Researchers Are Now Tracking Monkeypox in Wastewater


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If the past two years have taught us anything, it’s that testing for viral diseases is complicated. Sometimes, the tests are difficult to get, like in the early days of COVID-19. And even if people have access to testing, they might not feel they need it. People with COVID-19 often don’t have symptoms and may not always know to get tested. And now, with the availability of at-home self-tests, most people test themselves and don’t report the results. With other diseases—such as monkeypox—stigma surrounding the disease and the group most affected can deter access to testing.

These limitations hinder health authorities’ ability to learn more about infectious diseases and control their spread. If you can’t detect a problem, you can’t direct resources to help fix it.

Wastewater analysis can help skirt some of these issues. Scientists have tracked COVID-19 through wastewater since early in the pandemic, and now they’re doing the same for monkeypox. A new program led by researchers at Stanford University, Emory University, and Verily, an Alphabet Inc. company, is monitoring monkeypox cases by analyzing sewage from 41 communities in 10 states. So far, they have detected the monkeypox virus in 22 of those sites. As monkeypox case numbers around the country continue to climb, such information is proving valuable as doctors and patients wrestle with testing challenges. “We have now detected monkeypox DNA in sewersheds before any cases were reported in those counties,” says Bradley White, senior staff scientist at Verily. The group is planning to publish their first findings from their monkeypox work in a preprint soon. Other academic and public-health groups are working with their local sewage facilities to track the virus, but this program, called WastewaterSCAN, is focused on getting a national picture of where cases are.

The data are shared publicly on a website hosted by Stanford, and the group is sharing its findings with the U.S. Centers for Disease Control and Prevention (CDC).

Read More: How the Monkeypox Virus Does—and Doesn’t—Spread

Because sewage is a composite from the thousands of people, it provides an ideal, anonymous way to detect levels of virus in communities. “We are capturing cases even if people are asymptomatic,” says Marlene Wolfe, professor of environmental health at Emory and co-principal investigator of WastewaterSCAN. “When there is limited testing capacity, and there is stigma associated with the disease, to have a population-level measurement of infections that isn’t impacted by those things is really powerful.”

Another reason why sewage is a sophisticated way to track monkeypox relates to the fact that it contains effluent from not just urine and feces, where the virus can be excreted, but also from saliva and water that drain while people brush their teeth and shower. Because monkeypox virus is active in skin lesions, such secretions are particularly effective vehicles for trapping and detecting the virus.

Researchers have analyzed wastewater for decades, most notably during the 1940s to track polio in the U.S. But the COVID-19 pandemic proved its utility on a large scale. Studies have shown that waste samples generally pick up signs of SARS-CoV-2 up to a week before clinics in a region start seeing positive cases. Wastewater can even detect new variants of SARS-CoV-2—something a rapid test can’t do.

In late 2020, the CDC launched the National Wastewater Surveillance System (NWSS), the first federal system to track an infectious disease pathogen—in this case, SARS-CoV-2—in sewage. It’s an attempt to standardize the way wastewater is collected, analyzed, and interpreted. NWSS now includes data from local programs—like WastewaterSCAN—and cities with their own tracking systems. New York City’s Biosurveillance Program, for example, has been testing wastewater for signs of SARS-CoV-2 since February, and now 11 hospitals in the group will start scanning for monkeypox and polio, which have been detected in New York City sewage.

When monkeypox cases first began popping up in the U.S., the researchers at Stanford, Emory, and Verily saw an opportunity to apply a wastewater lens to the disease, especially since testing for monkeypox wasn’t widely available. They had been tracking SARS-CoV-2 at a few sites in California through the Sewer Coronavirus Alert Network (SCAN) since November 2020, and had been adding analyses of other viruses, including influenza and RSV. When monkeypox cases began spreading around the world and while access to testing was still limited, they added that virus to their investigation as well and expanded their network to include more sites around the country. WastewaterSCAN was born.

Wolfe says the group’s platform for isolating the genetic material of microbes made it relatively easy to create the proper assay for detecting the monkeypox virus in mid-June. They targeted a portion of the monkeypox genome that was relatively unique, and the probe successfully identified the virus in their lab tests. But, says White, “the first few tests we ran on wastewater samples didn’t pick anything up.” That might have been because the concentration of virus in sewage at that point was so low. While WastewaterSCAN’s probe is designed to pick up very diluted amounts of virus, at the time of the tests, there were few cases in northern California. On June 19, WastewaterSCAN started testing samples provided daily from two treatment plants in the San Francisco area. The next day, both sites had positive tests for monkeypox.

Read More: What It Really Feels Like to Have Monkeypox

The monkeypox virus’ genetic material differs from that of SARS-CoV-2 because it’s in the form of DNA, while the COVID-19 virus and all of the group’s previous tests had been directed against RNA. But, White says, “DNA is much more stable than RNA, so as long as the genetic material is extracted from the sample, we’re pretty confident that if people are excreting a virus in wastewater, we will eventually detect it.”

The scientists say that there are still a few important unanswered questions about monkeypox in wastewater. They don’t have enough data to say for sure how much of a lead time wastewater can give health officials about rising cases, compared to testing at clinics and hospitals. They are also continuing to analyze the data to get a better sense of how much virus needs to be circulating in the community, or how many cases need to accumulate in a given region, before their analysis can pick up signs of the virus in sewage. That could give doctors an important head start in preparing adequate numbers of tests, vaccines, and treatments for the disease before cases peak.

The WastewaterSCAN team is now applying what they’ve learned from COVID-19 and monkeypox to explore ways to monitor influenza, RSV, and other seasonal diseases. In the case of RSV, a respiratory infection that often sickens babies, knowing where cases are starting to circulate could help doctors treat the most vulnerable babies with a monoclonal antibody drug before they get exposed, and thus spare them from contracting a potentially dangerous illness.

The key to having such a national system, however, is coordination among partners who share their findings, says Wolfe. “Having a network of sites that use the same collection and analytic methods so we can compare data gives us a national picture of what is going on,” she says. “We’d love to have more federal investments in systems like this.”