Thread by @ewanbirney

It's been a hot half term in the UK; at the end of this week here are my thoughts on Coronavirus. TL;DR the delta variant has changed the calculus in the UK but we don't know how much the vaccination calculus makes this less of a concern. Still more concern globally than UK.

Context: I am an expert geneticist + computational biologist; I know experts in infectious epidemiology, viral genomics, immunology and clinical trials. I have COIs. I am long established paid consultant to Oxford Nanopore and I am on Oxford/AZ clinical trial

Reminder: SARS-CoV-2 is an infectious virus which causes a horrible, sometimes lethal, disease; COVID. Left unchecked every healthcare system would not be able to process the number of diseased individuals.

Thankfully vaccines work very well on preventing severe disease, and they work reasonably well in preventing transmission between individuals. This is above expectations from 2020 and the vaccine rollout in the developed world has broadly been good to excellent.

In India the relaxation of lockdown measures earlier in the year before widespread vaccination allowed strong transmission and a number of variants became dominant; one, now called "Delta" came to dominate and also spread to many other countries, from Japan to UK.

Unlike the previous faster transmitting variant ("Alpha", B.1.1.7) the Delta variant came in via importation (alongside some other circulating variants in India), and it was - still is - complex to untangle this importation signal from transmission advantage.

However, as the variant has spread across the UK into many situations which had controlled the Alpha variant the likelihood of faster biological transmission properties has strengthened over time. The UK (along with Denmark) has excellent sequencing so we can track this well.

(I will note there are still some conundrums for this variant; it, itself comes in 3 sub-types with deep phylogenetic branches - this means it's history in India must have been complex - and it is not obviously growing as fast in Denmark or Germany but >>

<< both these countries are, like the UK is doing, providing stronger track and trace and other schemes around observed breakouts. The UK's biggest hotspot - Bolton - now has dropping cases, but we do have a half-term effect on testing of school children.

Furthermore the community Delta first came into in the UK, ie, South Asian with links to India, is a different epidemiological context, eg, more multi-generational households. All in all its not easy to untangle all these things going on at the same time)

Both laboratory antibody neutralisation assays and real world epidemiological data suggest this variant has some level of immune escape, in particular vs 1 dose of a vaccine for transmission. It seems that the protection vs severe disease, in particular post 2 doses, is good.

(Again, so complex to handle with real data! Remember that the laboratory antibody assays is one arm of the immune system; the T-cell arm, probably more involved in severe disease, in fact largely an *overreaction* is not assayed here. Hence severe disease can be quite different

For the epidemiological data, one needs time and numbers to be able to work out impact on severe disease, and the lack of numbers - largely a good thing! - also means distinguishing different vaccines types - Pfzier vs AZ in the UK and doses impacts complex)

Taking some of the earliest hotspots in the UK as exemplars, one can see how vaccination has changed things - the case numbers of double vaccinated older groups have not gone up anywhere near as fast as in previous waves, and hospitalisations are (currently) lowish.

We are, in effect, in a different space in the UK from Jan 2021 or October 2020, though still the fundamentals of exponential increase can easily make a very small percentage of people being hospitalised a big problem for the NHS.

Scenario modellers and decision makers informed by scenarios now have their work cut out for them over the next period. My personal framing is to accept that we need a new plan, but that this new plan *might* be pretty close to the old plan.

(this is because plenty of reasonable worse case scenario parameters of February - of vaccine effectiveness and of vaccine uptake in particular - have turned out in our favour. However one can't just weigh these "in our favour" vs Delta variant "faster transmission" trivially)

Stepping back from the slightly feverish details of the Delta variant in the UK and change to UK plan, the UK, along with many developed countries are in a good place because vaccines continue to work in particular vs severe disease. Basically : Vaccines work, plan to this.

It will be interesting to see how other countries adjust plans or not over this summer, and some of the countries which have done so well on suppression (Japan) or border control (Australia and New Zealand) will be running bigger risks until they are appropriately vaccinated.

But the elephant in the room is that with even faster transmitting variants, the global race between vaccination and transmission has shifted strongly towards transmission. This is awful and heartbreaking; it is most obvious in India.

The commitment of actual vaccines from the developed world is a necessary part of the solution and this is good for both humane reasons - many people will die in awful situations without this - and for selfish, narrow reasons - we want less of this virus circulating.