Thread by @ewanbirney

Thoughts on COVID in Europe from a crisp morning in London; we understand this virus, its likely endpoint, but it is hard road to follow. Central/Northern Europe start a 4th nasty wave; South West Europe has vaccinated well, (currently) less of a wave; the UK remains a conundrum

Context: I am an expert in human genetics and computational biology. I know experts in infection biology, viral genomics, clinical trials. I have COIs - I am longstanding consultant to Oxford Nanopore (makes sequencing machines) and was on the Ox/Az trial.

Reminder: Assumming there is no major new SARS-CoV-2 variant, we have the measure of this virus and its horrible disease - it transmits rapidly between humans, causing a nasty, often lethal disease (COVID) in some (older, more overweight) people who are immunlogically naive.

remarkably science has created a suite of effective vaccines, the best of which are the mRNA type, which educate peoples' immune systems. These dramatically reduce hospitalisations, somewhat reduce transmission. A 3rd dose ("booster") strongly increases efficacy of both endpoints

Due to waning immunity (a hallmark of Coronaviruses), of new humans (babies) and animal resevoirs we are very unlikely to eliminate this virus; the most likely endpoint is an seasonal endemic virus which adds to the list of viruses that cause disease, mainly in the elderly

However, to get to this state, effectively everyone must have had exposure to either vaccine or infection, and many people both; the question is how much - and the rate - of hospitalisations happen during this exposure process.

For countries with high levels of vaccination, such as Denmark, Spain and Portugal, once they have completed their booster campaigns there are as armed as one can be for this transition. With the colder weather providing more indoor settings Denmark is walking this road first.

Eastern and Central Europe suffered heavily previous winter and it looks like another tough winter due to the lack of depth of vaccination in many countries. I am not so atuned to these countries to understand them in the same depth as western European countries.

For countries with a significant gap in vaccination, in particularly across society, such as Austria and Germany (in particular Eastern and Southern Lander) they have a far more complex path; no healthcare system can cope with exponentially rising hospitalisations at this level.

This is why lockdowns have been enforced again (eg, Austria, Netherlands) though note this really just buys time to do something else; the most important thing being vaccination. Unpicking, cajouling, reseting or somehow unwinding the anti-vax sentiment I think is key.

The federalised health system in Germany, its poor digital health and the inevitable need to share healthcare capacity in this coming wave is going to give Germany - a country with an excellent track record so far - it's harshest test this pandemic. I hope it is not too awful.

France has previously clustered closer to the Spain and Portugal on transmission (warmer weather?) but has just seen a strong uptick in transmission. The French vaccination is pretty deep (in aggregate numbers similar to UK) but has a bigger gap than the UK in the older ages

This means, like everywhere, the French booster campaign is critical. Given the last week's case numbers I think France is heading closer to a (north) German situation than (say) Spain/Portugal.

(this goes to the massive age-dependent aspect of this disease - a vaccinated 70-year old is 10-50 fold more beneficial to lowering healthcare burden than a vaccinated 35 year old, and why one needs to really stratify vaccination by age.

This also goes to the gaps in the German system where for example the age stratification of vaccination is hard to get out to even know the risks different regions are running).

The UK made a choice to relax restrictions over the summer, with scenario modelling show the possibility of an "early" 4th wave as a result. To the surprise of many people this did not happen, but rather a long, drawn out plateau of infections and healthcare burden.

Quite why this has occurred is complex; there must be some sort of feedback loop (free and easy to get LFD tests?) and potentially the strengthening of the previously meandering booster campaign late in the autumn really helped.

Undoubtly the UK system would have taken this outcome (they had predictions of far worse) though the constant effort for the UK healthcare system to process all the hospitalisations for COVID is taking its toll.

Looking ahead across Christmas, it is clear Germany, Austria and Netherlands are likely to have another disrupted christmas (the question is how much), perhaps with France; Denmark and Sweden I don't know; I hope Italy, Spain and Portgual have a relative normal Christmas.

As a Brit and London resident, I hope the current reasonable restrictions remain, boosters continue to be injected, and people here don't go Christmas party mad, meaning our disruption is lower, but anyone with confident predictions is being foolish.

This time last year we were waiting for the results of the Ox/Az and BioNTech/Pfzier trials - and that positivity I remember counteracted the characterisation of the first of the more transmissible variants, Alpha. It was both awful (a lockdown christmas) but hopeful (vaccines)

This November we're in a far better place, but the fundamentals of the virus and the disease has not changed, and if people don't get vaccinated they will run just the same chances of being in hospital as people back in March 2020.

Stepping back, Europe can still learn plenty - and I mean *plenty* from Asia (my favourite go to place - Japan) - on public health for respiratory viruses. Same virus, same host, different systems and different behaviours which have lead to different outcomes.

Although some might be untranslateable to the European setting, most I think can be mapped, and it is really worth us unpicking why things have worked well and then how to move the same mechanisms over into European systems.

(On the flip side, the excellent RECOVERY clinical trial and the vaccine technology basis in Europe - both BioNtech and Ox/Az - are worth Japan understanding how to get to same level in the future as well).