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

A new Covid variant feared to be ultra infectious and vaccine resistant is driving a Covid surge in South Africa and could become dominant in the country ‘very quickly’, scientists warned today.

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 the red travel list to be reimposed to prevent the strain being seeded in the country. 

Professor Christina Pagel, from Independent SAGE, urged ministers to ‘get ahead of this right now’. And Chris Snowdon, from the Institute of Economics Affairs who has previously called for borders to be kept open, said the Government needed to act ‘ASAP’ to stop this variant being imported.

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 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.

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.    

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 Pagel, who is also 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.’ 

In a hastily organised press conference today South African scientists warned that the B.1.1.529 variant was likely already in almost every province of the country and spreading.

So far it has officially been detected in three of the nine provinces — Gauteng where the capital is based, Limpopo and the North West.

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.

A graph of cases detected in Gauteng province was shown at the conference. It showed cases of the B.1.1.529 variant surging ahead of Delta infections. But scientists cautioned this was based on very few cases that were detected.

Another graph showed that cases with a specific mutation — which is easily detected and seen on B.1.1.529 but not Delta — appear to be rising rapidly across most of South Africa’s regions. 

Dr Richard Lessells, an infectious diseases doctor also in South Africa, said at the brifeing: ‘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.

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. 

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.

But Professor Oliveira warned it could already be in ‘nearly every province’. 

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.

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. 

Leave a Reply

Your email address will not be published. Required fields are marked *