Home South African KZN research team discovered new Covid-19 variant

KZN research team discovered new Covid-19 variant


The KZN Research Innovation and Sequencing Platform has discovered a new variant that is driving the second Covid-19 wave washing across the nation.

Professor Tulio de Oliveira the director of Krisp and leader of the team that discovered the new, dominant Covid-19 variant. Picture: Motshwari Mofokeng / ANA

DURBAN – A KZN team who discovered the 501.V2 variant of Covid-19, which experts describe as highly transmissible, say it is the driving force behind the country’s second wave and is making young and once healthy people now severely ill.

The announcement was made by Health Minister Zweli Mkhize, ministerial advisory committee co-chair Professor Salim Abdool Karim and Professor Tulio de Oliveira, the director of the KwaZulu-Natal Research Innovation and Sequencing Platform (Krisp), on Friday.

The professors emphasised that the discovery was not a new strain but a variant of the same virus that has multiple mutations. This was uncharacteristically high for a variant, and allows for easier binding within the human body.

De Oliveira and his Krisp team made the discovery with the use of genomic sequencing that they say they hoped could teach them more about Covid-19. They have sequenced hundreds of samples from across the country since the pandemic began in March.

“Genomic sequencing is vital to understand Covid-19. In the first wave, it was clear there were a few variants that accounted for more cases than others but these were nowhere near as dominant as the new variant. This new lineage appeared very quickly and started dominating almost all the genomes we analysed from the past two months. Ninety percent of this second wave is dominated by this single lineage, yet in the first wave, three or four lineages accounted for between a third to 40% of all cases,” he said.

De Oliveira said scientists did not know where it originated but knew it began spreading rapidly in Nelson Mandela Bay, then moved down the Garden Route and was also dominant in Gauteng and the Western Cape.

“The next steps are to gather further clinical and epidemiological evidence as well as expanding and strengthening genomic surveillance. We intend to intensify sampling in the Eastern Cape, Western Cape and KwaZulu-Natal to understand the persistence of this lineage. We should also expand sampling to assess the extent of its dissemination within the country and link with clinical investigations of suspected re-infections and severe disease development,” he said.

Karim added that while the discovery was still new and more time was needed, teams were already putting in hours to answer some of the more burning questions.

“We don’t know where it came from or why it formed and why, in Nelson Mandela Bay. It is also too early to tell if it is more severe, will re-infect those who were infected by the first wave or if the current vaccines will work against this variant. But what remains known are the isolation period and preventative measures, like mask-wearing, social distancing and sanitising. We will also continue with vaccine plans.”

Mkhize said De Oliveira and his genomics team shared their findings with the World Health Organisation and the scientific community at large.

He said it was the Krisp team which alerted the the UK to the 501.V2 variant, which prompted them to study their own samples and later found that a similar mutation was the variant that drove their resurgence in London.

“This led to a UK parliamentary announcement and the institution of a lockdown on Wednesday in London, to curb the spread of this variant. This is the calibre of our scientists,” said Mkhize.

Mkhize said no further lockdown recommendations were made to Ramaphosa and that current regulations remained.

“We did not expect the second wave to emerge so quickly or to come during the festive season, which is one of the worst periods, as holiday behaviour could increase infections. Complacency has set in and people have grown tired of adhering to regulations,” he said.

Mkhize lambasted the country’s youth for negligent behaviour in circulating videos depicting drinking and a lack of mask-wearing and social distancing, which could increase infections.

“A bump in infections was experienced when citizens travelled this holiday season. We expect another bump in January when return travel commences.”

Blade Nzimande, Minister of Higher Education, Science and Technology, said a budget of R45 million was requested to continue further research and studies but only R25 million would be allocated.