Multicenter comparison of the Cobas 6800 system with the RealStar RT-PCR kit for the detection of SARS-CoV-2

  1. Marc Wirden
  2. Linda Feghoul
  3. Mélanie Bertine
  4. Marie-Laure Nere
  5. Quentin Le Hingrat
  6. Basma Abdi
  7. David Boutolleau
  8. Valentine Marie Ferre
  9. Aude Jary
  10. Constance Delaugerre
  11. Anne-Genevieve Marcelin
  12. Diane Descamps
  13. Jérôme Legoff
  14. Benoit Visseaux
  15. Marie-Laure Chaix

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Abstract

Background

RT-PCR testing is crucial in the diagnostic of SARS-CoV-2 infection. The use of reliable and comparable PCR assays is a cornerstone to allow use of different PCR assays depending on the local equipment. In this work, we provide a comparison of the Cobas® (Roche) and the RealStar® assay (Altona).

Methods

Assessment of the two assays was performed prospectively in three reference Parisians hospitals, using 170 clinical samples. They were tested with the Cobas® assay, selected to obtain a distribution of cycle threshold (Ct) as large as possible, and tested with the RealStar assay with three largely available extraction platforms: QIAsymphony (Qiagen), MagNAPure (Roche) and NucliSENS-easyMag (BioMérieux).

Results

Overall, the agreement (positive for at least one gene) was 76%. This rate differed considerably depending on the Cobas Ct values for gene E: below 35 (n = 91), the concordance was 99%. Regarding the positive Ct values, linear regression analysis showed a determination correlation (R 2 ) of 0.88 and the Deming regression line revealed a strong correlation with a slope of 1.023 and an intercept of -3.9. Bland-Altman analysis showed that the mean difference (Cobas® minus RealStar®) was + 3.3 Ct, with a SD of + 2.3 Ct.

Conclusions

In this comparison, both RealStar® and Cobas® assays provided comparable qualitative results and a high correlation when both tests were positive. Discrepancies exist after 35 Ct and varied depending on the extraction system used for the RealStar® assay, probably due to a low viral load close to the detection limit of both assays.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.29.179184: (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
    Statistical analysis: Statistical analyses were performed on GraphPad Prism version 6.0.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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:
    This is a limitation of our study as we did not assessed comparatively the limit of detection of the two methods but the reliability of their Ct values among COBAS 6800 positive samples, excluding those that could be negative with COBAS 6800 and positive with RealStar in this range of low viral loads. Our work highlights the impact of the extraction system on the sensitivity of the RealStar assay. Overall, we demonstrated the good performances and concordance between the two assays, at least for viral loads above the detection limit of both assays. This concordance allows to reliably compare Ct values obtained from both methods. However, the variations observed between the Ct values of the two assays, evaluated here as about 3.5 additional Ct with the Cobas 6800 assay, has to be taken into account for Ct values follow-up done for the most severe patients in case of successive use of the two methods, depending of reagent and analyser availability.

    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 10.1101/2020.06.29.179184 on bioRxiv