A neutralizing epitope on the SD1 domain of SARS-CoV-2 spike targeted following infection and vaccination

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predo...

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Published in:	Cell reports (Cambridge) Vol. 40; no. 8; p. 111276
Main Authors:	Seow, Jeffrey, Khan, Hataf, Rosa, Annachiara, Calvaresi, Valeria, Graham, Carl, Pickering, Suzanne, Pye, Valerie E., Cronin, Nora B., Huettner, Isabella, Malim, Michael H., Politis, Argyris, Cherepanov, Peter, Doores, Katie J.
Format:	Journal Article
Language:	English
Published:	United States Elsevier Inc 23.08.2022 The Author(s)
Subjects:	Antibodies, Neutralizing Antibodies, Viral antibody COVID-19 Cryoelectron Microscopy cryogenic electron microscopy Epitopes Humans hydrogen-deuterium exchange Neutralization Tests neutralizing epitope omicron SARS-CoV-2 Spike Glycoprotein, Coronavirus spike subdomain 1 Syndactyly Vaccination hydrogen-deuterium exchange CP: Immunology SARS-CoV-2 spike subdomain 1 antibody omicron CP: Microbiology neutralizing epitope cryogenic electron microscopy
ISSN:	2211-1247, 2211-1247
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Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization. [Display omitted] •A neutralizing epitope on spike subdomain 1 (SD1) is identified•The SD1 epitope is conserved between current SARS-CoV-2 variants and SARS-CoV•SD1 antibodies arise from infection and vaccination•Cryo-EM reveals the SD1 epitope is occluded on many SARS-CoV-2 spike structures Seow et al. identify a class of broadly neutralizing antibodies that bind a conserved epitope on the spike subdomain 1 (SD1) and that are elicited following infection and vaccination. The SD1 epitope is occluded on spike prefusion structures, suggesting binding to a conformational state of spike.
AbstractList	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization. Seow et al. identify a class of broadly neutralizing antibodies that bind a conserved epitope on the spike subdomain 1 (SD1) and that are elicited following infection and vaccination. The SD1 epitope is occluded on spike prefusion structures, suggesting binding to a conformational state of spike. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization. [Display omitted] •A neutralizing epitope on spike subdomain 1 (SD1) is identified•The SD1 epitope is conserved between current SARS-CoV-2 variants and SARS-CoV•SD1 antibodies arise from infection and vaccination•Cryo-EM reveals the SD1 epitope is occluded on many SARS-CoV-2 spike structures Seow et al. identify a class of broadly neutralizing antibodies that bind a conserved epitope on the spike subdomain 1 (SD1) and that are elicited following infection and vaccination. The SD1 epitope is occluded on spike prefusion structures, suggesting binding to a conformational state of spike. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization.Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization.
ArticleNumber	111276
Author	Cherepanov, Peter Calvaresi, Valeria Graham, Carl Seow, Jeffrey Cronin, Nora B. Rosa, Annachiara Pye, Valerie E. Khan, Hataf Pickering, Suzanne Malim, Michael H. Politis, Argyris Huettner, Isabella Doores, Katie J.
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Keywords	hydrogen-deuterium exchange CP: Immunology SARS-CoV-2 spike subdomain 1 antibody omicron CP: Microbiology neutralizing epitope cryogenic electron microscopy
Language	English
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Present address: Faculty of Medicine, Wolfson Education Center, Hammersmith Campus, Imperial College London, Du Cane Road, London W12 0NN, UK These authors contributed equally Lead contact
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Snippet	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination....
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SubjectTerms	Antibodies, Neutralizing Antibodies, Viral antibody COVID-19 Cryoelectron Microscopy cryogenic electron microscopy Epitopes Humans hydrogen-deuterium exchange Neutralization Tests neutralizing epitope omicron SARS-CoV-2 Spike Glycoprotein, Coronavirus spike subdomain 1 Syndactyly Vaccination
Title	A neutralizing epitope on the SD1 domain of SARS-CoV-2 spike targeted following infection and vaccination
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