South African scientists detect new virus variant amid spike

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JOHANNESBURG — A new coronavirus disease has been detected in South Africa, scientists say is a concern because of its high number of mutations in the country’s most populous province, Gauteng, and its rapid spread among young people. Minister Joe Fahla made the announcement on Thursday.

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The coronavirus evolves as it spreads and many new forms, including those with worrying mutations, often die. Scientists monitor potential changes that could be more transmissible or lethal, but finding out whether the new forms will have an impact on public health may take time.

Fahla said in an online press briefing that there has been a dramatic increase in new infections in South Africa.


“In the last four or five days, there has been a rapid increase,” he said, adding that the new variant is driving a spike in cases. Scientists in South Africa are working to determine what percentage of new cases are caused by the new variant.

Currently identified as B.1.1.529, the new variant has also been found in South African travelers in Botswana and Hong Kong, he said.

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The World Health Organization’s technical working group was due to meet on Friday to assess the new version and may decide whether to give it a name from the Greek alphabet.

The British government announced that it is banning flights from South Africa and five other southern African countries and anyone who has recently arrived from those countries will be asked to take a coronavirus test.

UK Health Secretary Sajid Javid said the new variant “may be more permeable” than the dominant Delta strain, and “the vaccines we currently have may be less effective” against it.

The new variant has a “constellation” of new mutations, said Tulio de Oliveira of the Network for Genomic Surveillance in South Africa, who has tracked the spread of the delta variant in the country.

“The very high number of mutations is a concern for presumed immune evasion and transmissibility,” de Oliveira said.

“This new variant has many, many more mutations,” he said, “which includes more than 30 spike proteins that affect transmissibility.” “We can see that version potentially spreading very rapidly. We expect to start seeing pressure in the healthcare system over the next few days and weeks.”

De Oliveira said a team of scientists from seven South African universities is studying the variant. He said that he has 100 full genomes of it and many more are expected in the next few days.

“We are concerned about the jump in development in this version,” he said. He said that the good news is that it can be detected by PCR test.

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After a period of relatively low transmission, in which South Africa recorded just over 200 new confirmed cases per day, daily new cases rose sharply over the past week to more than 1,200 on Wednesday. They jumped to 2,465 on Thursday.

Health Minister Fahla said the first surge was in Pretoria and the surrounding Tshwane metropolitan area and that the cluster outbreak appeared from student gatherings at the region’s universities. Amid a surge in cases, scientists studied genomic sequencing and discovered the new variant.

“This is clearly the type that we need to be very serious about,” said Ravindra Gupta, professor of clinical microbiology at the University of Cambridge. “It has a high number of spike mutations that can affect transmission and the immune response.”

Gupta said scientists in South Africa needed time to determine whether the increase in new cases was due to the new variant. “There is a high probability that this is the case,” he said. “South African scientists have done an incredible job of quickly identifying it and bringing it to the attention of the world.”

Fahla said South African officials had warned that a new resurgence was expected from mid-December to early January and that many more people were expected to make up for it by getting vaccinated.

About 41% of South African adults have been vaccinated and the number of shots given per day is relatively small, at less than 130,000, well short of the government’s target of 300,000 per day.

South Africa currently has about 16.5 million doses of vaccines by Pfizer and Johnson & Johnson in the country and about 2.5 million more are expected to be delivered in the next week, according to Nicholas Crisp, the acting director general of the National Department of Health.

“We are getting vaccines faster than we are currently using,” Crisp said. “So for a while now, we’re postponing deliveries, not reducing orders, but just postponing our deliveries so that we don’t hoard and stock 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 date, the Delta variant remains by far the most infectious and has crowdsourced other once-worrisome variants including Alpha, Beta and MU. More than 99 percent are deltas, according to sequences submitted by countries around the world in the world’s largest public database.

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