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)
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
• • •
Missing some Tweet in this thread? You can try to
force a refresh
I've been getting questions from friends about what to do if their child gets sent from home to quarantine, after a case is identified in their class or 'bubble' (or whatever is the local term) 1/n
First point, be pleased that the exposure was detected. Imagine if it had not been. The information is power which helps you and others avoid infection, that is what the quarantine is for 2/n
the alternative (not testing) means undetected transmission in schools could introduce the virus to many households. Younger children *are* less likely to become infected and suffer severe illness, but they can transmit 3/n
Will not be time for many of these and please understand may well be distracted so will miss put too many but given the thanksgiving holiday would like to should out to those like @ImpactMovie who have been admirable friends for months. Happy thanksgiving to you and yours!
I would add @SFDukie happy thanksgiving to you and yours - hopefully in a non generation mixing setting
Or the extraordinary @EIDGeek - this had been a bad year. Getting to know you better has been one of the better parts. Look forward to meeting in person, one day
First this is good news in that it shows yet more evidence efficacy can be achieved, and in a vaccine setup we understand better than mRNA vaccines - no disrespect to any platform, but having more weapons in our arsenal is always going to be better
But what’s bad is the relentless media focus on the “up to 90% efficacy” which makes me irritable. This was a result from a mistake in the vaccine trial regarding dosage. Vaccine trials are not the sort of places you want to make mistakes
A comment (to complement some parallel threads from @michaelmina_lab) on the value of rapid testing, even if it is imperfect. So how do you re open say... movie theaters in the midst of a pandemic where anyone could be infected, and many are at risk of fatal outcomes? 1/n
So bad things are that most movies theaters are indoors, probably poorly ventilated. Crowds. Lots of opportunities for close contact. A person at the peak of infectiousness could kick off a Superspreader event 2/n
If you could present reliable evidence you have been -ve in the last 24 hrs, well that would obviously be transformative. But wait - what if that test result is a false negative and there is a resulting false sense of security? That’s where the masks come in 3/n
The reason for the test was exposure to a suggestive but non-specific symptom in a member of the household who was also tested 2/n
While waiting for the test result, all members of the household quarantined. Child did not go to school. Prevented any risk of transmission outside the household 3/n
There's a lot of talk about 'preserving healthcare' as a primary goal of pandemic management. That's not wrong, but it begs the question of what exactly we mean by 'preserving healthcare'. I recommend this article in the @NEJM & will add a couple comments nejm.org/doi/full/10.10…
So for some 'preserving healthcare' means avoiding all ICU beds being occupied by the pandemic. This is obviously bad. It's also a very low bar. If we get even close to this, where do you put patients recovering from surgery? Or emergency ICU admissions for other things? 2/n
This is not a hypothetical☝️🏽. So let's say we stop short of crashing the ICUs with patients - we would still end up with shortages of skilled nurses elsewhere in the system, compromising healthcare. When they are redirected at the pandemic other care is affected 3/n