Health

‘More infectious and vaccine resistant’ Botswana Covid variant is driving South African surge

A new Covid variant that has more mutations than have ever been seen before is becoming dominant in South Africa and is feared to be ultra infectious and vaccine resistant, scientists warned today.

Experts said the variant is growing ‘very quickly’ in South Africa and is driving the country’s surge in infections. 

Around 100 cases of B.1.1.529, its scientific name, have been detected so far in three countries and the World Health Organization is convening an emergency meeting tomorrow to investigate the troubling strain. 

South Africa’s Health Minister Joe Phaahla described the variant as ‘a major threat’, warning that it was behind an ‘exponential’ increase in cases across the country.  

Experts in the UK today called for travel restrictions to be reimposed to prevent the strain being seeded here and avoid risking a repeat of this spring when the Delta variant was imported in huge numbers from India.

Zero-Covid scientist Professor Christina Pagel urged ministers to ‘get ahead of this right now’ by immediately’ reimposing the red travel list ‘ — which was only scrapped a few weeks ago.

And Chris Snowdon, an economist who is normally in favour of fewer restrictions, also called for an immediate travel ban.

The Government has left the door open to bringing back the notorious traffic light travel system with Transport Secretary Grant Shapps saying last month hundreds of hotel rooms were still on standby for quarantine. 

Nationally, infections in South Africa have surged tenfold from 100 per day to 1,100, after the variant was first detected in neighbouring Botswana on November 11. 

Professor Tulio de Oliveira, a director of Covid surveillance in the South African province of KwaZulu-Natal, told a hastily organised press conference today that it has been spotted in nearly every corner of South Africa.

He admitted he was still ‘uncertain’ about the impact of the variant — which could be named ‘Nu’ by the WHO within days — on the country’s epidemic, with other scientists saying that it might be so evolved that it becomes unstable.

But Professor Oliveria explained the new variant is ‘clearly very different’ from previous strains, including the fact that it has five times more mutations on a specific part of the spike protein than Delta — meaning it might be better at infecting vaccinated people than the world-dominant strain.

He said that officials ‘do expect, unfortunately, to start seeing pressure in the healthcare system in the next few days and weeks.’

Health minister Mr Phaahla warned at the same press conference: ‘Here is a mutation variant of serious concern.’ 

He added: ‘We were hopeful that we might have a longer break in between waves – possibly that it would hold off to late December or even next year January.’ 

Current jabs train the immune system to recognise an older version of the spike, and lots of changes to this protein make it harder for the vaccinated people to fight it off.  

The UK Health Security Agency, which took over from Public Health England, said it was monitoring the situation closely. But the Prime Minister’s official spokesman said the variant was ‘not seen as something that is an issue’ for the UK at present.

MailOnline first sounded the alarm about the variant yesterday after British scientists warned that it had 32 mutations and is the most evolved version of Covid yet. They said it likely emerged in a long-term infection in an immunocompromised patient, possibly someone with undiagnosed AIDS.

The fact that South Africa has the largest number of people living HIV out of any country in the world has complicated its fight against Covid, as immuno-compromised people can harbor the virus for longer, scientists say. 

It comes as Britain’s daily Covid cases began to flatline today, official data showed after weeks of falling deaths and hospitalisations. This was the first time the percentage jump was below one since November 10. 

This chart shows the proportion of cases that were the B.1.1.529 variant (blue) and Indian ‘Delta’ variant (red) over time in South Africa. It suggests that the mutant strain could outcompete Delta in the province within weeks

The above slide shows the proportion of tests that picked up a SGTF mutation, a hallmark of the B.1.1.529. It suggests that the Covid variant may be spreading rapidly in the country. The slide was presented at a briefing today run by the South African Government

The above slide shows the proportion of tests that picked up a SGTF mutation, a hallmark of the B.1.1.529. It suggests that the Covid variant may be spreading rapidly in the country. The slide was presented at a briefing today run by the South African Government

The above slide shows variants that have been detected by province in South Africa since October last year. It suggests B.1.1.529 is focused in Gauteng province. This was presented at a briefing today from the South African Government

The above slide shows variants that have been detected by province in South Africa since October last year. It suggests B.1.1.529 is focused in Gauteng province. This was presented at a briefing today from the South African Government

The above shows the test positivity rate — the proportion of tests that picked up the virus — across Gauteng province. It reveals that there is an uptick of cases in the northern part of the province. It is not clear whether this could be driven by B.1.1.529

The above shows the test positivity rate — the proportion of tests that picked up the virus — across Gauteng province. It reveals that there is an uptick of cases in the northern part of the province. It is not clear whether this could be driven by B.1.1.529

Professor Francois Balloux, a geneticist at University College London, said the variant could become dominant in South Africa ‘very quickly’.

Asked whether it could soon make up the majority of cases in South Africa, he told MailOnline: ‘The numbers [of cases] are very small and there is a lot of uncertainty… but I would say it might become dominant very quickly.’

He said it was ‘plausible’ that the variant was more infectious because it was ‘better at infecting’ people that had immunity from vaccines or previous infections.

But he said very little is known about how likely someone who catches the variant would be to become seriously ill and die from the virus. Experts say viruses normally become less virulent over time. 

Professor Oliveira said that the variant had spread rapidly in South Africa.

‘In less than two weeks it now dominates all infections following a devastating Delta wave in South Africa.

‘We estimate that 90 per cent of cases in Gauteng (at least 1,000 a day) [are this variant].’

And Dr Theo Sanderson, a geneticist at the Francis Crick Institute in London, warned it was likely that vaccines targeted at B.1.1.529 could be needed ‘in the not too distant future’. 

Professor Pagel, who is also a member of Independent SAGE and a mathematician at University College London, said: ‘Given the speed with which this variant has spread and mutations which might mean significant vaccine escape, in my opinion the UK should get ahead of this right now.’

She added: ‘As far as we know, it’s not here yet.’ 

Mr Snowdon, from the Institute of Economic Affairs, said: ‘Hong Kong had one imported case of this variant and that’s where it ended because they have proper quarantine.

‘We need to do that ASAP especially for anyone from sub-Saharan Africa.’

The deputy director of the European Medical Biology Laboratory — which has six labs in Spain, Rome, Austria, Germany and the UK — said: ‘It does definitely look like a code red on B.1.1.529 (in need of a Greek letter).

‘Time to — red list international travel from Southern Africa, monitor circulating SARS-CoV-2 (isolates, wastewater), drugs and vaccines to SA, biological assays on pseudo virus.’ 

The last countries were removed from the red list — which would require arrivals to quarantine in hotels for 11 nights at a cost of £2,285 — on November 1. 

But ministers said they would keep several hundred hotel rooms on standby in case it needed to be reimposed.

Mr Shapps said at the time officials would continue to closely monitor outbreaks abroad and reveiw travel restrictions every three weeks. The next review is due on December 9.

In a hastily organised press conference today South African scientists presented a slew of figures warning that B.1.1.529 was likely already spreading rapidly in their country — and dominant in one province.

One showed more than 90 per cent of infections checked for variants in Gauteng — where the capital Johannesburg is based — are now down to the variant. But scientists said this was based on only a small number of cases that had been checked.

A separate graph revealed that cases with a specific mutation found on B.1.1.529 but not the Delta variant — and which scientists can quickly test for without checking all the genetic material — are rising quickly in seven of the country’s nine provinces.

Professor Oliveira warned: ‘Unfortunately we have detected a new variant which is a reason for concern in South Africa.’

He said that in one specific site of the variant’s spike protein — which antibodies bind to to stop an infection — there were ten mutations.

For comparison, he said the Beta variant which caused concern last year after it was spotted in South Africa and found to be better at evading antibodies had just three mutations at this site. And Delta has two mutations here. 

Dr Richard Lessells, an infectious diseases doctor also in South Africa, said at the briefing: ‘What gives us some concerns (is) that this variant might have not just have enhanced transmissibility, so spread more efficiently, but might also be able to get around parts of the immune system and the protection we have in our immune system.

So far the variant has been seen spreading especially among young people. But the coming days and weeks will be key to determine the severity of the variant, Lessells said.

Neutralising the variant is ‘complicated by the number of mutations this variant’ contains, said one of the scientists Penny Moore.

‘This variant contains many mutations that we are not familiar with,’ she added.

What is the new ‘Botswana’ B.1.1.529 variant? 

Should I be concerned?

Britons should not be ‘overly concerned’ about the variant, scientists say.

Its mutations suggest it is better able to evade vaccine-induced antibodies and more transmissible than other variants.

But this is yet to be backed up by lab tests or real-world data. 

Where have the cases been detected? 

26 cases have been detected so far. 

There are three in Botswana, and 22 in South Africa.

A case has also been detected in Hong Kong in a 36-year-old man who had recently returned from the African continent.

South Africa’s outbreak is focussed in Gauteng, Limpopo and the North West province. Two of these are recording steep rises in infections. 

No cases have been recorded in Britain to date. UK officials said they were monitoring the situation closely. 

Can the strain dodge vaccine-induced immunity?

Scientists say the strains mutations suggest it is better able to dodge immunity from vaccines.

Some warned it ‘looks like’ it could be better at dodging jabs than all other variants, including the South African ‘Beta’ strain.

South African scientists say many infections in their country have been spotted in people been detected in people thought to have immunity from vaccines or previous infection. 

It carries mutations K417N and E484A, which are similar to those on the Beta variant that made it more jab resistant.

But it also has mutations N440K, found on Delta, and S477N, on the New York variant, that could also make it more resistant.

B.1.1.529 also carries mutations P681H and N679K which are ‘rarely seen together’ on a specific part of the spike protein.

South African scientists say many infections have been detected in people thought to have immunity from vaccines or previous infection. 

Daily infections in South Africa shot to more than 1,200 on Wednesday, up from around 100 earlier this month.

Before the detection of the new variant, authorities had predicted a fourth wave to hit South Africa starting around the middle of December, buoyed by travel ahead of the festive season.

South Africa this week began adding in cases from lateral flow tests to its daily total. Officials warned at the time this would likely trigger an uptick.

But the test positivity rate — the proportion of tests that detect the virus — has also doubled suggesting there is a real-terms increase in cases. 

The Government-run National Institute for Communicable Diseases (NICD) said that detected cases and the percentage testing positive are ‘increasing quickly’ in three of the country’s provinces including Gauteng, which includes Johannesburg and Pretoria.

A cluster outbreak was recently identified, concentrated at a higher education institute in the capital Pretoria, the NICD said.

Last year South Africa also detected the Beta variant of the virus, although until now its infection numbers have been driven by the Delta variant, which was originally detected in India.

The country has the highest pandemic numbers in Africa with around 2.95million cases, of which 89,657 have been fatal. 

After a rather slow start to South Africa’s vaccination campaign, around 41 percent of adults have received at least a single dose, while 35 percent are fully vaccinated.

The country’s health department has even had to ask Johnson and Johnson and Pfizer Inc. to hold off on new deliveries due to a drop in demand.

Meanwhile, the rest of the continent is faring worse, with just 6.6 per cent of Africa being fully vaccinated, according to Africa CDC Director John Nkengasong.

He said the lack of demand has been spurred by the challenge of securing enough supplies, with just under half, or 45 per cent, of the 403 million doses delivered yet to be administered.    

WHO officials said its Technical Advisory Group on Virus Evolution (TAG-VE) was assessing the variant.

They will be convening a meeting tomorrow to determine whether the variant should be marked as being of concern — the highest alert category — or of interest — meaning monitoring of the variant will be ratcheted up.

In a glimmer of hope, however, British experts told MailOnline yesterday that the extensive mutations might work against the virus, making it ‘unstable’. 

The first case was identified in Botswana on November 11, and it was picked up in South Africa the following day. 

A case was also spotted in Hong Kong on November 13 in a 36-year-old man who had travelled back from South Africa on November 11.

In South Africa it has been officially spotted in the Gauteng, Limpopo and North West provinces.

Worldwide it has been detected 100 times so far, but experts warn there are likely many more cases. World Health Organization officials said the majority were in South Africa. 

Dr Tom Peacock, a virologist at Imperial College London, who first sounded the alarm about its spread, described the variant’s combination of mutations as ‘horrific’.

He warned that B.1.1.529 had the potential to be ‘worse than nearly anything else about’.    

Professor David Livermore, a microbiologist at the University of East Anglia, told MailOnline the Botswana variant concerned him because of its ‘very extensive’ set of mutations. 

He said: ‘This increases the risk of vaccine escape, but doesn’t prove that it will occur. 

‘Nor is the strain’s infectiousness clear, and it too will be affected by the spike’s structure.’

The Botswana variant carries mutations K417N and E484A that are similar to those on the South African ‘Beta’ variant that made it better able to dodge vaccines.

But it also has the N440K, found on Delta, and S477N, on the New York variant, which are also linked to antibody escape. 

The variant also has mutations P681H and N679K which are ‘rarely seen together’ and could make it yet more jab resistant. 

And the mutation N501Y that makes viruses more transmissible and was previously seen on the Kent ‘Alpha’ variant and Beta among others.

Other mutations it has include G446S, T478K, Q493K, G496S, Q498R and Y505H, although their significance is not yet clear.

Dr Meera Chand, from the UKHSA, said: ‘The UK Health Security Agency, in partnership with scientific bodies across the globe, is constantly monitoring the status of SARS-CoV-2 variants as they emerge and develop worldwide. 

‘As it is in the nature of viruses to mutate often and at random, it is not unusual for small numbers of cases to arise featuring new sets of mutations. Any variants showing evidence of spread are rapidly assessed.’ 

It comes as Covid cases continued to rise across the UK but deaths and hospitalisations still firmly trended downwards.

Another 43,676 cases have been recorded in the last 24 hours, a rise of 14.1 per cent on the 38,263 confirmed positive cases last Wednesday.

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