Thread by @ewanbirney

More thoughts post the extension of Stage 3 in the UK on COVID restrictions to July 19th.

Not enough in the press in my view is made of the change in *biology* of the virus; the virus is both more transmissible *and* is less dampened by 1st doses (in particular Ox/AZ, but Pfzier also) >>

This means that current UK population, both the number of 1st doses and where the 1st dose window is is a far harsher transmission environment for the Alpha and other variants than Delta; we've seen this play out in the numbers

(BTW - this means the 1st dose 1st strategy has less of an impact on transmission, but it still has a big impact on hospitalisation, and the scheduling of doses doesn't actually change when you hit overall 2nd; ie, I don't think this changes the validity of the dose schedule)

The second memes out there is either that the UK is somehow cursed with new variants and/or that the UK should just not monitor as deeply. A fair bit of this is due to the fact that the UK's testing and sequencing is *really good* (though; Denmark, take a bow) +very transparent.

This means UK can see, assess and adjust to new biology. Of course more knowledge makes the risks all the more clear, but that's the ... point. Better know, assess and plan than wing it.

If only a handful of countries have a good assessment system then we will only understand the shifts in biology in this handful of places; other places we will speculate about all sorts of things and not understand. This is not good worldwide.

In the assessment side of this, even a couple of weeks of hindsight is a dangerous drug - things are far clearer now than 2 weeks or 4 weeks - certainly 8 weeks ago, and the signals around Delta were really unclear (still some conundrums on the evolution of Delta).

With the UK's depth of sequencing and transparency it does mean the world has an ascertainment issue - the variants which have an impact on the UK's COVID trajectory will (currently) be the best understood. This comes hand in hand with... knowing stuff.

The other thing is the feeling that this will just keep on going, seemingly forever. At one level we have to "live with the virus" (managed endemicity) which is ... for the foreseeable future, but vaccination *really changes* what "live with the virus" means.

It's worth having a historical view on this. We have 4 circulating Coronaviruses in the human population, and one of them, snappily named OC43, look like it jumped from its other species (Cows) into humans around 1890, similar time to "Russian Flu" pandemic.

We don't know if it really caused this pandemic, but it seems likely, and during the "Russian Flu" was noted that it spared the children and left people with "lethargy" and "bedridden" for a number of months - both similar to COVID disease.

Further back in history we can see through genetics that the human immune system has had to balance its aggressiveness against other infectious disease vs coronavirus -

his has lead to at least two regions of the genome to come from our close, interbreeding cousins of Neanderthals and Denisovans which have risen to higher frequency in current humans; one case our cousin's DNA has increased severity of disease, one case the reverse, ie, it helps

The directionality is not the important thing, it is more the practical example that we as a species has been through the trade offs between different types of infection, reminding ourselves that COVID as a disease is as much an "overreaction" to SARS-CoV-2 as a reaction.

This all should give us some perspective on a world with SARS-CoV-2 as the 5th circulating human Coronavirus - probably the nastiest of the five - but something we can live with.

So - for the UK readers - let's go this extra month which really reduces the risk of something nasty happening to lots of us, but let's be firm that we've got transition into the new world.

For non UK Readers - it is really worth using the UK to understand Delta and have a strategy/plan that works for your country, as it is pretty likely that you will have to navigate this variant as well.

And, back to the assessment side, we can be pretty confident that this wont be the last chess move SARS-CoV-2 makes in its evolutionary landscape; We will have to stay on top of this for a loooong time (depressing I know, but doable). Time to tool up.