Structural diversity of the SARS-CoV-2 Omicron spike

  1. Sophie M.-C. Gobeil
  2. Rory Henderson
  3. Victoria Stalls
  4. Katarzyna Janowska
  5. Xiao Huang
  6. Aaron May
  7. Micah Speakman
  8. Esther Beaudoin
  9. Kartik Manne
  10. Dapeng Li
  11. Rob Parks
  12. Maggie Barr
  13. Margaret Deyton
  14. Mitchell Martin
  15. Katayoun Mansouri
  16. Robert J. Edwards
  17. Amanda Eaton
  18. David C. Montefiori
  19. Gregory D. Sempowski
  20. Kevin O. Saunders
  21. Kevin Wiehe
  22. Wilton Williams
  23. Bette Korber
  24. Barton F. Haynes
  25. Priyamvada Acharya

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Abstract

No abstract available

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  1. Version published to 10.1016/j.molcel.2022.03.028
  2. ScreenIT

    SciScore for 10.1101/2022.01.25.477784: (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.

    Table 2: Resources

    Antibodies
    SentencesResources
    Assays were run in two formats i.e., antibodies/ACE2 coated, or spike coated.
    antibodies/ACE2
    suggested: None
    Antibodies were incubated at room temperature for 1 hour, washed and binding detected with goat anti-human-HRP (Jackson ImmunoResearch Laboratories, PA) and TMB substrate.
    anti-human-HRP
    suggested: None
    Mouse anti-monkey IgG-HRP (Southern Biotech, CAT# 4700-05) and Goat anti-human IgG-HRP (Jackson ImmunoResearch Laboratories, CAT# 109-035-098) secondary antibodies were used to detect antibody bound to the spike proteins.
    anti-monkey IgG-HRP
    suggested: (SouthernBiotech Cat# 4700-05, RRID:AB_2796069)
    anti-human IgG-HRP
    suggested: None
    Software and Algorithms
    SentencesResources
    All spike ectodomains were cloned into the mammalian expression vector pαH and have been deposited to Addgene (10) (https://www.addgene.org).
    https://www.addgene.org
    suggested: (Addgene, RRID:SCR_002037)
    Sensogram data were analyzed using the BiaEvaluation software (Cytiva, MA) Negative-stain electron microscopy: Fab-spike complex of DH1044 was generated by mixing 5.9 μg of spike with 6.2 μg of Fab in ~25 μl of HEPES-buffered saline (HBS) containing 20 mM HEPES and 150 mM NaCl, pH 7.4, and incubating at 37 °C for 1 hr and using sample directly for negative stain without further purification.
    BiaEvaluation
    suggested: (BIAevaluation Software, RRID:SCR_015936)
    Images were analyzed and 3D reconstructions generated using standard protocols with Relion 3.0 (28).
    Relion
    suggested: (RELION, RRID:SCR_016274)
    The cryoSPARC (29) software was used for data processing.
    cryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)
    Phenix (30, 31), Coot (32)
    Coot
    suggested: (Coot, RRID:SCR_014222)
    , Pymol (33), Chimera (34), ChimeraX (35) and Isolde (36) were used for model building and refinement.
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)
    Difference distance matrices (DDM): DDM were generated using the Bio3D package (39) implemented in R (R Core Team (2014).
    Bio3D
    suggested: None
    The collected diffraction images were indexed, integrated, and scaled using HKL2000 (40) Initial phases were calculated by molecular replacement using Phenix.
    Phenix
    suggested: (Phenix, RRID:SCR_014224)

    Results from OddPub: Thank you for sharing your code and 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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 34 and 27. 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.

  3. Version published to 10.1101/2022.01.25.477784v1 on bioRxiv