11/ 🤲🏻 As always, thank you to our submitters, curators, partners, and community 🙏
Upload your sequences, cite your SeqSets (DOIs matter!), and tell us what you'd like to see next!
🔗 Full update: pathoplexus.org/news/2026-03...
#OpenData #OpenScience #PublicHealth #Dengue #YellowFever
10/ 🎤 We've been busy on the road! Highlights:
- Talks at Imperial College London, LS2 , BRC Consortium, SSI Denmark, DeZi & UNITEDengue and more
📌 Next up: 18 March - Emma at the 35th Annual Meeting of the Society for Virology!
Screenshot showing that if you try to have a group name that already exists, Pathoplexus will now warn you to create a more unique name.
9/ 🛠️ More tech:
- Improved group management - warnings for duplicate group names & easier ways to find & join existing groups
- Expanded measles dataset via higher-level INSDC taxon ingestion (thanks to Jover Lee for the tip!)
Screenshot of the Pathoplexus website, showing the 'browse data' page for CCHF - highlighting how you can now add mutations in specific boxes for the S, M, & L segments, rather than having to append the segment to the mutation itself.
8/ 🛠️ Tech improvements:
- Reverse complement retries now boost alignment success
- New CCHF dataset with lineages for the S segment
- Simpler multi-segment upload with the new fastaIds field
- Mutation search redesigned for segmented viruses - no need to append segment name!
7/ 🌐 Policy & governance: Pathoplexus has been included as a 'Relevant Stakeholder' in the WHO Pathogen Access and Benefits Sharing IGWG negotiations - allowing us to participate directly and share our experience running an open-access, restricted-use system.
6/ 💰 Funding news: We're grateful to have received a $500,000 grant from Kanro, the philanthropic initiative supported by Vitalik Buterin. This helps sustain and expand our open infrastructure for transparent, equitable pathogen genomic data sharing. 🙏
picture of Dr Idrissa Dieng, smiling, in a green outfit
5/ 🧫 On the first full-genome measles sequences from Senegal, Dr Idrissa Dieng (Institut Pasteur de Dakar) noted: "By sharing through Pathoplexus, we ensure that African-generated data are visible, valued, and integrated into international public health action." 🌍
4/ 📊 Highlights include:
- 593 new RSV-A sequences (Australia, Kenya, Netherlands, Argentina & more)
- 445 new RSV-B sequences (Australia, Germany, Kenya, Brazil & more)
- 357 new measles sequences - see below!
- 130 new mpox sequences, including the 1st from Angola & India
3/ 📊 Data growth: Since November, over 1,500 new directly-submitted sequences have been added across six pathogens, from labs in Africa, Europe, Asia, and the Americas. We now host over 10,400 directly-submitted sequences total.
2/ 🗣️ Dr Anderson Brito (ITpS, Brazil) explained the importance of this: "Integrating Dengue & Yellow Fever into Pathoplexus means providing endemic countries a transparent, equitable way to share data under terms that protect generators' rights - essential for public health."
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... 📰
4/ As with all pathogens on Pathoplexus, Marburg data can be uploaded as Open (immediately public + sent to INSDC) or Restricted-Use (up to 1 year). We hope this launch supports current response efforts and future preparedness. 🌍🌎🌏
3/ Jean Pierre Musabyimana (Rwanda Biomedical Centre) welcomed the addition, saying: “Having Pathoplexus support the inclusion of the Marburg virus will tremendously benefit our work in Rwanda and the region.”
2/ Our Executive Board prioritised adding Marburgvirus in light of the recent Ethiopia outbreak and community support.
Pathoplexus provides straightforward methods to upload, compare, and share sequences.
www.who.int/emergencies/...
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...
12/ 🔗 Read the full update here → pathoplexus.org/news/2025-11...
#PathogenGenomics #OpenData #OpenScience #PublicHealth #Bioinformatics
11/ 📌 Thank you to YOU - our submitters, users, partners and community - for helping us make Pathoplexus what it is.
If you haven’t checked in lately: log in, explore the new features, cite your SeqSets (yes, DOIs matter!), and let us know what you’d like to see next. 🎉💬💻
10/ 🤝 New members:
Please join us in welcoming our eight 8 members from Portugal, UK, Uganda (×2), Spain, Ireland (×2), and Bangladesh. Their expertise will help steer Pathoplexus to even greater heights.
pathoplexus.org/about/members
9/ 🏆 Awards & collaborations:
We’re excited to share that Loculus was awarded the SIB Remarkable Output 2024 - recognised for enabling efficient & secure sharing of pathogen genomic data: bsky.app/profile/sib....
Loculus is also joining the Pathogen Data Network!
Photographs of the PHA4GE pre-conference workshops. Showing first a photo of the workshop organizers, Patricia, Emma, Arthur, Stephen, and Chaoran. Then a photo of Stephen helping a workshop participant, and a photo of Chaoran helping a workshop participant.
8/ 🎤 Talks & media:
We’ve been on the road!
• A 2-part Pathoplexus feature on the MicroBinfie Podcast
• Tutorials at BC2, presentations at the IMMEM conference & the PHA4GE Conference & pre-workshop
Next up: See us at the Viruses in Silico (@evbc.bsky.social ) lecture series (27 Nov 16:00 CET)
A screenshot of the Tools page in RSV-A on Pathoplexus, highlighting GenSpectrum, Nextstrain, and some simple plots
7/ 🛠️ Tech improvements (cont.):
• Better UI banners for restricted sequences
• A new “Tools” tab - which highlights external apps/tools that use Pathoplexus data! If you’ve built one and want yours included, let us know! 👂🏻
Screenshot showing the search panel in Pathoplexus, showing that one can now select, for example, two Submitting Groups and two Countries in your sequence search
6/ 🛠️ Tech improvements:
• Support for accented characters in author names
• New means2id field for measles sequence upload, linking to the MeaNS2 database
• Improved groups pages highlight uploads per pathogen
• Multiple choice searches for better filtering!
5/ 🌐 Community & partnerships:
We’re proud to now be an institutional member of the International Pathogen Surveillance Network (IPSN) convened by the World Health Organization @who.int - strengthening our global ties and commitment to equitable pathogen data sharing. 🌐🤝
4/ 🧬 On RSV:
We updated our classification pipeline — switching from Taxon ID 11250 to 1868215 (Orthopneumovirus) to capture more human RSV sequences. This added ~2,325 RSV-A and ~1,335 RSV-B sequences to our system!
3/ 📊 Data growth (cont.):
• 68 new Ebola Zaire virus sequences from DRC (including the first samples from the recent outbreak)
• ~1,326 RSV-A & ~1,642 RSV-B sequences from global labs (USA, Australia, Switzerland)
👉 Showing the power of open, shared data.
2/ 📊 Data growth:
We now host over 8,900 directly-submitted sequences! Highlights since August include:
• ~1,464 new Mpox virus sequences from labs in DRC, Portugal, Ireland, Togo, Canada, Senegal & more
• 7 new West Nile virus sequences from Italy & France
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...
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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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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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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