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

By Yimin Huang, Annalee W Nguyen, Ching-Lin Hsieh, Rui Silva, Oladimeji S Olaluwoye, Rebecca Wilen, Tamer S Kaoud, Laura R Azouz, Ahlam N Qerqez, Kevin C Le, amanda L Bohanon, Andrea M DiVenere, Yutong Liu, Dzifa Amengor, Kevin Dalby, Sheena D'Arcy, Jason S McLellan, Jennifer A Maynard

Posted 01 Feb 2021
bioRxiv DOI: 10.1101/2021.01.31.428824

Three pathogenic human coronaviruses have emerged, with SARS-2 causing a global pandemic. While therapeutic antibodies targeting the SARS-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 three antibodies binding epitopes conserved on the pre-fusion MERS, SARS-1 and SARS-2 spike S2 domains. Antibody 3A3 binds a conformational epitope with ~2.5 nM affinity and neutralizes in in vitro SARS-2 cell fusion and pseudovirus assays. Hydrogen-Deuterium exchange mass spectrometry identified residues 980-1006 in the flexible hinge region at the S2 apex as the 3A3 epitope, consistent with binding to natural and engineered spike variants. This location at the spike trimer interface suggests 3A3 prevents the S2 conformational rearrangements required for virus-host cell fusion. This work defines a highly conserved vulnerable site on the SARS-2 S2 domain and may help guide design of pan-protective spike immunogens.

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