Diagnosis and Genomic Characterization of the Largest Western Equine Encephalitis Virus Outbreak in Uruguay During 2023–2024

Abstract

The Western Equine Encephalitis Virus (WEEV) is transmitted between mosquitoes and wild birds. Mosquitoes can spread the virus to horses and human populations, causing severe encephalitis and death. The most recent large outbreak of WEEV occurred in the Southern cone of South America from November 2023 to April 2024, affecting many equines and humans in Argentina and Uruguay. We identified and genetically characterized WEEV strains during this outbreak to understand their evolutionary trends and rapid expansion in the country and at international borders. The virus affected 1,086 horses and caused 388 deaths in all regions of Uruguay. We obtained genomes from 15 strains using a novel multiplex PCR assay combined with next-generation Illumina sequencing. The phylogenetic analysis revealed that samples from Uruguay and Brazil collected during 2023–2024 and an Argentine strain from 1958 share a common evolutionary origin and are distinct from North American strains. Phylogenetic and epidemiological data on the outbreak suggest that it originated in Argentina and spread to Uruguay and Brazil, likely by movements of infected birds. Genomic analysis also revealed mispairing in real-time PCR primers and probes that may affect official diagnostic protocols, highlighting the need for assay updates. Our research emphasizes the need to map the genetic diversity of WEEV in South America to understand their epidemiology and develop effective control approaches.