Antigenic cartography of SARS-CoV-2 reveals that Omicron BA.1 and BA.2 are antigenically distinct

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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.

Original languageEnglish
Article numbereabq4450
Pages (from-to)eabq4450
JournalScience immunology
Issue number75
Publication statusPublished - 23 Sep 2022

Bibliographical note


This work was financially
supported by the Netherlands Organization for Health Research and Development
(ZONMW) grant agreement 10150062010008 to B.L.H., the Health~Holland grants
EMCLHS20017 to R.D.d.V., and LSHM19136 to B.L.H cofunded by the PPP Allowance made
available by the Health~Holland, Top Sector Life Sciences & Health, to stimulate publicprivate partnerships, and the European Union’s Horizon 2020 research and innovation
program under grant no. 101003589 (RECoVER: to M.P.G.K.) and EU funding grant
agreement number 874735(VEO). B.L.H., R.A.M.F., B.R., D.J.S., and M.P.G.K. are supported by
the NIH/NIAID Centers of Excellence for Influenza Research and Response (CEIRR) under
contract 75N93021C00014-Icahn School of Medicine at Mt. Sinai.


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