• The latest data shows that South Africa's new Covid-19 variant has been found in almost 80% of samples from South Africa's coronavirus hotspots.
  • For the first time, the new variant also dominates in samples from KwaZulu-Natal, which now has the most active cases in the country.  
  • SA's lead genomic scientist says this is concerning, and that the new variant is now clearly driving the Covid surge in SA. 
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Over the past week, new data confirmed that South Africa’s Covid-19 variant is now also dominating genetic samples from KwaZulu-Natal, says Professor Tulio de Oliveira, director of the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP). KRISP coordinates the nationwide analysis of genetic samples of the virus.

"This is worrisome,” he told Business Insider SA, noting that the province now has the most active cases (more than 46,700) in the country.

READ | SA's Covid variant: How much more transmissible it may be, and what it could mean for vaccines

"We risk that the South African variant could be similar to the UK one, which may be 40% to 70% more transmissible than the original virus, De Oliveira said.

He says the new variant is now clearly driving the current coronavirus surge in South Africa, and warned that the health system is already close to breaking point. If urgent measures weren’t taken, hospitals will be overwhelmed, he added.

Earlier this month, KRISP confirmed the emergence of a new variant – called 501.V2 - which has 20 new mutations, eight of them in the main protein of the virus, the spike protein.

Scientist found that the new variant probably emerged from Nelson Mandela Bay, then spread through the Eastern Cape, to the Garden Route, and into KwaZulu-Natal.

The latest KRISP analysis of virus genomes from these areas found that the new variant was present in 79% of samples. For the first time, it also dominates in KZN.

While genomic sequencing data has not been released from Gauteng, De Oliveira expects that the new variant will also dominate samples there by the first week of January.

The new variant shares one key mutation with a new variant in the UK, the mutation 501Y, which has spread to a number of countries across the world.

But the South African variant has two mutations not present in the UK variant, which could interfere with antibody production and could have consequences for vaccine efficacy.

Cases of the South African variant have also been identified in the UK, which moved that country to ban air travel from South Africa. Another case of the South African variant has been confirmed in Switzerland as well, De Oliveira says.

"The UK variant, which dominates infection in London, [the 501Y.V1 (or B.1.1.7)] has already been found in more than 15 countries, which suggests that this will be initially the most widespread 501Y variant in the world as London is much more connected to the world than South Africa," he added.

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