Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies
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Abstract
The SARS-CoV-2 B.1.1.529 (Omicron) variant contains 15 mutations of the receptor-binding domain (RBD). How Omicron evades RBD-targeted neutralizing antibodies requires immediate investigation. Here we use high-throughput yeast display screening 1,2 to determine the profiles of RBD escaping mutations for 247 human anti-RBD neutralizing antibodies and show that the neutralizing antibodies can be classified by unsupervised clustering into six epitope groups (A–F)—a grouping that is highly concordant with knowledge-based structural classifications 3–5 . Various single mutations of Omicron can impair neutralizing antibodies of different epitope groups. Specifically, neutralizing antibodies in groups A–D, the epitopes of which overlap with the ACE2-binding motif, are largely escaped by K417N, G446S, E484A and Q493R. Antibodies in group E (for example, S309) 6 and group F (for example, CR3022) 7 , which often exhibit broad sarbecovirus neutralizing activity, are less affected by Omicron, but a subset of neutralizing antibodies are still escaped by G339D, N440K and S371L. Furthermore, Omicron pseudovirus neutralization showed that neutralizing antibodies that sustained single mutations could also be escaped, owing to multiple synergetic mutations on their epitopes. In total, over 85% of the tested neutralizing antibodies were escaped by Omicron. With regard to neutralizing-antibody-based drugs, the neutralization potency of LY-CoV016, LY-CoV555, REGN10933, REGN10987, AZD1061, AZD8895 and BRII-196 was greatly undermined by Omicron, whereas VIR-7831 and DXP-604 still functioned at a reduced efficacy. Together, our data suggest that infection with Omicron would result in considerable humoral immune evasion, and that neutralizing antibodies targeting the sarbecovirus conserved region will remain most effective. Our results inform the development of antibody-based drugs and vaccines against Omicron and future variants.
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Deep mutational scanning experiments of the SARS-CoV-2 receptor binding domain suggest that further mutations of Omicron BA.1/2 at sites 452 and 486 could lead to further immune evasion against antibodies isolated from individuals who had pre-Omicron and Omicron BA.1 breakthrough infections.
“Deep mutational scanning experiments of the SARS-CoV-2 receptor binding domain suggest that further mutations of Omicron BA.1/2 at sites 452 and 486 could lead to further immune evasion against antibodies isolated from individuals who had pre-Omicron and Omicron BA.1 breakthrough infections 21,28,29 .”
From Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa (2023) · cites this paper as [21]
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 [21]
Over reliance on immune memory may impact the breadth and strength of antibody and B-cell immunity as new antigenically drifted variants arise.
“Over reliance on immune memory may impact the breadth and strength of antibody and B-cell immunity as new antigenically drifted variants arise 15,21,32,33 .”
From Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa (2023) · cites this paper as [21]
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Molnupiravir and Its Antiviral Activity Against COVID-19
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Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants
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Self-citation
- Authors
- Cao, Y., Wang, J., Jian, F., Xiao, T., Song, W., Yisimayi, A., Huang, W., Li, Q., Wang, P., An, R., Wang, J., Wang, Y., Niu, X., Yang, S., Liang, H., Sun, H., Li, T., Yu, Y., Cui, Q., Liu, S., Yang, X., Du, S., Zhang, Z., Hao, X., Shao, F., Jin, R., Wang, X., Xiao, J., Wang, Y., & Xie, X. S.
- Affiliations
- Peking University (CN)
- National Institutes for Food and Drug Control (CN)
- Capital Medical University (CN)
- Chinese Academy of Sciences (CN)
- Corresponding author
- Cao, Yunlong
- Wang, Yao
- Wang, Xiangxi
- Xiao, Junyu
- Wang, Youchun
- Xie, Xiaoliang Sunney
- ORCID
- Venue
- Nature
- Published
- 2021-12-23
- Volume
- 602
- Issue
- 7898
- Pages
- 657-663
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC8866119
- OpenAlex
- W4220807057
- Cited by
- 2,006
- References
- 56
- Citations by year
- 2026: 143 · 2025: 242 · 2024: 329 · 2023: 525 · 2022: 735 · 2021: 20 · 2018: 1 · 2017: 1 · 2015: 1 · 2014: 2 · 2013: 1
- FWCI
- 127.72
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- Research Square (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Peking University
- 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
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Keywords
- Omicron variant, SARS-CoV-2, receptor binding domain, neutralizing antibodies, antibody escape, K417N, vaccine design
- MeSH terms
- Angiotensin-Converting Enzyme 2, COVID-19, SARS-CoV-2, COVID-19 Vaccines, Antibodies, Monoclonal, Antibodies, Viral, Cells, Cultured, Convalescence, Humans, Immune Sera, Models, Molecular, Mutation, Neutralization Tests, Epitopes, B-Lymphocyte, Immune Evasion, Antibodies, Neutralizing, Spike Glycoprotein, Coronavirus
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