An illustration of Covid-19. (Getty)
  • SA's new Covid-19 variant is still being analysed, but one of SA's top genetic scientists expects it to be between 40% to 70% more transmissible.  
  • Some of its unique mutations could also force vaccine producers to update their jabs. 
  • Scientists now think variants could originate in people with very weak immune systems due to illnesses like cancer.
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In the next few weeks, as laboratory work progressesSouth Africans should get a clearer picture of its new Covid-19 variant, says Professor Tulio de Oliveira, director of the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP). KRISP coordinates the genetic research into the virus in South Africa.

He warns that the new variant – called 501.V2 - is now clearly driving the surge in cases in South Africa, which is threatening to engulf its healthcare infrastructure.

Over the past nine days, more than 100,000 new Covid cases have been confirmed, with more than 200 people now dying every day.

While it is not expected that the new variant is causing more severe symptoms, De Oliveira says he won’t be surprised if the virus is found to be between 40% and 70% more transmissible than the original virus strain (in line with the UK’s 501Y variant). This means that you are much likelier to contract the virus when exposed to it.

How the variant was found

For many months, since the first confirmed case of Covid-19 was identified in March, local Covid samples were dominated by multiple lineages, which were initially introduced from Europe. But at the end of September, local scientists from across the country started seeing new mutations. 

Viruses typically evolve to ensure their own survival, but usually at a slow rate of around two mutations per month. However, the South African scientists noticed 20 new mutations develop within a couple of weeks.

Eight of these mutations affect the so-called spike protein in Covid-19. The virus uses spike proteins to gain entry into human cells. (Spike proteins give the coronavirus its name - they are bumps on the outside of the virus, which look like "crowns" under a microscope.) 

Three of the mutations (417, 484 and 501) are in the receptor binding domain of the virus, which “sticks” to the human cell receptor.

The mutations mean that if you are exposed to the virus (which is mainly transmitted through droplets from coughs, sneezes, or talking), there is potentially a bigger chance that it will infect you.

KRISP scientists presented their findings to the World Health Organisation’s Covid-19 Evolution Working Group at the start of December – and their presentation lead to the UK identifying its own variant. 

“(The South African scientists) were the first to recognise the importance of a genetic change in the spike protein, something that allows the virus to attach more easily to human cells making it more infectious than the original version,” The Times in the UK reported. 

Following the SA presentation, the UK scientists used the same approach to identify their own variant, which has since triggered stringent lockdowns in the UK, as well as travel bans from other countries.

Possible origin of the new variants

The latest hypothesis is that the UK variant originated from Covid patients who had very weak immune systems due to illnesses like cancer, as reported in Science magazine

De Oliveira says that because immune-compromised people don’t have sufficient immunity to fight Covid-19 as effectively, the virus can stay in their bodies for a longer time, and develop more mutations.

It is not yet clear whether the South African variant may also have possibly originated from a compromised immune system, says De Oliveira.

Professor Tulio de Oliveira, director of the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP)

He says it’s possible that other countries will confirm their own “spike” variants of Covid-19 in coming weeks as they increase their genomics surveillance.

SA's variant and vaccines

Concerningly, what sets the South African variant apart from the UK strain, are two mutations (417 and 484) that potentially reduce virus sensitivity to some antibodies. 

While the consequences are not yet clear, the fear is that this could potentially mean that someone who has had Covid-19 in the past, could be re-infected with the new variant. Crucially, it could also mean that South Africa’s variant may be more resistant to current vaccines.

De Oliviera says a national consortium of scientists, including the Medical Research Council, the National Institute for Communicable Diseases and the country’s universities, is now investigating “intensely” what the mutations could mean for vaccine efficacy.

He says two vaccine developers have already indicated that they could add new updates in the next batch of their vaccines to address the structure of the new variants. 

Eventually, Covid-19 vaccines could be like the flu jab, which is updated regularly, he adds.

But at the moment, South Africa’s biggest concern should not be the vaccine, says De Oliveira. “The biggest worry is the fast transmission of Covid that is overwhelming the health system, which is close to breaking point.”

The new variant means South Africans should be even more diligent in following Covid-19 protocols, by wearing masks (which covers the nose, mouth and chin), regularly washing their hands, frequent cleaning of surfaces, and maintaining a 1.5m distance from others. 

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