Antigenic cartography using variant-specific hamster sera reveals substantial antigenic variation among Omicron subvariants

Abstract

Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has developed substantial antigenic variability. As the majority of the population now has pre-existing immunity due to infection or vaccination, the use of experimentally generated animal immune sera can be valuable for measuring antigenic differences between virus variants. Here, we immunized Syrian hamsters by two successive infections with one of nine SARS-CoV-2 variants. Their sera were titrated against 16 SARS-CoV-2 variants, and the resulting titers were visualized using antigenic cartography. The antigenic map shows a condensed cluster containing all pre-Omicron variants (D614G, Alpha, Delta, Beta, Mu, and an engineered B.1+E484K variant) and considerably more diversity among a selected panel of Omicron subvariants (BA.1, BA.2, BA.4/BA.5, the BA.5 descendants BF.7 and BQ.1.18, the BA.2.75 descendant BN.1.3.1, the BA.2-derived recombinants XBB.2 and EG.5.1, and the BA.2.86 descendant JN.1). Some Omicron subvariants were as antigenically distinct from each other as the wildtype is from the Omicron BA.1 variant. Compared to titers measured in human sera, titers in hamster sera are of higher magnitude, show less fold change, and result in a more compact antigenic map topology. The results highlight the potential of sera from hamsters for the continued antigenic characterization of SARS-CoV-2.

Keywords: SARS-CoV-2; immunology; vaccines.

Fig. 1.

Neutralizing titers of 17 live virus isolates titrated against sera from hamsters twice infected with D614G, Alpha, Beta, Delta, Mu, B.1+E484K, Omicron BA.1, Omicron BA.2 (two isolates), Omicron BA.5, and Omicron XBB.2. Variants that were titrated are D614G, Alpha, Beta, Delta, Mu, B.1+E484K, Omicron BA.1, Omicron BA.2 (two isolates), Omicron BA.4, Omicron BA.5, Omicron BF.7, Omicron BQ.1.18, Omicron XBB.2, Omicron BN.1.3.1, Omicron EG.5.1, Omicron JN.1. Detectable titers are shown as filled in circles, nondetectable titers are shown as empty circles. Lines connecting nondetectable titers are dashed. Since not all variant and serum pairs were tested in all dilutions, nondetectable titers range from <1:160 to <1:20.

Fig. 2.

Antigenic map showing antigenic relationships between SARS-CoV-2 variants and sera. Distances between each variant and serum correspond to the fold change to the maximum titer for each serum. Viruses are shown as circles, sera as squares, with sera colored by the color of their homologous variant (blue: D614G, green: Alpha, dark-yellow: Beta, orange: Delta, green-blue: Mu, cyan: B.1+E484K, red: BA.1, orchid: BA.2 (2×, on top of each other), pink: BA.4 and BA.5, ochre: BQ.1.18, maroon: BF.7, sea-green: XBB.2, light-orchid: BN.1.3.1, dark blue: EG.4.1, yellow: JN.1). The side length of each grid square corresponds to a twofold serum dilution in the neutralization assay. The rotation of the map is arbitrary and is here oriented to correspond to previously published maps (8, 34).

Fig. 3.

Comparison of hamster and human sera. Comparison is shown according to titer magnitude (A and B), fold change (C and D), and antigenic maps (E and F). (A) GMT of hamster (green) and human (red) sera. Dots correspond to the GMT, lines to the estimated 95% highest posterior density interval (HPDI). (B) Posterior distributions of the estimated titer magnitude explained by whether a titer was measured using hamster (green) or human (red) sera, as well as the contrast of these distributions (Human–Hamster). The dot corresponds to the mean, the bar to the 95% HPDI. (C) Fold change estimated in hamster (green) and human (red) sera. Variants are ordered by decreasing fold change in the hamster sera. Dots correspond to the mean fold change, lines to the estimated 95% HPDI. Fold change is shown on the log₂ scale. (D) Posterior distributions of the estimated slope explained by whether a titer was measured using hamster (green) or human (red) sera, as well as the contrast of these distributions (Human–Hamster). The dot corresponds to the mean, the bar to the 95% HPDI. (E) Antigenic map constructed from a subset of the hamster data. (F) Antigenic map constructed using the human sera data. In panels E and F, the arrows point to the position of the variants in the human and hamster maps, respectively.