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Tracking viruses: The best clues may be in the sewer

Wastewater testing has captured rising COVID levels and even evidence of polio. Can it predict new viral outbreaks?

Aerial view of four tanks at a wastewater treatment plant with green trees and large-scale equipment dotted around the landscape

Yogi Berra said it well: “It’s tough to make predictions, especially about the future.”

Though he wasn’t talking about viral infections or the current pandemic, he might as well have been. Even the best scientists, infectious disease specialists, and epidemiologists have found it hard to accurately predict when new viral outbreaks will appear (think COVID-19), when old ones will reappear (think polio), and how to figure this out in time to make a difference. But what if they could? An already available tool called wastewater testing shows promise — and how we use the results could help rein in the next COVID surge or predict the rise of a surprising new virus.

COVID: When can we expect the next uptick?

For months now, the US has recorded well over 100,000 new COVID-19 cases and 300 deaths each day. And actually, the number of cases is probably much higher because rates of testing have fallen and positive home tests aren’t included in official counts. With numbers like these and new variants emerging, further spikes in cases seem inevitable.

But when?

Perhaps in the next few weeks, as new and highly contagious variants spread. Or possibly in the fall and winter, as we spend more time indoors. Or maybe this virus will surprise us again and wait until next year to resurge.

One huge challenge in containing the COVID-19 pandemic is that by the time we know that infections are rising rapidly in a community, it’s already been going on for some time. Because people often have no symptoms initially, the infection can spread for a while without notice.

If we could predict when the next uptick will happen, it’s possible that we could take appropriate preventive measures. And that’s where your stool — feces, poop, whatever you prefer to call it — comes in.

Detecting viral outbreaks using wastewater

The idea is simple: when people have a viral infection, the virus can often be detected in their stool. Therefore, wastewater from a town or city, or perhaps a community, can be tested to see if virus is present and, if so, whether the amount is rising over time.

This approach has been used since the 1940s, when polio was of major concern. But wastewater tests can also be used to detect several types of hepatitis, the flulike norovirus, and possibly measles.

The methods used to test wastewater have improved over time. The first efforts attempted to grow viruses from water samples; more recently, testing has moved toward the detection of viral genetic material.

Polio and COVID in wastewater

In June 2022, wastewater testing in London detected the virus that causes polio, a potentially life-threatening or disabling illness. Though no active cases of polio have been diagnosed yet in London, this finding triggered an investigation into where the virus originated, who might be infected, and whether there is any threat to public health.

In the US, a county in New York that had been testing wastewater for COVID levels also began testing for polio after an active case of polio occurred in an unvaccinated adult.

Has wastewater testing proven useful to detect and track SARS CoV2, the virus that causes COVID-19? Indeed, it has. Levels of this virus in wastewater have closely mirrored rates of infection in many cities around the world, and in some cases predicted an outbreak before a community has even noticed cases are rising. The CDC now includes wastewater data in its regular reporting of COVID-19 infection rates.

The results of wastewater testing are usually combined with other information, such as rates of infection reported by hospitals and doctors’ offices, trends of infection in nearby communities, and vaccination rates. Together, this information provides public health officials with better information on a range of worrisome viral infections and where case numbers may be headed.

How is wastewater data helpful?

Detecting the presence, or a rising level, of virus in wastewater can help public health officials, healthcare providers, and researchers

  • predict when a surge is happening or when it’s peaking
  • update messaging on measures for prevention (for example, advice to wear a mask in public spaces or to physically distance)
  • request more vaccines and antiviral medications
  • encourage more testing
  • identify new variants.

Allowing people to know if cases are rising in their community may be particularly important for those who face barriers to testing, including people who don’t have health insurance or a primary care doctor. Wastewater testing can be particularly helpful when undercounting is common, as in the case of COVID-19.

In the future, wastewater testing could improve to the point where we can narrow down the site of an outbreak to a single neighborhood, or a residential facility such as a nursing home or prison.

The bottom line

Unfortunately, the COVID-19 pandemic isn’t over. And we’re hearing alarming reports on the international spread of the virus causing monkeypox. In the future, it’s highly likely that old viruses like polio and measles will re-emerge and new pandemics will take hold.

We’ll need all the help we can get to stay ahead of these outbreaks. Some of that help will likely come from wastewater. So, as strange as it may seem, what you flush down the toilet may help health officials detect — and possibly even contain — a public health menace.

Follow me on Twitter @RobShmerling

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