What is S Gene dropout in Omicron? How can it confirm the presence of Omicron variant; All You Need to Know

Omicron virus symptoms include extreme fatigue, headache and body pain, instead of loss of smell and taste and high body temperature that is generally caused by other COVID Variants. 

What is S-Gene?
What is S-Gene?

S gene dropout: The missing S-gene is one of the proxy indicators for detection and diagnosis of Omicron COVID variant.  Dr. Naveen Dang, Director of Dr Dangs Lab confirmed that genome sequencing can confirm the presence of the new Omicron Covid variant.

As per the latest reports, Omicron virus symptoms include extreme fatigue, headache and body pain, instead of loss of smell and taste and high body temperature that is generally caused by other COVID Variants. This was informed by South African doctor  Dr Angelique Coetzee, who had a major role in the detection of the new COVID variant. 

Read more: SII seeks approval for Covishield vaccine as booster dose amid new variant concerns

Read  more: List of countries where Omicron COVID variant has been detected

What is S-Gene?

S-Gene is one of the S gene targets that is not detected due to mutations. It is termed as S gene dropout or S gene target failure, which is a marker to identify the Omicron variant.

How to detect whether S-gene is missing?

• Omicron covid variant has mutations in the S gene. While the regular RT-PCR kits will be able to identify whether the person is COVID positive or negative, they will not be able to identify if the positive result is due to mutation in the S gene.

• Most tests generally target a large number of genes. Currently, the tests in India test E, N and Rd Rp genes and if one of these genes is identified as positive, the test result would be positive. 

• Most of the tests in India have not been testing the S-gene as there was no need for it earlier. But in the case of a test where there are multiple genes and one of them is included in the SG, if the test comes out positive for all the genes but negative for S-gene, it can be assumed that this is an S-gene dropout or S-gene failure target failure. 

• If this happens, then by default the variant can be identified as Omicron and such sample should be on a priority basis, as per Dr. Dang. 

• Any sample that shows S-gene dropout will then be sent for gene sequencing studies and only after that it will be confirmed whether it is the Omicron variant or not.

Has Omicron been reported in India?

Not yet. India is on high alert in the wake of a rise in the number of countries reporting cases of Omicron, which is currently being reported as the new highly transmissible variant of COVID-19, more contagious than Delta. While few passengers traveling from 'high-risk' countries have tested positive for COVID-19 but no Omicron cases have been reported so far in India.

Omicron Covid variant reportedly has about 50 mutations, out of which almost 30 mutations are in its spike protein, which makes it different from other variants of concern (VoC). 

There is currently very little data on Omicron since it was detected very recently. It is still too early to say how contagious or severe the new Omicron variant is. 

Read more: Omicron Variant of COVID: High Risk Countries List Released by India

Travel bans unfair: UN Chief 

The Omicron variant was first identified in South Africa on November 26, 2021, just a week back. This was followed by countries imposing travel bans on South African nations to stop the spread of the variant.

WHO Director-General criticised the blunt measures stating that they are hurting the economy of the South African nations and penalising them, while instead they should be thanked for identifying and reporting the variant in time. 

UN Secretary-General Antonio Guterres also slammed the travel bans targeting specific countries and regions, calling them "unfair" and "ineffective." He said, "with a virus that is truly borderless, travel restrictions that isolate any one country or region are not only deeply unfair and punitive -- they are ineffective."

The UN Chief instead called for increased testing for travelers. Other experts have also called for vaccination of maximum people with both the doses and strict adherence to COVID protocols to curb the spread of the new strain of COVID-19. 

Read more: COVID ‘Omicron’ Variant: India issues revised guidelines for international arrivals


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