The implementation of a rapid sample preparation method for the detection of SARS-CoV-2 in a diagnostic laboratory in South Africa

  1. Gert Marais
  2. Michelle Naidoo
  3. Nei-yuan Hsiao
  4. Ziyaad Valley-Omar
  5. Heidi Smuts
  6. Diana Hardie

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  1. ScreenIT

    SciScore for 10.1101/2020.08.06.20169276: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethics approval for this work was granted by the University of Cape Town Human Research Ethics Committee (HREC reference number: 335/2020).
    RandomizationSamples that tested negative were selected randomly from the same intervals.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Ethics: Biological material of human origin was anonymised and all clinical and other personally identifiable data delinked with only study specific sample identifiers used along with sample SARS-CoV-2 assay performance data.
    Ethics: Biological
    suggested: None
    The diagnostic assays in use were the Abbott RealTime SARS-CoV-2 Assay (Abbott Laboratories, USA) running on the Abbott m2000 RealTime system and the Allplex™ 2019-nCoV assay (Seegene, South Korea).
    Abbott Laboratories
    suggested: None
    Abbott
    suggested: (Abbott, RRID:SCR_010477)
    Statistical analysis and graphics: Data visualisation and statistical analysis, including paired t-tests for comparison of target Ct values, a Fisher’s exact test for statistical significance determination of the positive percent agreement (PPA) and negative percent agreement (NPA) with NA extraction-based testing and the Wilson/Brown method for 95% confidence interval determination, was done using GraphPad Prism version 8.4.2 for macOS, GraphPad Software, San Diego, California USA, www.graphpad.com.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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.

  2. Version published to 10.1371/journal.pone.0241029
  3. Version published to 10.1101/2020.08.06.20169276v1 on medRxiv