What Do We Know About The B.1.1.529 ("Omicron") Variant?

Short Answer: Not Much

In the past day, the media has quite literally run amok over a new COVID-19 variant, now labeled “Omicron”, with its formal taxonomy given as B.1.1.529. Despite pleas from the WHO to not get ahead of the facts, speculations about the variant are spreading faster than the virus.

Medical experts, including the World Health Organization, warned against any overreaction before the variant that originated in southern Africa was better understood. But a jittery world feared the worst nearly two years after COVID-19 emerged and triggered a pandemic that has killed more than 5 million people around the globe.

The necessary question has quickly become “What do we know?” Other than that B.1.1.529 is a SARS-COV-2 variant, the short answer is “not much”. We do not know, and the experts do not know, how significant this variant will be.

A Short History Of B.1.1.529

The B.1.1.529 variant was first isolated in the south African country of Botswana on November 11. Cases with that variant were soon detected in South Africa and Hong Kong.

There have been 77 fully confirmed cases in Gauteng province in South Africa, four cases in Botswana and one in Hong Kong (which is directly linked to travel from South Africa). 

Cases since have been recorded in Belgium and Israel as well, attributed to travelers from South Africa. This last point is significant, because while there has technically been a case in Belgium, as of this writing there are no reports of local viral transmission.

That, in a nutshell, is the brief history of B.1.1.529

Lots And Lots Of Mutations

According to Tulio de Oliveira, the director of the Centre for Epidemic Response and Innovation in South Africa, the main cause of concern among virologists epidemiologists is the extraordinary number of mutations found within the genome, far more than is typically seen in a new variant.

In a media briefing Prof de Oliveira said there were 50 mutations overall and more than 30 on the spike protein, which is the target of most vaccines and the key the virus uses to unlock the doorway into our body's cells.

By comparison, the “Delta” variant only had nine to its spike protein. On the basis of mutation count alone, this variant is a significant evolutionary jump.

We also may be relatively certain that B.1.1.529 is not an offshoot of Delta. As epidemiologist and fellow Substack publisher Dr. Katelyn Jetelina, MPH PhD points out, nowhere in the variant's traceable lineage is there a link to the Delta variant.

We know that B.1.1.529 is not a “Delta plus” variant. The figure below shows a really long line, with no previous Delta ancestors. So this likely means it mutated over time in one, likely immunocompromised, individual.

The high number of mutations on the spike protein used by the various COVID-19 inoculations also raises the concern that the antibodies produced by the inoculations will be significantly less effective against B.1.1.529. However, at the present time, local transmission of the variant outside of Africa has not been documented; given Africa's low inoculation rate, the potential of the variant to sidestep the antibodies generated by the inoculations remains for now a speculation.

Coming On Strong?

While definitive metrics on how fast and how well B.1.1.529 spreads have yet to develop, early indications from South Africa suggest the variant can spread easily. Professor de Oliveira on the 25th tweeted that the variant was outcompeting Delta in South Africa:

According to de Oliveira, this new variant, B.1.1.529 "seems to spread very quick! In less than 2 weeks now dominates all infections following a devastating Delta wave in South Africa (Blue new variant, now at 75% of last genomes and soon to reach 100%)"

Early indications also suggest this variant is the culprit behind South Africa's recent surge in cases, which began late last week, less than two weeks after the previous outbreak had subsided.

However, that seeming transmissibility is contradicted by Botswana's outbreak experience, which saw a very brief outbreak that faded as quickly as it began by November 11.

If Botswana's mini outbreak was due to B.1.1.529, the variant seems to fade quickly.

We Know Where It Isn't

We may be reasonably assured the variant is not spreading in Europe yet. For now, the sequenced samples of SARS-COV-2 from Europe are literally all of the Delta lineage.

So far, the B.1.1.529 variant is in South Africa. How quickly it spreads into other regions is as yet unknown.

We may also be somewhat assured this variant did not arise in an inoculated host. While both South Africa and Botswana are ahead of Africa as whole on inoculations, they both lag Europe significantly.

As a matter of simple probabilities there are fewer inoculated hosts in either African country in which a new variant can arise. Whether this raises or lowers the odds inoculation-generated antibodies will be proof against the virus remains to be seen.

Botswana The Rare African Hotspot

The B.1.1.529 variant is also remarkable for where it first appeared and where it has spread so far. Botswana is very much the outlier in Africa with respect to the pandemic, having daily case numbers far more typical of Europe than of Africa. South Africa has had a somewhat better time than Botswana, but it, too, runs much higher daily case counts than Africa as a whole.

However, Botswana had already experienced a significant outbreak from July through October when this variant appeared. New variants typically arise at the beginning of an outbreak, not at the end.

That this variant appears to have then spread to Hong Kong, Israel, and Belgium and not the neighboring Democratic Republic of the Congo is for now another intriguing question.

Everything Else Is Speculation

This, in a nutshell, is what we know about the B.1.1.529 variant, aka Omicron. This is the factual data we have.

We do not have, and the experts do not have, good answers as to the exact significance of the many mutations in the strain.

We do not have, and the experts do not have, solid data on how transmissible the variant is, or how likely it is to cause severe infection.

We do not have, and the experts do not have, solid data on how this variant will fare against the inoculations.

This data will come in due time. That time is not yet due.

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