1. SciScore for 10.1101/2021.09.10.21262695: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: All participants included in this study provided written informed consent. 2.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Additionally, S gene dropout samples with cycle threshold less than 30 (Ct < 30.0) were submitted to whole genome sequencing (WGS) using the Illumina MiSeq high-throughput.
    WGS
    suggested: None
    Library preparation was conducted using QIAseq
    QIAseq
    suggested: (QIAGEN GeneGlobe Data Analysis Center, RRID:SCR_021211)
    Fifty-nine Brazilian SARS-CoV-2 complete genomes and the reference sequence (EPI_ISL_402124) (>29 kb) were retrieved from the GISAID database using Clustal Omega.
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    T-cell epitopes: The search in Immune Epitope Database (IEDB) considered T-cells epitopes for SARS-CoV-2 spike protein (region of 10 residues flanking the Y380Q) with 70% similarity in BLAST.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    Physicochemical properties: Electrostatic potential (EP) was verified through Delphi web server calculations and PIPSA [20,21].
    Delphi
    suggested: (DelPhi, RRID:SCR_008669)

    Results from OddPub: Thank you for sharing your data.


    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    This study has some limitations. The small sample size in which WGS was feasible may limit any conclusion about the clinical severity related to the mutations found. Moreover, individuals were enrolled in a single city in Southern Brazil, which may limit the generality of our findings. Nonetheless, despite such limitations, a novel mutation (Y380Q) in the RBD region of SARS-CoV-2 spike protein was described. The analysis based on crystal structures reinforces the importance of the Y380 and C379 residues in the NAbs binding, and thus mutations in these regions may affect the interaction effectiveness between the NAbs and SARS-CoV-2 protein, as inferred by computational analysis.

    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.

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