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Pathoplexus @pathoplexus.org · 28d

We encourage anyone interested in using these data for publications or preprints to reach out to the authors directly. Restricted-Use sharing protects their work and encourages collaborations, while ensuring the sequences are available for public health when needed most.

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Pathoplexus @pathoplexus.org · 28d

Restricted-Use sequences cannot be used for publications or preprints without permission from the data generators. This ensures credit and collaboration, while still supporting urgent response.

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Pathoplexus @pathoplexus.org · 28d

Restricted-Use sequences can be used immediately for public health, outbreak response, and preparedness. This is the main purpose of this option: enabling rapid access when it matters most.

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Pathoplexus @pathoplexus.org · 28d

Since these sequences are likely to attract interest, it’s worth highlighting again what ‘Restricted-Use’ means on Pathoplexus.

Data Use Terms for Restricted-Use data: pathoplexus.org/about/terms-...

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Screenshot of the Pathoplexus Data Use Terms, focusing on 4.2, Restricted Use Data introduction

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Pathoplexus @pathoplexus.org · 28d

We’re grateful these sequences were shared on Pathoplexus. The authors have chosen to share them as ‘Restricted-Use’ - enabling rapid access for public health, while limiting use in publications/preprints.

View the sequences here: pathoplexus.org/ebola-zaire/...

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Screenshot of the search page on Pathoplexus showing the first 4 sequences: their Pathoplexus accession, sample date, collection country and subdivision, authors, affiliations, and length.

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Pathoplexus @pathoplexus.org · 28d

Behind these sequences are the dedicated teams leading the public health response, sampling, testing, & sequencing. With thanks to Placide Mbala-Kingebeni & team at Institute National de Recherche Biomedicale DRC @inrb_kinshasa.

See the post for a full author list.

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Screenshot of list of authors, which can be seen in the post link in the first tweet

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Pathoplexus @pathoplexus.org · 28d

Amid the concerning news of a new Ebola Zaire outbreak in DRC, teams on the ground have already managed to sample, sequence, and share data. This rapid turnaround is a testament to their commitment and capacity to respond.

Read more: virological.org/t/the-16th-e...

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The 16th Ebola Virus Disease Outbreak in Bulape Health Zone, Kasai, Democratic Republic of the Congo: A new spillover event from an unknown reservoir host

Background The Democratic Republic of the Congo (DRC) is currently facing concurrent outbreaks including mpox, cholera and malaria (1-4). The Ministry of Public Health, DRC has declared the 16th Ebola...

virological.org

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Reposted by Pathoplexus

Theo Sanderson @theo.io · Aug 27

It's our birthday! Super proud of what this little database has become in the past year.

Today we launched support for measles and a bunch of new features 👇

Pathoplexus @pathoplexus.org · Aug 27

🗓 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...

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Pathoplexus @pathoplexus.org · Aug 27

We are so grateful to our contributors, curators, members & partners worldwide ❤️
Here’s to Year 2 - and an even more connected, equitable future for pathogen genomics! 🎊

Read our whole post here: pathoplexus.org/news/2025-08...

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Pathoplexus | Pathoplexus Turns One – and Adds Measles Virus!

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

pathoplexus.org

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Pathoplexus @pathoplexus.org · Aug 27

📢 We’re also celebrating a successful ETH4D Research Challenge grant with ETH Zurich @ethz.ch & Stephen Kanyerezi (Uganda) @kanyerezi30.bsky.social to grow Pathoplexus & Loculus – with workshops, training, user feedback & community building.

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Pathoplexus @pathoplexus.org · Aug 27

💡 New tech:

🔁GISAID accessions can now be linked in metadata for supported pathogens
🖱️Drag your mouse over checkboxes to quickly select multiple sequences
🔎Find sequences faster than ever with the new Accession search at the top of the home page

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Pathoplexus @pathoplexus.org · Aug 27

Other news:

We’ve received
🧬 256 new direct mpox sequences from Sierra Leone, Portugal, Germany, Côte d’Ivoire, DRC, Ireland & Central African Republic
🧬 308 new direct West Nile sequences from California & Nebraska, USA

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Pathoplexus @pathoplexus.org · Aug 27

Why now?
• Measles cases have surged in the US in 2025 - real-time genomic tracking is vital
• Global travel + declining vaccination rates raise outbreak risk
• More labs are sequencing MeV than ever before- enabling insights into spread & evolution

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Pathoplexus @pathoplexus.org · Aug 27

🎉 New in August: Measles virus joins Pathoplexus!

Following strong community support, we added MeV data submission (with Open & Restricted-Use options, as always) and powerful search & data access for MeV
pathoplexus.org/measles/search

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A screenshot of the Pathoplexus homepage, now showing Measles among the other pathogens supported.

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Pathoplexus @pathoplexus.org · Aug 27

And… 🏆
We received the 2024 Swiss National Open Research Data Prize for our commitment to openness & community governance – all while being powered largely by volunteer effort!

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A photo of key members of the Pathoplexus developer team receiving the ORD prize

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Pathoplexus @pathoplexus.org · Aug 27

We’ve also:
• Enabled rapid public-health use while protecting publication rights via Restricted-Use sharing
• Presented at WHO IPSN events, major conferences & workshops
• Featured in Lancet Microbe, Science, Nature, and national media

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Pathoplexus @pathoplexus.org · Aug 27

A Year of Milestones 🌍

Together with our community we have:
• Added mpox (Dec 2024) + RSV & HMPV (May 2025)
• Received direct uploads from 5 continents - incl. more mpox in 2025 than other databases
• Rolled out major software updates & new analysis integrations

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A diagram showing a timeline from August 2024 to May 2025, with one stop in the middle at December 2024.
In August, four viruses are shown: Ebola Sudan & Zaire, West Nile, and CCHF. In December 2024, mpox is added. Then in May 2025, RSV & HMPV

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Pathoplexus @pathoplexus.org · Aug 27

🗓 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...

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Pathoplexus @pathoplexus.org · Jul 15

👀Be sure to check out the full News Item to see all our technical updates (we couldn’t fit them all here), new sequences, and extra information!:
pathoplexus.org/news/2025-07-14-july-update

We can’t wait to celebrate one year with you all in August! 😁🎂

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Pathoplexus | Pathoplexus July Update

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

pathoplexus.org

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Pathoplexus @pathoplexus.org · Jul 15

As you may have already seen, ARTIC2, follow-up to the hugely successful ARTIC, has launched, and through @firefoxx66.bsky.social & @swisstph.ch, Loculus (the software underlying Pathoplexus) is part of the effort to make sequencing & data sharing easier!

bsky.app/profile/path...

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Nick Loman @pathogenomenick.bsky.social · May 22

Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...

Ambitious project to develop low-cost genome sequencing for pathogens known and unknown - University of Birmingham

Project will build on research that helped diagnostic labs to adopt sequencing capacity for COVID-19 and permit characterisation of future infectious threats

www.birmingham.ac.uk

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Pathoplexus @pathoplexus.org · Jul 15

We’ve also made donating to Pathoplexus easier - our new Funding page has helpful information - we will add additional donation methods soon! And we’d be happy to discuss institutional support as well - just reach out! 💶
pathoplexus.org/about/funding

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Pathoplexus | Funding

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

pathoplexus.org

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Pathoplexus @pathoplexus.org · Jul 15

If you’re an API user, you’ll be happy to hear we now support advanced queries including logical queries (like ‘and’, ‘not’, ‘&’, etc), regex, and ‘N-of’ & ‘exactly-of’ for more exact & flexible matching. 🧑🏻‍💻

See our full docs on using them here:
lapis.cov-spectrum.org/open/v2/docs...

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Advanced query

Generalized advanced queries

lapis.cov-spectrum.org

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Pathoplexus @pathoplexus.org · Jul 15

In an awesome new feature, you can now use the ‘Tools’ button to send sequences from Pathoplexus to other analyses and visualizations - like maps or Nextclade!

Have a tool that would be worth including? See our docs!
pathoplexus.org/docs/how-to/...

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Pathoplexus @pathoplexus.org · Jul 15

In new features - We’ve made it easy to include sublineages in your search! Use the ‘include sublineages’ checkbox on the website, or ‘A.2.*’ in the API to return both the top-level lineage and all sublineages:

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Pathoplexus @pathoplexus.org · Jul 15

Direct uploads in May & June have included the following sequences:
- 128 Mpox
- 15 West Nile
- 1089 RSV-A
- 1060 RSV-B
- 1 Ebola Zaire
An incredible diversity both in sequences and in contributing labs. We thank these contributors for choosing to share with Pathoplexus! 🙏🏻

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