This weekend is a festival of sport in the UK - Premier League action (sadly - Arsenal lost); Start of Rugby's 6 nations; Superbowl - against a background of a COVID still whipping around us. Some thoughts from sport-heavy London:
Reminder: SARS-CoV-2 is an infectious virus which causes a nasty disease (COVID) in a subset of people (more likely if older; male; overweight) and sadly a proportion of people die who get the disease.
If we let the virus follow its natural course in populations our health care systems would be overwhelmed; far more people would die both due to the virus and other things and it would be near catastrophic for the function of modern society
Many things have gone better than expected - most notably we have a large number of vaccines that work and additional treatments and clinical refinement have substantially improved treating the disease.
There have been some expected but against us moves - a number of mutations have occurred in different locations that have made the virus more transmissible and sometimes able to partially escape previous immunity.
(Both UK - England specifically - and now Portugal have gotten close to healthcare melt down in this B117 wave, and it seems clear that Europe as a whole - probably the world - will have to navigate B.1.1.7 / B1.351 / P.1 - and likely more changes in the future).
The exciting news though is vaccines - they work; we have a number of them. Most heartening is that Israel, which has had an excellent vaccine deployment shows clear impacts in reduction to mortality and hospitalisations due to vaccination
This primarily the Pfzier/BioNTech vaccine. The Ox/AZ vaccine (which I am on one of the trials) looks clear that a "long" 12 week dosing works if anything better than shorter (certainly not worse); I look forward to seeing real world data similar to Israel's from the UK.
Vaccines are brilliant, but they take time to just supply and deliver into people (there are a lot of people!) and time to take effect. Israel is only seeing its effects now and it vaccinated over twice as fast as nearly anyone else.
It's notable to me that Israel has not (yet) relaxed it's lockdown (though I think the debate is raging there). In one sense one has metrics of both cases and hospitalisations to be able to know if more transmission could be tolerated - not yet in Israel.
(One needs to work back 3 weeks from now to know what level one might have to hit for efficacy. My naive view is that 3 weeks ago Israel was ~25-30% vaccinated - so one has to wait to at this level, presumably further).
There is an unhelpful debate certainly in the UK about pitching scientists/modellers/healthcare leaders as risk adverse lockdown lovers with from my perspective very little desire to think this through.
to them: (a) we need to watch Israel, watch when they relax and what happens. We should learn from them and (b) don't forget that every week probably another 3 million people will be vaccinated in the UK, ie extending time here should simply buy us certainty of health+economy
It feels pretty bonkers (but that seems sometimes normal for COVID times) to discuss when UK is relaxing it's NPIs when Israel has not yet; Israel's reluctance is not being risk adverse, it is just ... complex and a long road from "vaccines work" to "vaccines means lower NPIs"
(Meta comment: one failure in the UK setting at least, if not worldwide is not merging technical science/healthcare scenario planning with technical economy planning. The end result is that it feels we do science+economy in the political arena without a joint understanding >>
<< this is bad; it's bad science and from my amateur economics side, bad economics. To stress - there are many decisions which must be made by elected officials across a complex and frankly really unattractive scenario landscape;
but by not fusing the technical advice we've ended up making the scenario landscape far mushier and messed up for politicians to see their way through it. Post pandemic we must have stronger economy+science policy schemes, thinking, "war games" etc)
Looking at Europe besides the UK, the complexity of securing vaccine supply with much high politics and complications is going to constrain EU for a while (as the German health minister has pointed out, at least a tight 10 weeks).
This is frustrating as every week is a week one could be vaccinating; however, I am sure the vaccine supply will be sorted out, and once that has happened the vaccine deployment and application rate must be as fast as possible.
Quite a lot of this sort of process is about rates above all, and one has to anticipate solving the current rate limiting step (supply) and thus ensure the downstream rates are good.
Across the developed nations (US, EU, UK, Canada etc) have over capacity in vaccine production will be good because... the real unit for vaccination in the world.
Here the cheap price, unfussy licensing and exponential growth as a (harmless, modified) virus itself of the Ox/AZ vaccine is brilliant; The 5 million doses delivered in India and 3 million in Brazil is a start along a very long road.
Rugby has started. I am ... optimistic, but 2021 is going to be a long road. It will get an easier road to walk.

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More from @ewanbirney

9 Feb
The @uk_biobank is ... amazing and is basically, in my view, rebooting the science of human physiology.
Why? First it is just a really well phenotyped cohort at scale. Back in the early 2000s a number of people did key power calculations and amazing (or not so amazingly for epidemiologists) 500,000 was the minimum prospective cohort to have to impact common disease
Secondly the phenotyping has been done centrally and consistently, and some key imaging phenotypes have been done at scale. This is remarkable logistics, fund raising/arguments and delivery. *so* many things could have gone wrong which didn't.
Read 13 tweets
31 Jan
COVID thoughts on a cloudy late January day in London - longer evenings, and our house lockdown rhythm has settled somewhat.
Context: I am an expert in human genetics and computational biology; I know experts in infectious epidemiology, viral genomics, clinical trials and immunology. I have some COIs: I am a long established consultant to Oxford Nanopore and I am on the Ox/AZ vaccine trial.
Reminder: SARS-CoV-2 is infectious virus which causes a severe disease in a subset of people (older; more obese; male risk factors) often leading to death. If we let the virus go through the population both a large number of people would die and healthcare systems would melt
Read 21 tweets
22 Jan
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.
Read 24 tweets
12 Jan
I am not full sure people appreciate the impact of B117 strain on the course of the pandemic. TL;DR B117 is "a pandemic inside a pandemic" and demands both monitoring and preparation for when it arrives in a location. Vaccination is even more of a priority due to B117.
Context: I am an expert on human genetics and computational biology. I know experts in viral evolution, testing, infectious epidemiology, clinical trials. I have COIs in that I am long established consultant to @nanopore and I am on the Ox/AZ vaccine trial.
B117 clearly transmits faster. This has been clear in a UK context now for over a month, with particularly insightful backtracking of growth of B117 from low levels through October/November; it is true in Denmark; it is true in Ireland.
Read 18 tweets
8 Jan
It is hard month in January in UK, in particular the NHS critical care, but also now in "schools out" lockdown. Here are some thoughts from grey January London on COVID.
Context. I am an expert in human genetics/genomics and computational biology; I know experts in viral genomics, infectious epidemiology, clinical trials and other fields. I have COIs: I am long established consultant to @nanopore that makes a COVID test + I am on the OX/Az trial
Reminder: SARS_CoV_2 is an infectious virus which causes a horrible disease (COVID) in a subset of people (more likely older, male and overweight). A substantial proportion of the people who get the disease die.
Read 25 tweets
3 Jan
A meta-thread on my take of how to "read" science as a scientist. This is to arm non-scientists about how to navigate a world where one sees the "leading edge" of science develop as we do now in COVID.
(Context: I am an expert in human genetics and computational biology - data science in biology. As Deputy Director General of @embl I have the pleasure of being involved in a lot of science in a strategic way both inside @embl and internationally).
The first point is that most scientists have sets of observations about the real world which are solid - they have been measured multiple times; multiple groups found the same thing; ideally measured in different ways.
Read 19 tweets

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