Mapping the geodispersal and evolutionary dynamics of regional Nipah virus strain in Bangladesh

Nipah virus (NiV) is a zoonotic pathogen causing severe respiratory and neurological disease in humans, with high fatality rates, primarily transmitted from fruit bats to humans through bat-tainted raw date palm sap and fruits. NiV outbreaks have occurred almost annually across 34 of 64 districts in Bangladesh. The study investigated the geodispersal patterns and evolutionary phylodynamics of NiV, aiding in more effective outbreak management strategies in Bangladesh. Phylodynamic and geographic evolutionary analyses were conducted using the nucleoprotein (N) gene sequence (n = 23) isolated from human and bat samples (2016-2023), along with publicly available NiV genomes up through November 2024. Bayesian evolutionary analysis of NiV spatiotemporal data suggested NiV clade expansion and the emergence of a new lineage, possibly driven by genetic mutations over time, and identified potential risk areas for NiV infections. The analysis revealed that Bangladeshi NiV strains diverged into two major lineages, BD-1 and BD-2, around 1984. BD-1 is split into NiV-BD1.1 and BD1.2 (first detected in 2004), while BD-2 emerged in 2008, later diverging into BD2.1 and BD2.2. As of 2023, most bat-derived NiV sequences belong to the BD-2 lineage. The estimated evolutionary rate of NiV in Bangladesh is 4.89 × 10⁻⁴ substitutions/site/year (95% HPD: 3.71 × 10⁻⁴ - 6.45 × 10⁻⁴), with genetic clusters spanning from 6.54 km to 116.09 km. Our findings highlight ongoing evolution, the emergence of sub-lineages, and the geographic expansion of NiV in Bangladesh, underscoring the value of phylogeographic approaches in guiding targeted surveillance and control strategies.IMPORTANCEA comprehensive understanding of the spread and evolution of the Nipah virus is critical, as it causes severe disease and frequent outbreaks in Bangladesh. This study provides a detailed look into how different strains of the Nipah virus have geographically moved and genetically changed over nearly two decades. By analyzing virus samples from fruit bats and infected human cases, the study reveals that the virus has formed two distinct sub-lineages, evolving separately at different times and regions of Bangladesh. Identifying these groups helps pinpoint areas most at risk for future outbreaks. These insights are important for identifying high-risk regions and informing surveillance priorities for early detection and preparedness, particularly in areas with recurring spillover events. Ultimately, this research emphasizes the importance of continuously monitoring Nipah virus evolution in both bats and humans, guiding public health strategies to manage and reduce the impact of this dangerous disease in Bangladesh and other regions.