🗓️CoVariants.org is updated🗓️, with some cool new additions:
- B.1.617.1/2 are added as 20A/S:154K & 20A/S:478K 🎉
- Beautiful new name table 📑🍾
- Mutation list displayed in full as a "side-sausage"🌭

Let's take a tour... 😁

1/7
I know this took a little time (thank you for your patience! 🙏🏻), but B.1.617 is now in CoVariants as the two sublineages 617.1 & 617.2, called respectively:
- 20A/S:154K (has 484Q)
- 20A/S:478K (no 484Q, has 478K)

2/7
We can see the two lineages best in the India graph of the 'Per Country' page - with S:154K in brighter green, & S:478K in darker green. (Note sequencing may not be representative)

They also show up in low numbers in some other countries.

3/7

CoVariants.org/per-country
And of course, both lineages are added to the 'Shared Mutations' table:
CoVariants.org/shared-mutatio…

4/7
Of course, S:154K & S:478K are also added to the front-page 'name table' (CoVariants.org) - which is now easier to read & dynamically resizes to fit your screen better! 📱💻

5/7
Finally, previously mutations were shown at the top of each variant page, taking up a lot of space. This meant I didn't always display every mutation (which a few of you caught!)

Now, mutations are shown down the side, ensuring a complete list while saving space!

6/7
Thanks again to everyone who messaged about adding the new variants (& everyone's patience while I got them in - it's been a busy week!).

And as always, a huge thanks to @ivan_aksamentov - this time in particular, for the new name table 👑 & fancy side-sausage 🌭! 👏🏻

7/7
PS - Contributions of more studies & links about B.1.617 for the 20A/S:154K & 20A/S:478K pages are welcome!
I wasn't able to take as much time to look everything up as I would normally, so suggestions of anything I missed are super-appreciated! 🙏🏻

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More from @firefoxx66

28 Apr
From the 'USA state' view (new) at CoVariants.org, I think the dynamics of 20C/S:484K (B.1.526) are intriguing.

Most variants that were circulating at end-2020 have declined after 501Y.V1 (B.1.1.7) (red) expanded - very noticeable with 20C/S:452R (purple) in CA:

1/7
But in states with 20C/S:484K (pink), this has seemed to grow alongside 501Y.V1 (B.1.1.7) (red) - sometimes growing, other times holding steady, or at least not declining significantly (may yet happen).

2/7
Some preprints have estimated the transmission of 20C/S:484K to be similar to 501Y.V1 (B.1.1.7).
20C/S:484K carries the 'Eek' 484K mutation in spike, which may be why neutralization (immune recognition) is lower.

medrxiv.org/content/10.110…
biorxiv.org/content/10.110…

3/7
Read 7 tweets
23 Apr
IT 💻 pulled out all the stops & the oven (server) is back online, so CoVariants is back in business!! 🛠️🎉

CoVariants.org is now updated - latest focal builds are in the oven 🥖🥐 -- & 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
Read 5 tweets
1 Apr
“I 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
12 Mar
🗓️CoVariants.org is now updated to data from 11 Mar!🗓️

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

⚙️The builds are already updated and live!🔍

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! 🎉

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
10 Mar
🗓️CoVariants.org now updated to data from 9 Mar🗓️

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
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

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