Cited by 1,514SARS-CoV-2 and COVID-19 ResearchAnimal Virus Infections StudiesCOVID-19 Clinical Research Studies

Considerable escape of SARS-CoV-2 Omicron to antibody neutralization

Open access
Planas, Delphine, Saunders, Nell, Maes, Piet, Guivel-Benhassine, Florence, Planchais, Cyril, Buchrieser, Julian, Bolland, William-Henry, Porrot, Françoise +24 more·2022·Nature

Published version of a preprint

Abstract

The SARS-CoV-2 Omicron variant was first identified in November 2021 in Botswana and South Africa 1-3. It has since spread to many countries and is expected to rapidly become dominant worldwide. The lineage is characterized by the presence of around 32 mutations in spike-located mostly in the N-terminal domain and the receptor-binding domain-that may enhance viral fitness and enable antibody evasion. Here we isolated an infectious Omicron virus in Belgium from a traveller returning from Egypt. We examined its sensitivity to nine monoclonal antibodies that have been clinically approved or are in development 4, and to antibodies present in 115 serum samples from COVID-19 vaccine recipients or individuals who have recovered from COVID-19. Omicron was completely or partially resistant to neutralization by all monoclonal antibodies tested. Sera from recipients of the Pfizer or AstraZeneca vaccine, sampled five months after complete vaccination, barely inhibited Omicron. Sera from COVID-19-convalescent patients collected 6 or 12 months after symptoms displayed low or no neutralizing activity against Omicron. Administration of a booster Pfizer dose as well as vaccination of previously infected individuals generated an anti-Omicron neutralizing response, with titres 6-fold to 23-fold lower against Omicron compared with those against Delta. Thus, Omicron escapes most therapeutic monoclonal antibodies and, to a large extent, vaccine-elicited antibodies. However, Omicron is neutralized by antibodies generated by a booster vaccine dose.

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  • The SARS-CoV-2 Omicron variant carries over 34 mutations in the spike protein.

    “The SARS-CoV-2 Omicron variant carries over 34 mutations in the spike protein”

    From Protection of the third-dose and fourth-dose mRNA vaccines against SARS-CoV-2 Omicron subvariant: a systematic review and meta-analysis (2023) · cites this paper as [2]

    The Discussion states that Omicron contains 32 mutations in its spike protein, not over 34. The Isolation and characterization section likewise reports 32 spike changes for the BA.1 variant studied. (LLM, conf=0.90)

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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 [3]

    The ‘Sensitivity of Omicron to sera from vaccinees’ section reports that sera collected five months after two Pfizer doses showed almost no detectable neutralization of Omicron, supporting escape from vaccine-elicited antibodies. The paper compares those sera with an ancestral viral strain, but the passages do not establish that the vaccines were based on ancestral spike-protein sequences. Its reported vaccine-serum experiments concern Omicron, not Beta; Beta has a separate citation in the citing sentence. (LLM, conf=0.82)

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  • The BA.1 Omicron variant became dominant worldwide quickly.

    “The BA.1 (B.1.1.529) Omicron variant, first identified in Botswana, became dominant worldwide quickly and was seen to evade immunity acquired from vaccines that were designed against the ancestral strain4.”

    From An Omicron-specific, self-amplifying mRNA booster vaccine for COVID-19: a phase 2/3 randomized trial (2024) · cites this paper as [4]

    The paper’s opening passage says Omicron had spread to many countries and was expected to rapidly become dominant worldwide; it does not say that worldwide dominance had already occurred. The Discussion likewise describes rapid spread in different countries. The copy identifies the studied strain as BA.1, but the claim turns a prediction into an accomplished event. Page numbers were not provided. (LLM, conf=0.87)

    Experimental — accuracy not yet measured
  • The BA.1 Omicron variant evaded immunity acquired from vaccines designed against the ancestral strain.

    “The BA.1 (B.1.1.529) Omicron variant, first identified in Botswana, became dominant worldwide quickly and was seen to evade immunity acquired from vaccines that were designed against the ancestral strain4.”

    From An Omicron-specific, self-amplifying mRNA booster vaccine for COVID-19: a phase 2/3 randomized trial (2024) · cites this paper as [4]

    The paper identifies the tested isolate as BA.1 (Isolation and characterization of an Omicron variant) and reports that it escaped vaccine-elicited antibodies to a large extent (opening summary; Sensitivity of Omicron to sera from vaccinees). The evidence concerns antibody neutralization, particularly five months after two vaccine doses; it does not establish escape from vaccine-acquired immunity as a whole, and the paper reports a neutralizing response after a booster. (LLM, conf=0.83)

    Experimental — accuracy not yet measured
  • The SARS-CoV-2 Omicron variant has an increased capacity to escape immunity and cause reinfections or breakthrough infections.

    “has an increased capacity to escape immunity and cause reinfections or breakthrough infections.2 3”

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Cites

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Research works printed but not linked: 13

  1. Karim, S. S. A. & Karim, Q. A. Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic. Lancet 398, 2126-2128 (2021).
  2. Viana, R. et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature, https://doi.org/10.1038/s41586-022-04411-y (2022). · DOI
  3. Grabowski, F., Kochańczyk, M. & Lipniacki, T. Omicron strain spreads with the doubling time of 3.2-3.6 days in South Africa province of Gauteng that achieved herd immunity to Delta variant. Preprint at https://doi.org/10.1101/2021.12.08.21267494 (2021). · DOI
  4. Cele, S. et al. Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization. Nature, https://doi.org/10.1038/s41586-021-04387-1 (2021). · DOI · Paper page
  5. Cameroni, E. et al. Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift. Nature, https://doi.org/10.1038/s41586-021-04386-2 (2021). · DOI
  6. Aggarwal, A. et al. SARS-CoV-2 Omicron: evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. Preprint at https://doi.org/10.1101/2021.12.14.21267772 (2021). · DOI
  7. Redd, A. D. et al. Minimal cross-over between mutations associated with Omicron variant of SARS-CoV-2 and CD8 + T cell epitopes identified in COVID-19 convalescent individuals. Preprint at https://doi.org/10.1101/2021.12.06.471446 (2021). · DOI
  8. Buchrieser, J. et al. Syncytia formation by SARS-CoV-2 infected cells. EMBO J. 39, e106267 (2020).
  9. Rajah, M. M. et al. SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced spike-mediated syncytia formation. EMBO J. 40, e108944 (2021).
  10. Kim, C. et al. A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein. Nat. Commun. 12, 288 (2021).
  11. Gallais, F. et al. Evolution of antibody responses up to 13 months after SARS-CoV-2 infection and risk of reinfection,EBioMedicine 71, 103561 (2021).
  12. Tzou, P. L. et al. Coronavirus Antiviral Research Database (CoV-RDB): an online database designed to facilitate comparisons between candidate anti-coronavirus compounds. Viruses 12, 1006 (2020).
  13. Van Cleemput, J. et al. Organ-specific genome diversity of replication-competent SARS-CoV-2. Nat. Commun. 12, 6612 (2021).

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Authors
Planas, D., Saunders, N., Maes, P., Guivel-Benhassine, F., Planchais, C., Buchrieser, J., Bolland, W.-H., Porrot, F., Staropoli, I., Lemoine, F., Péré, H., Veyer, D., Puech, J., Rodary, J., Baele, G., Dellicour, S., Raymenants, J., Gorissen, S., Geenen, C., Vanmechelen, B., Wawina-Bokalanga, T., Martí-Carreras, J., Cuypers, L., Sève, A., Hocqueloux, L., Prazuck, T., Rey, F. A., Simon-Loriere, E., Bruel, T., Mouquet, H., André, E., & Schwartz, O.
Affiliations
  • Centre National de la Recherche Scientifique (FR)
  • Rega Institute for Medical Research (BE)
  • Inserm (FR)
  • Hôpital Européen Georges-Pompidou (FR)
  • Université Libre de Bruxelles (BE)
  • KU Leuven (BE)
  • Universitair Ziekenhuis Leuven (BE)
  • Centre hospitalier universitaire d'Orléans (FR)
Corresponding author
  • Bruel, Timothée
  • Mouquet, Hugo
  • André, Emmanuel
  • Schwartz, Olivier
Venue
Nature
Published
2021-12-23
Volume
602
Issue
7898
Pages
671-675
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
OpenAlex
W4221072241
Cited by
1,514
References
8
Citations by year
2026: 51 · 2025: 115 · 2024: 206 · 2023: 400 · 2022: 725 · 2021: 17
FWCI
107.05
Type
journal article
Language
en
Open access
Locations
  • Nature (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Lirias (submittedVersion, other-oa)
  • HAL (submittedVersion)
  • Dépôt institutionnel de l'Université libre de Bruxelles (Université Libre de Bruxelles) (submittedVersion, other-oa)
Funders
  • European Commission (ANR-10-LABX-62-IBEID, HORIZON2020, ANR-10-INSB-04, COVID-19, 874850)
  • Agence Nationale de la Recherche (PROTEO-SARS-CoV-2, ANR-10–INSB–04, ANR-10-LABX-77, 10-LABX-62-IBEID, ANR-10–INSB–04-01, 10-INSB-04-01, ANR‐10‐LABX‐62‐IBEID, ANR‐10‐LABX‐69‐01, LABX-62-IBEID, ANR-21-CO14-0007, DIM1Health, 10‐LABX‐69‐01, ANR-10-LABX-0069, ANR-16-CONV-0005, ANR-11-INBS-0013, ANR-10-LABX-0077, ANR-10, ANR-10-LABX, ANR-10-LABX-0062, ANR-10-INBS-0004, ANR-10-LABX-62)
  • Institut National de la Santé et de la Recherche Médicale (ANR-10-INSB-04-01, ANR-10-LABX-77, ANR-10-LABX-62-IBEID)
  • Fonds De La Recherche Scientifique - FNRS (874850, G098321N)
  • Fondation pour la Recherche Médicale (ANR-10-LABX-62-IBEID, PROTEO-SARS-CoV-2, ANR-10-LABX-77, ANR-16-CONV-0005)
  • Fonds Wetenschappelijk Onderzoek (G098321N, G0H4420N, G0E1420N, C14/18/094, G0E1420N G098321N)
  • KU Leuven (C14/18/094)
  • Fondation de France (#00106077)
  • Vlaamse regering (G098321N)
Topics
  • Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
  • Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
  • Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
Keywords
Omicron variant, antibody escape, neutralizing antibodies, monoclonal antibodies, vaccine-elicited antibodies, booster vaccination, spike protein mutations, receptor binding domain, N-terminal domain, antibody resistance
MeSH terms
COVID-19, SARS-CoV-2, BNT162 Vaccine, ChAdOx1 nCoV-19, Adult, Antibodies, Monoclonal, Antibodies, Viral, Belgium, Convalescence, Female, Humans, Immunization, Secondary, Male, Mutation, Neutralization Tests, Phylogeny, Travel, Immune Evasion, Antibodies, Neutralizing

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