Deciphering Values

As COVID-19 self-test kits become as integral to our homes as other toiletries, the red lines are no longer as confounding as they once were. But what about the polymerase chain reaction (PCR) tests? What do they show and how do we interpret the results? Prof James Koh Kwee Choy, Consultant Infectious Diseases Specialist and Professor of Medicine in IMU, explains the basics of CT values and what we need to know about PCR tests.

“A CT value is the Cycle Threshold value,” says Prof James. During a PCR test, a nose or throat swab or both are taken and run through a PCR machine. The PCR test detects the RNA that the virus carries. However, it cannot detect this just from the original swab sample taken from you as the genetic material of the virus is too little for detection. The sample needs to be processed through a PCR machine which amplifies the genetic material to a sufficient amount for detection. The CT value tells us the number of cycles it took to multiply enough of the viral genetic material for us to detect it,” explains Prof James.

What is the difference between DNA and RNA? “DNA is our genetic makeup that determines for example, the color of our eyes and hair, facial features and so on,” says Prof James, “the RNA is a messenger that carries certain instructions. The COVID-19 virus carries RNA and once it enters the body, it releases the RNA. When our cells receive the viral RNA, they get the ‘instructions’ to replicate the virus and makes more of the virus.”

Interpreting CT values
When we get our PCR results, a low CT value indicates that it only took a few cycles to multiply enough of the viral genetic material to be detected. This means that you have a high viral load and that you are COVID-19 positive. On the other hand, a high CT value means that the machine has run through many cycles before the viral genetic material can be detected. In essence: the lower the CT value, the higher the viral load and risk of transmission. Conversely, the higher the CT value, the lower the viral load and risk of transmission. The CT value however, is often not correlated with the severity of a person’s symptoms. “Some people may have a low CT value (high infectivity) but are asymptomatic. Some people may have a high CT value (low infectivity) but are symptomatic,” says Prof James. Different countries have different CT values for interpretation of the PCR results. In Malaysia, the threshold is 40, i.e. a CT value of less than 40 means you are positive while more than 40 means you have tested negative. India uses a CT value threshold of 24 and China uses 30. Some test results will only tell you if you are positive or negative without indicating the CT value, as some laboratories want to simplify the results to create less confusion and anxiety. If you want to know your CT value, you can request for it.

Interpreting CT values

When we get our PCR results, a low CT value indicates that it only took a few cycles to multiply enough of the viral genetic material to be detected. This means that you have a high viral load and that you are COVID-19 positive. On the other hand, a high CT value means that the machine has run through many cycles before the viral genetic material can be detected. In essence: the lower the CT value, the higher the viral load and risk of transmission. Conversely, the higher the CT value, the lower the viral load and risk of transmission. The CT value however, is often not correlated with the severity of a person’s symptoms. “Some people may have a low CT value (high infectivity) but are asymptomatic. Some people may have a high CT value (low infectivity) but are symptomatic,” says Prof James. Different countries have different CT values for interpretation of the PCR results. In Malaysia, the threshold is 40, i.e. a CT value of less than 40 means you are positive while more than 40 means you have tested negative. India uses a CT value threshold of 24 and China uses 30. Some test results will only tell you if you are positive or negative without indicating the CT value, as some laboratories want to simplify the results to create less confusion and anxiety. If you want to know your CT value, you can request for it.

Other results In addition to CT values, a laboratory may also indicate an infectivity value. The infectivity value uses a CT threshold of 30-35 depending on the individual laboratory standards. “Above 30 means less risk of transmission, below 30 means high risk of transmission,” says Prof James. Some reports do not state the CT value directly but instead show values in other metrics: for example, the S gene, N Gene and ORF1ab gene. These are structural gene targets that manufacturers of test kits use for detection of COVID-19. “The S gene codes for the spike protein – these are the protrusions on the surface of the virus – is like the clothes of the virus. The N gene codes for the nucleocapsid is the protein coat that contains the viral RNA. And the ORF1ab genes are one of many accessory genes needed for viral replication. Detecting three target genes ensure greater accuracy in diagnosis of COVID-19. This makes the PCR test the gold standard for detecting the virus,” explains Prof James. He adds that you may find variations of these target genes such as the E gene instead of the S gene, depending on the manufacturer of the test.

To test or not to test?
There is a downside to dependence on PCR test, however. Prof James explains: “If you are tested positive, you may continue to test positive with the PCR test for the next few weeks because the PCR detects genetic materials – but does not differentiate between viable or non-viable viruses. Even if it’s non-viable, the PCR will still detect the genetic material and show a positive result.” This means that the PCR test should not be used as a criterion to release someone from quarantine. It is sufficient to go through the mandatory quarantine period as per SOP without requiring further tests. While the PCR test is more sensitive compared to the RTK test – the RTK only picks up the spike protein – the RTK allows quick diagnosis within minutes compared to the PCR which may take between 24-48 hours. This is why Health Minister, Khairy Jamaluddin, has advised the people to use the RTK instead of depending on the PCR tests. “This makes sense as PCR tests also require you to go to a laboratory or health facility, potentially exposing more people to the virus in the process. The PCR is very accurate in diagnosis but not very useful for regular self-monitoring purpose due to its high cost and logistic problems,” says Prof James. It is worth noting that regular testing, such as a weekly RTK test is not necessary if you have no symptoms or are not a close contact, but it is a good step to take to protect others if you are regularly in contact with people.

To test or not to test?

There is a downside to dependence on PCR test, however. Prof James explains: “If you are tested positive, you may continue to test positive with the PCR test for the next few weeks because the PCR detects genetic materials – but does not differentiate between viable or non-viable viruses. Even if it’s non-viable, the PCR will still detect the genetic material and show a positive result.” This means that the PCR test should not be used as a criterion to release someone from quarantine. It is sufficient to go through the mandatory quarantine period as per SOP without requiring further tests. While the PCR test is more sensitive compared to the RTK test – the RTK only picks up the spike protein – the RTK allows quick diagnosis within minutes compared to the PCR which may take between 24-48 hours. This is why Health Minister, Khairy Jamaluddin, has advised the people to use the RTK instead of depending on the PCR tests. “This makes sense as PCR tests also require you to go to a laboratory or health facility, potentially exposing more people to the virus in the process. The PCR is very accurate in diagnosis but not very useful for regular self-monitoring purpose due to its high cost and logistic problems,” says Prof James. It is worth noting that regular testing, such as a weekly RTK test is not necessary if you have no symptoms or are not a close contact, but it is a good step to take to protect others if you are regularly in contact with people.

Accuracy of tests All tests though are only as accurate as the samples taken. This becomes a bigger problem with home test kits as there is no control on the quality of the nasal or throat sample. There could also be contamination to the sample or test environment. “Buy MOH approved test kits and regardless of price – the variations in price are usually dependent on the quality of materials used for example in the packaging – follow the instructions that are given with the particular brand,” Prof James advises. Why are there times when repeated RTK tests show negative, but a PCR shows up positive? “If we test too soon using the RTK, the test won’t be able to detect the virus as viral replication takes time. The PCR is a lot more sensitive to pick up genetic material that the RTK is not able to.” However, the reverse can also be true, where an RTK test comes up positive, but a PCR is negative. “Many factors can contribute to a false-positive RTK test or even a false-negative PCR test, including time and method of sampling and contamination of samples,” explains Prof James.

Too close for comfort
What should you do if you are a close contact? First, Prof James says it is important to know what a close contact is: “You are a close contact if you are together with someone who has tested positive for more than 15 mins, were less than 1 metre apart, without masks, for example when dining together. Although close contacts who do not have symptoms are not required to self-quarantine now, it is prudent to be mindful of any symptoms that may develop within the next few days. Based on current guidelines from MOH, you are required to perform the RTK test on day 1 and 3. If you are symptomatic, you are required to self-quarantine and the duration depends on your vaccination status.” For those who have just recovered from an infection, there is no ‘honeymoon’ period where you are certain you won’t get the virus again. “There has been no study to show what the immunity duration is after contracting COVID-19. It’s very dependent on the individual and how infective the subsequent infection is and what variant the person is exposed to. I think it is safe to say recovery from COVID-19 does not guarantee immunity to subsequent infections,” says Prof James.

Too close for comfort

What should you do if you are a close contact? First, Prof James says it is important to know what a close contact is: “You are a close contact if you are together with someone who has tested positive for more than 15 mins, were less than 1 metre apart, without masks, for example when dining together. Although close contacts who do not have symptoms are not required to self-quarantine now, it is prudent to be mindful of any symptoms that may develop within the next few days. Based on current guidelines from MOH, you are required to perform the RTK test on day 1 and 3. If you are symptomatic, you are required to self-quarantine and the duration depends on your vaccination status.” For those who have just recovered from an infection, there is no ‘honeymoon’ period where you are certain you won’t get the virus again. “There has been no study to show what the immunity duration is after contracting COVID-19. It’s very dependent on the individual and how infective the subsequent infection is and what variant the person is exposed to. I think it is safe to say recovery from COVID-19 does not guarantee immunity to subsequent infections,” says Prof James.

Future challenges As we prepare to enter an endemic stage, we will see many more cases, but life will start to return to some semblance of what it was before the pandemic. The biggest problem however that will continue to be a threat to the community, says Prof James, is misinformation, “Fake news – and how it’s spread through word of mouth for example linking death and sickness to vaccinations, will remain one of our biggest problems.”