Head-to-head comparison of direct-input RT-PCR and RT-LAMP against RT-qPCR on extracted RNA for rapid SARS-CoV-2 diagnostics

  1. Max J. Kellner
  2. Martin Matl
  3. James J. Ross
  4. Jakob Schnabl
  5. Dominik Handler
  6. Robert Heinen
  7. Justine Schaeffer
  8. Peter Hufnagl
  9. Alexander Indra
  10. Marcus P.S. Dekens
  11. Robert Fritsche-Polanz
  12. Manuela Födinger
  13. Johannes Zuber
  14. Vienna Covid-19 Detection Initiative (VCDI)
  15. Franz Allerberger
  16. Andrea Pauli
  17. Julius Brennecke

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Abstract

Viral pandemics, such as Covid-19, pose serious threats to human societies. To control the spread of highly contagious viruses such as SARS-CoV-2, effective test-trace-isolate strategies require population-wide, systematic testing. Currently, RT-qPCR on extracted RNA is the only broadly accepted test for SARS-CoV-2 diagnostics, which bears the risk of supply chain bottlenecks, often exaggerated by dependencies on proprietary reagents. Here, we directly compare the performance of gold standard diagnostic RT-qPCR on extracted RNA to direct input RT-PCR, RT-LAMP and bead-LAMP on 384 primary patient samples collected from individuals with suspected Covid-19 infection. With a simple five minute crude sample inactivation step and one hour of total reaction time, we achieve assay sensitivities of 98% (direct RT-PCR), 93% (bead-LAMP) and 82% (RT-LAMP) for clinically relevant samples (diagnostic RT-qPCR Ct <35) and a specificity of >98%. For direct RT-PCR, our data further demonstrate a perfect agreement between real-time and end-point measurements, which allow a simple binary classification similar to the powerful visual readout of colorimetric LAMP assays. Our study provides highly sensitive and specific, easy to implement, rapid and cost-effective alternatives to diagnostic RT-qPCR tests.

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    SciScore for 10.1101/2021.01.19.21250079: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Clinical sample collection: Patient samples (oro/nasopharyngeal swabs and gargle) were obtained as part of a clinical performance study approved by the local Ethics Committee of the City of Vienna (#EK 20-292-1120).
    Consent: Informed consent was obtained from all patients.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The Fiji plugin ReadPlate was used to convert the smartphone image into numerical values according to the plugin’s manual instructions.
    Fiji
    suggested: (Fiji, RRID:SCR_002285)

    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.

  2. Version published to 10.1101/2021.01.19.21250079 on medRxiv