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A landmark study led by Duke-NUS Medical School has revealed that despite the lessons learned from the COVID-19 pandemic, many countries in South and Southeast Asia remain under-prepared to detect and respond to future outbreaks. The study, published in Nature Microbiology, highlights significant gaps in the integration of pathogen genomic surveillance into national plans, with only about half of the reviewed countries taking adequate steps toward this critical area of public health preparedness.
The comprehensive study, conducted over 12 months between 2022 and 2023, analyzed the genomic sequencing capabilities for pathogen detection across 13 of the 19 countries that make up South and Southeast Asia. While all 13 countries have some capacity for genomic sequencing, only seven have incorporated it into their national strategies for infectious disease surveillance. Furthermore, only six countries have established formal guidelines for utilizing pathogen genomics in tracking and controlling diseases.
The COVID-19 pandemic showcased the vital role of genomic surveillance in identifying SARS-CoV-2, monitoring its variants, and aiding in vaccine development. However, many countries in Asia are struggling to build on this momentum, with weak surveillance systems hindering their ability to detect and respond to a broad range of infectious threats.
Key Challenges Identified
The study identifies several critical challenges that are hampering the effective use of pathogen genomic surveillance in the region:
- Funding: Many countries rely heavily on external funding, with 57% of financial support for genomic surveillance coming from international donors. Only 32% comes from national governments, and a mere 6% from academic institutions.
- Manpower: The availability of trained laboratory staff, especially those skilled in bioinformatics, is severely limited across the region.
- Costs: Genomic sequencing equipment remains prohibitively expensive for lower-income countries in Asia. Several nations report paying higher prices for sequencing equipment than their wealthier counterparts.
- Supply Chain Issues: Delays in obtaining sequencing equipment and reagents are common, with many countries waiting up to two months for critical supplies to reach laboratories.
- Turnaround Time: Long delays between sample collection and the availability of genomic data undermine timely public health interventions.
Assistant Professor Ruklanthi de Alwis, Deputy Director of Duke-NUS’ Centre for Outbreak Preparedness, emphasized the need to strengthen genomic sequencing across the region. “While it is encouraging to see some capacity in lower-resourced countries, there is still room for improvement. It is vital that sequencing be fully utilized to maximize its public health impact,” she said.
The Importance of Genomics in Future Preparedness
Dr. Thimothy John Dizon from the Research Institute for Tropical Medicine in the Philippines noted that the pandemic has underscored the importance of genomics in shaping public health responses. He added, “The intricate nature of genomics demands a transformation in our surveillance practices and greater collaboration across laboratories, surveillance units, and academic institutions.”
Asia faces a heightened risk of emerging infectious diseases due to factors such as high population density, mobility, poor sanitation, human-animal interactions, and climate change. Strengthening genomic surveillance is essential to mitigating these risks, according to Dr. Khoo Yoong Khean from Duke-NUS. “Asia needs to invest in early detection systems and better preparedness,” he stated.
The Path Forward
The study was part of the Asia Pathogen Genomics Initiative (Asia PGI), a regional consortium hosted by Duke-NUS that aims to strengthen genomic surveillance in Asia. The initiative brings together governments, academic institutions, and public health bodies to address health threats through targeted training and collaboration.
Moving forward, Asia PGI is set to host a workshop in collaboration with the US Centers for Disease Control and Prevention (CDC) to guide national planning for pathogen genomics. The initiative’s long-term goal is to help countries not only detect future outbreaks more effectively but also leverage genomics to accelerate the development of new diagnostics and vaccines.
Professor Linfa Wang, Executive Director of Duke-NUS’ Programme for Research in Epidemic Preparedness and Response (PREPARE), emphasized the need for continued collaboration. “Genomics is essential for surveillance, but countries also need new tools to respond to outbreaks. We will continue working with regional partners to enhance resilience to future pandemics,” he said.
As Asia faces increasing threats from emerging diseases, this study highlights the urgent need for sustained investment in pathogen genomic surveillance to better prepare for the next pandemic. Without adequate resources and infrastructure, the region’s ability to effectively respond to future public health crises remains compromised.
