Performance of Abbott ID Now COVID-19 Rapid Nucleic Acid Amplification Test Using Nasopharyngeal Swabs Transported in Viral Transport Media and Dry Nasal Swabs in a New York City Academic Institution

  1. Atreyee Basu
  2. Tatyana Zinger
  3. Kenneth Inglima
  4. Kar-mun Woo
  5. Onome Atie
  6. Lauren Yurasits
  7. Benjamin See
  8. Maria E. Aguero-Rosenfeld

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Abstract

The recent emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has posed formidable challenges for clinical laboratories seeking reliable laboratory diagnostic confirmation. The swift advance of the crisis in the United States has led to Emergency Use Authorization (EUA) facilitating the availability of molecular diagnostic assays without the more rigorous examination to which tests are normally subjected prior to FDA approval. Our laboratory currently uses two real-time reverse transcription-PCR (RT-PCR) platforms, the Roche Cobas SARS-CoV2 and the Cepheid Xpert Xpress SARS-CoV-2.

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  1. Version published to 10.1128/jcm.01136-20
  2. ScreenIT

    SciScore for 10.1101/2020.05.11.089896: (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
    Collection instructions for the nasal swabs provided by Abbott were communicated to ED care providers.
    Abbott
    suggested: (Abbott, RRID:SCR_010477)
    Instruments: Statistical analysis: Qualitative Method Comparison was performed using EP Evaluator (Data Innovations, VT 05403), Evidence-Based Medicine Diagnostic Toolbox (https://ebm-tools.knowledgetranslation.net/calculator/diagnostic/) and the correlation coefficient using Excel 2010.
    Excel
    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:
    Limitations of our study include relatively small sample size, inability to control for sampling variability and lack of an additional comparator method to discern the discrepancies. In our laboratory, we periodically perform correlation studies between our 2 platforms, Cobas and Cepheid, and results consistently match. Another limitation was transporting the dry swabs specimens to the laboratory for testing rather than testing directly in a point-of-care setting as the Abbott ID NOW platform is intended. Nevertheless, this factor might not have influenced our results, since the samples were handled and tested in ID NOW within the appropriate time and conditions stipulated in the package insert. Overall, our study revealed low PPA of ID NOW when compared with Xpert Xpress irrespective of use of viral transport media or sample type, which raises concerns regarding its suitability as a diagnostic tool. An assay that detects a broad range of the SARS-CoV-2 RNA levels is highly desirable since it is difficult to control the sample quality and as a consequence, variations in viral concentrations. At this point, the significance of low viral levels in disease or transmission is largely unknown.

    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.
    • No funding statement was detected.
    • 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 10.1101/2020.05.11.089896v2 on bioRxiv
  4. Version published to 10.1101/2020.05.11.089896v1 on bioRxiv