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Antigenic cartography of SARS-CoV-2 reveals that Omicron BA.1 and BA.2 are antigenically distinct
Open accessAbstract
The emergence and rapid spread of SARS-CoV-2 variants may affect vaccine efficacy substantially. The Omicron variant termed BA.2, which differs substantially from BA.1 based on genetic sequence, is currently replacing BA.1 in several countries, but its antigenic characteristics have not yet been assessed. Here, we used antigenic cartography to quantify and visualize antigenic differences between early SARS-CoV-2 variants (614G, Alpha, Beta, Gamma, Zeta, Delta, and Mu) using hamster antisera obtained after primary infection. We first verified that the choice of the cell line for the neutralization assay did not affect the topology of the map substantially. Antigenic maps generated using pseudo-typed SARS-CoV-2 on the widely used VeroE6 cell line and the human airway cell line Calu-3 generated similar maps. Maps made using authentic SARS-CoV-2 on Calu-3 cells also closely resembled those generated with pseudo-typed viruses. The antigenic maps revealed a central cluster of SARS-CoV-2 variants, which grouped on the basis of mutual spike mutations. Whereas these early variants are antigenically similar, clustering relatively close to each other in antigenic space, Omicron BA.1 and BA.2 have evolved as two distinct antigenic outliers. Our data show that BA.1 and BA.2 both escape vaccine-induced antibody responses as a result of different antigenic characteristics. Thus, antigenic cartography could be used to assess antigenic properties of future SARS-CoV-2 variants of concern that emerge and to decide on the composition of novel spike-based (booster) vaccines.
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“These two population groups primed by different antigens will likely have different antibody responses as the sera of individuals primed by pre-Omicron variants or vaccines poorly neutralize the Omicron BA.1/2 variant and vice versa 26,27 .”
From Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa (2023) · cites this paper as [27]
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Metadata
- Authors
- Mykytyn, A. Z., Rissmann, M., Kok, A., Rosu, M. E., Schipper, D., Breugem, T. I., van den Doel, P. B., Chandler, F., Bestebroer, T., de Wit, M., van Royen, M. E., Molenkamp, R., Oude Munnink, B. B., de Vries, R. D., GeurtsvanKessel, C., Smith, D. J., Koopmans, M. P. G., Rockx, B., Lamers, M. M., Fouchier, R. A. M., & Haagmans, B. L.
- Affiliations
- Erasmus MC (NL)
- Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands.
- Department of Neurology, Erasmus University Medical Center, Rotterdam, Netherlands.
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands.
- University of Cambridge (GB)
- Corresponding author
- Rissmann, Melanie
- Kok, Adinda
- Rosu, Miruna E.
- Haagmans, Bart L.
- ORCID
- Mykytyn, Anna Z.
- Rissmann, Melanie
- Kok, Adinda
- Rosu, Miruna E.
- Schipper, Debby
- Breugem, Tim I.
- van den Doel, Petra B.
- Chandler, Felicity
- de Wit, Maurice
- van Royen, Martin E.
- Molenkamp, Richard
- Oude Munnink, Bas B.
- de Vries, Rory D.
- GeurtsvanKessel, Corine
- Smith, Derek J.
- Koopmans, Marion P. G.
- Rockx, Barry
- Lamers, Mart M.
- Fouchier, Ron A. M.
- Haagmans, Bart L.
- Venue
- Science Immunology
- Published
- 2022-09-30
- Volume
- 7
- Issue
- 75
- Pages
- eabq4450-eabq4450
- ISSN
- 2470-9468 (ISSN-L)
- PMC
- PMC9273038
- OpenAlex
- W4283330057
- Cited by
- 153
- References
- 35
- Citations by year
- 2026: 11 · 2025: 16 · 2024: 43 · 2023: 49 · 2022: 34
- FWCI
- 17.33
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- cc-by
- Locations
- Science Immunology (publishedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion, other-oa)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Funders
- Health~Holland (EMCLHS20017, LSHM19136)
- European Commission (874735, 101003589, 75N93021C00014)
- ZonMw (10150062010008)
- Erasmus Medisch Centrum
- National Institutes of Health (75N93021C00014, 874735, 101003589)
- National Institute of Allergy and Infectious Diseases (#75N93021C00014, 101003589, 874735)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Keywords
- SARS-CoV-2, Omicron BA.1, Omicron BA.2, antigenic cartography, antigenic drift, spike protein mutations, neutralizing antibodies, vaccine escape, spike protein, Calu-3 cells, Vero E6 cells, SARS-CoV-2 variants
- MeSH terms
- COVID-19, SARS-CoV-2, Animals, Cell Line, Cricetinae, Humans, Immune Sera
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