Covid-19 “super variant” surging in Gauteng — may be all over South Africa

Epidemiologists and virologists in South Africa have raised the alarm over a new Covid-19 variant first detected in Botswana, and found to have a heavy presence in South Africa.

Dubbed B.1.1.529, Imperial College London virologist Tom Peacock highlighted that the new variant contains a high number of mutations, including more than 30 in the spike protein.

This raised concerns that it may be more resistant to immune cells that attack the virus, and potentially more infectious.

The Department of Health, in conjunction with the National Health Laboratory Service (NHLS), held a media briefing on Thursday regarding the latest data gathered on the new variant.

Experts on the panel indicated that early signs show that infections of the new variant have increased rapidly in Gauteng. According to Tulio de Oliveira, the KRISP director at the University of KwaZulu-Natal, it is likely already present in other provinces.

According to Anne von Gottberg of the National Institute For Communicable Diseases (NICD), more than 100 genomes of the variant have been identified in South Africa.

The majority of these genomes are identified to have originated in Tshwane and other areas of Gauteng.

South Africa’s reproductive number for Covid-19 has increased to 1.47 (1.94 in Gauteng), and we are likely to see a rapid increase in cases over the coming weeks.

The reproductive number essentially indicates how many people each Covid-positive patient infects. If it is greater than 1, it means infections are expected to grow.

Internationally, South Africa has the highest number of confirmed cases (n=100) of this variant, with four identified in Botswana and one in Hong Kong.

The B.1.1.529 variant is predicted to have enhanced transmissibility, but its full significance is still uncertain.

One of the concerning aspects of this variant is the number of mutations within its genome, with nine mutations in the receptor-binding domain (RBM) alone.

As a comparison, the Beta variant had three mutations to the RBM, and the Delta variant had two.

This is concerning as mutations to the RBM are often associated with immune resistance.

De Oliveira said that mutations to the spike protein genome have allowed the variant to be identified by a particular PCR assay, which helps understand the variant’s spread throughout the country.

The NHLS team has noticed a rapid rise in positive tests showing the presence of this spike protein since the variant was first identified on Tuesday, 23 November.

While the B.1.1.529 variant is concerning, there is still a lot that is not understood, such as:

  • The transmissibility of the variant — the spike protein flagged in PCR assays is helping to develop an understanding of the variant’s transmissibility
  • The protection provided by vaccines against the variant
  • The risk of reinfection
  • Disease severity in both the vaccinated and unvaccinated

“We can make some predictions about the impact of mutations in this variant, but the full significance is uncertain, and the vaccines remain critical,” said Tulio de Oliveira, Director of the Centre for Epidemic Response & innovation.

“We expect to see an increased pressure in public healthcare over the coming weeks,” he added.

Members of the South African Department of Health and the NHLS team will meet with the World Health Organisation (WHO) representatives tomorrow.

“Probably by tomorrow, we will have one of the greek variant names to help us use the terminology,” said Richard Lessells, doctor of Infectious Diseases and HIV/TB researcher at the University of KwaZulu-Natal.


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Covid-19 “super variant” surging in Gauteng — may be all over South Africa