Scientists in South Africa are studying a recently identified new coronavirus variant of concern, stoking fears the country may face a potentially severe fourth wave that could spread internationally.
The new discovery, called B.1.1.529 until a Greek letter is assigned to it by the World Health Organization, carries an unusually large number of mutations and is “clearly very different” from previous incarnations, Tulio de Oliveira, a bio-informatics professor who runs gene-sequencing institutions at two South African universities, said at a briefing on Thursday.
“Here is a mutation variant of serious concern,” Health Minister Joe Phaahla said at the same media event. “We were hopeful that we might have a longer break in between waves — possibly that it would hold off to late December or even next year January.”
Virologists have detected almost 100 cases linked to the variant in the country to date, said Anne von Gottberg, clinical microbiologist and head of respiratory diseases at the National Institute for Communicable Diseases. WHO officials have met to discuss the virus, which has also been detected in Botswana and Hong Kong.
In Botswana — a neighbor of South Africa — the new variant has been detected in vaccinated people, Kereng Masupu, coordinator of the Presidential COVID-19 Task Force, said in statement.
On Friday, the Japanese government announced that it will strengthen its border controls for all arrivals — Japanese and foreign national — from South Africa and five other African countries starting Saturday.
The other nations are Namibia, Botswana, Zimbabwe, Lesotho and Eswatini, formerly known as Swaziland.
Japanese nationals returning home or foreign nationals entering Japan will be required to quarantine at designated facilities for 10 days — the longest in the nation’s quarantine category.
Chief Cabinet Secretary Hirokazu Matsuno told a news conference late Friday that with the possibility that the new variant is more infectious and more resilient against vaccines, Japan is taking its “highest level of precautions.”
The U.K., Singapore and Israel have also taken steps to tighten their borders in the wake of the news.
Two cases of the variant have been found in travelers arriving in Hong Kong. A traveler from South Africa was found to have the variant while the other case was identified in a person quarantined in the hotel room opposite them, the Hong Kong government said late Thursday. That person may have been infected as air flowed between the rooms, according to the government.
The B.1.1.529 variant is likely to have evolved during a chronic infection of an immunocompromised person, possibly in an untreated HIV/AIDS patient, said Francois Balloux, director of the UCL Genetics Institute. With 8.2 million people infected with HIV, the most in the world, South Africa’s efforts to fight the coronavirus pandemic have been complicated, as immunocompromised people can harbor the virus for longer, scientists say. De Oliveira has previously said that the beta variant, a mutation identified last year in South Africa, may have come from an HIV-infected person.
The findings come as several European countries battle a renewed surge in COVID-19 case numbers, with hospitals in some German cities starting to feel the strain. Governments are considering a fresh round of restrictions, largely against the unvaccinated, to try and curb the spread. South Africa is currently on the lowest level of lockdown measures, though the new variant prompted the cabinet and coronavirus council to call a meeting for the weekend.
One key difference is that while European countries have broadly got vaccination levels to a healthy majority and have moved on to booster shots, only about 35% of South African adults are fully inoculated. The health department has even asked Johnson & Johnson and Pfizer Inc. to hold off on new deliveries due to a slump in demand.
The rest of Africa is in an even worse position, with only 6.6% of the continent’s population fully vaccinated, Africa CDC Director John Nkengasong said at a virtual briefing. The challenge of securing supplies has given way to a lack of demand, with about 45% of the 403 million doses delivered to the continent yet to be administered, he said.
South Africa has started to see a renewed surge in COVID-19 case numbers, particularly in the most-populous province of Gauteng. There were 2,465 infections recorded on Thursday, up from fewer than 900 two days previously, with the positivity rate — or the ratio between cases and tests — rising to 6.5%.
Almost 2,000 of the new cases were detected in the hub that includes Johannesburg and Pretoria.
The new variant already accounts for 75% of the genomes tested in the country, De Oliveira said in a later tweet.
While the government opted for a very strict lockdown at the start of the pandemic in March 2020, subsequent curbs have generally been driven by hospitalization rates. A preferred tactic is to ban the sale of alcohol, as it spares health centers from the burden of drink-related accidents and fights.
The outbreak of the new variant is at an early stage and studies are ongoing, but officials “do expect, unfortunately, to start seeing pressure in the health care system in the next few days and weeks,” De Oliveira said.
Following news of the new variant, the U.K. said it will temporarily ban flights from South Africa and five neighboring countries. The travel restrictions were called a precautionary measure to keep the spread of the new variant in check, Health Secretary Sajid Javid said. The six African countries will be placed on the U.K.’s red list as of Sunday, requiring travelers to quarantine in hotels upon arrival. Israel also has banned travel from the six countries, along with Mozambique, another neighbor of South Africa, BNO News said in a tweet, without citing the source of the information.
“As part of our close surveillance of variants across the world, we have become aware of the spread of a new potentially concerning variant,” Javid said in a statement, adding that the new strain it’s now under investigation.
The restrictions come as a further blow to the airline industry, which was starting to recover from earlier travel restrictions and lockdowns but now faces fresh curbs and a resurgent virus in parts of Europe. The measures announced Thursday mark the biggest change in the U.K.’s COVID-19 travel rules since the so-called traffic light system was overhauled earlier in the autumn to ease border crossings.
From 500 to 700 people daily arrive in the U.K. via South Africa on flights, a number that would normally be expected to increase in the next four to six weeks due to seasonal travel.
No cases of the new variant have been identified in the U.K., the health department said.
“Armed by our experience and understanding of the alpha and delta variants, we know that early action is far better than late action,” Ewan Birney, deputy director general of the European Molecular Biology Laboratory, said in a Science Media Center briefing note. “It may turn out that this variant is not as large a threat as alpha and delta, but the potential consequences of not acting on the possibility it could be are serious.”
WHO experts are meeting Friday with authorities from South Africa, according to U.K. officials. It will take several weeks to see the impact of the new variant on hospitalizations and deaths and to study how it may interact with vaccines.
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