Pathogen genomic surveillance status among lower resource settings in Asia

Abstract

Asia remains vulnerable to new and emerging infectious diseases. Understanding how to improve next generation sequencing (NGS) use in pathogen surveillance is an urgent priority for regional health security. Here we developed a pathogen genomic surveillance assessment framework to assess capacity in low-resource settings in South and Southeast Asia. Data collected between June 2022 and March 2023 from 42 institutions in 13 countries showed pathogen genomics capacity exists, but use is limited and under-resourced. All countries had NGS capacity and seven countries had strategic plans integrating pathogen genomics into wider surveillance efforts. Several pathogens were prioritized for human surveillance, but NGS application to environmental and human-animal interface surveillance was limited. Barriers to NGS implementation include reliance on external funding, supply chain challenges, trained personnel shortages and limited quality assurance mechanisms. Coordinated efforts are required to support national planning, address capacity gaps, enhance quality assurance and facilitate data sharing for decision making.

Fig. 1

A system-wide assessment framework of pathogen genomic surveillance capacity.

Fig. 2. Pathogens for which genomic surveillance was conducted in the past 5 years across 13 countries in Asia.

For each pathogen, countries reported use of NGS for routine surveillance, outbreak or research purposes, as applied to human or environmental surveillance. Pathogens are listed in order of their median Likert score (1–2 = low priority, 3 = medium priority, 4–5 = high priority). RSV, respiratory syncytial virus; HIV, human immunodeficiency virus.

Fig. 3. Country summary score for pathogen genomic surveillance status.

Total scores for each country are aggregated across thematic areas within the system-wide assessment framework (Enabling environment, Capacity and data quality, Sharing and impact) and include binary scoring for 20 indicators. A higher score indicates a more robust system supporting NGS implementation. It reflects the presence of supportive policies, investment, infrastructure and expertise, as well as good data dissemination practices essential for enhancing genomic surveillance.

Fig. 4. Major barriers and future priorities for pathogen genomic surveillance across 13 countries.

Median Likert scores (1–5) and interquartile ranges (IQR) are displayed, with scores for major barriers ranging from 1 (not a barrier) to 5 (always a barrier), and future priorities from 1 (not a priority) to 5 (essential). Median Likert score is displayed by a dot, and IQR by a grey bar, where the lowest and highest of the grey bar marks the 25th and 75th percentile, respectively (*includes availability, lead time and expiry date on arrival; **includes electricity and internet connection; ***includes transportation time and quality; ****includes data processing, quality assurance and storage).