How Airport Traveler Testing Caught the BA.2.86 COVID-19 Variant Early, 2023

A new variant

On August 13–14, 2023, genomic sequencing in Denmark and Israel turned up a new SARS-CoV-2 Omicron subvariant with more than 30 amino acid differences in its spike protein from earlier BA.2 viruses. It was named BA.2.86. Detections came almost simultaneously in several countries, including the United States, and health officials needed to know how far it had spread.

That was harder than before: submissions to SARS-CoV-2 sequence databases had fallen 95% since January 2022, weakening the world's ability to spot new variants.

How traveler surveillance works

CDC's Traveler-based Genomic Surveillance (TGS) program gives early warning of variants arriving in the United States. At six major airports — Newark, JFK, Dulles, Seattle-Tacoma, San Francisco and Los Angeles — consenting international travelers anonymously give two nasal swabs and answer a short questionnaire on travel, vaccination and past COVID-19.

1. One swab from each traveler is pooled with up to nine others and tested by RT-PCR.
2. A positive pool is sequenced.
3. The travelers' second swabs are then tested one by one, and positives are sequenced; some go to CDC labs for virus isolation.

The detection

• On August 17, 2023, sequencing found BA.2.86 in a pool of 10 travelers' swabs collected August 10 at Dulles International Airport, near Washington, D.C.
• On August 20, individual testing confirmed it in one traveler: a U.S. resident returning from a 15- to 30-day trip to Japan, with no previous COVID-19 and a last vaccine dose in October 2022. Japanese health authorities were notified.
• It was the second BA.2.86 sequence reported in the United States and the seventh worldwide — 17 days before Japan's own first report.
• CDC could not grow the virus from the sample.

Early BA.2.86 sequences, August 2023. The traveler's sequence (USA VA-GBW) differs from the others, consistent with the variant circulating and diverging for months before it was detected. CDC.

Why it matters

Traveler testing caught BA.2.86 within days of its first identification anywhere, adding to what was known about the variant's spread and diversity. With global sequencing falling, early detection among travelers and quick laboratory study of new variants — how well antibodies and antiviral drugs work against them — are essential parts of CDC's respiratory illness surveillance.

Sources

Based on Stephen M. Bart et al., "Notes from the Field: Early Identification of the SARS-CoV-2 Omicron BA.2.86 Variant by the Traveler-Based Genomic Surveillance Program — Dulles International Airport, August 2023," Morbidity and Mortality Weekly Report, Centers for Disease Control and Prevention, by authors from CDC, Ginkgo Bioworks and XpresCheck; published by CDC.