Sustained Oropouche virus transmission in Rio de Janeiro’s Atlantic Forest: genomic evidence over a two-year 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 characterise the spatio-temporal dynamics and ecological factors associated with OROV transmission in Rio de Janeiro during 2024-2025.

METHODS  We analysed 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 OROV_RJ/ES sub-clade was likely introduced into the Southern Fluminense region around January 2024, spread primarily by short (> 2 km, 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 OROV_ES-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.

Key words:
Oropouche virus; Oropouche fever; Brazil; Rio de Janeiro; Atlantic Forest