Evaluating Diagnostic Accuracy of Saliva Sampling Methods for Severe Acute Respiratory Syndrome Coronavirus 2 Reveals Differential Sensitivity and Association with Viral Load

  1. Pieter Mestdagh
  2. Michel Gillard
  3. Sharonjit K. Dhillon
  4. Jean-Paul Pirnay
  5. Jeroen Poels
  6. Jan Hellemans
  7. Veronik Hutse
  8. Celine Vermeiren
  9. Maxime Boutier
  10. Veerle De Wever
  11. Patrick Soentjens
  12. Sarah Djebara
  13. Hugues Malonne
  14. Emmanuel André
  15. Marc Arbyn
  16. John Smeraglia
  17. Jo Vandesompele

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Abstract

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  1. Version published to 10.1016/j.jmoldx.2021.07.017
  2. ScreenIT

    SciScore for 10.1101/2020.10.06.20207902: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study S64125 was approved by the ethical review committee of the University Hospital of Leuven on May, 29 2020.
    Randomizationnot detected.
    Blindingnot detected.
    Power AnalysisWe accepted a confidence of 95%, a power of 80%, a sensitivity of the test in NP samples of 95%, a proportion of saliva-/NP+ samples 5% and 0.90 as benchmark for the relative positivity rate (saliva/NP), which yielded 84 SARS-CoV-2+ subjects needed.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The multiplex RT-qPCR was performed on 5 µl of RNA eluate using TaqPath
    TaqPath
    suggested: None
    Cq values were generated using the FastFinder software v3.300.5 (UgenTec).
    FastFinder
    suggested: None
    Droplets were analyzed by the QX200 Droplet Reader and QuantaSoft software.
    QuantaSoft
    suggested: None

    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.

  3. Version published to 10.1101/2020.10.06.20207902v1 on medRxiv