CT Values Should Not Be Used to Assess Performance of SARS-CoV-2 PCR Tests or Triage COVID-19 Patients, Finds Study

A novel study has shown that coronavirus test cycle threshold (Ct) values should not be used to assess the performance of coronavirus tests or to triage COVID-19 patients.

These findings of the study by an international group of scientists, led by the National Measurement Laboratory for Chemical and Bio-Measurement team at LGC (Middlesex, UK), could improve the development of coronavirus tests, which are crucial for managing the pandemic, as well as care for COVID-19 patients.

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When a patient gets a standard coronavirus test - known as a PCR test - Ct values are generated as part of the testing process. These values are also commonly known as Cq or Cp values. In WHO’s recommendations for coronavirus test developers and funders, the organization proposes a Ct of 25 as the minimum level of virus that should be detected by point-of-care coronavirus tests (i.e., tests that can be performed near the patient). Some research has also suggested that Ct values could potentially identify patients who have high viral loads and are at increased risk for serious disease. However, in July of this year, the American Association for Clinical Chemistry (AACC) had issued a public statement advising against the use of these values to guide COVID-19 public health efforts or treatment due to a lack of conclusive data supporting this.

In an effort to fill this data gap, the international team of researchers set out to determine how the WHO’s suggested Ct cut-off of 25 impacts coronavirus test performance. To do this, the researchers analyzed the results of more than 6,000 patients who underwent coronavirus PCR testing at three clinical laboratories in the UK, Belgium, and the Republic of Korea. For the purposes of this study, all PCR tests used were considered to have 100% clinical sensitivity (i.e., the ability to correctly identify patients with COVID-19 100% of the time). However, when the team interpreted the tests’ results using the WHO’s cut-off, the tests’ clinical sensitivity dropped, varying from approximately 16% to 90% depending on the patient cohort.

Further analysis of data from 732 additional laboratories found that an individual Ct value can correspond to widely differing viral loads depending on the lab. For example, in theory, the Ct value range of 25-30 corresponds to 106 copies of SARS-CoV-2/mL. In reality, however, the researchers found that that Ct range can correspond to as many as 108 copies/mL to as few as 103 copies/mL. When taken altogether, these results showed that Ct values should not be used to guide test development or to determine a patient’s prognosis.

“While [Ct] values may be useful in COVID-19 for epidemiological assessments of populations, they should be avoided as a quantitative measure for individual patient stratification or … analytical performance targets,” said Jim Huggett, PhD, of the U.K. National Measurement Laboratory at LGC, who led the research team. “If quantification is to be performed, copy based units calibrated to appropriate standards should be explored as applied in other areas of clinical virology. When dealing with a new pathogen, this fact is hampered by an initial absence of appropriate standards to calibrate the copy based units; consequently; their rapid production should be an important part of diagnostic response plan to a new epidemic.”

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