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AMP Cautions Against Using Cycle Threshold Values for PCR SARS-CoV-2 Tests in Clinical Practice

NEW YORK – In a blog post on Wednesday, the Association for Molecular Pathology cautioned healthcare providers against basing clinical decisions on cycle threshold values from PCR tests.

Blake Buchan, a member of the organization's Clinical Practice Committee and an associate professor in the department of pathology at the Medical College of Wisconsin, wrote the post, which laid out the key considerations providers should keep in mind before relying on Ct values for clinical decision making.

A test's cycle threshold value is the number of PCR cycles required to amplify the targeted viral nucleic acid to a detectable level, Buchan wrote. A lower Ct value is generally interpreted to correspond to a higher viral load from a patient's sample, and a test's Ct value could help determine patient prognosis and risk of transmission, but there is limited data currently available, he added. 

One issue Buchan brings up is that the use of different specimen collection devices, specimen types, nucleic acid extraction methods, genomic targets, and real-time PCR chemistries can contribute to variability in a reported Ct value. Although "there are some available prognostic correlates of Ct value within large populations, the variety of SARS-CoV-2 testing procedures and lack of a universally applicable threshold present barriers to the use of Ct values for individualized patient care," Buchan wrote.

Buchan's post comes after a joint statement was released last month by AMP and the Infectious Diseases Society of America laying out caveats to be considered when interpreting Ct values in clinical practice. In the statement, the two organizations noted that "Ct values generated by qualitative PCR assays do not reliably correspond to specific RNA concentrations" and "multiple factors other than viral load are known to affect Ct values." 

In IDSA and AMP's statement, the groups wrote that "due to the myriad of analytical and clinical factors known to impact Ct values, caution is advised when applying published correlations of Ct values with disease severity or as a predictor of active infection and hence transmissibility." 

Another concern is the need for validation or verification of test performance, as the reporting of Ct values "without rigorous evaluation of the test performance to support these uses can result in misinterpretation of results and potentially mismanagement of patients," Buchan wrote. 

In addition, many of the SARS-CoV-2 RT-PCR tests currently available are qualitative, providing only a binary positive or negative result. "To date, there are no commercially available molecular tests for SARS-CoV-2 that have data supporting an indication to report quantitative results, including Ct values," Buchan said.

He urged caution in reporting Ct values formally into a patient's medical record, despite the fact that reporting these values for public health or epidemiologic studies can help improve understanding of SARS-CoV-2 infection and transmission dynamics. If Ct values are reported, Buchan recommended adding a comment that states the test used and the lack of verification for use in individual patient care. 

Buchan noted that limiting SARS-CoV-2 reporting to a binary result allowed clinical labs to ramp up testing for the virus and provided additional flexibility for labs. He recommended that SARS-CoV-2 test reporting should be limited to binary results. Limiting results in this way will also "prevent laboratory-generated Ct values from being used for purposes that have not been substantiated by the rigorous performance evaluation process required to deem a test as reliable."

Standardization of test methods and more robust clinical data could alleviate these concerns, Buchan said, but currently the "routine use of Ct values to inform clinical decisions is not advised."