Evaluation of Nasopharyngeal Swab Collection Techniques for Nucleic Acid Recovery and Participant Experience: Recommendations for COVID-19 Diagnostics

  1. Natalie N Kinloch
  2. Aniqa Shahid
  3. Gordon Ritchie
  4. Winnie Dong
  5. Tanya Lawson
  6. Julio S G Montaner
  7. Marc G Romney
  8. Aleksandra Stefanovic
  9. Nancy Matic
  10. Chanson J Brumme
  11. Christopher F Lowe
  12. Zabrina L Brumme
  13. Victor Leung

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Abstract

Nasopharyngeal swabs are critical to the diagnosis of respiratory infections including coronavirus disease 2019, but collection techniques vary. We compared 2 recommended nasopharyngeal swab collection techniques in adult volunteers and found that swab rotation following nasopharyngeal contact did not recover additional nucleic acid (as measured by human DNA/RNA copy number). Rotation was also less tolerable for participants. Notably, both discomfort and nucleic acid recovery were significantly higher in Asian participants, consistent with nasal anatomy differences. Our results suggest that it is unnecessary to rotate the swab in place following contact with the nasopharynx and reveal that procedural discomfort levels can differ by ethnicity.

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  1. ScreenIT

    SciScore for 10.1101/2020.08.18.20177592: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study was approved by the Providence Health Care/University of British Columbia and Simon Fraser University Research Ethics Boards.
    Consent: All participants provided written informed consent.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Droplets were generated using an Automated Droplet Generator (BioRad) and cycled at 50°C for 60 minutes; 40 cycles of (94°C for 30 seconds, 55°C for 1 minute) and 98°C for 10 minutes and analyzed on a QX200 Droplet Reader using QuantaSoft software version 1.7.4 (BioRad)
    QuantaSoft
    suggested: None

    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:
    Some limitations of our study merit mention. We assume that human DNA/RNA targets are appropriate markers of respiratory pathogen collection quality [2], though this is consistent with the inclusion of RNase P in the US-CDC 2019-nCoV real-time RT-PCR diagnostic panel as part of quality control [15]. As swabs vary in design, the absolute discomfort scores and nucleic acid quantities recovered may not be applicable to all swabs, though our general observations should be. Protocol differences also prevent direct comparison of recovered nucleic acid across studies (e.g. the swab, silica input and elution volumes differed between the present and a previous study by our group [2]).

    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 10.1093/ofid/ofaa488
  3. Version published to 10.1101/2020.08.18.20177592v1 on medRxiv