RNA Viromics of Southern California Wastewater and Detection of SARS-CoV-2 Single-Nucleotide Variants

  1. Jason A. Rothman
  2. Theresa B. Loveless
  3. Joseph Kapcia
  4. Eric D. Adams
  5. Joshua A. Steele
  6. Amity G. Zimmer-Faust
  7. Kylie Langlois
  8. David Wanless
  9. Madison Griffith
  10. Lucy Mao
  11. Jeffrey Chokry
  12. John F. Griffith
  13. Katrine L. Whiteson

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Abstract

Wastewater-based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is useful for public health, industry, and ecological studies.

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  1. Version published to 10.1128/aem.01448-21
  2. ScreenIT

    SciScore for 10.1101/2021.07.19.21260815: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    We removed primers, adapter sequences, and low-quality bases with “bbduk” in the BBTools software package (69), then removed PCR duplicates with BBTools “dedupe.
    BBTools
    suggested: (Bestus Bioinformaticus Tools, RRID:SCR_016968)

    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 10.1101/2021.07.19.21260815 on medRxiv