Neutralization and Stability of SARS-CoV-2 Omicron Variant

  1. Cong Zeng
  2. John P. Evans
  3. Panke Qu
  4. Julia Faraone
  5. Yi-Min Zheng
  6. Claire Carlin
  7. Joseph S. Bednash
  8. Tongqing Zhou
  9. Gerard Lozanski
  10. Rama Mallampalli
  11. Linda J. Saif
  12. Eugene M. Oltz
  13. Peter Mohler
  14. Kai Xu
  15. Richard J. Gumina
  16. Shan-Lu Liu

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Abstract

The SARS-CoV-2 B.1.1.529/Omicron variant was first characterized in South Africa and was swiftly designated a variant of concern 1 . Of great concern is its high number of mutations, including 30-40 mutations in the virus spike (S) protein compared to 7-10 for other variants. Some of these mutations have been shown to enhance escape from vaccine-induced immunity, while others remain uncharacterized. Additionally, reports of increasing frequencies of the Omicron variant may indicate a higher rate of transmission compared to other variants. However, the transmissibility of Omicron and its degree of resistance to vaccine-induced immunity remain unclear. Here we show that Omicron exhibits significant immune evasion compared to other variants, but antibody neutralization is largely restored by mRNA vaccine booster doses. Additionally, the Omicron spike exhibits reduced receptor binding, cell-cell fusion, S1 subunit shedding, but increased cell-to-cell transmission, and homology modeling indicates a more stable closed S structure. These findings suggest dual immune evasion strategies for Omicron, due to altered epitopes and reduced exposure of the S receptor binding domain, coupled with enhanced transmissibility due to enhanced S protein stability. These results highlight the importance of booster vaccine doses for maintaining protection against the Omicron variant, and provide mechanistic insight into the altered functionality of the Omicron spike protein.

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  1. ScreenIT

    SciScore for 10.1101/2021.12.16.472934: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Then, cells were fixed in 4% formaldehyde in PBS, and stained with sACE2-humanFc fusion protein (construct is a gift of Jason McLellan, University of Texas at Austin) or mouse anti-Flag antibody (Sigma, F3165).
    anti-Flag
    suggested: (Sigma-Aldrich Cat# F3165, RRID:AB_259529)
    Anti-mouse-IgG-Peroxidase (Sigma, A5278) and anti-rabbit-IgG-HRP (Sigma, A9169) were used as secondary antibodies where appropriate.
    anti-rabbit-IgG-HRP
    suggested: None
    Anti-mouse-IgG-Peroxidase (Sigma, A5278) and anti-rabbit-IgG-HRP (Sigma, A9169) were used as secondary antibodies.
    Anti-mouse-IgG-Peroxidase
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Briefly, HEK293T cells were transfected with pNL4-3-inGluc and spike construct in a 2:1 ratio using polyethylenimine transfection.
    HEK293T
    suggested: None
    HEK293T-ACE2 or CaLu-3 cells were infected with pseudotyped virus for each strain, produced in parallel.
    CaLu-3
    suggested: BCRJ Cat# 0264, RRID:CVCL_0609)
    Virus and serum were incubated for 1 hr at 37°C and then transferred to HEK293T-ACE2 cells for infection.
    HEK293T-ACE2
    suggested: None
    24 hrs after transfection, HEK293FT-mCAT-Gluc and HEK293T cells were dissociated with PBS-EDTA, and cocultured at a 1:1 ratio.
    HEK293FT-mCAT-Gluc
    suggested: None
    Recombinant DNA
    SentencesResources
    Plasmids: We utilized a previously reported pNL4-3-inGluc lentivirus vector which is based on ΔEnv HIV-1 and bears a Gaussia luciferase reporter gene that is expressed in virus target cells but not virus producing cells15,28.
    pNL4-3-inGluc
    suggested: None
    Additionally, SARS-CoV-2 variant spike constructs with N- and C-terminal flag tags were produced and cloned into a pcDNA3.1 vector by GenScript Biotech (Piscataway, NJ) using Kpn I and BamH I restriction enzyme cloning.
    pcDNA3.1
    suggested: RRID:Addgene_79663)
    A pLenti-hACE2-GFP (a gift from Jacob Yount, The Ohio State University) was used transient expression of ACE2.
    pLenti-hACE2-GFP
    suggested: None
    For transient expression of the Tet-Off (tTA) transcription factor, a pQCXIP-Tet-Off expression plasmid was used (a gift from Marc Johnson, University of Missouri)
    pQCXIP-Tet-Off
    suggested: None
    Software and Algorithms
    SentencesResources
    NT50 values were determined by least-squares-fit, non-linear regression in GraphPad Prism 5 (San Diego, CA)
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Results were processed using FlowJo v7.6.5 (Ashland, OR)
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Residue examination and renumbering were carried out manually with program Coot.
    Coot
    suggested: (Coot, RRID:SCR_014222)
    Intra-protomer contacts of Omicron mutants were examined with the programs PyMOL and chimeraX.
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2021.12.16.472934 on bioRxiv