Structural and functional characterization of a conserved cryptic epitope on SARS-CoV-2 spike S2 subunit

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone extensive evolution since its emergence in 2019, underscoring the continuous need for vaccines and therapeutics effective against multiple variants of concern (VOCs). The S2 subunit of the viral spike (S) glycoprotein is highly conserved among sarbecoviruses, making it an attractive target for broadly protective countermeasures. To elucidate the S2 antigenic landscape, we employed yeast surface display to isolate S2-targeted antibodies from COVID-19 convalescent donors. Biophysical characterization revealed that these S2 apex-directed antibodies preferentially bind to open spike conformations and a stabilized S2 construct but not to the closed, trimeric prefusion spike. Cryo-electron microscopy structures defined a cryptic epitope encompassing the upper helix and fusion peptide proximal region on S2. This epitope is conserved among sarbecoviruses but remains largely occluded in the closed prefusion conformation of the spikes. As a result, the antibodies exhibited weak neutralization activity against SARS-CoV-2 pseudoviruses, failed to neutralize authentic viruses, and did not provide protection in a lethal mouse challenge model using a mouse-adapted SARS-CoV-2 strain. These findings highlight a non-neutralizing epitope on S2 capable of eliciting antibodies during SARS-CoV-2 infection in humans and provide valuable reagents for probing S2 conformational dynamics and optimizing S2-based vaccine antigens.

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Publication Details

Journal
PLoS Pathogens
Published
2026-08-03
DOI
https://doi.org/10.1371/journal.ppat.1014391
Primary Topic
SARS-CoV-2 and COVID-19 Research
Type
article
Field-Weighted Citation Impact
0.00

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article

Structural and functional characterization of a conserved cryptic epitope on SARS-CoV-2 spike S2 subunit

John M. Powers, Jason S. McLellan, Sarah R. Leist, Elizabeth C. Gardner et al.
PLoS Pathogens
SARS-CoV-2 and COVID-19 Research
article

Structural and functional characterization of a conserved cryptic epitope on SARS-CoV-2 spike S2 subunit

John M. Powers, Jason S. McLellan, Sarah R. Leist, Elizabeth C. Gardner, Sophie R. Shoemaker, Alexandra L. Tse, Emily Happy Miller, Jimmy Gollihar, Kamyab Javanmardi, Daniel R. Boutz, Nicole V. Johnson, Lily E. Adams, Kartik Chandran, Ling Zhou, Albert Wang, Ching‐Lin Hsieh, Ralph S. Baric, Jonathan Schisler, Susan Marqusee, Connor M. Mullins, Andrew P. Horton, Michael L. Mallory
article en

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone extensive evolution since its emergence in 2019, underscoring the continuous need for vaccines and therapeutics effective against multiple variants of concern (VOCs). The S2 subunit of the viral spike (S) glycoprotein is highly conserved among sarbecoviruses, making it an attractive target for broadly protective countermeasures. To elucidate the S2 antigenic landscape, we employed yeast surface display to isolate S2-targeted antibodies from COVID-19 convalescent donors. Biophysical characterization revealed that these S2 apex-directed antibodies preferentially bind to open spike conformations and a stabilized S2 construct but not to the closed, trimeric prefusion spike. Cryo-electron microscopy structures defined a cryptic epitope encompassing the upper helix and fusion peptide proximal region on S2. This epitope is conserved among sarbecoviruses but remains largely occluded in the closed prefusion conformation of the spikes. As a result, the antibodies exhibited weak neutralization activity against SARS-CoV-2 pseudoviruses, failed to neutralize authentic viruses, and did not provide protection in a lethal mouse challenge model using a mouse-adapted SARS-CoV-2 strain. These findings highlight a non-neutralizing epitope on S2 capable of eliciting antibodies during SARS-CoV-2 infection in humans and provide valuable reagents for probing S2 conformational dynamics and optimizing S2-based vaccine antigens.

PLoS PathogensVol. 22(8)
QB3 (US), University of North Carolina at Chapel Hill (US), Houston Methodist (US), Albert Einstein College of Medicine (US), Chan Zuckerberg Initiative (United States) (US), The University of Texas at Austin (US), University of California, Berkeley (US)
Bill and Melinda Gates Foundation, Welch Foundation, University of Texas at Austin, National Institutes of Health, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases
Good health and well-being
Openalex Percentile: Top 9%
SARS-CoV-2 and COVID-19 Research
DOIOpen Access PDFOpenAlex
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