The National Institute for Communicable Diseases (NICD) has announced the detection of a new Covid-19 strain in South Africa with one of the highest number of mutations.

The institute said 22 positive cases of the new variant have been recorded in the country following genomic sequencing. While South Africa’s Health Minister Joe Phaahla said the variant was behind an “exponential” increase in reported cases, making it “a major threat”.

What do scientists know about the new variant?

Scientists have said that the new COVID-19 variant, called B.1.1.529, has a very unusual constellation of mutations, which could help it evade the body’s immune response and make it more transmissible.

The new variant has more than 30 mutations to the spike protein, compared to the Beta and Delta variants which have 2 and 3 mutations respectively. These mutations in the spike protein of the virus that helps to create an entry point for the coronavirus to infect human cells.

Tulio de Oliveira, director of the KwaZulu-Natal Research and Innovation Sequencing Platform, said the variant has baffled experts. “It has a big jump in evolution, many more mutations than we expected,” de Oliveira said.

“The one piece of good news is that it can be detected by a PCR test”, de Oliveira added.

The mutations are associated with increased antibody resistance, which makes the virus more contagious.

The World Health Organisation (WHO) said it is “closely monitoring” the reported variant and is expected to meet on Friday to determine if it should be designated a variant of “interest” or of “concern”.

Have infection rates increased?

The number of daily infections in Africa’s hardest-hit country has increased 10-fold since the start of the month.

The NICD said the number of detected cases and the percentage testing positive are “increasing quickly” in three of the country’s provinces, including Gauteng.

The country’s daily number of infections hit 1,200 on Wednesday, up from 106 earlier in the month.

Before the detection of the new variant, authorities had predicted a fourth wave to hit South Africa ahead of the festive season, starting about the middle of December.

South Africa has the highest pandemic numbers in Africa with approximately 2.95 million cases and a death toll of 89,657.

Are COVID-19 vaccines effective against the new variant?

COVID-19 vaccines are based on the original coronavirus spike protein, raising concerns that the new dramatically different spike protein could render vaccines less effective.

“It will take a few weeks for us to understand what impact this variant has on any potential vaccines,” Van Kerkhove, head of Emerging Diseases and Zoonosis at WHO said when asked about the efficacy of existing vaccines against the new strain.

Any new variant that can evade vaccines or spread faster than the now-dominant Delta variant might pose a significant threat as the world emerges from the pandemic.

Detection and response

The variant has spread rapidly through the Gauteng province of South Africa, home to the economic hub Johannesburg and the capital Pretoria.

A total of about 50 confirmed cases have been identified in South Africa, Hong Kong and Botswana. The confirmed cases in Botswana and Hong Kong were detected among travellers from South Africa.

In response, Britain banned all travel from the country and five other southern African nations, namely Botswana, Eswatini, Lesotho, Namibia and Zimbabwe starting at noon local time on Friday.

Israel also announced on Thursday it was barring its citizens from travelling to South Africa. It also included Lesotho, Botswana, Zimbabwe, Mozambique, Namibia and Eswatini to its highest-risk travel list.

On Friday, the Israeli Health Ministry said a new coronavirus variant had been detected in a traveller who returned from Malawi.

EU Commission chief Ursula von der Leyen also said the EU will aim to halt air travel from the southern African region.