What is CT Value in RT-PCR?


In March 2020, the World Health Organisation (WHO) declared COVID-19 as a pandemic. This declaration meant that the SARS-CoV-2 coronavirus was a matter of global concern and was affecting millions of people daily. Today, there are various ways of determining if a person is infected by the SARS-CoV-2 virus. 

Antibody tests require medical experts to obtain the patient’s blood samples for testing, and there is a chance that someone previously infected with a mild case of the disease might not have antibodies. Another way of testing for COVID-19 is antigen testing. Antigen testing is the fastest testing method for COVID-19 as it involves a rapid test kit, which is typically used along with a nasopharyngeal swab to get results in under 15 minutes. Lastly, we come to the most commonly used testing method known as the RT-PCR test, which has proven to professionals that it is the most accurate COVID-19 test to date.

What is RT-PCR?

RT-PCR, also known as a molecular test, is a test for COVID-19 designed to detect the genetic material of SARS-CoV-2 using a technique called Reverse Transcription – Polymerase Chain Reaction (RT-PCR). The patient’s samples are collected by a trained professional through nasal swabs or oral swabs inserted into the back of the throat. 

The type of RT-PCR used by modern scientists to detect SARS-CoV-2 is called real-time RT-PCR. Real-time RT-PCR has previously been used to diagnose diseases like Ebola and Zika fever. It is the preferred choice of most scientists worldwide because it is a more efficient variation of the conventional RT-PCR test. In real-time RT-PCR, the use of fluorescent markers to detect targeted genetic material allows professionals to see the test results almost immediately. On the contrary, the conventional method will only give you results at the end of the test.

What is Ct Value in RT-PCR Tests?

Ct stands for cycle threshold, which is a value reflected in an RT-PCR report that helps professionals determine the amount in which the virus is present inside the patient’s body. After collecting the swab samples from the patient for an RT-PCR test, professionals extract the Ribonucleic Acid (RNA) and convert it into Deoxyribonucleic Acid (DNA) using Reverse Transcription. After converting the RNA into DNA, multiple copies of the specific DNA are made through various cycles until SARS-CoV-2 is present in a detectable amount. The number of RT cycles required to reach an amount perceptible in the test is called the Ct value in an RT-PCR test. A lower Ct value in PCR tests indicates that the patient is more infectious than others. On the other hand, a higher Ct value in RT-PCR means that the patient is less contagious and has a lesser quantity of the virus in their bodies. Scientists believe this theory because samples having more of the SARS-CoV-2 pathogen present in them will require less amplification to reach enough copies of the pathogen for detection. 

What Are The Factors Affecting Ct Value?

Although the Ct value in a person’s RT-PCR test indicates how much of the SARS-CoV-2 pathogen they have been carrying in their throats, several other factors can also cause variations in the Ct value shown in the results. Due to this, the Ct value can not determine how sick a person is or what course of treatment a doctor should offer to them based on their viral load. The factors that affect Ct Value in patients are:

  • What was the amount in which the SARS-CoV-2 pathogen was present in the person’s throat during sample collection?
  • What is the effectiveness of the collection method used to obtain the sample?
  • What were the storage conditions of the sample after collection?
  • What was the time of sample collection?
  • What was the type of sample used for testing (nasopharyngeal, saliva, sputum, and so on)?

Why is The Ct Value Important in RT-PCR Tests?

According to the Indian Council of Medical Research (ICMR) in New Delhi, the patient will be considered positive for COVID-19 if the Ct value is below 35. This number means that if the SARS-CoV-2 pathogen gets detected in the patient’s DNA sample after 35 cycles or earlier, the patient will be considered positive for COVID-19. 

Not too long ago, the state of Maharashtra, which has the highest number of COVID-19 cases amongst all Indian states, wrote a letter to the ICMR requesting them to lower the benchmark Ct value required for a patient to be deemed positive for COVID-19. The globally accepted Ct value for RT-PCR results ranges between 35 and 40 globally.

Having the current benchmark of 35 cycles means that more people, even with a lower viral load, will also test positive for COVID-19. Therefore, ICMR had to reject Maharashtra’s request to lower the threshold. The reason stated by the ICMR was that reducing the required CT value of RT-PCR tests would result in many comparatively milder cases going undetected, leading to many infectious patients going undiagnosed, which would, in turn, result in increased transmission of COVID-19. Doing this would result in a false decrease in the positive cases. Many patients with a lower viral load of SARS-CoV-2 in their bodies can also be severely ill without being diagnosed with COVID-19.

Do Severe Cases Have Lower Ct Values?

The Ct value tells us how much of the virus is present in the person’s body. Having a lower Ct value does not indicate that a person will be sicker than someone with a higher Ct value. There are cases where people have a viral load high enough to be detected in a low number of cycles but show no symptoms of COVID-19 whatsoever. The Ct value tells us about the viral load of SARS-CoV-2 in the patient’s throat and not the lungs. Getting to know the Ct value of a patient helps doctors determine how infectious the patient is, not how severely they are affected by COVID-19.

What to do if Someone Near You Has a Low Ct Value?

Thanks to security management apps such as MyGate, you can easily find out if someone in your society has been diagnosed with COVID-19 or is showing symptoms of the disease. If someone has a Ct value below 35, they will test positive for COVID-19. The infectivity of these patients is lesser than patients with comparatively lower Ct values. If someone near you has a lower Ct value than average, you should take more precautions than you normally would since the chances of you getting infected are much higher due to the high viral load of the patient.

Contact tracing is particularly important for patients who show a lower-than-average Ct value in pcr, as having a lower value in Rtpcr means they can spread the virus more than other infected patients. The quarantine of such patients should only end once their RT-PCR tests show a Ct value high enough for them to not be a danger to society.


With newer, more infectious strains of the SARS-CoV-2 virus, such as the Omicron variant sprouting up in different parts of the world, it is extremely important for us to know what the Ct value in an RT-PCR test means. Due to the highly infectious strains of today, it is becoming increasingly common for patients to have Ct values that are much lower than 30. This means that the SARS-CoV-2 virus has evolved to become more infectious than it was before, and we need to be extra cautious about our habits and activities.


What do you think?

Leave a Reply

Your email address will not be published. Required fields are marked *