A Comprehensive Assessment of the Use Cases of Pathogen Genomics in Asia: A Systematic Review

Abstract

ABSTRACT Title: Comprehensive Assessment of the Use Cases of Pathogen Genomics in Asia: A Systematic Review Background: Pathogen genomics has become an increasingly important component of modern infectious disease surveillance, enabling improved detection, characterization, and monitoring of pathogens. Advances in next-generation sequencing technologies have expanded the ability of public health systems to generate and analyze genomic data to support outbreak investigation, transmission analysis, antimicrobial resistance surveillance, and pandemic preparedness. In Asia, genomic surveillance capacity has expanded substantially in recent years, particularly during the COVID-19 pandemic. However, the extent to which pathogen genomics has been applied across public health functions, pathogens, and countries in the region has not been systematically examined. Purpose: This study aimed to comprehensively assess the reported use cases of pathogen genomics across Asian countries and to characterize patterns in applications, pathogens studied, sequencing technologies, sampling contexts, and research leadership. Methods: A systematic review of peer-reviewed literature was conducted to identify studies reporting pathogen genomic sequencing in Asia between 2018 and 2024. Studies were screened using predefined eligibility criteria and relevant data were extracted on genomic surveillance use cases, pathogen types, sequencing technologies, sampling contexts, and publication characteristics. Use cases were classified according to the World Health Organization Pathogen Genomic Surveillance framework and the International Pathogen Surveillance Network taxonomy. iii Findings: A total of 490 studies were included in the analysis. Publication output increased substantially during the COVID-19 period, peaking in 2022 before stabilizing in subsequent years. Sequencing activity was geographically concentrated in a small number of higher-output countries, particularly China, Japan, India, and South Korea. Viral pathogens dominated sequencing applications, with SARS-CoV-2 representing a major component of the literature, while bacterial sequencing was less frequent and fungal and parasitic pathogens were minimally represented. Pathogen characterization and genetic epidemiology were the most commonly reported use cases, whereas programmatic applications such as policy support, risk assessment, and routine surveillance integration were less frequently documented. Human-derived clinical samples accounted for the majority of sequencing studies, with limited environmental and cross-sectoral One Health sampling. Conclusions: Although pathogen genomics capacity in Asia has expanded rapidly in recent years, its applications remain uneven across countries and public health functions. The findings highlight the need for stronger integration of genomics into routine surveillance systems, diversification of pathogen coverage, and sustained investment in infrastructure, workforce development, and regional coordination to ensure equitable and effective genomic surveillance across the region.