Pooled Saliva Specimens for SARS-CoV-2 Testing

  1. Bidisha Barat
  2. Sanchita Das
  3. Valeria De Giorgi
  4. David K. Henderson
  5. Stacy Kopka
  6. Anna F. Lau
  7. Tracey Miller
  8. Theresa Moriarty
  9. Tara N. Palmore
  10. Shari Sawney
  11. Chris Spalding
  12. Patricia Tanjutco
  13. Glenn Wortmann
  14. Adrian M. Zelazny
  15. Karen M. Frank

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Abstract

We evaluated saliva (SAL) specimens for SARS-CoV-2 reverse transcriptase PCR (RT-PCR) testing by comparison of 459 prospectively paired nasopharyngeal (NP) or midturbinate (MT) swabs from 449 individuals with the aim of using saliva for asymptomatic screening. Samples were collected in a drive-through car line for symptomatic individuals ( n  = 380) and in the emergency department (ED) ( n  = 69).

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  1. ScreenIT

    SciScore for 10.1101/2020.10.02.20204859: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: After giving informed consent, participants were instructed to provide 3-5 mL of saliva using the drooling method into a sterile tube without any stabilizer or solution.
    IRB: The study was approved by the institutional review boards for both participating institutions.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    SARS-CoV-2 Assay: Nucleic acid from individual specimens was extracted from 200 μL of Saliva/NP/MT specimens using the NucliSENS® easyMAG® platform (bioMérieux, Marcy l’Etoile, France) with an elution volume of 50 μL.
    NucliSENS®
    suggested: None
    All statistical analyses were performed using GraphPad Prism version 8 (GraphPad Software, San Diego, CA).
    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: We detected the following sentences addressing limitations in the study:
    The limitations for our study included the low number of positive participants, testing of symptomatic patients to determine an approach for screening the asymptomatic population, and the combined use of two collection sites (drive-through center and ED). The positive specimens include seven MT of the total 38 positives, to increase likelihood of participation in the study. All positive NP samples from the ED did not have a Ct value from the easyMAG/ABI 7500 platform, as not all samples were available for repeat testing. For this reason, only data from the easyMAG/ABI 7500 platform are included in the figures that compare Ct ranges. A challenge for all centers offering saliva testing is that some individuals may have difficulty producing adequate saliva for the test. Saliva is also a more challenging specimen for the laboratory staff to handle and requires judgement about thickness to ensure the correct volume is pipetted, with a chance of an under-pipetted sample, due to viscosity or bubbles, leading to a false-negative result, as well as increased likelihood of extraction failure. Initially, mucolyse was added to individual thick saliva specimens prior to extraction, but data obtained during our pooling validation showed that proteinase K digestion for individual thick samples prior to extraction was just as effective. Therefore, thick specimens and pooled specimens follow the same processing procedure. When evaluating the effectiveness of saliva collection, it is important...

    Results from TrialIdentifier: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    NCT04424446RecruitingSaliva as Source of Detection for SARS-CoV-2

    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 10.1128/jcm.02486-20
  3. Version published to 10.1101/2020.10.02.20204859v1 on medRxiv