Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that bind a conserved membrane proximal epitope of the spike


Sieglinde De Cae, Inge Van Molle, Loes van Schie, Sophie R. Shoemaker, Julie Deckers, Nincy
Debeuf, Sahine Lameire, Wim Nerinckx, Kenny Roose, Daria Fijalkowska, Simon Devos,
Anne-Sophie Desmet, Jackeline Cecilia Zavala Marchan, Toon Venneman, Koen Sedeyn, Marlies
Ballegeer, Manon Vanheerswynghels, Caroline De Wolf, Hans Demol, Pieter
Vanhaverbeke, Gholamreza Hassanzadeh Ghassabeh, Chiara Lonigro, Viki Bockstal, Manuela
Rinaldi, Rana Abdelnabi, Johan Neyts, Susan Marqusee, Bart N. Lambrecht, Nico
Callewaert, Han Remaut, Xavier Saelens, Bert Schepens

bioRxiv preprint doi: https://doi.org/10.1101/2023.03.10.531533; posted March 10, 2023

Currently circulating SARS-CoV-2 variants have gained complete or significant resistance to all SARSCoV-2-neutralizing antibodies that have been used in the clinic. Such antibodies can prevent severe disease in SARS-CoV-2 exposed patients for whom vaccines may not provide optimal protection. Here, we describe single-domain antibodies (VHHs), also known as nanobodies, that can broadly neutralize SARS-CoV-2 with unusually high potency. Structural analysis revealed their binding to a unique, highly conserved, membrane proximal, quaternary epitope in the S2 subunit of the spike. Furthermore, a VHH-human IgG1 Fc fusion, efficiently expressed in Chinese hamster ovary cells as a stable antibody construct, protected hamsters against SARS-CoV-2 replication in a therapeutic setting when administered systemically at low dose. This VHH-based antibody represents a new candidate anti-COVID-19 biologic that targets the Achilles heel of the viral spike.