A new variant of COVID-19 identified in Botswana and Nigeria with dozens of mutations is being watched closely, amid fears it could be resistant to the effect of currently-used vaccines.

The B.1.1.529 variant has more mutations affecting the spike protein targeted by vaccines than any other strain identified to date, although it’s not yet clear if it is more or less transmissible.

There have only been a few confirmed cases so far, including 77 in Gauteng Province South Africa, three in Botswana, six in South Africa where surveillance is more robust, and one in Hong Kong in an individual who travelled from South Africa before being tested.

The mutations in the spike protein has been described as “really awful” by Tom Peacock, a virologist at Imperial College’s department of infectious disease. In pango-designation on Github he suggested the following new lineage

He also said that while case numbers are still very low, B.1.1.529 should be monitored carefully as the mutations suggest it “would be worse antigenically than nearly anything else about.”

Prof Francois Balloux, director of the UCL Genetics Institute in London, said that the large number of mutations might indicate the variant evolved “during a chronic infection of an immunocompromised person, possibly in an untreated HIV/AIDS patient.”

He also said that it would likely be poorly recognised by neutralising antibodies against the alpha or delta variants, but added it is difficult to predict how transmissible it may be 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,” said Balloux.

One the positive side, there are signs that another variant that was causing concern earlier in the year – B.1.628 – seems to have fizzled out.

The strain was identified in the US and drew attention because it was the first evidence of a recombinant form of SARS-CoV2, generated when two strains combine in a con-infected person.

There are fears recombination could be a driver for the creation of new, more aggressive strains, but in this case the variant reached a global prevalence of around 0.5% before becoming extinct.

“There is no evidence it [was] more transmissible, virulent or better at evading immune recognition than other SARS-CoV-2 lineages,” commented Balloux.

The Minister of Health Dr Joe Phaahla called an emergency media briefing on Thursday afternoon, 25 November, to update the country on the emergence of the B.1.1.529 COVID-19 variant.

Phaahla was joined by representatives of the National Institute of Communicable Diseases (NICD), the National Health Laboratory Service (NHLS) and the Network for Genomic Surveillance in South Africa (NGS-SA).

Professor Tulio de Oliveira, the director of the Centre for Epidemic Response and Innovation (CERI), and Dr Richard Lessells led the presentation that detailed what the authorities know about the B.1.1.529 thus far.

“Unfortunately, we have detected a new variant, which is a reason for concern in South Africa,” said de Oliveira.

The new variant detected in the country has a high number of mutations, which are concerning to the authorities because while they recognise some of the mutations – as they are present in other variants – the full significance of B.1.1.529 is not yet known.

However, it is predicted to have significant immune evasion and enhanced transmissibility.

De Oliveira said South Africa has requested an urgent meeting with the World Health Organization (WHO) – possibly on Friday – so that the new variant can be assigned a Greek name (Delta, Beta, etc).

“It is very important to understand that even though we detected it here, very quickly, it doesn’t mean that this variant is from South Africa and we shouldn’t use any country’s name to avoid discrimination.”

The first B.1.1.529 genomes were produced from samples collected between 12 and 20 November in Gauteng (77).

De Oliveira explained that the B.1.1.529 variant was first discovered on Tuesday 23 November at around 14:00. The samples it was detected were collected between 14 to 16 November, which coincides with the start of the rise in infections in Johannesburg.

An hour later, the NGS-SA, health department and DSI called an urgent meeting to discuss the results. On Wednesday, more tests and analysis confirmed that the variant was concerning and the first reports of similar cases being reported in Botswana and China trickled in.

On Thursday morning, the health and science ministers were briefed, and later the information was made public.

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