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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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“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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Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants
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“Mutation of glutamate to lysine at this position abrogates binding to certain antibodies and results in immune evasion, reinfection and reduced efficacy of vaccines [11, 18-22].”
SARS-CoV-2 Mutations and their Viral Variants
Coşar, B., KARAGÜLLEOĞLU, Z. Y., ÜNAL, S., İnce, A. T., Uncuoglu, D. B., Tuncer, G., Kilinc, B. R., Ozkan, Y. E., Ozkoc, H. C., Demir, I. N., et al. (2021) · Cytokine & Growth Factor Reviews · doi:10.1016/j.cytogfr.2021.06.001 · Cited by 205
“This mutation weakened antibody neutralization and increased the virus’s ability to infect [75].”
The Global Epidemic of the SARS-CoV-2 Delta Variant, Key Spike Mutations and Immune Escape
Tian, D., Sun, Y., Zhou, J., & Ye, Q. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.751778 · Cited by 201
Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far?
Lazarević, I., Pravica, V., Miljanovic, D., & Cupic, M. D. (2021) · Viruses · doi:10.3390/v13071192 · Cited by 193
SARS‐CoV‐2 Alpha, Beta, and Delta variants display enhanced Spike‐mediated syncytia formation
Rajah, M. M., Hubert, M., Bishop, E., Saunders, N., Robinot, R., Grzelak, L., Planas, D., Dufloo, J., Gellenoncourt, S., Bongers, A., et al. (2021) · The EMBO Journal · doi:10.15252/embj.2021108944 · Cited by 192
Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination
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Walls, 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
“These findings show that, as is the case for many convalescent individuals (Greaney et al., 2021b; Liu et al., 2021; Piccoli et al., 2020), an important fraction of vaccine-elicited neutralizing Abs in NHPs and humans is focused on the RBM (specifically around position 484), independently of the immunogen (RBD-NP, Hex…”
Truong, T., Ryutov, A., Pandey, U., Yee, R., Goldberg, L., Bhojwani, D., Aguayo-Hiraldo, P. I., Pinsky, B. A., Pekosz, A. S., Shen, L., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103355 · Cited by 177
Kuzmina, A., Khalaila, Y., Voloshin, O., Keren‐Naus, A., Cohen, L. B., Raviv, Y., Shemer‐Avni, Y., Rosenberg, E., & Taube, R. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.03.008 · Cited by 177
Nasal delivery of an IgM offers broad protection from SARS-CoV-2 variants
Ku, Z., Xie, X., Hinton, P. R., Liu, X., Ye, X., Muruato, A. E., Ng, D., Biswas, S., Zou, J., Liu, Y., et al. (2021) · Nature · doi:10.1038/s41586-021-03673-2 · Cited by 170
In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2
Szemiel, A. M., Merits, A., Orton, R. J., MacLean, O. A., Pinto, R. M., Wickenhagen, A., Lieber, G., Turnbull, M. L., Wang, S., Furnon, W., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009929 · Cited by 170
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SARS-CoV-2 Omicron boosting induces de novo B cell response in humans
Alsoussi, W. B., Malladi, S. K., Zhou, J. Q., Liu, Z., Ying, B., Kim, W., Schmitz, A. J., Lei, T., Horvath, S. C., Sturtz, A. J., et al. (2023) · Nature · doi:10.1038/s41586-023-06025-4 · Cited by 174
Self-citationNeutralization of BA.4–BA.5, BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1 with Bivalent Vaccine
Zou, J., Kurhade, C., Patel, S., Kitchin, N. R. E., Tompkins, K. R., Cutler, M. W., Cooper, D., Yang, Q., Cai, H., Muik, A., et al. (2023) · New England Journal of Medicine · doi:10.1056/nejmc2214916 · Cited by 166
“Cell Host Microbe 2021; 29(3): 477-488.”
SARS-CoV-2 evolution and vaccines: cause for concern?
Williams, T., & Burgers, W. A. (2021) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(21)00075-8 · Cited by 163
Huang, X., Tang, T., Zhang, G., & Liang, T. (2021) · Molecular Cancer · doi:10.1186/s12943-021-01342-6 · Cited by 157
SARS-CoV-2 one year on: evidence for ongoing viral adaptation
Peacock, T. P., Penrice-Randal, R., Hiscox, J. A., & Barclay, W. (2021) · Journal of General Virology · doi:10.1099/jgv.0.001584 · Cited by 155
Tada, T., Dcosta, B. M., Samanovic, M. I., Herati, R. S., Cornelius, A. R., Zhou, H., Vaill, A., Kazmierski, W., Mulligan, M. J., & Landau, N. R. (2021) · mBio · doi:10.1128/mbio.00696-21 · Cited by 155
Focosi, D., & Maggi, F. (2021) · Reviews in Medical Virology · doi:10.1002/rmv.2231 · Cited by 150
Chakraborty, C., Sharma, A. R., Bhattacharya, M., & Lee, S. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.801522 · Cited by 154
Case, J. B., Mackin, S., Errico, J. M., Chong, Z., Madden, E. A., Whitener, B. M., Guarino, B., Schmid, M., Rosenthal, K., Ren, K., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31615-7 · Cited by 146
Self-citationAntibody-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
Review of Current COVID-19 Diagnostics and Opportunities for Further Development
Mardian, Y., Kosasih, H., Karyana, M., Neal, A., & Lau, C. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.615099 · Cited by 153
“, Spike-E484K and SpikeS477N) have demonstrated ability to escape neutralization by convalescent sera and monoclonal antibodies (258).”
BackgroundFrom delta to Omicron: S1-RBD/S2 mutation/deletion equilibrium in SARS-CoV-2 defined variants
PAPANIKOLAOU, V. S., Chrysovergis, A., Ragos, V., Tsiambas, E., Katsinis, S., Manoli, A., Papouliakos, S. M., Roukas, D., Mastronikolis, S. N., Peschos, D., et al. (2022) · Gene · doi:10.1016/j.gene.2021.146134 · Cited by 149
Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell
Puray‐Chavez, M., LaPak, K. M., Schrank, T. P., Elliott, J. L., Bhatt, D. P., Agajanian, M. J., Jasuja, R., Lawson, D. Q., Davis, K., Rothlauf, P. W., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109364 · Cited by 139
“Monoclonal antibody SARS2-55 was generated and as previously described (Liu et al., 2021).”
Self-citationEvolutionary 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 150
SARS-CoV-2 neutralizing antibodies: Longevity, breadth, and evasion by emerging viral variants
Tea, F., Stella, A. O., Aggarwal, A., Darley, D. R., Pilli, D., Vitale, D., Merheb, V., Lee, F. X. Z., Cunningham, P., Walker, G. J., et al. (2021) · PLoS Medicine · doi:10.1371/journal.pmed.1003656 · Cited by 135
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 134
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 149
“With multiple critical mutations destabilizing the antibody interaction with spike or RBD, in vitro experiments also revealed the worrying performance of current antibodies against the SARS-CoV-2 variants.(201,202) Considering that in vitro neutralization for the same therapeutic agent might differ under different cir…”
MethodHeilmann, E., Costacurta, F., Moghadasi, S. A., Ye, C., Pavan, M., Bassani, D., Volland, A., Ascher, C., Weiss, A. K. H., Bante, D., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abq7360 · Cited by 145
Fast-spreading SARS-CoV-2 variants: challenges to and new design strategies of COVID-19 vaccines
Zhou, W., & Wang, W. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00644-x · Cited by 134
“All four mutants undergoing substitution at E484 are resistant to neutralization of human immune serum.(25) Bloom et al.”
BackgroundLi, 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
“These data demonstrate that in contrast to other antibodies that are attenuated against emerging variants (Greaney et al., 2021a; Liu et al., 2021; Starr et al., 2021; Weisblum et al., 2020), CV3-1 and CV3-25 remain potent against these variants and are therefore prime candidates to elucidate the…”
Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2
Laiton‐Donato, K., Franco-Muñoz, C., Álvarez-Díaz, D. A., Ruiz-Moreno, H. A., Usme-Ciro, J. A., Prada-Cardozo, D., Reales-González, J., Corchuelo, S., Herrera-Sepúlveda, M. T., Naizaque, J., et al. (2021) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2021.105038 · Cited by 123
SARS-CoV-2 immune evasion by variant B.1.427/B.1.429Preprint
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An intranasal vaccine durably protects against SARS-CoV-2 variants in mice
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Self-citationSpike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation
Chen, D. W., Chin, C. V., Kenney, D., Tavares, A. H., Khan, N., Conway, H. L., Liu, G., Choudhary, M. C., Gertje, H. P., O’Connell, A. K., et al. (2023) · Nature · doi:10.1038/s41586-023-05697-2 · Cited by 148
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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
“617, L452R, appears to reduce the sensitivity to certain antibodies and human convalescent sera [139,158].”
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SARS‐CoV‐2 Omicron variant: Immune escape and vaccine development
Ao, D., Lan, T., He, X., Liu, J., Chen, L., Baptista‐Hon, D. T., Zhang, K., & Wei, X. (2022) · MedComm · doi:10.1002/mco2.126 · Cited by 122
Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination
Cobey, S. E., Larremore, D. B., Grad, Y. H., & Lipsitch, M. (2021) · Nature reviews. Immunology · doi:10.1038/s41577-021-00544-9 · Cited by 119
LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variantsPreprint
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Mutations of SARS-CoV-2 spike protein: Implications on immune evasion and vaccine-induced immunity
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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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