Sensitivity of Nasopharyngeal, Nasal and Throat Swab for the Detection of SARS-CoV-2

  1. Byron Michael Berenger
  2. Kevin Fonseca
  3. Angela R Schneider
  4. Jia Hu
  5. Nathan Zelyas

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Abstract

Nasopharyngeal (NP), nasal and throat swabs are the most practical specimen sources to test for upper respiratory pathogens. We compared the sensitivity of NP, nasal and throat swabs to detect SARS-CoV-2 in community patients. Using detection at any site as the standard, the sensitivities were 90%, 80% and 87% for NP, nasal and throat respectively (n=30 positive at any site). Throat swabs are likely a suitable alternative to NP swabs for the detection of COVID-19 infections.

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  1. ScreenIT

    SciScore for 10.1101/2020.05.05.20084889: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: Oral consent by phone was obtained for collection of NP, nasal, and throat swabs in the participant’s home.
    IRB: The University of Calgary Research Ethics board approved this study (REB20-444).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Graph Pad Prism v8.4.1 (Graphpad Prism Softwar L.L.C, San Diego, CA) was used for statistical analysis.
    Graph Pad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Graphpad
    suggested: (GraphPad, RRID:SCR_000306)

    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:
    One limitation of our study is the small number of samples validated. We chose thirty to have a high likelihood to detect 90% agreement (11). A hindrance of performing studies of this nature with a large sample size is that sampling puts collectors at risk of infection even with appropriate personal protective equipment. Our study was also performed a mean of 10 days after symptom onset, so the site of optimal sampling may have differed if participants were swabbed closer to symptom onset. In early disease, throat swabs may be falsely negative compared to CT scan findings, though it is not clear whether NP and nasal swabs also lack sensitivity early in the disease progress (12). The sensitivity of the sample type is dependent on proper sampling procedure. In our jurisdiction, nasal swabs were initially implemented due to reports of lower Ct values than those seen in throat swabs (13). Despite education and routine observation of the technique used at COVID-19 community assessment centres, multiple accounts of sampling the anterior nares instead of the posterior nares/lower turbinates were reported to the laboratory by patients. Sampling errors may also occur with throat and NP swab and may have contributed to some of the false-negative NP swab results despite our collectors being trained health care professionals. Additionally, other studies have since reported that throat swabs have equivalent or higher SARS-CoV-2 viral loads compared to NP or nasal swabs, respectively (14, ...

    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 10.1101/2020.05.05.20084889 on medRxiv