COVID variant: Newly discovered strain leads to dramatic increase in cases in South Africa

JOHANNESBURG – A new variant of coronavirus has been discovered in South Africa, which researchers say is a 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 evolves as it spreads, and many new variants, including those with worrying mutations, often just die out. Researchers are monitoring for possible changes that may be more transmissible or fatal, but it may take time to find out if new variants will have an impact on public health.

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

“Over the last four or five days, there has been more of an exponential increase,” he said, adding that the new variant appears to be driving the peak in cases. Researchers in South Africa are working to determine what percentage of the new cases are 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 WHO Technical Working Group is due to meet on Friday to assess the new variant and can decide whether or not to give it a name from the Greek alphabet.

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

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

“This new variant has many, many more mutations,” including more than 30 to the tip protein that affect transmissibility, he said. “We can see that the variant is potentially spreading very fast. We expect to start seeing pressure in healthcare over 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 genomes of it and expect to have many more in the next few days, he said.

“We are concerned about the leap in development in this variant,” he said. The one good news is that it can be detected by a PCR test, he said.

After a period of relatively low transmission, with South Africa registering just over 200 new confirmed cases a day, daily new cases rose rapidly to more than 1,200 on Wednesday in the past week. On Thursday, they jumped to 2,465.

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

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

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

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

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

South Africa currently has about 16.5 million doses of vaccines from 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 get vaccines faster than we currently use them,” Crisp said. “So for some time now we have been postponing deliveries, not reducing orders, but simply postponing our deliveries so we are not accumulating and stocking 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 remains by far the most contagious and has displaced other once worrying 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% are delta.


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