The PCR test (polymerase chain reaction test) detects the presence of small fragments of genetic material from the coronavirus SARS-CoV-2 in nasal and throat mucus. It is the most widely used and most reliable test for the virus.

With a PCR test, a smear is taken from mucus in the nose and throat with a cotton swab. This sample goes to a laboratory for the PCR test. If the virus is present in the mucus, this test will make copies of part of the virus. A small fragment of genetic material from the virus is replicated repeatedly, in order to detect its presence. This is also referred to as an amplification test. The PCR test is very sensitive. That means that the PCR test also detects the virus in someone who is not carrying much of the virus  , or no longer has much virus left in their body.

The PCR test is used in the GGD test lanes or at other test sites. The test is also done in hospitals. It takes about 24 to 48 hours after the swab before the tested person receives the results. The procedure in the laboratory takes 4-8 hours. One laboratory technician can analyse 600 PCR tests a day. There are also PCR tests that work faster, but it is only possible to test a few samples at once using those tests. They are mainly used in hospitals for medical emergencies.

LAMP test
The LAMP (loop-mediated isothermal amplification) test, like the PCR test, is a form of testing in which small fragments of genetic material are copied or replicated. The method used for that purpose in the LAMP test is completely different from the PCR test. The major advantage of the LAMP test is that the fragments of genetic material are replicated at only one temperature. Therefore, this test is faster than the PCR test, which requires fluctuations in temperature. The LAMP test requires different equipment and chemical substances than are needed for PCR tests. As a result, they can complement each other in this respect, rather than competing if supplies become scarce.  

How reliable is the PCR test?

The PCR test is extremely sensitive. It is internationally regarded as the ‘gold standard’: it is considered the best test and is used to investigate the reliability of new tests. Each test, including the PCR test, always has a percentage of false positives (an individual is not infected, while the test indicates that they are) and false negatives (an individual is infected, while the test does not indicate that they are). There are a number of possible causes for this:

  • If you test very early after becoming infected, the test can still be negative (i.e. the test indicates that you do not have the virus). This is because it could take several days, or even more than a week, before the virus levels in the cells of your nose and throat are high enough before the test. In that case, there would not be enough of the virus present for the test to detect it.
  • If the test is performed too late, for example when someone has had symptoms for more than a week and has already recovered fully, it is possible that the virus would no longer be present in sufficient quantities in the nose and throat. In that case, virus levels are now low and there is little risk that the person will still infect others. 
  • On the other hand, it is possible that fragments of the virus could still be present in the throat for several weeks after the infection, even without contagious virus particles still being present. In that case, the person may still test positive for COVID-19, but is no longer contagious to others.
  • A test could also incorrectly show that you do not have COVID-19 if the swab did not take enough mucus from the nose and throat, or if the wrong type of swab was used, or because mucus was not sampled from the correct location in the nose and throat.
  • Every test has a margin of error, including the PCR. However, the probability of a false positive test result from a PCR is low. The chance of a positive test result in a person who is not infected or contagious is most likely in the event of a low and decreasing number of infections in a country, or when testing people who do not have symptoms. 

Extensive research has been done to check that the tests do not respond to the presence of other viruses or bacteria, such as cold and flu viruses. Results show that they do not.

Frequently asked questions

Q&As: What does the Ct value on the PCR test mean?

To explain the Cycle Threshold (Ct), we first need to explain what happens during a PCR test. After a swab is used to collect a specimen (the testing sample), this sample is sent to the lab. In the laboratory, lab technicians use equipment to check whether genetic material from SARS-CoV-2 is present in the sample.

To ensure that the test will be as sensitive as possible, a specific fragment of the genetic material is amplified (copied) using the polymerase chain reaction method, known as PCR. This fragment of genetic material is specific to the coronavirus SARS-CoV-2. That means that the test cannot give a positive result for other viruses, such as a flu or cold virus. 

The genetic material is copied in ‘cycles’. During each cycle, the genetic material doubles in volume; this continues until it is detected by the PCR device. The Cycle threshold or Ct value is the number of amplification cycles required to detect the first signal that the virus is present.

What does a high or low Ct value mean?

A low Ct value means that it did not take many cycles to detect the presence of the virus. In that case, there were a lot of virus particles in the sample. This does not necessarily mean that the patient is very ill, or very contagious. Not every patient becomes equally ill as a result of the virus, and not every patient spreads the virus easily. If the Ct value is high, then the patient had a lower viral load (fewer virus particles in the sample), so many amplification cycles were needed to detect the presence of the virus.

A PCR test is very sensitive. Relatively little genetic material from the virus is needed for a positive test result.

At the beginning of the COVID-19 epidemic, RIVMNational Institute for Public Health and the Environment advised taking a closer look at the PCR results of samples with a Ct value greater than 30. Based on the added experience gained with the PCR test for SARS-CoV-2 since then, it can be stated that the results below a Ct value of 35 are completely reliable. Taking an extra look to see if there is also a good S-curve is therefore only useful at Ct values of 35 or higher. Shifting the checkpoint from Ct 30 to Ct 35 does not increase the number of positive results, but it does save lab technicians a lot of time.

More information about PCR tests and Ct values (in Dutch)