South Africa discovers a new type of coronavirus amid a spike in cases
On Thursday, Health Minister Joe Vahla announced the discovery of a new type of coronavirus in South Africa, which scientists say is a cause for concern due to the high number of mutations and its rapid spread among young people in Gauteng, the country’s most populous province.
Corona virus evolves as it spreads and many new variants, including those with worrying mutations, often die. Scientists are watching for potential changes that could be more transmissible or lethal, but determining whether new variables will have an impact on public health may take time.
In an online press conference, Bhalla said South Africa has seen a spike in new infections.
“Over the past four or five days, there’s been more exponential rise,” he said, adding that the new variant appears to be driving the rise in cases. Scientists in South Africa are working to determine the percentage of new cases caused by the new variant.
He said the new variant, currently identified as B.1.1.529, was also found in Botswana and Hong Kong in South African travelers.
The World Health Organization’s technical working group will meet on Friday to assess the new variant and may decide whether or not to name it from the Greek alphabet.
The British government announced that it has banned flights from South Africa and five other countries in South Africa from noon on Friday, and that anyone who has recently arrived from those countries will be required to take a coronavirus test.
British Health Secretary Sajid Javid said there were concerns the new variant “may be more transmissible” than the dominant Delta strain, and that “the vaccines we currently have may be less effective” against it.
The new variant contains a “constellation” of new mutations, said Tulio de Oliveira, of the South African Genome Monitoring Network, who has followed the spread of the delta variant in the country.
“The large number of mutations is a concern for expected immune evasion and transmissibility,” de Oliveira said.
“This new species has many, many mutations,” he said, including more than 30 to the spiny protein that affects transmissibility. “We can see that the variant has the potential to spread very quickly. We expect to start to see pressure in the healthcare system in the next few days and weeks.”
De Oliveira said a team of scientists from seven universities in South Africa is studying the alternative. He said they have 100 complete genomes of it and expect to have more in the next few days.
“We are concerned about the leap in development in this alternative,” he said.
The only good news, he said, is that it can be detected with a PCR test.
After a period of relatively low transmission where South Africa recorded just over 200 new confirmed cases per day, last week daily new cases rapidly increased to more than 1,200 on Wednesday. On Thursday, they jumped to 2465.
Health Minister Bahla said the first increase was in Pretoria and the surrounding Twane metropolitan area, and appeared to be cluster outbreaks from student gatherings at universities in the area. Amid the growing cases, scientists studied the genetic sequence and discovered the new variant.
“This is clearly a variable that we have to be very serious about,” said Ravindra Gupta, professor of clinical microbiology at the University of Cambridge. “It has a large number of mutational mutations that can affect transmissibility and immune response.”
Gupta said scientists in South Africa need time to determine if the increase in new cases is attributable to the new variant. “There is a high probability that this will be the case,” he said. “South African scientists have done an amazing job quickly identifying this and bringing it to the world’s attention.”
Bhalla said South African officials had warned to expect a resurgence from mid-December to early January, and had hoped to prepare for that by vaccinating more people.
About 41% of adults in South Africa have been vaccinated, and the number of injections given 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 doses of vaccines, by Pfizer and Johnson & Johnson, in the country and expects to deliver about 2.5 million more doses in the next week, according to Nicholas Crisp, acting director-general of the national health ministry.
“We are getting vaccines faster than we are using them at the moment,” Crisp said. “So, for some time, we’ve been delaying deliveries, not reducing orders, but just delaying our deliveries so that we don’t collect and stock vaccines.”
South Africa, with a population of 60 million, has recorded more than 2.9 million cases of COVID-19 including more than 89,000 deaths.
To date, the Delta variant remains by far the most contagious and has crowded out other previously worrisome variants 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 deltas.