Inclusion of cycle threshold (CT) values when reporting SARS-CoV-2 RT-PCR results improves clinical Interpretation in suspected and confirmed COVID-19

  1. Peter V. Coyle
  2. Naema Hassan Al Molawi
  3. Mohamed Ali Ben Hadj Kacem
  4. Reham Awni El Kahlout
  5. Einas Al Kuwari
  6. Abdullatif Al Khal
  7. Imtiaz Gilliani
  8. Andrew Jeremijenko
  9. Hatoun Saeb
  10. Sheikh Mohammad Al Thani
  11. Roberto Bertollini
  12. Hanan F. Abdul Rahim
  13. Hiam Chemaitelly
  14. Patrick Tang
  15. Ali Nizar Latif
  16. Saad Al Kaabi
  17. Muna A. Rahman S. AlMaslamani
  18. Brendan David Morris
  19. Nasser Al-Ansari
  20. Anvar Hassan Kaleeckal
  21. Laith J. Abu Raddad

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Abstract

The Cycle Threshold (CT) value in Real-time Polymerase Chain Reaction (RT-PCR) is where a target specific amplification signal becomes detectable and can infer viral load, risk of transmission and recovery in SARS-CoV-2 infections. Adoption into routine practice is however uncommon.

Gap Statement

The lack of inclusion of CT values when reporting SARS-CoV-2 RT-PCR results in routine practice.

Aim

To use CT values when reporting SARS-CoV-2 RT-PCR results in Qatar to aid clinical interpretation and patient management.

Methodology

Routine CT values across 3 different RT-PCR platforms were reviewed for concordance at presentation and clearance in patients with COVID-19. An Indicative Threshold of CT 30 based on viral clearance kinetics categorized low and high CT values.

Results

There was very high Correlation and Kappa Score agreement between the different gene targets in each platform (p<0.001). Using the Indicative Threshold it was possible to autoverify and add average CT values and append Interpretive Comments to all RT-PCR reports. The new reporting algorithm impacted immediately and safely on: physician interpretation of SARS-CoV-2 results; patient management; staff surveillance protocols; length of stay in quarantine; a redefinition of patient recovery.

Conclusion

Incorporation of CT values into routine practice is possible across different RT-PCR platforms and adds useful information for patient management. The use of an Indicative Threshold and interpretive comments improves clinical interpretation of the result and could be a model for reporting other respiratory infections. The current accepted practice of withholding CT values should be reviewed by the profession, accreditation bodies and regulators.

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    SciScore for 10.1101/2021.02.11.21251557: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot 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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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.

    Results from scite Reference Check: We found no unreliable references.

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  2. Version published to 10.1101/2021.02.11.21251557 on medRxiv