Sensitivity of nasopharyngeal, oropharyngeal, and nasal wash specimens for SARS-CoV-2 detection in the setting of sampling device shortage

  1. Adrien Calame
  2. Léna Mazza
  3. Adriana Renzoni
  4. Laurent Kaiser
  5. Manuel Schibler

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Abstract

In the context of an unprecedented shortage of nasopharyngeal swabs (NPS) or sample transport media during the coronavirus disease 2019 (COVID-19) crisis, alternative methods for sample collection are needed. To address this need, we validated a cell culture medium as a viral transport medium, and compared the analytical sensitivity of SARS-CoV-2 RT-PCR in nasal wash (NW), oropharyngeal swab (OPS), and NPS specimens. Both the clinical and analytical sensitivity were comparable in these three sample types. OPS and NW specimens may therefore represent suitable alternatives to NPS for SARS-CoV-2 detection.

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  1. ScreenIT

    SciScore for 10.1101/2020.08.01.20166397: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Video demonstrating the NW procedure available at: https://www.youtube.com/watch?v=3cMoR7hSPF8&feature=emb_title
    https://www.youtube.com/watch
    suggested: (GENEtics Video, RRID:SCR_004770)
    Statistical analyses were performed using IBM SPSS Statistics 25.
    SPSS
    suggested: (SPSS, RRID:SCR_002865)

    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 to our study include the relatively small sample size, and further evaluation would be needed to reach a definitive conclusion. The statistical analyses were also underpowered and should be interpreted with caution. In conclusion, OPS and NW seem to be reliable alternative upper respiratory tract sampling methods for the molecular detection of SARS-CoV-2, and DMEM can be used as an alternative to commercial UTM, particularly in crisis settings. Further studies with a higher number of samples would still be needed to firmly conclude to an equivalence between these sampling methods. Nevertheless, the increased testing versatility offered by these substitutes should be greatly welcomed in the COVID-19 global crisis setting.

    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.

  2. Version published to 10.1007/s10096-020-04039-8
  3. Version published to 10.1101/2020.08.01.20166397v1 on medRxiv