Cited by 535SARS-CoV-2 and COVID-19 Researchvaccines and immunoinformatics approachesAnimal Virus Infections Studies

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Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

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McCallum, Matthew, Czudnochowski, Nadine, Rosen, Laura E., Zepeda, Samantha K., Bowen, John E., Walls, Alexandra C., Hauser, Kevin, Joshi, Anshu, Stewart, Cameron, Dillen, Josh R., Powell, Abigail E., Croll, Tristan I., Nix, Jay, Virgin, Herbert W., Corti, Davide, Snell, Gyorgy, Veesler, David·2022·Science

DOI 10.1126/science.abn8652PMC PMC9427005

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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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“The Omicron RBD is structurally similar to the Wuhan-Hu-1 RBD and both structures can be superimposed with an r.m.s.d. of 0.8Å over 183 aligned C ɑ residues (as compared to PDB 6m0j ( 42 )).”

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Influential
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Influential
Omicron mutations increase interdomain interactions and reduce epitope exposure in the SARS-CoV-2 spike
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Self-citation
Structural Dynamics and Molecular Evolution of the SARS-CoV-2 Spike Protein
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Self-citation
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Influential
Comprehensive Humoral and Cellular Immune Responses to SARS-CoV-2 Variants in Diverse Chinese Population
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“33 34 The omicron variant has reportedly challenged the effectiveness and neutralisation capacity of SARS-CoV-2 vaccines, developed initially against the Wuhan variant.”
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“5 (29-274) 113 (29-274) ) 20 (77) 30 (77) (1-257) 257 (1-257) 257 (1-257)”
Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships
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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: McCallum, Matthew
Czudnochowski, Nadine
Rosen, Laura E.
Zepeda, Samantha K.
Bowen, John E.
Walls, Alexandra C.
Hauser, Kevin
Stewart, Cameron
Dillen, Josh R.
Powell, Abigail E.
Croll, Tristan I.
Nix, Jay
Virgin, Herbert W.
Corti, Davide
Snell, Gyorgy
Veesler, David
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 2022-02-25
Volume: 375
Issue: 6583
Pages: 864-868
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.abn8652
PMC: PMC9427005
OpenAlex: W4220861013
Cited by: 535
References: 85
Citations by year: 2026: 25 · 2025: 56 · 2024: 85 · 2023: 122 · 2022: 246
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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Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

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