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...

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. 🌳

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.

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-...

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.

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.

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...