Thread by @ewanbirney

A view from COVID from sunny and wind blown Northumberland this time, not my normal London view. TL;DR - developed countries are making their way across the vaccine bridge to a better 2021 (~variants); the storm still rages in many other countries; the world has to work as one.

Context: I am an expert in human genetics and computational biology. I know experts in viral genomics, infectious epidemiology, clinical trials, public health+ immunology. I have COIs: I am a consultant to Oxford Nanopore, who makes sequencing machines+ I was on the Ox/AZ trial

Reminder: SARS-CoV-2 is infectious human virus which causes a horrible disease, COVID, in a subset of people, many of whom die. If one let the virus propagate naturally not only would many people die but no healthcare system could process the huge number of sick people so quickly

Remarkably a mixture of scientific institutes, biotech companies and large companies have come up with a large number of safe, effective vaccines. These virtually eliminate severe disease and, even better, significantly blunt the transmission of the virus.

A reflection here; the speed of development is simply remarkable (hats off to all the scientists and clinicians who made this happen), efficacy is at the high end (compared to some hard nuts to crack in terms vaccines previously). Humans... a clever bunch collectively!

Because of this success, the single sensible thing is to vaccinate certainly all your at risk of disease population, and given the transmission prevention, likely all the transmitting population. We will have some agonising about children to come up here (perhaps another thread)

I think of this as a bridge from a "unvaccinated high NPI, efficient TTI, high risk of fatal disease" world to "vaccinated far lower NPI, still make your TTI efficient, low risk of disease".

Israel is first over this bridge, then UK and US are close to the end, and EU is at least half way, but with what we've learnt about transmission suppression from Israel and UK, probably further along than one thought a month ago.

A side note here on EU; it is just great to see cases and deaths dropping in many countries: France and Germany are two I feel particularly attached to. Countries like Portugal are partially opening up after a horrible B.1.1.7 wave in the winter, and a "mid-way" vaccination

There are definitely risks here - less risk of death (due to vaccination starting at the most risky end - mainly age) more risks of hospitalisation and hospital capacity will be something to watch, but the vaccine supply is high, vaccination rates are high.

But the rest of the world is often only starting on this bridge. Some do not need to hurry so much due to excellent TTI (Japan, Tawain and South Korea) or good elimination and border control (Australia and New Zealand) but most countries are in a far far worse state.

I don't know the situation and nuances as well as I do Europe; I can't understand the local vs national politics in India or how different countries are coping really; it is all too opaque to me. However, it is clear to me that this is the issue to solve these coming months.

In some sense it is simple; vaccines (not pledges, not money, not IP - but vaccines) supplied to people at risk worldwide. It is logistics (from vaccine production to vaccine delivery) and politics.

You should be moved by the sheer humanity of seeing so many people suffer, for example in India. You should also be aware that solving this is to *everyone's benefit* because our world is one interconnected thing - economically, ecologically and socially.

Looking ahead, the concern is - rightly - variants of SARS-CoV-2 with new biology. (New variants happen *all* the time - every 3 infection cycles is one estimate - but variants that change biology in a way which is "useful" to the virus is thankfully far far rarer).

Side note: the SARS-CoV-2 genomicists name variants as numbers with dots because (a) there are so many of these, hence the numbers, and (b) they have to be related on a tree, so the "." scheme helps). I will also give the vernacular "first discovered in" but this wont scale well

The scariest would be variants that escape the immune response from natural infection or vaccines. B.1.351, first discovered in South Africa, is still the scariest on this axis from laboratory and real world evidence.

*thankfully* real world evidence from Qatar shows that at least the Pfzier/BioNTech vaccine protects against severe disease for B.1.351 - I expect more studies to emerge to show the same. It would be great to get a read out from Ox/Az, J&J and Moderna >>

But to reassure people here somewhat there is good reason to think that severe disease is more a T-cell mediated response (or rather inappropriate response; the human immune system - like all immune systems in fact - is very highly strung thing)

Most recently, B.1.617.2, one of the "sub lineages" (notice the .2) of the lineage first discovered in India looks like it transmits at least as fast as B.1.1.7 (the variant first discovered in the UK).

Laboratory studies suggest this is less likely to have (partial) immune escape than B.1.351, so again, reasons to be reassured, but we need to nail that down ideally with real world evidence. B.1.617.2 now has some community transmission in at least the UK as well as India

It is clear that new variants with potentially new biology will continue to arise, and, in my view, public health in every country will have to be "paranoid on our behalf" about this. There is a chance that one of these could be like "go back to square 1, January 2020"

But I am not sure it is appropriate for all of us to be paranoid all the time. Transparency on the paranoia is very good and necessary (thumbs up to Danish and UK sequencing, PHE VOC committee, data sharing etc)

I also worry that this necessary part of "a better 2021" (and it is not like a reset to 2019- that's not the way this works sadly) will be so interesting and something to pick over that it will be all too easy to tune out the SARS-CoV-2 storms elsewhere in the world.

Even on a variant only basis, these variants arise because of the sheer numbers of this virus. If we can suppress the virus better worldwide we will run fewer risks.