Dr Emma Hodcroft Profile picture
May 2, 2021 โ€ข 8 tweets โ€ข 4 min read โ€ข Read on X
๐Ÿ—“๏ธCoVariants.org is updated๐Ÿ—“๏ธ, with some cool new additions:
- B.1.617.1/2 are added as 20A/S:154K & 20A/S:478K ๐ŸŽ‰
- Beautiful new name table ๐Ÿ“‘๐Ÿพ
- Mutation list displayed in full as a "side-sausage"๐ŸŒญ

Let's take a tour... ๐Ÿ˜

1/7
I know this took a little time (thank you for your patience! ๐Ÿ™๐Ÿป), 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-mutatioโ€ฆ

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! ๐Ÿ“ฑ๐Ÿ’ป

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 ๐Ÿ‘‘ & fancy side-sausage ๐ŸŒญ! ๐Ÿ‘๐Ÿป

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! ๐Ÿ™๐Ÿป

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More from @firefoxx66

Sep 7, 2023
I'm excited to announce a new paper with @MLReichmuth and @C_Althaus, out now in @PLOSPathogens!

We used phylogenetics & modelling to investigate the introduction & expansion of #SARSCoV2 Alpha & Delta variants into #Switzerland & to simulate different interventions.

1/17 Image
First, we wanted to estimate the number of times Alpha & Delta were introduced into Switzerland before they were dominant.
For this we used sequences: we looked for where Swiss Alpha/Delta seqs descend from non-Swiss sequences - coming to Switzerland from elsewhere.

2/17
We looked at two ways of counting these introductions:

Liberal: every Swiss sequence coming from non-Swiss sequences is an introduction
Conservative: only the first Swiss sequence in a subtree of mixed-Swiss-non-Swiss sequences is an introduction

3/17 Image
Read 17 tweets
Jun 15, 2023
Benevolent dictators have no place in academic science.

I don't care if they usually make the right decision. Or if people don't think they've abused their power yet.

Science should not depend on one person being well-behaved.
Balance should be built in, power distributed.

1/5
"If you want to go fast, go alone, if you want to go far, go together" the African proverb says.

Can driven, visionary people start up groundbreaking ideas & cut through barriers to implement them? Absolutely! This 100% is part of science.

2/5
But if you want your idea to be a keystone of science communities & the public, you have to make it about more than *you*.

If you want to run a private business, go do that.
If you want to be keystone of public science, you have to be transparent, trustworthy, & stable.

3/5
Read 5 tweets
Apr 28, 2023
๐ŸŽ‰CoVariants.org Update!๐ŸŽ‰

23B (XBB.1.16) is now available on CoVariants! It's visible as part of Per Country & Per Variant plots, on the shared mutation page - and of course, has a page of its own.

1/10

#XBB116 #23B #Arcturus
๐Ÿ“ท Image
This is in line with the recent addition of 23B (XBB.1.16) as a @nextstrain clade - read more on that below ๐Ÿ‘‡๐Ÿป!

2/10

As I covered earlier, 23B (XBB.1.16) is descended from the recombinant 22F (XBB) variant, with some additional mutations. You can read more about how it evolved & acquired those mutations below ๐Ÿ‘‡๐Ÿป.

3/10

Read 10 tweets
Apr 20, 2023
A Q I've seen: "How did this stay quiet so long?"

Quote from the article:
"Many sources who spoke to Science declined to be named out of fear of legal action from Bogner or of losing GISAID access."

Scientists depend on GISAID access. Fear is powerful.

science.org/content/articlโ€ฆ
Also from this article:
'Marion Koopmans ... says she has received multiple calls from Bognerโ€œwith a rather intimidating tone.โ€ So have colleagues, she adds. โ€œI have heard similar experiences from quite a few.โ€'
And:
"And Science heard many stories about researchers who saw their data curtailed, or cut off, without explanation. Some linked the actions to their being critical of GISAID or being seen as a potential threat."
Read 8 tweets
Apr 4, 2023
If you're an early career researcher (yes even 'just' a PhD student!) 1 of my biggest pieces of advice would be:
Go claim/create your Google Scholar page!! ๐Ÿ‘ˆ๐Ÿปโœ๏ธ๐Ÿป

I put this off bc I thought I 'didn't have enough on it'. I also generally thought "nobody is looking for me".

1/4
Now that I'm (a little) on the other end, I see how wrong I was.

It's *just fine* to not have "much" in your Google Scholar profile - anyone worth their salt will be evaluating you relative to your career state.
Much more important: to be findable!

2/4
And alongside that: it's so useful to have an easy way for people to see what your field is & what you've been up to/who you work with/your expertise.

Google Scholar is also pretty easy to maintain (will vary depending on how unique your name is), as it auto-updates.

3/4
Read 6 tweets
Feb 14, 2023
๐ŸŽ‰ CoVariants.org Update! ๐ŸŽ‰

23A (XBB.1.5) is now available on CoVariants! It's visible as part of Per Country & Per Variant plots, on the shared mutation page - and of course, has a page of its own.

1/9

#XBB15 #23A Image
This is in line with the recent addition of 23A (XBB.1.5) as a @nextstrain clade - read more on that below ๐Ÿ‘‡๐Ÿป!

2/9

As I covered earlier, 23A (XBB.1.5) is descended from the recombinant 22F (XBB) variant, with some additional mutations. You can read more about how it evolved & acquired those mutations below ๐Ÿ‘‡๐Ÿป.

3/9

Read 10 tweets

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