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Dr Emma Hodcroft Profile picture
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16 Feb, 4 tweets, 3 min read
Tweets haven't been happening as times get busy, but CoVariants.org is now updated to data from 15 Feb! Focal builds are in the oven 🥖

This update also includes some neat new improvements - let's take a quick look!

1/4
Thanks to @jamesscottbrown, pages are now a little tidier, with the link icons placed after the links!

Thanks to a suggestion by @theosanderson the proportion of 'other' variants on the 'Per Country' page are now grey - easier to see and label!

2/4 ImageImage
@ivan_aksamentov has helped greatly improve the 'Per Variants' page! Tool-tip legends now show the lines so you can see the difference between solid & dashed!

And you can now select what kind or order you'd like the legend to show - frequency or country!

3/4 ImageImage
Thanks to everyone who continues to contribute & help make CoVariants.org better!

We still have plenty of ideas to implement - hope to unveil some more soon!

4/4

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More from @firefoxx66

Dr Emma Hodcroft Profile picture
15 Feb
We found the same #SARSCoV2 mutation at position 677 in Spike has appeared at least 7 times in US-focused clusters in the past few months. What have we seen, & what does it mean?

New preprint out now! With @DDomman @macroliter @macroliter & more!

medrxiv.org/content/10.110…

1/17
Sparked by @macroliter & @DDomman independently spotting a rise in Q677P mutants in New Mexico & Louisiana, we teamed up & started investigating!

We noticed an increase in both Q677H and Q677P mutants around the world and within the USA, in particular since autumn 2020.

2/17
On a S:Q677-focused Nextstrain build, it quickly became apparent that there were multiple separate branches where Q677 mutants had arisen independently. We focused in on those in the USA.

Nextstrain build, filtered to 677H & P in the USA: nextstrain.org/groups/neherla…

3/17
Read 17 tweets
Dr Emma Hodcroft Profile picture
11 Feb
It's #WomenInSTEM day today! 👩🏻‍💻👩🏾‍⚕️👩🏿‍🎓👩🏽‍🔬
I'm terrified of making lists of Twitter names as I know I'll leave someone off.

But I want to express how absolutely inspired I have been by the many brilliant women I've had the opportunity to work with this year & throughout my career!🎉
I absolutely remember how important it was (and is!) to be able to see myself in women who were in positions I aimed to achieve. Representation matters *so much.*

It helps to break down the expectations & stereotypes we often unknowingly internalise & realise what's possible!
Just 1 anecdote:

The first time I heard a brilliant women scientist whom I admired matter-of-factly state that she was looking forward both to the conference 🗒️ /and/ to shoe-shopping 👠 in the city it was in was *a revelation* for me. 🤯
Read 6 tweets
Dr Emma Hodcroft Profile picture
9 Feb
The focal builds for S:N501 & S:E484 are now updated to data from the 8th Feb!

nextstrain.org/groups/neherla…

nextstrain.org/groups/neherla…

Let's take a quick look at some snapshots of what we can see in the latest data.

1/15
Important note: the S:N501 build is now being more significantly impacted by downsampling.
I'm working on addressing this, but in the meantime, suggest looking at the S:E484 build for 501Y.V2 & 501Y.V3 & checking out the CoV Lineages report! cov-lineages.org/global_report.…

2/15
Israel now has over 200 sequences in 501Y.V1 (B.1.1.7). The latest additions indicate separate introductions (mostly from a month or two ago) and a large and still-growing local cluster.

3/15
Read 16 tweets
Dr Emma Hodcroft Profile picture
5 Feb
New focal builds for S:N501 & S:E484 are now live!

nextstrain.org/groups/neherla…

nextstrain.org/groups/neherla…

1/5
As well as the major variants of concern, we can spot a couple of other clusters stemming from an 'old' #SARSCoV2 clade, 19B (originating in late 2019).

19A & 19B haven't been around much since early 2020, as they were overtaken by 20A, B & C (which carry D614G).

2/5
However, a few branches of 19B seem to be popping back up again recently.

In the UK, we can see a recent cluster that's acquired S:E484K (along with other mutations in S).

@theosanderson illustrated this one a few days ago!

3/5
nextstrain.org/groups/neherla…
Read 5 tweets
Dr Emma Hodcroft Profile picture
4 Feb
I'm still getting a *lot* of media enquiries - more than I can even respond to! So here's some of my best tips for how to reach out to me to maximise your chances of success (though I imagine they're true of other scientists too!)

1/7
(Just as a disclaimer - even if you use all of these, I can't promise I write back, or that I can say yes. If emails slip off the 'front page' of my inbox they basically fall into a black hole 😬. And sometimes I just cannot take any more interviews, even great ones.)

2/7
1. Please tell me what time zone you're in!

If I want to say 'yes' that means a pencilled-in appointment goes into the calendar immediately - so I need to know when you're likely to be awake. If I have to email you to find out... it might not happen.

3/7
Read 7 tweets
Dr Emma Hodcroft Profile picture
3 Feb
The new focal builds are now up, with data up to 2nd Feb.

Updated S:N501 build:
nextstrain.org/groups/neherla…

Updated S:E484 build:
nextstrain.org/groups/neherla…

1/15
Unfortunately it takes too long for me to do the detailed tweet threads I did originally. However, I'll try to hit a few highlights...

In 20I/501Y.V1 (B.1.1.7):

2/15
The Netherlands now has over 300 sequences in 501Y.V1, with clear signs of community transmission.

3/15
Read 16 tweets

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