Test Agreement Between Roche Cobas 6800 and Cepheid GeneXpert Xpress SARS-CoV-2 Assays at High Cycle Threshold Ranges

  1. Kari Broder
  2. Ahmed Babiker
  3. Charles Myers
  4. Terri White
  5. Heather Jones
  6. John Cardella
  7. Eileen M. Burd
  8. Charles E. Hill
  9. Colleen S. Kraft

Reviewed by

Read the full article See related articles

Discuss this preprint

Start a discussion What are Sciety discussions?

Listed in

Log in to save this article

Abstract

The SARS-CoV-2 pandemic has changed the face of the globe and upended the daily lives of billions. In an effort to bring mass-testing to as many as possible, multiple diagnostic tests including molecular, antigen detection and serological assays have been rapidly developed. However, there is very little information on positive test agreement across modalities, especially for lower viral loads. Thirty-five nasopharyngeal samples that had cycle threshold (Ct) values greater than 30.0 from the Roche cobas 6800 assay were run on the Cepheid GeneXpert Xpress SARS-CoV-2 assay. Ct values ranged from 30.1 to 37.9 (mean 36.7 ± 1.9) on the Roche cobas 6800 assay and 24.6 to 42.4 (mean 32.8±4.1) on the Cepheid assay. There was a bias of 0.33 ± 3.21, (mean difference −1.59, 95% limits of agreement −5.97, 6.63) signifying close agreement between the 2 instruments with a high standard deviation. The close test agreement between the cobas 6800 and GeneXpert at high Ct values allows for utilization of both assays interchangeable in accordance with testing algorithms.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.05.05.078501: (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

    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:
    Limitations of this study include sample size, location within a single institutional system, and proprietary manufacturer information, including differences in E gene target sequence. Further studies are required to confirm percent agreement across different platforms and specimen types to expand on our findings. This is of particular importance as there is a lack of standardization of reference materials and quantitfication (copies/vol, TCID50, etc) for LoD determination. Overall, the Cepheid GeneXpert Xpress SARS-CoV-2 assay and the Roche cobas 6800 SARS-CoV-2 assay showed a high level of agreement among patients with high Ct values. This allows for the laboratories to utilize both assays concurrently as fits with local testing algorithms.

    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.

  2. Version published to 10.1101/2020.05.05.078501 on bioRxiv