Worrying variant of coronavirus, with many unknown mutations, driving resurgence of infections in Gauteng

Worrying variant of coronavirus, with many unknown mutations, driving resurgence of infections in Gauteng
This electron microscope image shows Covid-19 (round gold objects) emerging from the surface of cells cultured in a lab. (Photo: NIAID-RML CC BY 2.0)

A team of scientists in South Africa has identified a variant of the SARS-CoV-2, currently known as B.1.1.529 and also seen in Botswana and Hong Kong, as the possible driver of a sudden and sharp increase in coronavirus cases in Gauteng.

A new variant of SARS-CoV-2, currently only identified as B.1.1.529, has been identified by a team of South African scientists as the driver behind a huge and sudden spike in infections in Gauteng.

“You need to know the enemy that you are fighting,” one of the leading experts in the team, Professor Tulio de Oliveira, said. 

He said that while they are still unsure about the impact some of the mutations will have, they do know some of them and are concerned that this variant will be more transmissible and possibly better at evading some aspects of the body’s immune response.

Working as a collaborative network of scientists they were going as fast as they could to find out what the country was facing. 

Minister of Health Dr Joe Phaahla said the number of positive cases of coronavirus infections has been rising over the past seven to 10 days, with “more of an exponential rise” over the past few days. 

Eight days ago there were 273 new infections in the country. It doubled the next day and on Wednesday, 24 November there were more than 1,000.

Eighty percent of these cases, according to the National Institute for Communicable Diseases (NICD), are found in Gauteng, with the first evidence of a rise in infections seen in Tshwane metro but spreading to other parts of Gauteng, Johannesburg and Ekurhuleni.

Phaahla said they received a briefing on the new variant from De Oliveira’s team on Thursday at 8am.

The team includes scientists at seven universities in South Africa, the National Health Laboratory Service and the NICD, as well as private laboratories.

De Oliveira said the variant doesn’t have a name yet but the World Health Organization will sit on Friday to discuss this. 

Currently labelled as B.1.1.529, the variant, De Oliveira explained, had a very high number of mutations and has also been detected in samples from Botswana and Hong Kong.

He said that while they can make some predictions about the impact of these mutations, vaccines will remain a critical tool to fight them.

“It is very new. Two days ago we found the first signs of it,” he said, describing how they had set up urgent meetings within the hour after finding the new variant in samples.

D’Oliveira said the one good thing about it was that this specific variant can be picked up in PCR testing used to diagnose Covid-19.

He said the reproductive rate of the variant in Gauteng was now 2 – meaning every infected person is transmitting the virus to two others.

“We expect to see a fast increase in cases,” he said.

As a result, the positivity rate had shot up to 30% in some sub-districts of Gauteng.

He said this specific variant had more than 30 mutations on the spike protein. Beta had three and Delta had two. It has 10 mutations just on the part of the virus that binds with the human body.

Infectious disease specialist Dr Richard Lessells said many of the new mutations are not familiar to scientists but the ones they do know were creating concern that the variant was more transmissible and also could find ways to bypass parts of the body’s immune response.

Currently, they were not seeing a similar increase in cases in the rest of the country, but it was possible that this variant was already circulating in large parts of the country.

“There is a lot we don’t understand about it and what it means. We started working on characterising the impact of mutations on the behaviour of the virus. How transmissible is it? How efficiently can it spread?” 

Lessells said one of the key questions was around the severity of disease caused by the virus and they will be looking into it.

“This variant surprised us. It has many more mutations than we expected.”

Phaahla said they were hoping for a longer respite before the fourth wave.

“It reinforces that this invisible enemy is now very unpredictable.”

“This is very fresh news. We got a warning yesterday, met at 8am, had further meetings with the provincial MECs and heads of health departments. There has been no time to really reflect on possible decisions. We wanted this to be confirmed and not rumours,” Phaahla said.

He said the issue will now be discussed further with the coronavirus council, the President and the premiers.

The minister said that only 41% of adults have been vaccinated and the uptake of vaccines remains low at fewer than 130,000, especially in the 18-to-35 age group.

“This outbreak is largely in young people,” he said. “They are at high risk.”

Professor Ann von Gottberg from the NICD said of the 100 specimens they sequenced, 90% had the marker of the new variant and were from Tshwane and Gauteng. 

“There is an increase in other provinces,” she said. 

Professor Penny Moore from the University of the Witwatersrand said it is likely to take weeks to establish the impact of vaccines on the new variant.

“This variant contains a lot we don’t know about,” she added.

Lessells said they also do not know yet if the variant can cause severe disease as they are fooled into thinking that because it is mostly young people who are infected. DM/MC

This article was amended following initial publication to indicate the correct variant, B.1.1.529


"Information pertaining to Covid-19, vaccines, how to control the spread of the virus and potential treatments is ever-changing. Under the South African Disaster Management Act Regulation 11(5)(c) it is prohibited to publish information through any medium with the intention to deceive people on government measures to address COVID-19. We are therefore disabling the comment section on this article in order to protect both the commenting member and ourselves from potential liability. Should you have additional information that you think we should know, please email [email protected]"

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