Important Issues to Consider Before Interpreting and Applying Ct Values in Clinical Practice

AMP recently partnered with our colleagues at the Infectious Diseases Society of America (IDSA) to issue a joint statement on the use of SARS-CoV-2 PCR cycle threshold (Ct) values for clinical decision-making. As AMP’s representative on the project, I wanted to share a few additional thoughts on the caveats that need to be considered before interpreting and applying Ct values in clinical practice.

Current U.S. Food and Drug Administration (FDA) Emergency Use Authorized (EUA) real-time PCR tests for SARS-CoV-2 are designed as qualitative assays, which means that the test procedure generates a binary result of “positive” or “negative.”* Some, but not all, SARS-CoV-2 molecular tests (formally known as real-time polymerase chain reaction tests, or real-time PCR) also generate and report a cycle threshold (Ct) value, referring to the number of PCR cycles required to amplify the targeted viral nucleic acid to a detectable level.  While this information has potential value in determining patient prognosis and risk of transmission, AMP and IDSA urge caution to prevent health care providers from making clinical decisions based on Ct values given the limited data currently available. This all may change in the future based on expanded development and standardization of test methods and more robust clinical data, but at the current time, routine use of Ct values to inform clinical decisions is not advised.


  • Precision is a key factor when considering use of Ct values to manage individual patients. The use of different specimen collection devices, specimen types, nucleic acid extraction methods, genomic targets, and RT-PCR chemistries all contribute to variability in the final reported Ct value (Rhoads et al., PMID: 32785682). Data from Westblade, et al (PMID 32997958) demonstrate a correlation between Ct value and in-hospital mortality using two different RT-PCR tests; however, the Ct value thresholds used for each test were different even after controlling for all other factors. This clearly demonstrates a lack of Ct value commutability between test platforms. Further, while the difference in median Ct value between groups was statistically significant, the interquartile range (IQR) of values between groups overlapped by 20-50%.  While 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.


  • Validation or Verification of test performance is central to reporting of accurate and reliable results that can be used to improve patient care. The reporting and subsequent use of Ct values when making diagnostic, prognostic, or therapeutic decisions without rigorous evaluation of the test performance to support these uses can result in misinterpretation of results and potentially mismanagement of patients. Evaluation of performance characteristics, whether related to assessment of an EUA designated test or a laboratory developed testing procedure (LDP), falls under the purview of a laboratory director with specific expertise and is subject to regulatory oversight. The process includes examination of both analytical and clinical data to support the intended use of the test. 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.


  • Reporting Ct values for public health or epidemiologic studies may be important to the continued research and understanding of SARS-CoV-2 infection and transmission dynamics.  However, caution is urged in reporting these values formally into the medical record.  If a decision is made to routinely or sporadically (i.e., case by case) report Ct values, consideration should be given to inclusion of an interpretive comment that specifically states the test used and the lack of verification for use in individual patient care.

Example inclusion in a report: “This result was generated using the <insert test name here> for qualitative detection of SARS-CoV-2.  Resulting cycle threshold (Ct) values have not been standardized.  The Ct values are reported for epidemiologic investigation and are of limited utility for the management of individual patients.



While many clinical nuances and considerations are carefully laid out in the statement, I’d like to focus on the fact that limiting SARS-CoV-2 reporting to a qualitative result has allowed the clinical laboratory community to ramp up testing across the country in a manner never seen before. The use of LDPs to test for the novel coronavirus helped the U.S. scale up from just a few thousand tests per day to millions of tests per day, which was a truly astonishing accomplishment. Furthermore, the use of LDPs has provided laboratories with additional flexibility that helped alleviate staffing and supply shortages that would otherwise have been insurmountable, though significant pressures remain.

Flexibility in no way means lax regulatory oversight – clinical laboratories and the tests we develop are overseen by the Clinical Laboratory Improvement Amendments (CLIA), a program administered by the Centers for Medicare and Medicaid Services (CMS), in addition to other state and professional requirements. We support responsible oversight just as we support rigorous training for our community. Rather, flexibility in this scenario conveys a trust that trained professionals will use our skills and resources efficiently to provide the best patient care possible.

Right now, the best way to ensure patients have access to safe and prompt SARS-CoV-2 testing is to limit reporting to binary “positive” and “negative” results.* Use of all qualitative tests currently on the market, including those that do not generate a Ct value, avoids a potential bottleneck due to demand for only those tests reporting Ct value. Limitation of reporting to binary results for individual patient care 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.

*Some laboratories report “detected” and “not detected”


Blake W. Buchan, PhD, D(ABMM)
Member of the AMP Clinical Practice Committee (Infectious Diseases Subdivision)
Associate Professor, Department of Pathology
The Medical College of Wisconsin

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