Validation of a Self-administrable, Saliva-based RT-qPCR Test Detecting SARS-CoV-2

  1. Meghan Miller
  2. Michael Jansen
  3. Alexander Bisignano
  4. Shannon Mahoney
  5. Christine Wechsberg
  6. Nikita Albanese
  7. Louise Castillo
  8. Pia Farinas
  9. Gabriel A. Lazarin
  10. Malgorzata Jaremko

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Abstract

Background

Rapid and easy COVID-19 diagnostic testing is essential to controlling the pandemic and facilitating safe resumption of clinical care, employment and other social activities.

Methods

This study was conducted to validate an self-administrable saliva-based RT-qPCR test for the SARS-CoV2 virus under controlled laboratory conditions (analytical validation) according to federal guidance. An additional clinical study assessed positive (n = 34) and negative (n = 57) nasopharyngeal swab samples collected contemporaneously with saliva samples. Assessments for analytical specificity, sensitivity, cross reactivity and sample stability to simulate shipping conditions were conducted.

Results

Positive and negative agreement with third-party laboratory results were reported as 97.1% and 96.5–98.2%, respectively. Limit of detection was established at 5 copies/µL. Stability through simulated shipping conditions found 100% concordance up to 56 hours after collection. Discussion: These data validate a self-collected saliva-based COVID-19 RT-qPCR assay that performs comparably well to an assay of health care-provider administered nasopharyngeal swab samples. Accordingly, the United States Food and Drug Administration granted emergency use authorization in June 2020. Use of the saliva-based assay overcomes barriers to the necessary widespread testing, including strained health care resources, supply chain disruptions of laboratory materials, testing and protective equipment and exposure risks due to close interpersonal contact.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.05.20122721: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study was conducted with review and approval of the Aspire Institutional Review Board (Protocol #20200726).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Extracted RNA was reverse transcribed to cDNA and subsequently amplified using the CFX384 Touch Real-Time PCR Detection System with CFX Manager software version 3.1 (Bio-Rad Laboratories).
    CFX Manager
    suggested: (CFX Manager, RRID:SCR_017251)
    Bio-Rad Laboratories
    suggested: (Bio-Rad Laboratories, RRID:SCR_008426)
    Analysis of the fluorescence curves generated during the PCR process is done using the Bio-Rad CFX Manager software version 3.1.
    Bio-Rad CFX Manager
    suggested: None
    CFX
    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.
    • Thank you for including a protocol registration statement.

    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 10.1101/2020.06.05.20122721v1 on medRxiv