Spatial and phylogenetic insights into bovine rabies virus in Ecuador: Regional control implications

Bovine rabies caused by the rabies virus (RABV) represents a significant veterinary and economic problem in Ecuador, particularly in the Amazonian province. In this study, the transmission dynamics and genetic diversity of the virus are explored through phylogenetic and spatial analysis of Ecuadorian isolates from cattle, contextualized with sequences from neighboring countries. Cerebellum and brain samples were collected from 45 virus-infected farms across Ecuador between 2015 and 2020. Samples were obtained post-mortem from symptomatic animals and immediately processed for virus isolation. The phylogenetic analysis employed the maximum likelihood method, using the Tamura-Nei model. The spatial analysis employed kernel density estimation and Getis-Ord Gi* to identify disease hotspots. Ecuador reported 815 cases of bovine rabies during 2015–2020, of which 404 were confirmed. The Amazonian province of Zamora Chinchipe had the highest number of cases and high spatial clustering in 2017–2018. Time-structured phylogenetic analysis revealed province-specific clades with strong support, indicating localized persistence and regional transmission (TMRCA ≈ 1749). Low nucleotide diversity, negative Tajima's D, and ω < 1 confirmed strong purifying selection and constrained rabies virus evolution in Ecuador. These findings provide critical insights into the molecular epidemiology and geographic distribution of RABV in Ecuador, which are crucial for informing targeted and effective control interventions and activities for regional coordination.