A generalized framework to identify SARS-CoV-2 broadly neutralizing antibodies

Abstract

AbstractMonoclonal antibodies (mAbs) targeting the SARS-CoV-2 receptor-binding domain (RBD) showed high efficacy in the prevention and treatment of COVID-19. However, the rapid evolution of SARS-CoV-2 has rendered all clinically authorized mAbs ineffective and continues to stymie the development of next-generation mAbs. Consequently, the ability to identify broadly neutralizing antibodies (bnAbs) that neutralize both current and future variants is critical for successful antibody therapeutic development, especially for newly emerged viruses when no knowledge about immune evasive variants is available. Here, we have developed a strategy to specifically select for potent bnAbs with activity against both existing and prospective SARS-CoV-2 variants based on accurate viral evolution prediction informed by deep mutational scanning (DMS). By adopting this methodology, we increased the probability of identifying XBB.1.5-effective SARS-CoV-2 bnAbs from ∼1% to 40% if we were at the early stage of the pandemic, as revealed by a retrospective analysis of >1,000 SARS-CoV-2 wildtype (WT)-elicited mAbs. From this collection, we identified a bnAb, designated BD55-1205, that exhibited exceptional activity against historical, contemporary, and predicted future variants. Structural analyses revealed extensive polar interactions between BD55-1205 and XBB.1.5 receptor-binding motif (RBM), especially with backbone atoms, explaining its unusually broad reactivity. Importantly, mRNA-based delivery of BD55-1205 IgG to human FcRn-expressing transgenic mice resulted in high serum neutralizing titers against selected XBB and BA.2.86 subvariants. Together, the ability to identify bnAbs via accurate viral evolution prediction, coupled with the speed and flexibility of mRNA delivery technology, provides a generalized framework for the rapid development of next-generation antibody-based countermeasures against SARS-CoV-2 and potentially other highly variable pathogens with pandemic potential.