October saw continued progress across several PHA4GE Working Groups and subgroups, with activity spanning wastewater surveillance, genomic data infrastructure, artificial intelligence and pathogen data sharing.
Building stronger wastewater surveillance systems
The Wastewater Sequencing subgroup continued work on guidance for mpox wastewater surveillance, including the addition of references and examples relating to metagenomic sequencing.
The group is also exploring how wastewater surveillance data could be stored, accessed and shared more effectively across countries. Discussions included the possibility of a centralised platform capable of tracking organisms such as SARS-CoV-2 lineages and visualising changes in lineage prevalence over time.
Members considered a range of possible approaches to data storage, from cloud-based infrastructure to institutional systems hosted in different countries. Existing initiatives such as the Beacon Project were also discussed as potential models or sources of inspiration for developing more coordinated global wastewater surveillance infrastructure.
Strengthening infrastructure for genomic data
The Infrastructure Working Group continued discussions around sequence databases and the systems needed to support genomic surveillance.
Working Group co-chair Peter van Heusden also participated in a meeting in Kathmandu, Nepal, where discussions focused on strengthening the foundations needed to support pathogen genomic surveillance and data infrastructure.
These conversations form part of PHA4GE’s broader effort to ensure that genomic data can be stored, managed and exchanged in ways that are sustainable and useful to public health systems.
Growing the AI community
The Artificial Intelligence Working Group continued to build momentum during October, with members discussing opportunities for future speakers and contributors.
The group is developing a broader network of researchers and practitioners working at the intersection of artificial intelligence, pathogen genomics and public health, while identifying opportunities to share practical applications of AI with the wider PHA4GE community.
Pathoplexus expands to new pathogens
There was also significant progress from the Data Repositories Working Group, particularly through ongoing development of Pathoplexus.
The platform recently expanded its pathogen coverage with the addition of Zika virus and chikungunya virus, further broadening the range of genomic data that can be shared through the platform.
Pathoplexus has also introduced support for raw sequencing reads, allowing users to share data beyond assembled consensus sequences. Supporting tools and guidance are being developed to help users process and clean these reads before submission.
The team is now preparing improvements to the Loculus API, which underpins Pathoplexus, as the software moves towards its first official version 1 release.
Pathoplexus also continues to receive genomic sequences linked to the ongoing outbreak of Bundibugyo virus, including submissions from Kenya and Nigeria.
Looking ahead
In the coming months, the Working Groups will continue developing wastewater surveillance guidance, exploring options for globally coordinated data infrastructure, strengthening genomic sequence databases and expanding tools for pathogen data sharing.
Across these activities, a common theme remains clear: developing practical, interoperable systems that make pathogen genomic data easier to collect, share and use for public health.
