Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets

  1. Jiantao Zhang
  2. Qi Li
  3. Ruth S. Cruz Cosme
  4. Volodymyr Gerzanich
  5. Qiyi Tang
  6. J. Marc Simard
  7. Richard Y. Zhao

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Abstract

The ongoing COVID-19 pandemic caused by SARS-CoV-2 has claimed over 5.5 million lives with more than 300 million people infected worldwide. While vaccines are effective, the emergence of new viral variants could jeopardize vaccine protection.

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  1. Version published to 10.1128/mbio.00169-22
  2. Version published to 10.1101/2021.11.23.469747v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.11.23.469747: (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
    Target proteins were detected using the following antibodies: mouse anti-Strep tag II (Millipore Sigma: 71590); rabbit anti-Caspase 3 (Cell signaling: 9662); rabbit anti-Cleaved-Caspase 3 (Cell signaling: 9664) and mouse anti-GAPDH antibody (Cell signaling: 2118).
    anti-Strep tag II
    suggested: (Abnova Cat# PAB16601, RRID:AB_10677207)
    anti-Caspase 3
    suggested: None
    anti-Cleaved-Caspase 3
    suggested: (Affinity Biosciences Cat# BF0711, RRID:AB_2846190)
    anti-GAPDH
    suggested: (Cell Signaling Technology Cat# 2118, RRID:AB_561053)
    Experimental Models: Cell Lines
    SentencesResources
    A549 and 293T cell lines were maintained in the high glucose Dulbecco’s modified Eagle’s medium (DMEM) (Corning Cat#: 10-017-CV) with 10% fetal bovine serum (FBS, Gibco Cat#: 100-438-026) and 100 U/mL Penicillin-Streptomycin (Gibco Cat#:
    293T
    suggested: None
    Calu-3 cells were maintained in Eagle’s Minimum Essential medium (EMEM) (Quality Biological Cat#: 112-018-101) with 10% FBS and 100 U/mL Penicillin-Streptomycin.
    Calu-3
    suggested: BCRJ Cat# 0264, RRID:CVCL_0609)
    Measurement of Mammalian Cell-specific Activities: 2 x 104 293T or 1 x 104 A549 and Calu-3 cells/well were seeded into a 96-well plate and cultured at 37°C/5% CO2 overnight.
    A549
    suggested: None
    Recombinant DNA
    SentencesResources
    For the mammalian ORF3a study, a lentiviral constitutive expression vector pLVX-EF1alpha-IRES-Puro (Takara) that carries the ORF insert (provided by Dr. Nevan J.
    pLVX-EF1alpha-IRES-Puro
    suggested: None
    Fission Yeast Plasmid Transformation and Inducible SARS-COV-2 Gene Expression: The SARS-COV-2 gene-carrying pYZ1N plasmids were transformed into a wild type fission yeast SP223 strain by electroporation (5, 57).
    pYZ1N
    suggested: None
    Software and Algorithms
    SentencesResources
    Calu-3 cells were maintained in Eagle’s Minimum Essential medium (EMEM) (Quality Biological Cat#: 112-018-101) with 10% FBS and 100 U/mL Penicillin-Streptomycin.
    Quality Biological
    suggested: None
    Statistical Analysis: Pair-wise t-test or one-way ANOVA was calculated using software Prism 9 (GraphPad, San Diego, CA, USA).
    GraphPad
    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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 24 and 17. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

  4. Version published to 10.1101/2021.11.23.469747v1 on bioRxiv