All you need to know: How to make sense of your RT-PCR test report

A lot of scientific jargon related to the coronavirus has entered into our daily lingo. What is your CT levels in your RT-PCR test? people ask knowledgeably. That is important, it will determine whether you really have COVID or not, they say. But, how is the presence of the wily coronavirus in your body captured in all its complexities and reflected in this all-important CT value?

What is CT value?

An acronym for ‘Cycle Threshold’, CT is the value that appears in an RT-PCR test, which is currently the ultimate test being conducted to detect whether you have been infected by the SARS-CoV-2 coronavirus. It is this CT value which turns out to be the benchmark to prove that you are COVID positive or not.

The process to arrive at the CT value?

In an RT-PCR test, an RNA is extracted from the nasal and throat swab collected from the patient and converted into DNA. This DNA is amplified to create multiple copies of the genetic material — and this amplification gives an opportunity to search for miniscule pieces of the viral genes. Multiple copies of the genetic material are created to make it easier to nose out the virus if it is present.

If a trace amount of the genetic material of the virus is detected, it’s amplified, or copied, over and over again, cycle after cycle making many copies of the virus. The CT value then refers to the number of cycles, after which the virus gets detected.

Also read: Centre blames Maharashtra for slow RTPCR tests for detecting COVID

So, if it takes a higher number of cycles, it implies that the virus was not caught when the number of cycles was lower. If the CT value is low, then it automatically means that the virus was seen after fewer cycles and you have a high viral load. Therefore, a low CT value means the viral load is high, and inversely, if a high CT value is recorded, then the viral load is low.

Lower CT value= Higher Viral Load

Higher CT value= Lower Viral load

However, this does not have much relation to the severity of the disease but it works as a benchmark to assess if you are COVID positive or not.

On the critical question of number of cycles required to find proof of the virus?

This question was recently posed by the Maharashtra government, hit hard by the pandemic, to the Indian Council of Medical Research (ICMR). The state wanted to know if an asymptomatic person with a CT value of 24 can be considered as COVID-negative. Apparently, there have been varying views from different government bodies like NITI Aayog, and even several ICMR documents had mentioned different CT values.

The ICMR reportedly took inputs from virology laboratories across the country and arrived at a single CT value cut-off. All patients with a CT value of equal to or less than 35, may be considered as positive, while those with a CT value above 35 may be considered as negative, ICMR said in a letter dated April 5, said media reports.

“All samples with a CT value equal to or less than 35, which is seen as a poor sigmoidal curve, should be essentially retested. Implementing a CT value cut-off of 24 is not at all advisable as this would lead to missing of several infectious patients and increase disease transmission,” added the letter.

Also read: As cases spike, Centre asks states to ramp up RT-PCR tests

What is the significance behind this cut-off level?

If the virus is caught before 35 cycles then the person is considered to have a high viral load and is dubbed as a positive. But, if the criteria was lowered to 24 cycles, then the CT values between the 24-35 cycles will be overlooked, in short, there are more chances of catching the virus with longer cycles. The ICMR too observed that lowering the CT threshold parameter may lead to missing several infectious persons and increase chances of spreading the virus.

As reported in India Today, Dr Samiran Panda, head of epidemiology and communicable diseases at the ICMR said, “If you lower down the CT value, that will pose a serious problem because the person is still infected, he would have a low viral load – the person would be negative.” And added that false negative results may lead to the person not seeking treatment and ending up transmitting the infection to the family and the society.

What is the cut off CT value threshold in other countries?

Globally, the accepted cut-off for CT value for COVID-19 ranges between 35 and 40, depending on instructions from the respective manufacturers of testing equipment. For example, in Canada, most labs set the limit of cycles to detect the virus’ genetic material, or RNA, to between 35 and 40 cycles, though some Ontario labs have “positivity” cut-offs as high as 45 cycles.

Is there any link between CT value and severity of the disease?

No. A patient can have a low CT value, which means the viral load is high enough to be detected rapidly, but he or she may still be asymptomatic. According to an Indian Express report, a small study published in the Indian Journal of Medical Microbiology in January this year found no correlation between CT values and severity of disease or mortality in patients with COVID-19 disease. It is more linked to when the COVID-19 symptoms started rather than how severe the disease is.

Also read: Candidates must show -ve COVID report or jab proof to enter counting centres

The reason why CT value has no relation to severity of disease

This is because the CT value is related to the viral load in the throat not the lungs. It is only tagged with “infectivity”, or how much you can infect another person

Factors that impede capturing correct CT values?

An ICMR advisory in August last year noted that CT values depend on how the sample has been collected. A poorly collected sample may reflect inappropriate CT values. Also, the technical competence of the person performing the test, calibration of the equipment, and the analytical skills of the interpreters have also to be taken into account. Besides, the temperature, transportation, as well as the time taken from collection to receipt in the lab, can also adversely impact CT values.

Here’s a Catch:

A high CT value does not necessarily always mean a low viral load. Some experts have said that some patients can have a high CT value and yet have a very significant level of COVID-19 infection, and vice versa.