A new Covid-19 variant that poses cause for concern in South Africa has been identified, with the majority of cases recorded in Gauteng.
While the full significance remains uncertain at this stage, the new variant, with the lineage B.1.1.529, “has a high number of adaptations with a concern for predicted immune evasion and transmissibility”, the director of the KwaZulu-Natal Research and Innovation Sequencing Platform (Krisp), Tulio de Oliveira, told a media briefing on Thursday.
The National Institute for Communicable Diseases (NICD) said it could confirm 22 positive cases of the variant as of Thursday. The department of health, together with leading scientists, hosted the urgent virtual news conference after reports of the possible new variant emerged.
Oliveira said there had been quick action following the detection of the variant, and that experts were researching a possible cluster outbreak in Gauteng.
“What is very clear, recent data from detailed analysis show that in many areas of Gauteng, in the city of Johannesburg, we see in the last two days, this fast increase of infections, with a sustainable increase,” he said.
Drawing from data analysis, Oliveira said there was evidence of a “very unusual constellation of mutations” in the genomes of the variant, adding however that the full significance was still uncertain. The B.1.1.529 variant, which has also been recorded in neighbouring Botswana and further afield in Hong Kong, has more than 30 mutations.
Putting this in perspective, Oliveira noted that the Beta variant had three mutations and the Delta two, adding: “This new variant has 10 mutations just at the receptor-binding domain. And despite having over 30 mutations, [it is] very different from other circulating variants that were assigned a variant of interest.”
Oliveira added that not all mutations had been well characterised, and that vaccines remained the critical tool to protect people against the virus.
In a statement, acting NICD executive director Professor Adrian Puren said it was not surprising that a new variant had been detected in South Africa.
“Although the data are limited, our experts are working overtime with all the established surveillance systems to understand the new variant and what the potential implications could be. Developments are occurring at a rapid pace and the public has our assurance that we will keep them up to date,” Puren said.
Stakeholders are meeting the World Health Organisation technical working group on Friday, and expect to assign a Greek name for the new variant then.
South Africa has recorded a sharp increase in new Covid-19 infections in the past eight days. Detected cases and the percentage of positive tests is rising quickly, particularly in Gauteng, the North West and Limpopo.
Health Minister Dr Joe Phaahla told Thursday’s media briefing that there had been an “exponential rise” in new infections, “starting about eight days ago, where we had the total daily infections of 273 positive cases, rising steadily the next day to almost double to 700 and 800”.
“As of yesterday [Wednesday], we passed the 1 000 mark at over 1 200 positive cases,” he added. Of the newly reported infections, 80% were detected in Gauteng.