Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant
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 neut...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-12-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-43703-3 |
| _version_ | 1797397865144778752 |
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| author | 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 van Deventer Terry Marshall Nithendra Manickchund Bernadett I. Gosnell Richard J. Lessells Quarraisha Abdool Karim Salim S. Abdool Karim Mahomed-Yunus S. Moosa Tulio de Oliveira Anne von Gottberg Nicole Wolter Richard A. Neher Alex Sigal |
| author_facet | 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 van Deventer Terry Marshall Nithendra Manickchund Bernadett I. Gosnell Richard J. Lessells Quarraisha Abdool Karim Salim S. Abdool Karim Mahomed-Yunus S. Moosa Tulio de Oliveira Anne von Gottberg Nicole Wolter Richard A. Neher Alex Sigal |
| author_sort | Khadija Khan |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T01:16:23Z |
| format | Article |
| id | doaj.art-385191ebb6d244fb85921e20444d30a5 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-09T01:16:23Z |
| publishDate | 2023-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-385191ebb6d244fb85921e20444d30a52023-12-10T12:24:55ZengNature PortfolioNature Communications2041-17232023-12-011411910.1038/s41467-023-43703-3Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariantKhadija Khan0Gila Lustig1Cornelius Römer2Kajal Reedoy3Zesuliwe Jule4Farina Karim5Yashica Ganga6Mallory Bernstein7Zainab Baig8Laurelle Jackson9Boitshoko Mahlangu10Anele Mnguni11Ayanda Nzimande12Nadine Stock13Dikeledi Kekana14Buhle Ntozini15Cindy van Deventer16Terry Marshall17Nithendra Manickchund18Bernadett I. Gosnell19Richard J. Lessells20Quarraisha Abdool Karim21Salim S. Abdool Karim22Mahomed-Yunus S. Moosa23Tulio de Oliveira24Anne von Gottberg25Nicole Wolter26Richard A. Neher27Alex Sigal28Africa Health Research InstituteCentre for the AIDS Programme of Research in South AfricaBiozentrum, University of BaselAfrica Health Research InstituteAfrica Health Research InstituteAfrica Health Research InstituteAfrica Health Research InstituteAfrica Health Research InstituteAfrica Health Research InstituteAfrica Health Research InstituteCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory ServiceCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory ServiceCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory ServiceCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory ServiceCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory ServiceCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory ServiceAmpath Molecular BiologyAmpath Molecular BiologyDepartment of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-NatalDepartment of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-NatalCentre for the AIDS Programme of Research in South AfricaCentre for the AIDS Programme of Research in South AfricaCentre for the AIDS Programme of Research in South AfricaDepartment of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-NatalCentre for the AIDS Programme of Research in South AfricaCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory ServiceCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a Division of the National Health Laboratory ServiceBiozentrum, University of BaselAfrica Health Research InstituteAbstract 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.https://doi.org/10.1038/s41467-023-43703-3 |
| spellingShingle | 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 van Deventer Terry Marshall Nithendra Manickchund Bernadett I. Gosnell Richard J. Lessells Quarraisha Abdool Karim Salim S. Abdool Karim Mahomed-Yunus S. Moosa Tulio de Oliveira Anne von Gottberg Nicole Wolter Richard A. Neher Alex Sigal Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant Nature Communications |
| title | Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant |
| title_full | Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant |
| title_fullStr | Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant |
| title_full_unstemmed | Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant |
| title_short | Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant |
| title_sort | evolution and neutralization escape of the sars cov 2 ba 2 86 subvariant |
| url | https://doi.org/10.1038/s41467-023-43703-3 |
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