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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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AIDS patient with severe T cell depletion achieved control but not clearance of SARS‐CoV‐2 infection
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“…escape mutations K417T and F490S (https://jbloomlab.github.io/SARS2-RBD-escape-calc/) and the N-terminal neutralization escape deletion at 144 (McCallum et al. 2021), evolved spike N501Y, known to increase SARS-CoV-2 infectivity and to a lesser degree neutralization escape (Liu et al. 2022).”
BackgroundEvolving spike-protein N -glycosylation in SARS-CoV-2 variantsPreprint
Baboo, S., Diedrich, J. K., Torres, J. L., Copps, J., Singh, B., Garrett, P. T., Ward, A. B., Paulson, J. C., & Yates, J. R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.08.539897 · Cited by 10
“N17, along with N74, N122 and N149 border a multi-epitope “neutralization supersite” on NTD 62,84 .”
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“S255F is located within multiple T- and B-cell epitopes and was found to be associated with reduced neutralization by a monoclonal antibody, mAb_S2L28.(27) Despite its immune-escape properties, this mutation was not fixed in Delta lineages, and its prevalence remained limited.”
Structures of the SARS-CoV-2 spike glycoprotein and applications for novel drug development
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“also identified a supersite (site I, Figure 8), which could be recognized by all known NTD-specific neutralizing antibodies (McCallum et al., 2021).”
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“These comprehend both in vitro studies, conducted by culturing virus to monoclonal antibody [7] or polyclonal sera [8] selective pressure or by monitoring virus evolution within immunocompromised patients with a diminished or abolished immune response, often compensated by immunological treatments (convalescent plasma…”
BackgroundPrediction of antibody binding to SARS-CoV-2 RBDs
Wang, E. J. D. (2022) · Bioinformatics Advances · doi:10.1093/bioadv/vbac103 · Cited by 9
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“In this vein, 41 monoclonal antibodies recognized the NTD and neutralized SARS-CoV-2, allowing the definition of an antigenic NTD map.(30) The presence of several NTD substitutions, additions, and deletions indicates the domain is under selective pressure and should compose the targetable toolkit to avert SARS-CoV-2 p…”
Progressive membrane-binding mechanism of SARS-CoV-2 variant spike proteins
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Insertions in the SARS-CoV-2 Spike N-Terminal Domain May Aid COVID-19 TransmissionPreprint
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“Supporting references: Behloul et al., 2020; Fantini et al., 2020; Baker et al., 2021; Di Gaetano et al., 2021; McCallum et al., 2021.”
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SARS-CoV-2 variants associated with vaccine breakthrough in the Delaware Valley through summer 2021
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“The spike D253G substitution has been implicated in mAb evasion (44), and nucleocapsid P199L may alter the assembly of SARS-CoV-2 VLPs (45), functions possibly linked to their depletion in vaccine breakthrough.”
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Miller, N. L., Clark, T., Raman, R., & Sasisekharan, R. (2021) · Viruses · doi:10.3390/v13102009 · Cited by 10
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“This mutation was seen to result in a decreased efficiency of neutralization by antibodies (McCallum et al. 2021).”
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Warger, J., & Gaudieri, S. (2022) · Viruses · doi:10.3390/v15010070 · Cited by 11
“This deletion falls within the NTD antigenic supersite [96,98,136] and overlaps a 3-nucleotide deletion (∆143-145) observed in Omicron [137] (Table A1).”
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“Consistent with the antigenic distance between Beta or Gamma and Wuhan-Hu-1 or Delta viruses, infection with Beta produces plasma antibody responses that are more potent against Beta or Gamma than against Wuhan-Hu-1 or Delta (Cele et al., 2021; Moyo-Gwete et al., 2021; Reincke et al., 2022).”
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“Some mutations are apparently of particular interest since they are located within (M153I) or near (P9T, S12F and T22I) the antigenic supersite of the NTD domain, which represents the main target of antibodies produced by memory B cells after administration of mRNA vaccine [43,44].”
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Maturation of SARS-CoV-2 Spike-specific memory B cells drives resilience to viral escape
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“In most cases receptor-binding domain (RBD)-specific MBCs dominated the response to S, whereas N-terminal domain (NTD)- and S2-specific MBCs were present at lower frequencies, concurring with the fact that most mAbs cloned from the memory B cells of previously infected subjects target the RBD.(13,29) Overall, S-specif…”
InfluentialSelf-citationStructural diversity of the SARS-CoV-2 Omicron spike
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“1 that targets a site of vulnerability in the NTD (20, 24), no longer bound the Delta and Omicron S proteins (Fig.”
Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display
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“Of note, N-612-017 CDRH2 loop residues contact RBD positions frequently mutated among circulating variants (Deng et al., 2021; Kuzmina et al., 2021; McCallum et al., 2021a; Wang et al., 2021).”
InfluentialZhao, X., Zheng, A., Li, D., Zhang, R., Sun, H., Wang, Q., Gao, G. F., Han, P., & Dai, L. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.15.452504 · Cited by 10
ADNKA overcomes SARS-CoV2-mediated NK cell inhibition through non-spike antibodies
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The role of N-glycosylation in spike antigenicity for the SARS-CoV-2 gamma variant
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“NTD-directed antibodies are a major selective pressure against the virus, and promote the emergence of NTD escape mutations of SARS-CoV-2 variants (McCallum et al. 2021).”
InfluentialOmicron infection increases IgG binding to spike protein of predecessor variants
Mahalingam, G., Periyasami, Y., Arjunan, P., Subaschandrabose, R. K., Mathivanan, T. V., Mathew, R. S., Devi, R., Premkumar, P. S., Muliyil, J., Srivastava, A., et al. (2022) · Journal of Medical Virology · doi:10.1002/jmv.28419 · Cited by 10
Development of a Rapid Live SARS-CoV-2 Neutralization Assay Based on a qPCR Readout
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Multifaceted membrane binding head of the SARS-CoV-2 spike protein
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Identification of SARS-CoV-2 S RBD escape mutants using yeast screening and deep mutational scanning
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Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany
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“Mutations at this position were selected via in vitro passaging experiments and showed cross-resistance to monoclonal antibodies targeting NTD [25].”
BackgroundInfluentialNanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2
Mast, F. D., Fridy, P. C., Ketaren, N. E., Wang, J., Jacobs, E. Y., Olivier, J. P., Sanyal, T., Molloy, K., Schmidt, F., Rutkowska, M., et al. (2021) · bioRxiv · doi:10.1101/2021.04.08.438911 · Cited by 9
“the trimers of S1-23 and S1-RBD-35 do not show a similar fold improvement as to what was observed for the monomer to dimer transition (Koenig et al., 2021; Ma et al., 2021; Schoof et al., 2020a; Xiang et al., 2020; Xu et al., 2021).”
BackgroundShowers, W. M., Leach, S. M., Kechris, K., & Strong, M. (2021) · bioRxiv · doi:10.1101/2021.03.05.433666 · Cited by 8
“Several variants observed in the N-terminal domain and the signal peptide (L18F, Y144del, and D253G) have also been shown to decrease the effectiveness of antibodies.(43) It is essential to continue monitoring these variants and other variants in the RBD shown to escape antibodies(42,44) to ensure that vaccines”
BackgroundProtein nanoparticle vaccines induce potent neutralizing antibody responses against MERS-CoV
Chao, C. W., Sprouse, K. R., Miranda, M. C., et al. (2024) · bioRxiv · doi:10.1101/2024.03.13.584735 · Cited by 8
“For SARS-CoV-2, although effector functions from non-neutralizing antibodies can also protect ( 30 , 103 – 107 ), the most potently neutralizing antibodies target the RBD and a single immunodominant antigenic site in the NTD ( 74 , 76 , 80 , 108 , 109 ).”
Self-citationEnvironmental Impacts on COVID-19: Mechanisms of Increased Susceptibility
Cormier, S. A., Yamamoto, A., Short, K. R., Vu, L. D., & Suk, W. A. (2022) · Annals of Global Health · doi:10.5334/aogh.3907 · Cited by 8
“Furthermore, many potential neutralizing antibodies targeting NTD have been identified [21, 22].”
BackgroundViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants in space and time
Cilibrasi, L., Pinoli, P., Bernasconi, A., Canakoglu, A., Chiara, M., & Ceri, S. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac030 · Cited by 14
“Notably, mutations at Spike residues 142 and 158 have been previously reported to potentially (McCallum et al. , 2021) contribute evasion of the innate immune response, by reducing the affinity to potent neutralising antibodies derived from convalescent donors sera, suggesting potentially important…”
BackgroundMin, L., Liu, J., Lu, R., Zhang, Y., Du, M., Xing, M., Wu, Z., Kong, X., Zhu, Y., Zhou, X., et al. (2022) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2022.01.005 · Cited by 10
Immunology and Technology of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Vaccines
Pecetta, S., Kratochvil, S., Kato, Y., Vadivelu, K., & Rappuoli, R. (2022) · Pharmacological Reviews · doi:10.1124/pharmrev.120.000285 · Cited by 11
Design, immunogenicity and efficacy of a Pan-SARS-CoV-2 synthetic DNA vaccinePreprint
Reed, C. C., Schultheis, K., Andrade, V. M., Kalia, R., Tur, J., Schouest, B., Elwood, D., Walters, J. N., Maricic, I., Doan, A., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.11.443592 · Cited by 10
“351 has multiple unique changes to the N-terminal domain (NTD) which along with the RBD contains potent neutralization sites [47].”
Amanat, F., Strohmeier, S., Lee, W.-H., Bangaru, S., Ward, A. B., Coughlan, L., & Krammer, F. (2021) · mBio · doi:10.1128/mbio.01002-21 · Cited by 16
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) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.22.441007 · Cited by 8
SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise
Duerr, R., Crosse, K. M., Valero-Jimenez, A. M., & Dittmann, M. (2021) · Microorganisms · doi:10.3390/microorganisms9071389 · Cited by 12
“CD4bs: CD4 binding site; FP: fusion peptide; MPER: membrane-proximal external region; NTD: N-terminal domain; RBD: receptorbinding domain; SP: signal peptide; TM: transmembrane domain.”
BackgroundInfluentialLamb, K. D., Hughes, J., Lytras, S., Young, F., Koci, O., Herzig, J. C., Lovell, S., Grove, J., Yuan, K., & Robertson, D. L. (2024) · bioRxiv · doi:10.1101/2024.07.05.602129 · Cited by 7
“ESM-2 models spike protein constraints, maps low relative grammaticalities to the S2 and high relative grammaticalities to the S1, which is heavily targeted by host antibodies (NTD, RBD) 12,14– 17 and predominantly on the protein surface (Figure 2).”
Wang, Z., Li, L., Du, R., et al. (2024) · bioRxiv · doi:10.1101/2024.05.30.596664 · Cited by 7
SARS-CoV-2 S Glycoprotein Stabilization Strategies
Pedenko, B., Sulbarán, G., Guilligay, D., Effantin, G., & Weissenhorn, W. (2023) · Viruses · doi:10.3390/v15020558 · Cited by 8
Evolution of the SARS-CoV-2 pandemic in India
Potdar, V. A., & Cherian, S. (2022) · Medical Journal Armed Forces India · doi:10.1016/j.mjafi.2022.05.006 · Cited by 7
“21 As seen in Table 3, apart from the mutations in the S protein, changes in the other regions of the genome also need to be critically evaluated for functional significance.”
Arora, P., Kempf, A. M., Nehlmeier, I., Graichen, L., Winkler, M. S., Lier, M., Schulz, S. R., Jäck, H., Cossmann, A., Stankov, M. V., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110754 · Cited by 7
“Moreover, both variants harbor mutations in their N-terminal domain (NTD), which contains an antigenic supersite that is targeted by most neutralizing antibodies not directed against the RBD (McCallum et al., 2021).”
Contributions of single-particle cryoelectron microscopy toward fighting COVID-19
Rapp, M., Shapiro, L. S., & Frank, J. (2021) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2021.10.005 · Cited by 12
“Cryo-EM has revealed that these antibodies target a single supersite [57,58] in a highly prevalent response.”
Standardized Two-Step Testing of Antibody Activity in COVID-19 Convalescent Plasma
Gilchuk, P., Thomsen, I. P., Yoder, S. M., Brady, E. J., Chappell, J. D., Stevens, L. J., Denison, M. R., Sutton, R. E., Chen, R. E., VanBlargan, L. A., et al. (2021) · iScience · doi:10.1016/j.isci.2021.103602 · Cited by 7
“…in some individuals are directed against the N-terminal domain (NTD) of the SARS-CoV-2 spike protein, which lies outside of the RBD (Voss et al., 2021); however, these neutralizing antibodies do not inhibit binding to ACE2 (Chi et al., 2020; McCallum et al., 2021; Suryadevara et al., 2021).”
BackgroundAfzal, M., Melnyk, D., Courty, T., Schimanski, L. M., Hill, M. L., Neil, S. J. D., Tan, T. K., & James, W. (2025) · iScience · doi:10.1016/j.isci.2025.112451 · Cited by 4
Suryadevara, N., Kose, N., Bangaru, S., Binshtein, E., Munt, J. E., Martinez, D. R., Schäfer, A., Myers, L., Scobey, T., Carnahan, R. H., et al. (2024) · Journal of Clinical Investigation · doi:10.1172/jci178880 · Cited by 6
“Similar to mAb C1717, other mAbs, such as S2M24 (19), DH1052 (29), and polyclonal Fabs from donor COV57 (49), also were identified in individuals following SARS-CoV-2 infection.”
Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence featuresPreprint
Magaret, C. A., Li, L., deCamp, A. C., Rolland, M., Juraska, M., Williamson, B. D., Ludwig, J., Molitor, C., Benkeser, D. C., Luedtke, A. R., et al. (2023) · Research Square · doi:10.21203/rs.3.rs-2743022/v1
Addetia, A., Park, Y., Starr, T. N., Greaney, A. J., Sprouse, K. R., Bowen, J. E., Tilles, S. W., Voorhis, W. C. V., Bloom, J. D., Corti, D., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112621 · Cited by 24
“…harboring numerous mutations, some of them altering transmissibility, immune evasion, replication kinetics or disease severity relative to the ancestral SARS-CoV-2 isolate 7,23,25– 307, 23, 25, Conceptualization: AA, T.N.S., A.J.G., J.B., A.C.W. and DV. Pseudovirus entry assays: AA and ACW.”
Self-citationWayham, N. P., Niedecken, A. R., Simons, J. F., Chiang, Y., Medina‐Cucurella, A. V., Mizrahi, R. A., Wagner, E. K., Gras, A., Segal, I., Witte, P., et al. (2023) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiad102 · Cited by 7
Tang, H., Ke, Y., Liao, Y., Bian, Y., Yuan, Y., Wang, Z., Li, Y., Ma, H., Sun, T., Zhang, B., et al. (2022) · Virologica Sinica · doi:10.1016/j.virs.2022.11.005 · Cited by 6
Delta breakthrough infections elicit potent, broad and durable neutralizing antibody responsesPreprint
Walls, A. C., Sprouse, K. R., Joshi, A., Bowen, J. E., Franko, N., Navarro, M. J., Stewart, C., McCallum, M., Goecker, E. A., Degli-Angeli, E., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.08.471707 · Cited by 8
Self-citationLv, H., Tsang, O. T., So, R. T. Y., Wang, Y., Yuan, M., Liu, H., Yip, G. K., Teo, Q. W., Lin, Y., Liang, W., et al. (2021) · European Journal of Immunology · doi:10.1002/eji.202149234 · Cited by 6
Johnson, L., Bartlett, M. L., Ramirez, F., Heger, C. D., & Smith, D. R. (2023) · Journal of Immunological Methods · doi:10.1016/j.jim.2023.113586 · Cited by 4
The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37
Jodar, M. S. N., Torres, C., Mojsiejczuk, L. N., Acuña, D., Valinotto, L. E., Goya, S., Natale, M. I., Lusso, S. B., Alexay, S., Amadío, A., et al. (2023) · Viruses · doi:10.3390/v15061382 · Cited by 4
Khalaf, R. A., Bernasconi, A., Pinoli, P., & Ceri, S. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.07.051 · Cited by 5
Ji, C., Han, N., Cheng, Y., Shang, J., Weng, S., Yang, R., Zhou, H., & Wu, A. (2022) · Viruses · doi:10.3390/v14051087 · Cited by 5
ACE2 engagement exposes the fusion peptide to pan-coronavirus neutralizing antibodiesPreprint
Low, J., Jerak, J., Tortorici, M. A., et al. (2022) · bioRxiv · doi:10.1101/2022.03.30.486377 · Cited by 5
Self-citationSARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021
Marques, A. D., Sherrill-Mix, S. A., Everett, J. K., Reddy, S. G., Hokama, P., Roche, A. M., Hwang, Y., Glascock, A. L., Whiteside, S. A., Graham-Wooten, J., et al. (2022) · mBio · doi:10.1128/mbio.03788-21 · Cited by 15
“The spike D253G substitution has been implicated in MAb evasion (45), and nucleocapsid P199L may alter the assembly of SARS-CoV-2 VLPs (46), functions possibly linked to their depletion in vaccine breakthrough.”
BackgroundLevy, Y., Alcalay, R., Zvi, A., Makdasi, E., Peretz, E., Noy-Porat, T., Chitlaru, T., Mandelboim, M., Mazor, O., & Rosenfeld, R. (2022) · Vaccines · doi:10.3390/vaccines10020251 · Cited by 6
Structural basis for antibody resistance to SARS-CoV-2 omicron variantPreprint
Cerutti, G., Guo, Y., Liu, L., Zhang, Z., Liu, L., Luo, Y., Huang, Y., Wang, H. H., Ho, D. D., Sheng, Z., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.21.473620 · Cited by 5
“, and Ferrin, T.E. (2004). UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem 25, 1605-1612. Pettersen, E.F., Goddard, T.D., Huang, C.C., Meng, E.C., Couch, G.S., Croll, T.I., Morris, J.H., and Ferrin, T.E. (2021). UCSF ChimeraX: Structure visualization for researchers, educators…”
BackgroundInfluentialZimerman, R., Ferrareze, P. A. G., Cadegiani, F., et al. (2021) · medRxiv · doi:10.1101/2021.10.30.21265694 · Cited by 5
“Despite this site has not been the target of much attention as RBD, it is in fact a hotspot for mutations, including “indels” and other missense substitutions, which may affect the activity of neutralizing antibodies and/or lead fitness recovery activity (39, 40).”
BackgroundMutational profile confers increased stability of SARS-CoV-2 spike protein in Brazilian isolates
Santos, F. R. D. S., de Azevedo, M. S. P., Bielavsky, M., da Costa, H. H. M., Ribeiro, D. G., do Nascimento, G. G., Marcondes, G. M. P., de Castro, B. P., Neto, D. F. D. L., & Prudêncio, C. R. (2021) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2021.1982775 · Cited by 5
Sensitivity of two SARS-CoV-2 variants with spike protein mutations to neutralising antibodies
Müller, K., Girl, P., Giebl, A., Grützner, S., Antwerpen, M. H., Khatamzas, E., Wölfel, R., & von Buttlar, H. (2021) · Virus Genes · doi:10.1007/s11262-021-01871-8 · Cited by 4
“MUC-IMBB.1.351 carries mutations located within the NTD (i.e. two substitutions and one in-frame deletion) that were previously shown to influence NTD-specific NAbs [24].”
BackgroundInfluentialSokal, A., Spaeth, G. B., Fernández, I., Broketa, M., Azzaoui, I., Selle, A. D. L., Vandenberghe, A., Fourati, S., Roeser, A., Meola, A., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.17.448459 · Cited by 5
“(I) Proportion of Spike-specific memory B cells recognizing RBD in each individual at the two months time point.”
BackgroundInfluentialGüven, E. (2021) · Gene Reports · doi:10.1016/j.genrep.2021.101169 · Cited by 5
“While vaccines are developed and implemented at breakneck speed, the timeline for large-scale production and vaccination of the world’s enormous population stays vague (McCallum et al., 2021).”
Heterogeneous Evolution Among SARS‐CoV‐2 Genes and Variants of Concern
González-Vázquez, L. D., Iglesias-Rivas, P., Ferreiro, D., & Arenas, M. (2025) · Journal of Medical Virology · doi:10.1002/jmv.70604 · Cited by 5
“Some studies suggested that the NTD can be recognized by specific monoclonal antibodies, and mutations in this region can facilitate immune escape [78].”
Di, H., Pusch, E. A., Jones, J. E., Kovacs, N. A., Hassell, N., Sheth, M., Lynn, K. S., Keller, M. W., Wilson, M. M., Keong, L. M., et al. (2024) · Vaccines · doi:10.3390/vaccines12050505 · Cited by 4
“3 of 19 By January 2022, the Omicron wave replaced the Delta wave and was predominated by BA.1 and BA.1.1 first, then BA.2 and BA.2.12.1, followed by BA.5, BQ.1/BQ.1.1 and XBB.1.5 as of September 2023 [9–12] (Figure 1). neutralizing antibodies. supersite [20,21].”
BackgroundInfluentialStäb, S., Pearce, N. M., Tronrud, D. E., Ginn, H. M., Fadda, E., Santoni, G., & Thorn, A. (2024) · Crystallography Reviews · doi:10.1080/0889311x.2024.2363756 · Cited by 7
“Almost all inherently neutralising antibodies bind to the RBD, along with a smaller set which bind to an ‘anti-genic supersite’ on the N-terminal domain located at the most radially distant loops from the centre of the spike [227,229].”
Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2Preprint
Bianchini, F., Crivelli, V., Abernathy, M. E., Guerra, C., Palus, M., Muri, J., Marcotte, H., Piralla, A., Pedotti, M., Gasparo, R. D., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.24.515932 · Cited by 4
Kuhaudomlarp, S., & Imberty, A. (2022) · IUBMB Life · doi:10.1002/iub.2692 · Cited by 7
“Moreover, the structural context of escape mutations arising in variants of concerns can be mapped (19–21) allowing conserved epitopes to be identified and facilitating the design of pan-coronavirus antibodies and vaccines (22).”
Sorokina, M., Belapure, J., Tüting, C., Paschke, R., Papasotiriou, I., Rodrigues, J., & Kastritis, P. L. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167637 · Cited by 4
“Despite becoming widespread, it remains mysterious for its structural or functional impact, although 2 reports suggested that it does not affect antigenicity(51) and has minimal impact on viral entry.(50,51) The high frequency substitutions present in S1 should affect the unbound and bound states of the S protein and…”
Comparative Investigation of Methods for Analysis of SARS-CoV-2-Spike-Specific Antisera
Herrlein, M., Hein, S., Zahn, T. R., Mhedhbi, I., Raupach, J., Husria, Y., Benz, N. I., Eisert, J., Bender, D., Haberger, V., et al. (2022) · Viruses · doi:10.3390/v14020410 · Cited by 8
“In addition to the RBD-targeting antibodies, there are neutralizing antibodies, which bind to an antigenic “supersite” in the N-terminal domain involving residues 141 to 156 and residues 246 to 260 [5,6].”
BackgroundVolkwein, W., Pavlovic, M., Anton, M., Haase, M., Stellberger, T., Jarrar, A., Busch, U., & Baiker, A. E. (2021) · Journal of Virological Methods · doi:10.1016/j.jviromet.2021.114316 · Cited by 3
Mishra, T. K., Joshi, G., Kumar, A., Dalavi, R., Pandey, P., Shukla, S., Mishra, R. K., & Chande, A. G. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.04.463028 · Cited by 5
Quaranta, M., Via, A., & Pascarella, S. (2025) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26855 · Cited by 4
“Through structural and biophysical analyses of several mAbs bound to the Spike protein, an antigenic supersite on the NTD was identified [18], which is the target of 4A8.”
Ernst, C., Pires‐Afonso, Y., Bejko, D., Huberty, C., Dentzer, T. G., Wienecke-Baldacchino, A. K., Hugoson, E., Álvarez, D., Weydert, M., Vergison, A., et al. (2023) · Geriatrics · doi:10.3390/geriatrics8010019 · Cited by 2
“The aspartic-acidto-glycine substitution on position 614 (D614G) appears to have an advantage in terms of transmissibility and infectivity [31], and decreased antibody neutralization is linked to the L18F mutation [32].”
Background
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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