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Dr Emma Hodcroft Profile picture
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15 Dec, 7 tweets, 5 min read
There are many, many #SARSCoV2 #COVID19 variants out there! A few have caught the attention of scientists in Europe - we're trying to monitor them!

I'll be maintaining updated information here:
github.com/emmahodcroft/c…

#newvariant

1/7
This site includes a bit about what we know about specific mutations/clusters, including counts of sequences, some graphs, and links to dedicated @nextstrain runs (maintained by @richardneher Lab & myself) focused on each mutation

2/7
You can also check out graphs of the prevalence of the clusters in various countries:

3/7
github.com/emmahodcroft/c…
The focused @nextstrain builds pull out all sequences with the relevant mutation/part of the relevant cluster & then add closely related background. So they allow a fantastic way to take a close-up look at the variants.

Each is linked in the mutation's 'section'!

4/7
I'll be doing my best to keep information updated, but I *welcome* PRs & links to include the latest publications, preprints, & research!

Our best work on #SARCoV2 #COVID19 is done collaboratively! No one person can keep up with it all 😁

I aim to update at least weekly.

5/7
This page is currently incomplete: I was working on this already - but I've rushed this through to get it good enough to release, as I hope it will be useful straight away - but please be patient as I continue to add information!

6/7
And yes, there's a section on S:N501: 😉

I'll be tweeting some of the information here on my original thread on N501Y shortly!

7/7
#newvariant

github.com/emmahodcroft/c…

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Dr Emma Hodcroft Profile picture
14 Dec
As far as I know, the #SARSCoV2 variant identified by Hancock today is defined by a spike mutation at position 501 N->Y & a double-deletion at positions 69/70.

You can see it in orange in the dedicated Neher Lab S:N501 @nextstrain build below
nextstrain.org/groups/neherla…

1/N
I do not have more information about why scientists in the UK believe this variant may have increased transmission.
However, it does appear the proportion of UK sequences containing S:N501 mutations has increased recently (sorry, hard to see)

github.com/emmahodcroft/c…

2/N
This build is from last week (I'll try to update soon), but from this information, it seems like this particular variant has so far only been detected in the UK and Denmark. However, we may simply not have samples from other countries.

nextstrain.org/groups/neherla…

3/N
Read 19 tweets
Dr Emma Hodcroft Profile picture
14 Dec
1/ "The release of the scientists' views caused a furore. Until then, it had not been known how strongly the government's scientific advisors has lobbied for a lockdown in September. The next day Labour backed the scientists & called for a shutdown."

thetimes.co.uk/article/48-hou…
2/ It's a shame this article is behind a paywall, as it highlights critical moments in political #SARSCoV2 decision-making in the UK, & the impact of the false dichotomy that one can either save the economy or lives - rather than that reducing cases does both.
3/ As we've seen time & again in this pandemic, prioritizing actions based on the economy instead of impact on transmission has a tendency to come back to bite: 'back to normal' "now" is so often paid for with hospitalizations, deaths, & more severe restrictions later.
Read 13 tweets
Dr Emma Hodcroft Profile picture
3 Dec
*Very* surprised to hear this from @ECDC_EU & @EASA this morning. Our work on #SARSCoV2 20A.EU1 shows this variant spread incredibly effectively across Europe due to travel & now accounts for significant proportion of seqs circulating in many countries.

euronews.com/2020/12/03/cov…
While the variant initially spread from Spain, phylogenetic data shows that it also transmitted onward from secondary European countries.

Though we haven't studied other variants in as much detail, I have no doubt we'll find similar stories of travel-associated introductions.
Our work suggests that indeed, 'honour-based' quarantine alone may not be the ideal policy. But we suggest this because it doesn't seem to have worked as well in practice as one might have hoped - not because travellers posed no risk of introducing #SARSCoV2 (to the contrary).
Read 6 tweets
Dr Emma Hodcroft Profile picture
27 Nov
It's been a tough season for #ski resorts, but:
- Ski lifts & resort restaurants pose real #SARSCov2 transmission risks (Ischgl in spring)
- Attracting travel from across Europe could undo hard work getting cases down/stable (as we saw in summer)

1/4
nzz.ch/wirtschaft/eu-…
This summer, holiday travel spread #COVID19 cases across Europe easily. These 'sparks' were blown up to flames when the weather got colder.

The combination of lots of travel & ski resorts while cases are still too high across Europe is a risky one.



2/4
As many countries do not have to quarantine on arriving in Switzerland, we could be an attractive #Skiferien destination. Economically I see how that's tempting, but the longer term impact of rising cases & possibly more restrictions may cancel out the benefit.

3/4
Read 4 tweets
Dr Emma Hodcroft Profile picture
20 Nov
Gentle reminder that in Switzerland we are still feeling our way in the dark: with a #SARSCoV2 test positivity this high, the # of cases we report is largely linked to the # of tests we do.
While there are other signs cases are going down, we have a poor grasp on how much.

1/5
You can see this in this great cantonal graph by @gust_avius.
While tests & cases will always be linked somewhat, it's a bad sign when every jitter in testing is reflected perfectly in cases. It means we can't see exactly how case # are changing.

2/5
It's an even worse sign for places like Basel-Stadt, Schaffhausen, & Zug, where a decline in tests hasn't seen a same-size decrease in cases - in some cantons cases have even risen or plateaued despite the decrease in tests.

3/5
Read 5 tweets
Dr Emma Hodcroft Profile picture
20 Nov
The new #SARSCoV2 variant we identified recently, 20A.EU1, has jumped to New Zealand a few times (& been caught in quarantine) - but this interesting preprint shows how it seems to have transmitted in-flight, from individuals originating in Switzerland:
research.esr.cri.nz/articles/prepr…
Just for the avoidance of all doubt (I know I've been covering a lot of stuff lately!) this isn't linked to mink/Denmark, but the variant that's currently most prevalent in Europe, spread through summer travel. You can read more about it here:
This preprint was made possible by a long list of great people - unfortunately I do not know twitter handles for them all - but it was led by Tara Swadi & Jemma Geoghegan & involved @hamesjadfield @alexeidrummond @edwardcholmes & @Joepdl
Read 4 tweets

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