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 💯 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. 👐🏻
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. 🎉 But all of that is vital in building a stronger scientific community. ⛓️
The purpose of this thread isn't to blow @nextstrain's horn - but to hold up what's hopefully an example of what we should be expecting from every major body that's critically involved in the pandemic: it's simply too important to not invest in transparency & communication!
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🗓️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.
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.
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!:
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
“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.
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_.
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!
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.