Dr Emma Hodcroft Profile picture
Sep 23, 2020 11 tweets 6 min read Read on X
The 'Texas Paper' is getting sensationalist headlines. Remember:
- D614G is same mutation we've known about since spring & been in media all summer
- It happened in ~Jan & most of Europe & much of US had it
- Great to confirm previous work, but not 'breaking'

#SARSCoV2 #COVID19
Worth noting that the authors of this study sat on 5,000 sequences *all summer* meaning they couldn't be used by other scientists to explore any findings in these sequences. Or to better understand Texas's epidemic during its biggest spike.
The author laments the low sequencing rates of #SARSCoV2:

“I think we need to be doing this pretty aggressively in multiple locations on a real-time basis,” Musser said. “I think it’s shameful that we’re not doing that.”

/It's shameful to sit on sequences that could be public./
I maintain a #Texas @nextstrain build (I grew up partially in Texas; my mom lives there). I've repeatedly put out calls to connect to anyone willing to do TX sequencing to gather better information during the summer peak.

There are about ~600 sequences.

nextstrain.org/community/emma…
Using *only* 10% of the sequences of the new paper, what can we tell about the mutation they make such a fanfare about?

Here it is, plotted on the tree. D is ancestral (green), G is the new variant (yellow). Pie chart shows proportion of each, in Texas

nextstrain.org/community/emma…
As we already know: the G mutation arises very early in the pandemic (~Jan - where yellow starts). And, as in many other places in the west, it became the most common variant. From mid-April there were extremely few (if any) D (green) strains in Texas.
These trees alone can't show /why/ that happened - though many studies have been done that increasingly indicate the G variant has higher transmissibility (which could explain this pattern).

There's no evidence that it has changed clinical outcomes though - & def not recently
Certainly, since that variant has been circulating since early 2020 & since its the variant most people in Europe & USA had in spring - & the one circulating now - we can be confident it isn't responsible for things like a lower death rate - since it's the same variant.
The authors talk about seeing many mutations in their sequences. #SARSCoV2 mutates. We know this. We already see diversity in the sequences.

Here's all the amino-acid changes in the 600 TX seqs up until June. Quite a few! No different from what we see elsewhere, though.
Still - you can see how many sequences we lack from TX during the worst of the summer peak.

Those 5000 seqs might have helped us better understand imports vs local transmission, & connections within Texas & to other states, at a time when maybe that could have been useful.
We're in a pandemic. We're in this together. #Openscience & #opendata is responsible for *so much* of the research we've achieved on #SARSCoV2.

We need to put the greater good ahead of ourselves & our career goals. We need to do what's *right*. It's our best chance to succeed.

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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
🎉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
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
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
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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