Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant

Khadija Khan, Gila Lustig, Cornelius Römer, Kajal Reedoy, Zesuliwe Jule, Farina Karim, Yashica Ganga, Mallory Bernstein, Zainab Baig, Laurelle Jackson, Boitshoko Mahlangu, Anele Mnguni, Ayanda Nzimande, Nadine Stock, Dikeledi Kekana, Buhle Ntozini, Cindy Deventer, Terry Marshall, Nithendra Manickchund, Bernadett I. Gosnell, Richard J. Lessells, Quarraisha Abdool Karim, Salim S. Abdool Karim, Mahomed-Yunus S. Moosa, Tulio Oliveira, Anne Gottberg, Nicole Wolter, Richard A. Neher and Alex Sigal ()
Additional contact information
Khadija Khan: Africa Health Research Institute
Gila Lustig: Centre for the AIDS Programme of Research in South Africa
Cornelius Römer: Biozentrum, University of Basel
Kajal Reedoy: Africa Health Research Institute
Zesuliwe Jule: Africa Health Research Institute
Farina Karim: Africa Health Research Institute
Yashica Ganga: Africa Health Research Institute
Mallory Bernstein: Africa Health Research Institute
Zainab Baig: Africa Health Research Institute
Laurelle Jackson: Africa Health Research Institute
Boitshoko Mahlangu: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service
Anele Mnguni: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service
Ayanda Nzimande: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service
Nadine Stock: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service
Dikeledi Kekana: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service
Buhle Ntozini: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service
Cindy Deventer: Ampath Molecular Biology
Terry Marshall: Ampath Molecular Biology
Nithendra Manickchund: University of KwaZulu-Natal
Bernadett I. Gosnell: University of KwaZulu-Natal
Richard J. Lessells: Centre for the AIDS Programme of Research in South Africa
Quarraisha Abdool Karim: Centre for the AIDS Programme of Research in South Africa
Salim S. Abdool Karim: Centre for the AIDS Programme of Research in South Africa
Mahomed-Yunus S. Moosa: University of KwaZulu-Natal
Tulio Oliveira: Centre for the AIDS Programme of Research in South Africa
Anne Gottberg: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service
Nicole Wolter: Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service
Richard A. Neher: Biozentrum, University of Basel
Alex Sigal: Africa Health Research Institute

Nature Communications, 2023, vol. 14, issue 1, 1-9

Abstract: Abstract Omicron BA.2.86 subvariant differs from Omicron BA.2 as well as recently circulating variants by over 30 mutations in the spike protein alone. Here we report on the isolation of the live BA.2.86 subvariant from a diagnostic swab collected in South Africa which we tested for escape from neutralizing antibodies and viral replication properties in cell culture. We found that BA.2.86 does not have significantly more escape relative to Omicron XBB.1.5 from neutralizing immunity elicited by either Omicron XBB-family subvariant infection or from residual neutralizing immunity of recently collected sera from the South African population. BA.2.86 does have extensive escape relative to ancestral virus with the D614G substitution (B.1 lineage) when neutralized by sera from pre-Omicron vaccinated individuals and relative to Omicron BA.1 when neutralized by sera from Omicron BA.1 infected individuals. BA.2.86 and XBB.1.5 show similar viral infection dynamics in the VeroE6-TMPRSS2 and H1299-ACE2 cell lines. We also investigate the relationship of BA.2.86 to BA.2 sequences. The closest BA.2 sequences are BA.2 samples from Southern Africa circulating in early 2022. Similarly, many basal BA.2.86 sequences were sampled in Southern Africa. This suggests that BA.2.86 potentially evolved in this region, and that unobserved evolution led to escape from neutralizing antibodies similar in scale to recently circulating strains of SARS-CoV-2.

Date: 2023
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DOI: 10.1038/s41467-023-43703-3

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