IIf the past two years have taught us anything, it’s that testing for viral diseases is complicated. Sometimes tests are hard to get, like in the early days of COVID-19. And even if people have access to testing, they may not feel they need it. People with COVID-19 often have no symptoms and may not always know how to test. And now, with the availability of home self-tests, most people are testing themselves and not reporting the results. With other diseases – such as monkeypox— the stigma surrounding the disease and the most affected group can inhibit access to testing.
These restrictions hinder the ability of health authorities to learn more about infectious diseases and control their spread. If you can’t find a problem, you can’t direct resources to help fix it.
Wastewater analysis can help overcome some of these problems. Scientists have traced COVID-19 through sewage since the start of the pandemic, and are now doing the same with monkeypox. A new program led by researchers at Stanford University, Emory University and Verily, an Alphabet Inc. company, is monitoring monkeypox cases by analyzing wastewater from 41 communities in 10 states. So far, they have found the monkeypox virus in 22 of those places. As the number of monkeypox cases across the country continues to rise, such information is proving valuable as doctors and patients grapple with the challenges of testing. “We have now detected monkeypox DNA in the sewage before cases were reported in these counties,” said Bradley White, senior scientist at Verily. The group plans to publish its first findings from its monkeypox work in preprint soon. Other academic and health groups are working with local sewage facilities to track the virus, but this program, the so-called Waste water SCANfocuses on getting a national picture of where the cases are.
Data is shared publicly on a website hosted by Stanford, and the group shared its findings with the US Centers for Disease Control and Prevention (CDC).
Because sewage is a mixture of thousands of people, it provides an ideal, anonymous way to detect virus levels in communities. “We’re catching cases even if people are asymptomatic,” says Marlene Wolfe, professor of environmental health at Emory and co-principal investigator of WastewaterSCAN. “When there’s limited testing capacity and there’s stigma attached to the disease, measuring infection at a population level that’s not affected by those things is really powerful.”
Another reason why sewage is an advanced way to track down monkeypox is because it contains sewage not only from urine and faeces, where the virus can be shed, but also from saliva and water that drains away while people brush their teeth and bathe. Because the monkeypox virus is active in skin lesions, such secretions are particularly effective means of capturing and detecting the virus.
Researchers have analyzed sewage for decades, most notably in the 1940s to track polio in the US, but The COVID-19 pandemic has proven its usefulness on a grand scale. Studies show that waste samples usually 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 the rapid test can’t do.
In late 2020, the CDC launched National Wastewater Monitoring System (NWSS), the first federal system to follow-up of an infectious disease pathogen – in this case SARS-CoV-2 – in the sewage. It is an attempt to standardize the way wastewater is collected, analyzed and interpreted. NWSS now includes data from local programs — such as 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 poliowhich were found in the sewers of New York.
When cases of monkeypox first started appearing in the U.S., researchers at Stanford, Emory and Verrilli saw an opportunity to apply a wastewater lens to the disease, especially since testing for monkeypox was not widely available. They tracked SARS-CoV-2 at several locations in California during Sewage Alert Network for Coronavirus (SCAN) from November 2020 and added analyzes of other viruses, including influenza and RSV. As cases of monkeypox began to spread around the world, and while access to testing was still limited, they added this virus to their investigation and expanded their network to include more sites across the country. WastewaterSCAN was born.
Wolff says the group’s platform for isolating the genetic material of microbes made it relatively easy to create the right assay to detect the monkeypox virus in mid-June. They targeted a part of the monkeypox genome that was relatively unique, and the probe successfully identified the virus in their laboratory tests. But, White says, “the first few tests we ran on sewage samples didn’t find anything.” This may be because the concentration of virus in the sewage was so low at that time. While WastewaterSCAN’s probe is designed to capture very dilute amounts of the virus, there were few cases in Northern California during the tests. On June 19, WastewaterSCAN began testing samples provided daily by two treatment plants in the San Francisco area. The next day, both sites tested positive for monkeypox.
Read more: What it really feels like to have monkeypox
The genetic material of the monkeypox virus differs from that of SARS-CoV-2 because it is in the form of DNA, while the COVID-19 virus and all of the group’s previous tests have 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 sewage, we’ll eventually find it.”
Scientists say there are still several important unanswered questions about monkeypox in sewage. They don’t have enough data to say for sure how much time the sewage might give health officials for rising cases compared to testing in clinics and hospitals. They also continue to analyze the data to get a better idea of how much virus needs to circulate in the community, or how many cases need to accumulate in a region, before their analysis picks up signs of the virus in the sewers. This could give doctors a head start on preparing the right number of tests, vaccines and treatments for the disease before cases peak.
The WastewaterSCAN team is now applying what it 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 infants, knowing where cases begin to circulate can help doctors treat the most vulnerable infants with a monoclonal antibody drug before they are exposed, thereby protecting them from contracting a potentially dangerous disease.
The key to having such a national system, however, is coordination among partners who share their findings, Wolff says. “Having a network of sites that use the same collection and analysis methods so we can compare data gives us a national picture of what’s going on,” she says. “We would love to have more federal investment in systems like this.”
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