South Africa detects a new variant

Scientists in South Africa (SA) on Thursday identified a concerning new coronavirus variant with mutations that one scientist said marked a “big jump in evolution,” prompting several countries to quickly limit travel from the region.

Within hours, Britain, Israel and Singapore had restricted travel from South Africa and some neighboring countries, citing the threat of the new variant. By Friday, markets were down in Japan in response to the discovery, and officials in Australia and in New Zealand said that they were monitoring the new variant closely.

The European Commission will also propose restricting air travel to the bloc from southern Africa based on concerns over the variant, Ursula von der Leyen, the commission’s president, said in a Twitter post on Friday. She referred to it by its scientific name, B.1.1.529.

In the past two days, scientists detected the variant after observing an increase in infections in South Africa’s economic hub surrounding Johannesburg. So far, 22 positive cases have been identified in the country, according to South Africa’s National Institute for Communicable Diseases. Two cases were detected in Hong Kong, both apparently linked to someone who had traveled from South Africa. No cases have been detected yet in Britain.

A number of variants have emerged since the onset of the pandemic. One underlying concern about them is whether they will stymie the fight against the virus or limit the effectiveness of vaccines. South African scientists will meet with the World Health Organization technical team on Friday to discuss the new variant, and the authorities will assign it a letter of the Greek alphabet.

But governments are not waiting to impose restrictions. By Thursday evening, Britain had banned flights from South Africa, Botswana, Eswatini, Lesotho, Namibia and Zimbabwe, starting at noon local time on Friday. The six nations will be added to the country’s red list, which would require British travelers coming from those nations to quarantine on arrival.

“More data is needed but we’re taking precautions now,” Sajid Javid, the health secretary, said on Twitter.

In a statement posted Friday on a government website, South Africa said it would urge Britain to reconsider the measure, saying: “The U.K.’s decision to temporarily ban South Africans from entering the U.K. seems to have been rushed, as even the World Health Organization is yet to advise on the next steps.”

Within a few hours, officials from Israel and Singapore had announced that they, too, would add the same countries to their red lists, along with Mozambique.

In December 2020, South Africa was the first nation to report the appearance of the Beta variant, which has now spread to nearly 70 countries. Scientists have been concerned that some clinical trials have shown that vaccines offer less protection against the Beta variant. Since then, the more virulent and aggressive Delta variant has spread all over the world and is believed to be fueling the latest surge in cases.

The variant has also been identified in Botswana. The country’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.

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.The variant has also been identified in Botswana. The country’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.

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, Mr. de Oliveira said. 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.Scientists are still unclear on how effective existing vaccines will be against the new variant, which displays mutations that might resist neutralization.

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,” Mr. Lessells said.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 in South Africa 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, Mr. Phaahla said.