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A new variant of Covid-19 has been detected in SA. Picture: 123RF/PERIG76
A new variant of Covid-19 has been detected in SA. Picture: 123RF/PERIG76

The government will convene a series of high-level meetings at the weekend to discuss how to respond to the detection of a swiftly spreading new coronavirus variant dubbed B.1.1.529, which appears to be driving Gauteng’s rapid increase in cases, health minister Joe Phaahla said on Thursday.

It is too soon to say whether the government would tighten lockdown restrictions or whether the emergence of B.1.1.529 would lead to travel restrictions, but these issues will be discussed by the national coronavirus command council, cabinet and the president’s co-ordinating council, he said.

SA has experienced three waves of coronavirus infections, each more severe than the last. The second wave was driven by the Beta variant, which was more contagious than older lineages, while the third wave was driven by the even more infectious Delta strain. Each surge has seen the government step up its curbs on gatherings, travel and economic activity, with devastating economic consequences.

The latest variant was first identified in Botswana on November 11. It has been confirmed in about 100 samples collected in SA, but hundreds more are being analysed and the figure is expected to rise.

The variant is fuelling a resurgence of cases in Gauteng in the past fortnight and is likely to be circulating in other provinces too, said Stellenbosch University bioinformaticist Tulio de Oliveira.

“We can see it spreading very fast, and we do expect unfortunately to start seeing pressure on the health system in the next few days and weeks,” he said.

Koleka Mlisana, co-chair of the ministerial advisory committee on Covid-19, urged people who are not yet vaccinated to get inoculated as soon as possible. “The only solution we have for the pandemic is vaccination. If we look at the other variants of concern, we have seen that even though vaccines may not protect against infection, they have protected [people] against severe disease, hospitalisation and death,” she said.

Only 35% of SA’s adults are fully immunised, with coverage lowest among younger people: approximately 26% of those aged between 18 and 34 have had at least one vaccine dose, compared to 64% of those aged 60 or above.

A high proportion of the cases recently identified in Gauteng were among younger adults, and work was under way to determine whether they were vaccinated or not, said Mlisana

The upswing in cases was initially clustered in Tshwane, but there is now a sustained increase across all five Gauteng metros, according to analysis from the SA Covid-19 modelling consortium, co-ordinated by the National Institute of Communicable Diseases (NICD).

The new variant has a unique constellation of dozens of mutations, more than 30 of them on the spike protein, which the SARS-CoV-2 virus uses to enter human cells. But it is not yet clear how transmissible it is, whether it is more virulent than older lineages, and the extent to which it is able to evade the immune response triggered by prior infection or vaccination, said University of KwaZulu-Natal infectious disease specialist Richard Lessells.

While many of the mutations have been identified in older variants and are well understood, many others are new, and the full significance of the combination seen in B.1.1.529 is not yet understood, he said.

Researchers have begun laboratory-based studies to try to tease out the implications of B.1.1.529’s mutations, but it will be several weeks before they get results, said NICD senior scientist Penny Moore.

SA has requested a meeting with the World Health Organization (WHO) on Friday to discuss the new variant, and anticipated it would be given a new name based on a letter from the Greek alphabet, said D’Oliveira.

The WHO introduced a naming system based on the Greek alphabet in May, to avoid stigmatising the countries where new variants are first detected.



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