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

Introduction: 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.