September saw continued progress across PHA4GE’s Working Groups, with activity spanning data standards, artificial intelligence, infrastructure, wastewater surveillance, data repositories and workforce development.
This month’s updates reflect the range of technical and capacity-building work underway across the network, as Working Groups continue to develop practical resources, guidance and opportunities for collaboration.
Data Structures Working Group
The Data Structures Working Group continued work on a minimal contextual data specification for pathogen surveillance.
The proposed pathogen-agnostic specification currently includes approximately 12 core fields covering information such as pathogen details, sample collection and researcher or institutional involvement.
Discussions this month focused on the intended audience and purpose of the specification, with members emphasising its use for routine surveillance and internal data exchange rather than solely for public repository submission.
The group also discussed plans for wider community consultation. A survey will be developed to gather feedback on the proposed specification, supported by an information session that will introduce the work and provide additional context before the survey is circulated.
Data Repositories Working Group
The Data Repositories Working Group highlighted the second anniversary of Pathoplexus.
Pathoplexus supports the sharing of pathogen genomic data and associated metadata and continues to contribute to efforts to improve access to genomic surveillance data.
The milestone provided an opportunity to recognise the platform’s development and its role within the wider pathogen genomics ecosystem.
Wastewater Sequencing Sub-Working Group
The Wastewater Sequencing Sub-Working Group continued refining its guidance on the use of wastewater surveillance for Mpox.
The group discussed the complementary roles of qPCR and genomic sequencing, noting that while qPCR can distinguish between major Mpox clades, genomic sequencing provides additional information on genomic origin and can help distinguish known transmission lineages from potentially novel strains.
Members also agreed that the guidance should better reflect the global nature of Mpox transmission. Updates are being made to reduce an Africa-centred framing and include evidence of local transmission and locally acquired cases outside Africa, including Clade 1b where relevant.
The group also reviewed recent literature on Mpox sequencing strategies, wastewater surveillance and lessons from SARS-CoV-2 wastewater monitoring.
Infrastructure Working Group
The Infrastructure Working Group discussed several areas relevant to the future of public health genomics infrastructure.
These included the relationship between artificial intelligence, infrastructure and cybersecurity, as well as opportunities to harmonise and reuse data integration approaches across public health laboratories.
Members considered how genomic databases, epidemiological systems and laboratory information management systems could be better integrated.
Other topics included database design principles, accreditation, infrastructure maintenance costs and approaches to cost recovery when providing services to external clients.
Artificial Intelligence Working Group
The Artificial Intelligence Working Group continued exploring practical ways to support the adoption of AI in public health genomics.
Members proposed the development of hands-on workshops to provide practical experience with AI tools and approaches.
The group also discussed a possible webinar series featuring experts working on AI implementation in public health genomics.
Work is also continuing on an AI perspective paper, with contributors from across the PHA4GE community helping to shape the publication.
Training and Workforce Development Working Group
The Training and Workforce Development Working Group hosted Dr Harris Onywera of Africa CDC, who presented on Building Africa’s Public Health Genomics Workforce for Sustainable Impact: An Africa CDC Perspective.
Dr Onywera is a Bioinformatics Data Scientist and Workforce Development Coordinator for the Africa Pathogen Genomics Initiative within Africa CDC.
His presentation focused on efforts to strengthen genomic surveillance capacity across the continent, including workforce development, integrated genomic surveillance, pathogen detection and wastewater and environmental surveillance.
Africa CDC’s workforce development initiatives have contributed to the training of more than 2,600 public health laboratory scientists across 54 African Union member states.
The session also highlighted online genomics training resources that can support continued learning and capacity development.
Looking ahead
Across the Working Groups, September’s activities continued to focus on practical outputs, including standards, guidance, training opportunities, technical resources and community engagement.
Several groups are now moving into the next stages of their work, including community consultation, document refinement, webinar planning and the development of new training and AI-focused activities.
Get involved
PHA4GE’s Working Groups are open to members of the global public health genomics community who would like to contribute to ongoing projects and discussions.
Those interested in data standards, infrastructure, artificial intelligence, workforce development, repositories, bioinformatics or related areas are encouraged to join PHA4GE and get involved in a Working Group.
