Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: a guide and case study in setting up an emergency-use, laboratory-developed molecular microbiological assay

  1. Melis N Anahtar
  2. Bennett M Shaw
  3. Damien Slater
  4. Elizabeth H Byrne
  5. Yolanda Botti-Lodovico
  6. Gordon Adams
  7. Stephen F Schaffner
  8. Jacqueline Eversley
  9. Graham E G McGrath
  10. Tasos Gogakos
  11. Jochen Lennerz
  12. Hetal Desai Marble
  13. Lauren L Ritterhouse
  14. Julie M Batten
  15. N Zeke Georgantas
  16. Rebecca Pellerin
  17. Sylvia Signorelli
  18. Julia Thierauf
  19. Molly Kemball
  20. Christian Happi
  21. Donald S Grant
  22. Daouda Ndiaye
  23. Katherine J Siddle
  24. Samar B Mehta
  25. Jason B Harris
  26. Edward T Ryan
  27. Virginia M Pierce
  28. Regina C LaRocque
  29. Jacob E Lemieux
  30. Pardis C Sabeti
  31. Eric S Rosenberg
  32. John A Branda
  33. Sarah E Turbett

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Abstract

Developing and deploying new diagnostic tests are difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important. During a pandemic, laboratories play a key role in helping healthcare providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, PCR remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular-based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to establishing fast and accurate diagnostic testing in crisis conditions.

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  1. Version published to 10.1136/jclinpath-2020-207128
  2. ScreenIT

    SciScore for 10.1101/2020.08.26.20157297: (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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    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 10.1101/2020.08.26.20157297v1 on medRxiv