South African authorities reported Thursday that they have detected a new variant of coronavirus in the country that, according to scientists, is worrying due to its high number of mutations and its rapid spread among Gauteng youth, the most populous province, Health Minister Joe Phaahla announced Thursday.
In the last 36 hours after observing an increase in infections in South Africa’s economic center, Gauteng province, scientists detected variant B1.1.529. So far, 22 positive cases have been identified, according to the South African National Institute for Communicable Diseases.
The coronavirus evolves as it spreads, and many new variants, including those with worrisome mutations, often simply disappear. Scientists monitor possible changes that could be more communicable or deadlyBut determining whether the new variants will have an impact on public health can 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 a more exponential increase,” he said, adding that the new variant appears to be driving the increase in cases. Scientists in South Africa are working to determine what percentage of the new cases have been caused by the new variant.
The new variant has also been found in Botswana and Hong Kong in travelers from South Africa, he said.
The World Health Organization 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.
The British government announced that ban flights from South Africa and five other southern African countries beginning at noon on Friday, and that anyone who has recently arrived from those countries will be asked to undergo a coronavirus test.
High number of mutations
UK Health Secretary Sajid Javid said there were concerns that the new variant “could be more transmissible” that 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 Genomic Surveillance Network 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 predicted immune evasion and transmissibility,” de Oliveira said.
“This new variant has many, many more mutations,” including more than 30 in peak protein affecting transmissibility, said. “We can see that the variant is potentially spreading very fast. We hope to start seeing pressure on the healthcare system in the coming days and weeks. “
De Oliveira said that a team of scientists from seven South African universities is studying the variant. They have 100 complete genomes and expect to have many more in the coming days, he said.
“We are concerned about the leap in the evolution of this variant,” he said. The only good news is that it can be detected by a PCR test, he said.
Unusual increase in infections
After a relatively low transmission period in which South Africa recorded just over 200 new confirmed cases per day, last week the daily new cases rose rapidly to more than 1,200 on Wednesday. On Thursday they jumped to 2,465.
The first increase was in Pretoria and the surrounding metropolitan area of Tshwane and appeared to be cluster outbreaks of student gatherings at area universities, Health Minister Phaahla said. Amid the surge in cases, scientists studied genomic sequencing and discovered the new variant.
“This is clearly a variant that we must take very seriously,” said Ravindra Gupta, professor of clinical microbiology at the University of Cambridge. “It has a large number of spike mutations that could affect transmissibility and the immune response.”
Gupta said that South African scientists need time to determine if the increase in new cases is attributable 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 this and getting the world’s attention.”
South African officials had warned that a new resurgence was expected from mid-December to early January and were hoping to prepare for that by vaccinating many more people, Phaahla said.
About the 41% of adults in South Africa have been vaccinated and the number of injections given per day is relatively low, less than 130,000, significantly below target of the government 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 the delivery of about 2.5 million more next week, according to Nicholas Crisp, acting director general of the national health department.
“We are getting vaccines faster than we are using them right now,” Crisp said. “That is why, for some time now, we have been putting off deliveries, not decreasing orders, but simply putting off our deliveries so as not to accumulate 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 date, the delta variant remains by far the most infectious and has displaced other variants that were once of concern, including alpha, beta, and mu. According to the sequences submitted by countries around the world to the world’s largest public database, more than 99% are delta.