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Dr Emma Hodcroft Profile picture
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23 Apr, 5 tweets, 3 min read
IT πŸ’» pulled out all the stops & the oven (server) is back online, so CoVariants is back in business!! πŸ› οΈπŸŽ‰

CoVariants.org is now updated - latest focal builds are in the oven πŸ₯–πŸ₯ -- & a very cool new breakdown feature has been added! (Read on!)

1/5
Overall variant frequencies per country sometimes don't reflect the whole picture. As a first step to hoping to support more regional views, you can now select a "USA" view on CoVariants' "Per Country" page & view by state!:

2/5
master.covariants.org/per-country
As always, be cautious when interpreting:
- Last data points, when data may still be coming in
- Data points/states with low numbers of samples - may not be representative

3/5
As hinted by the top of the page - I hope to include areas in Switzerland next (CoVariants is based in Switzerland πŸ‡¨πŸ‡­πŸ«• πŸ”οΈ) - and we will see what the future brings for more regional breakdowns!

4/5
Finally, thanks to @henryaj for catching & fixing a typo, & @ivan_aksamentov for always ensuring my wildest ideas for the CoVariants.org website always come true.

Hoping to get more improvements/expansions on CoVariants out soon!

5/5

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Dr Emma Hodcroft Profile picture
1 Apr
β€œI am precariously employed; I don’t have a long-term job. I feel a lot of pressure that this is my opportunity and I cannot waste that" says Hodcroft.

Fantastic article by @meredithwadman on how scientists are coping (or not) in this pandemic marathon.

sciencemag.org/careers/2021/0…
I know PIs whose valuable pandemic staff are quitting because *they just can't take it anymore.* I know academics who are counselling post-docs while juggling next-day demands from governments - & of course balancing a family & sometimes homeschooling kids.
It's not sustainable.
You may have noticed I've been absent from Twitter a lot the past few weeks. It's the same phenomenon. I'm lucky: I have no staff or dependents. I'm gainfully employed. But I've spent more than a year feeling guilty *every waking moment* that _I'm not doing enough_.
Read 5 tweets
Dr Emma Hodcroft Profile picture
12 Mar
πŸ—“οΈCoVariants.org is now updated to data from 11 Mar!πŸ—“οΈ

Plus, 2 new variants, and new additions to the Shared Mutations page!

βš™οΈThe builds are already updated and live!πŸ”

1/4
First, the S:Q677 USA variants S:677H (Robin1) and S:677P (Pelican) are added to the lists of variants & Per Country plots.

These variants arose at the end of 2020 & are found across the US, but prominently in the north-central & south-central USA (respectively).

2/4
We know the Shared Mutations table has been helpful for many people to compare Spike mutations shared between Variants - & now it's got even more variants! πŸŽ‰

Sort by commonness or position & see what keeps popping up.
We aim to add even more soon!

3/4
covariants.org/shared-mutatio…
Read 4 tweets
Dr Emma Hodcroft Profile picture
10 Mar
πŸ—“οΈCoVariants.org now updated to data from 9 MarπŸ—“οΈ

Plus, 2 new variants and 5 new mutations added!

Let's have a look at what's new...

1/10
To help track variants of interest, we've added 20C/S:484K (B.1.526, sometimes called the 'New York variant') & 20A/S:484K (B.1.525)!

2/10
20C/S:484K (blue) carries the S:E484K mutation as well as a mutation at S:A701V (shared with 501Y.V2). Interestingly, 2 independent sister-clades nearby (yellow) do *not* have 484, but have S:S477N (same mutation as is in 20A.EU2 & 20F.

3/10

covariants.org/variants/20C.S…
Read 10 tweets
Dr Emma Hodcroft Profile picture
4 Mar
All the focal builds linked from CoVariants.org are now updated with data from 2 Mar.

This includes the new focal builds for 501Y.V1, 501Y.V2 & 501Y.V3 (B.1.1.7, B.1.351, P.1) - links in the thread....

1/7
501Y.V1 (B.1.1.7) is still significantly downsampled due to the extremely high number of sequences in this cluster - but the focal build helps a bit!

2/7
nextstrain.org/groups/neherla…
501Y.V2 is not downsampled much now, which means it gives a pretty good view of where the variant has spread. Shown in large dots here are the clusters in Mayotte, the French territory off the coast of Africa (yellow circle near Africa).

3/7
nextstrain.org/groups/neherla…
Read 7 tweets
Dr Emma Hodcroft Profile picture
3 Mar
πŸ“…CoVariants.org is updated with data from 2 MarchπŸ“…, as well as a very exciting new change:

Variants & mutations are now separated & clearly labelled - & each Variant of Concern has it's own page & data! πŸŽ‰

1/8
A new, improved left-menu now clearly indicates whether a page is concerned with a Variant (collection of mutations in one part of the tree) or a Mutation (one change, could be in many places on the tree).

Updated naming helps, too!
And menus collapse to keep things tidy.

2/8
And to help you find what you're looking for - a table to help you link up nomenclature!! πŸŽ‰

A lot of people have asked for this - it's not yet beautiful but it's already hopefully useful.

And you can go straight to the CoV-Lineages reports on the 3 main VoCs, too!

3/8
Read 8 tweets
Dr Emma Hodcroft Profile picture
24 Feb
While not downplaying our current careful situation, I think we've got a lot to be optimistic about in 2021, if we can think globally 🌍 & act appropriately πŸ’‰πŸ˜·

I thoroughly enjoyed reading this interview with @fabiennekatrin: '1 year of #SARSCoV2'

1/5
blick.ch/schweiz/epidem…
On conspiracy theories:
"Unfortunately, conspiracy theories have become very dominant in the pandemic. I can understand: [they often] provide much simpler explanations. We scientists should learn from this, to make what we say more accessible and understandable."

2/5
On mutations:
"If many people have already been infected, it is an advantage for a virus [to evade] this immunity. A year ago that would not have been of any use to the virus. But now... we just have to be aware that the pandemic is not static. It is constantly changing."

3/5
Read 5 tweets

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