Self-Collected Anterior Nasal and Saliva Specimens versus Health Care Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2

  1. K. E. Hanson
  2. A. P. Barker
  3. D. R. Hillyard
  4. N. Gilmore
  5. J. W. Barrett
  6. R. R. Orlandi
  7. S. M. Shakir

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Abstract

We prospectively compared health care worker-collected nasopharyngeal swabs (NPS) to self-collected anterior nasal swabs (ANS) and straight saliva for the diagnosis of coronavirus disease 2019 (COVID-19) in 354 patients. The percent positive agreement between NPS and ANS or saliva was 86.3% (95% confidence interval [CI], 76.7 to 92.9%) and 93.8% (95% CI, 86.0 to 97.9%), respectively. The percent negative agreement was 99.6% (95% CI, 98.0 to 100.0%) for NPS versus ANS and 97.8% (95% CI, 95.3 to 99.

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  1. Version published to 10.1128/jcm.01824-20
  2. ScreenIT

    SciScore for 10.1101/2020.07.17.20155754: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: After obtaining consent, subjects were instructed to swab both nostrils, pool saliva in their mouth, and then repeatedly spit a minimum of 1 mL saliva into a sterile tube in the presence of a healthcare worker.
    IRB: The University of Utah Institutional Review Board approved all study procedures.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    GraphPad Quick Calcs software was used to calculate kappa coefficients (k) and proportions (p value) by the Chi Square test.
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Percent positive or negative agreement for categorical variables were calculated in Microsoft Excel using the Analyse-it software package.
    Microsoft Excel
    suggested: (Microsoft Excel, RRID:SCR_016137)

    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:
    We did not collect information on the duration or type of symptoms at the time of specimen collection, which is an additional limitation of the study. Lastly, in an attempt to exclude RNA degradation in straight saliva as a potential explanation for “false negatives”, we performed stability studies at ambient and refrigerated temperatures for up to 5 days and saw no reduced TMA or PCR signal (data not shown). In conclusion, NPS and saliva were superior to ANS alone for the detection of SARS-CoV-2 in symptomatic patients. These observations, along with other recent reports (9, 12), suggest that straight saliva is an acceptable specimen type for symptomatic patients especially if swab or PPE supplies are limited. However, not all patients could provide adequate volume and saliva is a complex matrix that requires clinical laboratories to validate this specimen type on their respective NAAT platforms. An increased indeterminate or invalid rate (3.3% for saliva vs. 0% for swabs in saline) was observed using the Hologic Panther despite a 1:1 dilution in UTM. This could be related to issues of sample viscosity affecting the automated pipetting and/or internal control inhibition. We did not test whether an additional dilution step would reduce the invalid rate without loss of sensitivity. Combination testing with simultaneous sample collection from multiple anatomic sites may increase SARS-CoV-2 detection rates slightly, but multisite testing could be impractical given current swab a...

    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 10.1101/2020.07.17.20155754v1 on medRxiv