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Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization
Open accessAbstract
Neutralizing antibodies against the SARS-CoV-2 spike (S) protein are a goal of COVID-19 vaccines and have received emergency use authorization as therapeutics. However, viral escape mutants could compromise efficacy. To define immune-selected mutations in the S protein, we exposed a VSV-eGFP-SARS-CoV-2-S chimeric virus, in which the VSV glycoprotein is replaced with the S protein, to 19 neutralizing monoclonal antibodies (mAbs) against the receptor-binding domain (RBD) and generated 50 different escape mutants. Each mAb had a unique resistance profile, although many shared residues within an epitope of the RBD. Some variants (e.g., S477N) were resistant to neutralization by multiple mAbs, whereas others (e.g., E484K) escaped neutralization by convalescent sera. Additionally, sequential selection identified mutants that escape neutralization by antibody cocktails. Comparing these antibody-mediated mutations with sequence variation in circulating SARS-CoV-2 revealed substitutions that may attenuate neutralizing immune responses in some humans and thus warrant further investigation.
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In the citing paper
“F490S mutation helps the Lambda variant to escape convalescent sera and neutralizing antibodies from the CoronaVac vaccine and also reduced in vitro susceptibility to neutralization [54].”
From Waves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe (2022) · cites this paper as [54]
Experimental — accuracy not yet measuredIn the citing paper
“several were previously shown to modulate ACE2 binding and/or antibody evasion”
From The Omicron variant is highly resistant against antibody-mediated neutralization: Implications for control of the COVID-19 pandemic (2022) · cites this paper as Liu et al., 2021
In the citing paper
“Our results establishing the E484K substitution as a vulnerability for multiple neutralizing mAbs are consistent with deep mutational scanning or VSV-SARS-CoV-2-based neutralization escape screening campaigns31,33,34.”
From Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies (2021) · cites this paper as [34]
In the citing paper
“E484K has resulted in 3-fold to 10-fold reduced susceptibility to about 30% and >10-fold reduced susceptibility to about 10% of convalescent plasma samples”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [160]
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Cites
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“Processing of S by host cell proteases, typically TMPRSS2, TMPRSS4, or endosomal cathepsins, facilitates the S2-dependent fusion of viral and host-cell membranes (Hoffmann et al., 2020; Zang et al., 2020).”
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InfluentialWill Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines?
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“Spike mutants that are resistant to monoclonal antibodies against RBD [121] would be useful tools for identifying viral determinants of alternative receptors.”
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SARS-CoV-2 Causes Lung Infection without Severe Disease in Human ACE2 Knock-In Mice
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“Plates were washed and sequentially incubated with an oligoclonal pool of SARS2-2, SARS2-11, SARS2-16, SARS2-31, SARS2-38, SARS2-57, and SARS2-71 (48) anti-S antibodies and HRP-conjugated goat anti-mouse IgG (Sigma, catalog number 12-349) in PBS supplemented with 0.1% saponin and 0.1% bovine serum albumin.”
MethodInfluentialSelf-citationImmunity to SARS-CoV-2 up to 15 months after infection
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InfluentialSelf-citationA potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification
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“The RBD is also prone to naturally occurring mutations, along with the N-terminal domain (NTD) and other non-RBD and non-NTD regions, where insertions and deletions have also been found (Greaney et al., 2021b; Kemp et al., 2021; Liu et al., 2021; McCarthy et al., 2021; Starr et al., 2020; Tegally et al., 2021; Van Ege…”
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“However, S477N has also been described as escape mutation [32].”
A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy
Greaney, A. J., Starr, T. N., Eguia, R. T., Loes, A. N., Khan, K., Karim, F., Cele, S., Bowen, J. E., Logue, J. K., Corti, D., et al. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010248 · Cited by 58
Souza, P. F. N., Mesquita, F. P., Amaral, J. L., Landim, P. G. C., Lima, K. R. P., Costa, M. B., Farias, I. R., Belém, M. O., Pinto, Y. O., Moreira, H. H. T., et al. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.03.058 · Cited by 67
SARS-CoV-2’s Variants of Concern: A Brief Characterization
Scovino, A. M., Dahab, E. C., Vieira, G. F., Freire‐de‐Lima, L., Freire-de-Lima, C. G., & Morrot, A. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.834098 · Cited by 69
“These mutations in the VOCs, without changing the viral fitness, can be selected during the course of the infection, by the host’s immune system, by therapy with convalescent plasma, by vaccines and also by treatment with antibodies (64).”
BackgroundAn atlas of continuous adaptive evolution in endemic human viruses
Kistler, K. E., & Bedford, T. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.09.012 · Cited by 65
“…viruses as those with high rates of adaptation in the protein that mediates receptor-binding, as this is a primary location of antibody neutralization and the locus of antigenic escape mutations in seasonal influenza viruses 19,20,9,21 , coronavirus 229E 7 and SARS-CoV-2 22,23,24,25 .”
SARS-CoV-2 Subgenomic RNAs: Characterization, Utility, and Perspectives
Long, S. (2021) · Viruses · doi:10.3390/v13101923 · Cited by 67
SARS-CoV-2 variants – Evolution, spike protein, and vaccines
Chen, K.-W. K., Huang, D. T., & Huang, L. (2022) · Biomedical Journal · doi:10.1016/j.bj.2022.04.006 · Cited by 63
“There is no clear evidence suggesting an association of this variant with increased mortality, but some reports have shown that E484K mutation may affect neutralization by several mAbs, including casirivimab, bamlanivimab, and etesevimab [28,32,48].”
InfluentialSARS-CoV-2 Variants and Their Relevant Mutational Profiles: Update Summer 2021
Alkhatib, M., Svicher, V., Salpini, R., Ambrosio, F. A., Bellocchi, M. C., Carioti, L., Piermatteo, L., Scutari, R., Costa, G., Artese, A., et al. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.01096-21 · Cited by 62
“can favor viral escape from a large variety of monoclonal antibodies and from convalescent-phase sera of recovered individuals (40, 47, 48).”
BackgroundMethodDiscovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers
Vanshylla, K., Fan, C., Wunsch, M., Poopalasingam, N., Meijers, M., Kreer, C., Kleipass, F., Ruchnewitz, D., Ercanoglu, M. S., Gruell, H., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.010 · Cited by 58
“R346 and N440 mutants were previously only reported in cell culture-based escape assays (Liu et al., 2021;Weisblumet al., 2020).”
Valdés-Balbín, Y., Santana-Mederos, D., Paquet, F., Fernández-Castillo, S., Climent, Y., Chiodo, F., Rodríguez, L., Ramírez, B. S., León, K., Hernández, T., et al. (2021) · ACS Central Science · doi:10.1021/acscentsci.1c00216 · Cited by 53
Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2
Prévost, J., Richard, J., Gasser, R., Ding, S., Fage, C., Anand, S. P., Adam, D., Vergara, N. G., Tauzin, A., Benlarbi, M., et al. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.101151 · Cited by 64
The trispecific DARPin ensovibep inhibits diverse SARS-CoV-2 variants
Rothenberger, S., Hurdiss, D. L., Walser, M., Malvezzi, F., Mayor, J., Ryter, S., Moreno, H., Liechti, N., Bosshart, A., Iss, C., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01382-3 · Cited by 75
Zhang, L., Cui, Z., Li, Q., Wang, B., Yu, Y., Wu, J., Nie, J., Ding, R., Wang, H., Zhang, Y., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-02728-4 · Cited by 58
Pre-existing immunity modulates responses to mRNA boosters
Dangi, T., Sanchez, S., Lew, M. H., Awakoaiye, B., Visvabharathy, L., Richner, J. M., Koralnik, I. J., & Penaloza‐MacMaster, P. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112167 · Cited by 55
Understanding Mutations in Human SARS-CoV-2 Spike Glycoprotein: A Systematic Review & Meta-Analysis
Kumar, R., Srivastava, Y., Muthuramalingam, P., Singh, S. K., Verma, G., Tiwari, S., Tandel, N., Beura, S. K., Panigrahi, A. R., Maji, S., et al. (2023) · Viruses · doi:10.3390/v15040856 · Cited by 57
“Thus, S477N mutation plays a significant role in the interaction with hACE2 and confers resistance to convalescent sera and antibodies, subsequently increasing infectivity [45,46].”
BackgroundEmergence and outcomes of the SARS-CoV-2 ‘Marseille-4’ variant
Fournier, P., Colson, P., Levasseur, A., Devaux, C. A., Gautret, P., Bedotto, M., Delerce, J., Bréchard, L., Pinault, L., Lagier, J., et al. (2021) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2021.03.068 · Cited by 57
Wilton, T., Bujáki, E., Klapsa, D., Majumdar, M., Zambon, M. C. F. A., Fritzsche, M., Mate, R., & Martín, J. E.-S. (2021) · mSystems · doi:10.1128/msystems.00353-21 · Cited by 55
Predicting Mutational Effects on Receptor Binding of the Spike Protein of SARS-CoV-2 Variants
Bai, C., Wang, J., Chen, G., Zhang, H., An, K., Xu, P., Du, Y., Ye, R. D., Saha, A., Zhang, A., et al. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c07965 · Cited by 51
Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants
Gupta, D., Sharma, P., Singh, M., Kumar, M., Ethayathulla, A. S., & Kaur, P. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-04008-0 · Cited by 56
“This mutant serves as an escape mutant against SARS-CoV-2 infection as it interferes with the ability of the antibodies to bind with the RBD region [53, 82, 90, 100, 101].”
BackgroundPondé, R. A. D. A. (2022) · Virology · doi:10.1016/j.virol.2022.05.003 · Cited by 54
“…since it favors the virus spread, compromises the neutralizing activity of therapeutic monoclonal antibodies (Weisblum et al., 2020) and also gives the virus a ability to evade immunity induced by natural infection and by vaccination (Wang et al., 2021b; Jangra et al., 2021; Liu et al., 2021a).”
InfluentialUnderstanding 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
“L452 residue did not directly interact with ACE2, but the L452R mutation could affect the structural stability of the region where S protein interacts with ACE2 and facilitate SARS-CoV-2 to enter into human respiratory organs (37), which accounted for the prevalence of B.1.427/429 in North America and B.1.617 in India.”
BackgroundInfluentialLu, M., Chamblee, M., Zhang, Y., Ye, C., Dravid, P., Park, J., Mahesh, K., Trivedi, S., Murthy, S. S., Sharma, H., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2110105119 · Cited by 55
Rajasekharan, S., Bonotto, R. M., Alves, L. N., Kazungu, Y., Poggianella, M., Martínez-Orellana, P., Skoko, N., Polez, S., & Marcello, A. (2021) · Viruses · doi:10.3390/v13050808 · Cited by 54
“A recent addition to the armamentarium of strategies to inhibit SARS-CoV-2 is represented by neutralizing monoclonal antibodies, although their narrow window of applicability and sensitivity to Spike immunological escape mutations makes them non-resolutive [8].”
BackgroundPadilla, C., Jimenez‐Vasquez, V., Hurtado, V., Mestanza, O., Molina, I. S., Barcena, L., Ruiz, S. M., Acedo-Lazo, S. V., Lizárraga, W. C., Bailón, H., et al. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27261 · Cited by 54
“Noteworthy, the L452Q mutation uniquely present in this variant is very similar to the L452R present in the delta variant and in the epsilon variants, which together with the D614G mutation, are considered to increase the transmissibility.(13,14)”
BackgroundThe way of SARS-CoV-2 vaccine development: success and challenges
Dong, Y., Dai, T., Wang, B., Zhang, L., Zeng, L., Huang, J., Yan, H., Zhang, L., & Zhou, F. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00796-w · Cited by 53
Du, W., Hurdiss, D. L., Drabek, D., Mykytyn, A. Z., Kaiser, F. K., González-Hernández, M., Muñoz‐Santos, D., Lamers, M. M., van Haperen, R., Li, W., et al. (2022) · Science Immunology · doi:10.1126/sciimmunol.abp9312 · Cited by 56
SARS-CoV-2 drug resistance and therapeutic approaches
Batool, S., Chokkakula, S., Jeong, J. H., Baek, Y. H., & Song, M. (2025) · Heliyon · doi:10.1016/j.heliyon.2025.e41980 · Cited by 55
Dominance of Alpha and Iota variants in SARS-CoV-2 vaccine breakthrough infections in New York City
Duerr, R., Dimartino, D., Marier, C., Zappile, P., Wang, G., Lighter, J., Elbel, B. D., Troxel, A. B., & Heguy, A. (2021) · Journal of Clinical Investigation · doi:10.1172/jci152702 · Cited by 53
Immune Escape Associated with RBD Omicron Mutations and SARS-CoV-2 Evolution Dynamics
Kudriavtsev, A. V., Vakhrusheva, A., Novoseletsky, V. N., Bozdaganyan, M. E., Шайтан, К. В., Kirpichnikov, M. P., & Sokolova, O. S. (2022) · Viruses · doi:10.3390/v14081603 · Cited by 52
“The presence of this mutation led to an almost complete absence of neutralization by monoclonal antibodies C121 and C144 [43] and convalescent plasma [40,44].”
BackgroundOne-shot identification of SARS-CoV-2 S RBD escape mutants using yeast screening
Francino-Urdaniz, I. M., Steiner, P. J., Kirby, M. B., Zhao, F., Haas, C. M., Barman, S., Rhodes, E. R., Leonard, A. C., Peng, L., Sprenger, K. G., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109627 · Cited by 47
“There have been a number of recent approaches to identify specific S escape mutants (summarized in Data S2; Baum et al., 2020; Greaney et al., 2021; Li et al., 2020; Liu et al., 2021; Weisblum et al., 2020).”
On the road to ending the COVID-19 pandemic: Are we there yet?
Case, J. B., Winkler, E. S., Errico, J. M., & Diamond, M. (2021) · Virology · doi:10.1016/j.virol.2021.02.003 · Cited by 47
Self-citationSARS-CoV-2: phenotype, genotype, and characterization of different variants
Saberiyan, M., Karimi, E., Khademi, Z., Movahhed, P., Safi, A., & Ghahfarrokhi, A. M. (2022) · Cellular & Molecular Biology Letters · doi:10.1186/s11658-022-00352-6 · Cited by 56
Huang, S., & Wang, S. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22063060 · Cited by 50
“• Enhance the infectivity and compensate the decrease of infectivity due to emerge of RBD immune escape mutations, such as D796H.”
BackgroundInfluentialMullick, B., Magar, R., Jhunjhunwala, A., & Farimani, A. B. (2021) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2021.104915 · Cited by 49
“This mutation lies in the region 473 – 487 which includes another mutation of significance S477 N [16,54].”
Laurini, E., Marson, D., Aulić, S., Fermeglia, A., & Pricl, S. (2021) · Scientific Reports · doi:10.1038/s41598-021-99827-3 · Cited by 45
Verkhivker, G. M., Agajanian, S., Öztaş, D. Y., & Gupta, G. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00372 · Cited by 40
Omicron variant of SARS-CoV-2 imposes a new challenge for the global public health
Xu, Z., Liu, K., & Gao, G. F. (2022) · Biosafety and Health · doi:10.1016/j.bsheal.2022.01.002 · Cited by 49
“K417N tends to affect the binding of Class 1 antibodies and is less important for polyclonal antibodies targeting RBD, which mainly relate to Class 2 antibodies [7].”
CVnCoV protects human ACE2 transgenic mice from ancestral B BavPat1 and emerging B.1.351 SARS-CoV-2
Hoffmann, D., Corleis, B., Rauch, S., Roth, N., Mühe, J., Halwe, N. J., Ulrich, L., Fricke, C., Schön, J., Kraft, A., et al. (2021) · doi:10.1101/2021.03.22.435960 · Cited by 48
Ameratunga, R., Longhurst, H. J., Steele, R. H., Lehnert, K., Leung, E. Y., Brooks, A. E. S., & Woon, S. (2021) · The Journal of Allergy and Clinical Immunology In Practice · doi:10.1016/j.jaip.2021.06.019 · Cited by 49
Çeli̇k, İ., Yadav, R., Düzgün, Z., Albogami, S. M., El‐Shehawi, A. M., Fatimawali, F., Idroes, R., Tallei, T. E., & Emran, T. B. (2021) · Biology · doi:10.3390/biology10090880 · Cited by 49
Ahmad, L. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.742167 · Cited by 46
Bhattacharya, M., Chatterjee, S., Sharma, A. R., Lee, S., & Chakraborty, C. (2022) · Folia Microbiologica · doi:10.1007/s12223-022-01001-3 · Cited by 48
Cheng, M. H., Krieger, J., Banerjee, A., Xiang, Y., Kaynak, B., Shi, Y., Arditi, M., & Bahar, İ. (2022) · iScience · doi:10.1016/j.isci.2022.103939 · Cited by 50
“…been studied in deep scanning mutagenesis (Dong et al., 2021; Greaney et al., 2021a, 2021c; Starr et al., 2020, 2021a, 2021b), in vitro evolution (Liu et al., 2021d; Muecksch et al., 2021; Wang et al., 2021c; Weisblum et al., 2020; Zahradnik et al., 2021), cryo-EM (Cai et al., 2021;…”
InfluentialChen, Y., Sun, L., Ullah, I., Beaudoin-Bussières, G., Anand, S. P., Hederman, A. P., Tolbert, W. D., Sherburn, R. T., Nguyen, D. N. P., Marchitto, L., et al. (2022) · Science Advances · doi:10.1126/sciadv.abn4188 · Cited by 49
“neutralizing antibodies (nAbs) elicited through natural infection and vaccination act by disrupting 64 this interaction; however, selection pressure results in viral escape mutations, in many cases 65 generating VOCs with an enhanced ability to bind host receptors (12-16).”
Long, S. W., Olsen, R. J., Christensen, P. A., Subedi, S., Olson, R., Davis, J. J., Saavedra, M. O., Yerramilli, P., Pruitt, L., Reppond, K., et al. (2021) · American Journal Of Pathology · doi:10.1016/j.ajpath.2021.03.004 · Cited by 46
Upadhyay, V., Lucas, A., Panja, S., Miyauchi, R., & Mallela, K. M. G. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.101208 · Cited by 44
A review: Antibody-dependent enhancement in COVID-19: The not so friendly side of antibodies
Sánchez‐Zuno, G. A., Matuz-Flores, M. G., González-Estévez, G., Nicoletti, F., Turrubiates‐Hernández, F. J., Mangano, K., & Muñóz-Valle, J. F. (2021) · International Journal of Immunopathology and Pharmacology · doi:10.1177/20587384211050199 · Cited by 48
“To date, 4150 mutations have been identified in the S-gene of SARSCoV-2 isolated from humans, resulting in 1246 changes in amino acids, including 187 RBD substitutions compared to the reference genome.(72) The main variants identified that seem to have high relevance in the immunogenicity of the virus are D614G, N501Y…”
Metadata
- Authors
- 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., Alford, B., Buchser, W. J., Ellebedy, A. H., Fremont, D. H., Diamond, M. S., & Whelan, S. P. J.
- Affiliations
- Washington University in St. Louis (US)
- Harvard University (US)
- Mayo Clinic (US)
- Corresponding author
- Diamond, Michael S.
- Whelan, Sean P.J.
- ORCID
- Venue
- Cell Host & Microbe
- Publisher
- Elsevier BV
- Published
- 2021-03
- Volume
- 29
- Issue
- 3
- Pages
- 477-488.e4
- ISSN
- 1931-3128 (ISSN-L)
- PMC
- PMC7839837
- OpenAlex
- W3121995178
- Cited by
- 725
- References
- 38
- Citations by year
- 2026: 11 · 2025: 22 · 2024: 57 · 2023: 77 · 2022: 255 · 2021: 302
- FWCI
- 55.27
- 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, 374 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 Host & Microbe (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Funders
- Washington University in St. Louis
- University of Washington
- Saint Louis University
- National Institutes of Health (75N93019C00062, R01 AI127828, R01 AI157155, R37 AI059371)
- AbbVie
- Defense Advanced Research Projects Agency (HR001117S0019)
- 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, antibody escape mutants, neutralizing monoclonal antibodies, receptor binding domain, E484K mutation
- MeSH terms
- Angiotensin-Converting Enzyme 2, COVID-19, SARS-CoV-2, COVID-19 Vaccines, Animals, Antibodies, Monoclonal, Antibodies, Viral, Chlorocebus aethiops, Female, Humans, Mice, Inbred BALB C, Models, Molecular, Mutation, Neutralization Tests, Protein Binding, Receptors, Virus, Vero Cells, Amino Acid Substitution, Mice, Antibodies, Neutralizing, Spike Glycoprotein, Coronavirus
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