Molecular Architecture of the SARS-CoV-2 Virus

  1. Hangping Yao
  2. Yutong Song
  3. Yong Chen
  4. Nanping Wu
  5. Jialu Xu
  6. Chujie Sun
  7. Jiaxing Zhang
  8. Tianhao Weng
  9. Zheyuan Zhang
  10. Zhigang Wu
  11. Linfang Cheng
  12. Danrong Shi
  13. Xiangyun Lu
  14. Jianlin Lei
  15. Max Crispin
  16. Yigong Shi
  17. Lanjuan Li
  18. Sai Li

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Abstract

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  1. ScreenIT

    SciScore for 10.1101/2020.07.08.192104: (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.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: Thank you for sharing your data.

    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.cell.2020.09.018
  3. Version published to 10.1101/2020.07.08.192104v2 on bioRxiv
  4. ScreenIT

    SciScore for 10.1101/2020.07.08.192104: (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
    Despite recent advances in the structural elucidation of SARS-CoV-2 proteins and the complexes of the spike (S) proteins with the cellular receptor ACE2 or neutralizing antibodies, detailed architecture of the intact virus remains to be unveiled.
    ACE2
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    SARS-CoV-2 virions (ID: ZJU_5) were collected on January 22nd, 2020, from a patient with severe symptoms, and were propagated in Vero cells.
    Vero
    suggested: CLS Cat# 605372/p622_VERO, CVCL_0059
    Software and Algorithms
    SentencesResources
    T. A. M. Bharat, S. H. W. Scheres, Resolving macromolecular structures from electron cryotomography data using subtomogram averaging in RELION. Nat. Protoc. 11, 9-20 (2016). M. Chen et al., Convolutional neural networks for automated annotation of cellular cryo-electron tomograms. Nat. Methods 14, 983-985 (2017). J. T. Huiskonen et al., Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo. JOVE-J. VIS. EXP., e51714 (2014). E. F. Pettersen et al., UCSF chimera - A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612 (2004). T. D. Goddard et al., UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
    RELION
    suggested: (RELION, SCR_016274)

    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 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).

    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.

  5. Version published to 10.1101/2020.07.08.192104v1 on bioRxiv