Understanding Molecular Testing of COVID-19

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Vigneshwar Senthilvel
23rd May 2020

Molecular testing used to be a term which was confined within the walls of science institutions. Not anymore in the times of COVID19. The term can now be heard in everyday news reports and also in social media. The term is used for any experiment which is carried out to identify/detect anything that is impossible to be seen with a naked eye.

Viruses have proteins on their surface which it uses to meet and greet with the cells, its cognate hosts in our body. These proteins are selective and can only bind to certain receptor proteins on the cell surface. When the two proteins bind, our cells invite these viruses inside. They take over our cells from the inside and start their multiplication with the help of the instructions in their own genetic material, and using the cells machinery to do the hard work.

Once inside a cell, our immune system initially cannot see these viruses and therefore they cannot differentiate an infected cell from a healthy cell. To overcome this ‘bug’ in the system, the infected cells presents pieces/fragments of proteins (antigens) from within the cell on its surface. Special immune cells in the body called cytotoxic T cells identify these presented fragments and releases factors which eliminate the infected cell.

When the initial infection is removed, the fragments of the infected viruses circulate in the body and these antigens are recognized by B cells of the immune system. These cells differentiate and become plasma cells. These plasma cells create antibodies for a specific antigen and are released into the circulation. These antibodies are our immune systems response to the infection. The antibodies can tackle viruses in various ways and can eliminate them from our body.

How can we humans identify for ourselves, the patients who are infected. The three main things discussed above act as markers for infection in our body.

1. The presence of a foreign genetic material in our body.

2. The presence of foreign protein fragments a.k.a antigens in our body

3. The indication of an immune response against an infection.

These markers are smaller than the viruses themselves. Hence, we use different experiments to identify these molecular markers to check for a viral presence in our body.

The most widely used testing method is the presence of the genetic material that is unique to the virus. It is popularly known as the Nucleic Acid Amplification Tests (NAAT). As the name suggests, the detection is based on amplification of the viral nucleic acid present in the isolated samples. Ideal sampling method is a nasal or a buccal swab. As SARS-CoV-2 is an RNA virus, the RNA is isolated from the samples, and are converted to cDNA using reverse transcription. The cDNA is amplified using primer sequences specific to the viral DNA and are quantified using fluorescent probes which bind to the amplified viral sequences. Nucleic acid testing is the most recommended method of testing for COVID-19 by the World Health Organization. A positive result shows the current status of infection in a patient and does not guarantee immunity in the future, when tested negative.

Serological tests, on the other hand, identify the circulating antibodies in our body which are produced as an immune response to an infection in the past. A blood draw is required from the patient to check the circulating antibody levels in the serum. These tests can help identify the rate of infection in a community. They can also help identify individuals who can serve as donors to current COVID-19 patients.

Antigen testing method was approved by the US-FDA recently and hence, the newest method of detection of SARS-CoV-2 in a patient. This method identifies the presence of broken fragments of the virus in the body through a buccal swab. The antigens present in the samples bind to labelled antibodies immobilized on a strip and can be easily visualized without special equipment. It is cheaper and gives rapid results when compared to NAAT, and is very specific to the virus, but is not as accurate. This means, that the positive tests are highly accurate, but there is a high rate of false negatives. They can be easily mass produced and the simple chemistry helps in deploying these tests even in primary healthcare centres and clinics.

The types of molecular testing for COVID-19 are summarized in the infographic attached below. 

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