Immunoglobulin isotype switching ceases in germinal centres

B cell-derived antibodies are essential to protect against infection and underpin the success of most existing vaccines. Class switch recombination (CSR) is a tightly controlled DNA recombination that replaces the constant region of an antibody for the isotype that can best protect against the invading pathogen. Germinal centres (GCs) are thought to favour immunoglobulin (Ig) diversification through somatic hypermutation (SHM) and CSR at least in part because activation-induced cytidine deaminase (AID), the enzyme required for both processes, is highly expressed in GC B cells. Nevertheless, CSR also occurs in extrafollicular (EF) responses and can be initiated soon after T cell priming. Here we show that CSR is initiated prior to B cell commitment to follicular or EF differentiation and comparable proportions of switched cells are found at both sites, with little or no enrichment within GCs. Single-cell analysis of germline transcripts (GLTs) showed that CSR is triggered prior to B cell entry into the follicle and rapidly declines as B cells become GC cells. Analysis of the clonal distribution and phylogeny of individual IgM-expressing GC B cells demonstrated that CSR events largely occurred in GC B cell precursors ceasing within the first two days of differentiation into GC B cells and soon after the onset of SHM. This data also demonstrated the existence of IgM-dominated GCs. Mathematical modelling showed that IgM-dominated GCs are unlikely to occur under the assumption of ongoing switching. Lack of ongoing switching in GCs may be crucial to maintain IgM+ memory B cells that can produce adequate protective isotypes upon reinfection with antigenically-related pathogens. The chromosomal breaks required for CSR can also cause pathogenicity, gene insertions and translocations, resulting in the formation of self-reactive BCRs or giving rise to B cell lymphomas. Therefore, understanding the timing and anatomical location in which CSR occurs is a crucial aspect of B cell biology to better comprehend autoimmunity, B-cell derived lymphomas, and eventually improve the design of future vaccines