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[Preprint]. 2024 Dec 9:2024.12.06.625234. [Version 1] doi: 10.1101/2024.12.06.625234

Defining a highly conserved B cell epitope in the receptor binding motif of SARS-CoV-2 spike glycoprotein

Sameer Kumar Malladi, Deepika Jaiswal, Baoling Ying, Wafaa B Alsoussi, Tamarand L Darling, Bernadeta Dadonaite, Alesandro Civljak, Stephen C Horvath, Julian Q Zhou, Wooseob Kim, Jackson S Turner, Aaron J Schmitz, Fangjie Han, Suzanne M Scheaffer, Christopher W Farnsworth, Raffael Nachbagauer, Biliana Nestorova, Spyros Chalkias, Michael K Klebert, Darin K Edwards, Robert Paris, Benjamin S Strnad, William D Middleton, Jane A O’Halloran, Rachel M Presti, Jesse D Bloom, Adrianus C M Boon, Michael S Diamond, Goran Bajic, Ali H Ellebedy
PMCID: PMC11661108  PMID: 39713327

Abstract

SARS-CoV-2 mRNA vaccines induce robust and persistent germinal centre (GC) B cell responses in humans. It remains unclear how the continuous evolution of the virus impacts the breadth of the induced GC B cell response. Using ultrasound-guided fine needle aspiration, we examined draining lymph nodes of nine healthy adults following bivalent booster immunization. We show that 77.8% of the B cell clones in the GC expressed as representative monoclonal antibodies recognized the spike protein, with a third (37.8%) of these targeting the receptor binding domain (RBD). Strikingly, only one RBD-targeting mAb, mAb-52, neutralized all tested SARS- CoV-2 strains, including the recent KP.2 variant. mAb-52 utilizes the IGHV3-66 public clonotype, protects hamsters challenged against the EG.5.1 variant and targets the class I/II RBD epitope, closely mimicking the binding footprint of ACE2. Finally, we show that the remarkable breadth of mAb-52 is due to the somatic hypermutations accumulated within vaccine-induced GC reaction.

One Sentence Summary

Booster SARS-CoV-2 mRNA vaccine recruits and broadens GC B cell responses targeting a highly conserved site on receptor binding domain of spike glycoprotein.

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