An improved method for determining frequency of multiple variants of SARS-CoV-2 in wastewater using qPCR assays

  1. Meghan Fuzzen
  2. Nathanael B.J. Harper
  3. Hadi A. Dhiyebi
  4. Nivetha Srikanthan
  5. Samina Hayat
  6. Leslie M. Bragg
  7. Shelley W. Peterson
  8. Ivy Yang
  9. J.X. Sun
  10. Elizabeth A. Edwards
  11. John P. Giesy
  12. Chand S. Mangat
  13. Tyson E. Graber
  14. Robert Delatolla
  15. Mark R. Servos

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Abstract

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  1. Version published to 10.1016/j.scitotenv.2023.163292
  2. ScreenIT

    SciScore for 10.1101/2022.04.12.22273761: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: Wastewater sample collection, concentration, and extraction: Wastewater from the Regions of Peel (wastewater treatment plant influents GE Booth and Clarkson), York (access points Humber Air Management Facility (AMF) and Warden) and Waterloo (wastewater treatment plant influents Kitchener and Waterloo) Ontario, Canada.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The template sequence used for designs were retrieved from accession numbers provided by TWIST Bioscience (South San Francisco, CA, USA) for synthetic controls 14 (Alpha), 16 (Beta), 17 (Gamma) and 23 (Delta) and sequences were aligned using MAFFT (Katoh et al., 2002).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Candidate primers were screened for hairpins, homodimers and heterodimers in silico using OligoAnalyzer by integrated DNA technologies (IDT; RRID:SCR_001363) with the “qPCR” parameter selected.
    OligoAnalyzer
    detected: Integrated DNA Technologies OligoAnalyzer ( RRID:SCR_001363)
    Probes were designed with the mutated base(s) at their center using PrimerExpress v3.0.1 with a GC content of 40-60%.
    PrimerExpress
    suggested: None
    Candidate probes were also screened for % identity to non-target sequences using NCBI’s BLAST tool (Agarwala et al., 2016).
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)

    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.

    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 10.1101/2022.04.12.22273761v1 on medRxiv