Month: November 2021

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:

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:

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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.

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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.

12) When I see a 🧬mutation divergence tree like this, it gives me pause. #Omicron is leaps & bounds different than other #SARSCoV2 variants. Evolution selected this unique combination for a reason—it wasn’t a regular rate of accumulating mutation errors. This is why the caution. pic.twitter.com/uRxTraxcMl

— Eric Feigl-Ding (@DrEricDing) November 29, 2021

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.

Europe (and other countries worldwide) seems to be in a starting phase of the new wave. To be honest, I am myself puzzled by the severity of the outbreak in some European countries; perhaps less in others.

So why suddenly are we seeing rapid growth in cases when we already thought the pandemic is over?

I can think of a range of reasons. A relatively low vaccine coverage or use of lower efficacy vaccines, vaccine efficacy waning, behavioural changes (abandoning all restrictions), winter (bringing people inside).

It is possible that we will not have a single explanation for all these countries and we might indeed be seeing different epidemics (i.e. driven by different factors) which we interpret as the same wave.

We might also be seeing countries at different stages of the outbreak, some (Bulgaria?) already being past the “fourth wave”, some having entered it in September (Austria, Poland), October (Denmark), some entering now (Germany, France, Portugal), and perhaps some that will either enter it later (USA), or never (Israel?).

It is also possible that Israel already had its “fourth wave” and thanks to its “burning out” effect and a rapid third vaccination campaign, managed to stop it.

So, what we are looking at in Europe now is Israel’s August-September wave shifted to November and perhaps magnified by other factors like lower overall vaccination and much lower restrictions.

The UK seems to be standing out, by having a rather steady, high level of epidemic cases. Again, possibly a combination of factors, including little effort in preventing spread in schools, a large proportion of AZ vaccines, no masks (in England).

Mark McLaughlin from The Times Scotland has recently asked me what I think about the current COVID-19 situation in Scotland and the direct and indirect impact of the pandemic on excess deaths. The resulting article can be found here (behind paywall). Here is a bit more detailed response to the question:

Why does coronavirus now account for less than half of excess deaths in Scotland?

Mark McLaughlin, rephrased

Two sources of data can be used to look at it in more detail. Firstly, Human Mortality Database (which I used in the past here) provides information on excess deaths, i.e. the number of deaths above (or below) the long-term average. Mortality varies from year to year, with particular increases in winters of bad seasonal flu. It also varies between seasons, with lower mortality in summer and higher in winter (in the Northern Hemisphere, and in the temperate climate zone). Over the last 19 months, most countries in the world have experienced many more deaths than usual – far exceeding the ‘usual’ variation.

Secondly, I have recently been looking in great detail at Scottish COVID-19 data, from the Public Health Scotland web page, particularly the number of reported cases and the number of deaths attributed to COVID-19.

Both sets of data are potentially problematic. Excess deaths have arguably been the best indicator of how severe the COVID-19 has been. It is because they are ‘clean’ and not prone to misinterpretation (The only possible query is for the date of death – is it when it is reported, or when it actually occurred? But this is really a minor quibble not affecting the magnitude and general pattern.). In most developed countries there is a very solid system of reporting deaths and it is not easy to either hide them or artificially inflate them.

Deaths attributed to COVID-19 might be more questionable. Most developed countries have adopted a criterion, usually a person whose death doctors attribute to COVID-19 within 28 days from the date of COVID-19 being diagnosed. But it is open to interpretation of whether a person died from or with COVID-19. Still, as long as the attribution is consistent, we can look at the general patterns, even if the numbers might be a bit uncertain.

In both data sets, we get three large waves, March-July 2020, September 2020-April 2021, and the most recent one. Mortality – both COVID-19 related and excess – is clearly reduced in the most recent wave, thanks to the vaccination rollout which thankfully preceded the third wave.

The first two excess mortality waves are clearly correlated with the case numbers and COVID-19-attributed deaths. Look how massive – and concentrated – the early 2020 peak was. Later on, we can clearly see the two peaks of the second wave – one in late 2020 and one in early 2021. In the first two waves, excess deaths follow COVID-19-attributed deaths quite closely, rising up and falling down in remarkable accord.

But not any more. In contrast, the current excess death wave is a slow-growing one which does really follow the ups and downs of the COVID-related deaths in the pictures.

My reading of it is that we now see a combination of three factors:

1. A delayed wave of non-COVID health problems caused by people not accessing health care over the last 19 months and by unhealthy life style last year – it might take several months for people who delayed their treatment last year and earlier this year to get to the point when they actually die of cancer, heart, or kidney failure.

2. A growing wave of COVID and non-COVID health problems caused by the effective collapse of health system now. Given my own experience of health care in Scotland I am not surprised – I have had some health problems recently and getting quality medical help was not easy as my GPs were clearly under duress. Additionally, getting medication in the local pharmacy is a challenge and takes days when previously it was either in stock or next day. A friend had to wait over the weekend to get an antibiotic for a serious infection.

3. Finally, an increase in COVID deaths caused by the current epidemic wave. Vaccines seem to work very well for 45-84 year olds, but I was surprised to see how close the data for cases and deaths follow each other for 85+ – meaning that a similar proportion of them have died with and without vaccines throughout the whole period.

Note also that we are now seeing many more cases – a lot of this is due to much better reporting but the current wave must be putting a lot of pressure on GP and hospitals.

So, what is the conclusion? It looks like we are in for a difficult winter of a double whammy – a combination of COVID-19 (which we as a society and our governments are not able or not willing to stop) and a long-lasting, slow but relentlessly growing wave of health problems caused indirectly by the pandemic.