AACC Doubles Down on Not Using CT Values to Evaluate Performance of SARS-CoV-2 PCR Tests

Laboratories and health care providers should not use cycle threshold (CT) values to measure the performance of polymerase chain reaction (PCR) tests for SARS-CoV-2. That was the advice of the American Association of Clinical Chemistry (AACC) in a public statement issued on July 7.  And the results of a new study reinforce that the AACC’s recommendation is a sound one.

Use of CT Value for Managing COVID-19 Patients

According to the Clinical and Laboratory Standards Institute (CLSI), the CT value is the “number of cycles needed for an amplicon to become detectable above background.” Stated differently, the CT value is the lowest PCR cycle number at which the fluorescent probe signal for the amplified target sequence is greater than the minimal detection level determined during validation by the user. Lower CT values are associated with a higher amount of target viral sequence (copy number) in the sample tested. During the pandemic, a number of healthcare providers and public health agencies have asked laboratories to report the numerical CT value along with the qualitative result when a specimen has detectable SARS-CoV-2 nucleic acids.

The AACC’s Opposition

The AACC has made it known that it thinks this is a bad idea. Its July 7 statement notes that validation of a quantitative test is more complex and requires more rigorous testing to ensure performance, such as determining the lower limit of quantification rather than the lower limit of detection.

The new independent study, which was published in the organization’s Clinical Chemistry, offers evidence that reinforces the validity of the AACC’s recommendation against use of CT value for measuring performance PCR tests for SARS-CoV-2. The study was led by researchers at the UK National Measurement Laboratory at life sciences company LGC. The team applied the World Health Organization’s recommended CT cutoff of 25 to the test results of more than 6,000 patients who were tested for SARS-CoV-2 with PCR at three laboratories in the UK, Belgium and South Korea. They found that clinical sensitivity dropped from 100 percent to between 16 percent and 90 percent, depending on the patient cohort.

After looking at an additional 732 laboratories, they determined that an individual CT value can correspond to different viral loads depending on the laboratory. While CT values may be useful for epidemiological assessments, “they should be avoided as a quantitative measure for individual patient stratification or analytical performance targets,” noted research team leader Jim Huggett in a statement.

“If quantification is to be performed, copy-based units calibrated to appropriate standards should be explored,” he said. Such standards may not be available yet for a new pathogen and should be produced quickly as “an important part of a diagnostic response plan to a new epidemic,” he added.