How CDC Tracked the BA.2.86 COVID-19 Variant From the First Sequence

Summary

BA.2.86, a SARS-CoV-2 variant with more than 30 spike-protein mutations compared with other circulating variants, was first reported from Israel on August 13, 2023. So many changes raised concern that it might evade immunity from past infection and vaccination. This CDC report describes how several complementary surveillance systems caught and tracked it in real time — even as sequencing had declined.

Key points

• The first U.S. case was reported on August 17, from a patient tested on August 3. Within a month, eight more states had detected it.
• By October 23, sequences had come from at least 32 countries on five continents, but BA.2.86 was under 1% of U.S. variants.
• Early lab findings suggested existing antibodies from infection or vaccination neutralize it, though real-world data were still needed.

Four systems

Tracking the emergence

• August 13: first sequence, submitted from Israel. August 14: two unrelated cases in Denmark.
• August 17: the fourth case worldwide, in Michigan — and, the same day, the first U.S. wastewater detection, in Ohio, from a sample collected July 30.
• Over the next 10 days, nine more cases, including in the United Kingdom and South Africa; Switzerland and Denmark reported wastewater detections.
• August 20: traveler surveillance confirmed BA.2.86 in a traveler from Japan sampled August 10 at Dulles Airport.
• August 26: Ohio reported a case collected July 29, in the same area as the wastewater detection 9 days earlier — wastewater was the leading signal. At least one early U.S. case had no international travel.

The earliest specimens were collected on July 24 (Denmark) and July 29 (United States), so BA.2.86 was probably circulating in the United States before the end of July.

Lag times from sample collection to reported sequence: a median of 14 days (range 5–29) for the first 11 respiratory detections, 18 days for early wastewater, and 15 days (range 4–53) across 945 specimens by October 23.

Countries reporting BA.2.86 by respiratory specimens, wastewater, or both: (A) August 26 and (B) October 23, 2023. CDC.

The response

• Risk communication through CDC's weekly Respiratory Virus Updates.
• Lab work: sequencing labs shared leftover virus samples, and CDC isolated the virus, characterized it, shared isolates and ran neutralization studies.
• Rapid, high-quality sequences showed its wide spread and fed lab and computer studies of immune escape.
• Next steps if it spread: Nowcast reporting once it passed 1%, and field studies of transmissibility and severity if concern grew.

Lessons

Each system sees part of the picture; together they gave early warning despite less testing. Limitations: uneven clinical and demographic data and global sequencing capacity; labor-intensive digital monitoring; variable lag times; no standard way to report sequences — especially from wastewater — to public databases; and a need for data standards. Keeping these multipurpose systems running — for this virus and future threats — requires sustained funding.

Sources

Based on Anastasia S. Lambrou, Erin South et al., "Early Detection and Surveillance of the SARS-CoV-2 Variant BA.2.86 — Worldwide, July–October 2023," Morbidity and Mortality Weekly Report, Centers for Disease Control and Prevention; published by CDC.