Notes from the Field: Early Identification of the SARS-CoV-2 Omicron BA.2.86 Variant by the Traveler-Based Genomic … – CDC

Stephen M. Bart, PhD1; Andrew P. Rothstein, PhD2; Casandra W. Philipson, PhD2; Teresa C. Smith, MPH1; Birgitte B. Simen, PhD2; Azaibi Tamin, PhD3; Lydia J. Atherton, DVM, PhD3; Jennifer L. Harcourt, PhD3; Allison Taylor Walker, PhD1; Daniel C. Payne, PhD1; Ezra T. Ernst4; Robert C. Morfino, MBA2; Ian Ruskey, MPA1; Cindy R. Friedman, MD1 (View author affiliations)

Views equals page views plus PDF downloads

During August 1314, 2023, a new SARS-CoV-2 Omicron subvariant with a large number of mutations compared with previously circulating BA.2 variants (>30 amino acid differences in its spike protein) was identified by genomic sequencing in Denmark and Israel and subsequently designated BA.2.86 (1,2). Given near-simultaneous detections in multiple countries, including the United States, further information was needed regarding geographic spread of BA.2.86. Since January 2022, submissions to SARS-CoV-2 sequence repositories have declined by 95%,* substantially decreasing global capacity to monitor new variants. To fill gaps in global surveillance, CDCs Traveler-based Genomic Surveillance (TGS) program was developed to provide early warning of new variants entering the United States by collecting samples from arriving international travelers (3).

The TGS program anonymously collects two nasal swab samples from consenting international travelers arriving at six major U.S. airports. Participants complete a brief questionnaire that collects information including travel history, COVID-19 vaccination status, and previous COVID-19 history. One sample collected from each traveler is pooled together with up to nine other travelers samples and tested for SARS-CoV-2 using reverse transcriptionpolymerase chain reaction. If a pooled sample tests positive, it undergoes viral genomic sequencing. The second nasal samples from each traveler in that pool are then tested for SARS-CoV-2, and positive individual samples are sequenced. Select positive individual samples are sent to CDC laboratories for virus isolation and characterization. This activity was reviewed by CDC, deemed not research, and was conducted consistent with applicable federal law and CDC policy.

On August 17, 2023, genomic sequencing identified BA.2.86 in a pooled sample of swabs from 10 TGS participants collected on August 10 at Dulles International Airport near the District of Columbia. Testing and sequencing of the individual samples confirmed the presence of BA.2.86 in one individual sample on August 20. The sample was collected from a U.S. resident returning from a 1530-day trip to Japan; health authorities in Japan were notified upon confirmation. The traveler reported no previous COVID-19 infection and had last received a COVID-19 vaccine dose in October 2022. This sequence was the second publicly reported BA.2.86 sequence in the United States and the seventh reported globally, preceding the first BA.2.86 sequence submission reported from Japan by 17 days.** The TGS sample was sent to a CDC laboratory, but virus isolation was not successful. Phylogenetic analyses indicated that the TGS sample contained distinct genetic differences from other BA.2.86 sequences collected in August 2023 (Figure), consistent with BA.2.86 circulation and divergence from BA.2.86.1 viruses several months before detection (4,5).

As a component of comprehensive U.S. SARS-CoV-2 genomic surveillance, TGS detected the BA.2.86 variant within days of its first identification globally, highlighting its importance for the detection of variants entering the United States. This identification provided important context regarding BA.2.86 geographic spread and diversity. Although virus isolation was not successful in this case, continued surveillance and sample collection are important to enable rapid laboratory characterization of variant sensitivity to antibody neutralization and antiviral drugs. Early variant detection among travelers and laboratory characterization of new variants are essential components of CDCs respiratory illness surveillance, especially as global sequencing volumes decline.

Traveler-based Genomic Surveillance program participants and airports; Thomas Aichele, Claire Altieri, Tim Lyden, Xueting Qiu, Amy Schierhorn, Ginkgo Bioworks; Patti Ward, XpresCheck; Nicole Cohen, Lauren Elsberry, Heather Hicks, Brendan Jackson, Hannah Kirking, Anastasia Lambrou, Samantha Loh, Duncan MacCannell, Ryan Novak, Clinton Paden, CDC; originating and submitting laboratories for the BA.2.86 sequence data in the Global Initiative on Sharing All Influenza Data.

1Division of Global Migration Health, National Center for Emerging and Zoonotic Infectious Diseases, CDC; 2Ginkgo Bioworks, Inc., Boston, Massachusetts; 3Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, CDC; 4XpresCheck, XWELL, New York, New York.

Abbreviation: GISAID = Global Initiative on Sharing All Influenza Data.

* https://gisaid.org

Consensus genome sequences from BA.2.86 GISAID submissions on or before August 21, 2023, were aligned, and mutational profiles were generated using Nextclade (version 2.14.1; https://joss.theoj.org/papers/10.21105/joss.03773). Consensus reference genomes for BA.2 were available at https://github.com/corneliusroemer/ncov-simplest/tree/main/data. A maximum likelihood phylogenetic tree was generated using iqTREE software (version 1.6.12) with 1,000 bootstraps. Using the iqTREE model finder tool, the HKY+F+I model was selected as the most appropriate model according to Bayesian Information Criterion. The maximum likelihood tree was visualized and annotated using iTOL (version 6; https://academic.oup.com/nar/article/49/W1/W293/6246398). Branch labels indicate confidence in phylogenetic placement as a percentage.

https://academic.oup.com/bioinformatics/article/34/23/4121/5001388

https://academic.oup.com/mbe/article/32/1/268/2925592

** The BA.2.86 sample identified through the Traveler-based Genomic Surveillance program (hCoV-19 USA VA-GBW-H20-330-6734 2023 EPI ISL 18121060 2023-08-10) was collected at Dulles International Airport on August 10, 2023.

Suggested citation for this article: Bart SM, Rothstein AP, Philipson CW, 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. MMWR Morb Mortal Wkly Rep 2023;72:11681169. DOI: http://dx.doi.org/10.15585/mmwr.mm7243a3.

MMWR and Morbidity and Mortality Weekly Report are service marks of the U.S. Department of Health and Human Services. Use of trade names and commercial sources is for identification only and does not imply endorsement by the U.S. Department of Health and Human Services. References to non-CDC sites on the Internet are provided as a service to MMWR readers and do not constitute or imply endorsement of these organizations or their programs by CDC or the U.S. Department of Health and Human Services. CDC is not responsible for the content of pages found at these sites. URL addresses listed in MMWR were current as of the date of publication.

All HTML versions of MMWR articles are generated from final proofs through an automated process. This conversion might result in character translation or format errors in the HTML version. Users are referred to the electronic PDF version (https://www.cdc.gov/mmwr) and/or the original MMWR paper copy for printable versions of official text, figures, and tables.

Questions or messages regarding errors in formatting should be addressed to mmwrq@cdc.gov.

Read the rest here:

Notes from the Field: Early Identification of the SARS-CoV-2 Omicron BA.2.86 Variant by the Traveler-Based Genomic ... - CDC