Abstract
Class switch recombination (CSR) allows B cells to produce antibodies with distinct effector functions, but its dynamics during a primary human response remain poorly understood. We sampled COVID-19-naïve healthy volunteers every other day during the first three weeks after SARS-CoV-2 vaccination, combining bulk and single-cell cell receptor repertoires, single-cell transcriptomics, immunophenotyping, and IGHC sterile transcript analysis. Vaccine-specific B cells show sterile transcription across all IGHC genes up to IGHG2, contradicting the prevailing idea of single-gene sterile transcription. Clonal tracking confirms that sequential CSR exists: e.g. IGHG3 to IGHG1, IGHG1 to IGHA1 and IGHG2, with sparse switching beyond IGHG2. VDJ gene usage associates with specific isotype subclasses and differential CSR timing. CSR and somatic hypermutation are temporally decoupled, with antigen-specific clones remaining hypomutated up to ten weeks post-immunization. These findings complement textbook models of CSR and inform strategies for vaccines requiring switching to key isotypes such as IgG1 or IgA2.