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Analysis of a SARS-CoV-2-Infected Individual Reveals Development of Potent Neutralizing Antibodies with Limited Somatic Mutation
Open accessAbstract
Antibody responses develop following SARS-CoV-2 infection, but little is known about their epitope specificities, clonality, binding affinities, epitopes, and neutralizing activity. We isolated B cells specific for the SARS-CoV-2 envelope glycoprotein spike (S) from a COVID-19-infected subject 21 days after the onset of clinical disease. 45 S-specific monoclonal antibodies were generated. They had undergone minimal somatic mutation with limited clonal expansion, and three bound the receptor-binding domain (RBD). Two antibodies neutralized SARS-CoV-2. The most potent antibody bound the RBD and prevented binding to the ACE2 receptor, while the other bound outside the RBD. Thus, most anti-S antibodies that were generated in this patient during the first weeks of COVID-19 infection were non-neutralizing and target epitopes outside the RBD. Antibodies that disrupt the SARS-CoV-2 S-ACE2 interaction can potently neutralize the virus without undergoing extensive maturation. Such antibodies have potential preventive and/or therapeutic potential and can serve as templates for vaccine design.
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“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 [22]
In the citing paper
“SARS-CoV-2 infection rapidly elicits nAbs (16, 21–24) that decline, but remain detectable, over several months (25–29).”
From mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection (2021) · cites this paper as [22]
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“In addition, neutralizing IgG MBCs isolated from COVID-19 patients may have none or very few somatic mutations (97) thus suggesting that the preimmune or innate MBC repertoire may contain SARS-CoV-2 specificities (82).”
BackgroundSARS-CoV-2 evolution in an immunocompromised host reveals shared neutralization escape mechanisms
Clark, S. A., Clark, L. E., Pan, J., Coscia, A., McKay, L. G. A., Shankar, S., Johnson, R. I., Brusic, V., Choudhary, M. C., Regan, J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.027 · Cited by 193
“VH3-53 and VH3-66 antibody genes are identical except for a single amino acid change in an antibody framework region (FWR) (Lefranc and Lefranc, 2001), and potent neutralizing antibodies derived from these germline genes have been isolated from multiple COVID-19 convalescent individuals (Du et al., 2020; Robbiani et a…”
Recognition of the SARS-CoV-2 receptor binding domain by neutralizing antibodies
Yuan, M., Liu, H., Wu, N. C., & Wilson, I. A. (2020) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2020.10.012 · Cited by 184
Structural basis for broad coronavirus neutralization
Sauer, M. M., Tortorici, M. A., Park, Y., Walls, A. C., Homad, L. J., Acton, O. J., Bowen, J. E., Wang, C., Xiong, X., de van der Schueren, W., et al. (2021) · Nature Structural & Molecular Biology · doi:10.1038/s41594-021-00596-4 · Cited by 175
“…2020; Corti et al., 2015; Hansen et al., 2020; Hassan et al., 2020a; Liu et al., 2020; Piccoli et al., 2020; Pinto et al., 2020; Rockx et al., 2008; Rockx et al., 2010; Rogers et al., 2020; Seydoux et al., 2020; Tortorici et al., 2020; Walls et al., 2019; Wang et al., 2020a; Zost et al., 2020).”
Self-citationDesigned proteins assemble antibodies into modular nanocages
Divine, R., Dang, H. V., Ueda, G., Fallas, J. A., Vulovic, I., Sheffler, W., Saini, S., Zhao, Y. T., Raj, I. X., Morawski, P. A., et al. (2021) · Science · doi:10.1126/science.abd9994 · Cited by 184
“1) formed with the SARS-CoV-2 S-binding antibodies CV1 or CV30 ( 38 ) were more effective at neutralizing pseudovirus entry into angiotensin-converting enzyme 2 (ACE2) – expressing cells than freeCV1 or CV30, dropping the apparent median inhibitory concentration (IC 50 ) by more than 200-fold and…”
Self-citationMolecular determinants and mechanism for antibody cocktail preventing SARS-CoV-2 escape
Ku, Z., Xie, X., Davidson, E., Ye, X., Su, H., Menachery, V. D., Li, Y., Yuan, Z., Zhang, X., Muruato, A. E., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20789-7 · Cited by 160
Germinal center responses to SARS-CoV-2 mRNA vaccines in healthy and immunocompromised individuals
(2022) · doi:10.1016/j.cell.2022.01.027 · Cited by 179
“Multiple groups reported that several near-germline nAbs, endowed with potent in vitro neutralizing activity, are elicited during natural SARS-CoV-2 infection in humans (Brouwer et al., 2020; Kreer et al., 2020; Schultheiß et al., 2020; Seydoux et al., 2020).”
Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation
Hurlburt, N. K., Seydoux, E., Wan, Y.-H., Edara, V. V., Stuart, A. B., Feng, J., Suthar, M. S., McGuire, A. T., Stamatatos, L., & Pancera, M. (2020) · Nature Communications · doi:10.1038/s41467-020-19231-9 · Cited by 162
Self-citationImmunity to SARS‐CoV‐2 induced by infection or vaccination
Dopico, X. C., Ols, S., Loré, K., & Hedestam, G. B. K. (2021) · Journal of Internal Medicine · doi:10.1111/joim.13372 · Cited by 172
Antibodies and Vaccines Target RBD of SARS-CoV-2
Min, L., & Sun, Q. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.671633 · Cited by 159
Shan, S., Luo, S., Yang, Z., Hong, J., Su, Y., Ding, F., Fu, L., Li, C., Chen, P., Ma, J., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2122954119 · Cited by 157
An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain
Wu, N. C., Yuan, M., Liu, H., Lee, C.-C. D., Zhu, X., Bangaru, S., Torres, J. L., Caniels, T. G., Brouwer, P. J. M., van Gils, M. J., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108274 · Cited by 158
Graham, C., Seow, J., Huettner, I., Khan, H., Kouphou, N., Acors, S., Winstone, H., Pickering, S., Galão, R. P., Dupont, L., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.03.023 · Cited by 155
“RBD-specific nAbs isolated here targeted epitopes similar to those reported previously (Barnes et al., 2020; Brouwer et al., 2020; Piccoli et al., 2020; Seydoux et al., 2020; Yuan et al., 2020b; Zost et al., 2020) and included nAbs that directly block ACE2 binding through binding RBM and nAbs targeting epitopes distal…”
Focosi, D., & Maggi, F. (2021) · Reviews in Medical Virology · doi:10.1002/rmv.2231 · Cited by 150
Antibody-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 150
Nanomaterials for photothermal and photodynamic cancer therapy
Nasseri, B., Alizadeh, E., Bani, F., Davaran, S., Akbarzadeh, A., Rabiee, N., Bahadori, A., Ziaei, M., Bagherzadeh, M., Saeb, M. R., et al. (2022) · Applied Physics Reviews · doi:10.1063/5.0047672 · Cited by 148
Galson, J. D., Schätzle, S., Bashford-Rogers, R. J. M., Raybould, M. I. J., Kovaltsuk, A., Kilpatrick, G. J., Minter, R., Finch, D. K., Dias, J. C., James, L. K., et al. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.605170 · Cited by 136
Neerukonda, S. N., Vassell, R. A., Herrup, R., Liu, S., Wang, T. T., Takeda, K., Yang, Y., Lin, T.-L., Wang, W., & Weiss, C. D. (2021) · PLoS ONE · doi:10.1371/journal.pone.0248348 · Cited by 133
Zhou, Y., Liu, Z., Li, S. N., Xu, W., Zhang, Q., da Silva, I. T., Li, C., Wu, Y., Jiang, Q., Liu, Z., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108699 · Cited by 137
“, 2020), and single B cell antibody cloning from SARS-CoV-2 convalescent donors (Andreano et al., 2020; Brouwer et al., 2020; Cao et al., 2020; Chen et al., 2020; Chi et al., 2020; Ju et al., 2020; Kreer et al., 2020; Liu et al., 2020a; Robbiani et al., 2020; Rogers et al., 2020; Seydoux et al., 2020; Wan et al., 2020…”
Dogan, M., Kozhaya, L., Placek, L., Gunter, C., Yiğit, M., Hardy, R., Plassmeyer, M. L., Coatney, P., Lillard, K., Bukhari, Z., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-01649-6 · Cited by 126
Zhang, Q., Ju, B., Ge, J., Chan, J. F., Cheng, L., Wang, R., Huang, W., Fang, M., Chen, P., Zhou, B., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24514-w · Cited by 114
Emerging SARS-CoV-2 Variants of Concern (VOCs): An Impending Global Crisis
Thye, A. Y.-K., Law, J. W., Pusparajah, P., Letchumanan, V., Chan, K., & Lee, L. (2021) · Biomedicines · doi:10.3390/biomedicines9101303 · Cited by 121
King, R. G., Silva-Sánchez, A., Peel, J. N., Botta, D., Dickson, A. M., Pinto, A. K., Meza‐Perez, S., Allie, S. R., Schultz, M. D., Liu, M., et al. (2021) · Vaccines · doi:10.3390/vaccines9080881 · Cited by 134
Beaudoin-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
“…CV3-13) used in the work were isolated from blood of male convalescent donor CV3 recovered 41 days after symptoms onset using fluorescent recombinant stabilized Spike ectodomains (S2P) as probes to identify antigen-specific B cells as previously described (Lu et al., 2020; Seydoux et al., 2020).”
Self-citationJette, C. A., Cohen, A. A., Gnanapragasam, P. N. P., Muecksch, F., Lee, Y. E., Huey‐Tubman, K. E., Schmidt, F., Hatziioannou, T., Bieniasz, P. D., Nussenzweig, M. C., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109760 · Cited by 99
“Consistent with their obligate role in viral entry, sarbecovirus S trimers are the primary targets of neutralizing antibodies (Brouwer et al., 2020; Cao et al., 2020; Fung and Liu, 2019; Kreer et al., 2020; Liu et al., 2020b; Robbiani et al., 2020; Rogers et al., 2020; Seydoux et al., 2020; Shi et al., 2020; Zost et a…”
Carrillo, J., Izquierdo‐Useros, N., Ávila‐Nieto, C., Pradenas, E., Clotet, B., & Blanco, J. (2020) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2020.10.108 · Cited by 120
Neutralizing antibodies targeting SARS-CoV-2 spike protein
Shi, X., Yu, L., Yan, L., Guang, Y., & Qiang, M. (2020) · Stem Cell Research · doi:10.1016/j.scr.2020.102125 · Cited by 114
“and potently neutralize the virus without undergoing extensive maturation (Seydoux et al., 2020).”
Johnson, M., Wagstaffe, H. R., Gilmour, K. C., Mai, A., Lewis, J. E. A., Hunt, A., Sirr, J., Bengt, C., Grandjean, L., & Goldblatt, D. (2020) · Journal of Clinical Virology · doi:10.1016/j.jcv.2020.104572 · Cited by 107
Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects
Jennewein, M. F., MacCamy, A. J., Akins, N. R., Feng, J., Homad, L. J., Hurlburt, N. K., Seydoux, E., Wan, Y.-H., Stuart, A. B., Edara, V. V., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109353 · Cited by 108
“We recently reported an initial characterization of the anti-S antibody responses generated by CV1 (Seydoux et al., 2020).”
InfluentialSelf-citationDual Nature of Type I Interferons in SARS-CoV-2-Induced Inflammation
King, C., & Sprent, J. (2021) · Trends in Immunology · doi:10.1016/j.it.2021.02.003 · Cited by 104
Chen, E. C., Gilchuk, P., Zost, S. J., Suryadevara, N., Winkler, E. S., Cabel, C. R., Binshtein, E., Chen, R. E., Sutton, R. E., Rodriguez, J. L., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109604 · Cited by 102
Pandemic Preparedness: Developing Vaccines and Therapeutic Antibodies For COVID-19
Sempowski, G. D., Saunders, K. O., Acharya, P., Wiehe, K. J., & Haynes, B. F. (2020) · Cell · doi:10.1016/j.cell.2020.05.041 · Cited by 102
Zeng, C., Evans, J. P., Pearson, R., Qu, P., Zheng, Y.-M., Robinson, R., Hall‐Stoodley, L., Yount, J. S., Pannu, S. R., Mallampalli, R. K., et al. (2020) · JCI Insight · doi:10.1172/jci.insight.143213 · Cited by 87
Markers of Polyfunctional SARS-CoV-2 Antibodies in Convalescent Plasma
Natarajan, H., Crowley, A. R., Butler, S. E., Xu, S., Weiner, J. A., Bloch, E. M., Littlefield, K. E., Wieland‐Alter, W., Connor, R. I., Wright, P. F., et al. (2021) · mBio · doi:10.1128/mbio.00765-21 · Cited by 99
Signatures 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
Stamatatos, 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
“As a consequence, several mAbs that potently neutralize SARS CoV-2 fail to bind SARS-CoV-1 (16, 22-24).”
BackgroundMethodInfluentialSelf-citationEvaluation of Cell-Based and Surrogate SARS-CoV-2 Neutralization Assays
Sholukh, A. M., Fiore-Gartland, A. J., Ford, E. S., Miner, M. D., Hou, Y. J., Tse, L. V., Kaiser, H., Zhu, H., Lu, J., Madarampalli, B., et al. (2021) · Journal of Clinical Microbiology · doi:10.1128/jcm.00527-21 · Cited by 119
“This is not surprising, as much of the immunodominant response associated with neutralization involves binding and/or blocking the spike RBD to inhibit viral entry to host cells (26, 28, 47).”
Self-citationChallenges and opportunities for antiviral monoclonal antibodies as COVID-19 therapy
Cruz-Teran, C. A., Tiruthani, K., McSweeney, M. D., Ma, A. L., Pickles, R. J., & Lai, S. K. (2020) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2020.12.004 · Cited by 90
COVID-19 Vaccines: “Warp Speed” Needs Mind Melds, Not Warped Minds
Moore, J. P., & Klasse, P. J. (2020) · Journal of Virology · doi:10.1128/jvi.01083-20 · Cited by 87
Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma
Soler, L. F., Daguer, J., Barluenga, S., Vadas, O., Cohen, P., Pagano, S., Yerly, S., Kaiser, L., Vuilleumier, N., & Winssinger, N. (2020) · PLoS ONE · doi:10.1371/journal.pone.0238089 · Cited by 89
SARS-CoV-2 induces robust germinal center CD4 T follicular helper cell responses in rhesus macaques
Lakshmanappa, Y. S., Elizaldi, S. R., Roh, J. W., Schmidt, B., Carroll, T. D., Weaver, K. D., Smith, J. C., Verma, A., Deere, J. D., Dutra, J., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20642-x · Cited by 92
Structural Basis of SARS-CoV-2 and SARS-CoV Antibody Interactions
Gavor, E., Choong, Y. K., Er, S. Y., Sivaraman, H., & Sivaraman, J. (2020) · Trends in Immunology · doi:10.1016/j.it.2020.09.004 · Cited by 83
“CV30 Human mAb Neutralizes SARS-2 SARS-2 RBD but not with SARS RBD Competes with hACE-2 Blocks hACE2 RBD binding N/A N/A [79]”
Li, W., Chen, C., Drelich, A. K., Martinez, D. R., Gralinski, L. E., Sun, Z., Schäfer, A., Kulkarni, S. S., Liu, X., Leist, S. R., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2010197117 · Cited by 82
“Interestingly, Fab ab1 had only several somatic mutations compared to the closest germline predecessor genes, which was also observed for many neutralizing antibodies from COVID-19 patients (36 – 38).”
A Global Picture: Therapeutic Perspectives for COVID-19
Chavda, V. P., Kapadia, C., Soni, S., Prajapati, R., Chauhan, S. C., Yallapu, M. M., & Apostolopoulos, V. (2022) · Immunotherapy · doi:10.2217/imt-2021-0168 · Cited by 88
“Examples of some monoclonal antibodies under review for the management of COVID-19 are summarized in Supplementary Table 4 [147,148,149,150,151,152,153,154,155,156,157,158,159].”
BackgroundSilva-Cayetano, A., Foster, W. S., Innocentin, S., Belij-Rammerstorfer, S., Spencer, A. J., Burton, O. T., Fra-Bidó, S., Le Lee, J., Thakur, N., Conceicao, C., et al. (2021) · Med · doi:10.1016/j.medj.2020.12.006 · Cited by 84
Sequence signatures of two public antibody clonotypes that bind SARS-CoV-2 receptor binding domain
Tan, T. J. C., Yuan, M., Kuzelka, K., Padron, G. C., Beal, J. R., Chen, X., Wang, Y., Rivera-Cardona, J., Zhu, X., Stadtmueller, B. M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24123-7 · Cited by 75
The immunodominant and neutralization linear epitopes for SARS-CoV-2
Lu, S., Xie, X.-X., Zhao, L., Wang, B., Zhu, J., Yang, T.-R., Yang, G.-W., Ji, M., Lv, C.-P., Xue, J., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2020.108666 · Cited by 79
“To assess neutralization antibodies induced by S protein epitopes, we incubated the immunization sera with D614 or G614 SARS-CoV-2 pseudo-viruses and then the mixture was added to ACE2-293FT cells which stably expressed ACE2.”
BackgroundInfluentialStructural 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
“…cDNA for the HKU1 spike was PCR amplified from pCMV-HCoV-HKU1 (SinoBiological Cat# VG40606-UT) and subcloned into pTT3. pTT3-SARS-CoV-2-S (Seydoux et al., 2020), pHDM-MERS-CoV-Spike, pTWist-WIV1-CoV, pHDM-MERS-CoV-1 Spike, pTT3-HKU1 or pTT3-OC43 Spike were transfected into…”
MethodSelf-citationTang, J., Ravichandran, S., Lee, Y., Grubbs, G., Coyle, E. M., Klenow, L., Genser, H., Golding, H., & Khurana, S. (2021) · Nature Communications · doi:10.1038/s41467-021-21463-2 · Cited by 81
Metadata
- Authors
- Seydoux, E., Homad, L. J., MacCamy, A. J., Parks, K. R., Hurlburt, N. K., Jennewein, M. F., Akins, N. R., Stuart, A. B., Wan, Y.-H., Feng, J., Whaley, R. E., Singh, S., Boeckh, M., Cohen, K. W., McElrath, M. J., Englund, J. A., Chu, H. Y., Pancera, M., McGuire, A. T., & Stamatatos, L.
- Affiliations
- Fred Hutch Cancer Center (US)
- University of Washington (US)
- National Institutes of Health (US)
- Corresponding author
- Pancera, Marie
- McGuire, Andrew T.
- Stamatatos, Leonidas
- ORCID
- Seydoux, Emilie
- Homad, Leah J.
- MacCamy, Anna J.
- Parks, K. Rachael
- Hurlburt, Nicholas K.
- Jennewein, Madeleine F.
- Akins, Nicholas R.
- Wan, Yu-Hsin
- Feng, Junli
- Whaley, Rachael E.
- Singh, Suruchi
- Boeckh, Michael
- Cohen, Kristen W.
- McElrath, M. Juliana
- Englund, Janet A.
- Chu, Helen Y.
- Pancera, Marie
- McGuire, Andrew T.
- Stamatatos, Leonidas
- Venue
- Immunity
- Publisher
- Elsevier BV
- Published
- 2020-07
- Volume
- 53
- Issue
- 1
- Pages
- 98-105.e5
- ISSN
- 1074-7613 (ISSN-L)
- PMC
- PMC7276322
- OpenAlex
- W3033450058
- Cited by
- 364
- References
- 44
- Citations by year
- 2026: 9 · 2025: 12 · 2024: 13 · 2023: 27 · 2022: 70 · 2021: 143 · 2020: 89
- FWCI
- 10.79
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Immunity (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Fred Hutchinson Cancer Research Center
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Immunology and Microbiology › Immunology › Monoclonal and Polyclonal Antibodies Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- SARS-CoV-2, COVID-19 pandemic, neutralizing antibodies, spike protein, receptor binding domain, ACE2 receptor, somatic mutations, B-cell clonality, monoclonal antibodies, antibody epitope specificity, antibody affinity, antibody maturation, vaccine design
- MeSH terms
- Betacoronavirus, Angiotensin-Converting Enzyme 2, COVID-19, SARS-CoV-2, Antibodies, Monoclonal, Antibodies, Viral, B-Lymphocytes, Binding Sites, Humans, Peptidyl-Dipeptidase A, Pneumonia, Viral, Protein Binding, Receptors, Virus, Viral Vaccines, Coronavirus Infections, Epitopes, B-Lymphocyte, Somatic Hypermutation, Immunoglobulin, Antibodies, Neutralizing, Pandemics, Spike Glycoprotein, Coronavirus
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