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

Abstract

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.

Fig. 1.. Neutralizing activity of human post-vaccination sera against Omicron BA.1 and BA.2.

(A-C) Neutralization titers against 614G, Delta, Omicron BA.1 and Omicron BA.2 of vaccinated individuals after vaccination with one (A), two (B) or three (C) doses of BNT162b2. Geometric mean is displayed above each graph. PRNT50: plaque reduction neutralization titers resulting in 50% plaque reduction. Dotted lines indicate limit of detection. One way ANOVA was performed for statistical analysis. *p<0.05. N=10.

Fig. 2.. SARS-CoV-2 variants efficiently infect hamsters, inducing high neutralizing antibody titers.

(A) Hamsters were inoculated with the indicated SARS-CoV-2 variants. Nasal washes were collected 7 days post-infection and sequenced. At 26 days post-infection blood was collected for serological analysis. (B) Hamster antisera were assessed for neutralizing antibodies against pseudotyped and authentic SARS-CoV-2. PRNT50 values were used to generate antigenic maps using a multidimensional scaling algorithm. (C) RNA titers of nasal washes collected one day post-infection. (D) Homologous PRNT50 titers were determined using authentic SARS-CoV-2. Geometric mean is displayed above graph. PRNT50: plaque reduction neutralization titers resulting in 50% plaque reduction. Dotted line indicates limit of detection. Error bars indicate SEM. Panels A and B were created with BioRender.com.

Fig. 3.. Antigenic maps comparing neutralizations with SARS-CoV-2 pseudoviruses and authentic SARS-CoV-2.

(A-B) MDS was used to create an antigenic map from the PRNT50 titers generated against 614D, 614G, Alpha, Beta, Delta, Kappa and Omicron pseudoviruses on either VeroE6 (A) or Calu-3 (B) cells. (C) MDS was used to create an antigenic map from the PRNT50 titers generated against 614G, Alpha, Beta, Delta and Omicron authentic SARS-CoV-2. (D) Re-display of antigenic map in C with lilac arrows indicating antigen positions in map A and black arrows indicating antigen positions in map B. Viruses are shown as colored circles and antisera as squares with the same outline color as the matching viruses. Viruses and antisera are positioned in the map so that the distances between them are inversely related to the antibody titers, with minimized error. The grid in the background scales to a 2-fold dilution of antisera in the titrations. MDS: multidimensional scaling. PRNT50: plaque reduction neutralization titers resulting in 50% plaque reduction.

Fig. 4.. Antigenic cartography using authentic SARS-CoV-2.

(A-H) Neutralizing titers of hamsters infected with either (A) 614G, (B) Alpha, (C) Beta, (D) Gamma, (E) Zeta, (F) Delta, (G) Mu or (H) Omicron BA.1 viruses. (I) Multidimensional scaling was used to create an antigenic map utilizing PRNT50 titers generated from authentic SARS-CoV-2 on Calu-3 cells. See legend to Fig. 3 for details. Subdivided by dotted ellipses are variants possessing overlapping substitutions as indicated. Geometric mean is displayed above each graph. PRNT50: plaque reduction neutralization titers resulting in 50% plaque reduction. Dotted lines indicate limits of detection. Error bars indicate SEM.