πŸŽ‰.@WHO and @nextstrain names come to CoVariants.org!πŸŽ‰

Now it's easier than ever to identify the variant you're interested in - and with beautiful new badges! πŸ”

Also, the date plotting on the Per Country page has been made clearer!πŸ“ˆ

Let's take a look... πŸ‘€

1/4
CoVariants now uses the same clades (including WHO names) you see on Nextstrain.org, making it easy to find a variant of interest!

This comes with beautiful new variant badges - & an updated Name Table that includes Pango & WHO badges, & old CoVariants names! 🎨🌈4

2/4 Image
Of course, this carries over to the Per Country page, where the variant order is also more intuitive. πŸ“œ

Additionally, the date axes have been made clearer with more lines, & mouse-over now shows exactly what period the data comes from! πŸ—“οΈ

3/4 ImageImage
As usual, a huge thanks to @ivan_aksamentov, who plays a huge role in making CoVariants.org as beautiful & functional as it is! πŸ™πŸ»πŸ‘πŸ»πŸ‘πŸ»

4/4

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More from @firefoxx66

7 Jun
It's incredibly thrilling to have this paper out at last! πŸŽ‰

"Spread of a #SARSCoV2 variant through Europe in the summer of 2020"

(aka The Tale of Europe, Summer Travel, & EU1)

But why should we care about summer 2020 now? Let's take a look...

nature.com/articles/s4158…

1/24
Last Sept, while looking for #SARSCoV2 sequences that could help us understand transmission across #Switzerland, I noticed a cluster that was present not just across Switzerland, but also the UK & Spain. This is the cluster that eventually came to be known as 20E (EU1).

2/24
EU1 had a mutation at position 222 in spike - this caught my eye.

From mid-summer 2020, EU1 (orange) expanded across Europe - becoming the most prevalent variant in most of Western Europe, & accounting for >30% of sequences in Europe by the end of 2020.

3/24
Read 24 tweets
3 Jun
I am incredibly grateful to have received the 1st dose of the #COVID19 vaccineπŸ’‰today!

A year ago, I never imagined we'd have multiple vaccines available & being distributed now.
At the same time, I'm saddened the privilege I've been granted is still unavailable to so many.

1/4
This is often particularly the case in countries where continuing high case numbers & outbreaks mean lives are still being lost & people being hospitalized. We must continue to ask countries to do more to realise equitable & fair vaccination access.

2/4

nature.com/articles/s4156…
This is esp true for Western countries which are starting to reach high vaccine levels.

I call on wealthy countries to propose a plan for how they are going to contribute to better & more equal vaccine distribution.πŸ“’πŸ’‰

We aren't safe until all of us are safe. πŸ€²πŸ»πŸ§‘πŸΏβ€πŸ€β€πŸ§‘πŸ»πŸ§‘πŸΌβ€πŸ€β€πŸ§‘πŸ»πŸ§‘πŸΎβ€πŸ€β€πŸ§‘πŸ»

3/4
Read 4 tweets
14 May
Transparency & open communication is *so key* in this pandemic.

At @nextstrain we don't claim to be perfect - but you know who we are, how we work, & we try incredibly hard to have open conversations with the community: building trust & better research.

#openscience #opensource
It can be easy to say things like "we are too busy to tweet" or "we don't have time to talk to everyone." I πŸ’― get it! Not every one of our emails is answered, not every discussion post responded to. But if you want to truly be part of a community: you have to open up to it. πŸ‘πŸ»
It's painful sometimes: it means being open to change, being transparent about how everything works & how decisions are made -- it means openly crediting & celebrating others' work and contributions. πŸŽ‰ But all of that is vital in building a stronger scientific community. ⛓️
Read 4 tweets
2 May
πŸ—“οΈCoVariants.org is updatedπŸ—“οΈ, with some cool new additions:
- B.1.617.1/2 are added as 20A/S:154K & 20A/S:478K πŸŽ‰
- Beautiful new name table πŸ“‘πŸΎ
- 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! πŸ™πŸ»), 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
Read 8 tweets
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 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
Read 5 tweets

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