San Francisco airport will monitor plane waste for COVID-19 variants

International travelers can now contribute valuable data to COVID-19 surveillance efforts in the United States from above the clouds.

San Francisco International Airport has launched a new program to test airplane wastewater for variants of SARS-CoV-2, the virus responsible for COVID-19, the airport announced May 9. The program is the first in the country to continuously monitor sewage from airplanes, after previous studies demonstrated the potential value of this work.

Airplane wastewater is a key source for COVID-19 surveillance because international travelers frequently bring new variants into the country, experts say. As fewer people get their noses swabbed in health care facilities, the U.S. Centers for Disease Control and Prevention is looking for new ways to keep tabs on how the coronavirus mutates. Searching for genetic material in airplane bathroom waste can help fill that data gap — and even provide early warnings for future health crises (SN: 5/28/20).

“We know variants have been imported from around the globe,” says Alexandria Boehm, an environmental engineer at Stanford University who leads WastewaterSCAN, one of the biggest wastewater surveillance programs in the United States. Testing airplane waste “can give us a sense of which variants are being imported and help us prepare.”

For the new project, the San Francisco airport is collaborating with the CDC and Concentric by Ginkgo, a biosecurity and public health team in Boston.

Testing started on April 20, according to a spokesperson for the airport. Airport workers are taking samples from vacuum trucks that suck waste out of airplane bathrooms, using an automatic machine that plugs into a central dumping point. “We’re basically creating a composite sample of the trucks, which themselves are a composite sample of aircraft,” says Andrew Franklin, director of business development at Concentric.

The San Francisco airport has one dumping point dedicated to international flights, which are a priority for testing because passengers are more likely to use the restroom — and deliver solid samples — when they spend many hours on the plane. The airport is shipping one composite sample per day, six days a week, back to a lab, where scientists isolate the coronavirus’ genetic material and put the results through machines that map the virus’ genes.

The resulting data are complicated, says Casandra Philipson, director of bioinformatics at Concentric, as each sample includes hundreds of passengers from around the world. “Trying to figure out how to determine actual frequencies of mutations or variants” in the sewage samples will be a challenge, she says, though simply seeing certain variants pop up in the data will warn health officials about what to watch out for.

Concentric has worked with the CDC on monitoring COVID-19 among international travelers since fall 2021, when the company started offering free PCR tests to people returning from long flights. About 170,000 travelers have contributed to the program, which has picked up new variants before they spread widely in the United States.

But wastewater surveillance is more efficient than voluntary nose swabs, leading scientists to focus on this approach for future monitoring efforts (SN: 9/29/22). In August and September 2022, Concentric and CDC researchers ran a pilot program at John F. Kennedy International Airport in New York City to test the idea. Out of 88 samples collected from airplane bathrooms, the team was able to perform PCR tests on 80, and 65 of those tested positive for SARS-CoV-2, the scientists reported in the Feb. 24 Morbidity and Mortality Weekly Report. Analysis of genetic material from 25 samples turned up a variety of coronavirus variants.

Other research projects and pilot programs have similarly demonstrated this technique’s potential for detecting variants. The European Commission has issued guidance for airports in the European Union that may want to try it out. As with other forms of wastewater surveillance, though, scientists are still working to understand how they might interpret and act on the data. “It will be a new data stream that we’ll have to learn to use as it evolves,” Boehm says.

In addition to tracking coronavirus variants, scientists hope that future programs like the one at the San Francisco airport can lay the groundwork for monitoring new diseases that might enter the United States through international airports. “It’s easy to also test the samples for other emerging pathogens,” says Colleen Naughton, an environmental engineer at the University of California, Merced.

The Concentric team is excited about this potential and looking for other types of health data that might come out of airplane waste. “We’re building this future technology,” Philipson says, “to expand the toolkit for pathogens of public health concern.”