Poop Could Be Our New Secret Weapon Against Mutant COVID Strains

There’s a golden opportunity to track deadly new variants of the virus in the sewers.
Gabriela Esparza and Zach Wu, wastewater control inspectors with EBMUD, cap 24 separate bottles while retrieving collection equipment and the samples in Oakland, Calif. on Tuesday, July 14, 2020.
Gabriela Esparza and Zach Wu, wastewater control inspectors with EBMUD, cap 24 separate bottles while retrieving collection equipment and the samples in Oakland, Calif. on Tuesday, July 14, 2020. (Paul Chinn/The San Francisco Chronicle via Getty Images)

The coronavirus mutants are here. And scientists say the U.S. should use a new weapon against them: your poop. 

America’s failure to track the rise of dangerous variants has left the country at risk of a new wave of sickness and death, with only vague estimates of where, and how quickly, they’re spreading. The so-called “UK variant,” which may be both more deadly and 50 percent more transmissible, is now thought to be doubling in infections in the U.S. every 10 days, and could become the country’s dominant strain by March. 


But public health experts say there’s an opportunity to track the spread, and it’s hiding in our sewers. Because everyone who catches COVID sheds virus fragments in feces and urine, a national program to monitor wastewater for virus mutations would help close the gap. 

“This is the most cost-effective, objective, and equitable approach we’ve got,” said Ted Smith, an environmental medicine researcher at the University of Louisville. “It’s far more convenient than shipping around swabs from labs.” 

A poop program powerful enough to meet the crisis wouldn’t be cheap. But it would hand experts an almost real-time map of where the new variants are spreading, allow authorities to surge resources to trouble spots, and help experts evaluate vaccine effectiveness at the community level and detect new strains even before they start sending people to the hospital. And it would help us all better predict how long we’ll be stuck dealing with this global crisis, experts told VICE News.

“There's a lot of utility in being able to understand, kind of as a sentinel surveillance system, what's going on within a community without having to go out and and stick a swab up thousands of people's noses,” said Patrick Ayscue, an epidemiologist and senior biosecurity fellow at the nonprofit Chan Zuckerberg Biohub. 

Into the sewers

The beautiful part about checking feces for coronavirus is that everyone poops, so you catch a lot that you’d otherwise miss. 

By design, such a system includes people who aren’t getting tested, either because they’re asymptomatic or only recently caught the virus, or they aren’t taking the pandemic seriously. 


A patchwork of communities around the country are already monitoring sewage for coronavirus. But these programs are focused on the amount of virus rather than the type. 

The University of Arizona tests wastewater coming out of individual dorms, in a program that allowed administrators to find three COVID-positive students during the first week of classes last fall, before they sparked a wider contagion. 

The city of Cambridge, Massachusetts, uses a wastewater testing system run by the private company BioBot to help determine whether schools should be open or shut. The city posts results on a website, which says that as of February 1, local wastewater contained 446 viral particles per milliliter.  

In these communities, wastewater testing has already proven it can spot problems early. 

“It’s not just a measure of how much there is right now; it’s also a measure of what’s coming,” said Nour Sharara, a public health expert at BioBot.

“As soon as people are infected, they start shedding the virus, before they start showing symptoms. Some people take five days to develop symptoms. But during those five days, we can already see it in the sewage, because it’s in their stool.”

To combat the new variants, the same technology would need to be ramped up and paired with a process known as “genomic surveillance,” which means analyzing samples to determine their strain.


Ramping up a wastewater genomic surveillance program could give authorities advance warning that a new, dangerous variant has spread to a particular location, so they can take action early. 

“If you found a town with a lot of the B117 [UK] variant, you could recommend more PCR testing, or say that all of North Cambridge should get N95 masks in the mail,” Sharara said. “That’s the hope.”

American toilets

American toilets weren't designed as portals to a biotech lab, of course—and the program would face some key challenges. 

For starters, in some places, the country’s aging sewer system would need a serious upgrade.

Testing wastewater for coronavirus generally involves inserting a device into a manhole to pull out samples of sludge at regular intervals—for example, 50 milliliters every 15 minutes. But the best access points are hardly located in ideal spots. In some towns, researchers might have to prop up manholes in the middle of Main Street to get the kind of access they’d need. 

Then, once researchers get the sewage, it needs to be evaluated. That process involves using computers to sift through enormous piles of genetic information, to separate the signal from the noise, according to Jared Auclair, who leads the genomic sequencing lab at Northeastern University. 

“The largest problem is the sheer amount of data,” Auclair told VICE News. “It's finding a needle in a haystack.” 


The cost of a national program could easily run into the hundreds of millions of dollars, if not billions, even though advocates say it’s worth the money.

The U.S. should allocate roughly 10% of its overall coronavirus testing budget to a new national wastewater program, said Smith. 

“In my opinion, there’s an unbelievable upside to making this investment,” Smith said.  

Such a program would help America’s catch the ground and time lost thanks to its dismal failure to track the spread of coronavirus mutations so far. 

The Trump administration simply never bothered to enact a robust national genomic surveillance program, and the country now lags far behind. The U.S. genetically analyzes less than 1 percent of all cases; experts say we should be analyzing at least 5 percent just to have an idea of what’s out there. The UK, Denmark and Iceland are closer to 10 percent. 

In addition to variants first identified in the UK, Brazil and South Africa, scientists have recently identified seven more variants in the U.S. that researchers are naming after birds in order to make them easier to remember. 

The so-called Robin 1 has spread to some 30 states, especially in the midwest. Another called Pelican was first found in Oregon and has since spread to 12 states. Others are being called Quail, Bluebird, Yellowhammer and Robin 2. 

Yet the real danger may be the variants that haven’t yet been identified—because we aren’t looking hard enough.

“The variants from South Africa, from the UK and from Brazil, you know, we're watching,” said Auclair. “But the ones that scare me the most? It's the ones I don't know about.”