Asia Pathogen Genomics Initiative

Asia Pathogen Genomics Initiative

Genomic sequencing for infectious disease elimination

The Asia Pathogen Genomics Initiative (Asia PGI) was established in late 2021 with the support of the Gates Foundation. As the flagship initiative of the Duke-NUS Centre for Outbreak Preparedness, Asia PGI is a coordination and capacity development hub advancing pathogen genomic sequencing for early detection, control, and elimination of infectious diseases in the region. The Asia PGI network includes over 40 regional partners from 14 Asian countries, representing government, academia, industry, and non-governmental organisations.

Areas of work

Capacity development

Health systems

Legal frameworks

Novel tools

Asia Pathogen Genomics Academy

The Academy aims to accelerate capacity development for pathogen genomic sequencing of novel and endemic pathogens. The facility is equipped to provide hands-on technical training on a range of pathogen genomic sequencing platforms and workflows. Training covers both laboratory and bioinformatics, with workshops focusing on priority pathogens for genomic surveillance in Asia. Additionally, the Academy envisions utilising new educational technologies and delivery modes to enhance technical trainings and strengthen pandemic preparedness.

Key activities include:

Singapore based training workshops
Off-site regional workshops
Deployable genomics outbreak response
Virtual learning platforms
Webinars and seminars
Monitoring and evaluation

Visit our Training Repository to access a wide range of training materials.

National planning

The health systems enhancement (HSE) team aims to translate the Global Genomic Surveillance Strategy developed by the World Health Organization (WHO) into national health plans. Contextualising the global mandate into local settings is a critical first step in developing national capacity and securing sustainable domestic financing. The HSE team also offers technical support for investment case development and cross-country learning via knowledge-sharing platforms and activities, to enable policymakers to make strategic decisions on implementing and scaling up cost-effective health interventions and policies.

Key activities include:

National investment case development
National planning support
Best-practice documentation
Cross-country learning exchange
Regional working groups on Asian priority pathogens

Check out our Roadmap for Pathogen Genomics in Asia and published paper in Cell Genomics: 'Advancing pathogen genomics in resource limited settings.'

View our HSE resource repository to access all resources, including country profiles and external guidance documents.

Supply chain responsiveness

Addressing supply chain constraints has emerged as a key priority for countries in Asia. At present, low-income countries pay substantially more than high-income countries for genomic sequencing equipment and reagents. Supply chain challenges lead to long delays in repair and re-supply time. The supply chain team works with genomics manufacturers and countries to address these challenges.

Key activities include:

Generating market intelligence on genomics pricing
Supporting national forecasting and costing for pathogen genomics
Establishing a regional supply chain community-of-practice network
Engaging with manufacturers to negotiate preferential access schemes for country partners

Use case: Wastewater & environmental surveillance

We are strengthening emerging efforts and expanding the utility of wastewater and environmental surveillance (WES) for novel and endemic pathogens of public health importance in Asia. A Regional WES Expert Working Group has been established to foster ongoing strategic engagement, guidance development, knowledge exchange and capacity building activities. The WES team partners with Singapore’s National Environment Agency to develop training programs on WES best practice.

Key activities include:

Regional expert working group
Technical training
Webinar series
Strategy design for sampling and surveillance
Innovation hub
Country use-cases and investment cases

Use case: Drug-resistant tuberculosis

Tuberculosis (TB), particularly drug-resistant TB (DR-TB), remains a major public health threat in Asia, and is a key priority use-case for pathogen genomics. Targeted next-generation sequencing (tNGS) provides a transformative solution by enabling rapid, comprehensive detection of resistance mutations directly from clinical samples. Over the past year, Asia PGI has launched a series of targeted initiatives to advance the adoption and integration of tuberculosis (TB) genomics within national programs across the region.

Key activities include:

Regional TB genomics stakeholder meeting
Cross-country knowledge exchange, including a TB Genomics Expert Working Group
Capacity building for TB genomics
Evidence-based implementation guidance for tNGS for DR-TB management

Legal frameworks & data governance

Legal frameworks in pathogen genomics establish clear guidelines and standards for every step of the process – from research and development, data collection and usage, to data sharing and collaboration for the surveillance and response of global infectious disease outbreaks. Together with the Centre for International Law (CIL) at NUS, we support countries in strengthening their legal infrastructure in pathogen genomics to promote sustainable efforts in the region.

Key activities include:

Landscape mapping
Ethics for pathogen genomic surveillance
Supporting the development of standards for data sharing
Supporting innovations and building capacity around intellectual property

Novel tool development

Asia PGI works to establish scientific and technical partnerships to advance innovations in the interpretation and use of pathogen genomic data. This includes support to the development of diagnostics, therapeutics and vaccines through linking scientists in partner countries to laboratories in Singapore at Duke-NUS, Singapore PREPARE and others, and to local manufacturers with the aim of regional self-sufficiency and commercial product generation.

Key activities include:

AI-enabled platform linking pathogen genomics to large language models to enhance public health and clinical decision-making
New tool development through translational research projects
Workshops for new tool design and development
Landscaping and reviews on the regional landscape and the applications of pathogen genomics to human health in Asia