How our sewage could warn us of future outbreaks of coronavirus

Down a gravel pathway, past a scattering of needle caps and food wrappers and beneath a graffiti-sprayed overpass for Tacoma’sEast 32nd Street, lies a portal into the public’s health.

For millennia, sewer systems have carried off waste and disease. More recently, they’ve drawn coronavirus-searching scientists in their wake.

On a Friday last month, Chad Atkinson, a senior environmental technician for Tacoma, lifted up a maintenance hole cover with a metal hook.

The stench of decomposition pricked the nostrils as a flashlight beam illuminated a stream of untreated wastewater flowing past globs of fatty muck below.

The waste of some 17,000 Tacoma residents drains through this site, including sewage from several retirement communities and the nearby Emerald Queen Casino.

Senior environmental specialist Steve Shortencarrier jabbed an extendible pole into the sanitary sewer, rubbed an attached shop towel on the sludge and pulled it to the surface.

Then, Gina Chang, a student intern volunteering with a nearby biotech laboratory, dabbed and twisted a pair of swabs on the soiled towel, before snapping the samples off into vials with preservative liquid for testing.

“The nastier, the better,” Chang said of the samples. “If it’s ripe, it’s good.” Chang is one of many researchers involved in an international and fast-developing hunt for sewer system clues to the virus that causes Covid-19.

Scientists say developing methods to test and track remnants of the virus in wastewater and sewer sludge could help build an early warning system for future COVID-19 outbreaks, help epidemiologists understand trends in infection and lead to a better understanding of the virus’s reach in communities with less access to clinical testing.

Researchers have monitored for viruses like polio in wastewater for years, but the coronavirus is new, and while studies indicate scientists can find its genetic fingerprints, they’re still sorting out what that means and how it could help contain the disease.

“Covid-19 is in our community and circulating the drainage in our sewer,” said David Hirschberg, founder of the RAIN Incubator for biotechnology, which is leading the testing in Tacoma. With that information, “What do you do now?”

Scientists sampling and testing the sewers are not, necessarily, finding live virus or even enough virus to infect humans.

Rather, they’re identifying the presence of the genetic signal of SARS-CoV-2, the virus that causes Covid-19, through ribonucleic acid (RNA), which ultimately breaks down in the environment.

“RNA doesn’t last very long outside of a host or a body or a cell,” Hirschberg said. But in sewage, “there’s enough fat in there or organic material that allows parts of it to exist without being degraded.”

The virus’s genes, of course, are transported into wastewater by human feces, where they intermingle with everything else in the system.

“It shows up and sheds pretty commonly and sheds in pretty high concentrations in human stool,” said Jordan Peccia, a professor of chemical and environmental engineering at Yale University who is examining wastewater sludge for remnants of the coronavirus in Connecticut.

That makes sewage a convenient method for sampling communities broadly and at once.

“Everybody on average passes a stool sample each day that is conveniently flushed down a toilet and transported, within typically two hours, to a wastewater treatment plant,” Peccia said, referencing his work in Connecticut. “It’s a low-cost, pretty easy surveillance method.”

And there might be nothing more egalitarian than the sewer system.”When you measure the sewage, you measure everybody – not just the wealthy,” Hirschberg said, noting that inequalities in the health care system have created disparities in access to clinical testing and that Covid-19 disproportionately affects people of color. “Sewage is a way to unbiasedly test populations.”

The nascent scientific work produced by sewer sleuths across the world is emerging quickly, but it remains messy, and these promising ideas offer as many questions as answers.

Are samples representative of upstream populations? Could the concentration of RNA detected indicate how many infections are spreading in a community? How precise are sewer tests? How much, and how quickly, does the genetic material decay in water?

Scientists don’t yet know for sure. “It’s the wild West right now,” said Scott Meschke, a professor of environmental and occupational health sciences at the University of Washington who specializes in environmental pathogens and has been testing samples of raw wastewater from King County’s treatment plants each week to determine the most consistent analytical methods for detecting the virus. “Everything is happening in parallel.”

A peer-reviewed study conducted in the Netherlands, which began sampling before Covid-19 had spread to some Dutch communities, identified the virus’s RNA six days before the first clinical cases were reported in one Dutch town.

Peccia’s team at Yale published a paper, which has yet to be peer-reviewed by other scientists, that suggests the concentration of viral RNA in samples taken from a central wastewater plant in New Haven, Connecticut, was a “leading indicator” of an outbreak’s course.

Peccia said the rise and fall of clinical testing data and hospitalizations correlated to sample concentration data collected days earlier.

A Barcelona scientist suggested Covid-19 emerged earlier than thought after his preliminary study reported he had found the virus in a March 2019 wastewater sample, according to The New York Times. Independent experts doubted the claim, the newspaper reported.

Other scientists have attempted to extrapolate the number of Covid-19 cases in communities based on wastewater samples, which has drawn skepticism.

“Some folks are over-interpreting,” Meschke said of the research. “The peer review process will help.” The Tacoma researchers are exploring a novel approach they hope could inform public health decisions.

About an hour after the sewer sample was plucked from beneath the Tacoma overpass, research technician Darrell Lockhart sat before a biosafety hood and gingerly used a pipette to mix samples with a solvent solution and begin analytical testing that targets genetic sequences.

Workers and volunteers at the RAIN Incubator laboratory in Tacoma, a nonprofit hub Hirschberg founded in hopes of sparking a biotech renaissance in Tacoma, each week gather and process about eight samples – five from nearby sewer sites and three from Tacoma’s wastewater plants.

The RAIN scientists are skeptical that wastewater data can foretell how many people are infected with Covid-19, and merely seek to determine the presence or absence of the virus.

“This is a binary signal,” said Stanley Langevin, a virologist and principal scientist at the incubator. “That’s why you have to go into sewers for resolution.”

Central wastewater plants process tens of thousands of people’s waste, but increasingly small branches in the sewer system offer a more specific and narrow perspective.

“Some drain neighborhoods, some drain shopping malls, some drain from schools, hospitals,” Hirschberg said. The smallest branch the team is currently sampling comprises about 1,500 residents, Hirschberg said.

“The more signals we have, the more likely we can understand the parameters of the outbreak to put prevention measures to stop it,” Langevin said.

Langevin harbors doubts over whether a vaccine can be developed for Covid-19, and believes Washington state does not perform enough clinical testing nor contract tracing to contain the outbreak. (Hirschberg is more bullish on a vaccine, but skeptical it will be developed soon.)

The RAIN scientists believe public health officials could use wastewater data to marshal resources to affected areas before people start showing up sick at hospitals.

“We have to have a way to narrow the population,” Langevin said. “This can be an early warning.”

As US case numbers rise quickly and as many expect a worldwide second wave of Covid-19 cases, the Water Research Foundation has asked some 30 laboratories pursuing this research to share and compare methodology for a study it’s leading.

“We want to have greater confidence in the methods,” said Peter Grevatt, chief executive officer of the international nonprofit research foundation. Grevatt said the organization will lead a second study that focuses on how and when to sample, and how the genetic material moves or degrades in sewers.

“It needs to be reined in a bit to make good public health use,” Meschke said of the research environment. Could what’s flowing through the sewers one day drive governments’ Covid-19 responses?

By fall, the Netherlands plans to establish a Covid-19 sampling program for every wastewater treatment facility in the country, Grevatt said.

Washington State is not moving with the Netherlands’ haste.

The state Department of Health did create an informal group to look into wastewater monitoring for the virus that causes Covid-19, said Ginny Streeter, a spokesperson for the department.

“There is definitely an interest in this type of testing at the agency and more broadly, the state response. That being said, the current priorities are really on more established tools such as clinical testing and contact tracing,” Streeter said. “We do have constraints on resources.”

To Grevatt, the promise of testing the pulse of an entire community at once with only a handful of samples is worth pursuing.

“Wastewater has a story to tell,” he said.