Airplane Toilets Could Catch the Next COVID Variant

Airplane bathrooms are not most people’s idea of ​​a good time. It’s barely big enough to turn around. Its doors slammed shut, as if it was trying to trap you in place. This is to say nothing of the smell. But for the Centers for Disease Control and Prevention, those same bathrooms may be a data mine.

This month, the agency spoke with Concentric, the public health and biosecurity arm of biotechnology company Ginkgo Bioworks, about screening airline wastewater for COVID-19 at airports across the country. Although testing of in-flight sewage was already in the works (a pilot program was completed at New York City’s JFK International Airport last summer), there are concerns about a new variant that has emerged in China after the “zero COVID” program ends. . The policies acted as a “catalyst” for the project, Matt McKnight, general manager of biosecurity at Ginkgo, told me. According to Ginkgo, even airport managers are excited. “There have been a couple of airports that have already reached out to the CDC asking to be part of the program,” Laura Bruner, vice president of commercial strategies for Ginkgo, told me.

Airplane sewage testing is poised to revolutionize how we track the ongoing surges of coronavirus around the world, along with other common viruses like influenza and RSV — and public health threats scientists don’t yet know about. Unlike sewer-level surveillance, which shows us how diseases spread among large communities, aircraft surveillance is precisely targeted to catch new variants entering the country from outside. And unlike a PCR test, passengers do not have to sign up individually. (The results remain anonymous either way.) McKnight compares the technology to radar: Instead of responding to an attack after it is detected, America can get advance warning of new threats before they cause problems. As we enter an age when most people are not focused on avoiding COVID-19, our best contribution to public health may be using a toilet at 30,000 feet.

Essentially, testing sewage on airplanes is a smaller version of the surveillance that’s been taking place in municipal water systems since early 2020: Researchers run genetic tests on wastewater samples to determine the presence of coronavirus, variants included. But adapting the methodology to levels will require researchers to be creative. For one thing, aircraft wastewater has a higher solid-to-liquid ratio. Municipal sewage derives from showering, cooking, washing clothes and other activities, says Kata Farkas, a Bangor University microbiologist, while airplane sewage “primarily comes from the toilet.” In a recent study tracking COVID-19 at UK airports, Farkas and her colleagues had to adjust their analytical methods, adjusting the chemicals and laboratory techniques used to isolate the coronavirus from aircraft sewage.

Researchers also need to choose trips carefully to ensure that the data they collect is worth the effort. To put it bluntly, not everyone on the plane gets out — and if the total number of travelers sampled is very small, the analysis is unlikely to turn up much useful data. “The number of conversations we’ve had about how we know how many people went to the toilet inconspicuously on the plane is hysterical,” says Cassandra Phillipson, who leads the focused bioinformatics program. (Concentric later clarified that they have no plans to actually monitor occupants’ bathroom use.) The researchers ended up settling on an easier scale: Longer flights tend to use more bathrooms, and therefore should be the focus of sewage testing. (Philipson and her colleagues are also working with the CDC to test flights from countries where the government is particularly interested in identifying new variants.)

Besides those technical challenges, scientists face the daunting task of collaborating with airports and airlines — large corporations unaccustomed to being involved in public health surveillance. “It’s a tough environment to work in,” says Jordan Schmidt, director of product applications at LuminUltra, a Canadian biotechnology company that is testing wastewater at Toronto Pearson Airport. Li said the tight security measures and complex bureaucracy in air travel can make collecting samples from individual planes difficult. Instead, LuminUltra samples from airport terminals and from trucks hauling sewage from multiple planes, so the company doesn’t need to get a buyout from airlines.

Airplane surveillance seeks to track new variants, not individual passengers: Researchers don’t track exact contact with the person who brought a particular virus strain into the country. For this reason, companies like Concentric do not plan to alert passengers that COVID-19 has been found on their flight, as some of us might appreciate that warning. Airplane sewage testing can identify variables from around the world, but it won’t necessarily tell us about new spikes in the city those planes land in.

Aircraft wastewater testing offers several advantages for epidemiologists. Overall, testing wastewater is “dramatically cheaper” and “significantly less risky” than testing a nasal swab of everyone in a town or on an airplane, says Rob Knight, a professor of medical engineering at the University of California, San Diego who leads Water University sanitation – monitoring program. Earlier this month, a landmark report from the National Academies of Sciences, Engineering, and Medicine (Knight co-authored) highlighted international airports as ideal places to search for new variants of the coronavirus and other pathogens. “You’ll catch people traveling from other parts of the world where they might bring new variables,” Knight told me. Early detection of these new variants is key to updating our vaccines and treatments to ensure they continue to work well against COVID-19. Collecting more data from people who travel within the country could also be beneficial, Knight said, as variants can evolve at home as easily as abroad. (XBB.1.5, the latest variant to dominate the spread of COVID-19 in the United States, is believed to have originated in the American Northeast.) To that end, Lee said, the CDC should consider monitoring large train stations or seaports as well.

When wastewater testing first began during the pandemic, the focus was mostly on municipal utilities, because they could provide data for an entire city or county at once. But scientists have since realized that a more specific look at our waste could be useful, especially in places that are critical to informing public health measures. For example, at NYC Health+ hospitals, the city’s public healthcare system, sewage data helps officials “see 10 to 14 days in advance if there is any surge” of coronavirus, influenza, or mpox, Leopolda Silvera, Health+ Hospitals deputy global health, told me. Silvera said officials use the data in decisions about safety measures and where to send resources: If a hospital’s sewage indicates an upcoming spike in COVID-19 cases, additional staff can be added to the emergency department.

Schools are another obvious target for small-scale wastewater testing. In San Diego, Rebecca Fielding Miller ran a two-year monitoring program for elementary schools. It focused particularly on disadvantaged communities, including refugees and low-income workers who were reluctant to seek out a PCR test. Regular sewage testing picks up asymptomatic cases with high accuracy, Fielding Miller told me, providing school staff and parents with “accurate” information about the spread of COVID-19 in their buildings. But this school year, the program has run out of funding.

Even neighborhood-level monitoring, while not as accurate as in-plane, hospital, or school sampling, can provide more useful data than city-level testing. “In Boston, we really wanted hyperlocal surveillance” to inform the placements of the city’s vaccine clinics, testing sites, and other public health services, says Katherine Hall, deputy commissioner at the city’s public health agency. She and her colleagues identified 11 manhole covers that provide “good coverage” for certain neighborhoods and can be tested without causing too much traffic disturbance. When the testing site lights up with soaring COVID-19 numbers, Hall’s colleagues reach out to community organizations like health centers and senior living facilities. “We make sure they have access to boosters, that they have access to PPE, that they understand what’s going on,” Hall told me. In the nearby city of Revere, a similar program run by CIC Health showed an uptick in RSV in nearby wastewater before the virus started making headlines. CIC shared the news with day care centers and helped them respond to the surge with educational information and personal protective equipment.

According to sewage experts, local superprograms cannot herald a future of omnipotence on their own. Colleen Naughton, a professor of environmental engineering at the University of California, Merced who runs the COVIDPoops19 dashboard, told me she would like to see communities without wastewater monitoring get the resources to prepare them before more funding goes to testing individual buildings or manhole covers. The latest National Academies report outlines a future for wastewater monitoring that includes both broad surveillance across the country and targeted testing where new health threats may emerge or where specific communities need local information to stay safe.

That future will require sustained federal funding beyond the current COVID-19 emergency, which is set to expire if the Biden administration does not renew it in April. Knight said the United States needs “more and better technology, with a financing model to support its development,” in order to realize the true potential of wastewater. Airplane toilets may be the best first step toward a future of mass sewage control.


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