A new variant probably responsible for the rise in Covid infections has been identified after the country was left scratching its head when it came weeks after the predicted increase following the superspreader events during elections never happened.
Its current name is B.1.1.529, the new Covid variant detected initially in three cases in Botswana, six in South Africa, and one in Hong Kong in a traveller returning from South Africa.
As of Thursday, South Africa had detected 22 new cases “following genomic sequencing collaborations between the NICD [National Institute for Communicable Diseases] and private laboratories”.
In addition, other NGS-SA laboratories are confirming “more cases as sequencing results come out”.
“Unfortunately, we have detected a new variant which is a reason for concern in South Africa,” said virologist Prof Tulio de Oliveira on Thursday.
“What we have done is to act very quickly … as the cases have just started to increase, to really know what we are facing.
“You have to know the enemy to know what you are fighting.”
In his presentation, De Olivera noted early signs showed the new variant had rapidly increased in Gauteng and may be already present in most provinces.
“We can make some predictions about the impact of mutations in this variant but the full significance is uncertain and vaccines remain the critical tool to protect us against severe disease.”
The Delta variant was first detected in India in December and has since spread across the world.
It was found to be twice as contagious as previous variants and in South Africa wreaked havoc when the third wave hit, harder than the previous two waves.
Infectious Diseases Specialist at the University of KwaZulu-Natal Dr Richard Lessells said on Thursday there was “some concern this variant might not just have enhanced transmissibility but might also be able to get around parts of the protection in our immune system”.
He noted the C.1.2 variant detected a few months ago remained at relatively low levels.
However, in the first two weeks of November, Lessells noted B.1.1.529 was already becoming dominant. Lessells said hundreds of recently collected samples were being sequenced and the results could be available by the end of this week.
Prof Adrian Puren, NICD acting executive director, said it was not surprising the new variant was detected in South Africa.
“Although the data is limited, our experts are working overtime with all the established surveillance systems to understand the new variant and what the potential implications could be,” Puren said.
“Developments are occurring at a rapid pace and the public has our assurance that we will keep them up to date.”
Detected cases and the percentage of people testing positive are both increasing quickly, particularly in Gauteng, North West and Limpopo, said Dr Michelle Groome, head of the NICD’s division of public health surveillance and response.
Provincial health authorities remain on high alert and are prioritising the sequencing of Covid positive samples.
Scientists have warned the new variant, with a “high amount of spike mutations”, could lead to widespread outbreaks of the virus.
Health Minister Joe Phaahla was concerned about the low level of vaccination, meanwhile, with government’s aim of having 70% of the population immunised to avoid a festive season lockdown now a pipe dream.
Meanwhile, Cabinet has approved the extension of the national state of disaster by one month until 15 December, said Minister in the Presidency Mondli Gungubele yesterday during a media briefing.
“These measures continue to assist in the country’s fight to stop the spread of Covid,” Gungubele said.
As of Thursday, South Africa has been in various stages of lockdown for at least 600 days following the declaration of the national State of Disaster by President Cyril Ramaphosa in March 2020.
Ramaphosa then locked the country down for 21 days from 26 March to April 16.
Since then, the economy was brought to its knees under severe lockdown restriction – no open toed sandals allowed – and corruption ran rampant in the health sector, and allegations cost then health minister Dr Zweli Mkhize his job.
The country is currently on adjusted level 1 lockdown, which has eased restrictions on gatherings and people’s movements.
On Wednesday, the NICD reported 1,275 new Covid infections in the country.
This is the highest number of Covid-19 infections that has been recorded since 6 October, just after the country exited the third wave.
“This is not the end of this matter,” Phaahla said.
“We will be discussing this further. As we get more information the necessary structures will meet and decisions will be taken on available information.”