Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants
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Abstract
Neutralizing antibodies elicited by prior infection or vaccination are likely to be key for future protection of individuals and populations against SARS-CoV-2. Moreover, passively administered antibodies are among the most promising therapeutic and prophylactic anti-SARS-CoV-2 agents. However, the degree to which SARS-CoV-2 will adapt to evade neutralizing antibodies is unclear. Using a recombinant chimeric VSV/SARS-CoV-2 reporter virus, we show that functional SARS-CoV-2 S protein variants with mutations in the receptor-binding domain (RBD) and N-terminal domain that confer resistance to monoclonal antibodies or convalescent plasma can be readily selected. Notably, SARS-CoV-2 S variants that resist commonly elicited neutralizing antibodies are now present at low frequencies in circulating SARS-CoV-2 populations. Finally, the emergence of antibody-resistant SARS-CoV-2 variants that might limit the therapeutic usefulness of monoclonal antibodies can be mitigated by the use of antibody combinations that target distinct neutralizing epitopes.
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Class 1 antibodies are resisted by A475V; class 2 by E484K and Q493R; class 3 by R346S, N439K, and N440K.
“A475V is resistant to class 1 antibodies (structurally defined as described29); E484K and Q493R are resistant to class 2 antibodies7,8,12,13,29,30,32,33; while R346S, N439K, and N440K are resistant to class 3 antibodies7,8,12,13,29,33.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [13]
Mutations found in emergent S variants decrease sensitivity to neutralization by mAbs, convalescent plasma, and sera from vaccinated individuals.
“Mutations found in emergent S variants decrease sensitivity to neutralization by mAbs, convalescent plasma, and sera from vaccinated individuals (27, 37, 58, 61–70).”
From mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection (2021) · cites this paper as [64]
NTD-specific mAbs were suggested to interfere with viral entry based on other accessory receptors, such as DC-SIGN and L-SIGN, and their neutralization potency was found to be dependent on different in vitro culture conditions.
“NTD-specific mAbs were suggested to interfere with viral entry based on other accessory receptors, such as DC-SIGN and L-SIGN46, and their neutralization potency was found to be dependent on different in vitro culture conditions24.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [24]
Multiple variants, including the 501Y.V2 and B.1.1.7 lineages, harbor multiple mutations and deletions in NTD, most of which are located in a site of vulnerability targeted by all known NTD-specific neutralising antibodies.
“Multiple variants, including the 501Y.V2 and B.1.1.7 lineages, harbor multiple mutations as well as deletions in NTD, most of which are located in a site of vulnerability that is targeted by all known NTD-specific neutralising antibodies24,45.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [24]
Deletion of residue 144 abrogates binding by 4 out of 6 NTD-specific mAbs tested, possibly accounting for viral neutralization escape by most NTD-specific antibodies.
“We previously showed that the deletion of residue 144 abrogates binding by 4 out of 6 NTD-specific mAbs tested, possibly accounting for viral neutralization escape by most NTD-specific antibodies24.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [24]
The lack of neutralization of B.1.1.7 by the 4A8 mAb observed in this study is likely caused by Δ144 due to loss of binding.
“This result is in line with the lack of neutralization of B.1.1.7 by the 4A8 mAb observed in this study, likely caused by Δ144 due to loss of binding24.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [24]
The variants share known escape mutations previously identified under antibody pressure selection in vitro.
“Although distinct, the variants share common characteristics, including known escape mutations that were previously identified under antibody pressure selection in vitro 2,3,[13][14][15][16][17] .”
From Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies (2021) · cites this paper as [13]
E484K substitution is a vulnerability for multiple neutralizing mAbs.
“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 [33]
Even though E484Q is more likely than T478K to evade antibody neutralization, only the Delta variant has demonstrated increased transmissibility, spreading to 54 countries and rapidly replacing the Alpha variant in the UK and the USA.
“Even though E484Q is more likely than T478K to evade antibody neutralization 48,100,165 , only the Delta variant has demonstrated increased transmissibility, spreading to 54 countries and rapidly replacing the Alpha variant in the UK 32,35 and the USA 33 .”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [48]
Breakthrough cases observed might be due to immune evasion mediated by particular alterations present in these strains.
“From a biological point of view, the breakthrough cases observed in this study might be due to immune evasion, mediated by particular alterations present in these strains 9,[23][24][25][26][27] .”
From Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals (2021) · cites this paper as [24]
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N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
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The biological and clinical significance of emerging SARS-CoV-2 variants
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Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection
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Self-citationSARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway
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SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies
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Vaccine Breakthrough Infections with SARS-CoV-2 Variants
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Self-citationSensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
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Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
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mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection
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SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity
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Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement
McCallum, M., Czudnochowski, N., Rosen, L. E., Zepeda, S. K., Bowen, J. E., Walls, A. C., Hauser, K., Joshi, A., Stewart, C., Dillen, J. R., et al. (2022) · Science · doi:10.1126/science.abn8652 · Cited by 535 · see citing works
“%) harbor the R346K substitution which in conjunction with N440K (present in the main haplotype) leads to escape from C135 mAb-mediated neutralization ( 25 , 51 ).”
Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
McCarthy, K. R., Rennick, L. J., Nambulli, S., Robinson-McCarthy, L. R., Bain, W. G., Haidar, G., & Duprex, W. P. (2021) · Science · doi:10.1126/science.abf6950 · Cited by 535 · see citing works
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SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern
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Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies
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Self-citationSARS-CoV-2 spike E484K mutation reduces antibody neutralisation
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Plasma Neutralization of the SARS-CoV-2 Omicron Variant
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Self-citationStructural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants
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SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., et al. (2021) · doi:10.1101/2021.01.18.427166
Increased memory B cell potency and breadth after a SARS-CoV-2 mRNA boost
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Self-citationGenetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail
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“E484K is present in emerging lineages B.1.351 38 and B.1.1.28 39 , along with substitutions at K417, and has been demonstrated to alter the binding of some monoclonal antibodies 40,43,44 as well as human polyclonal serum antibodies 45 .”
InfluentialSARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2
Amanat, F., Thapa, M., Lei, T., Ahmed, S. M. S., Adelsberg, D. C., Carreño, J. M., Strohmeier, S., Schmitz, A. J., Zafar, S., Zhou, J. Q., et al. (2021) · Cell · doi:10.1016/j.cell.2021.06.005 · Cited by 273 · see citing works
A human coronavirus evolves antigenically to escape antibody immunity
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Recurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70
Kemp, S. A., Meng, B., Ferriera, I. A., Datir, R., Harvey, W. T., Papa, G., Lytras, S., Collier, D. A., Mohamed, A., Gallo, G., et al. (2020) · doi:10.1101/2020.12.14.422555 · Cited by 252 · see citing works
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“This lack of concordance between the epitopes of serum and monoclonal antibodies is consistent with other studies reporting that the specificities of potent monoclonal antibodies often do not recapitulate the sera from which they were isolated (Barnes et al., 2020b; Weisblum et al., 2020).”
BackgroundResultInfluentialWalls, 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 · see citing works
“Conversely, some mutations found in circulating SARS-CoV-2 isolates were shown to promote escape from mAbs and to reduce neutralization by immune sera (Baum et al., 2020b; Collier et al., 2021; Li et al., 2020; McCallum et al., 2021a, 2021b; Wang et al., 2021a; Weisblum et al., 2020; Wibmer et al., 2021).”
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
Cele, S., Gazy, I., Jackson, L., Hwa, S.-H., Tegally, H., Lustig, G., Giandhari, J., Pillay, S., Wilkinson, E., Naidoo, Y., et al. (2021) · doi:10.1101/2021.01.26.21250224 · Cited by 651 · see citing works
“In a number of separate in vitro studies using monoclonal antibodies (mAbs), mutations at E484 have emerged as immune escape mutations, often conferring broad cross-resistance to panels of mAbs [8, 9, 10, 11].”
BackgroundN-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
McCallum, M., Marco, A. D., Lempp, F., Tortorici, M. A., Pinto, D., Walls, A. C., Beltramello, M., Chen, A., Liu, Z., Zatta, F., et al. (2021) · doi:10.1101/2021.01.14.426475 · Cited by 901 · see citing works
Comparison of Four SARS-CoV-2 Neutralization Assays
Riepler, L., Rössler, A., Falch, A., Volland, A., Borena, W., von Laer, D., & Kimpel, J. (2020) · Vaccines · doi:10.3390/vaccines9010013 · Cited by 117 · see citing works
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Tada, T., Dcosta, B. M., Samanovic-Golden, M., Herati, R. S., Cornelius, A., Mulligan, M. J., & Landau, N. R. (2021) · doi:10.1101/2021.02.05.430003 · Cited by 153 · see citing works
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., et al. (2020) · doi:10.1101/2020.11.06.372037 · Cited by 135 · see citing works
The Emergence of Sars-CoV-2 Variant Lambda (C.37) in South America
Romero, P. E., Dávila-Barclay, A., Salvatierra, G., González, L., Cuicapuza, D., Solís, L., Marcos-Carbajal, P., Huancachoque, J., Maturrano, L., & Tsukayama, P. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.00789-21 · Cited by 85 · see citing works
Tackling COVID-19 with neutralizing monoclonal antibodies
Corti, D., Purcell, L. A., Snell, G., & Veesler, D. (2021) · Cell · doi:10.1016/j.cell.2021.07.027 · Cited by 78 · see citing works
“Importantly, most of the RBD mutations found in current VOCs/VOIs were already previously identified as resistant variants in vitro by using mAbs and convalescent or vaccine-elicited serum antibodies (Andreano et al., 2020; Baum et al., 2020b; Liu et al., 2021b; Weisblum et al., 2020), suggesting that the emergence of…”
InfluentialFerrareze, P. A. G., Franceschi, V. B., Mayer, A. D. M., Caldana, G. D., Zimerman, R. A., & Thompson, C. E. (2021) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2021.104941 · Cited by 82 · see citing works
Suryadevara, N., Shrihari, S., Gilchuk, P., VanBlargan, L. A., Binshtein, E., Zost, S. J., Nargi, R. S., Sutton, R. E., Winkler, E. S., Chen, E. C., et al. (2021) · doi:10.1101/2021.01.19.427324 · Cited by 361 · see citing works
Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail
Dong, J., Zost, S. J., Greaney, A. J., Starr, T. N., Dingens, A. S., Chen, E. C., Chen, R. E., Case, J. B., Sutton, R. E., Gilchuk, P., et al. (2021) · doi:10.1101/2021.01.27.428529 · Cited by 55 · see citing works
Peng, J., Liu, J., Mann, S. A., Mitchell, A. M., Laurie, M. T., Sunshine, S., Pilarowski, G., Ayscue, P., Kistler, A., Vanaerschot, M., et al. (2022) · Clinical Infectious Diseases · doi:10.1093/cid/ciab283 · Cited by 41 · see citing works
Muecksch, F., Weisblum, Y., Barnes, C. O., Schmidt, F., Schaefer-Babajew, D., Lorenzi, J. C. C., Flyak, A. I., DeLaitsch, A. T., Huey-Tubman, K. E., Hou, S., et al. (2021) · doi:10.1101/2021.03.07.434227 · Cited by 39 · see citing works
Self-citationAnti- SARS-CoV-2 Receptor Binding Domain Antibody Evolution after mRNA Vaccination
Cho, A., Muecksch, F., Schaefer-Babajew, D., Wang, Z., Finkin, S., Gaebler, C., Ramos, V., Cipolla, M., Mendoza, P., Agudelo, M., et al. (2021) · doi:10.1101/2021.07.29.454333 · Cited by 275 · see citing works
Self-citationCoincident rapid expansion of two SARS-CoV-2 lineages with enhanced infectivity in Nigeria
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Shooting at a Moving Target—Effectiveness and Emerging Challenges for SARS-CoV-2 Vaccine Development
Günl, F., Mecate-Zambrano, A., Rehländer, S., Hinse, S., Ludwig, S., & Brunotte, L. (2021) · Vaccines · doi:10.3390/vaccines9101052 · Cited by 27 · see citing works
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Structural Analysis of Spike Protein Mutations in the SARS-CoV-2 P.3 Variant
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- Authors
- Weisblum, Y., Schmidt, F., Zhang, F., DaSilva, J., Poston, D., Lorenzi, J. C., Muecksch, F., Rutkowska, M., Hoffmann, H.-H., Michailidis, E., Gaebler, C., Agudelo, M., Cho, A., Wang, Z., Gazumyan, A., Cipolla, M., Luchsinger, L., Hillyer, C. D., Caskey, M., Robbiani, D. F., Rice, C. M., Nussenzweig, M. C., Hatziioannou, T., & Bieniasz, P. D.
- Affiliations
- Rockefeller University (US)
- Laboratory of Molecular Immunology The Rockefeller University, New York, United States
- New York Blood Center (US)
- Institute for Research in Biomedicine (CH)
- Howard Hughes Medical Institute (US)
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
- Corresponding author
- Nussenzweig, Michel C
- Bieniasz, Paul D
- ORCID
- Weisblum, Yiska
- Schmidt, Fabian
- Zhang, Fengwen
- DaSilva, Justin
- Poston, Daniel
- Muecksch, Frauke
- Rutkowska, Magdalena
- Hoffmann, Hans-Heinrich
- Michailidis, Eleftherios
- Gaebler, Christian
- Agudelo, Marianna
- Cho, Alice
- Wang, Zijun
- Gazumyan, Anna
- Cipolla, Melissa
- Luchsinger, Larry
- Caskey, Marina
- Robbiani, Davide F
- Rice, Charles M
- Nussenzweig, Michel C
- Bieniasz, Paul D
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2020-10-28
- Volume
- 9
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC7723407
- OpenAlex
- W3096064145
- Cited by
- 1,308
- References
- 55
- Citations by year
- 2026: 17 · 2025: 34 · 2024: 82 · 2023: 151 · 2022: 393 · 2021: 583 · 2020: 48
- FWCI
- 38.54
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institute of Allergy and Infectious Diseases (R37AI64003, R01AI078788, P01AI138398-S1, R01AI091707-10S1, 2U19AI111825)
- George Mason University (Fast Grant)
- European ATAC Consortium (EC101003650)
- National Institutes of Health (UL1 TR001866)
- G. Harold and Leila Y. Mathers Charitable Foundation
- Robert S. Wennett Post-Doctoral Fellowship
- Shapiro-Silverberg Fund (Advancement of Translational Research)
- Howard Hughes Medical Institute (Investigators)
- National Institute of General Medical Sciences (T32GM007739)
- 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 variants, neutralizing antibodies, antibody resistance, receptor-binding domain mutations, monoclonal antibodies, convalescent plasma, antibody escape, passive immunization, antibody combinations, epitope diversity
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