Investigation of neurotropic arboviruses in wild and domestic animals in Amazon region, 2023-2024

BACKGROUND Arboviruses represent a potential threat to global public health due to their ability to infect various vertebrate hosts and vectors, as well as their adaptability to diverse ecosystems, allowing them to expand geographically across continents. OBJECTIVE The present study aimed to describe the molecular epidemiology of encephalitic arboviruses, including Venezuelan equine encephalitis virus (VEEV), Eastern equine encephalitis virus (EEEV), Western equine encephalitis virus (WEEV), West Nile virus (WNV), Saint Louis encephalitis virus (SLEV), Toscana virus (TOSV), and Rift Valley fever virus (RVFV) in nervous tissue samples from domestic and wild animals from the Northern region of Brazil, between February 2023 and June 2024. METHODS Samples negative for rabies virus were analysed by reverse transcription real-time polymerase chain reaction (RT-qPCR) targeting Alphavirus, Orthoflavivirus and Phlebovirus species. Positive samples were subjected to viral isolation in cell culture and whole-genome sequencing using next-generation sequencing. Phylogenetic and molecular clock analyses were performed to characterise viral lineages and evolutionary relationships. FINDINGS Two samples tested positive for arboviruses by RT-qPCR: one SLEV sample from the state of Amazonas, which showed a low viral load, preventing virus isolation and sequencing, and one Madariaga virus (MADV) sample from the state of Pará, which could be isolated and sequenced. The isolated agent belongs to lineage III of EEEV, showing most similarity to strains from Guyana and Argentina. MAIN CONCLUSIONS The present study detected two arboviruses in animals, suggesting its circulation in the study area.