When an infectious disease outbreak emerges, sharing pathogen genomic data quickly can make a difference to how public health teams understand and respond to the threat. But for the teams generating that data, sharing it can also raise difficult questions: Will their work be acknowledged? Will they still have the opportunity to publish their findings?
These questions have been central to Pathoplexus since its launch in August 2024. Two years after its launch, the platform’s experience shows how a different approach to data sharing is being put into practice, from responding to emerging outbreaks to building a tool around the needs of the people who use it.
Making Data Sharing Work in Practice
Built on the open-source Loculus software and governed as a non-profit association, Pathoplexus is a community-governed, open-access platform for sharing pathogen genomic data. It has grown to support 16 pathogens, with direct submissions from dozens of countries across every inhabited continent.
For the Pathoplexus team, one of the biggest lessons has been that speed and trust need to go hand in hand. Teams may want to share sequences during an outbreak but hesitate if doing so could mean losing the opportunity to publish their own analyses or having their work used without acknowledgement.
Pathoplexus addresses this through two sharing options: data can be made openly available immediately or shared under Restricted-Use terms for up to a year, with conditions covering authorship, SeqSets and citation. The aim is to allow data to be shared when it is needed while protecting the credit of those who generated it.
When the Need Is Immediate
The value of this approach became clear during two recent outbreaks.
When the Andes virus outbreak linked to the MV Hondius emerged in May 2026, Pathoplexus added support for the virus within days. Four teams from four countries submitted genomes shortly afterwards.
Following the announcement of the Ebola Bundibugyo outbreak affecting the Democratic Republic of the Congo and Uganda, the Pathoplexus team added support for the virus before the sequences were off the sequencer. Laboratories in both countries had near-complete genomes available on the platform shortly afterwards.
For the teams generating those sequences, Restricted-Use sharing offered a way to make data available for outbreak response without giving up the opportunity to publish their own findings first.
These examples show how quickly the platform can adapt to emerging public health needs, while giving teams a way to share data without setting aside the recognition they deserve.
Built Around the People Who Use It
Pathoplexus has also grown in response to requests from its community. Mpox, respiratory syncytial virus (RSV), human metapneumovirus (HMPV) and measles were added following community requests, while other additions, including Marburg, dengue and yellow fever, responded to outbreak needs and interest from researchers in endemic countries.
The platform’s technical development has followed a similar path. Improvements to searching and submissions, tools for comparing sequence versions and tracking citations, and the addition of raw sequencing reads have all helped make data easier to share and use.
For contributors, citation tracking is particularly relevant. Pathoplexus addresses this need through SeqSets. SeqSets are collections of sequences tagged with a citable digital object identifier (DOI), allowing the use of sequences in scientific literature to be linked back to the records on Pathoplexus. It is one practical way the platform can recognise the work behind the data.
Pathoplexus now has 32 members from 14 countries, reflecting the collaborative effort behind the platform and its continued development.
Looking Ahead
In its third year, Pathoplexus plans to continue expanding pathogen coverage in response to community needs. The team is also working to improve its API so the platform fits more smoothly into analysis pipelines, while exploring better ways to display quality-control information and sequencing coverage.
The longer-term goal is to make it easier for more groups and countries to participate in data sharing with confidence.
Two years on, Pathoplexus is showing what can be possible when accessible infrastructure and fair data-sharing practices work together. As the platform continues to grow, its focus remains on making it easier for more teams and countries to share pathogen genomic data with confidence, helping ensure that the information needed for public health responses can be available when it matters most.
