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Molecular Epidemiology of Western Equine Encephalitis Virus, South America, 2023-2024

Aline Scarpellini Campos et al. Emerg Infect Dis. 2024 Sep.

Abstract

Western equine encephalitis virus (WEEV) is a mosquitoborne virus that reemerged in December 2023 in Argentina and Uruguay, causing a major outbreak. We investigated the outbreak using epidemiologic, entomological, and genomic analyses, focusing on WEEV circulation near the Argentina‒Uruguay border in Rio Grande do Sul state, Brazil. During November 2023‒April 2024, the outbreak in Argentina and Uruguay resulted in 217 human cases, 12 of which were fatal, and 2,548 equine cases. We determined cases on the basis of laboratory and clinical epidemiologic criteria. We characterized 3 fatal equine cases caused by a novel WEEV lineage identified through a nearly complete coding sequence analysis, which we propose as lineage C. Our findings highlight the importance of continued surveillance and equine vaccination to control future WEEV outbreaks in South America.

Keywords: Argentina; Brazil; South America; Uruguay; Western equine encephalitis virus; alphavirus; arbovirus; central nervous system infection; meningitis/encephalitis; mosquito-borne alphavirus; vector-borne infections; viruses; zoonoses.

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Figures

Figure 1
Figure 1
Western equine encephalitis cases in Argentina, Uruguay, and Brazil. A) Cumulative western equine encephalitis laboratory-confirmed cases in Argentina and Uruguay reported to the Pan American Health Organization (PAHO) during October 2023‒June 2024 (9). B) Locations of deaths among horses in Rio Grande do Sul state, Brazil, that tested positive (blue) and negative (yellow) for WEEV by RT-PCR during December 2023‒April 2024. The cases were identified by our molecular epidemiology study in Barra do Quaraí on December 21, 2023 (EQ1090), in Uruguaiana on December 28, 2023 (EQ1122), and in Jaguarão on January 30, 2024 (EQ237). WEEV, western equine encephalitis virus.
Figure 2
Figure 2
Maximum-likelihood phylogenetic tree of 3 new WEEV strains from Rio Grande do Sul state, Brazil (bold text), and reference sequences. Tip colors indicate WEEV lineage. We used an uncorrelated log-normal relaxed molecular clock model with an exponential rate distribution for generating the time-rooted tree. Posterior probability scores appear next to key well-supported nodes. Dates at key nodes are the estimated dates of divergence from a common ancestor, with Bayesian credible intervals. WEEV, western equine encephalitis virus.
Figure 3
Figure 3
Phylogenetic analysis of WEEV strains from Rio Grande do Sul state, Brazil, and reference sequences. A) Regression of sequence sampling dates against root-to-tip genetic distances in a maximum likelihood phylogeny of the WEEV strains. Sequences are colored according to geographic source. Line indicates the correlation; shading indicates 95% CIs. B) Effective population size of WEEV through time using the Skygrid model. Thin blue lines represent 95% Bayesian credibility interval, and the thick blue line represents the posterior median. Vertical dotted lines indicate the best estimates for the time of the root of the tree (left) and the upper highest posterior density (right). WEEV, western equine encephalitis virus.
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