Thread by @ewanbirney

Final thread in a series of 3 - what does this new variant mean for the next stages of the pandemic?

So - first off, if the biology has changed, we need to check all the biological and clinical parameters, some of them urgently. Most obviously do the vaccines work against them. There are good reasons to think this is v. likely which I outlined yesterday.

Briefly they are 1. The vaccine trials all happened with a mixture of different variants circulating (as happens everywhere - there's far more than this B.1.1.7 strain circulating). The fact all 3 work in this mixture is reassuring.

2. Inherently T-cell immunity - which is harder to measure but just as important as B-cell immunity - sees fragments of proteins not the entire thing, so this is why broad specificity is feasible.

In the absolute worst case, as the 3 vaccines are all from designs, one can imagine adapting the design for them to match this (though the testing and regulatory regime for such a "tweak" would be super super interesting)

But there are other parameters to work out - incubation peroid, symptoms, clinical progression, over-dispersion. We should have strong priors that these are the same or similar to the other strains, and Kent / SE of England is consistent only changes in transmission

...but... there is a host of details to check through here. Clinical researchers, infectious epidemiologists, genomics experts are going to have a busy time this Christmas.

If there is a big change, one might need to adapt tactics but it seems v. unlikely that the overall strategy needs to change - ie, vaccinate the population as fast as is safe, monitor everything whilst and afterwards.

This "bridge to vaccine" was the strategy before hand, but now that bridge has .... got a steeper incline on it. Clearly the UK Tier 3 rules could not reduce R of this strain in Kent/SE england, so some combination of NPI+TTI needs to get that ability.

(In a UK context people love to trash talk TTI for a variety of reasons without (a) actually seeing the improvements and (b) realising that steady improvement is feasible.)

Outside of the UK you might wonder 3 things (a) is this strain in my country or nearby? (b) could a new variant arise in my country and (c) what does this change for us.

(a) Like the spread of the virus from in March across Europe and other variants, I think it is quite unlikely (I'm afraid) that this virus strain is not elsewhere in Europe. I might be wrong, but viruses do not respect borders. Europe - or rather the world - is one unit.

(b) Could a new variant that transmits faster arise in my country? For sure - indeed, we have always expected this mutation of higher transmissibility and now seeing this at least once strengthens this.

(c) Similar to the UK I think the basic strategy is likely unchanged - vaccinate safely and quickly, but one will need more in the armoury of NPIs and TTI if this strain is present and/or if a new strain arises. And this implies monitoring+surveillance.

(Slightly tediously I should mention my COI - I am a longstanding consultant to Oxford Nanopore who makes a portable DNA sequencing platform; one way of a number to sequence this virus).

Finally - where should we be on the concern scale for this? As many people know I am an optimist, and I have discovered optimism is a curse in the pandemic; here my optimism is that (a) we've seen this early (b) there has been a response pretty quickly and (c) ... vaccines

It goes without saying that one should leave national concerns at the door though. This is humanity's struggle against a virus. We're all on the same side here, and there is still a far better 2021 waiting for us. Let's get there together.