Predictions of the SARS-CoV-2 Omicron Variant (B.1.1.529) Spike Protein Receptor-Binding Domain Structure and Neutralizing Antibody Interactions
Open accessPublished version of a preprint
Abstract
The genome of the SARS-CoV-2 Omicron variant (B.1.1.529) was released on November 22, 2021, which has caused a flurry of media attention due the large number of mutations it contains. These raw data have spurred questions around vaccine efficacy. Given that neither the structural information nor the experimentally-derived antibody interaction of this variant are available, we have turned to predictive computational methods to model the mutated structure of the spike protein's receptor binding domain and posit potential changes to vaccine efficacy. In this study, we predict some structural changes in the receptor-binding domain that may reduce antibody interaction without completely evading existing neutralizing antibodies (and therefore current vaccines).
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
ColabFold - Making protein folding accessible to all
Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2021) · doi:10.1101/2021.08.15.456425 · Cited by 9,391 · see citing works
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
Rambaut, A., Holmes, E. C., O’Toole, Á., Hill, V., McCrone, J. T., Ruis, C., du Plessis, L., & Pybus, O. G. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0770-5 · Cited by 2,543 · see citing works
Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2
Liu, L., Iketani, S., Guo, Y., Chan, J. F.-W., Wang, M., Liu, L., Luo, Y., Chu, H., Huang, Y., Nair, M. S., et al. (2022) · Nature · doi:10.1038/s41586-021-04388-0 · Cited by 1,290 · see citing works
Barnes, C. O., West, A. P., Huey-Tubman, K. E., Hoffmann, M. A. G., Sharaf, N. G., Hoffman, P. R., Koranda, N., Gristick, H. B., Gaebler, C., Muecksch, F., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.025 · Cited by 795 · see citing works
Structural basis of a shared antibody response to SARS-CoV-2
Yuan, M., Liu, H., Wu, N. C., Lee, C.-C. D., Zhu, X., Zhao, F., Huang, D., Yu, W., Hua, Y., Tien, H., et al. (2020) · Science · doi:10.1126/science.abd2321 · Cited by 589 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Ford, C. T., Yasa, S., Jacob Machado, D., White, R. A., & Janies, D. A. (2023) · Frontiers in Virology · doi:10.3389/fviro.2023.1172027 · Cited by 9 · see citing works
Self-citationAli, M. A., & Caetano-Anollés, G. (2024) · Viruses · doi:10.3390/v16091358 · Cited by 6 · see citing works
“In the absence of experimental protein structures from VOCs, numerous studies utilized AlphaFold2 to explore the differences between the wild-type (WT) Wuhan strain, which is used as reference, and the emerging variants [15,34–36].”
Method
- Authors
- Ford, C. T., Jacob Machado, D., & Janies, D. A.
- Affiliations
- University of North Carolina at Charlotte (US)
- Corresponding author
- Ford, Colby T.
- Venue
- Frontiers in Virology
- Publisher
- Frontiers Media SA
- Published
- 2022-02-07
- Volume
- 2
- ISSN
- 2673-818X (ISSN-L)
- OpenAlex
- W4225575973
- Cited by
- 52
- References
- 6
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 6 · 2023: 9 · 2022: 29 · 2021: 3
- FWCI
- 5.87
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Virology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- DeepMind
- University of North Carolina at Charlotte
- 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 › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- Omicron variant, spike protein, receptor binding domain, structure prediction, neutralizing antibodies, antigen-antibody reaction, vaccine efficacy, viral mutations, COVID-19 pandemic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
