‘Serious concern’ as South Africa detects new coronavirus variant

South African Health Minister Joe Phaahla says the variant is behind an ‘exponential’ increase in COVID infections.

COVID South Africa
Gambia truth panel urges prosecutions for Jammeh-era crimes [File: Sumaya Hisham/Reuters]

South African scientists have expressed concern about a new COVID-19 variant that has been detected in small numbers, and are working to understand its potential implications.

The variant – called B.1.1.529 – has a “very unusual constellation” of mutations, which are concerning because they could help it evade the body’s immune response and make it more transmissible, scientists said on Thursday.

The National Institute for Communicable Diseases (NICD) said 22 positive cases of the new variant have been recorded in the country following genomic sequencing.

“Unfortunately we have detected a new variant which is a reason for concern in South Africa,” Tulio de Oliveira, from the Network for Genomic Surveillance in South Africa, told a news conference.

The variant “has a very high number of mutations”, he said. “It’s unfortunately causing a resurgence of infections,” he added.

It has also been detected in Botswana and Hong Kong among travellers from South Africa, he said.

Health Minister Joe Phaahla said the variant was of “serious concern” and behind an “exponential” increase in reported cases, making it “a major threat”.

Daily infections jumped to more than 1,200 on Wednesday, up from about 100 earlier this month.

Before the detection of the new variant, authorities had predicted a fourth wave to hit South Africa starting around the middle of December, buoyed by travel ahead of the festive season.

The NICD said in a statement on Thursday that detected cases and the percentage testing positive were “increasing quickly” in three of the country’s provinces including Gauteng, which includes Johannesburg and Pretoria, the capital.

A cluster outbreak, concentrated at a higher education institute in Pretoria had recently been identified, the NICD said.

“Although the data are limited, our experts are working overtime with all the established surveillance systems to understand the new variant and what the potential implications could be,” it said.

Since the beginning of the pandemic, South Africa has recorded about 2.95 million cases of COVID-19, of which 89,657 have been fatal.

More mutations

The new variant has a “constellation” of new mutations, which was a “concern for predicted immune evasion and transmissibility,” de Oliveira said.

More than 30 mutations to the spike protein that affects transmissibility had been found, he added. “We can see that the variant is potentially spreading very fast. We do expect to start seeing pressure in the healthcare system in the next few days and weeks.”

Researcher Richard Lessells said the coming days and weeks would be key to determining the severity of the variant.

“What gives us some concerns (is) that this variant might have not just have enhanced transmissibility, so spread more efficiently, but might also be able to get around parts of the immune system and the protection we have in our immune system,” he said.

So far the variant has been seen spreading mostly among young people.

Professor Helen Rees, of the WHO’s African Regional Immunization Technical Advisory Group, urged people not to panic.

“[Currently] we are trying to identify how widely spread this is. There will be a lot of work looking at: Is it more transmissible? Is it associated with any more severity of disease? Does it render the vaccines less effective?” Rees told Al Jazeera.

“In the meantime, our big request to the world, in terms of vaccinating the African region, is please get the vaccines out into the region because as we know variants don’t stay in one country,” she added.

Travel restrictions

On Thursday, Britain announced it would temporarily suspend all flights from South Africa, Namibia, Lesotho, Eswatini, Zimbabwe and Botswana from 12:00 GMT on Friday as a precaution amid concerns over the new variant.

“The early indication we have of this variant is it may be more transmissible than the Delta variant and the vaccines that we currently have may be less effective against it,” UK Health Secretary Sajid Javid said.

Javid said the new variant had not been found so far in Britain, but that British scientists were “deeply concerned”.

“We will be requiring anyone that arrives from those countries from 4:00am on Sunday to quarantine in hotels,” Javid added. “If anyone arrives before then they should self-isolate at home and take a PCR test on day two and day eight.

“And if anyone has arrived from any of those countries over the last 10 days, we would ask them to take PCR tests.”

Al Jazeera’s Fahmida Miller, reporting from Johannesburg, said there was concern over the economic impact of the new restrictions.

“Southern African countries depend on tourism and trade,” Miller said, adding that the expected uptick in tourism during the holiday season now seemed unlikely.

South Africa had recently obtained its removal from a UK red list only to see new restrictions being put in place. “At the moment, around 1,000 people travel between the UK and South Africa and that was expected to increase in the coming days,” Miller said.

Israel also imposed a travel ban for those six countries, as well as Mozambique, adding them to its “red” or highest-risk travel list after the new variant was announced.

The move means that Israelis are barred from travelling to the southern African nations, while citizens of those countries would not be allowed into Israel.

Israelis returning home from those countries will be required to spend between 7 and 14 days in a quarantine hotel after arrival, the government said.

The Israeli Health Ministry detected the country’s first case of a new coronavirus variant in a traveler who returned from Malawi on Friday.

The Health Ministry said in a statement that the traveler and two other suspected cases have been placed in isolation. It said all three are vaccinated but that it is currently looking into their exact vaccination status.

New travel restrictions were also imposed by Singapore, Japan, Italy and the Czech Republic. The Czech government has imposed new measures to contain the spread of the virus within the country as it grapples with the worst wave of contagions since the pandemic begun.

On Friday, Australia said it was investigating the strain and could close its borders to those countries depending on World Health Organisation (WHO) advice.

“As we have always been, we are flexible. And if the medical advice is that we need to change that, we won’t hesitate,” Health Minister Greg Hunt told reporters in Sydney. “That is what we have done as a country, whether it has been closing borders, whether it has been ensuring there is quarantine.”

The WHO technical working group is to meet on Friday to assess the new variant and could decide whether or not to give it a code name from the Greek alphabet.

Health Minister Phaahla said it was too early to say whether the South African government would impose tougher restrictions in response to the variant.

South Africa was the first country to detect the Beta variant last year.

Beta is one of only four labelled “of concern” by the WHO because there is evidence that it is more contagious and vaccines work less well against it.

Source: Al Jazeera and news agencies