Is Botswana variant behind sudden Covid surge in South Africa?

Is Botswana variant behind sudden Covid surge in South Africa? Cases have risen fivefold in a week as experts fear super strain could be outcompeting Delta

  • South Africa’s infection rate has surged more than five-fold in a week
  • Some 22 cases of the mutant strain have now been detected in the country
  • They are in three provinces, suggesting it is likely more widespread 

Fears are mounting that the new Botswana Covid variant is driving a rise in cases in neighbouring South Africa.

The national infection rate in South Africa has surged more than fivefold in the past week since the variant was first detected on November 11. 

Just 22 infections of B.1.1.529, its scientific name, have been officially detected in the country so far, with a cluster in the province of Gauteng.

But it’s been spotted in nearly every province, public health experts in South Africa revealed today, and is already in three countries — including Hong Kong.  

Alarm about the variant was first sounded yesterday after it was revealed it has 32 mutations and is the most evolved version of Covid yet.  

Concerned health chiefs in South Africa revealed in a hastily organised press conference today that the variant may be outcompeting the dominant Delta variant because it can infect vaccinated people more easily. 

Professor Tulio de Oliveira, a director of Covid surveillance in the South African province of KwaZulu-Natal, admitted experts were still ‘uncertain’ about the impact of the variant on the country’s epidemic.

But he explained the virus has five times more mutations on the specific part of the spike that antibodies bind to compared to Delta. 

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

British experts told MailOnline yesterday that the extensive mutations might work against the virus, making it ‘unstable’.

They said it likely emerged in a lingering infection in an immunocompromised patient, possibly someone with undiagnosed AIDS.   

They added that South Africa has good Covid surveillance thanks to its experience with HIV/AIDS.  

It is expected that the World Health Organization will assign this variant the name ‘Nu’ in the coming days, which is the next letter available in the Greek alphabet. 

Professor Tulio de Oliveira, who runs Covid surveillance in the South African province of KwaZulu-Natal, warned that B.1.1.529 is likely more widespread.

He told a press briefing that samples detected from November 12 to 20 are mostly from Gauteng province.

He added: ‘This lineage has a very high number of mutations with concern for predicted immune evasion.

‘[But] even though it was detected here very quick it doesn’t mean it is from South Africa.’

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. 

Dr Simon Clarke, a microbiologist at Reading University, told MailOnline it was not clear whether this variant had just emerged or been lingering for a while.

He said: ‘The South Africans have pretty good surveillance because of their experience with HIV. 

‘On this basis, they do not appear to be picking it up in great numbers yet.

‘[But] we need to be careful here because we have got transmissibility and it is quite rare this strain.

‘That might be because it is not very fit, or that might be because it is very new.’   

British experts yesterday sounded the alarm over the Covid strain believed to have emerged in Botswana.

Some 26 cases have now been detected globally, the majority in South Africa.

The first case was identified in Botswana on November 11, followed by South Africa on November 12.

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 spotted in the Gauteng, Limpopo and North West provinces. 

It carries 32 mutations, many of which suggest it is highly transmissible and vaccine-resistant, and has more alterations to its spike protein than any other variant.

Professor Francois Balloux, a geneticist at University College London, said it likely emerged in a lingering infection in an immunocompromised patient, possibly someone with undiagnosed AIDS.

Changes to the spike make it difficult for current jabs to fight off, because they train the immune system to recognise an older version of this part of the virus. 

Dr Tom Peacock, a virologist at Imperial College who first picked up on its spread, described the variant’s combination of mutations as ‘horrific’.

He warned that B.1.1.529, its scientific name, had the potential to be ‘worse than nearly anything else about’ — including the world-dominant Delta strain. 

Scientists told MailOnline, however, that its unprecedented number of mutations might work against it and make it ‘unstable’, preventing it from becoming widespread. 

They said there was ‘no need to be overly concerned’ because there were no signs yet that it was spreading rapidly.

Three infections have been detected in Botswana to date and six in South Africa — where variant surveillance is more robust.

One case has also been spotted in a 36-year-old man in Hong Kong who recently returned from the continent. 

There are no cases in Britain. But the UK Health Security Agency, which took over from Public Health England, said it was monitoring the situation closely. 

The Prime Minister’s official spokesman said the variant was ‘not seen as something that is an issue’ for the UK at present.

The mutant variant has sparked concern because of its ‘very extensive’ set of mutations. 

Professor Francois Balloux, a geneticist at University College London, said it was likely the variant would be much more able to dodge antibodies than Delta.

He told MailOnline: ‘For the time being, it should be closely monitored.

‘But there’s no need to be overly concerned, unless it starts going up in frequency.’

He said its many mutations suggested it could have emerged during a lingering infection in an immunocompromised person, such as an AIDS patient.

In patients with weakened immune systems infections can linger for months because the body is unable to fight it off.

This gives the virus time to acquire mutations that allow it to get around the body’s defences. 

Scientists previously said the Kent ‘Alpha’ variant may have emerged in this way.

Professor Lawrence Young, a virologist at Warwick Medical School, said it ‘looks like’ this mutant strain could be better at dodging vaccine-triggered immunity than other mutants based on its mutations.

But he added: ‘It’s always difficult to say just by looking at [mutations], and so much depends on how the immune system sees the change and responds.

‘But it looks like just because of the severe load of [mutations] — some of which we know about quite a bit in terms of harming transmission — it looks like it might be slightly more qorrying than the South African variant.’

He said it was hard to tell whether the virus would be more transmissible than Delta at this stage.

Professor David Livermore, a microbiologist at the University of East Anglia, said the Botswana variant had sparked concern 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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