Thread by @ewanbirney

A Covid view, back in lovely Northumberland. TL;DR - Europe continues to vaccinate; UK, further in vaccination, has some concerning outbreaks associated with imported strains from India; much of the world continues to worsen with lack of vaccine supply.

Context: I am an expert in human genetics and computational biology. I know experts in infectious epidemiology, viral genomics, clinical trials, immunology. I have COIs: I am paid consultant to Oxford Nanopore and I was on the Ox/Az vaccine clinical trial.

Reminder: SARS-CoV-2 is an infectious virus which causes a horrible disease, COVID19, in a subset of people often leading to death. If we let the virus transmit unimpeded many people would die/hospitalised; no healthcare system could cope with the rate of hospitalisation.

Vaccines brilliantly work - currently for severe disease we don't know a variant which can evade them (though one always has concerns - see below) and so there is a rather now a conceptually simple, logistically and politically more complex solution of vaccinating everyone

Israel has achieved a new state; UK and US next behind, and the EU countries as a block with some ahead due to other vaccines (hungary) and some somewhat behind due to logistics. Vaccines are working better than expected, so this is a good thing.

Before I turn to the complications in the UK, I want to stress that the big picture problem is that vaccine supply is still constrained *globally* and we simply wont be in a happy, "safer" place until everyone has either had a vaccine or gone through an infection.

This is a simple thing to state but a complex thing to action, and the consequences of losing control before large scale vaccination are being played out in India in horrible scenes. I really hope control is achieved, and vaccination (not infection) is the majority route

The pandemic continues to evolve. Japan, a country with strong border controls and excellent Track-and-Isolate (indeed, at the start, with the absence of a strong Test mode) is now seeing widespread infection in Osaka. I presume these are faster transmitting variants.

Japan is not out of tools or abilities to control - the state of emergency NPIs in some prefectures will I hope control it better, and this will I hope sharpen a sluggish vaccination campaign so far.

The UK has been stepwise relaxing restrictions, with a big ish step happening on Monday May 17th. However, a massive concern has been localised growth of variants from India in a variety of locations around the UK.

Some perspective is needed here; this growth is in the context of low numbers, and for sure we had higher and broader growth of clusters in late summer 2020 in more locations, actually from a slight faster transmitting variant which probably emerged from Spain.

As we weren't testing or sequencing deeply then we didn't see it, nor quantify it in the same way we can for these Indian outbreaks. So our ability to know what is happening has gone up massively.

When importation happens it is inevitable that it looks like 'growth' at the start; this is just really a numbers game of the number of imports and the fact that many people are asymptomatic carriers (so it is not a straightforward task to work out the number of imports).

However, inside of the UK system we can track where strains come from (kudos to testing system and sequencing, where the UK, like Denmark, is sequencing everything it can). There is a straightforward concern that a particular variant, B.1.617.2, is expanding in a number of areas

Currently the available public evidence is that this variant is still largely stopped by vaccination. It is surprisingly fiddly to go beyond a rough "vaccines have an impact on this variant" to "is it the same as B.1.1.7" and I presume clever people in NHS are doing this now.

[A side note on names. if we named every variant we'd go mad; there are already 100,000s of thousands, and they are grouped in trees. Naming them after the country they first were discovered in is both divisive and also wont scale, and B.1.617.2 shows this.

B.1.617.2 is a lineage from B.1.617, and has two sister lineages B.1.617.1 and B.1.617.3. All three can validly be called "the Indian variant" and given the numbers I fully expect another variant to arise from India. The concern in the UK is only about B.1.617.2 *not* the others]

However, this is not slam dunk evidence that this is due to biological properties of the virus. It is expanding pretty fast in Bolton and Blackburn and Darwen, but far less fast in west London for example, and then there is a technical conundrum about the genesis of B.1.617.2

Furthermore careful work by phylogenetics experts (something the UK does well; eg @arambaut ) shows that the pattern of mutations in this suggest the lineage B.1.617.2 originated back in the summer of 2020, almost certainly in India, and hasn't grown that fast by this analysis.

One headache for decision makers is effectiveness of interventions are much much higher the earlier you take them (as @JeremyFarrar says the best time to act is often yesterday, the next best is today, and tomorrow is worse).

This means decision makers (local PHE, national PHE/HSA, NHS, UK Government) have to act early without resolving this conundrum between clear observed growth in some areas but more patchily distributed and this mismatch with phylogenetics.

It's important to note this is not like the B.1.1.7 scenario (where we saw growth everywhere it went, and we could backtrace its history to the source).

After a pretty tense week of data+analysis, the UK is basically throwing the kitchen sink of local interventions at this - more testing, more vaccination, more TTI. If anyone thinks the decision making here is easy or obvious... they haven't wrapped their head around the problem.

We are likely to be living with new variants for a long time. They will pop up in complex ways as this one. The decision making bias will always be weighted on deciding things early with incomplete information or analysis, but we can't be having mass response on every new variant

As you can see, I'm probably in the less concerned than some people on twitter on this, but I am happy some strong local interventions have started (I'd be crawling up the walls a bit more if not).

How this resolves I am not sure - we simply need more data - it's that straightforward and speculation is just that. Plan for the worst, hope for the best is a reasonable mindset.

Outside of UK across Europe, the steady and effective vaccine roll out has occurred. Broadly most European countries are planning to relax in some way earlier than the UK roadmap (I think with some justification as they can learn from Israel and UK). Vaccine supply is now strong.

However, opening up with less vaccinated individuals does have more risks - risks of hospitalisations (less deaths as most countries have vaccinated the most at risk first) and long COVID. These are ... things to be concerned about.

As such countries will need to titrate their NPIs (non pharmaceutical interventions) with their TTI with their vaccination levels. It is a complex world to navigate this summer. I sort of wish more countries would just ... wait for vaccination, but I get that there are drivers.

In the big picture though the concern in the UK over B.1.617.2, or the worries about the Terraces reopening in France is small beer compared to the serious risks in the rest of the world with faster transmitting variants from 2020 and lower vaccination levels.

As I have said before, both for humane reasons of wanting to minimise suffering and narrow, selfish reasons of wanting to reduce new variants and have a growing world economy... we need to vaccinate a large proportion of the world. Nothing else matters than this in 2021.