Sewage testing gives clues of coronavirus

Scientists looking for new ways to identify potential coronavirus outbreaks are turning their attention to what could be an early warning sign: the stuff you flush down the toilet.

New studies increasingly show that the coronavirus’s genetic code can be detected in the remnants of fecal matter that flows through sewers and into sewage facilities, either in raw wastewater or in what is euphemistically known as sludge.

The genetic information represents such a good cross-section of a city or region that taking just a few samples can be the equivalent of testing millions of people in a given day. Using one method, just 14 samples could test the prevalence of the virus in all of New York City.

“In the same way that we can understand the health of an individual by looking at urine and stool, we can also do it at the city level,” said Newsha Ghaeli, the co-founder of Biobot, a Massachusetts-based wastewater epidemiology startup.

Sewer systems work as well or better than any other type of community surveillance network, experts said, because so many people are connected to one. About three-quarters of the U.S. population are connected to their local sewer systems.

“We all know that we have this billion dollar infrastructure in all of our cities called sewers,” said Jordan Peccia, a professor of chemical and environmental engineering at Yale who led a team studying the coronavirus in New Haven’s sewer system. “We’re all giving a sample to the wastewater treatment plant every day.”

More importantly, the testing represents more than simple confirmation of the presence of the coronavirus. The amount of RNA extracted from the sludge can show how prevalent the virus is in a community, effectively building an epidemiological curve that can show prevalence of the virus rising or falling as much as a week before those who are infected test positive or show up at the hospital.

That added time can give cities, states and regions the ability to see an outbreak coming, long before anyone begins developing symptoms.

“It’s a leading indicator, it seems to be ahead of cases and it’s ahead of hospital admissions as well,” Peccia said. “If I were a governor or a mayor, I would want to know that seven days in advance of what I already know.”

Biobot is testing about 400 wastewater facilities across 42 states, facilities that together cover about 10 percent of the population. They use samples sent from those facilities to test for the presence of the virus and to estimate just how widespread it might be in a given area.

The University of Michigan and Oakland University are tracking the spread of the virus in Detroit and Macomb County using similar techniques. Researchers in Spain and Australia have begun planning for nationwide sewage testing, and the United Kingdom is considering similar steps.

In a sign of just how valuable the genetic information can be, scientists in Holland detected the presence of the coronavirus at a wastewater treatment facility in Amersfoort on March 5, days before anyone in the city tested positive for the virus. Ghaeli said Biobot had detected initial cases in some American cities, though she declined to identify those cities for privacy reasons.

“We definitely believe that wastewater can be such a powerful early warning for the detection of COVID-19 cases,” Ghaeli said. “We need to be really mindful of how we are going to pick up an early warning of another outbreak, and so we think wastewater testing or sewage testing can be one of the surveillance tools in the toolkit that any governor can use.”

The testing has also raised questions about just how many people have been infected by the coronavirus, and just how many cases health officials have missed. In late March, when the Boston area had just 446 confirmed coronavirus cases, Biobot found enough RNA in sewage samples to estimate that as many as 115,000 people had been infected. 

Massachusetts soon became one of the epicenters of the outbreak in the United States. As of Wednesday, the state had reported more than 93,000 confirmed cases.

“What we’re seeing on average is that our case estimates are 10 times more or an order of magnitude higher than what’s been clinically reported in all of the communities we’re working with,” Ghaeli said. “It would suggest the case numbers a month ago were likely a lot higher than was reported.”

The process for collecting the samples is not a pleasant business. Solids that flow with wastewater into a treatment facility are separated from liquids in what is effectively a large colander. The end product is called primary sludge.

Those who work there “will all tell you the primary sludge smells worse than anything in a wastewater treatment plant,” Peccia said.

Fortunately for Peccia, the New Haven facility where his team got its samples is practicing social distancing, so staffers leave samples in a cooler outside. RNA is extracted from the sludge and amplified using a polymerase chain reaction, a common method of turning a few strands of RNA into millions or billions of strands so it can be detected by diagnostic equipment.

The process of sampling wastewater to find the presence of a virus is nothing new. The World Health Organization routinely uses the same method to identify potential polio clusters in developing nations. Like polio, the coronavirus is also present in feces. 

And it recalls some of the very foundational lessons of epidemiology, as when the father of the field, John Snow, traced a cholera outbreak in London to a single water pump on Broad Street in 1854.

“The people who thought of testing sewage points for Covid-19 are brilliant; they are tapping into an old tradition of using detective work to trace how infections spread,” said Prabhjot Singh, a physician and health systems expert at the Mount Sinai Health System and the Icahn School of Medicine. “Testing sewage from specific areas can serve as an early warning system of community transmission.”

Snow’s work inspired London, and eventually other cities around the globe, to install the first modern sewer systems to improve public health.

“We are big John Snow fans,” Ghaeli said. “He’s the grandfather of sewer systems and sewer infrastructure.”