A glycan cluster on the SARS-CoV-2 spike ectodomain is recognized by Fab-dimerized glycan-reactive antibodies

Acharya, Priyamvada; Williams, Wilton; Henderson, Rory; Janowska, Katarzyna; Manne, Kartik; Parks, Robert; Deyton, Margaret; Sprenz, Jordan; Stalls, Victoria; Kopp, Megan; Mansouri, Katayoun; Edwards, Robert J; Meyerhoff, R. Ryan; Oguin, Thomas; Sempowski, Gregory; Saunders, Kevin; Haynes, Barton F.

The COVID-19 pandemic caused by SARS-CoV-2 has escalated into a global crisis. The spike (S) protein that mediates cell entry and membrane fusion is the current focus of vaccine and therapeutic antibody development efforts. The S protein, like many other viral fusion proteins such as HIV-1 envelope (Env) and influenza hemagglutinin, is glycosylated with both complex and high mannose glycans. Here we demonstrate binding to the SARS-CoV-2 S protein by a category of Fab-dimerized glycan-reactive (FDG) HIV-1-induced broadly neutralizing antibodies (bnAbs). A 3.1 Ã… resolution cryo-EM structure of the S protein ectodomain bound to glycan-dependent HIV-1 bnAb 2G12 revealed a quaternary glycan epitope on the spike S2 domain involving multiple protomers. These data reveal a new epitope on the SARS-CoV-2 spike that can be targeted for vaccine design. Highlights Fab-dimerized, glycan-reactive (FDG) HIV-1 bnAbs cross-react with SARS-CoV-2 spike. 3.1 Ã… resolution cryo-EM structure reveals quaternary S2 epitope for HIV-1 bnAb 2G12. 2G12 targets glycans, at positions 709, 717 and 801, in the SARS-CoV-2 spike. Our studies suggest a common epitope for FDG antibodies centered around glycan 709.