Identification of a conserved neutralizing epitope present on spike proteins from all highly pathogenic coronaviruses

Huang, Yimin; Nguyen, Annalee W.; Hsieh, Ching-Lin; Silva, Rui; Olaluwoye, Oladimeji S.; Wilen, Rebecca E.; Kaoud, Tamer S.; Azouz, Laura R.; Qerqez, Ahlam N.; Le, Kevin C.; Bohanon, Amanda L.; DiVenere, Andrea M.; Liu, Yutong; Lee, Alison G.; Amengor, Dzifa; Shoemaker, Sophie R.; Costello, Shawn M.; Marqusee, Susan; Dalby, Kevin N.; D’Arcy, Sheena; McLellan, Jason S.; Maynard, Jennifer A.

Three pathogenic human coronaviruses have emerged within the last 20 years, with SARS-CoV-2 causing a global pandemic. Although therapeutic antibodies targeting the SARS-CoV-2 spike currently focus on the poorly conserved receptor-binding domain, targeting essential neutralizing epitopes on the more conserved S2 domain may provide broader protection. We report an antibody binding an epitope conserved in the pre-fusion core of MERS-CoV, SARS-CoV and SARS-CoV-2 spike S2 domains. Antibody 3A3 binds a conformational epitope with ~2.5 nM affinity and neutralizes spike from SARS-CoV, SARS-CoV-2 and variants of concern in in vitro pseudovirus assays. Hydrogen-deuterium exchange mass spectrometry identified residues 980-1006 in the flexible hinge region at the S2 apex as the 3A3 epitope, suggesting 3A3 prevents the S2 conformational rearrangements required for conversion to the spike post-fusion state and virus-host cell fusion. This work defines a conserved vulnerable site on the SARS-CoV-2 S2 domain and guides the design of pan-protective spike immunogens.