The national coronavirus command council will meet at the weekend to discuss whether the Covid-19 lockdown should be intensified after the discovery of a worrying new variant.
Health minister Joe Phaahla said the cabinet would also meet and President Cyril Ramaphosa would discuss the matter with premiers, raising fears of another Covid Christmas under lockdown.
Scientists are concerned the new variant of Sars-Cov2 could spread rapidly, reduce protection from natural immunity and vaccines and cause a hospital crisis ahead of the festive season.
Discovered by genome sequencers in just the last 36 hours, it is expected to be allocated a Greek letter name by the World Health Organisation on Friday.
Right now, what’s known as B.1.1.529 has been detected in Gauteng and is probably in “most other provinces too”.
At an urgent press briefing called by the health department on Thursday, Krisp genome sequencer Prof Tulio de Oliveira said: “it is concerning for predicted immune-evasion and transmissibility.”
He and other scientists had, over the past 36 hours, discovered and researched it as quickly as possible and found that it has a “very high number of mutations” with more than 30 such mutations located at the spike protein.
“It is a very unusual constellation of mutations,” said De Oliveira, adding that “this variant did surprise us as a big jump in evolution”.
He said this was especially so after such a severe third wave caused by the Delta variant.
“We think it could spread very fast. And we do expect to start seeing pressure on the healthcare system in the next few days and weeks.
"The only good thing is that we’ve detected it quite early and we have to use that time wisely to prepare the health system but as a public we should try to avoid superspreader events and help to prevent cluster outbreaks.
“Many are finishing school and university and they want to go away for the holiday season but this is the real time to all play our part.
Phaahla said: “We had hoped for a long recess between waves but this has just descended on us. We were hoping the rise in numbers in Gauteng could be contained and were caused by the Delta variant but this new variant being identified reinforces the fact that our invisible enemy is very unpredictable”.
Eighty percent of cases of this new variant have been found in Gauteng where numbers have been climbing over the past few days.
“Initially it looked like cluster outbreaks and a spread of the Delta variant on university campuses but from yesterday we got indication from scientists that there could be another variant at play," said Phaahla.
The reproductive number in SA is 1.47 and in Gauteng it is approaching two. This means each infected person will infect two others, “so we will see a very fast increase of cases going forward,” said De Oliveira.
According to Dr Richard Lessells of Krisp, there is a “large number of mutations across all the different proteins of this virus and while some of these are familiar to us, many are not”.
He said the team can see “mutations that suggest enhanced transmissibility and the virus’s ability to get around other parts of the immune system and not just the neutralising antibodies”.
He added: “This is what gives us some concern, and we are also concerned that it is not just isolated in Gauteng.”
It is already becoming dominant, but on the upside, unlike other variants, its presence can be flagged even at the stage of a PCR test rather than a process of whole genome sequencing.
Urgent research is under way to understand how it changes transmissibility, immune evasion, and also importantly, severity of disease.