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.

亚洲仍然容易受到新出现的传染病的影响。了解如何改进下一代测序 （NGS） 在病原体监测中的应用是区域卫生安全的当务之急。在这里，我们开发了一个病原体基因组监测评估框架，以评估南亚和东南亚资源匮乏环境中的能力。2022 年 6 月至 2023 年 3 月期间从 13 个国家的 42 个机构收集的数据显示，病原体基因组学能力存在，但使用有限且资源不足。所有国家都有 NGS 能力，7 个国家制定了将病原体基因组学纳入更广泛的监测工作的战略计划。几种病原体被优先用于人类监测，但 NGS 在环境和人-动物界面监测中的应用受到限制。NGS 实施的障碍包括依赖外部资金、供应链挑战、训练有素的人员短缺和有限的质量保证机制。需要协调努力来支持国家规划、解决能力差距、加强质量保证并促进决策数据共享。