India is reeling from an explosive third wave of Covid outbreak led by the Omicron variant, as the country reports over two lakh cases for the sixth consecutive day.
With cases spiking in nearly all districts in India, the focus has again switched to testing to detect and diagnose the infection. Among the various types of testing, RT-PCR (Reverse Transcription-Polymerase Chain Reaction) is considered the gold standard to detect the presence of SARS-CoV-2 virus.
This brings us to a crucial scientific term in the RT-PCR report, called Ct value, short for Cycle Threshold, a vital test parameter.
It refers to the number of cycles needed in the test, after which the virus in the sample reaches a detectable level. The Ct value is inversely proportional to the amount of viral load in the human body. For instance, lower the value, higher will be the viral level in the sample collected as the virus was detected only after a few cycles, and vice-versa.
During RT-PCR test, the sample swab collected from the patient is used to extract RNA (Ribonucleic Acid), which is then converted to DNA (Deoxyribonucleic Acid). This DNA is then amplified, i.e. its multiple copies are created. The process of amplification of DNA happens through various cycles until a detectable virus level is attained. Here, the number of cycles needed to detect the virus is the Ct value.
Speaking to India Today, Dr SP Kalantri, Professor of Medicine at Maharashtra’s Mahatma Gandhi Institute of Medical Sciences, said, “A typical RT-PCR assay will have a maximum of 40 thermal cycles. A Ct value less than 40 is clinically reported as PCR positive.”
He further added that Ct values obtained in severely ill hospitalised patients are lower than those of mild cases.
On interpreting the Ct value, Dr AK Singh, Endocrinologist at Kolkata’s GD Hospital & Diabetes Institute, told India Today, “When looking at Ct value, we need to know whether this has been done with qualitative or quantitative PCR methodology. Most labs in India report qualitative RT-PCR, and thus Ct value is difficult to interpret and gives confusing results in the same patients. If Ct value is reported through a qualitative RT-PCR, it will differ from one kit to another since they have different Ct cut-offs and different gene targets.”
In reply to the query on correlation between Ct value and severity of the disease, Dr Singh added that although a low Ct value suggests high viral load, it does not necessarily cause severe disease disease manifestation the largely depends on host factors.
He further stressed, “Since Ct values in RT-PCR depend on sampling method, the temperature during transportation, time taken from collection to testing, technical competence and analytical skill of the technician, calibration of equipment and types of samples (nasal vs oropharyngeal swab) tested, its role in prognostication of disease severity is extremely difficult.”
An advisory issued by ICMR in August 2020 also stressed on the importance of the testing process.
Speaking to India Today on the connection between how infectious a person can be and the Ct value, Dr Rajeev Jayadevan, scientific adviser and former president of the Indian Medical Association, said, “Though initially considered to be a marker of how infectious a patient was, recent studies have shown that Ct value does not necessarily mean more amount of actual virus that can spread to other people.”
He further added, “What matters is the amount of virus that can be isolated from the sample. The maximum amount of viruses that can be isolated is found between Days 3 and 6 of onset of symptoms in a person with Omicron infection. Beyond Day 10, no ‘live’ virus is found that can be isolated. However, the RT-PCR can still be positive beyond 14 days because of fragments of ‘dead’ viral RNA lying around the nose and throat.”
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