Two new variants of COVID-19 which appear to have emerged in Southern Africa are raising extremely serious concerns around the world. The variants—known as C.1.2 and B.1.1.529—appear to have a worrisome combination of changes, including changes that could make them highly evasive of antibodies from both vaccines and previous infections. Of particular concern: these variants appear to be more contagious than the already highly infectious delta, with the B.1.1.529 variant in particular going from a small cluster of cases, to local dominance, almost overnight.

The B.1.1.529 variant, which could gain the label “nu” following a World Health Organization meeting on Friday, is raising concerns great enough that both Israel and the U.K. have moved quickly to ban travel to and from the region where this variant has been identified. First identified in Botswana, the variant was initially tagged as a “very small cluster” (4 cases in Botswana, 77 in South Africa, and 1 case in Hong Kong). However, as virologist Tom Peacock of Imperial College quickly noted, the number of mutations seen in this variant are “really awful” and give it a “horrific spike profile.”

Other variants showing extreme mutations on the spike protein have been identified before, and several of these have contained changes that suggested they could be more evasive of antibodies from existing vaccines and past infections. However, these past variants have proven to be less infectious than delta and haven’t become dominant outside of small areas. That doesn’t seem to be the case this time around. The C.1.2 variant had been gaining ground against delta in South Africa over the last few weeks, and now early data suggests that the B.1.1.529 is ferociously infectious. Possibly 500% more infectious than delta. 

Friday, Nov 26, 2021 · 6:20:52 PM +00:00 · Mark Sumner

The WHO Technical Advisory Group has officially tagged B.1.1.529 as “Omicron.” Which sounds more than a little threatening.

The upside to this: You will not have to go through the next six weeks with people correcting how you pronounce “Nu.”

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            Friday, Nov 26, 2021 ·  7:09:29 PM +00:00

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      Mark Sumner
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            Friday, Nov 26, 2021 ·  7:37:45 PM +00:00

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    <a href="https://www.reuters.com/world/americas/canada-closing-borders-citizens-seven-southern-african-nations-over-covid-19-2021-11-26/">Reuters</a> reports that Canada is also closing its borders to travelers from seven southern Africa nations. 

At the moment, there are no known cases of the omicron variant in either the U.S. or Canada. However, it seems unlikely that either nation has avoided some cases, either arriving directly from the nations involved, or secondhand. 

Bioinformatician Tulio de Oliveira, in discussing the variant on Thursday, notes that the variant carries 32 mutations on the spike protein alone. That protein is the portion of the virus which it uses to attach to human cells. Portions of the spike protein were targeted by vaccines for triggering an immune response. So changes to this region can both alter how effective the virus is at causing infection, and make it more difficult to halt with existing vaccines.

Initial hopes were that the number of changes to the spike protein might actually make this variant less transmissible, due to the critical role that region plays in allowing the virus to invade human cells. However, this does not seem to be the case. Following the small cluster identified earlier in the week, it now appears that this variant makes up 100% of the cases subsequently identified in a  part of the Gauteng province of South Africa. The single case in Hong Kong—a traveler from South Africa—was followed by another in Israel. Following this case, Israel ended travel to South Africa, Lesotho, Botswana, Zimbabwe, Mozambique, Namibia and Eswatini. The U.K. also moved to temporarily ban travel to six countries, with returning U.K. travelers to be quarantined.

What’s raising the greatest concern may be that, within the areas where the variant has been identified, it seems to have rapidly displaced other variants, including delta, with early estimates suggesting that it could be roughly five times more contagious. As the BBC notes, this variant seems to contain several changes that are thought to make it easier for the virus to spread.

All of this sounds very much like a worst case scenario — a version of COVID-19 that’s much more infectious than the variant that is still causing enormous spikes even in areas where vaccination levels are relatively high. Germany is now seeing new cases at a rate that far exceeds past records. The U.K. seems to be locked into a perpetually high rate of cases that has persisted for months. While case counts fell in the U.S. from August to early October, they have been rising again with expectations that holiday travel could trigger a new surge of cases. Daily deaths in the United States remain around 1,000. And all that’s without any new super-variant.

Epidemiologist Eric Feigl-Ding, who was one of the first to warn that even the original European variant of COVID-19 was “thermomolecular panic level bad,” is extremely concerned about the apparent level of contagion represented by B.1.1.529. That’s especially true since that one traveler to Hong Kong has already generated a second case from casual hotel contact.  Feigl-Ding also noted that, even before the emergence of the variant that has been generating so much concern, the C.1.2 variant has been displacing delta in South Africa. 

Despite all the fearful warnings, Reuters reports that the World Health Organization is urging nations not to move too quickly in imposing travel restrictions until the situation is better understood. The number of cases is still small, and the apparent super-dominance of B.1.1.529 could be largely an artifact of selective sampling. The WHO will convene a meeting on Friday to evaluation the new variant, and whether it rates being given the “nu” label — the next available Greek letter for variants of concern. 

The WHO Weekly epidemiological update for November 23, actually showed a 30% decrease in deaths across Africa. There is no available data at this point to determine whether the B.1.1.529 or C.1.2 variants are more or less virulent than other variants.

BioNTech, whose vaccine is distributed around the world by Pfizer, has indicated that it will take them weeks to determine how this new variant changes the effectiveness of existing vaccines. Both BioNTech and Moderna developed their original mRNA vaccines using RNA sequencing provided by China in January, 2020, and while another vaccine could also be developed to match the new profile of variants such as delta or B.1.1.529, it’s unclear how much time would be required to test, produce, and distribute an updated vaccine. 

Friday, Nov 26, 2021 · 3:22:54 PM +00:00 · Mark Sumner

Friday, Nov 26, 2021 · 3:38:42 PM +00:00 · Mark Sumner

Friday, Nov 26, 2021 · 4:22:52 PM +00:00 · Mark Sumner

Clinking through the Reuters link, you can join the Q&A in progress.