Thread by @ewanbirney

Post-christmas COVID thoughts from dark Northumberland. TL;DR Omicron is rising across the world, and hospitalisations are following, but it seems clear Omicron-COVID is different from previous variants; the actions needed to steer a safe path in Omicron Europe are still murky

Context: I am an expert in human genetics and computational biology. I know expets in infectious epidemiology, viral genomics, immunology and clinical trials. I have some conflicts of interest; I am consultant and shareholder of Oxford Nanopore and was on the Ox/Az trial.

Brief recap; SARS-CoV-2 is a new human coronavirus which jumped from an animal host in late 2019. It causes a horrible disease, COVID, which often leads to death in a subset of people (older, more likely to be male and obesse) and can triggers a CFS-like disease, LongCOVID.

Over 2020 and most of 2021 societies reacted to this threat first by significantly dampening transmission of the virus and then by vaccines which were created in record time. Clinicians rapidly improved how they handled the disease, aided by large, fast clinical trials.

In late 2021 the first "endemic" variant appeared, Omicron, rapidly characterised by excellent work from South Africa. It had enough differences to evade immune systems educated either by previous non-Omicron infection or by 2-doses of vaccine.

(This "drift the major spike antigen" to prevent neutralising host immunity is how Coronaviruses roll; the 4 endemic human coronaviruses all do this, and its well documented in coronavirus infection patterns. So this is all expected if very concerning and complex to sort out)

Omicron is both immune evading (like Beta and Gamma before it) and fast transmitting (like Alpha and Delta), a potent combination which led to doubling rates of every 2 to 3 days; 10-fold in a week, 100-fold in 2 weeks. Case charts leap up as Omicron hits a country.

Thankfully good data linkage and tracking in England and Scotland both confirmed the immune evasion properties of Omicron and that 3-doses ("boosters") provided neutralising immunity to infection - hence the importance of booster and vaccination campaigns.

South Africa had relatively low hospitalisations and deaths compared to previous waves, suggesting that Omicron on top of previous infection at least was not as severe; this was confirmed by English+Scottish data showing less severity (in particular in double or triple vax)

Furthermore there is consistent reports of different biology (less ICU and Oxygen needs, different location of viral replication being more throat and less lung and nose) - all points to a different viral infection biology as well as immunity differences.

However, this shift in biology and less severity - extremely welcome - doesn't wipe out the risks as all healthcare serivces almost certainly cannot handle everyone who could get sick from this getting sick in the same 2 weeks.

The complications of the holiday season in Europe and America has made it even more complex to manage; Politicians responding to broad societal wishes of family celebrations have held off changes either post Christmas (eg Wales, Scotland, Germany) or beyond (England, France, US).

Holidays has also changed mixing patterns ( intergenerational), testing behaviour (far more deployment and use of rapid tests) + reporting. As such it is extremely hard to use current stats over these two weeks to know what is happening, though hospitalisations are most reliable.

(If there is a pundit on this site or other location who talk with confidence about the trajectory of any country from this week I would be very skeptical of claims).

As such countries have set the course this week; in something like 10 days from now we will be settling into new "exit from Omicron wave" schemes. Worth noting that South Africa has pretty much got through Omicron (at least my reading from SA epidemiology twitter).

What does an exit from Omicron need? We still don't know how much of Omicron's low severity extends to immunologically naive people, though the fast rising hospitalisations in US suggests not (though sorting out Delta from Omicron is still complex).

Clearly the safest position is to have as many people vaccinated (3-doses, first dose the most important). It seems unlikely one can easily prevent exposure as Omicron moves through the population, so unexposed, vaccine hestitant people are the biggest risk.

Here there is often I think too much focus on aggregate country numbers (78% vaccinated) and not enough on age-stratified vaccination numbers; more complex, harder to aggregate, sometimes not easily available (eg, Germany) and harder to explain, but the most important variable.

Omicron's infectiousness over 2-vax, previous also means there is a new workforce issue of isolation - important to really be on top of for healthcare workers. This greatly complicates navigating Omicron.

But we also have new weapons - eg anti-viral drugs (note a UK scheme to have pre-positioned test-at-home for vulnerable people with express couriered anti-virals to home to try to stop hospitalisations) and in-home monitoring for low risk discharge (oxygen meters)

Faster, immune evading Omicron infection but with less inherent severity and new clinical approaches means we have multiple variables moving around at the same time; even more complexity for analysts and ultimately decision makers.

It is tempting just to go slow - lockdown to get time to see perhaps mistakes or successes other countries make - and yet lockdowns themselves cause harm (we've not been collectively good at measuring them) and some things we desparately don't want to lockdown, notably schools.

Just as UK agonised in mid-december about how much one could extrapolate from South Africa on severity (somewhat it turns out, but it's complex), other European countries are going to agonise about how much they can extrapolate/understand from UK and DK, the early Omicron leaders

(France though looks like it is catching up with UK and DK quickly, in particular in Paris / Ile-de-France, and if Omicron takes off in PACA I guess we will understand even better Omicron severity in unvaccinated individuals).

No matter the course taken I think though it will go fast, because Omicron's infection rate is so fast. Hold tight, take care, and look after yourself, your family and your friends because Omicron is coming to everyone, quickly.