Would you volunteer for a nasal swab after a long flight? Why the CDC wants you to

After being stuffed into an airplane cabin for a long, redeye flight from overseas, you’re finally on your way home — but first, the government wants to shove a cotton swab up your nose.

The Centers for Disease Control and Prevention is asking passengers returning from international destinations at four U.S. airports to volunteer for its Traveler-based Genomic Surveillance (TGS) program.

Passengers at New York’s John F. Kennedy International Airport, Boston Logan International Airport, Dulles International Airport near Washington, D.C., and San Francisco International Airport can now have their nasal discharge anonymously sampled as they leave the travel hubs.

The new TGS pilot program is an expansion of a CDC initiative started in 2021 to test nasal swabs for the spread of COVID-19. Over the past two years, TGS has enrolled more than 360,000 air travelers, according to a CDC news release.

Now, the CDC will test for more than 30 pathogens, including flu, RSV and other respiratory viruses. In addition to the nasal swabs, the CDC will sample the wastewater from aircraft to test for the presence of viruses.

“The expansion of the Traveler-based Genomic Surveillance program to flu, RSV, and other pathogens is essential as we head into fall respiratory season,” said Dr. Cindy Friedman, chief of the CDC’s Travelers’ Health Branch.

“The TGS program, which began during the COVID-19 pandemic, acted as an early warning system to detect new and rare variants of the SARS-CoV-2 virus and will do the same for other respiratory viruses going forward,” Friedman added.

TGS detected the SARS-CoV-2 variant BA.2.86 from a traveler entering the U.S. within days of its global identification, according to the CDC.

Because the infected traveler had originated travel in Japan, the discovery also informed the public health community that the new variant had also spread to Asia.

The new testing program, which will last for several months, will be implemented by private companies Ginkgo Bioworks and XpresCheck.

“The dream is that you’re running similar programs across the world in many, many places, so you get much earlier detection than if somebody shows up at a hospital,” Matthew McKnight, the general manager of biosecurity at Ginkgo Bioworks, told CNN.

“The idea would be, how do you prevent a pandemic? You catch something really early, which allows you to put it into a vaccine manufacturing process much faster. Today we don’t have as much of that early warning as we want. And these are the first stages of it,” McKnight added.

The current rate of COVID-19 hospitalizations includes more than 15,700 hospital admissions per 100,000 people for the week ending Oct. 28, according to the CDC, which also noted the number of COVID-19-related deaths at just under 600 reported for the period.

And as flu season begins, for the week ending Oct. 28, 189 cases of influenza were reported by public health laboratories.

“We are interested in these fall respiratory pathogens,” Friedman told CNN. “We want to able to sequence them, so we know the genomics of the strain.

“There are a lot of blind spots globally where there’s limited testing and monitoring,” she added. “In general, our focus is on airports that are international hubs, and have flights coming in from a broad array of international locations.”