Analysis: why the South African coronavirus variant is so worrying

If the coronavirus was a horror film, we have now reached the obligatory ‘not dead yet’ scare, in which the seemingly conquered monster returns from the grave to give a final fright. 

Just as light was beginning to emerge at the end of a very long and gloomy tunnel, the South African variant of the virus threatens to undermine the vaccine and testing gains of recent months.

Brian Pinker, 82, received the first Oxford vaccine on Jan 4, yet there are real concerns that he and the hundreds of thousands of others who have had their jabs may not be fully protected against this latest mutation.

Clearly the Medicines and Healthcare products Regulatory Agency (MHRA) is expecting some vaccine tweaks to be needed as it has already begun to look at how quickly an altered jab could be approved, and Matt Hancock has said he is "very worried".

The problem lies in how the virus has mutated. Variants of coronavirus have been around since the beginning of the pandemic and are a natural evolutionary process by which viruses adapt to their hosts as they replicate.

Most of these mutations have no effect, but occasionally they can improve the ability of the virus to infect or become more resistant to the body’s immune response. This is one such occasion.

The South African variant has three mutations in important genes. One, the N501Y mutation, has already been found in the UK variant and could be responsible for it being so infectious.

However, the South African version carries two more mutations (E484K and K417N) that are absent in the British version and make it far more worrying. 

“These two additional mutations may interfere more with vaccine effectiveness in the South African variant than in the UK variant,” said Dr Julian W Tang, honorary associate professor and clinical virologist, University of Leicester.

“This does not mean that the existing Covid-19 vaccines will not work at all, just that the antibodies induced by the current vaccines may not bind and neutralise the South African variant as well as it would the other circulating viruses, including the UK variant.”

Global vaccinations doses administered

The South African variant carries mutations in a gene which builds spike proteins – the rod-like structures on the outside of the virus which attaches to human cells.

Spike proteins are also produced by vaccines so that the body knows what to look for and what to fight off. 

So, any significant changes to the spike protein may mean the body can no longer spot the virus, even after vaccination or a previous infection, and antibodies produced in anticipation may not be able to attach properly in order to clear it away.

Worryingly, the mutations may also mean that it is harder to pick up cases through the normal Polymerase chain reaction (PCR) testing, so it could have already spread widely. It quickly became the dominant variant in the Eastern and Western Cape provinces of South Africa.

Yet there is still hope. Even if the new variant is more infectious, it may not cause more severe disease. England’s chief medical officer, Chris Whitty, and chief scientific officer, Patrick Vallance, are believed to have briefed Boris Johnson, claiming they are not overly concerned about the new variant.

And even if the South African variant becomes more widespread and dominant, both vaccines can be modified to be more effective against this variant in as little as six weeks. 

Most scientists believe that existing vaccines will still work to some extent, even if the new variant lowers the overall efficacy. 

The mutations have not altered the shape of the spike protein to such an extent that antibodies cannot bind at all, they just may be less effective. 

“It is not anticipated that this mutation is sufficient for the ‘South African’ variant to bypass the protection provided by current vaccines,” said Prof Francois Balloux, professor of computational systems biology, University College London (UCL). 

Vaccination rates scenarios

“It’s possible that new variants will affect the efficacy of the Covid-19 vaccines, but we shouldn’t make that assumption yet about the South African one.”

Researchers are working round the clock to find out just how dangerous this new variant is, and new lockdown measures introduced by the Government will undoubtedly help to stem the tide, and give scientists room to find a new solution.

Prof James Naismith, director of the Rosalind Franklin Institute, and University of Oxford, said: "We can all help if we redouble our efforts to wash our hands, wear a mask and socially distance. The faster and further the vaccine is rolled out, the quicker the end to this nightmare.”

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