Thread by @ewanbirney

A perspective on COVID from a sunny, crisp London house, in a break between zoom calls.

Context: I am an expert in human genetics and computational biology; I know experts in infectious epidemiology, viral evolution, clinical trials and (now) public health delivery. As Deputy Director General of @embl means I have a working knowledge of many European countries

I have two conflicts of interest - I am a consultant to Oxford Nanopore that makes SARS-CoV-2 tests+sequencing kits and I am trial participant on the Oxford/AstraZeneca vaccine trial.

Reminder: SARS-CoV-2 is an infectious human virus which causes a horrible disease (COVID) in a subset of people, often leading to death, and sometimes leading to a lingering, longer lasting auto-immune disease (LongCOVID).

If we allowed the virus to freely infect people an extremely large number of people would need healthcare and hospital support; this would overwhelm healthcare delivery and many more people would die (both from COVID and other diseases due to capacity stretch)

Many parts of the UK are at - or rather somewhat above - this level right now, and the healthcare staff working through this ... are to be praised and creditted.

The arrival of new more infectious variants - B117 first discovered in South East England, B1.351 first discovered in South Africa and P.1 First discovered in Manaus Brazil is changing the pandemic - these more infectious variants are causing a epidemic within a pandemic.

Although the headline number of "50% more transmissable" sounds like only a bit worse, due to nature of expontential increase this can lead to 6 to 8 fold more cases *each month*.

At @embl we have contributed to the research behind this and provided an summary of this and other evidence in Deutsch, Français, Italiano and Español for B117 here. embl.org/news/science/s…

B117 exploded in the South East in the UK in late November, early December, and then spread across the UK; it moved quickly into Ireland and Portugual. In all these locations only strict lockdown has held it, and even then perhaps only just.

It is reasonably inevitable that this will become the dominant variant in Europe and likely that every country will have to tighten NPIs (lockdown rules) to prevent run away exponential growth. This has happened already in Germany and Denmark, winter lockdowns extended.

We have hope though, and that hope is predominantly vaccines. Both for theoretical grounds and increasing laboratory and real world evidence the vaccines do offer protection to at least the B117 variant (the other variants need more evidence).

All vaccines so far have been more efficacious at preventing disease than preventing infection and so the progressive vaccination by age strata has been adopted in many locations.

A leading country in terms of depth vaccinated is Israel, and worth watching as vaccination impacts. Although the efficacy of preventing infection was not perhaps as high as hoped, it clearly is happening, and the efficacy of preventing disease shows strong signs

(My go to Twitter handle here is @segal_eran who tweets in Hebrew - though twitter translated is pretty good - and English, and the people Eran retweets).

Outside of Israel, UAE and Bahrain, the UK has the next highest level of vaccination, and with the easy to distribute Oxford/AZ vaccine now more rolled out I think the pace will increase even more. Every person vaccinated is a step forward for 2021!

Denmark, Ireland, Spain and Italy are some of the fast moving EU countries on vaccination. The coordination of vaccine procurement, supply and then national and regional vaccination is a complex beast, but every increase in rate at all steps is beneficial here

(this is because more vaccines are very likely to be approved by the EMA, and so even if the rate limiting step in some countries is vaccine supply, this wont persist into the next months potentially).

Ultimately the unit for vaccination is not nations though but the planet; we will have to think about how to get the entire planet vaccinated over the coming months. Thankfully many vaccines can be scaled in production and are cheap to make and sold at a close to production price

This is the COVAX scheme and other from @WHO and the all too national conversations needs to often have their eyes raised to this goal.

Back to more national concerns, at some point the impact of vaccination will counter act the higher transmission rate of B117 and the lower risk for hospitalisation - but this is not trivial - transmission suppression by vaccination is a long road, and >>

<< there is plenty of earlier, nasty disease (Long COVID) and the use of ICUs is for an younger age range. It will not be a simple exit via vaccinating the older population, even though this will be extremely useful, save lives and reduce healthcare pressures.

Israel is likely to meet this challenge first, and then UAE/Bahrain. UK is likely to be the first European country to navigate this. It wont be easy to work out when to reduce NPIs and what the new schemes should be, and we will need good data, analysis and modelling on this.

So - it has been an awful winter in the UK - and is not improving that fast - but we can see a better future. Many parts of Europe have some tough decisions before then. Vaccination rates are key. But we can -should- be hopeful.