Want to Predict the Next Big COVID-19 Variant to Hit the U.S.? Look to Airports

With the summer travel season about to begin, public-health officials face a daunting challenge in keeping on top of ever-evolving COVID-19 variants. Most countries—including the U.S.—have scaled down or eliminated pandemic measures, including pre-flight testing and screening, giving the virus a greater opportunity to slip into countries undetected and start spreading.

But even though the U.S. now has less robust COVID-19 data collection, one important but little-known source remains: samples from international passengers flying into the U.S.

Launched by the U.S. Centers for Disease Control and Prevention (CDC) in late 2021, the Traveler-Based Genomic Surveillance program is still running in seven of the busiest international airports in the U.S.: John F. Kennedy International Airport (JFK), Newark Liberty International Airport (EWR), San Francisco International Airport (SFO), Hartsfield-Jackson Atlanta International Airport (ATL), Los Angeles International Airport (LAX), Seattle-Tacoma International Airport (SEA), and Washington Dulles International Airport (IAD).

Officials with the CDC’s partner XpresCheck, which runs spa operations in many airports but began conducting COVID-19 testing during the pandemic, meet passengers on select international flights once they clear customs and ask them to voluntarily provide nasal swabs that are pooled and tested by Ginkgo Bioworks, CDC’s lab partner.

“This program is critical for early detection and filling in many blind spots in global surveillance,” says Dr. Cindy Friedman, chief of the travelers’ health branch at the CDC. “This is really critical right now as many countries, including the U.S., are decreasing testing by as much as 90%. It’s a key piece of biosecurity.” Keeping tabs on passengers from abroad is an ideal way to track how the virus is changing and moving around the world, says Friedman, who recently participated in the program herself after returning home from a trip abroad. “We can fill in the gaps using travelers as sentinels; they are like the FedEx package bringing the sample in them to the U.S.”

Each week, CDC officials decide which flights to test based on global case trends. During the latest case surge in China and elsewhere in Asia, for example, Friedman says the program detected the increase in positive tests from the region just before case numbers began peaking. “A lot of times we are ahead of reported cases,” she says. “We see increases in cases before there are news stories or before something is reported in the public-health community.”

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More than 200,000 passengers have provided samples after arriving in the U.S. so far. Passengers provide anonymous information including their age, travel itinerary and COVID-19 infection and vaccination history, along with two nasal swabs. One is added to a pooled sample that includes up to 10 other samples, and the other is stored for possible later testing. If the pooled sample is positive, then the second sample is tested to determine which of the pooled ones were positive, and then genetically sequenced at a lab. If the genetic sequence shows novel changes, the second sample is sent to the CDC labs in Atlanta for further characterization and is added to the agency’s growing database of SARS-CoV-2 sequences.

In 2021, the program detected the first versions of the Omicron BA.2 variant one week before cases were reported in the U.S., and the BA.3 variant in travelers six weeks ahead of reported cases.

While the number of volunteers offering to provide nasal swabs has been impressive so far, that continued altruism may not be a given as the urgency of the pandemic wanes. That’s why the CDC is bulking up its airport wastewater testing program as the basis for potentially more consistent screening. For about a year, the agency has been collecting wastewater directly from the lavatories on overseas flights at three to four airports as well as from the communal drain at SFO. Early testing showed that the wastewater reflected the same variants picked up by nasal-swab testing, and those results were also supported by studies from Australia where officials conducted similar wastewater collection. “There is good data showing that wastewater is reflective of what is going on in people,” says Friedman.

Health officials say it’s important to learn from this program’s success and make sure that the lessons aren’t wasted—especially as precautions wind down. “Imagine how much better off the world might have been in January 2020 if a surveillance system like this could have picked up these strains of a new coronavirus in multiple countries after it was first detected in China,” says Marty Cetron, former director of global migration and quarantine at the CDC. “To know in advance would have helped in developing diagnostics and identifying outbreaks more quickly, and would have been a game changer.”

Wastewater screening in particular holds lots of promise as a permanent pathogen screening tool since it can be adapted to test for any new disease-causing agent that might emerge, making it an important part of preparing for future biological threats. “If we are not wise in taking what we’ve learned and investing in anticipatory, proactive, 21st-century tools for surveillance, we’re at risk of getting whacked again and repeating our mistakes,” says Cetron, “which would really be a shame.”