How to read a Covid-19 test report: What is the Ct value?


Among the various scientific terms that the Covid-19 pandemic has been part of the public vocabulary, one is the “ Ct value ” in RT-PCR tests to determine if a patient is positive for Covid-19.

This was the subject of a recent request by the government of Maharashtra to the Indian Council for Medical Research (ICMR). The state has requested clarification on whether to treat a person as Covid-negative if the Ct value is greater than 24 and the person is asymptomatic. State officials said that various ICMR documents mentioned different Ct values ​​and that there were divergent views even between Niti Aayog and the National Center for Disease Control.

A few days later, the ICMR CEO responded to the Secretary of State for Health that the ICMR had taken input from virology labs across the country to arrive at a single Ct threshold. All patients with a Ct value less than 35 can be considered positive while those with a Ct value greater than 35 can be considered negative, the ICMR said.

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But what is the Ct value?

Short for cycle threshold, Ct is a value that emerges during RT-PCR testing, the gold standard for detection of the SARS-CoV-2 coronavirus. In an RT-PCR test, RNA is extracted from the swab taken from the patient. It is then converted into DNA, which is then amplified. Amplification refers to the process of creating multiple copies of genetic material – in this case, DNA. This improves the test’s ability to detect the presence of viruses. Amplification occurs through a series of cycles – one copy becomes two, two becomes four, and so on – and it is after several cycles that a detectable amount of virus is produced.

According to the ICMR opinion, the Ct value of an RT-PCR reaction is the number of cycles at which fluorescence of the PCR product is detectable above the background signal. Simply put, the Ct value refers to the number of cycles after which the virus can be detected. If a higher number of cycles is required, it means that the virus was not detected when the number of cycles was lower. The lower the Ct value, the higher the viral load – because the virus was spotted after fewer cycles.

Why is this important?

To put this in context, let’s look at the ICMR opinion and the Maharashtra letter to the ICMR. According to the ICMR, a patient is considered positive for Covid if the Ct value is less than 35. In other words, if the virus is detectable after 35 cycles or earlier, then the patient is considered positive. If the benchmark were lowered to 24 – the value mentioned in the letter from Maharashtra – it would mean that Ct values ​​between 25 and 34 would not be considered positive. A benchmark of 35, therefore, means that more patients would be considered positive than we would get if the benchmark were 24. ICMR said lowering the Ct cutoff parameter could lead to the disappearance of Ct. several infectious people.

One can think of the Ct value as a measure of the potential for transmission, said lead virologist Dr Shahid Jameel. “So if there is more virus in my throat and nose, I will transmit it better,” said Dr Jameel, director of the Trivedi School of Biosciences at Ashoka University.

What is the significance of the ICMR threshold of 35?

Overall, the accepted cut-off value for the Ct value for Covid-19 varies between 35 and 40, depending on the instructions of the respective manufacturers of the test equipment. The ICMR arrived at the Ct value of 35 based on laboratory experiments and inputs from several virology laboratories.

There was no new notice, but the ICMR has informed the government of Maharashtra that it is not advisable to use a lower cycle threshold setting as it will lead to the disappearance of several infectious people and increase transmission of the disease, said Dr Balram Bhargava, CEO of ICMR.

Is there a correlation between a Ct value and the severity of the disease?

No. Although the Ct value is inversely correlated with viral load, it does not affect the severity of the disease, the experts said. A patient may have a low Ct value, which means her viral load is high enough to be detected quickly, but she may still be asymptomatic.

A small study published in the Indian Journal of Medical Microbiology in January of this year found that there was no correlation between Ct values ​​and disease severity or mortality in patients with Covid disease. -19. He found that the time since symptom onset has a stronger relationship with Ct values ​​relative to disease severity.

The Ct value tells us about the viral load in the throat, not the lungs, said Dr Parikshit Prayag, consultant for infectious diseases at Deenanath Mangeshkar Hospital in Pune. “The Ct value does not correlate with severity – only with infectivity. In the first report, I don’t really look at the Ct value, but for patient follow-up in the hospital, I consider the Ct value, because then I can decide whether or not to transfer the patient to the non-Covid building. . From an infectivity perspective, it may matter, not severity, ”said Dr Prayag.

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Does a high Ct value always mean a low viral load?

While this may be the obvious conclusion, some experts point out that some patients may have a high Ct value while having a very high level of Covid-19 infection, and vice versa. Many factors are important in interpreting an RT-PCR test, and the results may also depend on the method of specimen collection and the time between infection and collection and analysis.

An ICMR notice in August last year noted that Ct values ​​depend on how the sample was collected. A poorly collected sample may reflect inappropriate Ct values. In addition, Ct values ​​are also determined by the technical competence of the person performing the test, the calibration of the equipment and the analytical skills of the interpreters.

Again, Ct values ​​may differ between nasal and oropharyngeal samples taken from the same individual. Transport temperature, as well as the time between collection and reception in the laboratory, can also have a negative impact on Ct values.

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