Another coronavirus variant detected in SA, but no reason to panic, says KRISP director

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  • A new SARS-CoV-2 variant, which has dominated Covid-19 infections in Uganda and Rwanda, has been detected in South Africa
  • The announcement was made by Professor Tulio de Oliveira, director of the KRISP lab
  • However, de Oliveira told Health24 that is not a variant of concern, and that genome surveillance will monitor this and other variants

A new coronavirus variant has been detected in South Africa, Professor Tulio de Oliveira, director of KRISP (Kwazulu-Natal Research Innovation and Sequencing Platform) announced in a tweet last week. The virus genome sample that de Oliveira and his team sequenced has been linked to Nelson Mandela Bay in the Eastern Cape.

The variant, named, A.23.1, originally emerged in Uganda and Rwanda late last year, and is now the dominant variant in these two countries, de Oliveira told Health24. As of today, it has been identified in 17 other countries, including the UK, Canada, the US, and South Africa, he said.

However, de Oliveira stressed that A.23.1 is not a variant of concern (VoC), but a variant of interest. It is being closely monitored by genomic surveillance networks as it has a mutation in a particular position of the spike gene that may make it more transmissible than the original virus variant – but further data are needed. It is also on the World Health Organization’s (WHO) variant watchlist.

Genomic sequencing allows scientists to identify SARS-CoV-2, the virus that causes Covid-19 disease, and monitor how it changes over time into new variants, explains the Centers for Disease Control and Prevention. 

Variants of concern (VoC)

The emergence of new variants was expected as viruses change and adapt in order to survive, Professor Willem Hanekom, director at the Africa Health Research Institute (AFRI) previously told News24.

“If there's an advantage in their change, then that [variant] with the huge advantage will become much more common in society. And they do this because they make mistakes when they replicate and they don't actually have the machinery to fix those mistakes,” he explained.

These "mistakes", Hanekom added, are called mutations – referring to the genetic code of a virus – and when there are many mutations, they are known as variants of concern (VoC).

At present, there are three coronavirus VoC. They are 501Y.V1, first identified in the UK; 501Y.V2 first identified in South Africa; and 501Y.V3, first identified in Japan in travellers from Brazil.

Giving an update on these variants during a webinar last week, de Oliveira, who is also a member of the WHO Virus Evolution group, mentioned that in addition to the three VoC, and the A.23.1 variant of interest, there is another variant of interest that is being closely monitored.

“So in total, you have five variants – two of them [501Y.V1 and 501Y.V2] have been detected in South Africa and are variants of concern, and two are variants of interest, with one of them having been detected in South Africa.”

De Oliveira said the second variant of interest, which was first identified in the UK but later linked to Nigeria, has not been detected in South Africa, but that he and his team are constantly monitoring it. “That’s why it’s important to do this genomic surveillance weekly,” he said.

New variant must be monitored

In a paper published in preprint server medrxiv last week, researchers noted that while the impact of the A.23.1 variant is not yet clear, it is essential to continue careful monitoring of this variant.

If A.23.1 increases in circulation, it will mean that it has a clear advantage over previous variants and will end up dominating infections in East Africa, said de Oliveira. However, he added that it will likely be responsible for a minority of infections in South Africa.

READ | Coronavirus variants update: One has spread to over 90 countries, two on WHO watchlist

READ | Covid-19 immunity: New coronavirus variant increases risk of reinfection, says local expert

READ | 'Calling it the SA variant is a stigmatising approach' - Prof Salim Abdool Karim on 501Y.V2

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