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Pathoplexus @pathoplexus.org · 22/09/2026

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.

Screenshot of the submission page showing the section to upload raw-reads - with a description and link to the documentation on the left, and a place to upload folders and files on the right.

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Pathoplexus @pathoplexus.org · 22/09/2026

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...

AI-generated image showing raw reads (short reads) lining up above a consensus sequence, with both the raw reads and consensus sequence labelled. Vague images below show a virus, coverage, and DNA.

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Pathoplexus @pathoplexus.org · 27/08/2026

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.

Grid of photographs of all 32 members of Pathoplexus

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Pathoplexus @pathoplexus.org · 27/08/2026

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

Screenshot of a sequence page of RSV-B, showing how a manuscript the sequence has been cited in shows up on the sequence page

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Pathoplexus @pathoplexus.org · 27/08/2026

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.

Screenshot of the Pathoplexus website home page, showing all 15 supported viruses

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Pathoplexus @pathoplexus.org · 27/08/2026

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)

Map of the world with regions Africa, Asia, North America, South America, Oceania, and Europe colored different colors, with each showing their total direct uploads per region

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Pathoplexus @pathoplexus.org · 27/08/2026

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...

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Pathoplexus @pathoplexus.org · 26/08/2026

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... 📰

Screenshot of the Pathoplexus website homepage, where the new Zika virus button is circled in red

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Pathoplexus @pathoplexus.org · 05/08/2026

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...

Screenshot of a different SeqSet Details page on Pathoplexus - this SeqSet has been used and cited. It shows the name, description, and other metrics, but importantly, below the DOI, shows a list of citations. This SeqSet shows it's been cited in a paper called 'Improving the Scalability of Bayesian Phylodynamic Inference through Efficient MCMC Proposals'

Screenshot a Pathoplexus Sequence Details page, of a sequence that is within the SeqSet shown previously. This shows the sequence name, sample date, and other sequence metrics, but since it is included in a SeqSet that has been cited, it also shows a 'Cited by' section, which lists all citations. It shows it has been cited by the same paper in the SeqSet, 'Improving the Scalability of Bayesian Phylodynamic Inference through Efficient MCMC Proposals'

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Pathoplexus @pathoplexus.org · 05/08/2026

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!

Screenshot of the SeqSet Details page on Pathoplexus, showing the name, description, and other metrics - now also showing a DOI in place of the previous link to generate a DOI. Highlighted is the location of the button showing 'Export/Cite' which allows generation of citation/reference text.

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Pathoplexus @pathoplexus.org · 05/08/2026

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/...

Screenshot of the SeqSet Details page on Pathoplexus, showing the name, description, size, and other metrics - but highlighting that there's a link one can click that says 'Generate a DOI'

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Pathoplexus @pathoplexus.org · 05/08/2026

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/...

Screenshot of the 'Create a SeqSet' page on Pathoplexus, showing where one can fill in the SeqSet name, description, and the sequences used, divided into Focal and Background

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Pathoplexus @pathoplexus.org · 23/07/2026

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! 🎉

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Pathoplexus @pathoplexus.org · 23/07/2026

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

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Pathoplexus @pathoplexus.org · 23/07/2026

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

Screenshot of our rich XLSX template showing dropdowns for fields with defined values - this one shows a list of Countries

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Pathoplexus @pathoplexus.org · 23/07/2026

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...

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Pathoplexus @pathoplexus.org · 23/07/2026

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...

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Pathoplexus @pathoplexus.org · 23/07/2026

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

Screenshot of a SeqSet page, showing that the SeqSet has been cited in a paper, with a link to that paper.

Screenshot showing the 'cited in' section on a sequence page - showing the paper a sequence was used in, and a link to that paper.

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Pathoplexus @pathoplexus.org · 23/07/2026

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...

Screenshot of the Pathoplexus website homepage

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Pathoplexus @pathoplexus.org · 01/07/2026

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...

Screenshot of the first page of the pathoplexus annual report 2024-2025, which includes the first few lines of the report, describing the founding of Pathoplexus in August 2024

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Pathoplexus @pathoplexus.org · 30/06/2026

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... 📰

A screenshot of all supported viruses on the Pathoplexus front page, with ANDV and BDBV highlighted.

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Pathoplexus @pathoplexus.org · 15/05/2026

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

Image of some of the available pathogens on Pathoplexus, with a red rectangle outlining the new tile for Ebola Bundibugyo virus, with 44 sequences.

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Pathoplexus @pathoplexus.org · 09/05/2026

1/ 🚀 Pathoplexus now supports the Andes variant of Hantavirus (ANDV). ANDV is the variant identified in the recent MV Hondius cases, & the Hantavirus variant previously identified as having occasional human-to-human transmission. pathoplexus.org/andv #hantavirus #hondius

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Pathoplexus @pathoplexus.org · 12/03/2026

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 showing that if you try to have a group name that already exists, Pathoplexus will now warn you to create a more unique name.

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Pathoplexus @pathoplexus.org · 12/03/2026

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!

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.

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Pathoplexus @pathoplexus.org · 12/03/2026

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." 🌍

picture of Dr Idrissa Dieng, smiling, in a green outfit

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Pathoplexus @pathoplexus.org · 12/03/2026

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... 📰

A screenshot of the new Pathoplexus homepage showing all viruses now supported, including Dengue and Yellow Fever, which are circled in red

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Pathoplexus @pathoplexus.org · 28/11/2025

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...

A screenshot of the front page of Pathoplexus' website, showing the addition of a tile for Marburg Virus.

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Pathoplexus @pathoplexus.org · 18/11/2025

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)

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.

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Pathoplexus @pathoplexus.org · 18/11/2025

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! 👂🏻

A screenshot of the Tools page in RSV-A on Pathoplexus, highlighting GenSpectrum, Nextstrain, and some simple plots

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Pathoplexus @pathoplexus.org · 18/11/2025

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!

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

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Pathoplexus @pathoplexus.org · 18/11/2025

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...

Graph showing the change in number of directly submitted sequences to Pathoplexus since August 2024. 0 in Aug 2024 to almost 9000 today.

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Pathoplexus @pathoplexus.org · 10/09/2025

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-... 4/7

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

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Pathoplexus @pathoplexus.org · 10/09/2025

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/... 3/7

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 · 10/09/2025

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. 2/7

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

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Pathoplexus @pathoplexus.org · 27/08/2025

📢 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. 9/10

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Pathoplexus @pathoplexus.org · 27/08/2025

💡 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 8/10

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Pathoplexus @pathoplexus.org · 27/08/2025

🎉 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 5/10

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

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Pathoplexus @pathoplexus.org · 27/08/2025

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! 4/10

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

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Pathoplexus @pathoplexus.org · 27/08/2025

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 2/10

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 · 27/08/2025

🗓 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

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Pathoplexus @pathoplexus.org · 15/07/2025

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/... 5/9

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Pathoplexus @pathoplexus.org · 15/07/2025

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: 4/9

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Pathoplexus @pathoplexus.org · 15/07/2025

We’ve been thrilled to see that May & June have brought with them a surge in direct uploads to Pathoplexus, across 5 of our supported pathogens, 5 continents, and 8 countries! 🎉🌎🌏 In fact, so far in 2025, Pathoplexus has received more direct mpox submissions than INSDC. 2/9

Graph showing 6 months of Mpox sequences added to Pathoplexus, from Feb 2025 - July 2025, as a bar-chart. Bars are split into blue (sequences ingested from NCBI) and orange (sequences uploaded directly to Pathoplexus). The totals are approximately:
- Feb: 75 from NCBI, 725 direct
- Mar: 50 NCBI, ~5 direct
- Apr: 75 NCBI, 225 direct
- May: 100 NCBI, 100 direct
- June: 50 NCBI, 75 direct
- July: too small to see clearly

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Pathoplexus @pathoplexus.org · 15/07/2025

🗓️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

Screenshot of the July Update News article on the Pathoplexus website

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Pathoplexus @pathoplexus.org · 22/05/2025

📨As with other organisms, you can share data openly immediately or request that data be Restricted-Use for up to 1 year. Restricted-Use data is still openly available but is restricted in how it can be used in publications or preprints. 📖 3/4

A diagram showing how users can easily upload data to Pathoplexus and choose to share this as 'Open data' which can be used by other without restriction, or 'Restricted-use' data which requires permission to publish or preprint on. Restricted-use data can be restricted for up to 1 year, after which it becomes Open, and is always available to view. Open data is automatically submitted to INDSC (Genbank, ENA, DDBJ) by Pathoplexus on behalf of the submitter.

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Pathoplexus @pathoplexus.org · 22/05/2025

📢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

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.

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Pathoplexus @pathoplexus.org · 16/04/2025

You can also now more easily see what filters you’ve applied to your search, as they appear above the search results - making clearing them easier too! 7/9

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Pathoplexus @pathoplexus.org · 16/04/2025

And if you just have one sequence to submit, that’s now simple too - as you can now submit individual sequences via an easy-to-use web form. Spot a mistake? Scroll to the bottom of any sequence page and use the new "Report an Issue" button to let our curators know! 6/9

A screenshot of the pathoplexus website, showing a form where you can upload a single sequence by filling in the fields.

A screenshot of the Pathoplexus website, highlighting the "create github issue" button at the bottom of a sequence information page.

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Pathoplexus @pathoplexus.org · 16/04/2025

In updates to Pathoplexus, you can now upload metadata as Excel files - making data sharing easier than ever (we have templates too!) In the same vein, we now let you specify what columns in metadata files should be mapped to - no more worries if your column names differ! 5/9

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