ddPCR Reveals SARS-CoV-2 Variants in Florida Wastewater

  1. Eben Gering
  2. Jacob Colbert
  3. Sarah Schmedes
  4. George Duncan
  5. Joe Lopez
  6. Jessy Motes
  7. James Weiss
  8. Taj Azarian
  9. Omer Tekin
  10. Jason Blanton

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Abstract

Wastewater was screened for the presence of functionally significant mutations in SARS-CoV-2 associated with emerging variants of concern (VOC) by ddPCR, and results accorded with sequencing of clinical samples from the same region. We propose that PCR-based screening of wastewater can provide a powerful tool for rapid and inexpensive screening of large population segments for VOC-associated mutations and can hone complementary sampling and sequencing of direct (human) test material to track emerging VOC.

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  1. ScreenIT

    SciScore for 10.1101/2021.04.08.21255119: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    RNA was purified by multiple methods, including: Kingfisher combined with the Thermo Fisher MagMAX Viral/Pathogen II (MVP II) Nucleic Acid Isolation kit (Applied Biosystems by Thermo Fisher Scientific, Waltham,
    Thermo Fisher MagMAX
    suggested: None
    MA); Abbott m2000 System combined with the Abbott RealTime SARS-CoV-2 assay (Abbott, Lake County, IL;
    Abbott
    suggested: (Abbott, RRID:SCR_010477)
    Quality metrics were generated for raw sequence reads using fastqc v0.11.9 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and raw fastqs were quality filtered and trimmed (SLIDINGWINDOW:4:30 MINLEN:75 TRAILING:20) using trimmomatic v0.39 (Bolger, et al. 2014)
    http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
    suggested: (FastQC, RRID:SCR_014583)
    trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    Sequence adapter and Phix contamination were removed using bbduk (BBMap v38.79) (
    BBMap
    suggested: (BBmap, RRID:SCR_016965)
    Variants were called using samtools mpileup v1.9 (Li, et al. 2009) and ivar variant v1.2.2 (Grubaugh, et al. 2019), and consensus assemblies were generated using samtools mpileup v1.9 (Li, et al. 2009) and ivar consensus v1.2.2 (Grubaugh, et al. 2019).
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)

    Results from OddPub: Thank you for sharing your 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.

    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.

  2. Version published to 10.1101/2021.04.08.21255119v1 on medRxiv