An airport-based coronavirus surveillance program in the United States for travelers arriving from abroad detected the first known U.S. case of the highly contagious Omicron subvariant BA.2 in December, according to a new study.
The results, which have not yet been published in a peer-reviewed journal, suggest that pooled testing of international travelers may be an effective and efficient way to keep tabs on new variants and pathogens.
“Travelers are really an important population when tracking new and emerging infectious diseases because they’re mobile, they have the potential for exposure to disease during travel and they can spread disease from one place to another,” said Dr. Cindy R. Friedman, chief of the Travelers’ Health Branch at Centers for Disease Control and Prevention, and the study’s lead investigator.
The program actually detected the first known U.S. cases of two Omicron subvariants, BA.2 and BA.3, which are similar to, but genetically distinct from, BA.1 and B.1.1, the versions of Omicron that drove a winter surge in U.S. cases.
The voluntary program, which screened more than 16,000 travelers this fall and winter, was conducted by the C.D.C. and two commercial partners: the XpresSpa Group, which offers testing in airports, and Ginkgo Bioworks, a biotech company with a testing initiative and a network of laboratories across the country. The program combined nasal samples from multiple people arriving from the same country or on the same flight — an approach, known as pooled testing, that allows scientists to search for the virus in multiple people at once.
The program was not the first to catch every version of Omicron; BA.1, the subvariant that was initially most prevalent worldwide, did not show up in one of the airport samples until Dec. 1, the same day that officials announced that another team of researchers had found the first U.S. Omicron case.
The researchers hope to expand the traveler surveillance program and are also preparing to launch a pilot study that will search for signs of the virus in the wastewater from airplane bathrooms, Dr. Friedman said.
The program began in late September, focusing on travelers on selected flights from India to three major U.S. airports: John F. Kennedy International Airport in New York, Newark Liberty International Airport in New Jersey and San Francisco International Airport in California. In late November, after Omicron emerged, the program was expanded to Hartsfield-Jackson Atlanta International Airport and to people arriving from South Africa, Nigeria, Britain, France, Germany and Brazil.
(Omicron prompted the Biden administration to tighten travel rules. It temporarily banned travelers from eight African countries — the restrictions did not apply to U.S. citizens or permanent residents — and required international passengers to present evidence that they had tested negative for the virus within a day before departure. Previously, travelers could test within three days of departure. As of Nov. 8, only vaccinated foreign travelers were allowed into the country.)
Eligible travelers could volunteer to provide a self-collected nasal swab at the airport. Swabs from five to 25 travelers — from the same flight or country — were added to a single tube and then tested for the virus using P.C.R. testing. Positive samples were then sequenced to determine which version of the virus was present.
Between Sept. 29 and Jan. 23, 10 percent of 161,000 eligible travelers enrolled in the study, and 1,454 sample pools were tested for the virus.Despite the preflight testing requirement, more than 15 percent of the pools were positive.
This relatively high positivity rate may indicate that travelers were early in the course of their infections — and thus had viral loads too low for some tests to detect — when they took their predeparture tests, or that they contracted the virus in the time between being tested and landing in the United States, the researchers say. People may also have submitted fraudulent test results.
Before Nov. 28, nearly all of the positive sample pools contained the Delta variant, the researchers found. (The only exception was a positive sample whose exact genetic lineage could not be determined.)
After that, however, Omicron quickly came to dominate; from Nov. 28 to Jan. 23, two-thirds of the positive samples were Omicron. Most of the Omicron samples were the BA.1 subvariant, which was initially the most prevalent version worldwide. BA.1 remains the most common lineage in the United States, though BA.2 has been gaining ground and now accounts for 35 percent of infections, according to C.D.C. estimates.
But the researchers found the BA.3 subvariant in a pool of samples collected from travelers arriving from South Africa on Dec. 3. They reported the finding in GISAID, an international repository of viral genomes, on Dec. 22.It was the first reported case of BA.3 in the United States; it would be more than a month before the next was reported.
The airport program also detected the first known U.S. case of BA.2, in samples collected from South African travelers on Dec. 14. The researchers reported the finding a week before the next U.S. case of BA.2 was reported.
“This is a new tool in the C.D.C. tool kit that works, and we’ve shown it’s effective and it can be layered with all of our other mitigation measures,” Dr. Friedman said.