Broadly neutralizing and protective nanobodies against diverse sarbecoviruses

Abstract

As SARS-CoV-2 Omicron and other variants of concern continue spreading around the world, development of antibodies and vaccines to confer broad and protective activity is a global priority. Here, we report on the identification of a special group of nanobodies from immunized alpaca with exceptional breadth and potency against diverse sarbecoviruses including SARS-CoV-1, Omicron BA.1, and BA.2. Crystal structure analysis of one representative nanobody, 3-2A2-4, revealed a highly conserved epitope between the cryptic and the outer face of the receptor binding domain (RBD). The epitope is readily accessible regardless of RBD in up or down conformation and distinctive from the receptor ACE2 binding site. Passive delivery of 3-2A2-4 protected K18-hACE2 mice from infection of authentic SARS-CoV-2 Delta and Omicron. This group of nanobodies and the epitope identified should provide invaluable reference for the development of next generation antibody therapies and vaccines against wide varieties of SARS-CoV-2 infection and beyond.

Accelerating PERx reaction enables covalent nanobodies for potent neutralization of SARS-CoV-2 and variants

“…We therefore used a different nanobody (Nb70) capable of binding with Omicron variants by contacting two RBDs in their up state. 38 We decided to incorporate FSY at site G56, Y103, or D115 of nanobody Nb70 according to the crystal structure 38 to target the K386, Y369, or K378 site of the spike RBD, respectively (Figure S10A). All three sites in Nb70, after FSY incorporation, allowed efficient covalent cross-linking of both the Omicron BA.1 and BA.2 spike RBDs (Figure S10B).…”