Why SARS-CoV-2 Omicron variant is milder? A single high-frequency mutation of structural envelope protein matters

  1. Bingqing Xia
  2. Yi wang
  3. Xiaoyan pan
  4. Xi Cheng
  5. Hongying Ji
  6. Xiaoli Zuo
  7. Jia Li
  8. Zhaobing Gao

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Abstract

SARS-CoV-2 Omicron variant is highly transmissible and extensive morbidity, which has raised concerns for antiviral therapy. In addition, the molecular basis for the attenuated pathogenicity and replication capacity of Omicron remains elusive. Here, we report for the first time that a high-frequency mutation T9I on 2-E of SARS-CoV-2 variant Omicron forms a non-selective ion channel with abolished calcium permeability and reduced acid sensitivity compared to the WT channel. In addition, T9I caused less cell death and a weaker cytokine production. The channel property changes might be responsible for the Omicron variant releases less efficiently and induces a comparatively lower level of cell damage in the infected cells. Our study gives valuable insights into key features of the Omicron variant, further supporting 2-E is a promising drug target against SARS-CoV-2 and providing critical information for the COVID-19 treatment.

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  1. ScreenIT

    SciScore for 10.1101/2022.02.01.478647: (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
    The PVDF membranes were incubated with primary antibodies against HA-Tag (C29F4) (3724, CST, USA) or GAPDH (30201ES20, Yeasen, China), then incubated with second antibodies against IgG (Yeasen, China)
    HA-Tag
    suggested: (Cell Signaling Technology Cat# 3724, RRID:AB_1549585)
    GAPDH
    suggested: None
    IgG
    suggested: None
    Then, second antibodies FITC-AffiniPure Goat Anti-Rabbit IgG (33107ES60, Yeasen, China) and Cy3-AffiniPure Goat Anti-Mouse IgG (33208ES60, Yeasen, China)were used to incubate the cells at a 1:1,000 dilution.
    Anti-Rabbit IgG
    suggested: None
    Anti-Mouse IgG
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Cell culture and treatment: Vero E6 and Raw 264.7 cells were grown in 90% DMEM basal medium (Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, USA) at 37°C under 5% CO2.
    Raw 264.7
    suggested: None
    It was propagated and titrated with Vero E6 cells, and its associated operations were performed in a biosafety level 3 (BSL-3) facility.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Determination of lysosome pH: Vero cells were transfected with Lyso-pHluorin (addgene, 70113) and 2-E plasmid.
    Vero
    suggested: None
    Recombinant DNA
    SentencesResources
    Vector pET28a was used for protein purification; vector pcDNA5 and pcDNA3.1 were used for cell survival assay and cell imaging.
    pET28a
    suggested: RRID:Addgene_114145)
    pcDNA5
    suggested: RRID:Addgene_49428)
    pcDNA3.1
    suggested: RRID:Addgene_79663)
    Determination of lysosome pH: Vero cells were transfected with Lyso-pHluorin (addgene, 70113) and 2-E plasmid.
    2-E
    suggested: None
    Software and Algorithms
    SentencesResources
    The data were processed using pClamp 10.2 software (Molecular Devices, US).
    pClamp
    suggested: (pClamp, RRID:SCR_011323)
    The percentages of differently labeled cells were calculated by FlowJo 7.6.
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Flow cytometric data were collected and quantified using CytoExpert 2.4 software.
    CytoExpert
    suggested: None
    These ten structures were employed to construct ten homology models of the mutant envelope protein using Modeller [A. Sali, T.L. Blundell, Comparative protein modelling by satisfaction of spatial restraints, J Mol Biol 234 (1993) 779-815. 10.1006/jmbi.1993.1626.].
    Modeller
    suggested: (MODELLER, RRID:SCR_008395)
    Statistics were performed in GraphPad Prism.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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 did not find any issues relating to the usage of bar graphs.

    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 10.1101/2022.02.01.478647 on bioRxiv