Fig. 3: B cell immune imprinting after repeated Omicron infections.

a–d, Flow cytometry analysis of pooled B cells from individuals who had recovered from Omicron infection. BA.1 (top) and BA.2 (bottom) RBD double-positive CD20⁺IgM⁻IgD⁻CD27⁺ B cells were isolated for paired-single-cell V(D)J sequencing. Flow cytometry analyses were performed in cohorts of the following: 2 months after BA.1 (top) or BA.2 (bottom) breakthrough infections (a), 8 months after BA.1 (top) or BA.2 (bottom) breakthrough infections (b), 1 month after BA.5/BF.7 reinfection after BA.1 (top) and BA.2 (bottom) breakthrough infections (c), and 2–3 months after BA.5/BF.7 reinfection after BA.1 (top) or BA.2 (bottom) infection without SARS-CoV-2 vaccination history (d). APC, allophycocyanin; FITC, fluorescein isothiocyanate; PE, phycoerythrin; BV605, Brilliant Violet 605. e, Proportions of WT-binding and non-WT-binding antibodies from Omicron breakthrough infection and repeated Omicron infection cohorts. Binding specificity was determined by ELISA. The antibodies were expressed in vitro using the sequence of the RBD-binding memory B cells from various cohorts. f, The heavy-chain variable domain somatic hypermutation rate of the monoclonal antibodies (mAbs) from various cohorts. Two-tailed Wilcoxon rank-sum tests. Boxes indicate the 25th percentile, median and 75th percentile, and whiskers extend to median ± 1.5 times the interquartile range. Violin plots show kernel density estimation curves of the distribution. The numbers and ratios of samples in each group are labelled above the violin plots. g,h, The BA.1 (g) or BA.2 (h) pseudovirus-neutralizing ability (IC₅₀) of monoclonal antibodies from various cohorts. Detection limit is denoted as a dashed line, and geometric mean is denoted as black bar. Geometric mean, fold changes and the number of antibodies are indicated above the plots. f–h, Two-tailed Wilcoxon rank-sum tests.