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N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
Open accessPreprint — published as 10.1016/j.cell.2021.03.028 · Paper page
Abstract
SARS-CoV-2 entry into host cells is orchestrated by the spike (S) glycoprotein that contains an immunodominant receptor-binding domain (RBD) targeted by the largest fraction of 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 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. SARS-CoV-2 variants, including the 501Y.V2 and B.1.1.7 lineages, harbor frequent mutations localized in the NTD supersite suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs to protective immunity.
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“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 [39]
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“In older adults mean GMT was only 12 in a preliminary analysis of 12 participants19 and increased to 109 after the second dose.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [19]
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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 150
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“The D Y144 deletion, which has a prevalence of 1.7% in 37 countries (McCallum et al., 2021), has been shown to abrogate binding to other NTD mAbs including S2M28, S2X28, S2X333, and 4A8 (Chi et al., 2020; McCallum et al., 2021).”
InfluentialWang, 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 145
“…supersite consisting of variable loops flanked by glycans (Amanat et al., 2021; Cerutti et al., 2021b; Chi et al., 2020; Dussupt et al., 2021; Haslwanter et al., 2021; Li et al., 2021; Liu et al., 2021; McCallum et al., 2021a; Planas et al., 2021b; Suryadevara et al., 2021b; Voss et al., 2021).”
InfluentialNeutralizing antibodies for the prevention and treatment of COVID-19
Du, L., Yang, Y., & Zhang, X. (2021) · Cellular and Molecular Immunology · doi:10.1038/s41423-021-00752-2 · Cited by 133
Characterizations of enhanced infectivity and antibody evasion of Omicron BA.2.75
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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 215
“In addition, mutations in the N-terminal domain (NTD) of the SARSCoV-2 S protein are associated with neutralization escape (McCallum et al., 2021).”
Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York
West, A. P., Wertheim, J. O., Wang, J. C., Vasylyeva, T. I., Havens, J. L., Chowdhury, M. A., Gonzalez, E., Fang, C. E., Lonardo, S. S. D., Hughes, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25168-4 · Cited by 134
Grabowski, F., Preibisch, G., Giziński, S., Kochańczyk, M., & Lipniacki, T. (2021) · Viruses · doi:10.3390/v13030392 · Cited by 112
Recurrent SARS-CoV-2 mutations in immunodeficient patients
Wilkinson, S., Richter, A., Casey, A., Osman, H. K. E., Mirza, J. D., Stockton, J., Quick, J., Ratcliffe, L., Sparks, N., Cumley, N., et al. (2022) · Virus Evolution · doi:10.1093/ve/veac050 · Cited by 120
“Two occurrences of S:Δ243, another NTD supersite mutation, were also observed, another deletion that has been demonstrated to decrease Ab neutralisation in vitro (McCarthy et al. 2021; McCallum et al. 2021b).”
BackgroundBeaudoin-Bussières, G., Chen, Y., Ullah, I., Prévost, J., Tolbert, W. D., Symmes, K., Ding, S., Benlarbi, M., Gong, S. Y., Tauzin, A., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110368 · Cited by 122
“…nAbs whose structures have been determined recognized a similar glycan-free epitope (Cerutti et al., 2021; Chi et al., 2020; Liu et al., 2020; McCallum et al., 2021; Sun et al., 2021; Voss et al., 2021), named the NTD supersite (residues 14–20, 140–158, and 245–264) (Harvey et al., 2021;…”
BackgroundMethodInfluentialMutations of SARS-CoV-2 spike protein: Implications on immune evasion and vaccine-induced immunity
Mengist, H. M., Kombe, A. J. K., Mekonnen, D. S., Abebaw, A., Getachew, M., & Jin, T. (2021) · Seminars in Immunology · doi:10.1016/j.smim.2021.101533 · Cited by 115
Cryo-EM structure of the SARS-CoV-2 Omicron spike
Cerutti, G., Guo, Y., Liu, L., Liu, L., Zhang, Z., Luo, Y., Huang, Y., Wang, H. H., Ho, D. D., Sheng, Z., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110428 · Cited by 108
“…et al., 2021c; Chen et al., 2020; Ju et al., 2020; Liu et al., 2020b; Pinto et al., 2020; Rapp et al., 2021; Shi et al., 2020; Tortorici et al., 2020; Zost et al., 2020), and N-terminal domain (NTD) (Cerutti et al., 2021a, 2021b; Chi et al., 2020;McCallum et al., 2021a; Suryadevara et al., 2021).”
BackgroundTherapeutic targets and interventional strategies in COVID-19: mechanisms and clinical studies
Zhou, Y., Xie, Y., Tang, L., Pu, D., Zhu, Y., Liu, J., & Ma, X. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00733-x · Cited by 116
“All 144 and 242–244 deletions and R246I fall within the supersite of NTD.120,121 P.1 does not have NTD deletions but NTD mutations (R190S, D138Y, P26S, T20N, and L18F), which could influence the binding of mAbs.”
BackgroundInfluentialThe global epidemic of SARS‐CoV‐2 variants and their mutational immune escape
Tian, D., Sun, Y., Zhou, J., & Ye, Q. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27376 · Cited by 106
“7 pseudovirus to escape the neutralization of mAbs (4A8, S2X28, S2M28, and S2X333).(73) Another study showed that the B.”
BackgroundSelf-citationCho, H., Gonzales-Wartz, K. K., Huang, D., Yuan, M., Peterson, M., Liang, J. Y., Beutler, N., Torres, J. L., Cong, Y., Postnikova, E. N., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abj5413 · Cited by 123
SARS-CoV-2 spike protein: pathogenesis, vaccines, and potential therapies
Almehdi, A. M., Khoder, G., Alchakee, A., Alsayyid, A. T., Sarg, N. H., & Soliman, S. S. M. (2021) · Infection · doi:10.1007/s15010-021-01677-8 · Cited by 116
“On the other hand, 41 human monoclonal Abs (mAbs) derived from memory B cells have been identified and showed potent neutralizing activity against SARS-CoV-2 S N-terminal domain (NTD), specifically supersite I, suggesting its importance for protective immunity and vaccine design [70].”
BackgroundStamatatos, L., Czartoski, J., Wan, Y.-H., Homad, L. J., Rubin, V., Glantz, H., Neradilek, M., Seydoux, E., Jennewein, M. F., MacCamy, A. J., et al. (2021) · doi:10.1101/2021.02.05.21251182 · Cited by 559
“Neutralizing mAbs targeting epitopes on the NTD of S1 (24, 34, 38-40) and S2 have also been identified (41, 42).”
BackgroundCryo-EM structures of SARS-CoV-2 Omicron BA.2 spike
Stalls, V., Lindenberger, J. J., Gobeil, S., Henderson, R. C., Parks, R., Barr, M., Deyton, M., Martin, M., Janowska, K., Huang, X., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111009 · Cited by 101
Li, W., Chen, Y., Prévost, J., Ullah, I., Lu, M., Gong, S. Y., Tauzin, A., Gasser, R., Vézina, D., Anand, S. P., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110210 · Cited by 128
“…antibodies have been identified (Hoffmann et al., 2020; Jennewein et al., 2021; Jette et al., 2021; Li et al., 2021b; Ma et al., 2020; Ng et al., 2020; Rap-pazzo et al., 2021; Song et al., 2021; Tian et al., 2020; Tortorici et al., 2021; Wang et al., 2020, 2021a; Wec Anna et al., 2020).”
Tortorici, M. A., Walls, A. C., Joshi, A., Park, Y., Eguia, R. T., Miranda, M. C., Kepl, E., Dosey, A. M., Stevens‐Ayers, T., Boeckh, M. J., et al. (2022) · Cell · doi:10.1016/j.cell.2022.05.019 · Cited by 89
“…immune evasion, replication kinetics or disease severity relative to the ancestral SARS-CoV-2 isolate (Cele et al., 2021; Collier et al., 2021; Davies et al., 2021; Edara et al., 2021; Liu et al., 2021a, 2021b; McCallum et al., 2021a, 2021b; Plante et al., 2020; Wibmer et al., 2021).”
Self-citationSignatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies
Alenquer, M., Ferreira, F., Lousa, D., Valério, M., Medina-Lopes, M., Bergman, M., Gonçalves, J., Demengeot, J., Leite, R. B., Lilue, J., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009772 · Cited by 101
“All the antibodies analyzed are neutralizing antibodies, which is not the case in nature [54].”
Background(2021) · doi:10.21203/rs.3.rs-228079/v1 · Cited by 840
Self-citationStructural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit
Hurlburt, N. K., Homad, L. J., Sinha, I. R., Jennewein, M. F., MacCamy, A. J., Wan, Y.-H., Boonyaratanakornkit, J. B., Sholukh, A. M., Jackson, A. M., Zhou, P.-P., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03262-7 · Cited by 80
“The neutralizing potency of CV3-25 is not affected by mutations found in SARS-CoV-2 variants of concern, which harbor mutations that escape from many anti-NTD and anti-RBD antibodies.”
BackgroundInfluentialMannar, D., Saville, J. W., Zhu, X. Q., Srivastava, S. S., Berezuk, A., Zhou, S., Tuttle, K. S., Kim, A., Li, W., Dimitrov, D. S., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110156 · Cited by 90
“Although we have focused the present study on RBD mutations present within VoCs, it is possible that mutations elsewhere in the S protein (particularly in the N-terminal domain) also play a significant role in antibody evasion and may affect ACE2 binding (McCallum et al., 2021).”
InfluentialTackling COVID-19 with neutralizing monoclonal antibodies
Corti, D., Purcell, L. A., Snell, G., & Veesler, D. (2021) · Cell · doi:10.1016/j.cell.2021.07.027 · Cited by 78
“…Cell 184, June 10, 2021 bodies, possibly reducing vaccine effectiveness and the duration of protection (Cele et al., 2021; Chen et al., 2021c; Collier et al., 2021; Kustin et al., 2021; Liu et al., 2021a; McCallum et al., 2021a; Muik et al., 2021; Wang et al., 2021b, 2021c; Wu et al., 2021).”
InfluentialSelf-citationSaville, J. W., Mannar, D., Zhu, X. Q., Srivastava, S. S., Berezuk, A., Demers, J., Zhou, S., Tuttle, K. S., Sekirov, I., Kim, A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28324-6 · Cited by 85
Bianchini, F., Crivelli, V., Abernathy, M. E., Guerra, C., Palus, M., Muri, J., Marcotte, H., Piralla, A., Pedotti, M., Gasparo, R. D., et al. (2023) · Science Immunology · doi:10.1126/sciimmunol.ade0958 · Cited by 88
A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy
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Self-citationSun, S., He, L., Zhao, Z., Gu, H., Fang, X. D., Wang, T., Yang, X., Chen, S., Deng, Y., Li, J., et al. (2021) · Cellular and Molecular Immunology · doi:10.1038/s41423-021-00658-z · Cited by 68
Venkatakrishnan, A., Anand, P., Lenehan, P. J., Suratekar, R., Raghunathan, B., Niesen, M. J. M., & Soundararajan, V. (2021) · doi:10.31219/osf.io/f7txy · Cited by 58
Dussupt, V., Sankhala, R. S., Mendez-Rivera, L., Townsley, S., Schmidt, F., Wieczorek, L., Lal, K. G., Donofrio, G. C., Tran, U., Jackson, N. D., et al. (2021) · Nature Immunology · doi:10.1038/s41590-021-01068-z · Cited by 59
An overview of the vaccine platforms to combat COVID-19 with a focus on the subunit vaccines
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“The basis for the restriction of potent neutralization to site 1 is unclear; however, preliminary studies are consistent with a conformational mechanism for supersite-directed antibodies in which membrane fusion is inhibited (McCallum et al., 2021b; Suryadevara et al., 2021).”
Dynamics of SARS-CoV-2 Spike Proteins in Cell Entry: Control Elements in the Amino-Terminal Domains
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A review on evolution of emerging SARS-CoV-2 variants based on spike glycoprotein
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mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates
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Understanding the Secret of SARS-CoV-2 Variants of Concern/Interest and Immune Escape
Lou, F., Li, M., Pang, Z., Jiang, L., Guan, L., Tian, L., Hu, J., Fan, J., & Fan, H. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.744242 · Cited by 54
“In addition, the L18F mutation located in the NTD was shown to be related to immune escape potentiality (32).”
BackgroundSARS-CoV-2 spike N-terminal domain modulates TMPRSS2-dependent viral entry and fusogenicity
Meng, B., Datir, R. P., Choi, J., Baker, S. G., Dougan, G., Hess, C., Kingston, N., Lehner, P. J., Lyons, P., Matheson, N. J., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111220 · Cited by 58
“Although Kappa, the earliest detected B.1.617 variant in India, displayed greater escape to vaccine-elicited antibody responses (McCallum et al., 2021a), Delta surpassed Kappa to become the dominant strain in India and worldwide by mid-2021 (Mlcochova et al., 2021).”
InfluentialTaylor, A. L., & Starr, T. N. (2023) · PLoS Pathogens · doi:10.1371/journal.ppat.1011901 · Cited by 57
“Therefore, the continued presence of affinity-enhancing mutations in the BQ.1.1 and XBB.1.5 landscapes will likely facilitate ongoing antigenic evolution via compensatory epistasis.”
BackgroundInfluential
Metadata
- Authors
- McCallum, M., Marco, A. D., Lempp, F., 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., Caroline Foo, S.-Y., 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 (Switzerland) (CH)
- VIR Biotechnology (United States) (US)
- Centre National de la Recherche Scientifique (FR)
- 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
- Marco, Anna De
- Lempp, Florian
- 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
- openRxiv
- Published
- 2021-01-14
- Volume
- 184
- Issue
- 9
- Pages
- 2332-2347.e16
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC7814825
- OpenAlex
- W3136616180
- Cited by
- 901
- References
- 0
- Citations by year
- 2026: 38 · 2025: 64 · 2024: 92 · 2023: 154 · 2022: 270 · 2021: 269
- FWCI
- 62.32
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- 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
- Burroughs Wellcome Fund
- University of Washington
- Fast Grants
- National Institutes of Health (1s10od023476-01)
- Natural Sciences and Engineering Research Council of Canada (HHSN272201700059C)
- National Institute of General Medical Sciences (R01GM120553, T32GM008268)
- National Institute of Allergy and Infectious Diseases (HHSN272201700059C, DP1AI158186)
- 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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