Skip to main content

For the Delta Variant - and Future Threats - Scientists Eye the Toilet

Wastewater disease surveillance has gone mainstream, say experts, and it holds the potential to spot known and unknown infections among travelers, students and more.
  • Author:
  • Publish date:

Sunlight has always been touted as the best disinfectant, but when it comes to spotting disease-causing pathogens like the novel coronavirus, scientists are increasingly looking where the sun doesn’t shine: human feces.

Throughout the pandemic, the practice of wastewater-based epidemiology has rapidly advanced, as researchers around the world have been racing to devise new ways to detect SARS-CoV-2 – the virus that causes COVID-19 – in sewage. The work by university scientists, public health officials, governments and private companies over the past year and a half since the outbreak began in China has become so precise that even in major metropolises like New York City and Hong Kong infections with specific variations of the virus – such as the delta variant – can be identified before patients start showing up in emergency rooms. Advances in this sewage-monitoring technology now stands to help shape our ability to stave off future outbreaks. It even holds the potential to help alert health officials of infected passengers on global flights and cruises, spot sick students at college campuses and pinpoint novel threats among residents of entire cities.

“In theory, you could potentially detect any pathogens present – given that they are in high enough concentrations,” said John J. Dennehy, a professor of biology at Queens College and the Graduate Center of City University of New York, in an email exchange with TheStreet.

Dennehy, who is working on wastewater monitoring projects with the city, is one of many scientists around the world helping to create new methods of virus detection. His colleagues have come up with a pasteurization procedure that could broaden the ability for SARS-CoV-2 monitoring by making the waste safer to work with.

Others, meanwhile, are advancing techniques in different ways. In Tokyo, Shimadzu Techno-Research Inc. is offering polymerase chain reaction tests on raw sewage running from buildings that could notify health officials of people with the novel coronavirus infection. And in Hong Kong, which has relied heavily on sewage monitoring for SARS-2, Tong Zhang, a professor at Hong Kong University’s Department of Civil Engineering, has helped develop a new testing method that can identify specific variants in sewage. His work that was used largely in Hong Kong's fourth wave, has already helped spot dozens of COVID-19 cases in the city that has largely kept the pandemic at bay. 

In the U.S., local elementary schools in states like Texas, Michigan and Washington have also started surveillance systems, and so have university campuses around the country. In a national effort to expand the testing, the U.S. Department of Health & Human Services recently tapped Massachusetts-based company Biobot Analytics to create a national disease surveillance program for COVID-19 that will include collecting and analyzing samples from hundreds of wastewater treatment plants serving about a third the population. The same company had throughout the pandemic played a role in giving early warnings of cases in Massachusetts and elsewhere.


Bringing the publicly available data together from the various projects around the globe is a team of researchers at the University of California at Merced’s Department of Civil and Environmental Engineering. The group, led by Colleen C. Naughton, an assistant professor in the department who focuses on water health and sustainability,  created a disease-tracking site called COVIDPoops19 which can be found at, and is modeled after the COVID dashboard by Johns Hopkins.

“Through the COVIDPoops19 dashboard, we have a record of some monitoring in all 50 U.S. states,” said Naughton. “We have this network and hopefully we can build on it to monitor future pandemics.”

The Potential of No. 2

While experts are still trying to digest the current state of the research, several say future tracking systems could be expanded to detect many other types of pathogens, known and unknown, in many types of waste sources – ships, hotels, apartment complexes and beyond. 

Viruses like norovirus and sapovirus, and those causing hepatitis; bacteria like cholera, salmonella, and E. coli;  and protozoa like giardia and cryptosporidium, could potentially be monitored, said Dennehy. In the past, systems have been used for tracking polio virus and toxins such as opioids.

“If you just sequenced everything and did not specifically amplify, you would get sequences from everything in that sample. You could then map that pool of sequences to known sequences, and fish out anything that resembled a known pathogen,” said Dennehy. “Even better, there are some methods that you can specifically enrich for viruses and eliminate” other pathogens.

Prof. Zhang in Hong Kong, agrees that the advances in research could be used for spotting many other pathogens. Generally, he said, as long as a virus is discharged into a sewage system from people or animals, the principles and basic methodology used in SARS-2 detection could be used for other bugs.

Fernando Adali Roman, Jr., a recent graduate from the Environmental Engineering program at UC Merced, is pictured over a manhole with a printout of the COVIDPoops19 dashboard.

Fernando Adali Roman, Jr., a recent graduate from the Environmental Engineering program at UC Merced, is pictured over a manhole with a printout of the COVIDPoops19 dashboard.

Even more promising is that the work can be highly accurate, researches say. The projects that Dennehy works with, for example, can sample from watersheds that have flow from tens of millions of gallons per day of wastewater serving hundreds of thousands of people.

“At the other end of the scale, we sample from a campus dorm, and we've been able to detect a single positive case,” Dennehy said.

Another advantage is that people with no or few symptoms of diseases such as COVID can be found, because they still shed evidence of the virus in waste. These people would likely be missed by traditional screening tools like temperature taking and symptom checklists. 

“There are several examples," he said, "where the presence of SARS-CoV-2 has been detected in wastewater prior to clinical cases appearing in the same area.”

The possibilities of where to test are many, too, say experts. A study by Australian researchers last year found that surveillance of wastewater from large ships and aircraft with their own sanitation systems “has potential as a complementary data source to prioritize clinical testing and contact tracing among disembarking passengers” and could help spot pathogens such as SARS-CoV-2 infections among passengers.

“Imagine you have an aircraft carrier with 5,000 sailors. Do you want to test each sailor individually each week or test all sailors simultaneously with one assay? If you get a positive hit, then you can initiate a lockdown and subsample to identify the infected sailors,” said Dennehy.

Testing for viruses like SARS-CoV-2 and its variants could be used at hotels if there is a suitable sampling site, added Zhang. This could help officials spot imported cases of pathogens before they lead to local -- or national --outbreaks.

That Stinks: Limits Remain

But there are limits, ethical questions and obstacles to the technology. For one is funding. While the past year has seen an explosion in support for COVID-19 research, questions remain over how much the public will want to back funding for work on future disease threats they can't see.

“A lot of people have become trained and know the methods” over the past year, said Naughton, but she suggested, they may leave the field as demand dries up and the COVID pandemic passes.

In addition, the data in use is variable, many researchers are using many different methods, and only a small fraction of all the sewage monitoring data around is even publicly available.

“There are quite a few different methods to accomplish the same objective,” said Dennehy. “Right now, there's a lot of noise and unclarity on what is the best approach.”

Contradictory results could be caused by different types watersheds – such as industrial vs. residential. Some sources might get diluted by rain or an evidence of pathogens can become degraded by detergents or other chemicals.

The work can be labor intensive, too. People might be taking samples in poorer countries while in other rich ones robots are used. And while experts agree great potential exists for where to test – both in big cities and in small apartments and even on commercial transit – testing on places like international aircraft and at airports could be give false negatives because of their sanitation systems and because some people might skip using the toilet. At the same time, ethical and legal problems could come into play. 

For example, pointed out Naughton, if tests could zero-in on individual travelers on aircraft or cruises, their health privacy could be compromised. Also, if testing were conducted for drugs or illegal substances, it could open a legal and ethical can of worms.

And most agree that sewage surveillance should be used as a complement to other forms of disease watching and not as the only method.

“Others in the field and myself like to emphasize, wastewater testing isn't a silver bullet and needs to be combined with other preventative measures, clinical testing, and genomic sequencing,” said Naughton. Still, she said, wastewater monitoring shows great possibilities for spotting other novel pathogens – and for detecting antibiotic resistance, which she refers to as the “silent pandemic.”

It’s a technology that, she and other experts agree, should not go to waste.

This story has been updated.