Broad Sarbecovirus Neutralization by an S2-Directed Plasma Antibody Defines a New Site of Vulnerability in SARS-like Viruses

Abstract

The repeated emergence of pathogenic coronaviruses highlights the continual threat of zoonotic spillover events and the need to understand conserved regions of the viral spike protein that influence immune recognition. Here, we employ high-resolution proteomic analysis of circulating immunoglobulins to characterize the antibody response to the SARS-CoV-2 spike protein in vaccinated and infected individuals. We recombinantly expressed abundant plasma IgG lineages and identified nine antibodies targeting the highly conserved S2 spike subunit. Most of these S2-reactive plasma mAbs (7 of 9) exhibited neutralizing activity against pangolin coronavirus, while one mAb (SC45) demonstrated potent (IC50 < 1 {micro}g/mL) neutralizing activity against both pangolin and bat sarbecoviruses RsSHC014 and WIV1. Additionally, SC45 exhibited potent prophylactic efficacy in the K18-hACE2 mouse model challenged with Pangolin-Guangdong CoV MP789 (Pg-CoV), significantly reducing lung viral replication at day 4 post-infection. The cryo-EM structure of SC45 bound to the prefusion-stabilized S2 domain of Pg-CoV reveals that SC45 targets a novel, conserved epitope in the connector domain. Strikingly, even though SC45 was the most abundant antibody ([~]13%) of anti-spike plasma IgG in an infected patient and binds to both SARS-CoV-2 and Pg-CoV spike with comparable affinities, it fails to neutralize early (D614G and Omicron BA.1) SARS-CoV-2 variants. Together, these findings identify a conserved site of vulnerability in the spike S2 subunit which informs on potential mechanisms of antibody immunity to zoonotic coronaviruses.