Thread by @ewanbirney

A COVID perspective: TL;DR - the pandemic in the developed world has shifted due to successful vaccines, though plenty of complex and tricky scenarios to navigate; the developed world is in the midst of even harsher transmission rate from Delta.

Context: I am an expert in human genetics and bioinformatics. I know experts in viral genomics, infectious epidemiology, public health, clinical trials and immunology. I have some COIs: I am longstanding consultant to Oxford Nanopore (sequencing company) and am on the Ox/AZ trial

With the perspective of a glorious holiday in Northumberland, the last week disconnected from work and twitter, I have some bigger picture musings on the pandemic from my perspective.

The first is just how good the vaccines are - and thus how lucky we are - we have at least 4 really good vaccines in that they radically change the likelihood of severe disease from SARS-CoV-2 infection and clearly at least blunt transmission.

This was not a given; the vaccines could have plain not worked (some vaccines candidates for SARS-CoV-2 didn't). There could have been unacceptable adverse effects (adverse effects are present but very rare). They could have only moderately ameliorated severe disease.

As such the rather straightforward strategy of vaccinating as closely to everyone at risk of severe disease (crudely >50) and as large a proportion of the rest population as one can reach is sound; Europe (UK included) and Israel are showing the way here and it... looks sound.

(I note that the vaccines also seem to reduce the incidence of LongCOVID, which makes sense, and so there is an extra benefit for vaccinating people not at risk beyond suppressing transmission as clearly LongCOVID exists and is not nice)

However, UK and Israel are also showing the outline of the new normal; SARS-CoV-2 still in circulation, and the Delta variant infecting a number of double vaxxed people - far far less likely to lead to severe disease, but still transmitting. This looks like to me the new normal.

This is ... in line with the other 4 circulating human coronaviruses, where there is differential (and waning) immunity coupled with antigenic drift of the viruses (the viruses tweaking their key "display" regions) is the endemic, long term situation for these infectious agents

And so we will likely have a 5th coronavirus, SARS-CoV-2 giving many people "the common cold" which causes sometimes "viral pneumonia" and "viral triggered auto-immunity"; I suspect SARS-CoV-2 will be the nastiest of the 5 for a long time.

Hence the discussion and plans around vaccine boosters for the most at risk, and the new normal is going to have darker clouds from coronavirus infection for a while.

(Note: elimination of SARS-CoV-2 is gone from "very unlikely" to "very very unlikely, impossible in the mid term" in my view - just the numbers of humans, the infectivity, and also now documented animal reservoirs means this is not a credible short or mid term strategy)

Getting to this new normal means that very nearly everyone on the planet must either be vaccinated or infected. And the supply and distribution of vaccines is going to be the main reason for which route people take, though anti-vax/vaccine hesitancy sentiment is next.

I am *not* an expert (nor know well experts) on vaccine production and then distribution - the main thing I know is it is very complex both in actually doing it and regulation, but this is where the drama is worldwide. All wind to the sails of the production sites.

The impact on the developing world of lower vaccine supply is going to be ... harsh. Watching the Delta wave propagate through the largely unvaccinated India, and the impact of people and healthcare delivery is awful.

This means improving vaccine production and its supply globally is the single most important thing that can happen over the next months.

In developed countries with vaccine supply, there seems to be two phases: vaccinating the vast majority of high risk individuals and a large proportion of others, and then titrating infection across this population at a sensible rate.

The Delta variant has enough infectivity/transmission in a largely vaccinated society for there to be another wave "on top" - Israel having achieved something like community immunity with Alpha is now navigating this Delta-on-vaccination wave.

Other countries are approaching this from the other side of increasing vaccination and titrating out NPIs - the country I know best here is the UK, and it seems this strategy looks sensible but with an angst filled last titration step of release with poor messaging and tactics

Most of Western Europe will be in broadly the same place as Israel and UK sometime over this summer (or already there); France's somewhat lower vaccine uptake makes their navigation of the summer probably the most complex in Western Europe.

However, there are other countries in Europe which really need to accelerate their vaccine delivery before the faster transmitting Delta wave crashes over them. The growth in infection in UK and Netherlands just shows how much faster Delta is vs Alpha or the earlier variants.

Australia + New Zealand - which had an excellent elimination + quarantine scheme at start of the pandemic now need to transition to this high vaccination strategy - the elimination + quarantine is harder to hold vs Delta (as seen in Sydney now) and is not a mid term strategy

Here vaccine hesitancy (spiced with the weird anti-vax conspiracy theories) needs to be overcome, ideally without having to have serious transmission and healthcare impact to "make it real".

But the developed world country I worry about the most is the US. By the numbers the US vaccination level is reasonable if slowing; but the aggregate numbers I think hides a stronger regional variation, and in particular a larger number of at risk people not vaccinated.

Other people will know the numbers and drivers better than me, but from afar this is both the complexity of reaching marginalised communities in the US + also the alignment of anti-vax sentiment to partisan politics. The latter gets the press; the former is probably as important.

Again, one might expect that the reality of people going into hospital at high rate will be the backstop to get over vaccine hesitancy, but I worry about just the speed and momentum of infection compared to how fast one can turn around vaccination rates.

I think therefore the US is going to have a tough summer - in particular in the South and Midwest - and the frustrating is that this is all so avoidable.

But the developed world problems - even this - are small in the context of the global problem of vaccine supply. Plenty of complex production issues at the heart of this; then logistics and with politics stirred in across this.

We are definitely not out of the pandemic yet.