Sustained Oropouche virus transmission in Rio de Janeiro’s Atlantic forest: genomic evidence over a twoyear period

Abstract

BACKGROUND: Oropouche virus (OROV), an arbovirus endemic to the Amazon region, has recently expanded into non-endemic areas including Rio de Janeiro state, Brazil. OBJECTIVE: To characterize the spatio-temporal dynamics and ecological factors associated with OROV transmission in Rio de Janeiro during 2024–2025. METHODS: We analyzed OROV case-associated ecological factors and performed a phylodynamic analysis on 40 viral genomes, comprising 35 new and five published sequences, sampled from 15 municipalities across the state during 2024-2025. FINDINGS: OROV cases showed significant positive correlations with forest area (r = 0.50, p < 0.0001), banana harvest area (r = 0.39, p < 0.01), and cassava harvest area (r = 0.29, p < 0.05); but these factors were autocorrelated, suggesting a confounded relationship. We identified two OROV sub-clades circulating in the Rio de Janeiro state. The OROVRJ/ES sub-clade was likely introduced into the Southern Fluminense region around January 2024, spread primarily by short (>2km, 50% of events) and mid-distance movements (2-9 km; 30%) with a mean dispersal rate of 0.3 km/day, and seed outbreaks in Metropolitan and Northwest Fluminense regions in 2025. The OROVES-I clade was likely introduced into Central Fluminense and Coastal Lowlands regions, later spreading to the Northern Fluminense region. MAIN CONCLUSIONS: Following its introduction in early 2024, OROV persisted in Rio de Janeiro state by spreading through short-distance movements among municipalities with high forest cover and agricultural areas. The sustained multi-year OROV transmission in the Atlantic Forest biome highlights the potential for establishment of endemic cycles beyond the Amazon region and the need for enhanced surveillance in extra-Amazonian areas, where OROV will evolve in a different ecosystem.