Performance of RT-PCR on Saliva Specimens Compared With Nasopharyngeal Swabs for the Detection of SARS-CoV-2 in Children

  1. Yves Fougère
  2. Jean Marc Schwob
  3. Alix Miauton
  4. Francesca Hoegger
  5. Onya Opota
  6. Katia Jaton
  7. Rene Brouillet
  8. Gilbert Greub
  9. Blaise Genton
  10. Mario Gehri
  11. Ilaria Taddeo
  12. Valérie D’Acremont
  13. Sandra A. Asner

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Abstract

Saliva reverse transcriptase-Polymerase chain reaction (RT-PCR) is an attractive alternative for the detection of severe acute respiratory syndrome coronavirus 2 in adults with less known in children.

Methods:

Children with coronavirus disease 2019 symptoms were prospectively enrolled in a 1-month comparative clinical trial of saliva and nasopharyngeal (NP) RT-PCR. Detection rates and sensitivities of saliva and NP RT-PCR were compared as well as discordant NP and saliva RT-PCR findings including viral loads (VLs).

Results:

Of 405 patients enrolled, 397 patients had 2 tests performed. Mean age was 12.7 years (range, 1.2–17.9). Sensitivity of saliva was 85.2% (95% confidence interval: 78.2%–92.1%) when using NP as the standard; sensitivity of NP was 94.5% (89.8%–99.2%) when saliva was considered as the standard. For a NP RT-PCR VL threshold of ≥10 3 and ≥10 4 copies/mL, sensitivity of saliva increases to 88.7% and 95.2%, respectively. Sensitivity of saliva and NP swabs was, respectively, 89.5% and 95.3% in patient with symptoms less than 4 days ( P = 0.249) and 70.0% and 95.0% in those with symptoms ≥4–7 days ( P = 0.096). The 15 patients who had an isolated positive NP RT-PCR were younger ( P = 0.034), had lower NP VL (median 5.6 × 10 3 vs. 3.9 × 10 7 , P < 0.001), and could not drool saliva at the end of the sampling ( P = 0.002). VLs were lower with saliva than with NP RT-PCR (median 8.7 cp/mL × 10 4 ; interquartile range 1.2 × 10 4 –5.2 × 10 5 ; vs. median 4.0 × 10 7 cp/mL; interquartile range, 8.6 × 10 5 –1 × 10 8 ; P < 0.001).

Conclusions:

While RT-PCR testing on saliva performed more poorly in younger children and likely after longer duration of symptoms, saliva remains an attractive alternative to NP swabs in children.

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  1. Version published to 10.1097/inf.0000000000003198
  2. ScreenIT

    SciScore for 10.1101/2021.02.27.21252571: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: Informed consent from the legal guardians or adolescents ≥14 years were mandatory for inclusion.
    IRB: This study was approved by the ethics committee of Canton de Vaud (CER-VD 2020-02269) and conducted in accordance with the principles of the Declaration of Helsinki, the standards of Good Clinical Practice, and Swiss regulatory requirements.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    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:
    Limitations are predominantly related to the inclusion of outpatients and not hospitalized nor asymptomatic children, which might affect the generalizability of our findings. Furthermore, young children were under-represented and only a few of them were detected SARS-CoV2 positive, thus limiting extrapolation to this age-group. In addition, our study was conducted during a high prevalence of SARS-CoV-2 (up to 30%), thereby affecting our positive predicted values. Finally, our study was conducted before the introduction of 501Y mutants in Switzerland, which currently represent 8 to 15% of the analyzed samples. As such, we were not able to compare the performance of mutant typing in saliva vs NP. Yet, recent evidence supports that the lower VLs detected from saliva limit mutant typing analyses 27.

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

    IdentifierStatusTitle
    NCT04613310RecruitingPCR and Rapid Diagnostic Test on Saliva and Nasopharyngeal S…

    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 10.1101/2021.02.27.21252571 on medRxiv