SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant

  1. Yoriyuki Konno
  2. Izumi Kimura
  3. Keiya Uriu
  4. Masaya Fukushi
  5. Takashi Irie
  6. Yoshio Koyanagi
  7. Daniel Sauter
  8. Robert J. Gifford
  9. So Nakagawa
  10. Kei Sato

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  1. ScreenIT

    SciScore for 10.1101/2020.05.11.088179: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Western Blotting: Western blotting was performed as described (Kobayashi et al., 2014; Konno et al., 2018; Nakano et al., 2017; Yamada et al., 2018) using an HRP-conjugated anti-HA rat monoclonal antibody (clone 3F10; Roche) and an anti-alpha-tubulin (TUBA)
    anti-HA
    suggested: None
    anti-alpha-tubulin
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Transfection, SeV Infection and Reporter Assay: HEK293 cells were transfected using PEI Max (Polysciences) according to the manufacturer’s protocol.
    HEK293
    suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)
    Software and Algorithms
    SentencesResources
    We first aligned the viral genomes using the L-INS-i program of MAFFT version 7.453 (Katoh and Standley, 2013).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    We visualized the tree using a FigTree software (http://tree.bio.ed.ac.uk/software/figtree).
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    Nucleotide sequences were determined by a DNA sequencing service (Fasmac), and the sequence data were analyzed by Sequencher v5.1 software (Gene Codes Corporation)
    Sequencher
    suggested: (Sequencher, RRID:SCR_001528)
    Statistical Analysis: Data analyses were performed using Prism 7 (GraphPad Software).
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    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: 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.

    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 10.1016/j.celrep.2020.108185
  3. ScreenIT

    SciScore for 10.1101/2020.05.11.088179: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.Randomizationnot detected.Blindingnot detected.Power Analysisnot detected.Sex as a biological variablenot detected.Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Western Blotting Western blotting was performed as described (Kobayashi et al., 2014; Konno et al., 2018; Nakano et al., 2017; Yamada et al., 2018) using an HRP-conjugated anti-HA rat monoclonal antibody (clone 3F10; Roche) and an anti-alpha-tubulin (TUBA) mouse monoclonal antibody (clone DM1A; Sigma-Aldrich).
    anti-HA
    suggested: None
          <div style="margin-bottom:8px">
        <div><b>anti-alpha-tubulin (TUBA)</b></div>
        <div>suggested: None</div>
      </div>
    </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Experimental Models: Cell Lines</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Materials and Methods Cell Culture HEK293 cells (a human embryonic kidney cell line; ATCC CRL-1573) were maintained in Dulbecco’s modified Eagle's medium (Sigma-Aldrich) containing fetal calf serum and antibiotics.</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>HEK293</b></div>
        <div>suggested: None</div>
      </div>
    </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Software and Algorithms</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We first aligned the viral genomes using the L-INS-i program of MAFFT version 7.453 (Katoh and Standley, 2013).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>MAFFT</b></div>
        <div>suggested: (MAFFT, <a href="https://scicrunch.org/resources/Any/search?q=SCR_011811">SCR_011811</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We visualized the tree using a FigTree software (http://tree.bio.ed.ac.uk/software/figtree).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>FigTree</b></div>
        <div>suggested: (FigTree, <a href="https://scicrunch.org/resources/Any/search?q=SCR_008515">SCR_008515</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Nucleotide sequences were determined by a DNA sequencing service (Fasmac), and the sequence data were analyzed by Sequencher v5.1 software (Gene Codes Corporation).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>Sequencher</b></div>
        <div>suggested: (Sequencher, <a href="https://scicrunch.org/resources/Any/search?q=SCR_001528">SCR_001528</a>)</div>
      </div>
    </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical Analysis Data analyses were performed using Prism 7 (GraphPad Software).</td><td style="min-width:100px;border-bottom:1px solid lightgray">
      <div style="margin-bottom:8px">
        <div><b>Prism</b></div>
        <div>suggested: (PRISM, <a href="https://scicrunch.org/resources/Any/search?q=SCR_005375">SCR_005375</a>)</div>
      </div>
    
      <div style="margin-bottom:8px">
        <div><b>GraphPad</b></div>
        <div>suggested: (GraphPad Prism, <a href="https://scicrunch.org/resources/Any/search?q=SCR_002798">SCR_002798</a>)</div>
      </div>
    </td></tr></table>

    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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2020.05.11.088179v1 on bioRxiv