Cited by 739SARS-CoV-2 and COVID-19 Researchvaccines and immunoinformatics approachesAnimal Virus Infections Studies

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Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization

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Liu, Zhuoming, VanBlargan, Laura A., Bloyet, Louis-Marie, Rothlauf, Paul W., Chen, Rita E., Stumpf, Spencer, Zhao, Haiyan, Errico, John M., Theel, Elitza S., Liebeskind, Mariel J., Alford, Brynn, Buchser, William J., Ellebedy, Ali H., Fremont, Daved H., Diamond, Michael S., Whelan, Sean P.J.·2021·Cell Host & Microbe

DOI 10.1016/j.chom.2021.01.014PMC PMC7839837

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Abstract

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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SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor
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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).”
Background
A new coronavirus associated with human respiratory disease in China
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BackgroundInfluential
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Background
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“Its neighbouring residue E484 is of great interest to the scientific community with the mutation E484K contributing to antigenic escape (Greaney et al., 2021; Liu et al., 2021).”
Background
Development of highly potent non-covalent inhibitors of SARS-CoV-2 3CLproPreprint
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Background
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“Interestingly, P29 had a treatment history of I n v i t r o c o n fi r m e d s i t e s c o n f e r a r e d u c t i o n i n s u s - c e p t i b i l i t y t o b e b t e l o v i m a b [ 33 , 34 ] L a t e r O m i c r o n B Q .”
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“Further, multiple spike substitutions at 477 (S477G, S477N and S477R) and 484 positions (E484A, E484D and E484K) have characteristically shown resistance toward convalescent sera [28,31,35].”
Background
Structural communication fingerprinting and dynamic investigation of RBD-hACE2 complex from BA.1 × AY.4 recombinant variant (Deltacron) of SARS-CoV-2 to decipher the structural basis for enhanced transmission
Wang, J.-G., Muhammad, S. F., Aman, S., Khan, A., Munir, S., Khan, M., Mohammad, A., Waheed, Y., Munir, M., Guo, L., et al. (2022) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2022.2123399 · Cited by 5
“37 variant discovered in Pero, regarded as the ‘variant of interest’ had mutations (L452Q and F490S in the RBD) assumed to be related with decreased antibody neutralizing susceptibility, predominantly due to the F490S mutation in the RBD (Liu et al., 2021; Wink et al., 2021).”
Background
Surrogate Virus Neutralisation Test Based on Nanoluciferase-Tagged Antigens to Quantify Inhibitory Antibodies against SARS-CoV-2 and Characterise Omicron-Specific Reactivity in a Vaccination Cohort
Schöfbänker, M., Neddermeyer, R., Günther, T., Mueller, M., Romberg, M.-L., Classen, N., Hennies, M. T., Hrincius, E. R., Ludwig, S., Kühn, J., et al. (2023) · Vaccines · doi:10.3390/vaccines11121832 · Cited by 5
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“…sustained replication and are amenable to evolution studies. rVSVs expressing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike were used to evaluate monoclonal and serum antibody escape, enabling the identification of therapeutic candidates and future antigenic variants (25, 26).”
Detecting Potentially Adaptive Mutations from the Parallel and Fixed Patterns in SARS-CoV-2 Evolution
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
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Soluble wild-type ACE2 molecules inhibit newer SARS-CoV-2 variants and are a potential antiviral strategy to mitigate disease severity in COVID-19
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Receptor-Binding Domain Proteins of SARS-CoV-2 Variants Elicited Robust Antibody Responses Cross-Reacting with Wild-Type and Mutant Viruses in Mice
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Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India
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A CLUSTER OF SARS‐COV‐2 DELTA VARIANT OF CONCERN ADDITIONALLY HARBORING F490S, NORTHERN LOMBARDY, ITALY
Novazzi, F., Baj, A., Pasciuta, R., Genoni, A. P., Ferrante, F. D., Tripiciano, R., Catanoso, G., Focosi, D., & Maggi, F. (2022) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2021.12.362 · Cited by 5
First description of two immune escape indian B.1.1.420 and B.1.617.1 SARS-CoV2 variants in FrancePreprint
Garcia, V., Vig, V., Peillard, L., Ramdani, A., Mohamed, S., & Halfon, P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.12.443357 · Cited by 5
in silico Assessment of Antibody Drug Resistance to Bamlanivimab of SARS-CoV-2 Variant B.1.617Preprint
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Nasally-delivered interferon-λ protects mice against upper and lower respiratory tract infection of SARS-CoV-2 variants including OmicronPreprint
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Self-citation
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SARS-CoV-2 B.1.214.1, B.1.214.2 and B.1.620 are predominant lineages between December 2020 and July 2021 in the Republic of Congo
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“This substitution was shown to strengthen binding of S protein with the human ACE2 receptor(52,53) and to be resistant against multiple mAbs.(54) Additionally, S477 was observed to mutate to arginine (S477R) and isoleucine (S477I) (Figure 2(e)).”
Investigation of SARS-CoV-2 lineages and mutations circulating in a university-affiliated hospital in South Korea analyzed using Oxford Nanopore MinION sequencing
Kim, H., Chung, S. H., Kim, H. S., Kim, H.-S., Song, W., Hong, K. H., & Kim, J. (2022) · Osong Public Health and Research Perspectives · doi:10.24171/j.phrp.2022.0183 · Cited by 4
“In a study using 19 monoclonal antibodies, substitutions at this position occurred the most frequently [20], and all amino acid changes to A, K, Q, P, D, and G reduced recognition by antibodies [20,21].”
ChAdOx1 nCoV-19, BNT162b2 and CoronaVac Vaccines Do Not Induce as Strong Neutralising Antibodies with Broad Variant Protection as Infection and Suggest Vaccines that Induce Broader Sterilising Immunity are Essential to Stop the Pandemic
Chua, J. X., Durrant, L. G., Chok, Y. L., & Lai, O. M. (2022) · iScience · doi:10.1016/j.isci.2022.105379 · Cited by 4
The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37
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“Two mutations (L452Q, F490S) are present in the receptor‐binding protein, and one of them (F490S) has shown reduced susceptibility to antibody neutralization.(5) Although it”
Background
Early detection and improved genomic surveillance of SARS-CoV-2 variants from deep sequencing data
Ramazzotti, D., Maspero, D., Angaroni, F., Spinelli, S., Antoniotti, M., Piazza, R., & Graudenzi, A. (2022) · iScience · doi:10.1016/j.isci.2022.104487 · Cited by 4
“Moreover, mutation S:G446V has been associated to attenuate monoclonal and serum antibody neutralization (Liu et al., 2021).”
A Novel Conserved Linear Neutralizing Epitope on the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein
Hua, R.-H., Zhang, S., Niu, B., Ge, J., Lan, T., & Bu, Z. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.01190-23 · Cited by 4
Molecular epidemiological characteristics of SARS-CoV-2 in imported cases from 2021 to 2022 in Zhejiang Province, China
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“Specific Omicron variants outnumbered Delta variants, such as S339G, S373P, S375F, N440K, S477N, E484A, Q498R, N501Y, Y505H, H655Y, N679K, N764K, D796Y, Q954H, and N969K.”
Background
SARS-CoV-2 Serological Investigation of White-Tailed Deer in Northeastern Ohio
Boley, P. A., Dennis, P. M., Faraone, J. N., Xu, J., Liu, M., Niu, X., Gibson, S., Hale, V. L., Wang, Q., Liu, S., et al. (2023) · Viruses · doi:10.3390/v15071603 · Cited by 4
“Interestingly, a 484 aspartic-acid-to-lysine (E494K) substitution has been associated with resistance in convalescent serum neutralization [44], which may also contribute to the discrepancies among the ELISA positivity, with a lack of neutralizing antibody titer in some samples.”
Background
To be remembered: B cell memory response against SARS‐CoV ‐2 and its variants in vaccinated and unvaccinated individuals
Ahmed, N., Athavale, A., Tripathi, A. H., Subramaniam, A., Upadhyay, S. K., Pandey, A. K., Rai, R. C., & Awasthi, A. (2023) · Scandinavian Journal of Immunology · doi:10.1111/sji.13345 · Cited by 4
“139,140 The convalescent serum can neutralize viruses having the wild-type Spike protein (non-mutated).”
BackgroundInfluential
A mouse xenograft long‐term replication yields a SARS‐CoV‐2 Delta mutant with increased lethality
Kim, D., Kim, M., Kim, J.-S., Baek, K., Park, H., Park, S., Kang, B. M., Kim, S., Kim, M., Mostafa, M. N., et al. (2024) · Journal of Medical Virology · doi:10.1002/jmv.29459 · Cited by 4
An Overview on Lambda, Epsilon, Kappa, Iota and Zeta Variants of Covid-19 and its Probability to Merge with Delta & Delta Plus, why it is a Concern
(2021) · Biointerface Research in Applied Chemistry · doi:10.33263/briac125.68956914 · Cited by 4
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Background
SARS-CoV-2 Pandemic Tracing in Italy Highlights Lineages with Mutational Burden in Growing Subsets
Boccia, A. S., Tufano, R., Ferrucci, V., Sepe, L., Bianchi, M., Pascarella, S., Zollo, M., & Paolella, G. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23084155 · Cited by 4
Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern
Flores-Alanis, A., Delgado, G., Espinosa-Camacho, L. F., Rodríguez‐Gómez, F., Cruz‐Rangel, A., Sandner-Miranda, L., Cravioto, A., & Morales-Espinosa, R. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.886585 · Cited by 4
Simultaneous measurement of the antibody responses against SARS-CoV-2 and its multiple variants by a phage display mediated immuno-multiplex quantitative PCR-based assay
Chen, H., Li, S., Wang, J., He, S., Wang, D., Qian, Z., Hu, D., Qi, F., Hu, K., Luo, C., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.968036 · Cited by 4
Impact of New Variants on SAR-CoV-2 Infectivity and Neutralization: A Molecular Assessment of the Alterations in the Spike-Host Protein InteractionsPreprint
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Cohort-specific serological recognition of SARS-CoV-2 variant RBD antigensPreprint
Fraser, D. D., Miller, M. R., Martin, C. M., Slessarev, M., Hahn, P., Higgins, I., Melo, C., Pest, M. A., Rothery, N., Wang, X., et al. (2022) · medRxiv · doi:10.1101/2022.01.10.21268250 · Cited by 4
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Result
An ACE2-blocking antibody confers broad neutralization and protection against Omicron and other SARS-CoV-2 variantsPreprint
Du, W., Hurdiss, D. L., Drabek, D., Mykytyn, A. Z., Kaiser, F. K., González-Hernández, M. C., Muñoz‐Santos, D., Lamers, M. M., van Haperen, R., Li, W., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.17.480751 · Cited by 4
Adaptive evolution of SARS-CoV-2 during a persistent infection for 521 days in an immunocompromised patient
Schmidt, H., Schick, L., Podlech, J., Renzaho, A., Lieb, B., Diederich, S., Hankeln, T., Plachter, B., & Kriege, O. (2025) · npj Genomic Medicine · doi:10.1038/s41525-025-00463-x · Cited by 3
Identification of severity related mutation hotspots in SARS-CoV-2 using a density-based clustering approach
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“Q677 exists as two variants: Q677P and Q677H, contributing to host cell entry of SARS-CoV-2 [29].”
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Seadawy, M. G., Binsuwaidan, R., Alotaibi, B. S., El-Masry, T. A., El-Harty, B. E., Gad, A. F., Elkhatib, W. F., & El-Bouseary, M. M. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.923137 · Cited by 3
Novel neutralizing mouse-human chimeric monoclonal antibodies against the SARS-CoV-2 receptor binding domain
Vanan, A. G., Maghsood, F., Yadegari, H., Bahadori, T., Zarnani, A., Razavi, S. A., Jeddi‐Tehrani, M., Amiri, M. M., & Shokri, F. (2023) · Journal of Medical Microbiology · doi:10.1099/jmm.0.001728 · Cited by 3
Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins
Hasan, M., He, Z., Jia, M., Leung, A. C. F., Natarajan, K., Xu, W., Yap, S., Zhou, F., Chen, S., Su, H., et al. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.05.037 · Cited by 3
“Their locations within the epitope of several important neutralizing antibodies enable them to enhance the immune escape capabilities of the virus [69,76–78].”
Enhanced detection and molecular modeling of adaptive mutations in SARS-CoV-2 coding and non-coding regions using the c/µ test
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Features of Highly Homologous T-Cell Receptor Repertoire in the Immune Response to Mutations in Immunogenic Epitopes
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Prevalence of COVID-19 and Possible Antigenic Drifts in SARS-CoV-2 Spike Protein in Kurdistan Region-Iraq
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A Bacterial Cell-Based Assay To Study SARS-CoV-2 Protein-Protein Interactions
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Variation Analysis of SARS-CoV-2 Complete Sequences from Iran
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Retrospective in silico mutation profiling of SARS-CoV-2 structural proteins circulating in Uganda by July 2021: Towards refinement of COVID-19 disease vaccines, diagnostics, and therapeutics
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Benchmark Investigation of SARS-CoV-2 Mutants’ Immune Escape with 2B04 Murine Antibody: A Step Towards Unraveling a Larger Picture
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Antiviral Resistance against Viral Mutation: Praxis and Policy for SARS-CoV-2
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“An in vitro study for the SARS-CoV-2 spike protein mutations responsible for antibody evasiveness has identified that the S494P mutation reduces SARS-CoV-2 neutralization by 3–5-fold in some convalescent sera [45].”
Background
How concerning is a SARS-CoV-2 variant of concern? Computational predictions and the variants labeling system
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“455 456 In addition to Glu484, other mutations on RBD binding hot spots residues, have been also linked 457 to antibody binding and neutralization including mutations on Lys417, Gly446, Phe456, Asn501, 458 Gly477 and Asp614 [28-31].”
Background
Evaluation of Analytical and Clinical Performance and Usefulness in a Real-Life Hospital Setting of Two in-House Real-Time RT-PCR Assays to Track SARS-CoV-2 Variants of Concern
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Mutational analysis of the spike protein of SARS-COV-2 isolates revealed atomistic features responsible for higher binding and infectivity
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“277); destabilizing the structure of the respective protein was also previously reported to confer resistance to four different types of sera tested (Figure 2A) (Liu et al., 2021).”
SARS-CoV-2 variant with higher affinity to ACE2 shows reduced sera neutralization susceptibilityPreprint
Vogel, M., Chang, X., Augusto, G. S., Mohsen, M. O., Speiser, D. E., & Bachmann, M. F. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.04.433887 · Cited by 3

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: Liu, Zhuoming
VanBlargan, Laura A.
Bloyet, Louis-Marie
Rothlauf, Paul W.
Chen, Rita E.
Stumpf, Spencer
Zhao, Haiyan
Errico, John M.
Theel, Elitza S.
Liebeskind, Mariel J.
Buchser, William J.
Ellebedy, Ali H.
Fremont, Daved H.
Diamond, Michael S.
Whelan, Sean P.J.
Venue: Cell Host & Microbe
Publisher: Elsevier BV
Published: 2021-03
Volume: 29
Issue: 3
Pages: 477-488.e4
ISSN: 1931-3128 (ISSN-L)
DOI: 10.1016/j.chom.2021.01.014
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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Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization

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