Clonal expansion, dissemination, and SHM at different time points. (A) Bubble plot showing the relative expansion of representative Env-specific B cell lineages in Rep-seq data generated from blood after the second, fourth, or sixth immunizations. The sizes of the bubbles correspond to the number of somatic variants identified for each lineage (data from one independent experiment). (B) Intraclonal analysis of SHM shown as percentage divergence from the assigned germline V gene sequence at the nucleotide level. Each box shows one clonal lineage, with each variant of the lineage identified in the Rep-seq represented as one dot. Data from Rep-seq libraries generated from the blood post-2, post-4, and post-6 time points (data from one independent experiment). (C) Average V region SHM of all the variants identified at the different time points per Ab lineage. The experiment was performed once, and the analyses, at least twice.