Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike
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Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic continues, with devasting consequences for human lives and the global economy 1,2. The discovery and development of virus-neutralizing monoclonal antibodies could be one approach to treat or prevent infection by this coronavirus. Here we report the isolation of sixty-one SARS-CoV-2-neutralizing monoclonal antibodies from five patients infected with SARS-CoV-2 and admitted to hospital with severe coronavirus disease 2019 (COVID-19). Among these are nineteen antibodies that potently neutralized authentic SARS-CoV-2 in vitro, nine of which exhibited very high potency, with 50% virus-inhibitory concentrations of 0.7 to 9 ng ml-1. Epitope mapping showed that this collection of nineteen antibodies was about equally divided between those directed against the receptor-binding domain (RBD) and those directed against the N-terminal domain (NTD), indicating that both of these regions at the top of the viral spike are immunogenic. In addition, two other powerful neutralizing antibodies recognized quaternary epitopes that overlap with the domains at the top of the spike. Cryo-electron microscopy reconstructions of one antibody that targets the RBD, a second that targets the NTD, and a third that bridges two separate RBDs showed that the antibodies recognize the closed, 'all RBD-down' conformation of the spike. Several of these monoclonal antibodies are promising candidates for clinical development as potential therapeutic and/or prophylactic agents against SARS-CoV-2.
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Extraction of neutralizing antibodies from COVID-19 patient serum verified the S protein's high immunogenicity, and the receptor binding domain (RBD) and N-terminal domains were also equally immunogenic.
“The extraction of neutralizing antibodies from COVID-19 patient’s serum verified the S protein’s high immunogenicity, whereas the receptor binding domain (RBD) and N-terminal domains were also equally immunogenic (NTD).”
From Modifications of mRNA vaccine structural elements for improving mRNA stability and translation efficiency (2022) · cites this paper as Liu et al. 2020
The opening summary (p. 1) reports neutralizing antibodies from five COVID-19 patients and says the potent antibodies were about equally divided between RBD and NTD targets, indicating that both spike regions are immunogenic. But “Isolation and construction of mAbs” (p. 2) describes sorting spike-binding memory B cells from blood and producing monoclonal antibodies from their sequences, not extracting antibodies from patient serum. (LLM, conf=0.90)
Experimental — accuracy not yet measuredMost of the strongest neutralizing antibodies against SARS-CoV-2 identified so far bind the RBD.
“We focused on the RBD since it is the target of the majority of the more potent SARS-CoV-2 neutralizing antibodies discovered to date21–26.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [25]
Antibodies in classes 1 and 2 are both highly potent and highly abundant.
“Class 1 and 2 antibodies are among the most potent and also the most abundant antibodies7,8,21,22,25,39.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [25]
mRNA vaccines induce antibodies to RBD, the main target of neutralizing antibodies, in a way that resembles natural infection.
“The vaccines elicit antibody responses against the RBD, the major target of neutralizing antibodies21–26, in a manner that resembles natural infection.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [25]
Pseudovirus neutralization does not always faithfully reproduce live-virus neutralization.
“These discrepant results highlight a previous observation 20 that pseudovirus neutralization does not always faithfully”
From Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 (2021) · cites this paper as [20]
Eighteen mutant pseudoviruses were made as previously described, and each had a robust titre adequate for neutralization studies.
“A total of 18 mutant pseudoviruses were made as previously described 20,21 , and each was found to have a robust titre (Extended Data Fig. 1c) that was adequate for neutralization studies.”
From Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7 (2021) · cites this paper as [20]
Neutralizing mAbs that bind regions of the viral spike have also been identified.
“Neutralizing mAbs that bind regions of the viral spike have also been identified (24, 33, 38–42).”
From mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection (2021) · cites this paper as [33]
Numerous neutralizing anti-RBD monoclonal antibodies have been characterized, the most potent of which block the RBD-ACE2 interaction.
“Numerous neutralizing anti-RBD monoclonal antibodies (mAbs) have been characterized, the most potent of which block the RBD-ACE2 interaction (16, 17, 22–24, 32–37).”
From mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection (2021) · cites this paper as [33]
Other spike epitopes, notably the NTD and also S2, contain neutralizing epitopes.
“other epitopes within the spike protein, notably the N-terminal domain (NTD) but also S2, do harbor neutralizing epitopes”
From SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2 (2021) · cites this paper as Liu et al., 2020
Vaccinating against the entire Spike protein, rather than only one of its structural components, is expected to result in an improved response that is less affected when the virus undergoes genetic drift.
“This implies that vaccinating against the entire S protein, rather than only one of its structural components, is expected to result in an improved response which will be less affected when the virus undergoes genetic drift [28]”
From The dawn of mRNA vaccines: the COVID-19 case (2021) · cites this paper as [28]
Isolation of neutralizing antibodies from COVID-19 patient serum confirmed strong immunogenicity of the Spike protein but showed equal immunogenicity of the receptor-binding domain and the N-terminal domain.
“isolation of neutralizing antibodies from the serum of COVID-19 patients confirmed the strong immunogenicity of the S protein, but showed an equal immunogenicity of the RBD and the N-terminal domain (NTD)”
From The dawn of mRNA vaccines: the COVID-19 case (2021) · cites this paper as [28]
Immunizing against the full S protein rather than just one of its structural units may lead to a better response that is not impacted by genetic drift.
“Therefore, immunizing against the full S protein rather than just one of its structural units may lead to a better response that is not impacted by genetic drift (Liu et al. 2020).”
From Modifications of mRNA vaccine structural elements for improving mRNA stability and translation efficiency (2022) · cites this paper as Liu et al. 2020
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“2B shows that D253G resides in the antigenic supersite within the N-terminal domain (15), which is a target for neutralizing antibodies (16), whereas the E484K is situated at the RBD interface with the cellular receptor ACE2.”
BackgroundSelf-citationN-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
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- Authors
- Liu, L., Wang, P., Nair, M. S., Yu, J., Rapp, M., Wang, Q., Luo, Y., Chan, J. F.-W., Sahi, V., Figueroa, A., Guo, X. V., Cerutti, G., Bimela, J., Gorman, J., Zhou, T., Chen, Z., Yuen, K.-Y., Kwong, P. D., Sodroski, J. G., Yin, M. T., Sheng, Z., Huang, Y., Shapiro, L., & Ho, D. D.
- Affiliations
- Aaron Diamond AIDS Research Center (US)
- Mortimer B. Zuckerman Mind Brain Behavior Institute (US)
- Harvard University (US)
- University of Hong Kong (HK)
- Columbia University (US)
- National Institutes of Health (US)
- Corresponding author
- Huang, Yaoxing
- Shapiro, Lawrence
- Ho, David D.
- ORCID
- Venue
- Nature
- Published
- 2020-07-22
- Volume
- 584
- Issue
- 7821
- Pages
- 450-456
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W3044660350
- Cited by
- 1,349
- References
- 56
- Citations by year
- 2026: 34 · 2025: 55 · 2024: 111 · 2023: 161 · 2022: 310 · 2021: 548 · 2020: 129
- FWCI
- 37.67
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Simons Foundation (SF 349247)
- JPB Foundation
- Tencent
- Innovation and Technology Commission
- National Institutes of Health (GM 103310)
- National Institute of General Medical Sciences (P41GM103310, GM103310, U24GM129539)
- Common Fund (U24 GM129539)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Keywords
- SARS-CoV-2, COVID-19 pandemic, neutralizing monoclonal antibodies, spike protein, receptor binding domain, N-terminal domain, epitope mapping, quaternary epitope, therapeutic antibodies
- MeSH terms
- Betacoronavirus, COVID-19, SARS-CoV-2, Animals, Antibodies, Monoclonal, Antibodies, Viral, Disease Models, Animal, Female, Humans, Immunoglobulin Fab Fragments, Lung, Male, Mesocricetus, Models, Molecular, Neutralization Tests, Pneumonia, Viral, Coronavirus Infections, Epitope Mapping, Epitopes, B-Lymphocyte, Cryoelectron Microscopy, Antibodies, Neutralizing, Pandemics, Spike Glycoprotein, Coronavirus
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