Comparison of Commercially Available and Laboratory-Developed Assays for In Vitro Detection of SARS-CoV-2 in Clinical Laboratories

  1. Joshua A. Lieberman
  2. Gregory Pepper
  3. Samia N. Naccache
  4. Meei-Li Huang
  5. Keith R. Jerome
  6. Alexander L. Greninger

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Abstract

Multiple laboratory-developed tests (LDTs) and commercially available assays have emerged to meet diagnostic needs related to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. To date, there is limited comparison data for these different testing platforms. We compared the analytical performance of a LDT developed in our clinical laboratory based on CDC primer sets and four commercially available, FDA emergency use authorized assays for SARS-CoV-2 (Cepheid, DiaSorin, Hologic Panther, and Roche Cobas) on a total of 169 nasopharyngeal swabs.

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  1. ScreenIT

    SciScore for 10.1101/2020.04.24.20074559: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: This work was approved under a consent waiver from the University of Washington Institutional Review Board.
    IRB: This work was approved under a consent waiver from the University of Washington Institutional Review Board.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    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:
    Despite their limitations, these data provide a basis for differences in analytical sensitivity at different CTs that may be seen between platforms. For instance, recent reports have demonstrated a slightly higher analytical sensitivity of the Cepheid Xpert Xpress SARS-CoV-2 assay compared to the Roche Cobas SARS-CoV-2 test, and a slightly lower sensitivity of the DiaSorin Simplexa SARS-CoV-2 assay compared to a modified CDC assay, both of which are concordant with our data (7, 8). We also note that, while analytical sensitivity is of critical importance, many other considerations factor into assay platform selection including assay availability, cost, turnaround time, and throughput. Our results provide an early assessment of performance characteristics of five separate assays for the detection of SARS-CoV-2. During March 2020, reagent availability for SARS-COV-2 RT-PCR assays was heavily constrained, necessitating more limited assay comparisons. All platforms examined here had acceptable performance criteria for testing during the early part of this pandemic. As the supply chain for SARS-CoV-2 RT-PCR attempts to catch up with testing demand, we look forward to additional assay comparison data.

    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 10.1128/jcm.00821-20
  3. ScreenIT

    SciScore for 10.1101/2020.04.24.20074559: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementThis work was approved under a consent waiver from the University of Washington Institutional Review Board.Randomizationnot detected.Blindingnot detected.Power Analysisnot detected.Sex as a biological variablenot detected.

    Table 2: Resources

    Results from OddPub: We did not find a statement about open data. We also did not find a statement about open code. Researchers are encouraged to share open data when possible (see Nature blog).

    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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, please follow this link.

  4. Version published to 10.1101/2020.04.24.20074559v1 on medRxiv