A screenshot of the new Pathoplexus homepage showing all viruses now supported, including Dengue and Yellow Fever, which are circled in red
1/ 🦟 Big news: #Pathoplexus now supports Dengue virus & Yellow Fever virus - two arboviruses responsible for over 400 million infections and up to 94,000 deaths per year.
Here's what’s new in our latest update 👇🏻
Read the full update: pathoplexus.org/news/2026-03... 📰
> An alternative to GISAID has been gaining ground. In 2024, Chen, Stadler, and others launched Pathoplexus, a platform that also seeks to protect the interests of those uploading sequences but aims to allow data to be shared more freely.
And if you love podcasts:
open.spotify.com/episode/0wrp...
“[P]utting data into GISAID is like dropping it in a mail slot in an unmarked building,” says @colincarlson.bsky.social. “It’s wonderful that there’s so much cool stuff in that building. It would be great if we knew who owned it, or who paid for it, or what they plan to do with it.”
#IDsky 🧪
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...
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
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!
PI's of BSky: If you had to guess, What percentage of 2nd+ year PhD students in your lab have an @orcid.org?
And now NextStrain as well.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
Thank you very much to the UShER team (Jakob McBroome, @angieshinrichs.bsky.social, @russcd.bsky.social, Yatish Turakhia, and many more) for providing the daily-updated trees, @theo.io for developing Taxonium (and adding several features upon request!) and CDC AMD for funding. 4/4
The feature is only available on open.cov-spectrum.org which uses data from INSDC (GenBank/ENA/DDBJ), we unfortunately cannot provide it for data from GISAID.
If you have any questions or suggestions, please let us know! 3/4
You can choose to only display the sequences of the variant or the whole MRCA clade and color the tips by different metadata fields. You can also click on an inner node and search for a subtree. 2/4
Finally, CoV-Spectrum is meeting trees 🌳 – this week, we released a new feature to browse the SARS-CoV-2 UShER tree on CoV-Spectrum. With the new feature, you can see a subtree of your variant of interest. 1/4
An image of a birthday cake with scientific doodles around it, 9 colourful candles, and the Pathoplexus logo in the middle, with the words 'Happy 1 year'
🗓 Pathoplexus turns ONE! 🎂🎉
In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing.
📰 Read the full update: pathoplexus.org/news/2025-08...
1/10
If you would like to find out more about Loculus, you can still register for the Loculus tutorial at the [BC]2 Basel Computational Biology Conference 2025 on 8 September! Registration closes on 1 September.
www.bc2.ch/tutorials-wo...
“Loculus is remarkable for enabling efficient and secure sharing of pathogen genomic data, which is crucial for public health responses to infectious diseases."
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz
Image showing information on the BC2 (Basel Computational Biology Conference) from 8-10 Sept 2025. Says: "Tutorial: build a microbial genomic sequence database with Loculus - Register now. 8 Sept 2025 - Biozentrum, Basel. Early bird until 30 June 2025"
Interested to learn about how to run your own Loculus (the database code behind @pathoplexus.org)? 🤔🖥️
Sign up for the Loculus Tutorial on Mon 8 Sept at BC2 Conference (@sib.swiss) in Basel, run by @chaoranchen.de & Anya Parker! 🧬
Register: www.bc2.ch/registration...
#bioinformatics #openScience
Loculus, an open-source software for building pathogen sequencing databases, is on the shortlist for #SIBRemarkableOutputs 2024. It’s a joint project by the teams of @neher.io, @tanjastadler.bsky.social and @firefoxx66.bsky.social xx66.bsky.social. Congratulations!
An image showing the ARTIC and Pathoplexus logos connected by blue lines, with the text "Hiring: post-doc/software engineer" and "Global open-source pathogen tools" and "Join Swiss TPH, Work on ARTIC2 and Pathoplexus, Basel, Switzerland"
📢New job posting!📢
Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻💻🧬
My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on!
1/5
Screenshot of the July Update News article on the Pathoplexus website
🗓️As we close in on 11 months of Pathoplexus, we’re pleased to announce many new direct sequence uploads and some exciting new features that expand Pathoplexus’ utility!
📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update
1/9
You might be wondering why we haven't updated outbreak.info for months.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
Screenshot of the homepage of Pathoplexus, showing tiles to navigate to the supported pathogens CCHF, Ebola Sudan, Ebola Zaire, HMPV, Mpox, RSV-A, RSV-B, and West Nile virus.
📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV.
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
🤔Interested in building and managing microbial genomic databases? Join the hands-on tutorial on #Loculus & learn how to set up, customize & deploy Loculus for your projects.
🔹 Tutorial organized by @chaoranchen.de & Anna Parker, from @ethz.ch
📆8 sept at #BC2Basel
👉 Register: tinyurl.com/5n8w3pwb
🚀 New proof-of-principle:
An interactive, searchable MLST hash database... all in your browser! 🔥
Live demo ➡️ lskatz.github.io/mlst-hash-te...
A natural extension of the hash database spec I developed last year: lskatz.github.io/mlst-hash-te...
🧵
Interested in #Bayesian #phylogenetics? 🧬
Join the Taming the BEAST workshop — theory + hands-on tutorials incl. #singleCell, #devBio & #lineageTracing!
📍Beijing, July 14–18, 2025
📅 Apply by April 25
I'll teach on TiDeTree & cell trees
🔗 taming-the-beast.org/news/Deadlin...
The time is flying by.. Hard to believe that it has already been 7 months since we started Pathoplexus!
🗓️ Pathoplexus has now been around for 7 months!
And both we and our users have been busy - so we wanted to share some updates & highlights!
📰 You can see our full News Item here: pathoplexus.org/news/2025-04-16-spring-update
1/9
I think I may buy a few dozen copies of this book and just hand them out to strangers.
bookshop.org/p/books/who-...
The SIB Swiss Institute of #Bioinformatics is on Bluesky! We’re a non-profit organization dedicated to biological & biomedical #dataScience, supporting research & innovation. Follow us for updates on personalized health, biodiversity, pathogens, open science and more. Visit us at sib.swiss
Today I have resigned from my position as a Data Editor at Proceedings B. I believe the journal does great work, but it feels wrong to voluntarily spend my time holding authors to account on behalf of the Royal Society, while the Society refuses to hold its own Fellows to account.
