Testing Airplane Toilets for COVID-19 Variants at JFK Airport

As COVID-19 testing declined around the world, public health agencies were losing sight of which variants were spreading. One solution: test the planes. Because the virus can show up in the feces and urine of some infected people, a sample from an airplane's toilets can reveal which variants its passengers are carrying — and link them to the flight's country of origin — without anyone having to be swabbed.

The pilot

From August 1 to September 9, 2022, the biotech company Ginkgo Bioworks, working with CDC, collected wastewater from selected flights from the United Kingdom, the Netherlands and France arriving at John F. Kennedy International Airport in New York City. During routine maintenance, a device attached between the lavatory service port and the service truck's hose drew about 1 liter (0.25 gallon) from each plane.

The samples were concentrated with magnetic nanoparticles and tested by RT-PCR. Those with enough virus were genome-sequenced, analyzed for multiple lineages with a tool called Freyja, and assigned to sublineages with Pangolin. Results went to the airline, public genomic databases and CDC's National Wastewater Surveillance System.

What they found

From 88 flights to 25 sequenced samples. Credit: CDC, Morbidity and Mortality Weekly Report*.*

Of the 25 sequenced samples, 23 held a single Omicron sublineage — BA.5 in 21, BA.4.6 in one and BA.2.75 in one — and 2 held two distinct BA.5 sublineages.

Why it matters

The pilot showed that aircraft wastewater surveillance works: it is cheap compared with testing individuals, needs nothing from travelers and doesn't disrupt airport operations. It can monitor variants entering the country routinely, be scaled up for outbreaks or mass gatherings where variant surveillance is thin, and, alongside testing of travelers, act as an early warning for new variants and other dangerous pathogens.

Limits

Results depend on whether passengers use the toilet, which is more likely on longer flights. Passengers who connected from elsewhere can't be told apart, blurring where a variant came from. And virus left in a plane's system from an earlier flight could show up in the next sample; strict sequencing standards may make that less likely.

Sources

Based on Robert C. Morfino, Stephen M. Bart, Andrew Franklin, et al., "Notes from the Field: Aircraft Wastewater Surveillance for Early Detection of SARS-CoV-2 Variants — John F. Kennedy International Airport, New York City, August–September 2022," Morbidity and Mortality Weekly Report, volume 72, Centers for Disease Control and Prevention; a work of the United States government in the public domain. The authors included employees of Ginkgo Bioworks and XWELL.