New covid variant
A new Covid variant has been identified in South Africa. What’s different about the Omicron variant of Covid-19? Are the symptoms different? What precautions should one take? What has the WHO said?
The Network for Genomics Surveillance in South Africa (NGS-SA) identified the variant on Monday. It detected a group of related SARS-CoV-2 viruses, which belong to a lineage named B.1.1.529.
Early indications are that this variant is possibly even more transmissible than the highly infectious Delta variant and that current vaccines may be less effective against it.
This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa.
Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated 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 a 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.
How is India responding to the new covid variant?
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 Ministry 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 travelers 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.
So, what do we know new covid variant?
The variant has been named Omicron by the World Health Organization, following the pattern of Greek code names like the Alpha and Delta variants.
It is also incredibly heavily mutated. Prof Tulio de Oliveira, the director of the Centre for Epidemic Response and Innovation in South Africa, said there was an “unusual constellation of mutations” and that it was “very different” to other variants that have circulated.
“This variant did surprise us, it has a big jump on evolution [and] many more mutations that we expected,” he said.
In a media briefing, Prof de Oliveira said there were 50 mutations overall and more than 30 on the spike protein, which is the target of most vaccines and the key the virus uses to unlock the doorway into our body’s cells.
Zooming in even further to the receptor binding domain (that’s part of the virus that makes first contact with our body’s cells), it has 10 mutations compared to just two for the Delta variant that swept the world.
This level of mutation has most likely come from a single patient who was unable to beat the virus.
A lot of mutation doesn’t automatically mean: bad. It is important to know what those mutations are actually doing.
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