New Covid-19 variant arrives in SA as third wave starts to stir

SA has detected its first cases of a coronavirus variant initially identified in India, adding a highly infectious mutation of the Covid-19 virus just when some parts of the country are picking up early signs of a third wave of infections.

The National Institute for Communicable Diseases (NICD) said at the weekend that four cases of the variant — two from Gauteng and two from KwaZulu-Natal — have been found in individuals with a recent travel history to India.

The detection of the variant comes as some parts of Gauteng show early signs of a third wave, with the situation in the Sedibeng district, about 50km south of Johannesburg, particularly worrying. The risk, while still small, is rising in some subdistricts in Tshwane and Johannesburg.

The variant, known as B.1.617.2, has reached at least 17 countries, from Britain and Iran to Switzerland and the US, triggering global concern as experts worry it contains mutations that may give it an edge over the body’s immune defences.

"As the epidemic progresses, the detection of new variants is inevitable," health minister Zweli Mkhize said in a statement late on Saturday. "We reiterate that there is no need for panic as the fundamentals of the public health response (testing, contact tracing, isolation and quarantine) have not changed."

A wave of Covid-19 infections has been ravaging India over the past month, with an average of 390,000 new cases being confirmed each day over the past week. Cumulatively, the country has 22.3-million cases of the disease and on Saturday it reported its highest single-day Covid-19 death toll.

The World Health Organization has described it as a "variant of interest", suggesting it may have mutations that would make the virus more transmissible, cause more severe disease or even evade vaccine immunity.

But virologist Prof Barry David Schoub, who chairs the ministerial advisory committee on Covid-19 vaccines, said that while the country should be concerned about the B.1.617.2 variant, it is much more sensitive to vaccines than the variant dominating transmissions in SA.

"It is a variant that is more sensitive to the vaccine and also to people that have been previously infected. Unlike the one we have, which is more resistant to vaccination and previous infections," said Schoub. "The variant we have in SA is a much bigger problem … But we do need to monitor and see that it doesn’t spread too far."

The NICD said all cases of B.1.617.2 had been isolated and managed according to Covid-19 guidelines and contact tracing had been performed.

Linda-Gail Bekker, one of the principal investigators on the Sisonke study, which aims to inoculate 500,000 health-care workers, said the worry is new variants may "break through" vaccine protection, making the vaccine less effective.

"The big worry is that we’ll have breakthrough infections with the vaccine. It may be that they have some efficacy but we’ve seen evidence of reduction in that efficacy. I think that’s the concern that we need to continue to maintain," she said.

SA has ordered tens of millions of vaccine doses from Johnson & Johnson and Pfizer as it gears up to inoculate the general population after completing the inoculation of front-line health workers. The mass vaccination campaign is due to start on May 17.

The surge in infections in India has led to some countries closing their borders to travellers from India. Mkhize said travel restrictions will need to be balanced against scientific realities to protect the economy.

"These findings are urgently being processed by government and announcements pertaining to travel regulations will be made after all appropriate consultations … by cabinet," he said.

SA has also picked up 11 cases of the B.1.1.7 variant first detected in the UK, which is dominating infections in Europe and North America.

Update: May 9 2021
This article has been updated throughout with new information.

gavazam@businesslive.co.za