Comparison of Two Commercial Molecular Tests and a Laboratory-Developed Modification of the CDC 2019-nCoV Reverse Transcriptase PCR Assay for the Detection of SARS-CoV-2

  1. Nicholas M. Moore
  2. Haiying Li
  3. Debra Schejbal
  4. Jennifer Lindsley
  5. Mary K. Hayden

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Abstract

We compared the ability of 2 commercial molecular amplification assays (RealTime SARS-CoV-2 on the m 2000 [abbreviated ACOV; Abbott] and ID Now COVID-19 [abbreviated IDNOW; Abbott]) and a laboratory-developed test (modified CDC 2019-nCoV reverse transcriptase PCR [RT-PCR] assay with RNA extraction by eMag [bioMérieux] and amplification on QuantStudio 6 or ABI 7500 real-time PCR system [abbreviated CDC COV]) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in upper respiratory tract specimens.

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  1. Version published to 10.1128/jcm.00938-20
  2. ScreenIT

    SciScore for 10.1101/2020.05.02.20088740: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The study was reviewed and given expedited approval by the RUMC institutional review board, with a waiver of written informed consent.
    Consent: The study was reviewed and given expedited approval by the RUMC institutional review board, with a waiver of written informed consent.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Abbott Molecular SARS-CoV-2 assay: Next, we verified the RealTime SARS-CoV-2 assay (Abbott Molecular, Des Plaines, IL), which is a qualitative real-time assay performed on the Abbott m2000 platform (12).
    Abbott
    suggested: (Abbott, RRID:SCR_010477)
    Instead, we calculated overall, positive, and negative agreement for the 3 assays (http://www.medcalc.org).
    http://www.medcalc.org
    suggested: (MedCalc, RRID:SCR_015044)
    Box plots for comparing Ct values between groups were created using SPSS version 22 (IBM, Armonk, NY)
    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:
    Our study has limitations. Because there is not a reference standard for SARS-CoV-2 infection, we were unable to calculate sensitivity or specificity of the assays. Instead, we calculated percent agreement, which is appropriate when a non-standard reference method is utilized to compare assay performance (16). We resolved discrepant results through review of patient medical records, which may have introduced bias, since concordant test results were not confirmed in the same way (17). We enriched for samples that were positive by the RealTime SARS-CoV-2 assay on the m2000, which may have biased in favor of this test. However, our inability to detect any samples that yielded a positive result by either of the other two assays under evaluation and a negative result by the RealTime SARS-CoV-2 assay in this study, or in our initial verification of the assay, suggests that the effect of bias is small. Not all testing was performed on the same day due to workflow and personnel limitations, although all testing was completed within 72 hours of sample collection. Storage of specimens at ambient room (22°C) or refrigerated (4°C) temperature has been shown to have little impact on detection of other RNA viruses by RT-PCR (18). In conclusion, we found that The RealTime SARS-CoV-2 assay on the m2000 detected more cases of COVID-19 infection than the modified CDC assay or the ID NOW™ COVID-19 test. The ID NOW™ COVID-19 test provided fastest results, and the small footprint of the instrumen...

    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.

  3. Version published to 10.1101/2020.05.02.20088740v1 on medRxiv