Pathogen genomic surveillance status among lower resource settings in Asia.
Getchell M., Wulandari S., de Alwis R., Agoramurthy S., Khoo YK., Mak T-M., Moe L., Stona A-C., Pang J., Momin MHFHA., Amir A., Andalucia LR., Azzam G., Chin S., Chookajorn T., Arunkumar G., Hung DT., Ikram A., Jha R., Karlsson EA., Le Thi MQ., Mahasirimongkol S., Malavige GN., Manning JE., Munira SL., Trung NV., Nisar I., Qadri F., Qamar FN., Robinson MT., Saloma CP., Setk S., Shirin T., Tan LV., Dizon TJR., Thayan R., Thu HM., Tissera H., Xangsayarath P., Zaini Z., Lim JCW., Maurer-Stroh S., Smith GJD., Wang L-F., Pronyk P., Asia Pathogen Genomics Initiative (Asia PGI) consortium .
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.