South Africa Identifies New Variant of Coronavirus

JOHANNESBURG — A concerning new variant of the coronavirus, whose mutations evidence a “big jump in evolution,” is driving a spike in new Covid-19 infections in South Africa, scientists said on Thursday.

In the last 36 hours after observing an increase in infections in South Africa’s economic hub, the Gauteng province, scientists detected the B1.1.529 variant. So far, 22 positive cases have been identified in South Africa, according to South Africa’s National Institute for Communicable Diseases.

Since the onset of the pandemic, a number of variants have emerged. One underlying concern about new variants is whether they will stymie progress against the pandemic or whether they will limit the vaccine’s effectiveness. South African scientists will meet with the World Health Organization technical team on Friday, where authorities will assign a letter of the Greek alphabet to this one.

Botswana’s health ministry confirmed in a statement that four cases of the new variant were detected in people who were all fully vaccinated. All four were tested before their planned travel. One sample was also detected in Hong Kong, carried by a traveler from South Africa, South African scientists said.

With over 1,200 new infections, South Africa’s daily infection rate is much lower than in Germany, where new cases are driving a wave. However, the density of mutations on this new variant raises fears that it could be highly contagious, leading scientists to sound the alarm early.

“This variant did surprise us, it has a big jump in evolution, many more mutations than we expected, especially after a very severe third wave of Delta,” said Tulio de Oliveira, director of the KwaZulu-Natal Research and Innovation Sequencing Platform.

The B1.1.529 variant has a “very unusual constellation of mutations,” with more than 30 mutations in the spike protein alone, said Mr. de Oliveira. On the ACE2 receptor — the protein that helps to create an entry point for the coronavirus to infect human cells — the new variant has 10 mutations. In comparison, the Beta variant has three, the Delta variant has two, said Mr. de Oliveira.

Displaying mutations that might resist neutralization, scientists are also still unclear how effective existing vaccines will be against the new variant. The variant shares similarities with the Lambda and Beta variants, which are associated with an innate evasion of immunity, said Richard Lessells, an infectious diseases specialist at the KwaZulu-Natal Research and Innovation Sequencing Platform.

“All these things are what give us some concern that this variant might have not just enhanced transmissibility, so spread more efficiently, but might also be able to get around parts of the immune system and the protection we have in our immune system,” said Mr. Lessells.

The new variant has largely been detected among young people, the cohort that also has the lowest vaccination rate in South Africa. Just over a quarter of those ages between 18 and 34 are vaccinated, said Dr. Joe Phaahla, the country’s minister of health.

While cases of the new variant are mainly concentrated in the country’s economic hub, particularly in the capital Pretoria, it is “only a matter of time” before the virus spreads across the country as schools close and families prepare to travel for the holiday season, said Mr. Phaahla.

Alexandra E. Petri contributed reporting.

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