Somatic evolution of a cross-reactive germline antibody that expands its breadth to neutralize new SARS-CoV-2 variants

Abstract

Rapid antigenic drift of the SARS-CoV-2 receptor-binding domain (RBD) underlies immune escape and continues to challenge the durability of antibody-mediated protection. Among the major classes of RBD-directed antibodies, germline-encoded IGHV3-53 responses are highly potent against early SARS-CoV-2 variants but are generally compromised by Omicron-associated mutations. Here, we identify an intrinsically cross-reactive IGHV3-53 germline antibody that recognizes multiple pre-Omicron variants, including SARS-CoV-2 wild-type, Alpha, and Delta. Notably, we demonstrate that targeted somatic evolution can further expand this breadth to overcome the immune escape of different Omicron variants. Guided by integrated structural and sequence analyses, we introduce four somatic mutations (G26E, T28I, S53P, and Y58F) into the germline antibody, resulting in markedly enhanced binding and neutralization of Omicron BA.1, BA.2, and BA.4/5. High-resolution crystal structures reveal that these mutations re-establish critical interactions disrupted by substitutions on Omicron RBD and optimize affinity at a remodeled epitope interface. Collectively, our findings delineate a structural and mechanistic pathway through which an inherently cross-reactive germline antibody lineage can be adaptively refined to counter highly divergent SARS-CoV-2 variants. This work highlights the underappreciated breadth encoded within the naive B-cell repertoire and provides a conceptual framework for engineering and eliciting antibody responses resilient to future antigenic drift.