Molecular Evolution and Epidemiological Dynamics of Foot‐and‐Mouth Disease Virus O/ME‐SA/Ind‐2001e Circulating in East Java, Indonesia, in 2022–2025

Background Indonesia has been free from foot‐and‐mouth disease virus (FMDV) for decades, but in April 2022, the first major re‐emerging of FMDV was detected in Gresik, East Java, and later spreading nationwide. To understand how dynamic virus spread occurs in Indonesia, we performed an epidemiological study and molecular evolution analyses. Methods A total of 40 FMDV suspected samples collected in 2023–2025 from cattle in East Java, Indonesia. Phylogeny were inferred using the neighbor‐joining method, and Bayesian Markov Chain Monte Carlo (MCMC) was employed to estimate the evolutionary rate and time to the most recent common ancestor (tMRCA) compared with global reference and vaccine strains. Results Sanger sequencing was performed for 10 out of 40 positive VP1 genes, and results were confirmed as O/ME‐SA/Ind‐2001e. Amino acid substitutions were identified within the G‐H loop region of the VP1 protein and play an important antigenic site involved in receptor binding and immune recognition. The Bayesian evolutionary analyses suggested that estimated evolutionary rate was 1.1 × 10 −3 substitutions/site/year and tMRCA was 2012 (95% HPD interval 2008–2025). Conclusion Amino acid mutations in G‐H loop region may affect viral infectivity, host tropism, and vaccine match. These findings emphasize the need for continuous molecular surveillance of FMDV in Indonesia to detect emerging variants, understand transmission dynamics, and maintain effective antigenic matching between vaccines and circulating field strains.