Pathoplexus

22 Sept

1/ 🧬 A big #Pathoplexus milestone: you can now optionally include raw sequencing reads alongside your consensus sequences! Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses. 📰 Read more: pathoplexus.org/news/2026-09...

22 Sept

2/ ⚙️ How it works: raw reads follow all the same policies as consensus sequences - your chosen Data Use Terms apply to both, and raw reads are openly downloadable as soon as processing completes. Pathoplexus handles INSDC submission for you, just like today.

22 Sept

3/ 📤 Ready to try it? Upload raw reads files alongside your next submission (individual or bulk), add them to your existing consensus sequences, and check out our docs for the details on required metadata. 🔗 pathoplexus.org/news/2026-09... #OpenData #OpenScience #PathogenGenomics

1/ 🎂 Pathoplexus turns TWO! 🎉 Two years ago we launched with an idea: what if pathogen data sharing put open access, speed, ease of use, & credit for data generators at its center? Here's what our community has built since: 📰 Read the full update: pathoplexus.org/news/2026-08...

8/ 🙏 None of this happens on its own. Thank you to our Executive Board, our members who guide and hold us accountable, our developer team, and every researcher, lab, and institute who has chosen to share data through Pathoplexus.

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

9/ ❤️ To everyone who's submitted a sequence, flagged a curation issue, joined our Scientific Advisory Board, presented a poster, funded our work, or told a colleague about us - thank you. 2️⃣ Here's to year two, and many more to come! 🎊 🔗 Full post: pathoplexus.org/news/2026-08...

6/ 🔓 In the past two years, we've seen many Restricted-Use sequences have gone fully Open once manuscripts were published - showing that researchers want to share and want their data reused - they just want credit for generating it.

7/ 🦟 And just this week: Zika virus joined Pathoplexus, our newest addition! bsky.app/profile/path...

Pathoplexus@pathoplexus.org

1/ 🦟 New on @Pathoplexus: Zika virus (ZIKV) is now supported! Share your ZIKV sequences as Open or Restricted-Use, just like our other pathogens. Read more: pathoplexus.org/news/2026-08... 📰

4/ 🧬 Steady, ongoing sharing across our pathogens: - Dengue (3,557) - Mpox (3,686) - RSV-A (3,618) - RSV-B (3,653) - Measles (1,908) - West Nile (993) - BDBV (648) - HMPV (488) - Ebola Zaire (72) - plus critical additions to ANDV, Marburg, CCHF, Yellow Fever & Ebola Sudan.

5/ 💡 New capabilities added this year: - SeqSet DOI tracking - see when your sequences are cited in publications - Hierarchical taxonomy search - find all sequences from a host in one query - Link-out Tools - jump straight to Nextclade, Sealion, UShER & Taxonium

2/ 🦠 We've grown from 4 founding pathogens to 15 - including outbreak-driven additions like Ebola Bundibugyo & Andes virus. ⏲️Teams in the DRC and Uganda shared the first BDBV genomes within days of outbreak confirmation 🌍Labs across 4 countries did the same for ANDV

3/ 📊 Two years, in numbers: - 18,659 sequences directly submitted across 14 pathogens - Contributions from every populated continent: North America (4,737), Africa (4,194), South America (3,612), Europe (3,597), Oceania (2,157), Asia (362)

26 Aug

1/ 🦟 New on @Pathoplexus: Zika virus (ZIKV) is now supported! Share your ZIKV sequences as Open or Restricted-Use, just like our other pathogens. Read more: pathoplexus.org/news/2026-08... 📰

26 Aug

2/ 🧬 ZIKV often causes mild or no symptoms - but can rarely lead to Guillain-Barré syndrome or birth defects, making surveillance important. 🙏 Thanks to Arthur Shem Kasambula for leading this addition, & as always, to our submitters, curators, & community for helping expand Pathoplexus!

5 Aug

1/ Using @pathoplexus.org sequences in a preprint or publication? Remember to cite them correctly! It's easy - here how! 1. 🧺 Create a SeqSet containing all the sequences used. You can divide them into Focal & Background pathoplexus.org/docs/how-to/...

3/ 3. ✒️ Cite the DOI *in the references*, like a paper! (This is how CrossRef 'sees' it & how we track it) Getting a citation is easy - click the 'Export/Cite' button & pick your style Copy this *into the references* just like you'd cite a paper!

5 Aug

4/ That's it! 🎉 Now, as soon as CrossRef indexes your manuscript, your SeqSet, and all sequences within that SeqSet, will show that paper/preprint! See examples - A preprint citation in a SeqSet: pathoplexus.org/seqsets/PP_S... A preprint on a sequence page: pathoplexus.org/seq/PP_000TC...

2/ 2. 🔁 Generate a DOI for your SeqSet, by clicking the link available on your SeqSet page Since DOIs are recognised, trackable tags already in the publication ecosystem, this is key to 'following' how sequences are used! pathoplexus.org/docs/how-to/...

1/ 🛠️ Our July update is here - and it's a technical one! New features for citations, search, submission, and more. Here's what's new in #Pathoplexus 👇 🔗 Full post: pathoplexus.org/news/2026-07...

9/ 🏛️ Governance update: Pathoplexus held its General Assembly on 10 June, approving the annual report and planning the year ahead. Minutes & report here 👉 pathoplexus.org/about/govern... We're also delighted to welcome Prof. Placide Mbala to our Scientific Advisory Board! 🎉

10/ As always - share sequences, cite your SeqSets & DOIs, and let us know what you'd like to see next 💬 🔗 Full July update: pathoplexus.org/news/2026-07... #OpenData #OpenScience #PathogenGenomics #PublicHealth

7/ 🔎 Search got smarter: - Filters reorganized into collapsible sections - New 'Required segments' filter for multi-segmented organisms - Search across accession, INSDC, BioProject, BioSample & more in one field - Free-text search now available across all About & Docs pages

8/ 🧬 For #EbolaVirus Bundibugyo: amino acid substitutions relative to the outbreak clade founder are now visualized at a glance. Plus: new LinkOut to view alignments in Sealion - or place sequences on phylogenetic trees via viral UShER + Taxonium.

5/ Submission improvements: - 📄Download a rich XLSX template with field definitions & accepted values - 📥 Batch-download original data for multiple sequences to simplify bulk revisions - ⏪Revocations now process immediately on confirmation - no extra release step needed

6/ More submission updates: - 🗓️ You can now submit date ranges (ISO or Lucene format) when exact dates aren't known. - 🪰 Host species are now validated against NCBI taxonomy, powering consistent metadata & the new taxonomy search.

3/ 🔍 New: hierarchical taxonomy search for host species. Search "mosquitos" and get all sequences from Aedes, Culex, and every other mosquito genus - automatically. Try it for dengue 👉 pathoplexus.org/dengue/searc...

4/ 🔄 Compare sequence versions side-by-side! Click 'Version' on any multi-version sequence page to see exactly what changed between versions - and share the view via URL. Example 👉 pathoplexus.org/seq/PP_006W6...

2/ 📄 SeqSets/DOIs now show citations! We've integrated with @crossref.bsky.social so you can see which scientific publications have used a SeqSet - on the SeqSet page *and* on individual sequence pages. Using seqs in a paper? Don't forget to cite the DOI! 👉 pathoplexus.org/about/citation

1 July

Our first Annual Report is here! 📊 Covering Aug 2024 (our founding) through 2025: new viruses added, global submissions, software upgrades, & community & governance milestones. True to our values, it includes a full financial report + an audit 🔗 pathoplexus.org/about/govern...

1/ 🌍 Our June update is here! Two new pathogens added in response to active outbreaks, over 5,700 new sequences, and a growing community of labs from around the world. Here's what's new in #Pathoplexus 👇 Read the full update: pathoplexus.org/news/2026-06... 📰

9/ 💰 Donation news: You can now support Pathoplexus directly via credit card and other payment methods through Payrexx! Visit our Funding page to find out more 👉 pathoplexus.org/about/funding 🙏

pathoplexus.orgPathoplexus | Pathoplexus June Update: Outbreak Response, Global Firsts, and a Growing CommunityPathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

10/ 🙏 As always, thank you to our submitters, curators, partners, and community. Upload your sequences, cite your SeqSets/DOIs, & tell us what you'd like to see next! 💬 🔗 Full update: pathoplexus.org/news/2026-06... #OpenData #OpenScience #PublicHealth #PathogenGenomics

7/ 🌍 On the 1st yellow fever seqs from Gambia, Dr Idrissa Dieng (Institut Pasteur, Dakar): "Africa's genomic map still has too many blind spots. Uploading to Pathoplexus isn't just about depositing data - it's about lighting a fire under African viral genomics, 1 seq at a time."

8/ 🦠 7 Marbug sequences from Ethiopia, were shared via Wolday Lab, McMaster University, Canada. Dr Maysa Niazy (McMaster): "Making these data available allows researchers worldwide to build on this work and strengthen preparedness for future outbreaks."

5/ 📊 More data highlights: - 510 new RSV-A & 460 new RSV-B sequences (Canada, Australia, USA, Spain, Brazil & more) - 429 new measles sequences (Canada, Bangladesh, South Africa, Senegal, Tanzania)

pathoplexus.orgPathoplexus | Ebola: Rapid response to the Bundibugyo virus outbreak in the DRC and UgandaPathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

6/ 🧬 On sharing measles seqs during Bangladesh's outbreak, Dr. Omar Nasif (IEDCR, Dhaka) said: "The almost immediate release of sequences helps us share findings in real-time with the global scientific community - a significant advancement during public health emergencies."

3/ 🦠 New pathogen: Ebola Bundibugyo virus (BDBV) was added on 19 May in response to the concurrent outbreak in the DRC & Uganda. Teams in both countries shared the 1st genomes through Pathoplexus within days of outbreak confirmation. Read more: pathoplexus.org/news/2026-05...

pathoplexus.orgPathoplexus | Andes virus: supporting response to the current hantavirus outbreakPathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

4/ 📊 Data growth: Pathoplexus has over 5,700 new uploads since March! - 3,296 new dengue sequences 🦟 (Brazil, Bangladesh, Angola & more) - 576 new mpox sequences (Uganda, Portugal, Pakistan, Norway & more) - 467 new HMPV sequences (Spain, Brazil)

2/ 🦠 New pathogen: Andes virus (ANDV) - the hantavirus behind the outbreak linked to the MV Hondius - was added on 9 May. Four teams from four countries submitted genomes within days of launch. Read more: pathoplexus.org/news/2026-05...

19 May

Teams in the Democratic Republic of the Congo & Uganda have now shared the first sequences from the current Ebola (Bundibugyo virus) outbreak using Pathoplexus, just days after cases were confirmed. Read more about the response to Bundibugyo virus here: pathoplexus.org/news/2026-05...

15 May

1/ 🚀 Pathoplexus now supports Bundibugyo virus (BDBV), a species of Ebolavirus. BDBV has been associated with past outbreaks of Ebola in the DR Congo and Uganda, & a case has been reported today during response to the current Ebola outbreak. pathoplexus.org/ebola-bdbv #ebola #bdbv #ebolaoutbreak

5/ The process of adding BDBV to Pathoplexus, from beginning technical work, to EB vote, to launch, took about 7 hours. We’re proud of our ability to be able to enable data sharing for new outbreaks in such a short time, and hope it enables rapid public health response.

15 May

6/ 🙏We are grateful to everyone involved in caring for patients, testing samples, coordinating response, and sharing data. Our thoughts are with everyone impacted by the outbreak, and involved in the response efforts in DRC and Uganda.

3/ Sequences shared as Restricted-Use are available for all unpublished public-health uses (dashboards, reports, open analyses, website) with appropriate credit as outlined in our Data Use Terms - but their status provides protection from publication before the original submitters can publish.

15 May

4/ This is an ongoing outbreak of high interest, with few sequences available. In such a situation, Restricted-Use sequences are highly unlikely to be ‘background’ sequences. Please ensure you follow our Data Use Terms in preprints/publications & co-author with other submitters.

2/ The addition of BDBV to Pathoplexus was fast-tracked by our Exec Board today, to aid data sharing when sequences are available. Pathoplexus lets sequences to be uploaded as Open (immediately public + sent to INSDC) or Restricted-Use (up to 1 year) - to encourage fast sharing.