A Coronavirus view from London and Europe: TL;DR The Omicron storm is hard for healthcare management in the UK, but less deadly than feared; London leads the UK out with many indicators dropping; Is the UK experience going to replicate elsewhere?
Context: I am an expert in human genetics and computational biology. I know experts in infectious epidemiology, viral genomics, public health and clinical trials. I have some COIs - I am consultant and shareholder to Oxford Nanopore and was on the Ox/Az trial.
Key recap; the latest substantially different in biology variant of SARS-CoV-2, Omicron, will infect on top of previous SARS-CoV-2 infection and on top of double vaccination; triple vaccination less so.
Omicron causes different symptoms, replicates in different places in the airways and, at least for people with previous infection (often the case in South Africa) or at least double vaccination (often the case in UK) an infection is less likely to lead to ICU admission.
Omicron's immune invasion and eye-wateringly fast transmission means it moves very fast through populations - all countries have it. This fast transmission places a different type of stress on healthcare than the earlier waves.
Firstly there are many people with milder COVID or asymptomatic infection and another ailment in hospital, but these people *still must be treated in infection-control wards*. Hospitals are (unsurprisingly) enriched in at risk people with poor health, so infection control is key.
Secondly good management of the infection means many healthcare workers must be kept out if infected and/or risk of infection if close contact. This reduction in staff numbers makes dealing with this complex rush hard.
These are different stresses, but very real stresses on hospitals, and key to prevent more harm (infected people in a moment of poor health is exactly how to cause more harm). Although the individual risk is far lower, the system risk is different and high.
I know colleagues in the NHS, and they seem broadly like they are coping, but I am not an expert or know experts in hospital stress/workforce management etc. Like a lot of the UK COVID twitter, I rely on @ChrisCEOHopson as an active barometer on this.
London has turned in virtually all indicators (though the resumption of school might upset all of that); North West is plateauing on admissions, and North East looks like it might have the highest peak in this wave.
Looking beyond UK many places in Europe, such as Denmark, France, Italy, Spain, Portgual and Republic of Ireland are broadly going for the same "flatten the curve somewhat, but accept most people will be exposed, many infected".
I personally think the key metric here is triple vaccination levels >60; this will I think be "at risk" people for hospitalisation, and if this is too big, flattening curves wont be able to impedence match the exponential growth of cases wrt fixed/linearly scaleable healthcare
Here if the UK can get through this Jan, so should Portgual, Spain, Denmark, Ireland. By the aggregate numbers UK and France's vaccination are v. similar, but France has a bigger gap in the older ages (UK's gap in the younger). France's healthcare has more capacity though.
(though if I am not an expert on UK Healthcare operations I am even less informed on French! But this is what I pick up).
The other aspect is not to forget about Delta; both in the US and in South East France, a fair bit of the current hospitalisation and ICU is Delta continuing to grow, in some ways hidden by the huge Omicron case numbers.
Netherlands and Germany are in a somewhat different position; their control of Delta (which broadly worked in both places, with the usual aspects of reducing life/economy) merged into controlling Omicron but now cases are rising again, driven by Omicron
(Asides: One for the transmission officiandos is that the relative growth of Omicron in Germany vs Delta has been less than in the UK; basic hypothesis is that the shorter generation time of Omicron makes NPIs (eg, FFP2 mask wearing) more effective.
The other endless conundrum is that in the UK there is some "smudging" of the top of infection curves locally - falling off exponential growth at higher case levels. I personally think this a feedback loop of local cases and free+easy testing in the UK (this has worked well)
In Germany the Omicron rise is in the cities (eg, Hamburg + Berlin) and the west. Even the usually best-in-class Schleswig-Holstein has high case levels. The German East (former East Germany) is about 1 or 2 weeks behind.
However, Germany has an even bigger older vaccination gap, in particular in former East German states (Saxony and Thuringia). Closing this gap is key, and I personally think more engagement (door to door?) and carrots (vouchers?) rather than sticks (mandates)
This gap is also present in Austria, which has a similar problem of how to close that gap or somehow navigate Omicron's hopsitalisation flows. Netherlands booster campaign was slower than much of the rest of Europe last autumn so they have play catch up.
I am ... broadly hopeful (as ever) and we're shifting phases, but the fact we're shifting doesn't make it *easy* to do (in particular, to stress, in healthcare delivery in this) and we've got plenty of things that can still go against us.
However, I do think 2022 will be better than 2021.

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More from @ewanbirney

2 Jan
Gather around again for a tweet-thread about "models", their types, what they are (and aren't) and how to use and comment and/or critique them.
First off, models are always ways of understanding the real world. The well worn adage, "all models are wrong, some models are useful" serves you well, and focuses on *utility* of models rather than correctness.
Already you can see you might change what is useful in different settings - indeed, there are some very practical constraints about what things one can or cannot do because we have both time and decisions - this is a system with *lots* of endogenity as the economists would say.
Read 25 tweets
1 Jan
Paging English grammarians. My daughter and I are exploring conditional clauses with objects that change, eg meteor (can be hurtling through space or burning up in the atmosphere) vs shooting star (must be in burning in the atmosphere)
This sentence seems kosher “if Jupiter hadn’t blocked it, a shooting star would have hit earth” whereas “if Jupiter hadn’t blocked the shooting star, it would have hit earth” feels wrong (when Jupiter is doing the blocking it’s not a shooting star)
Both sentences are right if we swap in meteor as it’s valid in both contexts.
Read 5 tweets
31 Dec 21
I think for the second day running of high wind across the UK the North Sea link has run at full capacity in both directions - over night back to Norway, during the day to the UK (great website grid.iamkate.com from @KateRoseMorley) Image
This is to my very amateur energy eyes the system working as expected - using Norway as a massive grid scale battery (as one can often control trad hydro flow doesn’t need to be pumped hydro - just offsetting Norwegian electricity supply)
More wind farms in the U.K. will increase the frequency of this and the Viking link will increase the ability to offset into the high hydro Scandinavian market I think
Read 7 tweets
28 Dec 21
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.
Read 25 tweets
23 Dec 21
COVID thoughts from beautiful, misty Northumberland. TL;DR As expected, Omicron is exploding in numbers in cities and beyond worldwide. Reassuringly Omicron infections are less likely to end up in hospital, but whether this reduction in severity is enough to be safe is unclear
Context: I am an expert in human genetics and computational biology. I know experts in infectious epidemiology, viral genomics, immunology and clinical trials. I have some conflicts of interest: I am a consultant and sharehold of Oxford Nanopore and I was on the Ox/Az trial.
Reminder: Omicron is the first "antigen drift" variant with fast transmission from SARS-CoV-2. This drifting antigen presentation on spike is one of the ways Coronaviruses shift their appearance to our immune system, so it was expected, though always not fully appreciated.
Read 32 tweets
22 Dec 21
With Scottish, English and South African data all in hospitalisation risk given infection all coming in below 50% (range I think 80% lower SA to 60% lower, English some endpoints) this key parameter is firming up. Frustratingly in the balance from my reading of the SPI-M models
(plus "what does xx% lower mean - xx% per infection or per equivalent infection knowing that Omicron reinfects etc," and how does one factor this vs vaccination and age - so much detail here to nail down)
Basically, good news, and provides narrower spaces for models (both forward models and backward models on infection levels as hospitalisations are more completely ascertained than cases etc).
Read 4 tweets

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