Examine reveals gaps in outbreak detection assets in Asia

A landmark research led by Duke-NUS Medical Faculty revealed that regardless of the current pandemic, outbreak detection efforts stay under-resourced in South and Southeast Asia, with solely about half the international locations reviewed having built-in pathogen genomic surveillance initiatives of their nationwide plans. Printed in Nature Microbiology immediately, the research additionally identifies key priorities to reinforce the preparedness of the area towards future pandemics.

The research, performed over 12 months between 2022 and 2023, analyses responses on genomic sequencing capability for pathogen detection from 13 out of 19 international locations that make up South and Southeast Asia.

The COVID-19 pandemic underscored the significance of genomic surveillance, which was important in figuring out SARS-CoV-2, monitoring its variants and designing COVID-19 vaccines. Initially centered on monitoring SARS-CoV-2, these investments are actually getting used to handle different illness priorities together with drug-resistant tuberculosis, food-borne bacterial infections, dengue or to trace the avian influenza A (H5N1) present outbreak.

Whereas all 13 international locations have nationwide capability for genomic sequencing, solely 7 of the 13 assessed international locations have built-in pathogen genomic sequencing into their nationwide strategic plans for infectious illness surveillance. Moreover, solely 6 international locations have established pointers for utilizing pathogen genomics for infectious illness surveillance. The absence of nationwide pointers for pathogen genomic surveillance complicates implementation and useful resource allocation. Closing these gaps is essential for bettering the effectiveness and sustainability of infectious illness surveillance and response methods.

Though it’s encouraging to see some capability for pathogen genomics sequencing, together with in lower-resourced international locations in our area, there’s nonetheless room for strengthening it. It’s critical that pathogen sequencing is used to maximise public well being impression by way of infectious illness surveillance, response and management. Assessing the present state and wishes was a vital first step.”

Assistant Professor Ruklanthi de Alwis, Deputy Director of Duke-NUS’ Centre for Outbreak Preparedness

The paper additionally recognized 5 particular challenges confronted by the area in adopting genomics sequencing for infectious illness surveillance:

1. Funding: International locations reported a reliance on exterior funders for pathogen sequencing. Throughout the 13 international locations surveyed, 57 per cent of economic and different assets come from exterior donors, adopted by the general public sector (32 per cent) and tutorial establishments (6 per cent).
2. Skilled manpower: Restricted availability of educated laboratory workers and workers educated in bioinformatics for genomic sequencing processing and outcomes’ evaluation.
3. Price: The price of genomic sequencing-related gear is prohibitively excessive and plenty of resource-limited international locations in Asia report paying greater costs for genomic sequencing in contrast with higher-income nations.
4. Provide chain: The provision chain for genomic sequencing gear and reagents is sluggish, with new orders averaging two months to succeed in laboratories.
5. Turnaround time: Delays of a number of weeks between pattern assortment and the provision of genomic information hinder the well timed use of this info to information public well being actions.

Dr Thimothy John Dizon from the Analysis Institute for Tropical Medication within the Philippines mentioned:

“The COVID-19 pandemic has served as a essential wake-up name for well being methods worldwide, highlighting the immense worth of genomics in combating pathogens and shaping public well being responses. The intricate nature of genomics calls for a change in our surveillance practices and has considerably bolstered collaboration among the many Philippines’ public well being laboratories, surveillance models and tutorial establishments. To maximise these developments, it’s important to strengthen and maintain investments by fostering broader collaboration and partnerships each throughout the area and on a worldwide scale.”

Dr Khoo Yoong Khean, Scientific Officer from Duke-NUS’ Centre for Outbreak Preparedness, added:

“Pathogen genomics is an innovation with vital public well being impression, and our whole area would profit from steering on successfully planning and budgeting for genomics. Asia faces a excessive danger of rising infectious illness outbreaks as a consequence of components comparable to dense populations, excessive mobility charges, poor water and sanitation circumstances, frequent human-animal interactions, local weather stress, and a quickly altering atmosphere. Strengthening early detection by way of infectious illness surveillance is essential for regional outbreak preparedness.”

Methodology of the research

This research was performed in collaboration with companions from Bangladesh, Brunei Darussalam, Cambodia, Indonesia, Lao PDR, Malaysia, Myanmar, Nepal, Pakistan, Philippines, Sri Lanka, Thailand and Vietnam. Participation was voluntary and the research included information from all 13 international locations.

Key companions in every of the taking part international locations have been recognized to participate in an in-depth survey, leading to a complete of 42 main native establishments contributing information. These organizations hailed from various sectors, together with authorities entities, tutorial establishments, public laboratories, and non-governmental organizations.

Primarily based on survey responses, 25 abstract indicators have been then chosen and calculated to guage the regional standing of pathogen genomic surveillance. These indicators cowl areas comparable to partnerships, financing, insurance policies and pointers, provide chain, laboratory infrastructure, bioinformatics, high quality assurance, and information sharing and impression.

The research was revealed below the Asia Pathogen Genomics Initiative (Asia PGI), a regional consortium hosted by Duke-NUS that’s devoted to advancing pathogen genomics. The consortium has established a specialised coaching academy at Duke-NUS, enabling international locations to collaborate by way of tailor-made applications that deal with precedence well being threats in Asia. Key companions on this work embody the Bioinformatics Institute at Singapore’s Company for Science Know-how and Analysis.

In collaboration with the US Centres for Illness Management and Prevention (US CDC), Asia PGI can be organizing a joint workshop later this 12 months on nationwide planning and implementation of pathogen genomics for infectious illness surveillance.

Professor Linfa Wang, Govt Director, Programme for Analysis in Epidemic Preparedness and REsponse (PREPARE), added:

“Whereas genomics is important for surveillance, international locations additionally want new instruments of their outbreak response toolkit. PREPARE and Asia PGI will proceed working with regional companions to reinforce resilience to future epidemics and pandemics, and in the long term, leveraging genomics capability to quickly develop new diagnostics and vaccines shall be a vital space of help for our efforts.”