Dr Emma Hodcroft

Oh my god they found poisson steve

#poissonsteve

A screenshot of the front page of Pathoplexus' website, showing the addition of a tile for Marburg Virus.

1/ 🚀 Pathoplexus now supports Marburg virus (MARV) and Ravn virus (RAVN) (sister viruses in the same genus). MARV has two main clades and causes severe disease with reported fatality rates of 24–88%.

You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...

The change to the CDC website to reflect unscientific, agenda-driven mindsets is deeply upsetting.

But let's not forget there are a lot of excellent scientists still working there. Persisting. Trying to minimise damage.

Let's not stop supporting them - while condemning those in charge!

9/ 🔍 We invite clinicians, surveillance labs & researchers to explore the dataset & share your feedback.

Feedback? Questions? Drop a comment, DM or on GitHub. Like to join us in creating more EV datasets? Please reach out!

Thank you to everyone working on #Enteroviruses!🙏🏼

8/ 🙏🏻With our thanks:

This dataset was created by Nadia Neuner-Jehle, Alejandra Gonzalez Sanchez, & Emma Hodcroft - with help from Nextclade creators Richard Neher @neher.io & Ivan Aksamentov - and the input and advice of the ENPEN community!

7/ 🔜 Looking ahead:

We’re planning expansions - other non‐polio enteroviruses such as EV-A71, CVA10, CVA16.

🔭 Future features we hope to add: a recombination QC flag, gene-specific clade assignments.

Stay tuned & we welcome your input!

6/ 💻 Running locally:

You can also use the new EV-D68 dataset locally via the Nextclade CLI - perfect for integrating into workflows and sequencing pipelines!

Find out more about the CLI here: docs.nextstrain.org/projects/nex...

Screenshot showing the results screen of Nextclade, with example D68 sequences having been run, showing the sequence name, QC status, clade assignment, and mutations relative to the reference

Screenshot of the tree view in Nextclade, with the D68 sequences having been run. The sequences provided by the user show up as solid circles and thick lines, highlighting their position in the reference tree, which is shown as thin lines.

5/ 💡 How to use it (cont):

- In the results: you’ll see QC status (red/yellow/white), clade calls, mutation counts, coverage gaps, etc. 🔠🚩💯
- The tree view places your sequences into the global phylogeny alongside curated reference data. 🌳

Screenshot showing the EV-D68 dataset on Nextclade, with some example data loaded, ready to run

4/ 💡 How to use it:

- Go to nextclade.org → choose the EV-D68 dataset or go to clades.nextstrain.org?dataset-name...

- Drag & drop your FASTA (or load example)

- Click Run - alignment, QC & clade assignment happen in your browser (no data leaves your computer)

3/ What the D68 dataset can do:

- Clade assignments (A1–A2/D, B1–B3, C) 🔠
- Whole-genome mutation calling (not just VP1) Ⓜ️
- Quality-control (QC) metrics 🚩
- Gene annotations across the genome 🧬

👉🏻 So even if VP1 is missing, you can still assign the clade reliably.

Enterovirus D68 now on Nextclade! Check out the new Nextclade dataset for Enterovirus D68!

2/ Why this is important:

📈 EV-D68 cases are already rising this season.

📂 This dataset lets clinicians & researchers quickly run clade assignments, mutation calls, and QC checks directly in their browser - with no data uploaded

Detailed info here!: eve-lab.org/blog/EV-D68-...

1/ 🚀 Exciting news: we’ve just released the first Nextclade dataset for Enterovirus D68 (EV-D68), developed in collaboration with the European Non-Polio Enterovirus Network (ENPEN).

👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name...

#EVD68 #Enterovirus #OpenData

Graph showing the change in number of directly submitted sequences to Pathoplexus since August 2024. 0 in Aug 2024 to almost 9000 today.

1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻

Read the full update: pathoplexus.org/news/2025-11...

Looking forward to sharing @pathoplexus.org next week at the @evbc.bsky.social Viruses in Silico lecture! Tune in if you'd like to hear about open but protected data sharing, simple uploads, & transparent governance - all to help with easier, faster viral genome sharing!
#opendata #openscience

📢 Next Viruses in silico lecture:
🎙️ Pathoplexus: A Community-Driven Solution for Transparent and Equitable Viral Genomic Data Sharing
👩‍🔬 Emma Hodcroft @firefoxx66.bsky.social (@swisstph.ch @sib.swiss)
🗓️ 27 Nov 2025 🕑 4 PM CET
📍 Zoom - Register to receive login details
👉 tinyurl.com/VirInSilico

Particularly now, and for secure, respected, influential people in more democratic institutions, I think the excuses grow weak.

But as a limited-contract, early-career scientist who spent a lot of pandemic night awake, terrified of being targeted, I can vouch that it's a tough & shit situation.

On top of that, there's stories that certain people email & call your supervisor, boss, or even dean, calling for outright termination. That's scary.

And, there's interlinking at high levels. If there's friendships at govt level above you - you may not have any choice in what you can say publicly.

For many scientists, if they are dependant on the data for their work, they feel their backs are against the wall. It's not 'right' - but it's a cut-throat profession. Loose access to what you've but your career on, and you risk losing your entire career. That's tough to ask of anyone.

It was previously supported by an arm of the government, but I think current involvement is unclear. However, it was never part of the German government. Initially, it was a collaboration with SIB, currently it's officially a Verein in Germany, and more recently set up a US-based non-profit.

The blog post at Nextstrain details the reasons they gave us (nextstrain.org/blog) , but it can be different in each case, and for the overall reason, we aren't sure.

Open position at the Swiss Institute of Bioinformatics:
We are looking for a Director of the Center of Pathogen Bioinformatics
apply.refline.ch/499599/0346/...
I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and

The file came w an agreement and/or understanding that it was for display - & requirements to comply (credit, amount of detail, GISAID logo size).

Yes, the data is still available via GISAID website - but this is prohibited by DAA from display.

So GISAID decides what tools the public get.

I want to spell this out in case the implications aren't clear:

This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.

The file allowed this. Cut that - cut off all tools the public & others were using.

We've run a build based on NCBI + other open data for a long time now. However it doesn't contain all the data that is in GISIAID. You can find it here: nextstrain.org/ncov/open/gl...

Nextstrain does pull from NCBI - but does not contain all the data that is in GISAID. You can see our 'open data' (non-GISAID) build here: nextstrain.org/ncov/open/gl...

On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5

From @torstenseemann.bsky.social at @pha4ge.bsky.social Conference; "We are stealing from research money to support public health."

We need dedicated funding for maintaining & supporting public health infrastructure & pipelines. Not just startup, not just in pandemics.

Thrilled & honoured to have run the first @pathoplexus.org workshop with @chaoranchen.de @pagasi.bsky.social @kanyerezi30.bsky.social & Arthur Shem Kasambula at @pha4ge.bsky.social on Saturday! 🎉🤝

A fantastic turnout & wonderful time spent with curious users!

BREAKING: Friday night massacre underway at CDC. Doznes of "disease detectives," high-level scientists, entire Washington staff and editors of the MMWR (Morbidity and Mortality Weekly Report) have all been RIFed and received the following notice: