Molecular evolution and structural analyses of the spike glycoprotein from Brazilian SARS-CoV-2 genomes: the impact of selected mutations

  1. Patrícia Aline Gröhs Ferrareze
  2. Ricardo Ariel Zimerman
  3. Vinícius Bonetti Franceschi
  4. Gabriel Dickin Caldana
  5. Paulo Augusto Netz
  6. Claudia Elizabeth Thompson

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Abstract

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  1. Version published to 10.1080/07391102.2022.2076154
  2. ScreenIT

    SciScore for 10.1101/2021.07.16.452571: (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
    Spike phylogenetic analysis: The multiple sequence alignment with NC_045512.2 as reference was performed by the MAFFT v.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The phylogenetic tree reconstruction was performed by the Maximum Likelihood method in the IQ-TREE program (Nguyen et al., 2015), using 1,000 replicates of ultrafast bootstrap (Hoang et al., 2018) and a Shimodaira-Hasegawa-like approximate likelihood ratio test (SH-aLRT) with 1,000 replicates (Guindon et al., 2010), 2,000 iterations and the optimization of the UFBoot trees by NNI on bootstrap alignment.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    The tree visualization was performed by FigTree software (http://tree.bio.ed.ac.uk/software/figtree/).
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    Spike selection and coevolutionary analyses: The multiple sequence alignment of the 2,901 unique spike sequences and the phylogenetic tree previously built were used as input in the HyPhy program.
    HyPhy
    suggested: (HyPhy, RRID:SCR_016162)
    The PDB file 6M0J was selected as the best template (2.45 Å and 194 amino acids) to the modeling using the MODELLER pipeline (Webb and Sali, 2016).
    MODELLER
    suggested: (MODELLER, RRID:SCR_008395)
    The generation of the spike RBD - ACE2 complexes for each different lineage was performed by the PyMOL software using the structural alignment of the RBD models with the 6M0J template, which was the source of the ACE2 structural coordinates.
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 33 and 54. 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 10.1101/2021.07.16.452571v1 on bioRxiv