N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
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Abstract
The SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite (designated site i) recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge, albeit selecting escape mutants in some animals. Indeed, several SARS-CoV-2 variants, including the B.1.1.7, B.1.351, and P.1 lineages, harbor frequent mutations within the NTD supersite, suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs for protective immunity and vaccine design.
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Altered residues in the NTD are found in the NTD 'supersite' targeted by most anti-NTD neutralizing antibodies.
“These altered residues are found in the NTD 'supersite' that is targeted by most anti-NTD neutralizing antibodies 15 .”
From Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization (2021) · cites this paper as [15]
Mutations in the NTD and RBD can confer neutralization resistance by altering epitopes of neutralizing antibodies.
“Mutations in the N-terminal domain (NTD), which contains an antigenic supersite (McCallum et al., 2021), and the receptor-binding domain (RBD), which binds to the angiotensin-converting enzyme 2 (ACE2) receptor (Hoffmann et al., 2020b; Zhou et al., 2020), can confer neutralization resistance by altering epitopes of neutralizing antibodies.”
From The Omicron variant is highly resistant against antibody-mediated neutralization: Implications for control of the COVID-19 pandemic (2022) · cites this paper as McCallum et al., 2021
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 McCallum et al., 2021
Memory B cell-derived mAbs have also shown a key NTD antibody target role.
“The key role of NTD as target for antibodies has recently also been shown using memory B cell-derived mAbs (McCallum et al., 2021).”
From SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2 (2021) · cites this paper as McCallum et al., 2021
The Gamma variant contains five NTD mutations, of which L18F has been shown to interfere with the binding of NTD-targeting neutralizing antibodies.
“It also contains five NTD mutations, of which L18F has been shown to interfere with the binding of NTD-targeting neutralizing antibodies 51 .”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [51]
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Evaluation of the mRNA-1273 Vaccine against SARS-CoV-2 in Nonhuman Primates
Corbett, K. S., Flynn, B., Foulds, K. E., Francica, J. R., Boyoglu-Barnum, S., Werner, A. P., Flach, B., O’Connell, S., Bock, K. W., Minai, M., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2024671 · Cited by 1,066 · see citing works
Potently neutralizing and protective human antibodies against SARS-CoV-2
Zost, S. J., Gilchuk, P., Case, J. B., Binshtein, E., Chen, R. E., Nkolola, J. P., Schäfer, A., Reidy, J. X., Trivette, A., Nargi, R. S., et al. (2020) · Nature · doi:10.1038/s41586-020-2548-6 · Cited by 1,041 · see citing works
Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
Yurkovetskiy, L., Wang, X., Pascal, K. E., Tomkins-Tinch, C., Nyalile, T. P., Wang, Y., Baum, A., Diehl, W. E., Dauphin, A., Carbone, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.032 · Cited by 1,025 · see citing works
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“, 2020), and numerous monoclonal antibodies (mAbs) recognizing this domain have been isolated and characterized (Barnes et al., 2020a, 2020b; Baumet al., 2020b; Brouwer et al., 2020; Hansen et al., 2020; Ju et al., 2020; Piccoli et al., 2020; Pinto et al., 2020; Tortorici et al., 2020; Wang et al., 2020; Wu et al., 20…”
A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis
Zivanov, J., Nakane, T., & Scheres, S. H. W. (2018) · IUCrJ · doi:10.1107/s205225251801463x · Cited by 947 · see citing works
Real-time cryo–EM data pre-processing with Warp
Tegunov, D., & Cramer, P. (2018) · Nature Methods · doi:10.1038/s41592-019-0580-y · Cited by 923 · cited 1× · see citing works
“Cryo-EM data processing Movie frame alignment, estimation of the microscope contrast-transfer function parameters, particle picking and extraction (with a box size of 400 pixels(2)) were carried out usingWarp (Tegunov and Cramer, 2019).”
SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo
Hou, Y. J., Chiba, S., Halfmann, P., Ehre, C., Kuroda, M., Dinnon, K. H., Leist, S. R., Schäfer, A., Nakajima, N., Takahashi, K., et al. (2020) · Science · doi:10.1126/science.abe8499 · Cited by 900 · see citing works
EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
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“, 2010), EMringer(Barad et al., 2015), and Phenix (Liebschner et al.”
Visualizing density maps with UCSF Chimera
Goddard, T. D., Huang, C. C., & Ferrin, T. E. (2006) · Journal of Structural Biology · doi:10.1016/j.jsb.2006.06.010 · Cited by 876 · cited 1× · see citing works
“Cryo-EM model building and analysis UCSF Chimera (Goddard et al., 2007) and Coot (Casañal et al.”
Casañal, A., Lohkamp, B., & Emsley, P. (2019) · Protein Science · doi:10.1002/pro.3791 · Cited by 812 · cited 2× · see citing works
“Several subsequent rounds of model building and refinement were performed using Coot (Casañal et al., 2019) and Phenix-Refine (Adams et al.”
Barnes, C. O., West, A. P., Huey-Tubman, K. E., Hoffmann, M. A. G., Sharaf, N. G., Hoffman, P. R., Koranda, N., Gristick, H. B., Gaebler, C., Muecksch, F., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.025 · Cited by 795 · see citing works
Single-Shot Ad26 Vaccine Protects Against SARS-CoV-2 in Rhesus Macaques
Mercado, N. B., Zahn, R., Wegmann, F., Loos, C., Chandrashekar, A., Yu, J., Liu, J., Peter, L., McMahan, K., Tostanoski, L. H., et al. (2020) · Nature · doi:10.1038/s41586-020-2607-z · Cited by 789 · cited 1× · see citing works
“SARS-CoV-2 S is the main target of neutralizing antibodies (Abs) in infected individuals and the focus of the many nucleic acid, vectored, and protein subunit vaccines currently deployed or in development (Corbett et al., 2020a, 2020b; Erasmus et al., 2020; Hassan et al., 2020; Keech et al., 2020; Mercado et al., 2020…”
Structural insights into coronavirus entry
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“The S1 subunit comprises an N-terminal domain (NTD) and a receptor-binding domain (RBD), also known as domain A and B, respectively (Tortorici and Veesler, 2019).”
Self-citationProspective mapping of viral mutations that escape antibodies used to treat COVID-19
Starr, T. N., Greaney, A. J., Addetia, A., Hannon, W. W., Choudhary, M. C., Dingens, A. S., Li, J. Z., & Bloom, J. D. (2021) · Science · doi:10.1126/science.abf9302 · Cited by 743 · see citing works
SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R., Walls, A. C., Kemp S, S. A., Bassi, J., Pinto, D., Fregni, C. S., et al. (2021) · doi:10.1101/2021.01.19.21249840 · Cited by 729 · see citing works
Self-citationSensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., Kemp, S. A., Bassi, J., Pinto, D., Silacci-Fregni, C., et al. (2021) · Nature · doi:10.1038/s41586-021-03412-7 · Cited by 728 · cited 2× · see citing works
“, 2020), would circumvent neutralization by S2M28, S2X28, S2X333, and 4A8 (Collier et al., 2021).”
Self-citationCrawford, K. H. D., Eguia, R. T., Dingens, A. S., Loes, A. N., Malone, K. D., Wolf, C. R., Chu, H. Y., Tortorici, M. A., Veesler, D., Murphy, M., et al. (2020) · Viruses · doi:10.3390/v12050513 · Cited by 727 · cited 7× · see citing works
“For neutralization, stable 293T cells expressing ACE2 (Crawford et al., 2020) in DMEM supplemented with 10%FBS, 1%PenStrep were seeded at 40,000 cells/well into clear bottom white walled 96-well plates and cultured overnight at 37 C.”
InfluentialSelf-citationLiu, Z., VanBlargan, L. A., Bloyet, L.-M., Rothlauf, P. W., Chen, R. E., Stumpf, S., Zhao, H., Errico, J. M., Theel, E. S., Liebeskind, M. J., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.01.014 · Cited by 725 · see citing works
Self-citationAddendum: A pneumonia outbreak associated with a new coronavirus of probable bat origin
Zhou, P., Yang, X., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B., Huang, C.-L., et al. (2020) · Nature · doi:10.1038/s41586-020-2951-z · Cited by 715 · see citing works
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Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion
Walls, A. C., Xiong, X., Park, Y.-J., Tortorici, M. A., Snijder, J., Quispe, J., Cameroni, E., Gopal, R., Dai, M., Lanzavecchia, A., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.028 · Cited by 582 · see citing works
Self-citationA Single-Dose Intranasal ChAd Vaccine Protects Upper and Lower Respiratory Tracts against SARS-CoV-2
Hassan, A. O., Kafai, N. M., Dmitriev, I., Fox, J., Smith, B. K., Harvey, I. B., Chen, R. E., Winkler, E. S., Wessel, A. W., Case, J., et al. (2020) · Cell · doi:10.1016/j.cell.2020.08.026 · Cited by 568 · see citing works
Wrobel, A. G., Benton, D. J., Xu, P., Roustan, C., Martin, S. R., Rosenthal, P. B., Skehel, J. J., & Gamblin, S. J. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0468-7 · Cited by 544 · cited 1× · see citing works
“As a result of these distinct interactions, whereas the S2L28-bound NTD adopts an identical conformation to that observed in the apo S structures (Walls et al., 2020b; Wrapp et al., 2020; Wrobel et al., 2020b), S2M28 and S2X333 induce remodeling of the NTD supersite loop and b-hairpin, respectively (Figures 2G–2I).”
Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
McCarthy, K. R., Rennick, L. J., Nambulli, S., Robinson-McCarthy, L. R., Bain, W. G., Haidar, G., & Duprex, W. P. (2021) · Science · doi:10.1126/science.abf6950 · Cited by 535 · see citing works
Walls, A. C., Fiala, B., Schäfer, A., Wrenn, S., Pham, M. N., Murphy, M., Tse, L. V., Shehata, L., O’Connor, M. A., Chen, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.043 · Cited by 532 · see citing works
Self-citationBroad neutralization of SARS-related viruses by human monoclonal antibodies
Wec, A. Z., Wrapp, D., Herbert, A. S., Maurer, D. P., Haslwanter, D., Sakharkar, M., Jangra, R. K., Dieterle, M. E., Lilov, A., Huang, D., et al. (2020) · Science · doi:10.1126/science.abc7424 · Cited by 520 · see citing works
REGN-COV2 antibodies prevent and treat SARS-CoV-2 infection in rhesus macaques and hamsters
Baum, A., Ajithdoss, D., Copin, R., Zhou, A., Lanza, K., Negron, N., Ni, M., Wei, Y., Mohammadi, K., Musser, B., et al. (2020) · Science · doi:10.1126/science.abe2402 · Cited by 517 · see citing works
Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms
Tortorici, M. A., Beltramello, M., Lempp, F. A., Pinto, D., Dang, H. V., Rosen, L. E., McCallum, M., Bowen, J., Minola, A., Jaconi, S., et al. (2020) · Science · doi:10.1126/science.abe3354 · Cited by 510 · cited 15× · see citing works
“Evaluation of the neutralization potency of a subset of NTD-specific mAbs measured 6 h post-infection of Vero E6 cells infected with authentic SARS-CoV-2 virus confirmed that these mAbs did not completely block viral entry and instead plateaued at 80%– 90% neutralization, as opposed to the RBD-specific mAbs S309, S2E1…”
InfluentialSelf-citationChloroquine does not inhibit infection of human lung cells with SARS-CoV-2
Hoffmann, M., Mösbauer, K., Hofmann-Winkler, H., Kaul, A., Kleine‐Weber, H., Krüger, N., Gassen, N. C., Müller, M. A., Drosten, C., & Pöhlmann, S. (2020) · Nature · doi:10.1038/s41586-020-2575-3 · Cited by 476 · see citing works
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
Wang, R. Y.-R., Song, Y., Barad, B. A., Cheng, Y., Fraser, J. S., & DiMaio, F. (2016) · eLife · doi:10.7554/elife.17219 · Cited by 457 · see citing works
The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates
Jones, B. E., Brown-Augsburger, P., Corbett, K., Westendorf, K., Davies, J., Cujec, T., Wiethoff, C. M., Blackbourne, J., Heinz, B., Foster, D., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abf1906 · Cited by 420 · see citing works
Case, J. B., Rothlauf, P. W., Chen, R. E., Liu, Z., Zhao, H., Kim, A. S., Bloyet, L.-M., Zeng, Q., Tahan, S., Droit, L., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.06.021 · Cited by 410 · cited 2× · see citing works
“Selection of SARS-CoV-2 monoclonal antibody escape mutants (MARMS) VSV-SARS-CoV-2 chimera was used to select for SARS-CoV-2 S monoclonal antibody resistant mutants (MARMS) as previously described (Case et al., 2020; Liu et al., 2020b).”
Self-citationWinkler, E. S., Gilchuk, P., Yu, J., Bailey, A. L., Chen, R. E., Chong, Z., Zost, S. J., Jang, H., Huang, Y., Allen, J. D., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.026 · Cited by 366 · see citing works
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Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020Preprint
Hodcroft, E. B., Zuber, M., Nadeau, S., Vaughan, T. G., Crawford, K. H. D., Althaus, C. L., Reichmuth, M. L., Bowen, J. E., Walls, A. C., Corti, D., et al. (2020) · medRxiv · doi:10.1101/2020.10.25.20219063 · Cited by 326 · see citing works
Self-citationNeutralization of SARS-CoV-2 by Destruction of the Prefusion Spike
Huo, J., Zhao, Y., Ren, J., Zhou, D., Duyvesteyn, H. M. E., Ginn, H. M., Carrique, L., Malinauskas, T., Ruza, R. R., Shah, P. N. M., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.06.010 · Cited by 317 · see citing works
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Boudewijns, R., Thibaut, H. J., Kaptein, S. J. F., Li, R., Vergote, V., Seldeslachts, L., Weyenbergh, J. V., Keyzer, C. D., Bervoets, L., Sharma, S., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19684-y · Cited by 275 · cited 3× · see citing works
“RT-qPCR was performed on a LightCycler96 platform (Roche) using the iTaq Universal Probes One-Step RTqPCR kit (BioRad) with N2 primers and probes targeting the nucleocapsid (Boudewijns et al., 2020).”
InfluentialSelf-citationPrevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes
Voss, W. N., Hou, Y. J., Johnson, N. V., Delidakis, G., Kim, J. E., Javanmardi, K., Horton, A. P., Bartzoka, F., Paresi, C., Tanno, Y., et al. (2021) · Science · doi:10.1126/science.abg5268 · Cited by 248 · see citing works
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Self-citationSARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2Preprint
Clausen, T. M., Sandoval, D. R., Spliid, C. B., Pihl, J., Painter, C. D., Thacker, B. E., Glass, C. A., Narayanan, A., Majowicz, S. A., Yang, Z., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.14.201616 · Cited by 229 · see citing works
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SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma
Andreano, E., Piccini, G., Licastro, D., Casalino, L., Johnson, N., Paciello, I., Monego, S. D., Pantano, E., Manganaro, N., Manenti, A., et al. (2021) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.2103154118 · Cited by 187 · see citing works
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McCallum, M., Walls, A. C., Bowen, J. E., Corti, D., & Veesler, D. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0483-8 · Cited by 163 · cited 2× · see citing works
“Cryo-EM data processing of SARS-CoV-2 S bound to S2X28, S2L20, S2X316, or S2M24, related to Figures 2 and 3 (A) 6 Å low-pass filtered map of the SARS-CoV-2 2P DS S trimer (McCallum et al., 2020) bound to S2X28 (gold).”
Self-citationZhou, H., Chen, Y., Zhang, S., Niu, P., Qin, K., Jia, W., Huang, B., Zhang, S., Lan, J., Zhang, L., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10897-4 · Cited by 142 · cited 1× · see citing works
“Likewise, previous work on Middle East respiratory syndrome coronavirus (MERS-CoV) established that the NTD is the target of several potent and protective neutralizing mAbs and an attractive target for vaccine design (Chen et al., 2017; Jiaming et al., 2017; Wang et al., 2018, 2019; Zhou et al., 2019).”
Jones, B. E., Brown-Augsburger, P., Corbett, K., Westendorf, K., Davies, J., Cujec, T., Wiethoff, C. M., Blackbourne, J., Heinz, B., Foster, D., et al. (2020) · bioRxiv · doi:10.1101/2020.09.30.318972 · Cited by 140 · cited 1× · see citing works
“Several RBD-specific mAbs capable of protecting small animals and non-human primates from SARSCoV-2 challenge are able to neutralize viral infection by targeting multiple distinct antigenic sites (Baum et al., 2020a; Hansen et al., 2020; Jones et al., 2020; Pinto et al., 2020; Rogers et al., 2020; Tortorici et al., 20…”
Fc-optimized antibodies elicit CD8 immunity to viral respiratory infection
Bournazos, S., Corti, D., Virgin, H. W., & Ravetch, J. V. (2020) · Nature · doi:10.1038/s41586-020-2838-z · Cited by 139 · cited 1× · see citing works
“Since Fc-mediated effector functions contribute to protection by promoting viral clearance and anti-viral immune responses in vivo (Bournazos et al., 2020; Bournazos et al., 2016; Schäfer et al., 2021; Winkler et al., 2020), we evaluated the ability of site itargeting mAbs to trigger activation of FcγRIIa and FcγRIIIa…”
Self-citationThe role and function of Fcγ receptors on myeloid cells
Bournazos, S., Wang, T. T., & Ravetch, J. V. (2016) · Microbiology Spectrum · doi:10.1128/microbiolspec.mchd-0045-2016 · Cited by 138 · see citing works
Liu, Z., VanBlargan, L. A., Bloyet, L.-M., Rothlauf, P. W., Chen, R. E., Stumpf, S., Zhao, H., Errico, J. M., Theel, E. S., Liebeskind, M. J., et al. (2020) · doi:10.1101/2020.11.06.372037 · Cited by 135 · see citing works
Self-citationAutomatically Fixing Errors in Glycoprotein Structures with Rosetta
Frenz, B., Rämisch, S., Borst, A. J., Walls, A. C., Adolf‐Bryfogle, J., Schief, W. R., Veesler, D., & DiMaio, F. (2018) · Structure · doi:10.1016/j.str.2018.09.006 · Cited by 104 · cited 1× · see citing works
“The model was then refined into the map using Rosetta (DiMaio et al., 2015; Frenz et al., 2019; Wang et al., 2016), Phenix (Liebschner et al.”
Self-citationSARS-CoV-2 Spike Protein Interacts with Multiple Innate Immune ReceptorsPreprint
Gao, C., Zeng, J., Jia, N., Stavenhagen, K., Matsumoto, Y., Zhang, H., Jiang, L., Hume, A. J., Mühlberger, E., van Die, I., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.29.227462 · Cited by 102 · cited 3× · see citing works
“, 2020) and L-SIGN/DC-SIGN (Chiodo et al., 2020; Gao et al., 2020; Soh et al., 2020; Thépaut et al., 2020),whichwereproposed to serve as co-receptors, auxiliary receptors, or adsorption factors.”
Murine Leukemia Virus (MLV)-based Coronavirus Spike-pseudotyped Particle Production and Infection
Millet, J., & Whittaker, G. (2016) · BIO-PROTOCOL · doi:10.21769/bioprotoc.2035 · Cited by 91 · cited 1× · see citing works
“The in vitro neutralization activity of the NTD-specific mAbs was subsequently evaluated using a SARS-CoV-2 S pseudotyped murine leukemia virus (MLV) system (Millet and Whittaker, 2016; Walls et al., 2020b).”
Structural Definition of a Neutralization-sensitive Epitope on the MERS-CoV S1-NTD
Wang, N., Rosen, O., Wang, L., Turner, H. L., Stevens, L. J., Corbett, K. S., Bowman, C. A., Pallesen, J., Shi, W., Zhang, Y., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.08.052 · Cited by 86 · cited 1× · see citing works
“Likewise, previous work on MERS-CoV established that the NTD is the target of several potent and protective neutralizing mAbs and an attractive target for vaccine design (Chen et al., 2017; Jiaming et al., 2017; Wang et al., 2018; Wang et al., 2019; Zhou et al., 2019).”
Jiaming, L., Yanfeng, Y., Deng, Y. L., Yawei, H., Linlin, B., Baoying, H., Jinghua, Y., Gao, G. F., Chuan, Q., & Wenjie, T. (2016) · Vaccine · doi:10.1016/j.vaccine.2016.11.064 · Cited by 83 · cited 1× · see citing works
“Likewise, previous work on Middle East respiratory syndrome coronavirus (MERS-CoV) established that the NTD is the target of several potent and protective neutralizing mAbs and an attractive target for vaccine design (Chen et al., 2017; Jiaming et al., 2017; Wang et al., 2018, 2019; Zhou et al., 2019).”
Chen, Y., Lu, S., Jia, H., Deng, Y., Zhou, J., Huang, B., Yu, Y., Lan, J., Wang, W., Lou, Y., et al. (2017) · Emerging Microbes & Infections · doi:10.1038/emi.2017.50 · Cited by 81 · see citing works
Self-citationNeutralization of SARS-CoV-2 by Destruction of the Prefusion Spike
Huo, J., Zhao, Y., Ren, J., Zhou, D., Duyvesteyn, H. M. E., Ginn, H. M., Carrique, L., Malinauskas, T., Ruza, R. R., Shah, P. N. M., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.07.002 · Cited by 79 · see citing works
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A proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2
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“, 2020), FC05 (Zhang et al., 2020), and CM25 (Voss et al.”
InfluentialCharacterization of neutralizing antibodies from a SARS-CoV-2 infected individualPreprint
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“, 2020) and L-SIGN/DC-SIGN (Chiodo et al., 2020; Gao et al., 2020; Soh et al., 2020; Thépaut et al., 2020) which were proposed to serve as co-receptors, auxiliary receptors, or adsorption factors.”
InfluentialVoss, W. N., Hou, Y., Johnson, N., Kim, J. E., Delidakis, G., Horton, A. P., Bartzoka, F., Paresi, C. J., Tanno, Y., Abbasi, S. A., et al. (2020) · bioRxiv · doi:10.1101/2020.12.20.423708 · Cited by 57 · cited 4× · see citing works
“The neutralizing mAbs described here along with the mAbs 4A8 (Chi et al., 2020), FC05 (Zhang et al., 2020) and CM25 (Voss et al., 2020), which also target this antigenic supersite, use various germline V genes to recognize overlapping epitopes, thereby providing examples of convergent solutions to NTD-targeted mAb neu…”
InfluentialAntibody-mediated disruption of the SARS-CoV-2 spike glycoprotein
Wrobel, A. G., Benton, D. J., Hussain, S., Harvey, R., Martin, S. R., Roustan, C., Rosenthal, P. B., Skehel, J. J., & Gamblin, S. J. (2020) · Nature Communications · doi:10.1038/s41467-020-19146-5 · Cited by 55 · cited 1× · see citing works
“Moreover, these mAbs did not promote shedding of the S1 subunit from cell-surface-expressed fulllength SARS-CoV-2 S (Figure 6B), ruling out the possibility of premature S triggering, as previously shown for a SARS-CoV and several SARS-CoV-2 RBD-specific mAbs (Huo et al., 2020; Piccoli et al., 2020; Walls et al., 2019;…”
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“It is possible that NTD-specific mAb-mediated neutralization further relies on the steric hindrance provided by Fc positioning, similar to what was observed for anti-hemagglutinin influenza A virus neutralizing mAbs (Xiong et al., 2015).”
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SARS-CoV-2 escape <i>in vitro</i> from a highly neutralizing COVID-19 convalescent plasma
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SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
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Self-citationStructural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron
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“The NTD-1 epitope overlaps with that of mAb 4A8 ( 27 ) and other “supersite” binders ( 28 , 29 ).”
BackgroundSARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
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Self-citationCorrelates of protection against SARS‐CoV‐2 infection and COVID‐19 disease
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BackgroundThe emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
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“Most noteworthy of the 22 signature mutation sites that displayed the strongest evidence of lineage-specific positive selection are codons S/18, S/80, S/417, S/501, S/655, and S/681 in that all are either suspected or known to harbor mutations with potentially significant fitness impacts (Garry et al., 2021; Greaney e…”
InfluentialMolecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants
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“Although multiple antigenic sites are present at the surface of the NTD, a single supersite of vulnerability is targeted by neutralizing Abs elicited upon infection and vaccination (23, 24, 26).”
InfluentialSelf-citationAntibodies to combat viral infections: development strategies and progress
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“The key role of NTD as target for antibodies has recently also been shown using memory B cell-derived mAbs (McCallum et al., 2021).”
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A human coronavirus evolves antigenically to escape antibody immunity
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Self-citationRapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Viana, R. P. E. S., Moyo, S. M., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., Anyaneji, U. J., Bester, P. A., Boni, M. F., Chand, M., et al. (2022) · Nature · doi:10.1101/2021.12.19.21268028 · Cited by 250 · see citing works
Imprinted antibody responses against SARS-CoV-2 Omicron sublineages
Park, Y., Pinto, D., Walls, A. C., Liu, Z., Marco, A. D., Benigni, F., Zatta, F., Silacci-Fregni, C., Bassi, J., Sprouse, K. R., et al. (2022) · Science · doi:10.1126/science.adc9127 · Cited by 225 · see citing works
Self-citationWang, R., Zhang, Q., Ge, J., Ren, W., Zhang, R., Lan, J., Ju, B., Su, B., Yu, F., Chen, P., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.06.003 · Cited by 240 · see citing works
“To date, the most potent mAbs isolated from infected and vaccinated individuals are often dominated by those targeting the RBD, whereas many isolated NTD mAbs failed to reach 100% potency in neutralizing activity (Chi et al., 2020; Hansen et al., 2020; Ju et al., 2020; Liu et al., 2020; Robbiani et al., 2020; Wang et…”
Monoclonal antibodies for COVID-19 therapy and SARS-CoV-2 detection
Hwang, Y.-C., Lu, R.-M., Su, S.-C., Chiang, P.-Y., Ko, S.-H., Ke, F.-Y., Liang, K., Hsieh, T.-Y., & Wu, H.-C. (2022) · Journal of Biomedical Sciences · doi:10.1186/s12929-021-00784-w · Cited by 202 · see citing works
“Viral RNA copies/mg lung: 4 mg/kg, 10(6) → 10(3), ↓ 3 log TCID50/mg lung: 1 mg/kg, 10(4) → 10(1), ↓ 3 log 4 mg/kg, 10(4) → 10(1), ↓ 3 log [34]”
BackgroundImpact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity
Lucas, C., Vogels, C. B. F., Yildirim, I., Rothman, J. E., Lu, P., Monteiro, V., Gehlhausen, J. R., Campbell, M., Silva, J., Tabachnikova, A., et al. (2021) · Nature · doi:10.1038/s41586-021-04085-y · Cited by 226 · see citing works
SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape
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Structure of SARS-CoV-2 spike protein
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“High-resolution structures of the S protein in complex with NTD-directed neutralizing antibodies (4A8, FC05, CM25, 4-18, S2M28, and DH1205) have been determined [28 ,29 ,30,31 ,32], showing that these antibodies primarily bind to two glycan-free surfaces of the domain, designated NTD-1 and NTD-2 regions, respectively…”
BackgroundImmune responses to two and three doses of the BNT162b2 mRNA vaccine in adults with solid tumors
Shroff, R. T., Chalasani, P., Wei, R., Pennington, D., Quirk, G., Schoenle, M. V., Peyton, K. L., Uhrlaub, J. L., Ripperger, T. J., Jergović, M., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01542-z · Cited by 233 · see citing works
Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies
Cao, Y., Wang, J., Jian, F., Xiao, T., Song, W., Yisimayi, A., Huang, W., Li, Q., Wang, P., An, R., et al. (2021) · Nature · doi:10.1038/d41586-021-03796-6 · Cited by 227 · see citing works
Recurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70
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Self-citationSARS-CoV-2 infection generates tissue-localized immunological memory in humans
Poon, M. M. L., Rybkina, K., Kato, Y., Kubota, M., Matsumoto, R., Bloom, N. I., Zhang, Z., Hastie, K. M., Grifoni, A., Weiskopf, D., et al. (2021) · Science Immunology · doi:10.1126/sciimmunol.abl9105 · Cited by 214 · see citing works
The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance
Kimura, I., Kosugi, Y., Wu, J., Zahradník, J., Yamasoba, D., Butlertanaka, E. P., Tanaka, Y., Uriu, K., Liu, Y., Morizako, N., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110218 · Cited by 210 · see citing works
Mutations and Evolution of the SARS-CoV-2 Spike Protein
Magazine, N., Zhang, T., Wu, Y., McGee, M. C., Veggiani, G., & Huang, W. (2022) · Viruses · doi:10.3390/v14030640 · Cited by 218 · see citing works
“An interesting hallmark of antibodies tar‐ geting the NTD region is their ability to decrease cell–cell fusion, suggesting that the NTD may play a role in syncytium formation [32].”
BackgroundInfluentialBeyond neutralization: Fc-dependent antibody effector functions in SARS-CoV-2 infection
Zhang, A., Stacey, H. D., D’Agostino, M. R., Tugg, Y., Marzok, A., & Miller, M. S. (2022) · Nature reviews. Immunology · doi:10.1038/s41577-022-00813-1 · Cited by 212 · see citing works
High genetic barrier to SARS-CoV-2 polyclonal neutralizing antibody escape
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Structural Diversity of the SARS-CoV-2 Omicron Spike
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Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant
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SARS-CoV-2 Mutations and their Viral Variants
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SARS-CoV-2 breakthrough infections elicit potent, broad, and durable neutralizing antibody responses
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Self-citationA pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike
Dadonaite, B., Crawford, K. H. D., Radford, C. E., Farrell, A. G., Yu, T. C., Hannon, W. W., Zhou, P.-P., Andrabi, R., Burton, D. R., Liu, L., et al. (2023) · Cell · doi:10.1016/j.cell.2023.02.001 · Cited by 182 · see citing works
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The humoral response and antibodies against SARS-CoV-2 infection
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Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far?
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Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice
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“In fact, passive immunization with SARS-CoV-2 NTD-specific antibodies protect naïve mice from challenge, demonstrating that the NTD is a target of protective immunity ( 18, 24, 25 ).”
Structural basis for broad coronavirus neutralization
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Self-citationWalls, A. C., Miranda, M. C., Schäfer, A., Pham, M. N., Greaney, A., Arunachalam, P. S., Navarro, M.-J., Tortorici, M. A., Rogers, K., O’Connor, M. A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.09.015 · Cited by 185 · see citing works
Self-citationImplications of diversity in sperm size and function for sperm competition and fertility
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Effects of SARS-CoV-2 variants on vaccine efficacy and response strategies
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Predicting the mutational drivers of future SARS-CoV-2 variants of concern
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Self-citationResistance of Omicron subvariants BA.2.75.2, BA.4.6, and BQ.1.1 to neutralizing antibodies
Planas, D., Bruel, T., Staropoli, I., Guivel‐Benhassine, F., Porrot, F., Maes, P., Grzelak, L., Prot, M., Mougari, S., Planchais, C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36561-6 · Cited by 190 · see citing works
“Besides the RBD, antibodies targeting other regions of the spike, such as the NTD or S2 region may also broaden the humoral response 60,61 .”
Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75
Cao, Y., Song, W., Wang, L., Liu, P., Yue, C., Jian, F., Yu, Y., Yisimayi, A., Wang, P., Wang, Y., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.09.018 · Cited by 169 · see citing works
ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies
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Self-citationSARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines
Thakur, S., Sasi, S., Pillai, S. G., Nag, A., Shukla, D., Singhal, R., Phalke, S., & Velu, G. S. K. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.815389 · Cited by 158 · see citing works
Neutralization, effector function and immune imprinting of Omicron variants
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Self-citationEmerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy
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SARS-CoV-2 one year on: evidence for ongoing viral adaptation
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“binding inhibition, such as inhibiting membrane fusion (McCallum et al., 2021) or S1 shedding (Piccoli et al.”
InfluentialCao, Y., Yisimayi, A., Bai, Y., Huang, W., Li, X., Zhang, Z., Yuan, T., An, R., Wang, J., Xiao, T., et al. (2021) · Cell Research · doi:10.1038/s41422-021-00514-9 · Cited by 140 · see citing works
“The surface region formed by these three loops appears to be the focus of many NTD NAbs, such as 4A8 and FC05,(16,17) which is defined as an NTD antigenic supersite.(15,18) Importantly, residues 242–244 belong to part of a strand that precedes the N5 loop, and therefore deletion of these residues would drastically alt…”
BackgroundAntibody-mediated neutralization of SARS-CoV-2
Gruell, H., Vanshylla, K., Weber, T., Barnes, C. O., Kreer, C., & Klein, F. (2022) · Immunity · doi:10.1016/j.immuni.2022.05.005 · Cited by 145 · see citing works
Moodley, A., Stegger, M., BAĞCIGİL, A. F., Baptiste, K. E., Loeffler, A., Lloyd, D. H., Williams, N. J., Leonard, N., Abbott, Y., Skov, R. L., et al. (2006) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkl394 · Cited by 146 · see citing works
Wang, Z., Muecksch, F., Cho, A., Gaebler, C., Hoffmann, H.-H., Ramos, V., Zong, S., Cipolla, M., Johnson, B., Schmidt, F., et al. (2022) · Immunity · doi:10.1016/j.immuni.2022.04.003 · Cited by 142 · see citing works
Evolutionary trajectory of SARS-CoV-2 and emerging variants
Singh, J., Pandit, P., McArthur, A. G., Banerjee, A., & Mossman, K. L. (2021) · Virology Journal · doi:10.1186/s12985-021-01633-w · Cited by 144 · see citing works
SARS-CoV-2 Neutralizing Antibodies for COVID-19 Prevention and Treatment
Li, D., Sempowski, G. D., Saunders, K. O., Acharya, P., & Haynes, B. F. (2021) · Annual Review of Medicine · doi:10.1146/annurev-med-042420-113838 · Cited by 132 · see citing works
Scientific rationale for developing potent RBD-based vaccines targeting COVID-19
Kleanthous, H., Silverman, J., Makar, K., Yoon, I., Jackson, N. A. C., & Vaughn, D. (2021) · npj Vaccines · doi:10.1038/s41541-021-00393-6 · Cited by 137 · see citing works
Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants
Sun, C., Xie, C., Bu, G., Zhong, L., & Zeng, M. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01039-2 · Cited by 139 · see citing works
“For mutations not located on RBD, L18F in Gamma, T19R in Delta and Omicron, D80A in Beta, G142-/D, and Y144- in Omicron reduced S2L28, S2X28, S2M28, S2X333 and 4A8 (PDB:7C2L) binding to spike protein.(115,128) The deletion of amino acid residues 241~243 in NTD of the Beta variant nearly abolished the binding of 4A8, a…”
Background
- Authors
- McCallum, M., De Marco, A., Lempp, F. A., Tortorici, M. A., Pinto, D., Walls, A. C., Beltramello, M., Chen, A., Liu, Z., Zatta, F., Zepeda, S., di Iulio, J., Bowen, J. E., Montiel-Ruiz, M., Zhou, J., Rosen, L. E., Bianchi, S., Guarino, B., Fregni, C. S., Abdelnabi, R., Foo, S.-Y. C., Rothlauf, P. W., Bloyet, L.-M., Benigni, F., Cameroni, E., Neyts, J., Riva, A., Snell, G., Telenti, A., Whelan, S. P. J., Virgin, H. W., Corti, D., Pizzuto, M. S., & Veesler, D.
- Affiliations
- University of Washington (US)
- VIR Biotechnology (United States) (US)
- Centre National de la Recherche Scientifique (FR)
- Vir Biotechnology (Switzerland) (CH)
- Washington University in St. Louis (US)
- Rega Institute for Medical Research (BE)
- University of Milan (IT)
- Corresponding author
- Corti, Davide
- Pizzuto, Matteo Samuele
- Veesler, David
- ORCID
- McCallum, Matthew
- Lempp, Florian A.
- Tortorici, M. Alejandra
- Pinto, Dora
- Walls, Alexandra C.
- Beltramello, Martina
- Chen, Alex
- Liu, Zhuoming
- Zatta, Fabrizia
- Zepeda, Samantha
- Bowen, John E.
- Montiel-Ruiz, Martin
- Zhou, Jiayi
- Rosen, Laura E.
- Bianchi, Siro
- Guarino, Barbara
- Abdelnabi, Rana
- Rothlauf, Paul W.
- Bloyet, Louis-Marie
- Benigni, Fabio
- Cameroni, Elisabetta
- Neyts, Johan
- Riva, Agostino
- Snell, Gyorgy
- Telenti, Amalio
- Whelan, Sean P.J.
- Virgin, Herbert W.
- Corti, Davide
- Pizzuto, Matteo Samuele
- Veesler, David
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2021-04
- Volume
- 184
- Issue
- 9
- Pages
- 2332-2347.e16
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC7962585
- OpenAlex
- W3136616180
- Cited by
- 901
- References
- 130
- Citations by year
- 2026: 38 · 2025: 64 · 2024: 92 · 2023: 154 · 2022: 270 · 2021: 269 · 2020: 2 · 2018: 1 · 2017: 1 · 2015: 1 · 2014: 2 · 2013: 1
- FWCI
- 62.32
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 393 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Lirias (acceptedVersion, other-oa)
- PubMed Central (submittedVersion)
- HAL (submittedVersion)
- Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
- Lirias (submittedVersion, other-oa)
- Funders
- NIGMS
- 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
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Keywords
- SARS-CoV-2, spike protein, N-terminal domain, neutralizing antibodies, monoclonal antibodies, antigenic mapping, receptor binding domain, SARS-CoV-2 variants, Alpha variant, Beta variant, P.1 lineage, vaccine design
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