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Dr Emma Hodcroft Profile picture
@firefoxx66
Jun 24, 2021 • 9 tweets • 6 min read • Read on X
Scrolly
Another brief update: many of the latest focal builds are still baking🥖, but I've gone ahead and pushed up some finished Delta-related runs.

In particular, I wanted to look a little at what's being called 'Delta Plus' = Delta + S:417N mutation

1/9
nextstrain.org/groups/neherla…
S:417N has actually popped up multiple times in the Delta variant - it's of interest because it's thought to be related to immune escape & is also found in Beta.

But looking below, there are 2 main clusters - @PangoNetwork lineages AY.2 & AY.1

2/9
nextstrain.org/groups/neherla…
I don't have 1 build that shows these clusters perfectly yet (working on it!), so we'll use 2 - the focal builds for Delta & S:K417.

Delta: nextstrain.org/groups/neherla…
S:K417: nextstrain.org/groups/neherla…

3/9
Looking first at AY.1, it's found in Europe & Asia (a little US), with notable clusters in the UK, Switzerland, Portugal, Poland, & Japan.
(Delta build shown/linked first, then S:K417 build)

4/9
nextstrain.org/groups/neherla…

nextstrain.org/groups/neherla…
Looking at AY.2, it's predominantly in the USA, particularly in California.
(Delta build shown/linked first, then S:K417 build)

5/9
nextstrain.org/groups/neherla…

nextstrain.org/groups/neherla…
How do AY.1 & AY.2 differ?

In Spike, AY.1 has additional mutations at T95I (in Iota) & W258L, while AY.2 has additional mutations at V70F (deleted in Alpha & Eta) & A222V (in EU1).

AY.2 also has G142D, which is present in some AY.1 sequences.

6/9
Since I'm based in Switzerland, let's take a closer look at some of what we see there... 🇨🇭

7/9
Here's the Swiss AY.1 cluster - mostly in Geneva, Vaud & just over the border in France (location marked in red)
Note Geneva does a lot of sequencing, so more likely to pick up clusters!

Divergence view shows the order of transmission is unclear!

8/9
nextstrain.org/groups/neherla…
Switching to a Swiss-focused Delta build, we look at other Swiss Delta clusters.

The large Geneva cluster is the AY.1 we just looked at, but there are other clusters in Geneva, Basel Stadt & Land, & Bern.

9/9
nextstrain.org/groups/neherla…

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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 28, 2023
🎉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

Read 10 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

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