New Covid variant spreading in South Africa is ‘reason for concern’

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Scientists said more study was needed to establish if the coronavirus variant was more transmissible or could evade the immune system - iStockphoto
Scientists said more study was needed to establish if the coronavirus variant was more transmissible or could evade the immune system - iStockphoto

Scientists around the world are scrambling to understand a new coronavirus variant amid suggestions it could be driving a spike in cases in South Africa.

The B.1.1.529 variant has been found in 77 cases in South Africa, four in Botswana, and one in Hong Kong, in a patient who had recently visited South Africa.

Experts are sounding the alarm because of the variant’s unusually high level of mutations, some of which may make the virus more transmissible or undermine the effectiveness of vaccines.

South Africa has seen a spike in cases in recent weeks, particularly in Gauteng province where most of the cases of the new variant have been detected.

The World Health Organization is set to name the variant under its Greek letter system on Friday, according to researchers in South Africa. This would mean it is officially a variant of global interest, or concern - the next level up - and it is likely to be called ‘Nu’.

Professor Tulio De Oliveira, director of the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), which identified the 77 cases in South Africa, said the variant had a “very unusual constellation of mutations”.

“It is a reason for concern in South Africa,” he said.

However, he said its significance was still unclear, with scientists now monitoring it to assess how dangerous it may be. Viruses mutate all the time, and only some of the mutations change how the virus behaves.

Another member of the KRISP team, infectious diseases expert Dr Richard Lessells, added: "There is some concern that B.1.1.529 may have enhanced transmissibility and be able to get around parts of the immune system.”

Many of the 32 mutations on the variant are clustered around the spike protein, which the virus uses to infect cells. Some resemble mutations seen on previous variants of concern, including beta - which caused devastation in South Africa after first being identified by Prof de Oliveira’s team in late 2020 - and delta, which is now the dominant variant worldwide.

As well as sequencing, the new variant can be picked up by one kind of PCR test, and Prof de Oliveira said this was giving "early signs" that it may have already "rapidly" spread in Gauteng province and across South Africa.

However, experts around the world urged caution. Dr Emma Hodcroft, a molecular epidemiologist at the University of Bern, said: "We cannot perfectly predict virus behaviour from mutations. Even lab work doesn't perfectly mirror what happens in complex, whole-body real-life. Other, alarming variants have failed to spread very far in the past. We need more data."

However, other scientists said that it may be better to overreact before the variant is allowed to spread further, although it is unclear how it would behave in countries with higher vaccination rates than South Africa - which has only fully vaccinated 24 per cent of its population - or where delta is more widespread.

Professor Danny Altmann, an immunologist at Imperial College, London, told The Telegraph: “We thought delta was the dominant variant and nothing could displace it - this looks potentially horrible enough to displace it, if it is allowed to spread.

“We have all become pandemic fatigued, yet if this was a report of a terrorist threat, we would now be raising the threat level from amber to red.”

There were already calls on Thursday for the UK to crack down on travel from South Africa, which is considering tighter restrictions domestically to prevent further spread. The UK Health Security Agency said it was monitoring the variant.

Professor Christina Pagel from University College London said: “This is our window to act... Adding South Africa and close neighbours to the red list seems sensible.”

But Prof de Oliveira issued a plea for the world not to "discriminate and isolate" South Africa for sharing its data, saying they had done so to "protect our country and the world". He also said that the variant may already be causing 900 cases a day in Gauteng province, based on early data from PCR tests.

What could the future hold?

Predicting how the variant might behave if it is allowed to spread is complex; experts said that it may not necessarily have the same impact in countries with higher vaccination rates than South Africa - where only 24 per cent of people are fully vaccinated - or where delta is already widespread.

Dr Hodcroft said these were important things to bear in mind, adding: “We can step up monitoring, and we should. However, what fitness advantages it may have are still unclear, especially outside of initial spread.”

Global health experts have long warned that allowing the coronavirus pandemic to spread unchecked in poorer countries without access to vaccines could lead to the emergence of new variants.

In a paper published this summer, the UK’s Sage committee warned that new variants causing either more severe disease or able to evade the vaccines was a “realistic possibility”.

Professor Madhukar Pai, global health chair at McGill University, said: "This is what happens when we leave three billion plus people unvaccinated."

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