Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike

  1. Jiandong Huo
  2. Yuguang Zhao
  3. Jingshan Ren
  4. Daming Zhou
  5. Helen M.E. Duyvesteyn
  6. Helen M. Ginn
  7. Loic Carrique
  8. Tomas Malinauskas
  9. Reinis R. Ruza
  10. Pranav N.M. Shah
  11. Tiong Kit Tan
  12. Pramila Rijal
  13. Naomi Coombes
  14. Kevin R. Bewley
  15. Julia A. Tree
  16. Julika Radecke
  17. Neil G. Paterson
  18. Piyada Supasa
  19. Juthathip Mongkolsapaya
  20. Gavin R. Screaton
  21. Miles Carroll
  22. Alain Townsend
  23. Elizabeth E. Fry
  24. Raymond J. Owens
  25. David I. Stuart

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Abstract

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  1. Version published to 10.1016/j.chom.2020.06.010
  2. ScreenIT

    SciScore for 10.1101/2020.05.05.079202: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    All curves were plotted using GraphPad Prism 8.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Structural comparisons used SHP (Stuart et al., 1979), residues forming the RBD/Fab interface were identified with PISA (Krissinel and Henrick, 2007), figures were prepared with PyMOL (The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    CTF-estimation with GCTF (v1.06) (Zhang, 2016) and non-template-driven particle picking was then performed within cryoSPARC v2.14.1-live followed by multiple rounds of 2D classification (Punjani et al., 2017).
    GCTF
    suggested: (GCTF, RRID:SCR_016500)
    Both structures were then sharpened in cryoSPARC.
    cryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)
    An initial model for the spike (structure-A) was generated using PDB ID, 6VYB (Walls et al., 2020) and rigid body fitted into the final map using COOT (Emsley and Cowtan, 2004).
    COOT
    suggested: (Coot, RRID:SCR_014222)
    The model was further refined in real space with PHENIX (Liebschner et al., 2019) which resulted in a correlation coefficient of 0.84.
    PHENIX
    suggested: (Phenix, RRID:SCR_014224)

    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.

  3. Version published to 10.1101/2020.05.05.079202v1 on bioRxiv