Prospective Comparison of Saliva and Nasopharyngeal Swab Sampling for Mass Screening for COVID-19

  1. Mathieu Nacher
  2. Mayka Mergeay-Fabre
  3. Denis Blanchet
  4. Orelie Benoit
  5. Tristan Pozl
  6. Pauline Mesphoule
  7. Vincent Sainte-Rose
  8. Véronique Vialette
  9. Bruno Toulet
  10. Aurélie Moua
  11. Mona Saout
  12. Stéphane Simon
  13. Manon Guidarelli
  14. Muriel Galindo
  15. Barbara Biche
  16. William Faurous
  17. Laurie Chaizemartin
  18. Aniza Fahrasmane
  19. Devi Rochemont
  20. Nicolas Vignier
  21. Astrid Vabret
  22. Magalie Demar

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Abstract

Current testing for COVID-19 relies on reverse-transcriptase polymerase chain reaction from a nasopharyngeal swab specimen. Saliva samples have advantages regarding ease and painlessness of collection, which does not require trained staff and may allow self-sampling. We enrolled 776 persons at various field-testing sites and collected nasopharyngeal and pooled saliva samples. One hundred sixty two had a positive COVID-19 RT-PCR, 61% were mildly symptomatic and 39% asymptomatic. The sensitivity of RT-PCR on saliva samples vs. nasopharygeal swabs varied depending on the patient groups considered or on Ct thresholds. There were 10 (6.2%) patients with a positive saliva sample and a negative nasopharyngeal swab, all of whom had Ct values <25 for three genes. For symptomatic patients for whom the interval between symptoms onset and sampling was <10 days sensitivity was 77% but when excluding persons with isolated N gene positivity (54/162), sensitivity was 90%. In asymptomatic patients, the sensitivity was only 24%. When we looked at patients with Cts <30, sensitivity was 83 or 88.9% when considering two genes. The relatively good performance for patients with low Cts suggests that Saliva testing could be a useful and acceptable tool to identify infectious persons in mass screening contexts, a strategically important task for contact tracing and isolation in the community.

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  1. ScreenIT

    SciScore for 10.1101/2020.09.23.20150961: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: An investigator explained the objectives of the study and obtain the consent of the patient or his legal representative.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variableInclusion criteria were: males or females with an indication to perform a COVID diagnostic test (symptomatology, contact case, systematic screening, etc.), aged at least 3 years old.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Laboratory analysis: The same technique was used for the 2 samples throughout the study: the QIAsymphony and GeneFinder kit, a Real-time PCR assay.
    GeneFinder
    suggested: (GENEFINDER, RRID:SCR_009190)

    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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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 10.3389/fmed.2021.621160
  3. Version published to 10.1101/2020.09.23.20150961 on medRxiv