South African researchers discover a new variant of COVID-19

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A new variant of coronavirus has been discovered in South Africa, which researchers say is a cause for 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 virus that causes COVID-19 develops as it spreads and many new variants, including those with disturbing mutations, often just die out. Researchers are monitoring possible changes that may be more transmissible or fatal, but finding out if new variants will have an impact on public health may take time.

South Africa has seen a dramatic increase in new infections, Phaahla said at an online press conference.

“In the last four or five days, there has been more of an exponential increase,” he said, adding that the new variant seems to be driving the peak in cases. Researchers in South Africa are working to determine what proportion of the new cases have been caused by the new variant.

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

The World Health Organization’s technical working group will meet on Friday to evaluate the new variant and can decide whether or not to give it a name from the Greek alphabet – which is how the WHO names variants of interest and variants of concern.

Britain bans flights from South African countries

The British government announced that it is banning flights from South Africa and five other South African countries with effect from 12.00 local time on Friday, and that everyone who had recently arrived from these countries would be asked to do a coronavirus test.

Britain’s Health Minister 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” against it.

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

A health worker is preparing a dose of the Pfizer virus vaccine at a drive-thru vaccination center outside Johannesburg, South Africa, in May last year. About 41 percent of adults in South Africa have been vaccinated. (Themba Hadebe / Associated Press)

The “very high number of mutations is a problem for predicted immunosuppression and transmittance,” de Oliveira said.

“This new variant has many, many more mutations,” including more than 30 of the nail protein that affects its ability to transmit, he said. “We can see that the variant is potentially spreading very quickly. We expect to start seeing pressure in healthcare in the next few days and weeks.”

De Oliveira said a team of researchers from seven South African universities is studying the variant. They have 100 whole through of it and expect to have many more in the next few days, he said.

“We are concerned about the leap in evolution in this variant,” he said. One part of the good news is that it can be detected by a PCR test, he said.

New cases of covid-19 are increasing

After a period of relatively low transmission where South Africa registered just over 200 new confirmed cases per day, during the past week the daily new cases increased rapidly to more than 1,200 on Wednesday. On Thursday, they jumped to 2,465.

The first increase took place in Pretoria and the surrounding Tshwane metropolitan area and appeared to be cluster outbreaks from student gatherings at universities in the area, said Health Minister Phaahla. In the midst of the increase in cases, researchers studied the genomic sequencing and discovered the new variant.

“This is clearly a variant that we must be very serious about,” said Ravindra Gupta, a professor of clinical microbiology at the University of Cambridge. “It has a large number of nail mutations that can affect transmittance and immune response.”

Gupta said that researchers in South Africa need time to determine whether the increase in new cases can be attributed to the new variant. “It is very likely that this is the case,” he said. “South African researchers have done an incredible job of quickly identifying this and drawing the world’s attention to it.”

South African officials had warned that a new upswing was expected from mid-December to early January and had hoped to prepare for it by getting many more people vaccinated, Phaahla said.

Vaccination rate below government targets

About 41 percent of South Africa’s adults have been vaccinated and the number of injections given per day is relatively low, less than 130,000. This is well below the government’s target of 300,000 per day.

South Africa currently has about 16.5 million doses of vaccine, by Pfizer and Johnson & Johnson, in the country and expects delivery of about 2.5 million more by next week, according to Nicholas Crisp, acting director general of the national health department.

“We are getting vaccines faster than we are currently using them,” Crisp said. “So for some time now we have been postponing deliveries, not reducing orders, but just postponing our deliveries so that we do not collect and store vaccines.”

South Africa, with a population of 60 million, has registered more than 2.9 million COVID-19 cases – including more than 89,000 deaths.

To date, the delta variant is still by far the most contagious and has displaced other once disturbing variants including 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 participating.

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