New COVID-19 variant with high number of spike mutations a 'concern': researcher

toronto -

A scientist in the United Kingdom is taking note of a COVID-19 variant originating from Botswana with an astonishing number of mutations, though there have only been 82 confirmed cases to date.

The B.1.1.529 variant was first discovered in the southern African country and has since been discovered in South Africa and in a traveller in Hong Kong who had been to South Africa. In a briefing on Thursday, South African officials reported 82 cases of the variant, 77 of which are in South Africa.

Tom Peacock, a virologist at Imperial College London, said earlier this week that its potential is worth noting due to its 32 spike mutations, even though there had only been 10 confirmed cases at the time.

• Newsletter sign-up: Get The COVID-19 Brief sent to your inbox

“Export to Asia implies this might be more widespread than sequences alone would imply,” Peacock wrote on a website for genome sharing. “Also the extremely long branch length and incredibly high amount of spike mutations suggest this could be of real concern.”

Mutations in the spike protein, or spike mutations, can change the way a virus infects cells and spreads. These mutations can also make it harder to for the body’s immune system to attack it.

The World Health Organization currently lists B.1.1.529 as a “variant under monitoring,” which is below the agency’s classification of “variants of interest” and “variants of concern.”

On Thursday, the United Kingdom announced it would be banning flights from South Africa, Namibia, Botswana, Zimbabwe, Lesotho and Eswatini as a precaution. Travellers returning from these countries would have to quarantine.

Dr. Peter Juni, an epidemiologist at the University of Toronto and a member of Ontario’s COVID-19 Science Advisory Table, told CTV News Channel on Thursday that these sorts of cases are why border restrictions are important.

“This combination of two doses of a vaccine plus one negative test -- it can also be a rapid test -- that’s just a good safeguard against importing these sorts of variants too early into the province,” he said. “It happened before with Alpha, it happened with Delta, we don’t want it once more.”

In a Twitter thread about the variant, Peacock called the spike mutation profile “awful,” but emphasized the low case numbers make it only something to keep an eye on for now.

“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,” he said.

“It’s possible this is just an odd cluster that isn’t very transmissible. I hope that’s the case,” he wrote in another tweet.

Francois Balloux, professor of Computational Systems Biology and director of University College London’s Genetics Institute said in a statement that B.1.1.529 has an “unusual constellation of mutations” and likely evolved during a prolonged infection of an immunocompromised person.

“I would definitely expect it to be poorly recognised by neutralising antibodies relative to Alpha or Delta,” he wrote. “It is difficult to predict how transmissible it may be at this stage.” 

Balloux said that the variant is not one to be overly concerned with, unless “it starts going up in frequency in the near future.”

For Juni, this new variant is something to keep an eye on, but not one to make an drastic adjustments just yet.

“It’s important to monitor it, but we shouldn’t be overly concerned right now,” he said.

“Let’s remember (the virus is) about indeed invading the immune system – that’s one aspect – but it’s also about how well it transmits to other people and how well it can propagate. So when you just take all of that into account, we will see what happens.”

With files from Reuters

A final observation - this variant contains not one, but two furin cleavage site mutations - P681H (seen in Alpha, Mu, some Gamma, B.1.1.318) combined with N679K (seen in C.1.2 amongst others) - this is the first time I've seen two of these mutations in a single variant...

— Tom Peacock (@PeacockFlu) November 23, 2021