Temporal Detection and Phylogenetic Assessment of SARS-CoV-2 in Municipal Wastewater

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Abstract

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  1. SciScore for 10.1101/2020.04.15.20066746: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The study was reviewed by the Montana State University Institutional Review Board (IRB) For the Protection of Human Subjects (FWA 00000165) and was exempt from IRB oversight in accordance with Code of Federal regulations, Part 46, section 101.
    Consent: All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    20 ng of final library DNA was loaded onto the MinION flowcell for sequencing.
    MinION
    suggested: (MinION, RRID:SCR_017985)
    SARS-CoV-2 genome assembly: Nanopore raw reads (304.77 Mb) were basecalled with MinKNOW software in high-accuracy mode.
    MinKNOW
    suggested: None
    Phylogenetic and Position-specific Mutation Analysis: Phylogenetic analysis was performed by aligning the consensus sequence to 14,970 SARS-CoV-2 genomes retrieved from GISAID on 5/5/2020, 8:25:22 AM (https://www.gisaid.org/), using the FFT-NS-2 setting in MAFFT v7.429 (Katoh et al., 2019; Shu and McCauley, 2017).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Columns composed of more than 70% gaps were removed with trimAl v1.2rev59 (Capella-Gutierrez et al., 2009).
    trimAl
    suggested: (trimAl, RRID:SCR_017334)
    The APE v5.3 package in R was used to re-root the tree relative to RaTG13 bat coronavirus genome sequence (Paradis and Schliep, 2019), and the tree was plotted using ggtree v3.10 package in R (Yu et al., 2017).
    ggtree
    suggested: (ggtree, RRID:SCR_018560)
    The subtree, visualized in Figure 2B, was rendered in FigTree v1.4.4 (Rambaut, 2017).
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    Position specific mutation analysis was conducted in R using the BioStrings package (Pagès et al., 2019), and chromatograms of Sanger sequencing reads were rendered in SnapGene (GSL Biotech; available at snapgene.com).
    BioStrings
    suggested: (Biostrings, RRID:SCR_016949)
    SnapGene
    suggested: (SnapGene, RRID:SCR_015052)
    Quantification and Statistical Analyses: All statistical analyses were performed in RStudio v1.2.1335.
    RStudio
    suggested: (RStudio, RRID:SCR_000432)
    Data was plotted and analyzed using geom_smooth function from ggplot2 R package, with method = ‘lm’.
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)

    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:
    • 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.

    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.