Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail

Dong, Jinhui; Zost, Seth J.; Greaney, Allison J.; Starr, Tyler N.; Dingens, Adam S.; Chen, Elaine C.; Chen, Rita E.; Case, James Brett; Sutton, Rachel E.; Gilchuk, Pavlo; Rodriguez, Jessica; Armstrong, Erica; Gainza, Christopher; Nargi, Rachel S.; Binshtein, Elad; Xie, Xuping; Zhang, Xianwen; Shi, Pei-Yong; Logue, James; Weston, Stuart; McGrath, Marisa E.; Frieman, Matthew B.; Brady, Tyler; Tuffy, Kevin; Bright, Helen; Loo, Yueh-Ming; McTamney, Patrick; Esser, Mark; Carnahan, Robert H.; Diamond, Michael S.; Bloom, Jesse D.; Crowe, James E.

The SARS-CoV-2 pandemic has led to an urgent need to understand the molecular basis for immune recognition of SARS-CoV-2 spike (S) glycoprotein antigenic sites. To define the genetic and structural basis for SARS-CoV-2 neutralization, we determined the structures of two human monoclonal antibodies COV2-2196 and COV2-21301, which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor binding domain (RBD) of SARS-CoV-2. COV2-2196 forms an “aromatic cage” at the heavy/light chain interface using germline-encoded residues in complementarity determining regions (CDRs) 2 and 3 of the heavy chain and CDRs 1 and 3 of the light chain. These structural features explain why highly similar antibodies (public clonotypes) have been isolated from multiple individuals1–4. The structure of COV2-2130 reveals that an unusually long LCDR1 and HCDR3 make interactions with the opposite face of the RBD from that of COV2-2196. Using deep mutational scanning and neutralization escape selection experiments, we comprehensively mapped the critical residues of both antibodies and identified positions of concern for possible viral escape. Nonetheless, both COV2-2196 and COV2-2130 showed strong neutralizing activity against SARS-CoV-2 strain with recent variations of concern including E484K, N501Y, and D614G substitutions. These studies reveal germline-encoded antibody features enabling recognition of the RBD and demonstrate the activity of a cocktail like AZD7442 in preventing escape from emerging variant viruses.