Thread by @ewanbirney

A COVID viewpoint from increasingly cold London. TL;DR the world vaccination situation is improving, but there is a long way to go; Europe is entering a winter exit to endemicity surge; the UK is a leading country in this exit surge with internal angst, strife and screw ups

Context: I am an expert in human genetics and computational biology. I know experts in infectious disease epidemiology, viral genomics, immunology and clinical trials. I have COIs - I am consultant and shareholder of Oxford Nanopore and I was on the Ox/AZ trial.

Reminder: SARS-CoV-2 is now the fifth endemic coronavirus that infects humans, and by far the nastiest. For a subset (older, overweight, male) of people is causes a horrible disease, COVID, in which some people die, and many people have horrible time in hospital or longCOVID

Thankfully unprecedently fast clinical research have provided now a suite of vaccines that work well (and some that did not; but that's the nature of this) and when people are vaccinated hospitalisation and death are far less likely (~2 fold to 20 fold less depending on age)

48% of the world is now vaccinated with at least one dose; perhaps unsurprisingly this is not evenly distributed, with most of the rich world fully vaccinated except for ideological anti-vaxers. However, there are many countries with virtual no vaccination levels

For both moral reasons of preventing harm and death, for equity reasons worldwide and narrow economic and health reasons in rich countries given the interconnection of the world getting vaccines to everyone on the planet is the most important thing.

Over time SARS-CoV-2 has evolved primarily to become more transmissible - it is at least 2 fold more transmissible, and will infect and transmit in many vaccinated contexts. Furthermore it has found some animal resevoirs (which still need to be characterised).

This higher transmission level, global reach of the virus and likely animal resevoirs means the virus almost certainly will be with us for the forseeable future, ("endemic" in science speak), as the other 4 human coronaviruses are (they cause "the common cold").

As such the mid to long term strategy has been on working out how to reduce hospitalisations in the context of the circulating virus. This "exit to endemicity" is complex as it is unclear if any place has reached it and what the final balance of transmission/hospitalisations

Two particular developments are reasons to more hopeful; firstly 3rd doses of vaccines (boosters) seem to really improve protection, and the mRNA vaccines (Pfzier and Moderna) seem best. Secondly new effective drugs have been developed, with an earlier in hospitalisation drug.

However it seems likely that a substantial amount of transmission has to happen (natural infection seems to give more protection than vaccines), and it is hard to imagine "boosters" quickly into the European winter across the entire population.

As such it is likely that Europe (and US) will go into another wave, but this time a wave where more people are protected by vaccines, ideally with boosters if older. There is low appetite for lockdowns- unclear why buying time would help if you've vaxed as much as possible.

Some countries in Europe have recently started down this path, and the UK was more deliberately relaxed during the summer, with higher infection levels and has entered the autumn and winter with high transmission.

At one level this has been a remarkable proof of the efficacy of vaccines - this UK "plateau" of infections has not triggered the levels of hospitalisations in 2020 or 2021.

On the other side, the UK seemingly meandered in its vaccine decisions for boosters and teenage vaccines and did not prioritise the booster campaign in early autumn despite excellent initial vaccine roll out in Jan 2020.

This was not helped by the final step of Public Health England reorganisation (into HSA) which had a massive QA failure of an company that did PCR testing in the South West, with many people not getting their positive result.

This awful occurence has neatly shown the effectiveness of good testing and information (it clearly has an impact) but created even more transmission in the South West which they are getting over.

Furthermore, given this somewhat relaxed approach, simple things (in England) to slow transmission whilst boosters were administered, such as mask wearing or ventilation were handed over to "personal responsibility" /"company's judgement" and have become, sadly, tribal signifiers

This was most obviously seen in the House of Commons (an indoor setting with lots of people) with a split in the middle of the room of mask wearers and mask deniers. As masks *definitely slow down transmission* and the booster campaign *has not finished* this is all... stupid.

However, masks yes/no are probably more marginal than people think (most obviously shown by the high transmission rates in Wales and Scotland with mask mandates); in the big picture the anti-vax mentality in Saxony in Germany or US Red states is far more dangerous.

underlying all of this though seems a mix of indifference to taking one's eye off the ball in the UK (England in particular). This now has spooked everyone (probably should have earlier) and there is more urgency to the booster campaign (no reversal though on masks)

Much of Eastern Europe is joining the UK in higher transmission, with some countries going back to lockdown like conditions (eg Latvia). I think the key parameter is going to be 1st/2nd dose levels in over 50 year olds for weathering the winter, then booster roll out.

It seems pretty inevitable that most of western europe will join, and indeed Belgium, Netherlands and Germany have all seen sharp up ticks from far low transmission bases (though the UK tests deep now, so the raw case numbers are not apples to apples between countries).

The between country comparison is natural but only helpful for understanding what one can do (eg, FFP3 masks in shared indoor spaces is not some affront to democracy); one has to remind yourself this is not a between country race; it is a war between humanity and virus.

And that takes me back to the most important thing; getting the entire world (at least those >50) vaccinated. That is the single most important goal in the remainder of 2021 and no doubt 2022.