Fig. 2: Breakthrough infection induces durable SARS-CoV-2 RBD-specific memory B cell responses up to 6 months post-infection.

a Representative fluorescence-activated cell sorting gating strategy used to enumerate frequencies of (top) total (WT + BA.1) RBD-reactive B cells among class-switched (IgG⁺ or IgA⁺) CD19⁺ B cells and (bottom) WT-specific, BA.1-specific, and WT/BA.1 cross-reactive B cells among total RBD-reactive, class-switched (IgG⁺ or IgA⁺) CD19⁺ B cells. b, c Frequencies of b total RBD-reactive (P = 0.031) or c WT/BA.1 RBD cross-reactive (P = 0.032) B cells among class-switched CD19⁺ B cells at 1-month¹² (T1) and 5–6-month (T2) time points. Connected data points represent paired samples for each donor. Donors infected after two-dose mRNA vaccination (n = 3) are shown as circles and those infected after a third mRNA dose (n = 3) are shown as triangles. d Mean proportions of RBD-reactive, class-switched B cells that display WT-specific, BA.1-specific, or WT/BA.1 cross-reactive binding at each time point (n = 6 donors, P = 0.015). Proportions were derived from 36–417 RBD-specific B cells analyzed per donor. Error bars indicate the standard error of mean. Statistical significance is shown for WT-specific antibodies; differences in the proportions of cross-reactive and BA.1-specific antibodies were non-significant. e Clonal lineage analysis of RBD-directed antibodies isolated from four donors at the early¹² (T1) and late (T2) time points. Clonally expanded lineages (defined as antibodies with the same heavy and light chain germlines, same CDR3 lengths, and ≥80% CDRH3 sequence identity) are represented as colored slices. Each colored slice represents a clonal lineage, with the size of the slice proportional to the lineage size. Unique clones are combined into a single gray segment. The number of antibodies is shown in the center of each pie. Three of the donors (IML4042, IML4043, and IML4044) experienced BA.1 breakthrough infection following two-dose mRNA vaccination and the remaining donor (IML4045) was infected after a booster immunization. f Levels of somatic hypermutation, as determined by the number of nucleotide substitutions in the variable heavy (VH) region, at the early¹² (T1) and late (T2) time points among WT-specific (n = 146 and 283 at T1 and T2, respectively), WT/BA.1 cross-reactive (n = 10 and 24 at T1 and T2, respectively; P = 0.014), and BA.1-specific antibodies (n = 3 and 16 at T1 and T2, respectively; P = 0.002). Medians are shown by black bars. Statistical significance was determined by (b, c) two-tailed Wilcoxon matched-pairs signed rank test or (d, f) two-tailed Mann–Whitney U-test. swIg⁺, class-switched immunoglobulin. *P < 0.05; **P < 0.01. Source data and full statistical test results are provided as a Source Data file.