Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that clamp the spike at its base

Therapeutic monoclonal antibodies can prevent severe disease in SARS-CoV-2 exposed individuals. However, currently circulating virus variants have evolved to gain significant resistance to nearly all neutralizing human immune system-derived therapeutic monoclonal antibodies that had previously been emergency-authorized for use in the clinic. Here, we describe the discovery of a panel of single-domain antibodies (VHHs) directed against the spike protein S2 subunit that broadly neutralize SARS-CoV-1 and -2 with unusually high potency. One of these VHHs tightly clamps the spike's monomers at a highly conserved, quaternary epitope in the membrane proximal part of the trimeric Heptad Repeat 2 (HR2) coiled-coil, thereby locking the HR2 in its prefusion conformation. Low dose systemic administration of a VHH-human IgG1 Fc fusion prevented SARS-CoV-2 infection in two animal models. Pseudovirus escape selection experiments demonstrate that the very rare escape variants are rendered almost non-infectious. This VHH-based antibody with a highly potent mechanism of antiviral action forms the basis for a new class of pan-sarbecovirus neutralizing biologics, which are currently under development. In addition, the unique quaternary binding mode of the VHHs to the prefusion HR2 could be exploited for other class I fusion proteins. ; sponsorship: We are grateful to G. Zimmer for providing reagents to generate VSV pseudotype particles; J. McLellan and D. Wrapp for providing SARS-CoV-2, SARS-CoV, MERS-CoV, and HKU1 spike and SARS-CoV-2 RBD proteins and expression plasmids for these proteins; We thank L. de Waal from Viroclinics for coordinating the hamster challenge study. We thank Leander Meuris for helping with statistical analysis of the hamster study body weight loss. We thank Piet Maes for providing a SARS-CoV-2 Omicron BA.1 isolate and Florian I Schmidt for providing replication competent VSV pseudotyped with SARS-CoV-2 spike. We thank the staff of the VIB Flow Core Ghent for providing access to flow cytometry equipment and ...