Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement
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Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern evades antibody-mediated immunity that comes from vaccination or infection with earlier variants due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo–electron microscopy and x-ray crystal structures of the spike protein and the receptor-binding domain bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor. We provide a blueprint for understanding the marked reduction of binding of other therapeutic mAbs that leads to dampened neutralizing activity. Remodeling of interactions between the Omicron receptor-binding domain and human ACE2 likely explains the enhanced affinity for the host receptor relative to the ancestral virus.
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Several SARS-CoV-2 variants of concern, such as Beta and Omicron, evade humoral responses elicited by vaccines based on ancestral S-protein sequences.
“Several VOCs which have mutated, such as Beta1 and Omicron2, evade humoral responses elicited by vaccines based on ancestral S-protein sequences3.”
From Efficacy of an unmodified bivalent mRNA vaccine against SARS-CoV-2 variants in female small animal models (2023) · cites this paper as [2]
Reinfections and vaccine breakthrough infections accounted for the majority of Omicron BA.1/2 infections, likely attributable to a minority of population remaining naïve prior to the Omicron BA.1/2 wave and to Omicron BA.1/2's immune-escape properties.
“Reinfections and vaccine breakthrough infections accounted for the majority of Omicron BA.1/2 infections, likely attributable to a minority of population remaining naïve prior to the Omicron BA.1/2 wave and to Omicron BA.1/2's immune-escape properties 16,21,22 .”
From Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa (2023) · cites this paper as [22]
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Self-citationBroad and potent activity against SARS-like viruses by an engineered human monoclonal antibody
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Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail
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Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants
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“1D) ( 2 , 22 ).”
Self-citationBroad sarbecovirus neutralization by a human monoclonal antibody
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“Dampened S 1 subunit shedding might enhance the effector function activity of vaccine-or infection-elicited Abs along with that of therapeutic mAbs ( 21 ) that retain affinity for Omicron S.”
Self-citationBroadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift
Cameroni, E., Bowen, J. E., Rosen, L. E., Saliba, C., Zepeda, S. K., Culap, K., Pinto, D., VanBlargan, L. A., Marco, A. D., di Iulio, J., et al. (2021) · Nature · doi:10.1038/d41586-021-03825-4 · Cited by 247 · see citing works
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Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies
Cao, Y., Wang, J., Jian, F., Xiao, T., Song, W., Yisimayi, A., Huang, W., Li, Q., Wang, P., An, R., et al. (2021) · Nature · doi:10.1038/d41586-021-03796-6 · Cited by 227 · see citing works
Considerable escape of SARS-CoV-2 Omicron to antibody neutralization
Planas, D., Saunders, N., Maes, P., Guivel‐Benhassine, F., Planchais, C., Buchrieser, J., Bolland, W., Porrot, F., Staropoli, I., Lemoine, F., et al. (2021) · Nature · doi:10.1038/d41586-021-03827-2 · Cited by 193 · see citing works
Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice
Martinez, D. R., Schäfer, A., Leist, S. R., la Cruz, G. D., West, A., Atochina‐Vasserman, E. N., Lindesmith, L. C., Pardi, N., Parks, R., Barr, M., et al. (2021) · Science · doi:10.1126/science.abi4506 · Cited by 189 · see citing works
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“The identification of broadly reactive mAbs that neutralize multiple distinct sarbecoviruses, including SARS-CoV-2 variants, pave the way for designing vaccines eliciting broad sarbecovirus immunity ( 52 – 56 ).”
Self-citationZhu, X. Q., Mannar, D., Srivastava, S. S., Berezuk, A., Demers, J., Saville, J. W., Leopold, K., Li, W., Dimitrov, D. S., Tuttle, K. S., et al. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001237 · Cited by 176 · see citing works
Emerging SARS-CoV-2 variants expand species tropism to murines
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“Although the N501Y mutation has been described previously to enable some SARS-CoV-2 VOC to infect and replicate in mice, the Alpha and Beta variant RBDs only weakly bound mouse ACE2 ( 47 , 48 ).”
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 152 · cited 1× · see citing works
“S3, and table S3) and with previous analyses of the impact of individual mutations on neutralization by each of these two mAbs ( 9 , 38 – 40 ).”
A broadly cross-reactive antibody neutralizes and protects against sarbecovirus challenge in mice
Martinez, D. R., Schäfer, A., Gobeil, S., Li, D., la Cruz, G. D., Parks, R., Lu, X., Barr, M., Stalls, V., Janowska, K., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abj7125 · Cited by 136 · see citing works
Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry
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Self-citationTrack Omicron’s spread with molecular data
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Automatically Fixing Errors in Glycoprotein Structures with Rosetta
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Neutralization and Stability of SARS-CoV-2 Omicron VariantPreprint
Zeng, C., Evans, J. P., Qu, P., Faraone, J. N., Zheng, Y.-M., Carlin, C., Bednash, J. S., Zhou, T., Lozanski, G., Mallampalli, R. K., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.16.472934 · Cited by 86 · cited 1× · see citing works
“Putatively enhanced interactions between the S 1 and S 2 subunits in Omicron S along with pre-fusion stabilization, and altered processing at the S 1 /S 2 cleavage site due to the N679K and P681H mutations, might reduce S 1 shedding, consistent with recent studies ( 18 – 20 ).”
Pan, T. S., Chen, R., He, X., Yuan, Y., Deng, X., Li, R., Yan, H., Yan, S., Liu, J., Zhang, Y., et al. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00848-1 · Cited by 72 · cited 1× · see citing works
“Although the N501Y mutation has been described previously to enable some SARS-CoV-2 VOC to infect and replicate in mice, the Alpha and Beta variant RBDs only weakly bound mouse ACE2 ( 47 , 48 ).”
VanBlargan, L., Errico, J., Halfmann, P., et al. (2021) · bioRxiv · doi:10.1101/2021.12.15.472828 · Cited by 59 · cited 5×
“This finding likely explains the similarly moderate reduction of S309 potency against the single G339D S mutant ( 9 ) or the full constellation of Omicron S mutations ( 7 , 9 – 11 ).”
InfluentialOlmedillas, E., Mann, C. J., Peng, W.-W., Wang, Y.-T., Avalos, R. D., Bedinger, D. H., Valentine, K. M., Shafee, N., Schendel, S., Yuan, M., et al. (2021) · bioRxiv · doi:10.1101/2021.05.06.441046 · Cited by 30 · see citing works
SARS-CoV-2 spike conformation determines plasma neutralizing activityPreprint
Bowen, J. E., Walls, A. C., Joshi, A., Sprouse, K. R., Stewart, C., Tortorici, M. A., Franko, N., Logue, J. K., Mazzitelli, I. G., Tilles, S. W., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.19.473391 · Cited by 21 · cited 1× · see citing works
“The RBD is the main target of plasma neutralizing activity in convalescent and vaccinated individuals and comprises several antigenic sites recognized by neutralizing Abs with a range of neutralization potencies and breadth ( 12 , 13 , 21 , 23 – 36 ) (Fig.”
Self-citationAttenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variantPreprint
Sato, K., Suzuki, R., Yamasoba, D., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-1207670/v1 · Cited by 9 · see citing works
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Markov, P. V., Ghafari, M., Beer, M., Lythgoe, K., Simmonds, P., Stilianakis, N. I., & Katzourakis, A. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00878-2 · Cited by 1,179 · see citing works
Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity
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Self-citationSARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein–ACE2 complex
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SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters
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Self-citationAntibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum
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SARS-CoV-2 Omicron variant: recent progress and future perspectives
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“G339D and N440K are presumed to interfere with the combination of S309 and spike protein due to the proximity of the antigenic site, but the impact is limited.(76,127) BA.”
InfluentialShrestha, L. B., Foster, C. S. P., Rawlinson, W. D., Tedla, N. T., & Bull, R. A. (2022) · Reviews in Medical Virology · doi:10.1002/rmv.2381 · Cited by 469 · see citing works
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Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution
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Imprinted antibody responses against SARS-CoV-2 Omicron sublineages
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Molecular basis of receptor binding and antibody neutralization of Omicron
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Self-citationThe humoral response and antibodies against SARS-CoV-2 infection
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Omicron: increased transmissibility and decreased pathogenicity
Bálint, G., Vörös-Horváth, B., & Széchenyi, A. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01009-8 · Cited by 182 · see citing works
“Analysis using advanced structure determining methods such as cryo-electron microscopy and X-ray crystallography confirmed these results and directly connected novel mutations and new chemical interaction sites.(5) The ACE2 affinity was determined experimentally, using biolayer interferometry.”
The Evolution and Biology of SARS-CoV-2 VariantsPreprint
Telenti, A., Hodcroft, E. B., & Robertson, D. L. (2022) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a041390 · Cited by 183 · see citing works
Potent cross-reactive antibodies following Omicron breakthrough in vaccinees
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Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529
Zhou, T., Wang, L., Misasi, J., Pegu, A., Zhang, Y., Harris, D. R., Olia, A. S., Talana, C. A., Yang, E. S., Chen, M., et al. (2022) · Science · doi:10.1126/science.abn8897 · Cited by 160 · see citing works
Molecular fate-mapping of serum antibody responses to repeat immunization
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Omicron spike function and neutralizing activity elicited by a comprehensive panel of vaccines
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Self-citationClose relatives of MERS-CoV in bats use ACE2 as their functional receptors
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Self-citationNeutralization, effector function and immune imprinting of Omicron variants
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Structural and functional impact by SARS-CoV-2 Omicron spike mutations
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Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1
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Self-citationUnderstanding T cell responses to COVID-19 is essential for informing public health strategies
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“Furthermore, monoclonal antibodies used in a therapeutic capacity showed reduced neutralization and impaired binding to the Delta and Omicron spike protein (15, 16), and the Alpha and Beta variants are both refractory or resistant to therapeutic monoclonal antibodies directed against the spike protein (14).”
Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants
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Self-citationSARS-CoV-2: Evolution and Emergence of New Viral Variants
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“2022) and affinity for human and/or animal ACE2 proteins (Cameroni et al. 2022; Gobeil et al. 2022; Mannar et al. 2022; McCallum et al. 2022; Meng et al. 2022; Peacock et al. 2022); (2) between efficient proteolytic priming with TMPRSS2 which expedites cellular entry via the cell surface (Meng et al.”
InfluentialAdams, K., Rhoads, J. P., Surie, D., Gaglani, M., Ginde, A. A., McNeal, T., Talbot, H. K., Casey, J. D., Zepeski, A., Shapiro, N. I., et al. (2022) · BMJ · doi:10.1136/bmj-2022-072065 · Cited by 115 · see citing works
Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike
Stalls, V., Lindenberger, J. J., Gobeil, S., Henderson, R. C., Parks, R., Barr, M., Deyton, M., Martin, M., Janowska, K., Huang, X., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111009 · Cited by 101 · see citing works
“We and others have described structures of the Omicron BA.1 spike (Zhou, 2021, Mannar et al., 2022, Cerutti et al., 2022, Cui et al., 2022, McCallum et al., 2022, Ye et al., 2022, Gobeil et al., 2022).”
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“Thus, mutations in the N-terminal domain or receptor-binding domain (NTD and RBD, respectively) of S can increase resistance to neutralizing antibodies (Cao et al., 2022; Dai and Gao, 2021; Dejnirattisai et al., 2022; McCallum et al., 2022; VanBlargan et al., 2021).”
Tortorici, M. A., Walls, A. C., Joshi, A., Park, Y., Eguia, R. T., Miranda, M. C., Kepl, E., Dosey, A. M., Stevens‐Ayers, T., Boeckh, M. J., et al. (2022) · Cell · doi:10.1016/j.cell.2022.05.019 · Cited by 87 · see citing works
Self-citationB-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity
Lapuente, D., Winkler, T., & Tenbusch, M. (2023) · Cellular and Molecular Immunology · doi:10.1038/s41423-023-01095-w · Cited by 91 · see citing works
“Nevertheless, the RBD remains the most prominent target for nAbs, and the resulting immune pressure is re fl ected by an increasing number of escape mutations in the RBD, which is particularly the case for the omicron variant [33, 34].”
Bianchini, F., Crivelli, V., Abernathy, M. E., Guerra, C., Palus, M., Muri, J., Marcotte, H., Piralla, A., Pedotti, M., Gasparo, R. D., et al. (2023) · Science Immunology · doi:10.1126/sciimmunol.ade0958 · Cited by 83 · see citing works
SARS-CoV-2 evolution on a dynamic immune landscape
Raharinirina, N. A., Gubela, N., Börnigen, D., Smith, M. R., Oh, D., Budt, M., Mache, C., Schillings, C., Fuchs, S., Dürrwald, R., et al. (2025) · Nature · doi:10.1038/s41586-024-08477-8 · Cited by 86 · see citing works
Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein
Calvaresi, V., Wrobel, A. G., Toporowska, J., Hammerschmid, D., Doores, K. J., Bradshaw, R. T., Parsons, R. B., Benton, D. J., Roustan, C., Reading, E., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36745-0 · Cited by 82 · see citing works
Broad anti–SARS-CoV-2 antibody immunity induced by heterologous ChAdOx1/mRNA-1273 vaccination
Kaku, C. I., Champney, E. R., Normark, J., García, M., Johnson, C. E., Ahlm, C., Christ, W., Sakharkar, M., Ackerman, M. E., Klingström, J., et al. (2022) · Science · doi:10.1126/science.abn2688 · Cited by 72 · see citing works
Bowen, J. E., Park, Y., Stewart, C., Brown, J. T., Sharkey, W. K., Walls, A. C., Joshi, A., Sprouse, K. R., McCallum, M., Tortorici, M. A., et al. (2022) · Science Immunology · doi:10.1126/sciimmunol.adf1421 · Cited by 81 · see citing works
Self-citationBreakthrough infections after COVID-19 vaccination: Insights, perspectives and challenges
Amanatidou, E., Gkiouliava, A., Pella, E., Serafidi, M., Tsilingiris, D., Vallianou, N. G., Karampela, Ι., & Dalamaga, Μ. (2022) · Metabolism Open · doi:10.1016/j.metop.2022.100180 · Cited by 76 · see citing works
“Overall, emerging data have suggested that the omicron variant presents increased transmissibility and ability to dodge immunity whether from vaccination or previous infection as well decreased pathogenicity [11,12].”
Zhou, H., Møhlenberg, M., Thakor, J. C., Tuli, H. S., Wang, P., Assaraf, Y. G., Dhama, K., & Jiang, S. (2022) · Clinical Microbiology Reviews · doi:10.1128/cmr.00014-22 · Cited by 76 · see citing works
Evolution of the SARS-CoV-2 Omicron spike
Parsons, R., & Acharya, P. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113444 · Cited by 74 · see citing works
“4,39,55 Thus, the same mutations that remodeled the S protein architecture may have contributed to immune escape by the Omicron variant.”
Lee, I., Sun, C., Wu, P., Lan, Y.-H., Wang, I.-H., Liu, W., Yuan, J. P., Chang, Y.-W., Tseng, S.-C., Tsung, S.-I., et al. (2022) · Journal of Biomedical Science · doi:10.1186/s12929-022-00830-1 · Cited by 66 · see citing works
Structural insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction
Lan, J., He, X., Ren, Y., Wang, Z., Zhou, H., Fan, S., Zhu, C., Liu, D., Shao, B., Liu, T., et al. (2022) · Cell Research · doi:10.1038/s41422-022-00644-8 · Cited by 71 · see citing works
Xue, S., Han, Y., Wu, F., & Wang, Q. (2024) · Protein & Cell · doi:10.1093/procel/pwae007 · Cited by 72 · see citing works
“…of S protein is of primary importance for SARS-CoV-2 infection, thus distinct VOC mutations work together to maintain the ACE2 affinity and even enhance it to varying degrees (Cao et al., 2022a; Chakraborty, 2022; Liu et al., 2022; Ma et al., 2023; McCallum et al., 2022; Ozono et al., 2021).”
Seephetdee, C., Bhukhai, K., Buasri, N., Leelukkanaveera, P., Lerdwattanasombat, P., Manopwisedjaroen, S., Phueakphud, N., Kuhaudomlarp, S., Olmedillas, E., Saphire, E. O., et al. (2022) · Antiviral Research · doi:10.1016/j.antiviral.2022.105370 · Cited by 71 · see citing works
Brüssow, H. (2022) · Microbial Biotechnology · doi:10.1111/1751-7915.14064 · Cited by 69 · see citing works
“The spike proteins from the original Wuhan isolate and Omicron can be largely superimposed except for a 10 aa region preventing the binding of site II neutralizing monoclonal antibodies in Omicron (McCallum et al., 2022).”
Immune responses in Omicron SARS-CoV-2 breakthrough infection in vaccinated adults
Kared, H., Wolf, A., Alirezaylavasani, A., Ravussin, A., Solum, G., Tran, T. T., Lund‐Johansen, F., Vaage, J. T., Nissen‐Meyer, L. S. H., Nygaard, U. C., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31888-y · Cited by 65 · see citing works
Mannar, D., Saville, J. W., Sun, Z., Zhu, X. Q., Martí, M. M., Srivastava, S. S., Berezuk, A., Zhou, S., Tuttle, K. S., Sobolewski, M. D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32262-8 · Cited by 63 · see citing works
Imprinted antibody responses against SARS-CoV-2 Omicron sublineages
Park, Y.-J., Pinto, D., Walls, A. C., Liu, Z., De Marco, A., Benigni, F., Zatta, F., Silacci-Fregni, C., Bassi, J., Sprouse, K. R., et al. (2022) · doi:10.1101/2022.05.08.491108 · Cited by 251 · see citing works
Self-citationThe rapid replacement of the SARS-CoV-2 Delta variant by Omicron (B.1.1.529) in England
Paton, R. S., Overton, C. E., & Ward, T. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abo5395 · Cited by 63 · see citing works
“The variant has 37 mutations on the receptor binding domain (RBD) ( 10 ).”
The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution
Moulana, A., Dupic, T., Phillips, A. M., Chang, J., Roffler, A. A., Greaney, A. J., Starr, T. N., Bloom, J. D., & Desai, M. M. (2023) · eLife · doi:10.7554/elife.83442 · Cited by 62 · see citing works
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“This rapid 62 spread was at least in part brought about by a degree of immune evasion due to a 63 large number of mutations in the viral S-protein, which led to changes in epitopes 64 recognised by antibodies elicited by vaccination or previous infection [2].”
Structures of Omicron spike complexes and implications for neutralizing antibody development
Guo, H., Gao, Y., Li, T., Li, T., Lu, Y., Zheng, L., Liu, Y., Yang, T., Luo, F., Song, S., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110770 · Cited by 59 · see citing works
“As reported previously, S309 has shown enhanced SARS-CoV-2 neutralization when in combination with other antibodies (McCallum et al., 2022; Pinto et al., 2020).”
Choosing a cellular model to study SARS-CoV-2
de Souza, G. A. P., Bideau, M. L., Boschi, C., Wurtz, N., Colson, P., Aherfi, S., Devaux, C. A., & Scola, B. L. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.1003608 · Cited by 60 · see citing works
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“This vulnerability is further exacerbated by the emergence of viral variants that can evade these responses 9–11 .”
Grobbelaar, L. M., Kruger, A., Venter, C., Burger, E. M., Laubscher, G. J., Maponga, T. G., Kotze, M. J., Kwaan, H. C., Miller, J. B., Fulkerson, D. H., et al. (2022) · Seminars in Thrombosis and Hemostasis · doi:10.1055/s-0042-1756306 · Cited by 58 · see citing works
Recent insights into SARS‐CoV‐2 omicron variant
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Omicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2
Fang, Z., Peng, L., Filler, R. B., Suzuki, K., McNamara, A., Lin, Q., Renauer, P. A., Yang, L., Menasché, B. L., Sanchez, A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30878-4 · Cited by 54 · see citing works
SARS-CoV-2 spike N-terminal domain modulates TMPRSS2-dependent viral entry and fusogenicity
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“The lack of allostery of the Omicron NTD may reside in the unique nature of its spike (Cerutti et al., 2022; Cui et al., 2022; Gobeil et al., 2022; Mannar et al., 2022; McCallum et al., 2022; Stalls et al., 2022; Ye et al., 2022; Zhang et al., 2022).”
Generation of SARS-CoV-2 escape mutations by monoclonal antibody therapy
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“Label-free, real-time, fast, and on-site detection of biomolecular binding interactions and a variety of biomarkers is made possible by SPR-based biosensing technology, which offers several advantages such as simple operation, fast reaction times, and exceptional selectivity [249].”
Lai, J., Coleman, K. K., Tai, S., German, J. R., Hong, F. H., Albert, B., Esparza, Y., Srikakulapu, A. K., Schanz, M., Maldonado, I. S., et al. (2022) · Clinical Infectious Diseases · doi:10.1093/cid/ciac846 · Cited by 55 · see citing works
A highly efficient needle-free-injection delivery system for mRNA-LNP vaccination against SARS-CoV-2
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Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro
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“Some monoclonal antibodies have shown impaired binding to the spike protein of variants 51,54,60,61 .”
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 53 · see citing works
Structural basis for the evolution and antibody evasion of SARS-CoV-2 BA.2.86 and JN.1 subvariants
Yang, H., Guo, H., Wang, A., Cao, L., Fan, Q., Jiang, J., Wang, M., Lin, L., Ge, X., Wang, H., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-51973-8 · Cited by 49 · see citing works
“Previous studies on the S protein of SARS-CoV-2 primarily demonstrated either a complete “ up ” or “ down ” conformationinRBDs 15,16,41 .”
Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle
Yang, K., Wang, C., White, K. I., Pfuetzner, R. A., Esquivies, L. R., & Brünger, A. T. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2119467119 · Cited by 54 · see citing works
Luo, S., Zhang, J., Kreutzberger, A. J. B., Eaton, A., Edwards, R. J., Jing, C., Dai, H., Sempowski, G. D., Cronin, K. D., Parks, R., et al. (2022) · Science Immunology · doi:10.1126/sciimmunol.add5446 · Cited by 51 · see citing works
Arunachalam, P. S., Feng, Y., Ashraf, U., Hu, M., Walls, A. C., Edara, V. V., Zarnitsyna, V. I., Aye, P. P., Golden, N., Miranda, M. C., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abq4130 · Cited by 51 · see citing works
Self-citationLi, L., Han, P., Huang, B., Xie, Y., Li, W., Zhang, D., Han, P., Xu, Z., Bai, B., Zhou, J., et al. (2022) · Cell Discovery · doi:10.1038/s41421-022-00431-0 · Cited by 51 · see citing works
“Y34 Y453 (2), R493 (22), S494 (15, 1), S496 (1)”
InfluentialImmune 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 48 · see citing works
“Only therapeutic antibodies of class 3 (S309) and 4 (A3, CR3022, S2A4, S304, S2X35, H014, COVA1-16, S2X259, and DH1047) targeting regions that do not directly interact with ACE2, but interfere with its binding, can potently neutralize Omicron with some efficiency [48,49,50].”
Forsyth, C. B., Zhang, L., Bhushan, A., Swanson, B. A., Zhang, L., Mamede, J. I., Voigt, R. M., Shaikh, M. W., Engen, P. A., & Keshavarzian, A. (2022) · Microorganisms · doi:10.3390/microorganisms10101996 · Cited by 51 · see citing works
Structural Plasticity and Immune Evasion of SARS-CoV-2 Spike Variants
Ghimire, D., Han, Y., & Lu, M. (2022) · Viruses · doi:10.3390/v14061255 · Cited by 43 · see citing works
“Reduced: wide range >1- to >100-fold to total loss (D614G) [63,85,87,101] Completely reduced: [63,101] Increased: <10-fold (D614G) [63,102–104].”
InfluentialThe Current Status and Future Promise of SPR Biosensors
Chiu, N. (2022) · Biosensors · doi:10.3390/bios12110933 · Cited by 50 · see citing works
Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa
Sun, K., Tempia, S., Kleynhans, J., von Gottberg, A., McMorrow, M. L., Wolter, N., Bhiman, J. N., Moyes, J., Carrim, M., Martinson, N. A., et al. (2023) · Nature Communications · doi:10.1038/s41467-022-35652-0 · Cited by 45 · see citing works
Cao, L., Lou, J., Chan, S. Y., Zheng, H., Liu, C., Zhao, S., Li, Q., Mok, C. K. P., Chan, R. W. Y., Chong, K. C., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01877-1 · Cited by 47 · see citing works
Human coronavirus HKU1 recognition of the TMPRSS2 host receptor
McCallum, M., Park, Y., Stewart, C., Sprouse, K. R., Addetia, A., Brown, J. T., Tortorici, M. A., Gibson, C. A., Wong, E., Ieven, M. M., et al. (2024) · Cell · doi:10.1016/j.cell.2024.06.006 · Cited by 49 · see citing works
“These findings may explain the observed polymorphism of TMPRSS2-interacting residues among HKU1 isolates and are reminiscent of observations made for SARS-CoV-2 62,72,73 and 229E 71,74 .”
Self-citationMaeda, R., Fujita, J., Konishi, Y., Kazuma, Y., Yamazaki, H., Anzai, I., Watanabe, T., Yamaguchi, K., Kasai, K., Nagata, K., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03630-3 · Cited by 48 · see citing works
Immune evasion of neutralizing antibodies by SARS-CoV-2 Omicron
Wang, L., Møhlenberg, M., Wang, P., & Zhou, H. (2023) · Cytokine & Growth Factor Reviews · doi:10.1016/j.cytogfr.2023.03.001 · Cited by 45 · see citing works
“Secondly, although several point mutations reduce the binding of RBD to angiotensin-converting enzyme 2 (ACE2), the presence of compensatory mutations can restore the higher affinity of RBD to ACE2 [49] (Fig.”
InfluentialMultiple independent acquisitions of ACE2 usage in MERS-related coronaviruses
Ma, C., Liu, C., Park, Y., Tang, J., Chen, J., Xiong, Q., Lee, J., Stewart, C., Asarnow, D. E., Brown, J. T., et al. (2025) · Cell · doi:10.1016/j.cell.2024.12.031 · Cited by 47 · see citing works
“58,59 However, a recent study reported that PnNL2180B (PN-β CoV) primarily exhibits intestinal tropism in its natural bat host, suggesting a potential fecal-oral route used by these viruses in bats.”
Self-citationNi, D., Turelli, P., Beckert, B., Nazarov, S., Uchikawa, E., Myasnikov, A. G., Pojer, F., Trono, D., Stahlberg, H., & Lau, K. (2023) · PLoS Pathogens · doi:10.1371/journal.ppat.1011206 · Cited by 47 · see citing works
“1 variant was first reported with increased resistance to antibodies and significantly stronger binding to hACE2.[60,68] We also observe that mACE2 also shows drastically increased binding (almost 10-fold) to the Omicron BA.”
Nguyen, H. L., Thai, N. Q., Nguyen, P. H., & Li, M. S. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c01048 · Cited by 46 · see citing works
Antibody Titers and Protection against Omicron (BA.1 and BA.2) SARS-CoV-2 Infection
Dimeglio, C., Migueres, M., Bouzid, N., Chapuy‐Regaud, S., Gernigon, C., Da-Silva, I., Porcheron, M., Martin‐Blondel, G., Hérin, F., & Izopet, J. (2022) · Vaccines · doi:10.3390/vaccines10091548 · Cited by 45 · see citing works
“1 and the ancestral SARS-CoV-2 strain used in current vaccines and immunoassays [24].”
Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein
Yao, Z., Zhang, L., Duan, Y., Tang, X., & Lü, J. (2024) · Journal of Infection · doi:10.1016/j.jinf.2024.106121 · Cited by 46 · see citing works
SARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs
Iketani, S., & Ho, D. D. (2024) · Cell chemical biology · doi:10.1016/j.chembiol.2024.03.008 · Cited by 46 · see citing works
Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses
Park, Y., Liu, C., Lee, J., Brown, J. T., Ma, C., Liu, P., Gen, R., Xiong, Q., Zepeda, S. K., Stewart, C., et al. (2025) · Cell · doi:10.1016/j.cell.2024.12.032 · Cited by 46 · see citing works
Self-citationMechanism and evolution of human ACE2 binding by SARS-CoV-2 spike
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Kumar, S., Patel, A. B., Lai, L., Chennareddy, C., Valanparambil, R. M., Reddy, E. S., Gottimukkala, K. P., Davis-Gardner, M. E., Edara, V. V., Linderman, S. L., et al. (2022) · Science Advances · doi:10.1126/sciadv.add2032 · Cited by 42 · see citing works
“Structural studies have reported that SARS-CoV-2 bnAbs target only a few antigenic sites on the RBD, which are majorly recognized by class 3 and class 4 mAbs ( 12 , 13 , 18 , 19 ).”
Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses
Dijokaite-Guraliuc, A., Das, R., Zhou, D., Ginn, H. M., Liu, C., Duyvesteyn, H. M. E., Huo, J., Nutalai, R., Supasa, P., Selvaraj, M., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112271 · Cited by 45 · see citing works
“2–5, 13, 15, 21, 24, 34, 36) showed little or no ACE2-blocking function.”
- Authors
- 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., Powell, A. E., Croll, T. I., Nix, J., Virgin, H. W., Corti, D., Snell, G., & Veesler, D.
- Affiliations
- University of Washington (US)
- VIR Biotechnology (United States) (US)
- Howard Hughes Medical Institute (US)
- University of Cambridge (GB)
- Lawrence Berkeley National Laboratory (US)
- Washington University in St. Louis (US)
- Vir Biotechnology (Switzerland) (CH)
- Corresponding author
- McCallum, Matthew
- Czudnochowski, Nadine
- Snell, Gyorgy
- Veesler, David
- ORCID
- Venue
- Science
- Published
- 2022-02-25
- Volume
- 375
- Issue
- 6583
- Pages
- 864-868
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC9427005
- OpenAlex
- W4220861013
- Cited by
- 535
- References
- 85
- Citations by year
- 2026: 25 · 2025: 56 · 2024: 85 · 2023: 122 · 2022: 246 · 2021: 1
- FWCI
- 62.11
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- Science (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute (DE-AC02-05CH11231)
- U.S. Department of Energy (-AC02-05CH11231, Contract No. DE-AC02-05-CH11231, 05CH11231, No. DE-AC02-05-CH11231, DE AC02 05CH11231, DE-AC02-)
- Burroughs Wellcome Fund (DE-AC02-05CH11231)
- University of Washington
- Wellcome Trust (Z/17/Z, 209407/Z/17/Z)
- Fast Grants
- National Institutes of Health (S10 OD032290, DE-AC02–05CH11231, 1s10od023476-01, HHSN272201700059C)
- Office of Science (No. DE-AC02- 05-CH11231, DEAC02–05CH11231, AC02-05CH11231, DE-AC02, 05CH11231, Contract No. DE-AC02-05CH11231)
- National Institute of General Medical Sciences (DE-AC02-05CH11231, R01GM120553, T32GM008268, P30GM124169)
- National Institute of Allergy and Infectious Diseases (HHSN272201700059C, DP1AI158186)
- 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
- Omicron variant, spike protein, receptor binding domain, antibody escape, sotrovimab, ACE2 receptor, antigenic shift, spike protein mutations, antibody affinity
- MeSH terms
- Protein Domains, Broadly Neutralizing Antibodies, Receptors, Coronavirus, Angiotensin-Converting Enzyme 2, SARS-CoV-2, Antigenic Drift and Shift, Antibodies, Monoclonal, Antibodies, Viral, Humans, Models, Molecular, Mutation, Protein Binding, Protein Conformation, Crystallography, X-Ray, Amino Acid Substitution, Cryoelectron Microscopy, Protein Interaction Domains and Motifs, Immune Evasion, Spike Glycoprotein, Coronavirus
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