Now it's easier than ever to identify the variant you're interested in - and with beautiful new badges! π
Also, the date plotting on the Per Country page has been made clearer!π
Let's take a look... π
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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! π¨π4
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Of course, this carries over to the Per Country page, where the variant order is also more intuitive. π
Additionally, the date axes have been made clearer with more lines, & mouse-over now shows exactly what period the data comes from! ποΈ
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As usual, a huge thanks to @ivan_aksamentov, who plays a huge role in making CoVariants.org as beautiful & functional as it is! ππ»ππ»ππ»
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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.
I am incredibly grateful to have received the 1st dose of the #COVID19 vaccineπtoday!
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.
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.
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 π― 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. ππ»
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. π But all of that is vital in building a stronger scientific community. βοΈ
ποΈCoVariants.org is updatedποΈ, with some cool new additions:
- B.1.617.1/2 are added as 20A/S:154K & 20A/S:478K π
- Beautiful new name table ππΎ
- Mutation list displayed in full as a "side-sausage"π
Let's take a tour... π
1/7
I know this took a little time (thank you for your patience! ππ»), 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.
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:
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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).
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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.
IT π» pulled out all the stops & the oven (server) is back online, so CoVariants is back in business!! π οΈπ
CoVariants.org is now updated - latest focal builds are in the oven π₯π₯ -- & 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!:
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