All eyes on the lab to see if Indian variant has landed here

● SA will know this week whether the B.1.617 variant associated with the deadly new Covid wave in India is present in the country.

This is as fears mounted after health minister Zweli Mkhize announced this week that three travellers from the subcontinent had tested positive for Covid upon entry into SA.

India saw a record jump in Covid cases and deaths on Thursday when 412,262 new cases and 3,980 deaths were recorded.

Mkhize was speaking following pandemonium on Tuesday when 14 members of a Filipino crew aboard the Eaubonne — a cargo ship that had travelled from India to Durban transporting tonnes of rice — tested positive for the virus. The chief engineer had died due to a reported heart attack during the two-week voyage, raising alarm bells among port authorities in Durban.

The postmortem results are yet to determine whether the death was related to Covid. Later the same day, at the port of Gqeberha, at least 16 crew members from two vessels tested positive for the disease.

Mkhize said the government was on “high alert” for traces of the B.1.617 variant, but leading scientists and health experts said that according to current data the South African B.1.351 variant could be seen as more aggressive.

On Thursday Mkhize said the sequencing of one traveller’s results had been completed and it turned out to be the B.1.351 variant, the one that is circulating in SA.

“This tells us that one cannot assume that a traveller carries any particular variant and this is why we insist on being guided by the science,” he said.

The co-chair of the ministerial advisory committee, professor Koleka Mlisana, told the Sunday Times that sequencing to determine whether the B.1.617 variant is in SA will be complete this week and the information made public.

While scientists say it’s too early to say whether the B.1.617 variant is responsible for the rapid increase in infections, it is being treated as a possible cause.

Mlisana said as it stands there are only three variants of concern globally, namely the variants first discovered in the UK (B.1.1.7), Brazil (P1) and SA (B.1.351).

“The one discovered in India has not yet been classified as a variant of concern but it is rather a variant of interest,” she said.

She said the variant discovered in SA, and responsible for its deadly second wave, is on paper more aggressive than the one in India.

“The B.1.617 [Indian variant] has got a total of 13 mutations. Of those mutations, two occur at critical regions which result in it being highly transmittable or escaping the immunity. Whereas for the B.1.351 [South African variant] it’s got a lot more than 13 mutations and has three mutations occurring in critical regions.”

Mlisana said they remain concerned about a possible third wave and highlighted that Gauteng could likely see the worst of it.

“We might see a third wave and this will be based on what we call seroprevalence in the population, which means how many people have been infected by SARS-Cov-2 and have developed immunity that is still at protective level.

“In the first and second wave the infection rate in the Western Cape and KwaZulu-Natal was a lot higher as opposed to Gauteng, and that’s why we are concerned about Gauteng. Therefore the chances are that if we do get a third wave we can predict that it’s likely to be higher in Gauteng because there were less people exposed to the second wave.”

She emphasised that SA could not afford to have a third wave during the vaccination rollout.

“It will be very difficult because we will have a health-care system divide, looking after massive numbers while trying to get the vaccination process going at the same time.”

Acting vice-chancellor of research and innovation at the University of KwaZulu-Natal, professor Mosa Moshabela, said the government should consider stricter measures given the recent upward trend in positive cases.

He said SA’s second wave was the most severe because the government had reacted too late in implementing harsher restrictions to curb the spread of the virus.

“So the lesson there is that if SA wants to control the third wave with or without the variant that is circulating in India — accepting that the variant that is dominant in SA is also just as aggressive — then we need to act early rather than late.”