A recent investigation has shown that outbreak detection resources in South and Southeast Asia are lacking, even in the aftermath of the pandemic. Only around half of the countries examined have incorporated genomic surveillance for pathogens into their national strategies. The study outlines important strategies to bolster the region’s readiness for future pandemics.
A significant analysis conducted by Duke-NUS Medical School indicates that after the recent pandemic, efforts for outbreak detection in South and Southeast Asia are still inadequately funded, with just about 50% of the countries surveyed utilizing genomic surveillance for pathogens in their health plans. This study, published in Nature Microbiology today, outlines essential steps to improve the area’s preparedness against potential pandemics.
The research took place over a year, from 2022 to 2023, examining pathogen genomic sequencing capabilities in 13 out of 19 countries in South and Southeast Asia.
The COVID-19 crisis highlighted the critical role of genomic surveillance, which was essential for detecting SARS-CoV-2, tracking its variants, and creating COVID-19 vaccines. Initially aimed at monitoring SARS-CoV-2, these resources are now being redirected to other health issues, such as drug-resistant tuberculosis, foodborne bacterial diseases, dengue, and the latest avian influenza A (H5N1) outbreak.
All 13 countries possess national genomic sequencing capabilities, but only 7 of them have integrated these initiatives into their comprehensive plans for infectious disease monitoring. Furthermore, only 6 countries have set forth specific guidelines for utilizing pathogen genomics in their disease surveillance efforts. The lack of national protocols for genome surveillance hinders effective implementation and resource distribution. Addressing these shortcomings is vital for enhancing the sustainability and efficiency of infectious disease tracking and response mechanisms.
Assistant Professor Ruklanthi de Alwis, who is the Deputy Director of Duke-NUS’ Centre for Outbreak Preparedness, stated:
“It’s promising to observe some capabilities in pathogen genomic sequencing, even in less economically advantaged countries in our region, but there is still potential for development. Utilizing pathogen sequencing effectively is essential for maximizing the public health impact through disease surveillance, response, and control. Evaluating the current landscape and needs was a key initial step.”
The research also pinpointed five main obstacles the region faces in implementing genomic sequencing for disease surveillance:
- Funding: Many countries depend significantly on outside funding for pathogen sequencing, with 57% of financial resources in the surveyed nations coming from external donors, while the public sector contributes 32% and academic institutions 6%.
- Trained workforce: There is a shortage of skilled laboratory personnel and bioinformatics specialists for genomic sequencing and data analysis.
- Cost: The expenses associated with genomic sequencing technology are excessively high, leading resource-limited nations in Asia to pay considerably more for sequencing services compared to wealthier countries.
- Supply chain issues: The logistics of supplying genomic sequencing tools and materials is slow, with new orders typically taking around two months to arrive at laboratories.
- Delay in data availability: The several-week delay from sample collection to the receipt of genomic data complicates timely public health responses.
Dr. Thimothy John Dizon from the Research Institute for Tropical Medicine in the Philippines remarked:
“The COVID-19 pandemic has served as a significant signal for global health systems, demonstrating the vital role of genomics in combating pathogens and shaping public health strategies. The complex nature of genomics necessitates a shift in our monitoring practices while enhancing collaboration among the Philippines’ public health labs, surveillance units, and academic facilities. To amplify these improvements, it’s crucial to solidify and maintain investments while fostering broader partnerships both regionally and globally.”
Dr. Khoo Yoong Khean, a Scientific Officer at Duke-NUS’ Centre for Outbreak Preparedness, added:
“Pathogen genomics presents an innovation with substantial public health implications, and our entire region would gain from clear guidance on planning and budgeting for genomics initiatives. Asia is at a heightened risk of emerging infectious disease outbreaks due to factors like dense populations, high mobility, inadequate sanitation, frequent interactions with animals, climate change, and rapid environmental shifts. Improving early detection through infectious disease monitoring is essential for the region’s preparedness for outbreaks.”
Study Methodology
The study was carried out in partnership with participants from Bangladesh, Brunei Darussalam, Cambodia, Indonesia, Lao PDR, Malaysia, Myanmar, Nepal, Pakistan, Philippines, Sri Lanka, Thailand, and Vietnam. Involvement in this study was voluntary and data was gathered from all 13 countries.
Key stakeholders from each participating nation were selected for an extensive survey, resulting in contributions from 42 significant local institutions. These organizations came from various sectors, including government agencies, academic institutions, public laboratories, and NGOs.
Based on the survey responses, 25 summary indicators were developed to assess the regional state of pathogen genomic surveillance, including aspects such as partnerships, funding, policy frameworks, supply chains, laboratory capacity, bioinformatics, quality control, and data sharing.
This study was published through the Asia Pathogen Genomics Initiative (Asia PGI), a regional group led by Duke-NUS that focuses on advancing pathogenic genomics. The consortium has established a specialized training academy at Duke-NUS, allowing nations to collaborate on tailored programs that address priority health issues in Asia. Important collaborators in this initiative include the Bioinformatics Institute at Singapore’s Agency for Science, Technology, and Research.
In association with the US Centres for Disease Control and Prevention (US CDC), Asia PGI is also planning a joint workshop later this year regarding national strategy and the execution of pathogen genomics for infectious disease tracking.
Professor Linfa Wang, Executive Director of the Programme for Research in Epidemic Preparedness and Response (PREPARE), added:
“While genomics plays a crucial role in surveillance, countries must also equip themselves with new tools for their outbreak response strategies. PREPARE and Asia PGI will persist in collaborating with regional partners to build resilience against future epidemics and pandemics, and in the long run, utilizing genomic capabilities to swiftly develop new diagnostics and vaccines will be essential for supporting our efforts.”
