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News > Expanding Pathoplexus: Dengue and Yellow Fever Virus added

Expanding Pathoplexus: Dengue and Yellow Fever Virus added

By the Pathoplexus Team - 11 March 2026

Today Pathoplexus is launching support for yellow fever virus and dengue virus sequence sharing. Yellow fever virus and dengue virus (formally Orthoflavivirus flavi and Orthoflavivirus denguei, respectively) are both arboviruses transmitted by Aedes mosquitos. Yellow fever virus causes yellow fever, which is endemic in Africa and South America. Dengue fever — colloquially known as break-bone fever — occurs more broadly in tropical and subtropical climates around the world.

Together, these viruses are estimated to account for over 400 million infections and 43,000 to 94,000 deaths per year. Particularly concerning is the fact that global infections for dengue are rising steeply, and that the virus is spreading to new areas. By facilitating open sharing of yellow fever virus and dengue virus sequences, Pathoplexus seeks to support research and empower public health responses to these arboviruses.

Dr Anderson Brito, a research scientist at Instituto Todas pela Saude (ITpS), Brazil, and member of the Pathoplexus Executive Board, received expressions of interest from the community about adding dengue and yellow fever virus. He commented, “Integrating dengue and yellow fever virus into Pathoplexus means providing endemic countries a transparent, equitable way to share data under terms of use that protect generators’ rights. This creates a collaborative ecosystem where data can safely be contributed for the global public good, fostering the timely genomic surveillance essential for public health.”

Given the varied hosts for these species, we require the submission of the host scientific name metadata field for yellow fever virus and dengue (alongside our normally required fields of sample ID, country of collection, and date). We are adding this as samples from these viruses are often obtained from vectors, such as mosquitos, and infected animals, making this field important for analysis and surveillance.

The addition of these two arboviruses was resolved by our Executive Board after very strong expressions of community support.

Funding Update

Pathoplexus is grateful to have received a $500,000 grant from Kanro, the philanthropic initiative supported by Vitalik Buterin. This contribution will help sustain and expand our open infrastructure that enables transparent and equitable sharing of pathogen genomic data. We are deeply thankful for the trust placed in our mission.

Data and Pathogen Updates

Pathoplexus now hosts over 10,400 directly-submitted sequences. Since our last update in November 2025, over 1,500 new sequences have been directly submitted across six pathogens, from labs in Africa, Europe, Asia, and the Americas.

Our first direct upload of measles virus sequences to Pathoplexus came from Senegal. Dr Idrissa Dieng, a research scientist from Institute Pasteur de Dakar and Deputy Head of the Measles and Rubella National Reference Center, told us:

“Pathoplexus represents a new generation of genomic data platforms, one that balances rapid data sharing with recognition of the scientists generating the data. The measles sequences we uploaded are the first full-genome measles sequences generated from Senegal, marking an important milestone for genomic surveillance in the country. By sharing them through Pathoplexus, we are strengthening global measles monitoring while ensuring that African-generated data are visible, valued, and integrated into international public health action.”

A summary of our new uploads include:

As well as directly uploaded sequences, we also ingest data from INSDC databases, ensuring users can access all openly available sequences via Pathoplexus.

Community Highlights

Pathoplexus is dedicated to serving the pathogen community, and as such we aim to be active participants in initiatives that help us connect with and better understand the needs of our users (and potential users!).

Curations

WHO PABS Intergovernmental Working Group

Pathoplexus is grateful to have been included as a ‘Relevant Stakeholder’ for the ongoing WHO Pathogen Access and Benefits (PABS) Intergovernmental Working Group (IGWG) negotiations. This status allows Pathoplexus to participate directly in some of the sessions, and additionally be available to interact with Member States to answer questions about pathogen genomic data sharing and share our experience and success in running an ‘open-access, restricted-use’ system.

Technical Improvements

In the last three months, we’ve introduced several improvements across datasets, ingestion pipelines, mutation search, and submission workflows. Below is a summary of the latest updates.

Improved Alignment Success with Reverse Complement Retries

We now also attempt to align sequences to reference genomes using the reverse complement of the provided sequence, if the initial alignment fails. This has significantly increased the number of successfully aligned sequences ingested from the INSDC. Newly aligned sequences include:

  • 10 Ebola Zaire
  • 33 West Nile virus
  • 19 HMPV
  • 118 Mpox

Expanded Measles Dataset

We now ingest INSDC measles sequences from a higher taxonomic level: Morbillivirus hominis. This change allows us to mirror additional data and significantly increases the number of available sequences. This update was prompted by Jover Lee, who noticed that the measles taxon ID needed to be updated.

New CCHF Dataset with Lineages

A new nextclade dataset for Crimean-Congo Hemorrhagic Fever (CCHF) including lineage information for the S segment is now used for processing of CCHF sequences.

Improved Multi-Segment Upload for Segmented Pathogens

We have adjusted how multi-segmented virus data is uploaded. Now, you can include an additional metadata field called fastaIds, with the identifiers in the fasta file of all of the sequences to be linked to a specific metadata entry.

The field contains a space-separated list of FASTA identifiers, for example:

seq_12_A seq_12_B

Pathoplexus will automatically assign each sequence to the segment that it aligns to, simplifying the submission process for segmented pathogens. Read more about sequence submission here: https://pathoplexus.org/docs/how-to/upload-sequences.

Mutation Search Improvements for Segmented Viruses

Mutation search has been redesigned for segmented viruses. Nucleotide and amino acid mutation search now operates at the segment level. Users no longer need to append the segment name when querying nucleotide mutations. This makes mutation queries simpler and more intuitive.

An image showing the Pathoplexus user interface for mutation search on segmented viruses

Improvements to Group Management

We improved the group management interface to make collaboration easier: Users are now warned if a group name is already in use, and are shown ways to contact existing groups to request to join them. It is now also easier to discover existing groups. These improvements help avoid duplicate groups and streamline collaboration.

An image showing the new alert in Pathoplexus when a user attempts to create a group with a name that is already in use

Talks, Tutorials, and Media

Past talks

Upcoming:

Meetings, Minutes, and Resolutions

Remember that you can always check our minutes from General Assemblies and Executive Board meetings, as well as Executive Board resolutions.