Thread by @BillHanage

As might have been expected the UK is reintroducing more intense restrictions over the Christmas period. This may be tied to the 'new variant' common in the SE of the country, but should not obscure the fact that the relaxation in early December will have had an impact 1/n

There are several reasons to think this is an important variant, but notably it has increased extremely rapidly since emerging in mid sept (maybe a little earlier)

https://twitter.com/WvSchaik/status/1340332400023396352?s=20

2/n

Unlike the earliest stages of the pandemic, this variant has been competing with existing and established lineages, and it is against that backdrop that the increase has occurred, strongly suggesting IMO it is more transmissible 3/n

(apparently estimate of 0.4 increase in R, but not sure how we can exactly attribute the part due to the variant virus and the part due to more contacts permitted in early Dec. But both important) 4/n

This is a preprint describing the variant. Importantly it has *multiple* mutations, including 7 in the receptor binding domain of the Spike protein alone. Even if some of these have been seen before, they've not been in combination biorxiv.org/content/10.110… 5/n

(I am going to point out that I have been impressed by Chris Whitty and Patrick Vallance in this briefing) 6/n

Such large numbers of infections have been seen previously in patients who have been infected for long periods. For example one of the same mutations took place during this long term infection (work w the excellent @DrJLi and others) 7/n nejm.org/doi/full/10.10…

Or indeed this preprint, which includes multiple changes suggestive of some adaption to the immune system medrxiv.org/content/10.110… 8/n

We will need to do *much* more careful surveillance to see what if any impact this has on immune evasion. I'm not going to make any strong prediction and wait for empirical data. In other words, there's quite enough reason to take it seriously as it is 9/n

Someone asked in the presser where did the virus come from? Why England? It should be noted there are reports of something similar in South Africa, but I don't know enough to comment businessinsider.co.za/what-we-know-a… 10/n

But I will note that mutations happen all the time. The more infections, the more opportunities to explore the the space of possible mutations.

Basically you wouldn't have expected this to emerge in New Zealand 11/n

This figure illustrates how the 'new variant' (proper name lineage 'B.1.1.7') has more differences than you would expect. 12/n

There is much more discussion in this excellent and thorough blog post virological.org/t/preliminary-… (thx @WvSchaik for alerting me) but a few headline comments follow 13/n

The S:N501Y mutation is known to increase binding affinity to the receptor. Doesn't necessarily mean more transmissible. But has a phenotype and has been seen multiple times. The variant *also* has... 14/n

P681H. Which is next to the furin cleavage site. This is thought to be important (but I'd leave it to the likes of @angie_rasmussen to discuss as I don't think I know enough) cell.com/iscience/pdf/S… 15/n

and then a deletion in the spike protein. The 69 & 70th amino acids are deleted. This has been seen several times previously, and linked to immune evasion but also general stuff going on with the receptor binding domain 16/n

A note - it is a tribute to the extraordinary work of so many working with @CovidGenomicsUK that we know this much. I've been privileged to know and work with many of them for years. We are all in their debt. 17/end