Clonotype specificity distinguishes epitope-tailored and permissive somatic hypermutation

Identifying antibody features that reliably encode epitope specificity poses a major barrier towards modeling antigen-antibody interactions. Affinity maturation offers a unique opportunity to probe the molecular basis of antigen-antibody interactions by revealing how individual somatic hypermutations (SHM) refine antibody binding. Using SARS-CoV-2 spike-specific germinal center B-cell repertoires, we show that antibodies harboring multiple SHMs that are restricted to their respective clonotypes (clonotype-restricted SHMs) preferentially recognize cryptic epitopes. We structurally characterized three such antibodies: two recognized a cryptic epitope on the receptor-binding domain whereas a third bound an N-terminal domain epitope that is almost entirely occluded in prefusion spike. In contrast, SHMs shared across multiple clonotypes using the same V gene recur across antibodies targeting diverse antigens but generally fail to enhance affinity when introduced into diverse antibody backgrounds. Together, these findings define a spectrum of SHM behavior, distinguishing epitope-tailored mutations from broadly recurrent but largely permissive substitutions.