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Explained | What is the new coronavirus variant in South Africa?

People with masks walking at a shopping mall,= in Johannesburg, South Africa, on November 26, 2021. Advisers to the World Health Organization are holding a special session on Friday to flesh out information about a worrying new variant of the coronavirus that has emerged in South Africa, though its impact on COVID-19 vaccines may not be known for weeks.   | Photo Credit: AP

What do we know about Omicron, the new coronavirus variant in South Africa?

Formally known as B.1.1.529, the World Health Organisation had designated it as a Variant of Concern, that indicates it is quite likely to be extremely transmissible and potentially replace the dominant  Delta variant. Though knowledge on it is still nascent, researchers across the world have been pointing to the variant having an unusually large number of mutations that in theory could make them more transmissible. B.1.1.529 variant has about 50 mutations overall, including more than 30 on the spike protein alone. The spike protein is the part of the virus that latches on to the surface of the human cell and is the most conspicuous part of the virus. The existing vaccines are designed to target the spike protein and the more mutations there are on them, the greater the odds that the virus has the ability to evade them.

Explained | Understanding the Omicron variant of coronavirus

How widespread is it?

The WHO has now designated this variant as 'Omicron' following the convention of naming variants for Greek alphabets such as Delta, Gamma and Alpha. This is based on the extent of its spread, its severity and how quicky it can transmit. The South African Health Ministry said in a briefing that the variant so far has been found in Botswana, South Africa and Hongkong, from traveller returning from South Africa. Ten cases have so far been confirmed. In South Africa, the most cases are from Guateng province where in Tshwane, part of Guateng, test positivity in the last three weeks has risen from 1% to 30%. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021.

The current analysis suggests that in that region, the new variant maybe taking over the dominant Delta variant as well as another prominent variant called C.1.2.

 

How is India responding?

So far no cases have been reported and there are no direct flights between India and South Africa. However with the global easing of travel restrictions it wouldn't be surprising if cases eventually pop up here. The Ministry of Health and Family Welfare issued an alert late Thursday asking for more vigilance at airports.

" This variant is reported to have a significantly high number of mutations, and thus, has serious public health implications for the country, in view of recently relaxed visa restrictions and opening up of international travel," the Health Ministry said in its statement.

It has directed that travellers from South Africa and transiting between the countries where cases have been detected must be screened and those who test positive must have their samples sent to the India Sars Cov2 genome consortium (Insacog) by authorities. The INSACOG is a cluster of labs across the country that sequence a percentage of positive coronavirus samples to determine its variant.

India didn't report many cases of the Beta variant (B.1.351) that too was first identified in South Africa in October 2020 and was ultimately reported in at least 100 countries. This too was a threatening variant that was responsible for large surges in Africa but was eventually replaced by the Delta variant.

Beta was known to reduce the efficacy of vaccines and it remains to be seen what effects B.1.1.529 poses on this front.

Several labs have said that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.


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Printable version | Jan 18, 2022 10:07:59 AM | https://www.thehindu.com/news/international/explained-what-is-the-new-coronavirus-variant-in-south-africa/article37704642.ece

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