” said Rosalinda Guillen with Community to Community Development in Bellingham. “But we are not being considered as equitable community members that need to be notified that these efforts are going to be taken.”

Food and Drug Administration spokesperson Veronika Pfaeffle declined to be interviewed but said by email that the agency doesn’t expect results from variant tracking in Lynden and Shelton until May at the earliest.

Where this pandemic will be in May is anyone’s guess. Whether it has receded or yet another Covid wave has washed over Washington, our poop will always be there to reveal what viruses may be spreading through our communities.

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