Omicron – why so much concern

There has been quite a flurry of messages regarding the new strain of SARS-CoV-19, which now has a rather ominously sounding name, Omicron.

The name follows the WHO convention of using Greek letters to designate SARS-CoV-19 variants; omicron is the 15th letter, but two previous ones have been discarded due to similarities to a word ‘new’ in English and to ‘xi’, a common Chinese name).

We still do not know much about it, but I suspect it is the following information that has made the authorities concerned. Firstly, the number of new cases in South Africa have been dramatically increasing over the last two weeks:

Number of cases per 1 million people in Austria, UK and South Africa; updated 29th November

The rapid increase in South African data – note the logarithmic scale – mean that we are looking at a rapidly spreading virus.

I compare them here with Austria – where we did recently see a wave caused by the previous variant of concern, Delta, and with the UK which in recent months have seen a sustained epidemic of Delta.

Secondly, as seen below in a graph showing the most recent (November 29th) state of submissions of virus samples from different countries:

Within 2 weeks, Omicron managed to get from a few % to nearly 50% of all the reports from Africa. It is this rapid replacement of previous strains – most precisely, Delta – with the new strain (until recently South Africa had 96% Delta on 1st November and Botswana 97% on 15th November), that suggests that once the strain gets to the country, it will spread quickly.

This clearly reminds me of the spread of Alpha in late 2020 (below left) and of Delta in late May and early June 2021, (below right).

Such a rapid spread – associated with a very fast increase in disease incidence – suggests that we are possibly looking at a similar risk as in the previous (second/third and third/fourth) waves.

This stands in contrast to some “unsuccessful” mutations, like Mu which failed to take off:

The graph above clearly shows Mu originating in Colombia, then spreading to other countries and continents, but unable to compete with Delta and the pressure from vaccination.

Thirdly, Omicron seems to be spreading quickly across the world, as seen below, not only making single jumps but even travelling from South Africa to Australia to Europe (state of November 29th).

Fourthly, Omicron seems to be a completely new set of mutations that potentially can overcome the immunological protection inferred either by previous infection or vaccination.

A graph below – from Eric Feigl-Ding shows the mutation divergence tree – a way to explore how similar or dissimilar are different traits. Omicron seems to be very different to other traits which makes it an especially dangerous one.

Finally, to put to rest statements that Omicron arose in response to vaccination pressure, it is worth noting that while South Africa has made quite a lot of progress recently in vaccination, it has a relatively low proportion of people double vaccinated.

Clearly, this picture will change over the next few days and weeks, as we learn more about the spread. The key feature is that unlike some other recent variants (like Lambda of Mu), it caused quite a few red flags to be raised and so it is prudent to put control of it at the centre of our attention.

Graphs above from OWD and GISAID.

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