Wastewater is trying to tell us something about the future of COVID, polio, monkeypox, and the next epidemic to come

The method of community disease monitoring that has proved so useful during the COVID-19 pandemic is now coming in clutch in the global monkeypox outbreak, in addition to flagging potential polio epidemics. What else is it capable of?

Molecular biologist Emanuel Wyler examines wastewater samples for pathogens in the safety laboratory at the Max Delbrück Center for Molecular Medicine in Berlin. From the amount of bacteria and viruses found, conclusions can be drawn, for example, about the frequency of coronavirus infections. Bernd von Jutrczenka—Picture Alliance/Getty Images

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“The danger of polio is present in New York today.”

The statement seems ripped from the headlines during the 1916 New York polio epidemic, which killed 6,000—mostly children—and paralyzed 27,000 in just four months.

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“The danger of polio is present in New York today.”

The statement seems ripped from the headlines during the 1916 New York polio epidemic, which killed 6,000—mostly children—and paralyzed 27,000 in just four months.

But it was made just last week, by New York State Health Commissioner Dr. Mary Bassett, after the identification of poliovirus in both Rockland and Orange counties in June and July. New York City health officials on Friday announced the presence of the virus in wastewater there as well.

Health officials were recently notified of an unvaccinated Rockland County resident diagnosed in July with the potentially disabling and even deadly virus, which famously paralyzed President Franklin D. Roosevelt from the waist down. Most people with the virus don’t display symptoms. A handful present with flu-like complaints, but only one in roughly 100 develops serious side effects like paralysis

Public health officials likely wouldn’t be aware of wider spread so soon if it weren’t for wastewater surveillance, which some say is a bit of a crystal ball when it comes to identifying epidemics and pandemics to come. The technology rose to prominence during the beginning of the COVID-19 pandemic, and public health officials are now turning to it to try to gauge the true spread of monkeypox, with its sometimes atypical symptoms and spread. We wouldn’t know polio was spreading if not for it, either.

“In some regards, wastewater is a public health dream scenario,” Dr. Mark Siedner, an infectious disease doctor at Massachusetts General Hospital and associate professor at Harvard Medical School, told Fortune.

“Everyone poops, and most people poop every day. It provides real-time data on infection rates. In that regard, it’s an extremely powerful tool, particularly good at detecting early warning signs.”

“Before people get sick, we might get a signal.”

When toilets are telltale

Consider wastewater: a repelling reality of human existence with the blessed potential to warn public health officials of unexpected pathogens in the community—perhaps before cases present in doctor’s offices and emergency rooms. 

Global health emergencies like COVID-19 and monkeypox may seem like a new phenomenon, but they’re not. Such scourges typically occur at least once every quarter or half century—and they’re bound to become more frequent as climate change forces animals and humans into more frequent contact, experts say. And wastewater pathogen surveillance has a long history, too, dating back nearly 100 years. It was used to monitor for polio in the 1940s and hepatitis A in the 1980s, but in limited circumstances and capacity. It began to gain traction after the turn of the century, when it was used to monitor prescription and illicit drug levels, track the flu, and again, in efforts to detect and contain “silent” polio outbreaks.

But COVID-19 was its moment to shine.

Early in the pandemic, scientists discovered that SARS-CoV-2, the virus that causes COVID-19, is shed in fecal matter. Scientists increasingly began to rely on it as testing failed to meet demand. Soon it was picked up by colleges, in an attempt to rein in large outbreaks, then cities and states.

Less than a year into the pandemic, it had gained enough recognition that the U.S. launched the National Wastewater Surveillance System, which works with local health departments to track COVID levels throughout the nation.

Nearly three years into the pandemic, rates of traditional PCR and antigen COVID testing are abysmally low, and at-home test results are rarely reported to public health departments. This has put the U.S. and other countries with similar testing trends in a situation many experts have equated to “flying blind”—at a time, no less, when the most transmissible, immune-evasive COVID variant yet, BA.5, is sweeping the world.

Wastewater has become scientists’ eyes. Thanks to it, we know that COVID was recently at or near record highs in many locations in the U.S., including California’s Bay Area and Coeur d’Alene, Idaho.

“The levels we’re seeing in wastewater at a number of plants we monitor—and other plants around the country we don’t—are just as high or almost as high as they were during the first surge in January,” Alexandria Boehm, professor of environmental and civil engineering at Stanford University, told Fortune in July.

Stanford and Emory University have partnered with Alphabet-owned Verily, a precision health company formerly known as Google Life Sciences, to offer wastewater reporting of pathogens like COVID-19 for free to interested sewage treatment plants in the U.S.

The partnership started with reporting levels of COVID-19, flu, respiratory syncytial virus (RSV), and human metapneumovirus, another upper respiratory virus, in participating communities, which now number around 40.

It just recently added the ability to screen for monkeypox, given the global outbreak, and will soon have the ability to report which of two widely circulating monkeypox variants are more prevalent in a community, just as it reports on COVID-19 subvariants.

“As a scientist, I’m trained to be skeptical and test the null hypothesis that things don’t work—and wastewater again and again is proving to be a really amazing resource for probing infectious disease in the community,” noted Boehm.

Boehm said she’s amazed at how well levels of infectious diseases in wastewater correlate with those traditionally diagnosed in communities—even respiratory illnesses like flu and RSV, which one might not expect to find traces of in wastewater.

She’s hoping that levels of monkeypox in wastewater prove just as useful—but the jury is still out, as scientists can’t be sure if wastewater levels are predictive until they have a good handle on the presence of the disease in a community from traditional testing.

“What we can say is we know if we get a positive [in a community], at least one person is infected and excreting,” she said, adding that those with monkeypox shed virus via respiratory secretions, urine, feces, and open sores. “We can also look at trends and see if concentration is going up or coming down.”

‘Great for broad brushstrokes’

The handy thing about wastewater is that it’s nearly impervious to changes in human behavior, or hurdles to obtaining health care.

Regardless of whether someone knows they need to be tested for a disease—whether or not they want to get tested, are able to obtain a test, or report the results of an at-home test—their infection will be recorded, because, as people do, they’ll bathe, shower, brush their teeth, and use the restroom.

“Humans don’t have to opt in to their excretion going into the wastewater the way they’d have to when they go get a PCR test,” Boehm said. “They don’t have to make an appointment, drive there, wait in line, get that thing stuck up their nose.”

“If you’re hooked up to the system, your information is getting recorded in wastewater.”

It’s not perfect, however. Some pathogens, like group A Streptococcus, which causes strep throat—can’t be tracked in wastewater, Siedner said. In fact, many bacteria cannot be.

And while a positive result from wastewater alerts public health authorities to the presence of disease, it doesn’t alert them as to who is sick, and where, so they can intervene.

“It’s great for broad brushstrokes and early warning signs, but it’s not great if more detailed data is needed,” he said.

A lack of consistency in testing nationwide also hampers the potential utility of wastewater. Some areas don’t test, and not all areas that do test for the same pathogens, experts say.

Further, “you have to know what you’re testing for in wastewater” in order to find it, meaning it’s not a tool that can be used to detect new pathogens with pandemic potential, said Dr. Howard Forman, a professor of radiology, biomedical imaging, and public health, at Yale School of Medicine.

“In hospitals patients are only checked for whatever their symptoms are. Wastewater, I still think it really varies by location what people are testing for. I do think it would be great to have broader screening.

“It would be great if we had the type of analytics that would allow us to screen for every possible virus.”

Divining sewage

The knowledge afforded by wastewater does, however, allow public health workers to “move in rapidly” and promote prevention.

“People tend to be more receptive to immunizations when they see the threat, versus when they think it’s for some public health purpose.”

Dr. Morgan Katz, an infectious disease specialist at Johns Hopkins Bayview Medical Center in Baltimore and assistant professor at Johns Hopkins School of Medicine, told Fortune that wastewater alone is insufficient for community disease surveillance because it doesn’t provide the exact number and location of those with the disease. But it augments traditional methods like PCR and antigen testing, she said.

“It is a complement to our existing surveillance systems and a great way for us to get a marker of a brewing outbreak before we start seeing a lot of people with symptoms,” she said. It can be “particularly helpful in college dorms, nursing homes, or other congregate living facilities where it is particularly important to identify a developing outbreak early.”

While wastewater offers an incomplete view of community disease spread, it does offer invaluable insights.

One recent takeaway: Monkeypox could easily end up in “pretty much every major metro in the U.S.,” Bradley White, a senior scientist at Verily, recently told Fortune.

A look at the partnership’s monkeypox heat map, which displays data for its nearly 40 U.S. testing sites so far, shows levels spiking in California’s Bay Area, as well as monkeypox presence in Parker, Colo.; Roswell and College Park, Ga.; Coeur d’Alene, Idaho; Ann Arbor; and Garland and Sunnyvale, Texas.

“There’s clearly some spread going on across the entirety of the U.S.,” White said. “It seems like eventually this will probably get everywhere—something we had hoped stays isolated doesn’t seem like it will.”

One silver lining of the COVID-19 pandemic has been that it’s highlighted the utility of wastewater surveillance, and the ability to spot and potentially stop breeding outbreaks early on.

Using the same setup and even samples it was using to test for COVID-19 and subvariants, RSV, and flu, Verily was able to quickly pivot and add testing for monkeypox. It will soon add a test that determines which variants of monkeypox are appearing in local sewer systems and may add an assay for polio, if staff at local public health agencies ask for it, Boehm said.

“It’s the future, and a resource we haven’t yet taken full advantage of.”

The pandemic certainly did its part to make wastewater testing “vogue,” Siedner said. “It wasn’t something routinely done before. It’s a very creative tool. Hopefully, as we think about the lessons we’ve learned from COVID-19 and how to strengthen our public health systems, one thing that will be elevated will be wastewater detection. 

“It may be the way of the future.”