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Genome Sequencing Can Confirm Presence Of COVID-19 Variant Omicron: Expert

Dr Naveen Dang, Director of Dr Dangs Lab explains why the Omicron variant of COVID-19, which contains many of the mutations found in other variants in addition to its own, thus making it different from other variants of concern (VoC)

Genome Sequencing Can Confirm Presence Of COVID-19 Variant Omicron: Expert
COVID-19 variant Omicron was first detected in South Africa
Highlights
  • Different variants mean mutations in one or more of the genes: Dr Dang
  • COVID-19 variant Omicron is said to have 50 mutations
  • Over 30 mutations are on the spike protein - the outer layer of the virus

New Delhi: With a rise in the number of countries reporting an increase in cases of Omicron, the “highly transmissible” new COVID-19 variant, India continues to remain on high alert. Passengers travelling from ‘high-risk’ countries have tested positive for COVID-19 but so far no Omicron cases have been reported in India. Dr Naveen Dang, Director of Dr Dangs Lab explains why the Omicron variant, which contains many of the mutations found in other variants in addition to its own, thus making it different from other variants of concern (VoC).

Also Read: Omicron Variant Does Not Escape RT-PCR And RAT, Centre Tells States As It Asks Them To Ramp Up Testing

Different variants mean that there have been mutations in one or more of the genes. The previous mutants may also have a couple of mutations, but in Omicron we have a very large number of mutations that have occurred, nearly about 50 mutations, and out of these nearly 30 are in the spike protein. That is what makes it different from the other mutations of the COVID virus which we have experienced in the last two years, Dr Dang said.

Gene sequencing depending on the suspected cases and the missing S-gene is one of the indicators for detection and ultimate diagnosis for the potentially more infectious variant of concern, Omicron. One of the S gene targets is not detected due to mutations and this termed as the S gene dropout or S gene target failure, is a marker to identify the Omicron variant, says Dr Dang.

Also Read: Explained: What Are The Symptoms Of Omicron, A Variant Of Concern

The S-Gene dropout or as we say the S-Gene target failure or SGTF is one of the proxy indicators to (ascertain) whether or not it is the Omicron variant. But this is not necessarily so as the ultimate diagnostic tool is distinct for gene mutation. So, if there is a patient who is suspected (to be infected) with Omicron, the ultimate diagnosis relies on testing but testing for the mutations that are called gene sequencing, Dr Dang said.

Dr Dang further explained the process of detecting whether the S-gene has gone missing. The mutations in the latest variant have occurred in the S gene. The common RT-PCR kits being used will be able to identify positive or negative, but will not be able to identify if the positive result is due to the mutation in the S gene.

Also Read: A New Variant Of Concern: Is It More Dangerous? AIIMS Director Randeep Guleria Explains

When we are doing tests, most of them target a large number of genes. Now usually tests in India test the E, N and Rd Rp genes. Even if one of these genes (identifies as) positive, we can (identify) they tested positive for COVID-19. However, most of the tests in India are not (testing) the S-gene because there was no kind of requirement for it. But if we have a test in which you have multiple genes, and one of the genes included in the SG and if the test shows positive for all the genes but negative for S-gene, we can say that this is an S-gene dropout or S-gene failure target failure. So if that happened, then by proxy we can say by default, we can say that this is Omicron and such sample should be on a priority basis. We send for gene sequencing studies. So once that is done only then only it can confirm whether it is the variant or not.

According to the expert, since Omicron was very recently detected, there is very little data on its transmission and spread and scientific data is still being collected and is really early to say about how contagious the strain could be.

Also Read: South African Doctor Says Patients With Omicron Variant Have “Very Mild” Symptoms

We do not know how severe the cases are going to be. As you know very well that this virus was first identified and spoken about on November 26, is not even a week back. So it is too early to comment how severe the infection is going to be. Different kinds of data are coming in and everybody is working extremely hard to find out where we are and where we’re going to go, Dr Dang said.

As a precautionary measure Dr Dang emphasised on maximum vaccinations and if required, an additional booster dose to fight against COVID-19. He also strongly advocated following COVID appropriate behaviour.

Unfortunately, a large number of us have lowered our guards. Those guards should be back in place. The promotion should be more stringent now. And of course, most important is that you must make vaccinate as many of our population as possible by both the doses and when required. Even a booster may be in, Dr Dang added.

Also Read: Factbox: State Of Play Of India’s Healthcare Sector Exposed By COVID-19

(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)

NDTV – Dettol have been working towards a clean and healthy India since 2014 via Banega Swachh India initiative, which is helmed by Campaign Ambassador Amitabh Bachchan. The campaign aims to highlight the inter-dependency of humans and the environment, and of humans on one another with the focus on One Health, One Planet, One Future – Leaving No One Behind. It stresses on the need to take care of, and consider, everyone’s health in India – especially vulnerable communities – the LGBTQ populationindigenous people, India’s different tribes, ethnic and linguistic minorities, people with disabilities, migrants, geographically remote populations, gender and sexual minorities. In wake of the current COVID-19 pandemic, the need for WASH (WaterSanitation and Hygiene) is reaffirmed as handwashing is one of the ways to prevent Coronavirus infection and other diseases. The campaign will continue to raise awareness on the same along with focussing on the importance of nutrition and healthcare for women and children, fight malnutrition, mental wellbeing, self care, science and health, adolescent health & gender awareness. Along with the health of people, the campaign has realised the need to also take care of the health of the eco-system. Our environment is fragile due to human activity,  that is not only over-exploiting available resources, but also generating immense pollution as a result of using and extracting those resources. The imbalance has also led to immense biodiversity loss that has caused one of the biggest threats to human survival – climate change. It has now been described as a “code red for humanity.” The campaign will continue to cover issues like air pollutionwaste managementplastic banmanual scavenging and sanitation workers and menstrual hygiene. Banega Swasth India will also be taking forward the dream of Swasth Bharat, the campaign feels that only a Swachh or clean India where toilets are used and open defecation free (ODF) status achieved as part of the Swachh Bharat Abhiyan launched by Prime Minister Narendra Modi in 2014, can eradicate diseases like diahorrea and the country can become a Swasth or healthy India.

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