Thread by @ewanbirney

A view of COVID, heading into the Christmas period; ultimately a European, with strong focus on the UK view.

Context: I am an expert at (human/vertebrate) genetics and computational biology; I know experts in infectious disease testing and modelling, clinical trials, immunology. I have a COI in that I am long standing consultant to Oxford Nanopore, which makes a new COVID test.

A reminder: SARS-CoV-2 is coronavirus which jumped from another species late last year into humans; it is reasonably infectious in humans and causes a horrible disease in a subset of humans (older; male; obese) often leading to death.

If we let the virus infect all of us, not only would a subset of people die quickly, and another subset have a horrible long term disease, but also no healthcare system could cope with that number of ill people at once.

Thankfully medical research has given a host of better treatments (halving the rate of death of this disease) and, most amazingly, now a number of vaccines which interim analysis has shown 3 to be safe and work; one has passed regulation to be used.

But this is still a very fragile situation; despite the remarkable imminent vaccination, other regulators need to approve in their own jurisdictions, and the other vaccines need to go through this approval >>

<< more importantly, the logistics of vaccinating a large proportion, ideally nearly all, of a population is eye-wateringly complex. Every country has plans, and these plans will unfold over January. For sure there will be bumps in this road just because of the number of steps.

So, despite this respite on the horizon, countries are going to have to continue to suppress transmission of the virus for quite a few months yet; there is still a very mixed success across Europe for this

The most reliable and consistent way to suppress transmission is harsh restriction of socialisation - work, education and fun. Letting some of the above happen requires prompt testing, informing contacts ('manually' by phone or digitally) and enforcing hyper-local isolation.

Most European countries are working out how to titrate the right blanket measures across the population to work with the per-individual or per-region measures. It is complex work in itself, with many moving parts; much can go wrong.

One example is the North Kent coast in the UK, where the England-wide lockdown 2.0 did not prevent growth in cases. Similarly, Hildburghausen in Southern Germany grew in the context of "lockdown light" in Germany.

The upcoming holidays has challenges - how does Christmas and getting through the dark winter nights work when we're in the midst of this struggle? What do we do and what rules or guidance do governments make?

Other challenges include a large scale shift in contact patterns as university students come home (a bigger issue in the UK than say France or Germany where universities are often more local)

However, there might also be benefits - when university and school stop for the holidays there will be less contact patterns via those routes.

As suspected from the southern hemisphere, the restriction on socialisation is also slowing other respiratory diseases (eg, 'flu) but we really be sure of this until mid-Janurary.

Healthcare service capacity and morale is another careful thing. Winters are always hard work (in particular in the famously frugal UK NHS in terms of capacity) - navigating winter and COVID after the spring of 2020 is asking alot of doctors and nurses

(An aside - the stoic, let's get on with it and solve today's problems, see today's patients, repeat next shift that I see from so many of the clinical colleagues I know I am rather in awe of)

I think all healthcare services will breathe easier when the majority of their front-line staff are vaccinated - less shielding and isolation, less time off, more flexibile deployments inside hospitals.

I feel this world can be hopeful about the future, but it is a very fragile future - the vaccine roll out will have to be well established and working through the at risk groups until we can really say that safe future is growing in our hands.

And even then we will have to be careful, and play our parts until we have the new normal of 2021 at some point.

But there's proper hope. There is a better 2021 for us all - let's not mess up getting there.