Role of gene testing in identifying different variants of SARS-CoV-2 - Hindustan Times
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Role of gene testing in identifying different variants of SARS-CoV-2

ByHindustan Times
Feb 15, 2023 11:23 PM IST

The piece has been authored by Dr Subramanian Swaminathan, director, Infectious Diseases and Infection Control, Gleneagles Global Hospital, Chennai

The Covid-19 pandemic has been a tough time for the health care sector all over the world. While the country was recovering from the huge loss and explosion of cases resulting in a deadly second wave of the pandemic, a year later, a new variant of coronavirus, Omicron, started spreading rapidly. 

Genome sequencing is a time-driven procedure and even if we can sequence all Covid-19 samples in India, the S-gene target failure still be the fastest way to detect Omicron cases.(Praful Gangurde/HT Photo) PREMIUM
Genome sequencing is a time-driven procedure and even if we can sequence all Covid-19 samples in India, the S-gene target failure still be the fastest way to detect Omicron cases.(Praful Gangurde/HT Photo)

The variant Omicron was first detected in South Africa and Botswana and is believed to be even more transmissible, laying upon more challenges to detect. The virus just like any other virus proliferated into various sub-variants, namely, BA.1, BA.2, BA.3, and the most recently tracked ones like the XE, BA.4, and BA.5 sub-variant of Omicron. Doctors and scientists all over the world are trying to understand the behaviour of these new variants that have led to panic in different parts of the world. 

Since Covid-19 variants are continuously evolving over time, many tests like S-gene have turned out to be a game-changer in not only detecting a few of these variants but also understanding the patterns of mutation.

The Omicron variant of Covid-19 is currently the most dominant, and dangerous variant circulating globally while posing new challenges because of its fast transmission. The virus spreads faster as its gene mutation is comparatively faster than the other variants. This clearly indicates that this variant is more adaptable to changes in the human body. Omicron has 26 unique mutations and many of these mutations target the vaccine antibodies. The Omicron variant is made up of various lineages and sub-lineages. The three most common lineages found all over the world are BA.1, BA.1.1, and BA.2. The latest one, XE, has recently piqued people’s attention and raised concerns about increased severity and transmissibility. The newest development came in after World Health Organization (WHO) announced the tracking of two new sub-lineages of the Omicron variant known as BA.4 and BA.5.

Currently, at a global level, the proportion of BA.2 sequences have been increasing relatively to BA.1. BA.2 is different from BA.1 in its genetic sequence, the former has proven to have a growth advantage and further differs in some amino acids, spike proteins, and other proteins. As the reason behind the growth advantage is yet to be discovered, the initial data state that BA.2 appears inherently more transmissible than BA.1 and its siblings, however evidence suggests it is no more likely to cause severe disease.

The XE variant is a recombinant of two subvariants BA.1 and BA.2, stating it contains the mutations of both variants. According to WHO, XE is 10% more transmissible than the BA.2 variant. However, with increased vaccination around the world, it is hoped that the new sub-variants will be futile due to natural immunity from recoveries from earlier omicron infections. 

According to different reports, it has been seen that patients infected with these new variants have not reported any serious illness due to timely detection and can recover without getting hospitalised. It is important to also understand that not all Covid cases are tested for the Omicron variant. Some of the common symptoms of these new variants can be light fever, sore throat, and weakness. Therefore, it is recommended to get tested for signs of any of these symptoms and isolate them to avoid transmission of these sub-variants

Since the new variants of Covid are said to be more transmissible and dangerous, it is important to detect them at an early stage to start the right treatment. With the advancement of medical facilities, it is possible to track down this variant through simpler and affordable methods. The S-gene test is an important indicator for detecting these new variants of coronavirus. This test is another version of RT-PCR and amplifies the RNA of the virus to detect its genetic material. If the test detects the no presence of S-gene but the presence of other genes of SARS CoV-2 virus, it is a COVID infection.  

WHO’s report suggests that many countries lack proper infrastructure for genome sequencing and using S-gene target failure will enable faster identification of Omicron cases, especially where the genome sequencing capacity is low. In these circumstances, S-gene testing has turned out to be a milestone in the early detection and control the Covid transmission. The testing kits usually target more than one gene to detect and identify the presence of the virus. 

The S-gene failure testing kits make it a lot easier to screen suspected Covid cases and isolate them and prioritise them for genome sequencing. 

Also, while S-gene target failure was successful in detecting all the other Omicron sub-variants, the test is posed with the limitations of not being able to detect the BA.2 sub-variant. The mutations in BA.2 make the S-gene target failure impossible to detect S gene dropout. However, the test can confirm Covid-19 infection in a person infected with BA.2 variant. The experts call out genome sequencing as the confirmatory way of detecting the subvariants of Omicron, but its adequacy for a country like India is yet to get established. Genome sequencing is a time-driven procedure and even if we can sequence all Covid-19 samples in India, the S-gene target failure still be the fastest way to detect Omicron cases. 

 

(The piece has been authored by Dr Subramanian Swaminathan, director, Infectious Diseases and Infection Control, Gleneagles Global Hospital, Chennai)

 

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