Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica

  1. Jose Arturo Molina-Mora

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  1. Version published to 10.1016/j.genrep.2022.101554
  2. ScreenIT

    SciScore for 10.1101/2021.07.08.451640: (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
    The construction of the phylogenetic tree model was achieved with IQ-TREE v1.6.12 (Minh et al., 2020), including ModelFinder (Kalyaanamoorthy, Minh, Wong, Von Haeseler, & Jermiin, 2017) to select the best nucleotide substitution model (using the Bayesian Information Criterion BIC, the best model was TN+F+I).
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    Positive selection analysis of mutations: To detect sites in the spike protein of positive/adaptive (as well as negative/purifying) selection, we performed an analysis of natural selection using HyPhy (hypothesis testing using phylogenies) (Kosakovsky Pond, Frost, & Muse, 2005).
    HyPhy
    suggested: (HyPhy, RRID:SCR_016162)
    Coevolutionary analysis of spike sequences: All the spike sequences from SARS-CoV-2 genomes from Costa Rica were aligned using MAFFT v7.471 (Katoh et al., 2002).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The structural model of the spike (ID: 6VXX) was obtained from PDB (https://www.rcsb.org/), and the molecular structure of the nelfinavir drug, which is known, was downloaded from Drugbank (https://go.drugbank.com/).
    Drugbank
    suggested: (DrugBank, RRID:SCR_002700)

    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: We detected the following sentences addressing limitations in the study:
    Further analyses are required to validate experimentally predictions and results, which is the main limitation of this in silico study. Furthermore, this work offers a pipeline using distinct bioinformatics analyses, which can be applied to other mutations in the spike, proteins of SARS-CoV-2, or pathogens.

    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.

    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 10.1101/2021.07.08.451640v1 on bioRxiv