Genomic Informed Phylodynamic Modeling of Epidemic Acceleration in Conflict Affected Settings An Integrated Framework from Yemen

The study develops a genomic climate informed SEIR framework to forecast cholera epidemic dynamics in Yemen, a conflict-affected setting with fragile surveillance capacity. The model integrates genomic diversity of Vibrio cholerae (quantified using Shannon entropy) with composite climate forcing indices derived from rainfall anomalies, temperature deviations, and ENSO/IOD activity. Bayesian hierarchical estimation with MCMC was applied to calibrate parameters using surveillance data from 2015–2024. Forecasts for 2025–2030 reveal pronounced epidemic surges in 2026 and 2029, coinciding with ENSO-driven rainfall peaks, while moderate waves are anticipated in 2025, 2027, and 2030, and a smaller localized wave in 2028. Compared to classical SEIR models, the genomic-climate SEIR framework reduced forecasting error by nearly 50% (RMSE reduction 47%, MAE reduction 51%), enabling more accurate estimation of time-varying reproduction numbers. These findings highlight climate as the dominant driver of cholera amplification, with genomic variation contributing to acceleration under high-stress years. The proposed framework provides robust anticipatory risk assessment and supports Yemen’s alignment with the WHO roadmap for Ending Cholera by 2030.. The framework aims to improve outbreak prediction accuracy and enhance early warning systems in fragile health systems [1–4].