SARS-CoV-2 introduction and lineage dynamics across three epidemic peaks in Southern Brazil: massive spread of P.1

  1. Ana Paula Muterle Varela
  2. Janira Prichula
  3. Fabiana Quoos Mayer
  4. Richard Steiner Salvato
  5. Fernando Hayashi Sant'Anna
  6. Tatiana Schäffer Gregianini
  7. Letícia Garay Martins
  8. Adriana Seixas
  9. Ana Beatriz Gorini da Veiga

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Abstract

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  1. Version published to 10.1016/j.meegid.2021.105144
  2. ScreenIT

    SciScore for 10.1101/2021.07.29.454323: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: This study was approved by the Ethics Committee of Universidade Federal de Ciências da Saúde de Porto Alegre (Protocol n. 3.978.647, CAAE 30714520.0.0000.5345).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Bioinformatic analysis: Raw fastq files were trimmed to remove adapter sequences and low-quality reads using trimmomatic [13] (Parameters: leading:3 trailing:3 slidingwindow:4:25 minlen:36 illuminaclip: TruSeq3-PE.fa:2:30:10).
    trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    The quality of the resulting mapped BAM files was checked using Qualimap [15].
    Qualimap
    suggested: (QualiMap, RRID:SCR_001209)
    The software iVar (v1.2.2) was used to trim QIASEQ SARS-CoV-2 Primer Panel sequences and along with Samtools (v1.6) mpileup function [16] to variant calling (parameters: -A -d 20000 -Q 0) and consensus sequence generation (parameters: -q 20 -t 0).
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Analyses were carried out using Nextstrain ncov workflow (https://github.com/) (default parameters), which includes alignment, phylogenetic reconstruction, geographic and ancestral trait reconstruction, and inference of transmission events.
    https://github.com/
    suggested: (Laubach Lab GitHub Repository project, RRID:SCR_021464)
    Nextstrain uses by default the software IQ-Tree and the substitution model GTR.
    IQ-Tree
    suggested: (IQ-TREE, RRID:SCR_017254)

    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: 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 10.1101/2021.07.29.454323v1 on bioRxiv