A heavily-mutated Covid variant emerges in southern Africa: Here's what we know so far

The World Health Organization will meet on Friday to discuss a new heavily-mutated variant of Covid-19.

The variant known as B.1.1.529 has been detected in small numbers in South Africa, WHO officials said, with reports on Friday morning of cases being found in Israel and Hong Kong.

Here’s what we know so far:

South African scientist Tulio de Oliveira said in a media briefing held by the South Africa Department of Health on Thursday that the variant contains a “unique constellation” of more than 30 mutations to the spike protein, the component of the virus that binds to cells. This is significantly more than those of the delta variant.

Many of these mutations are linked to increased antibody resistance, which may affect how the virus behaves with regard to vaccines, treatments and transmissibility, health officials have said.

In total, de Oliveira said the variant contains around 50 mutations. The receptor binding domain (the part of the virus that first makes contact with cells) has 10 mutations, far greater than just two for the delta Covid variant, which spread rapidly earlier this year to become the dominant strain worldwide.

This level of mutation means it’s possible that it came from a single patient who could not clear the virus, giving it the chance to genetically evolve. The same hypothesis was proposed for the alpha Covid variant.

Dr. Maria Van Kerkhove, WHO’s technical lead on Covid-19, said in a livestreamed Q&A on Thursday that scientists “don’t know very much about this yet” and that it would take a few weeks to gain a full picture of how the variant reacts to existing vaccines.

‘Most significant variant’ to date

The U.K. immediately moved to ban flights from South Africa, Lesotho, Botswana, Namibia, Eswatini and Zimbabwe from noon on Friday to 4 a.m. local time on Sunday.

The U.K. Health Security Agency is investigating the variant, which Health Secretary Sajid Javid said is “potentially concerning.” No cases have yet been identified in the U.K., and Javid emphasized that although more data is needed at this early stage, the government had opted to take precautions.

“This is the most significant variant we have encountered to date and urgent research is underway to learn more about its transmissibility, severity and vaccine-susceptibility,” said U.K. HSA Chief Executive Jenny Harries.

Israel has also barred travel to several southern African nations over the new variant, as well as Singapore and several other nations. Israel has reported one case of the new variant in a traveler returning from Malawi.

Israeli Prime Minister Naftali Bennett met with health experts on Friday to discuss the country’s response, which could reportedly include declaring a state of emergency.

However, the WHO on Friday cautioned countries against the hasty imposition of travel restrictions. Spokesman Christian Lindmeier told a U.N. briefing in Geneva that governments should take a “risk-based and scientific approach,” and stressed that it will take researchers several weeks to understand the variant’s potential impact.

“It looks like this particular variant has a very concerning sets of mutations especially in the spike protein, which is needed for its transmission properties as well as its protection against the vaccines, so based on the genetic information we are quite concerned about it,” Pasi Penttinen, public health emergency response manager at the European Centre for Disease Prevention and Control, told CNBC Friday.

“We still have a lot more to learn about the situation in South Africa and all the efforts should now be not only in South Africa, but countries in the southern African region, to ensure that they get a full picture of this virus.”

However, Francois Balloux, an epidemiologist and director of University College London’s Genetics Institute, told the BBC on Friday that the early discovery of the variant could render it easier to contain.

Balloux added that even if B.1.1.529 is more transmissible than previous variants, it would not “bring us to square one” in the effort to contain the virus. He suggested that it should be seen an irritating setback rather than a rebirth of the pandemic.

The first genomes of the new variant were uploaded to the international GISAID database on Nov. 22, but genomes have now been uploaded from South Africa, Botswana, Hong Kong and Israel, with the extent of the spread not yet known.

Cases have been concentrated so far in Gauteng, South Africa’s most populated region and home to almost 16 million people, South African Health Minister Joe Phaahla said during Thursday’s briefing.

The two cases in Hong Kong were identified in a quarantine hotel, with one person who traveled from South Africa suspected to have passed the virus on to a person in a neighboring room.

The new development comes as cases of Covid-19, mostly the older delta variant, surge around the world heading into the winter months. Multiple countries in Europe, in particular, have seen record spikes, and have implemented strict containment measures.

William Schaffner, professor of preventive medicine at Vanderbilt University, told CNBC Friday that suggestions that the variant could be more transmissible than delta, and that it could evade vaccine protections, meant it is “a matter of some serious concern.”

“The delta variant is already extraordinarily transmissible. It is really difficult to think of another virus that is more transmissible,” Schaffner told CNBC’s “Squawk Box Asia.”

“If we have another Covid strain that can spread even more readily than delta, that would pose a challenge to all of us around the world, because when delta arrived this summer, it changed the game.”

One positive so far, however, is that the variant has not yet been associated with more severe cases of Covid-19, Schaffner noted.