Coronavirus: Everything you need to know about the nasal swab test

Dubai: As the world races against time to control the COVID-19 pandemic, pathology tests for confirming exposure to the virus have become crucial to managing its spread.

Since the virus has an incubation period that stretches from 0-14 days, getting a positive or negative result decides whether a person needs to be in isolation for treatment, and also how many people they came in contact with are required to go into self-quarantine.

How the COVID-19 virus is structured

A virus consists of genetic information - either DNA or RNA - coated by a protein. DNA is the acronym for Deoxyribonucleic acid and RNA for ribonucleic acid. DNA is a double stranded helix which also happens to be the carrier of genetic information for many generations. RNA is, on the other hand, generally a single strand of nucleotides, and it occurs in a variety of lengths and shapes.

A virus injects its genetic information into a host cell and then takes control of the cell’s machinery. This process enables the virus to make copies of its DNA or RNA and make the viral proteins inside the host cell. Since all coronaviruses including the novel coronavirus are RNA viruses, the nasal swab that is taken is used for isolating the RNA.

The nasal swab and other tests

Dr Kadria Al Sayed, Consultant Pathologist and Chief of Pathology Department at American Hospital Dubai that is already treating many patients who have tested positive for Covid 19 explained: “Currently, testing for COVID-19 is based on either molecular testing or serology. By molecular technology, most of the testing for COVID-19 is done by Real-Time Reverse Transcription Polymerase Chain Reaction (rRT-PCR). where the viral Ribo Nucleic Acid (RNA) is extracted from upper respiratory tract specimens, then amplified to produce a large number of viral copies. Subsequently, detection of three regions in the SARS-CoV-2 gene is done to identify the virus. This is a highly sensitive test and a large number of samples can be processed at the same time with a turnaround time of around 3-4 hours.”

How a test is deemed positive or negative?

Giving the stepwise breakdown for the rRT-PCR test, Dr Jyoti Sateesh Rampalliwar, Specialist Clinical Pathologist at the Biohealth Diagnostic Centre, Dubai said: “The rt-PCR test involves many complex steps that take place in the PCR machine in presence of different reagents & specific temperature.

In the first step, the nasal swab sample is processed and centrifuged to isolate the viral RNA.

Then the viral RNA protein is complemented with fragmented specific DNA & few copies of viral RNA are formed. These copies are amplified to create many copies of the viral RNA, that are measured for the viral count in the last step.

If the viral RNA attaches to the specific DNA fragment, to create the virus molecule, the test is positive. If it does not attach, means the RNA does not belong to the virus molecule and the test is negative."

Five minute swab tests or Point of Care (POC) tests

These tests are being conducted very quickly in drive through facilties. The testing method for rRT-PCR and POC tests is the same molecular method only the POC tests have a shorter waiting period. Dr Al Sayed explained: “The newer POC modality been approved for rapid testing of COVID-19 is based on the loop mediated isothermal nucleic acid amplification (LAMP) technolo. This method of testing can produce results in as little as five minutes depending on the viral load in the sample. This is a highly sensitive test and can be a reliable method to screen patients.”

However both Dr Al Sayed and Dr Rampallivar said the limitation of the POC testing was the number of patients it could test as limited at one time as compared to rRT-PCR. “In the POC tests the sample amplification period is short and the heat in the process is constant. In the centrifuge it takes one sample at a time as compared to the other test which can take 93 to over 100 samples in one go. But the rRT-PCR tests requires a longer period from the time the sample is taken, to the sample extraction, processing , putting it in negative pressure storage and conducting the reverse chain reaction process. However it gives out many more results in one go.”

Beware of false positives

Both the tests can give false positives. “The virus molecule is very fragile and can be contaminated at the time of collection, processing or storage. While storage the temperature has to be upto -70 degree celsius and after that it is subject to high temperatures during amplification. Any misstep during the storage can result in contamination,” said Dr Rampallivar.

Dr Al Sayed added the results could be influenced by the stage of the disease or the integrity of the sample submitted for testing.

Serology test

This is a new test for those who may have had some exposure to the virus in low doses and developed antibodies. This includes frontline health care professioanals – doctors, nurses, paramedics and lab technicians. The test will soon be made available and according to Dr Al Sayed, “serology testing for COVID-19 can identify patients who have already been affected by and recovered from the virus. This specific test detects antibodies in the patient’s blood to confirm current infection or previous exposure to the virus."