South African scientists warn new Botswana variant is likely behind sudden national Covid surge

South African scientists today warned that the new Botswana Covid variant may be driving a rise in cases in the country as the World Health Organization said it was convening an emergency meeting tomorrow to investigate the troubling strain.

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

Around 100 cases of B.1.1.529, its scientific name, have been officially detected so far. 

But 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 the country.

In total it has been detected in three countries — the third being Hong Kong. 

Professor Oliveria 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 a specific part of the spike that antibodies bind to compared to 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 recognise the virus and fight it off.  

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.   

In a glimmer of hope, however, 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.   

Professor Oliveira said he had asked for an ‘urgent’ meeting with the World Health Organization (WHO) to address the rising variant, which could be named ‘Nu’ in the coming days.

This chart shows the proportion of cases that were the B.1.1.529 variant (blue) and Indian 'Delta' variant (red) over time. It suggests that this mutant strain is outcompeting Delta. But experts warn Covid surveillance in South Africa is not picking up every case

This chart shows the proportion of cases that were the B.1.1.529 variant (blue) and Indian ‘Delta’ variant (red) over time. It suggests that this mutant strain is outcompeting Delta. But experts warn Covid surveillance in South Africa is not picking up every case

The above slide shows the proportion of tests that picked up a SGTF mutation, which marks out the variant B.1.1.529 from the Indian 'Delta' variant which is dominant. 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, which marks out the variant B.1.1.529 from the Indian ‘Delta’ variant which is dominant. 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

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

But a lack of testing analysis on continental Africa may me masking the true spread of the variant.

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. 

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.

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