Insights gained from the systemic use of whole genome sequencing (WGS) to monitor novel variants of SARS-CoV-2 during the COVID-19 pandemic have accelerated the wider integration of WGS for infectious disease and antimicrobial resistance (AMR) surveillance and a One Health approach to inform prevention and control strategies, including vaccination.

Pandemic preparedness requires worldwide deployment of agile integrated genomic, clinical, and epidemiologic surveillance systems with seamless interoperability and global interconnectivity—allowing real-time monitoring of the emergence, spread, virulence, and evolution of pathogens, using a One Health perspective.

One Health genomic surveillance requires wider cross-sectorial collaboration and data sharing in line with ethical regulations, between laboratories, health agencies, surveillance databases, and the broader scientific community—using FAIR principles regarding findability, accessibility, interoperability, and reusability.

International harmonization of methods and nomenclature for genomic surveillance as well as support for timely data sharing are key steps to enable coordinated global responses to cross-border threats from infectious diseases and AMR.

Continued investment to enhance laboratory capacity, provide access to validated genomic data analytical tools, train an expert workforce (including health professionals), and achieve a comprehensive digital health information infrastructure must address international resource inequalities to ensure universal access.

Academic, public health, and non-governmental organizations should share best practices to advance the equitable deployment of pathogen genomics through collaborative initiatives at regional and global levels.