Domain-Specific Impacts of Spike Protein Mutations on Infectivity and Antibody Escape in SARS-CoV-2 Omicron BA.1

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic began in Wuhan, China in late 2019, rapidly spreading worldwide and causing the COVID-19 pandemic. The virus evolved through multiple variants, with Omicron (first detected in late 2021) becoming dominant due to its extensive spike mutations, which enhanced immune evasion despite reduced infectivity compared to earlier strains. Here, we systematically evaluated the functional consequences of these mutations by generating pseudoviruses expressing spike proteins with domain-specific alterations. Mutations in the N-terminal domain (NTD) significantly enhanced pseudoviral infectivity, while receptor-binding domain (RBD) mutations markedly reduced infectivity. Importantly, NTD-mediated enhancement was attenuated when combined with RBD mutations, highlighting a complex interplay between spike regions. Despite lower infectivity compared to Delta, BA.1 pseudoviruses harboring RBD mutations exhibited robust resistance to neutralizing monoclonal antibodies, including casirivimab and imdevimab, with IC50 values exceeding assay limits. These findings indicate that Omicron BA.1’s rapid global spread is driven by enhanced immune evasion conferred by RBD mutations, even at the expense of viral entry efficiency. Our domain-specific analysis underscores the critical roles of spike protein mutations in shaping Omicron BA.1’s transmissibility and antibody escape, informing strategies for therapeutic and vaccine development.