Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop

  1. Javier A. Jaimes
  2. Nicole M. André
  3. Joshua S. Chappie
  4. Jean K. Millet
  5. Gary R. Whittaker

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  1. ScreenIT

    SciScore for 10.1101/2020.02.10.942185: (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
    Amino acid alignments and phylogenetic trees: Sequences alignments were performed on coronavirus S protein sequences using MAFFT v7.388 (Katoh et al., 2002; Katoh and Standley, 2013).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    A Maximum-Likelihood phylogenetic tree based on the S protein alignment was generated using PhyML (Guindon et al., 2010).
    PhyML
    suggested: (PhyML, RRID:SCR_014629)
    Sequence alignment display and formatting was performed using Geneious R10 (Biomatters) and phylogenetic tree display and formatting was performed using FigTree 1.4.3 (http://tree.bio.ed.ac.uk/).
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    S protein models were built using UCSF Chimera (v.1.14, University of California) through modeler homology tool of the Modeller extension (v.9.23, University of California) and edited using PyMOL (v.2.0.7
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)

    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:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • 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. ScreenIT

    SciScore for 10.1101/2020.02.10.942185: (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
    Amino acid alignments and phylogenetic trees: Sequences alignments were performed on coronavirus S protein sequences using MAFFT v7.388 ( Katoh et al. , 2002; Katoh and Standley , 2013) .
    MAFFT
    suggested: (MAFFT, SCR_011811)
    A Maximum-Likelihood phylogenetic tree based on the S protein alignment was generated using PhyML ( Guindon et al. , 2010) .
    PhyML
    suggested: (PhyML, SCR_014629)
    Sequence alignment display and formatting was performed using Geneious R10 ( Biomatters ) and phylogenetic tree display and formatting was performed using FigTree 1.4.3 ( http://tree.bio.ed.ac.uk/).
    FigTree
    suggested: (FigTree, SCR_008515)
    S protein models were built using UCSF Chimera ( v.1.14 , University of California ) through modeler homology tool of the Modeller extension ( v.9.23 , University of California ) and edited using PyMOL ( v.2.0.7
    PyMOL
    suggested: (PyMOL, SCR_000305)

    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.

  3. Version published to 10.1016/j.jmb.2020.04.009
  4. Version published to 10.1101/2020.02.10.942185v1 on bioRxiv