Concerning new Covid-19 variant detected in South Africa — What we know so far

A new Covid-19 variant with a high number of mutations has been detected in South Africa, and scientists have warned that it could be more resistant to immune cells that attack the virus.

Virologist at the Imperial College London, Tom Peacock, provided details about the variant in a series of tweets.

“Just spotted: very small cluster of variant associated with Southern Africa with very long branch length and really awful spike mutation profile,” Peacock stated.

The first case of the variant was detected in Botswana, where three total cases have now been confirmed.

Six cases have since also been detected in South Africa.

A Hong Kong resident also tested positive for the variant shortly after returning from a trip to South Africa.

The World Health Organisation has designated the variant as B.1.1.529 as “Variant Under Monitoring” on 24 November 2021.

The organisation describes such a variant as one “with genetic changes that are suspected to affect virus characteristics with some indication that it may pose a future risk, but evidence of phenotypic or epidemiological impact is unclear”.

It adds such a variant requires enhanced monitoring and repeat assessment pending new evidence.

Peacock emphasised that the number of cases was “super low” in a region of Africa that is reasonably well sampled, but warned that it should be monitored due to the “horrific” spike profile.

“Would take a guess that this would be worse antigenically than nearly anything else about,” he added.

Tom Peacock, a virologist at the Imperial College London

Cambridge University professor of clinical microbiology Ravi Gupta told The Guardian his lab found that two of the mutations found in B.1.1.529 increased infectivity and reduced antibody recognition.

“It does certainly look a significant concern based on the mutations present,” Gupta said.

However, he said the variant’s infectiousness was unknown. Transmissibility was the factor believed to be the main reason for the sharp increase in cases of the prolific Delta variant.

Director of the UCL Genetics Institute, professor Francois Balloux, also told the publication the large number of mutations in the variant apparently accumulated in a “single burst”.

This suggested it might have evolved during a chronic infection in someone with a weakened immune system, possibly an untreated HIV/Aids patient.

A case study previously found that a South African woman with uncontrolled HIV had the virus in her body for at least 216 days. During that time, the virus had mutated a lot.

Balloux also expected the new variant to be poorly recognised by neutralising antibodies relative to Alpha or Delta.

However, the transmissibility was challenging to predict at this stage.

“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,” Balloux said.

MyBroadband asked the National Health Department for feedback on the new variant, and we will update this article with their response.

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Concerning new Covid-19 variant detected in South Africa — What we know so far