A human monoclonal antibody neutralizes SARS-CoV-2 Omicron variants by targeting the upstream region of spike protein HR2 motif

The continuous emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants means there is a need to explore additional strategies to develop broad-spectrum vaccines or therapeutics for individuals remaining at risk of coronavirus disease 2019 (COVID-19). Neutralizing monoclonal antibody (mAb) that binds to the conserved S2 subunit of the SARS-CoV-2 spike (S) protein alone, or in combination with mAb that binds to the receptor-binding domain (RBD) of S protein, might be effective in eliciting protection from infection by a variety of SARS-CoV-2 variants. Using high-throughput single-cell immunoglobulin sequencing of B cells from COVID-19-convalescent donors, we identified a high-affinity S2-specific mAb-39, that could inhibit original SARS-CoV-2 strain, Omicron BA.1, BA.2.86, BA.4, BA.5, and EG.5.1 S protein-mediated membrane fusion, leading to the neutralization of these pseudoviral infections. Moreover, mAb-39 could also improve the neutralizing activity of anti-RBD antibody against the highly neutralization-resistant Omicron variants. Molecular docking and point mutation analyses revealed that mAb-39 recognized epitopes within the conserved upstream region of the heptad repeat 2 (HR2) motif of the S2 subunit. Collectively, these findings demonstrate that targeting the conserved upstream region of the HR2 motif (e.g., using mAbs) provides a novel strategy for preventing the infection of SARS-CoV-2 and its variants.