Scientists warn of new Botswana variant of Covid with ‘horrific’ number of mutations

A new Covid-19 variant has emerged that has an “incredibly high” number of mutations, scientists are warning.

It is feared that the B.1.1529, or Botswana variant – an off-shoot of the B.1.1 – could drive further transmission of the virus.

The first cases found were three in Botswana, followed by another six cases in South Africa, and one in Hong Kong involving a traveller returning from South Africa.

Generally, spike mutations allow viruses to adapt and become more virulent, and more able to evade natural and vaccine immunity.

Dr Tom Peacock, a virologist at Imperial College London, said the variant could be “of real concern” as its 32 mutations in its spike protein could enable it to more easily evade a person’s immune system and spread to more people.

On Twitter, he wrote that the variant “very, very much should be monitored due to that horrific spike profile” that could make it more contagious than any other variant so far.

He said: “Export to Asia implies this might be more widespread than sequences alone would imply.

“Also the extremely long branch length and incredibly high amount of spike mutations suggest this could be of real concern (predicted escape from most known monoclonal antibodies).

“Worth emphasising this is at super low numbers right now in a region of Africa that is fairly well sampled, however it very very much should be monitored due to that horrific spike profile (would take a guess that this would be worse antigenically than nearly anything else about).”

Virologists frequently identify new Covid variants that often do not exceed a small number of cases.

But Dr Peacock tweeted that he “hopes” the variant turns out to be one of these “odd clusters” and not as transmissible as feared.

Prof Francois Balloux, Professor of Computational Systems Biology and Director, UCL Genetics Institute, said the variant’s mutations are in “an unusual constellation” that “accummulated apparently in a single burst”.

He said that this indicates it could have evolved during a “chronic infection of an immunocompromised person, possibly in an untreated HIV/AIDS patient”.

Prof Balloux added: “I would definitely expect it to be poorly recognised by neutralising antibodies relative to Alpha or Delta. It is difficult to predict how transmissible it may be at this stage.

“So far, four strains have been sequenced in a region of Sub-Saharan with reasonable surveillance in place.

“It may be present in other parts of Africa. For the time being, it should be closely monitored and analysed, but there is no reason to get overly concerned, unless it starts going up in frequency in the near future.”

The first of the Botswana cases emerged on 11 November.

The first of the South Africa cases emerged on 14 November, the same day as the case involving a 36-year-old traveller – who had stayed in South Africa from 23 October to 11 November and tested positive three days into quarantine on his return to Hong Kong.

Dr Meera Chand, the Covid-19 incident director at the UK Health Security Agency, said that – in partnership with scientific bodies around the globe – the agency is constantly monitoring the status of new Covid variants worldwide.

She said: “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.”