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Dr Emma Hodcroft Profile picture
@firefoxx66
Apr 28, 2023 • 10 tweets • 7 min read • Read on X
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🎉CoVariants.org Update!🎉

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
📷 Image
This is in line with the recent addition of 23B (XBB.1.16) as a @nextstrain clade - read more on that below 👇🏻!

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 👇🏻.

3/10

On the 23B page, you can read about some initial 23B (XBB.1.16) work on neutralizing titres, see a list of defining mutations, a plot of the variant growth, link to Aquaria protein viz, & see a list of other mutations present in the variant.

4/10

covariants.org/variants/23B.O… ImageImage
There's also a link to the 23B (XBB.1.16) @nextstrain
focal build: nextstrain.org/groups/neherla…

Here, we can zoom in on the clade & get a closer look at how 23B sequences are distributed around the world, & their diversity. 🌏🌍

5/10

#XBB116 ImageImage
On the Per Country page, 23B (XBB.1.16) is already clearly visible in India & Singapore, & is starting to appear in smaller numbers in other countries, like Australia & the US. Remember, sequencing data is always a few weeks behind.

6/10

covariants.org/per-country Image
Finally, on the Shared Mutations page, you can see how 23B's / XBB.1.16's Spike mutations compare to other VoC, including its Omicron family, 22F (XBB) parent, and its 'sibling' 23A / XBB.1.5.

7/10

covariants.org/shared-mutatio… Image
More information on 23B (XBB.1.16) & its spread will become available in due course.

As always, CoVariants.org is open-source & we welcome your PRs & suggestions to add more studies & information to variant pages! (Or any error-catching!)

github.com/hodcroftlab/co…

8/10
As before, I've created a file for 23B (XBB.1.16) mapping all defining mutations (relative to ancestral), including nuc->AA. This is available on the CoVaritants Github!

Huge 🙏🏻to all who helped check it! (Esp @CorneliusRoemer @AngieSHinrichs)!

github.com/hodcroftlab/co…

9/10 Image
The eagle-eyed among you will have noticed that I've adjusted the 23A colour when adding 23B - the colours were probably always a bit too close together but this became even more obvious with 23B. I hope it doesn't cause any confusion! 🌈

10/10 Image

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More from @firefoxx66

Dr Emma Hodcroft Profile picture
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
Dr Emma Hodcroft Profile picture
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
Dr Emma Hodcroft Profile picture
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/articl…
Also from this article:
'Marion Koopmans ... says she has received multiple calls from Bogner“with a rather intimidating tone.” So have colleagues, she adds. “I have heard similar experiences from quite a few.”'
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
Dr Emma Hodcroft Profile picture
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!! 👈🏻✍️🏻

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
Dr Emma Hodcroft Profile picture
Feb 14, 2023
🎉 CoVariants.org Update! 🎉

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 👇🏻!

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 👇🏻.

3/9
Read 10 tweets
Dr Emma Hodcroft Profile picture
Feb 6, 2023
I've had this question a couple of times:

The recombinant XBB is shown as having mutation S:F486S (inc on CoVariants.org), from parent BM.1.1.1 - but looking at BM.1.1.1* now, it seems to have mostly S:486P!
So did XBB really get 486S?



1/5
As usual @GenSpectrum helps us dig into this at CoVSpectrum:
cov-spectrum.org/explore/World/…

Looking at "Mutations over time", we can see really nicely that BM.1.1.1* was mostly S:486S earlier, then 486P later - likely a daughter lineage outgrowing 'original' BM.1.1.1!

2/5
Indeed, daughter lineage CJ.1 has 100% S:486P and has been growing since Oct 22, when we see that switch.
cov-spectrum.org/explore/World/…

Similarly, looking at BM.1.1.1 (no star - so no descendants), show it has 96% S:486S & declined in Oct.
cov-spectrum.org/explore/World/…

3/5
Read 5 tweets

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