How Wastewater Could Help Track the Spread of the New Coronavirus

The virus that causes COVID-19 is unlikely to remain active in sewage, but its genetic material can still help researchers identify at-risk communities

Sampling wastewater could give scientists a new way to track the spread of the new coronavirus. Ivan Bandura / Unsplash

SARS-CoV-2, the virus that causes COVID-19, typically enters a person through the eyes, nose or mouth. But once it’s established itself in the airway, the pathogen doesn’t always stay in the respiratory system.

Recent evidence suggests that the new coronavirus may able to spread to sites throughout the body, such as the intestines. The virus could then use the gut as a jumping-off point to enter some patient’s feces, where researchers have detected its genetic footprint.

Experts aren’t yet sure whether SARS-CoV-2 can survive in stool or wastewater, or whether feces could constitute another way for COVID-19 to move from person to person. Health officials maintain that the risk of this mode of transmission is low.

But as researchers race to find answers, the SARS-CoV-2’s fecal signature could actually turn out to be a weapon to wield against COVID-19, helping track how and where disease is spreading. By analyzing bits of the virus’ genetic material in sewage, scientists may be able to identify the populations most at risk of infection—and most in need of lockdown—without painstakingly sampling every person, especially while individual tests remain in short supply.

Not everyone can get a diagnostic test. But everyone poops.

“This is an opportunity … to better understand the prevalence [of the new coronavirus],” says Andrea Silverman, a civil and urban engineer specializing in wastewater treatment at New York University. “The potential benefits are huge if you’re able to sample the whole community at once.”

A journey through the body

SARS-CoV-2 moves from person to person mainly through droplets that emerge when an individual coughs, sneezes, speaks or perhaps breathes. Since the early days of the outbreak, it’s been clear that the virus can also leave its calling card in feces. But whether COVID-19 can spread this way remains an open question.

Researchers and doctors have found large amounts of SARS-CoV-2’s RNA, or genetic material, in fecal samples taken from infected patients, says Saurabh Mehandru, a gastroenterologist and immunologist at Mt. Sinai’s Icahn School of Medicine. These genetic signatures can linger long after the virus itself has been destroyed. In the instances where scientists have looked for viable viruses in stool, some, but not all, have found them.

The Centers for Disease Control and Prevention and World Health Organization say the risk of the virus spreading through feces is low. No COVID-19 cases involving exposure contaminated stool been reported so far.

Still, there is not yet consensus whether SARS-CoV-2 can exit the body unscathed—just that “the possibility is real,” says Lijuan Yuan, who studies enteric viruses at the Virginia-Maryland College of Veterinary Medicine. To figure that out, researchers will need to survey the stool of many more patients and conduct controlled experiments on animal models and cells cultured in laboratories.

Perhaps these pieces of SARS-CoV-2 RNA are just debris—remnants of viruses swallowed from the airway into the gut, where digestive chemicals and enzymes ripped them to shreds. But should a virus survive this perilous journey through the GI tract, it could theoretically infect intestinal cells, which display the same surface protein that the new coronavirus uses to enter cells in the airway.

Mehandru says intestinal SARS-CoV-2 infections seem plausible simply because of the sheer volume of RNA found in some fecal samples. But the new coronavirus is shrouded in a delicate, fatty outer layer called an envelope that makes the pathogen sensitive to harsh chemicals—like what you’d find in a human’s GI tract. “It’s a very hostile environment,” he says. “It’s very possible the virus could be damaged in transit.”

If SARS-CoV-2 does occasionally seed a satellite population in the bowels, that might explain why around a third of COVID-19 patients have symptoms like nausea and diarrhea. From this stronghold in the gut, viruses—or at least their genetic material—could then be excreted into feces, Mehandru says, hitching a ride out of the body.

Signals in the sewer

Regardless of whether active SARS-CoV-2 persists in human waste, the presence of its RNA in stool could be a boon for disease surveillance. Around the world, researchers are now turning to wastewater monitoring as a means to track the virus’ prevalence in urban and suburban communities.

In areas where toilets are connected to sewage systems, flushed waste gets consolidated into progressively larger pipes en route to a water treatment facility. Sampling anywhere along this path could give researchers a quick and fairly comprehensive snapshot of health in a given city, borough or neighborhood, Silverman says.

Finding SARS-CoV-2 in sewer water works much like a diagnostic test for human patients. Researchers extract genetic material from wastewater, then search for a stretch of RNA exclusive to SARS-CoV-2. Public health officials have previously used similar forms of surveillance to keep tabs on flare-ups of polio, hepatitis A, norovirus and even antibiotic resistant strains of bacteria.

The strategy may prove especially useful for COVID-19, given that large-scale patient testing has continued to stall. Some infected individuals may start to shed bits of SARS-CoV-2 into stool before they feel symptoms (if they ever do at all), says Aaron Packman, a civil and environmental engineer at Northwestern University. Homing in on these sewage-borne clues could help pinpoint people who might be unknowingly spreading disease or give hospitals advance notice of an impending outbreak.

Early results appear to bear out this theory. Researchers sampling a wastewater treatment plant in the Netherlands found that viral RNA had entered local sewers before the city had reported any confirmed cases of COVID-19. A survey in Massachusetts discovered higher-than-expected concentrations of SARS-CoV-2 genetic material in local sewage, hinting that far more people had been infected with the coronavirus than were identified by testing.

How Wastewater Could Help Track the Spread of the New Coronavirus
Wastewater treatment facilities consolidate material from thousands or even millions of people, giving researchers a snapshot of an entire community's health status. Marcin Jozwiak / Unsplash

Silverman cautions that the technique is still being refined, and is not yet precise enough to determine how many infected individuals are in a given wastewater zone. To achieve that amount of resolution, “we’d need to know how much viral RNA each person is excreting,” she says. But that amount may not be consistent from person to person and may fluctuate over the course of the illness. For now, scientists are widening their lens to monitor broad trends in how viral RNA levels ebb and flow over time.

“If you start seeing the virus, that’s an early warning that there needs to be an intervention,” Packman says. Conversely, the gradual decline of the pathogen in a city’s wastewater might signal to local officials that a lockdown is working, helping inch residents along a tentative path toward reopening.

Virginia Pitzer, an epidemiologist at Yale University, says wastewater monitoring will help allocate tests and other limited resources to the places that need them most. “It’s easier than going out and testing everybody in the population,” she says. But once a community’s sewage water tests positive, researchers still have to figure out who is and isn’t harboring the coronavirus in their body. “This isn’t a replacement for individual testing,” Pitzer says.

Universal clean water

If it turns out the new coronavirus can spread through feces or contaminated water, the risks are exceedingly low in parts of the world with good sanitation. Because wastewater is typically treated with harsh chemicals, SARS-CoV-2 stands little chance of persisting in sewage, Silverman says. Besides, viruses must infect living cells to replicate. If they can’t locate a target, they fizzle out.

However, experts worry that people who live in places lacking adequate sanitation may be at greater risk of contracting the virus from wastewater. “The focus of all our containment measures have been very local,” Packman says. “Water is a long-distance transmission pathway. It can spread disease much faster than you’d expect.”

Other coronaviruses that infect animals like pigs are known to transmit through feces. Stool may have also played a small role in a handful of cases of the SARS outbreak that began in 2002, says E. Susan Amirian, an epidemiologist at Rice University. Several people living in an apartment building in Hong Kong were likely infected when a faulty sewage system aerosolized a plume of excrement.

To date, there is no evidence that the same will be true for SARS-CoV-2. But “if any virus is excreted in its viable form in feces... there’s definitely concern for the billions of people who don’t have access to sanitation,” Silverman says. This basic necessity is especially scarce in places like sub-Saharan Africa, southern Asia and eastern Asia.

Even in the United States, not everyone can regularly tap into a clean water supply. And many of the communities where clean water is scarce are already more vulnerable to disease because of infrequent access to medical care, overcrowding and higher rates of other health conditions. They’re also at risk of contracting the many pathogens known to be ferried from place to place by contaminated water. Many of these concerns have been highlighted in the Navajo Nation, where the number of COVID-19 cases and deaths continues to swell.

“We’re going to come out the other side of this pandemic with greater disparities between the haves and the have nots,” says Matthew Miller, a biologist at the University of Oklahoma. “That’s a very sobering reality.”

Get the latest Science stories in your inbox.