JOHANNESBURG – A new variant of the coronavirus has been discovered in South Africa, which scientists believe is of concern due to its high number of mutations and rapid spread among young people in Gauteng, the country’s most populous province, Health Minister Joe Phaahla said on Thursday.
The coronavirus continues to develop as it spreads and many new variants, including those with worrying mutations, often simply die out. Scientists are monitoring possible changes that could be more transmissible or deadly, but it can take time to figure out if new variants have public health implications.
South Africa has seen a dramatic increase in new infections, Phaahla said at an online press conference.
“There has been an exponential increase in the last four or five days,” he said, adding that the new variant appears to be driving the increase in some cases. Scientists in South Africa are working to find out what percentage of new cases were caused by the new variant.
Currently identified as B.1.1.529, the new variant was also found in Botswana and Hong Kong among travelers from South Africa, he said.
The World Health Organization’s technical working group is due to meet on Friday to evaluate the new variant and possibly decide whether or not to get a name from the Greek alphabet.
The UK government announced that it would be banning flights from South Africa and five other southern African countries as of Friday lunchtime and that anyone who recently entered from those countries will be asked to take a coronavirus test.
UK Health Secretary Sajid Javid said there were concerns that the new variant “may be more transmissible” than the dominant Delta strain and “the vaccines we currently have may be less effective”.
The new variant has a “constellation” of new mutations, said Tulio de Oliveira from the Network for Genomic Surveillance in South Africa, which has followed the spread of the Delta variant in the country.
The “very high number of mutations is a problem for predicted immune evasion and transmissibility,” said de Oliveira.
“This new variant has many, many more mutations,” including more than 30 of the spike protein that affects transmissibility, he said. “We can see that the variant may spread very quickly. We assume that we will see pressure in the health system in the next few days and weeks. “
De Oliveira said a team of scientists from seven South African universities are studying the variant. They have 100 whole genomes of them and expect to have many more in the next few days, he said.
“We are concerned about the evolutionary leap in this variant,” he said. The good news is that it can be detected by a PCR test, he said.
After a period of relatively low transmission in which South Africa recorded just over 200 new confirmed cases per day, the number of new cases on Wednesday rose rapidly to over 1,200 on Wednesday last week. On Thursday they jumped to 2,465.
The first surge was in Pretoria and the surrounding metropolitan area of Tshwane, and what appeared to be cluster outbreaks of student gatherings at universities in the area, Health Minister Phaahla said. Amid the surge in cases, scientists examined genome sequencing and discovered the new variant.
“This is clearly a variant that we have to take very seriously,” said Ravindra Gupta, professor of clinical microbiology at the University of Cambridge. “It has a high number of spike mutations that could affect transmissibility and the immune response.”
Gupta said scientists in South Africa need time to determine whether the surge in new cases is due to the new variant. “The probability is high,” he said. “South African scientists have done an incredible job of realizing this quickly and making the world aware of it.”
South African officials had warned that a resurgence was expected from mid-December to early January and hoped to prepare for it by vaccinating many more people, Phaahla said.
About 41 percent of South Africa’s adults are vaccinated, and the number of vaccinations per day is relatively low at less than 130,000, well below the government’s target of 300,000 per day.
South Africa currently has about 16.5 million Pfizer and Johnson & Johnson vaccine doses in the country and expects about 2.5 million more in the next week, according to Nicholas Crisp, acting director general of the national health department.
“We’re getting vaccines faster than we are using them right now,” said Crisp. “So we have been postponing deliveries for some time, not fewer orders, but just postponing our deliveries so that we don’t pile up and store vaccines.”
South Africa, with a population of 60 million, has recorded more than 2.9 million COVID-19 cases, including more than 89,000 deaths.
To this day, the Delta variant remains by far the most contagious, and has supplanted other once-worrying variants such as Alpha, Beta, and Mu. According to sequences submitted by countries around the world to the world’s largest public database, more than 99 percent are delta.
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