Fig. 3: Vaccination induces an IgA⁺ anti-S2 response on day 7 followed by an IgG⁺ anti-RBD response on days 21 and 28.

a, Flow cytometry data, showing percentages of S-specific plasmablasts in all IgG⁺ and IgA⁺ plasmablasts (left), S-specific S-B_mem cells in all IgG⁺ and IgA⁺ S-B_mem cells (center) and IgG⁺ S-specific S-B_mem cells in all S-specific IgG⁺ and IgA⁺ S-B_mem cells (right). Individual data points are averages of two independent experiments, including n = 9 participants at four time points. b–f, Single-cell transcriptome and BCR repertoire sequencing data of S-specific and nonspecific sorted B cells showing UMAP visualization with cluster assignments of S_R-B_mem cells, S_A-B_mem cells and plasmablasts (b, left) and antigen-specificity to S2, RBD and S1n (b, right). Proportions of cells shown in b, separated by antigen and cluster (c), day and antigen (d), antigen and clonality (e) and antigen and immunoglobulin class (f). g, Plasma IgG levels against S2 (left), RBD (center) and S1 (right) for n = 9 individuals at five time points. Area under the curve (AUC) for plasma dilutions are shown as individual data points. h, Ratio of IgG levels of day 120 AUC to day 28 AUC for antigens S2, RBD and S1. Gray dots represents the vaccinated participant who contracted COVID-19 2 weeks before day 120 and is excluded from statistics. Individual data points and medians for n = 9 participants are shown. i, Plasma neutralization of SARS-CoV-2 pseudovirus shown as dilution curves (left) and quantification (NT50) of neutralization titers (right) of n = 9 individuals at five time points. j, Single-cell BCR repertoire sequencing data showing IGHV and IGLV gene SHM frequencies of B cells specific for S2 (n = 210 cells, left), RBD (n = 124 cells, center) and S1n (n = 24 cells, right) at three time points after vaccination. Dashed line indicates the average mutation frequency of sorted nonspecific B cells. Individual data points represent single B cells from n = 9 individuals. Individual values, means and s.d. are shown (a,j). Exact P values according to two-tailed one-way ANOVA, followed by Dunnett’s multiple comparison test (a,g–i), chi-squared test (c–f), two-tailed Kruskal–Wallis test followed by Dunnett’s multiple comparison test (j). PB, plasmablast.

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