How the Covid-19 PCR test works

  • Science
  • Monday, 25 May 2020

Medical personnel taking a nasal swab from a motorist at a drive-through Covid-19 screening facility at the Unimas City Campus in Kuching, Sarawak. Private hospitals also offer this facility. — ZULAZHAR SHEBLEE/The Star

Testing for Covid-19 continues to be the primary form of defence in the fight to tackle, contain and prevent the spread of the SARS-CoV-2 virus that is ravaging the country and world.

Malaysia’s public healthcare system’s capacity to conduct testing for the virus has increased over the last couple of months.

However, these free tests are targeted at specific groups, like those who have contact with confirmed Covid-19 cases, e.g. in suspected clusters and enhanced movement control order (EMCO) areas, and Malaysians placed in quarantine after returning from overseas.

However, some people who are not in these groups might suspect that they have developed symptoms of Covid-19 and wish to test for the virus.

They can do so at certain private hospitals, which provide Covid-19 screening services on nasopharyngeal and oropharyngeal swabs, otherwise known as nasal and throat testing.

The swab test is usually done at a designated area next to the hospital’s Emergency Department in order to contain any possible positive Covid-19 cases to this area.

Drive-through testing is usually also available, where you can remain your car while getting swabbed.

Some hospitals are able to analyse all the samples in their own laboratory, enabling the results to be available more quickly.

Testing can help determine how the virus impacts different people based on age and health condition among other factors.

This will help determine treatment and course of action.

Wider spread testing will enable the healthcare sector to gain deeper understanding of this relatively unknown virus as quickly as possible.

A genetic test

The IMR lab for Covid-19 sample deactivation and RNA isolation. Labs testing the coronavirus should have the proper safety procedures and protocols in place. — FilepicThe IMR lab for Covid-19 sample deactivation and RNA isolation. Labs testing the coronavirus should have the proper safety procedures and protocols in place. — Filepic

The Covid-19 test is a molecular diagnostic test done in a controlled environment (in vitro) to detect the presence of the SARS-Cov-2 virus in a person’s swab sample, using the real-time RT-PCR (reverse transcription polymerase chain reaction) method.

The PCR test detects the virus directly, thus indicating whether an active infection of Covid-19 is present.

The test uses a set of DNA (deoxyribonucleic acid) fragments that complement three target RNA (ribonucleic acid) genes of the virus.

If any of the SARS-CoV-2 viral RNA is present, these DNA fragments will bind to it.

Chemical markers in the form of fluorescent dye or reporter molecules attached to the DNA fragments will release fluorescence during this DNA binding, which is visible on the result strip.

The entire process of analysing one swab test can take up to a day and involves the following three key steps:

  • Sample deactivation

    The sample will undergo heat inactivation at 65°C for one hour to kill the virus.

    This is to ensure that it is no longer infectious and safe to handle in a laboratory.

    Lab personnel handling the sample deactivation must wear full personal protective equipment (PPE), including a disposable isolation gown, double gloves, an N95 face mask, a face shield, a hair cap and shoe covers.
  • RNA isolation

    This step is carried out in a fully automated and closed system to isolate the RNA from the virus cells.
  • PCR amplification and data analysis

    The isolated RNA is amplified (duplicated many times) and analysed by a real time RT-PCR machine.

The testing must be done by staff who are trained and skilled in the meticulous process of doing the swab test, running the PCR machines and analysing the resulting data.

It is also important that the lab is equipped for safety and prevention of cross-contamination.

For example, the lab should have a negative pressure system, a HEPA (high-efficiency particulate air) filter and UV (ultra-violet) bulbs for sterilisation.

And all infectious procedures should be carried out in a validated biosafety cabinet.

Covid-19 safety protocols must also be strictly adhered to.

The designated area for testing needs to be disinfected after each procedure, in strict accordance with the World Health Organization’s (WHO) Guidelines in Safety Protocol for Covid-19.

Patient samples including the primary tubes, deactivated samples and RNA need to be kept at the required temperatures for a week before disposal.

All contaminated wastes are disposed in double biohazard bags, sealed and discarded in a designated waste bin for Covid-19.

Aside from the WHO Guidelines, the Health Ministry and Institute Medical Research (IMR) have also set up a national guideline that needs to be followed when dealing wtih Covid-19 samples.

Positive or negative

A positive test means that the sample swab contains RNA evidence that the SARS-CoV-2 virus is present.

As such, the person the swab was taken from is presumed to be contagious.

A negative test result means that there was no evidence of the virus’ RNA in the sample.

However, a negative result does not completely rule out Covid-19 and should not be used as the sole basis for treatment or patient management decisions.

Any positive results should be delivered by a doctor, so that he is able to advise the patient of their options.

The private hospital will also inform the District Health Office, as well as the designated Covid-19 admitting public hospital, to help coordinate the admission of the patient to the hospital.

Swab vs blood

As the nasal and throat swab test detects the presence of the SARS-Cov-2’s viral RNA, it is a much more definitive indicator that the patient has an active Covid-19 infection (at the time the swab was taken).A research officer loads RNA into the PCR machine in this filepic. The RT-PCR test allows detection of the actual virus in a sample. A research officer loads RNA into the PCR machine in this filepic. The RT-PCR test allows detection of the actual virus in a sample.

This is a vital to identify, isolate and treat Covid-19 patients.

It is also an essential tool to screen a Covid-19 patient’s contacts, who might have been exposed and infected by the patient before diagnosis.

A blood test on the other hand detects the presence of viral antibodies.

This indicates that a patient has developed antibodies as a result of a Covid-19 infection, but doesn’t tell whether the infection is current or in the past.

The antibody test is also less accurate than the PCR test.

Greg Brown is the group chief executive officer of Ramsay Sime Darby Health Care. For more information, email The information provided is for educational purposes only and should not be considered as medical advice. The Star does not give any warranty on accuracy, completeness, functionality, usefulness or other assurances as to the content appearing in this column. The Star disclaims all responsibility for any losses, damage to property or personal injury suffered directly or indirectly from reliance on such information.

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