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Home / Equine Research Bank / Npj Viruses / Diagnosis and genomic characterization of the largest wester...
Npj viruses2024; 2(1); 70; doi: 10.1038/s44298-024-00078-6

Diagnosis and genomic characterization of the largest western equine encephalitis virus outbreak in Uruguay during 2023-2024.

Abstract: The Western equine encephalitis virus is transmitted between mosquitoes and wild birds. Mosquitoes spread the virus to horses and human populations, causing severe encephalitis and death. The most recent large outbreak occurred in South America from November 2023 to April 2024. We identified and genetically characterized Uruguayan strains during this outbreak to understand their evolutionary trends and rapid expansion. We obtained genomes from 15 strains using a novel multiplex PCR assay combined with next-generation Illumina sequencing. The phylogenetic analysis revealed that viruses from Uruguay and Brazil collected during the outbreak and an Argentine strain from 1958 share a common evolutionary origin and are distinct from North American strains. Phylogenetic and epidemiological data suggest that the outbreak 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.
© 2024. The Author(s).
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Publication Date: 2024-12-31 PubMed ID: 40295695PubMed Central: PMC11721398DOI: 10.1038/s44298-024-00078-6Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • This study investigated the largest Western equine encephalitis virus (WEEV) outbreak in Uruguay during 2023-2024.
  • The researchers identified and genetically analyzed virus strains to understand the outbreak’s origin, evolution, and spread.

Background on Western Equine Encephalitis Virus (WEEV)

  • WEEV is an arbovirus transmitted primarily between mosquitoes and wild birds.
  • Mosquitoes act as vectors by spreading the virus to horses and humans.
  • The virus can cause severe encephalitis, an inflammation of the brain, which can be fatal in infected individuals.
  • Historically, large outbreaks of WEEV have been documented in various parts of the Americas.

Outbreak Context and Study Goals

  • The largest recent WEEV outbreak in South America occurred between November 2023 and April 2024.
  • The outbreak affected Uruguay, Brazil, and had connections to Argentina.
  • The study aimed to:
    • Isolate and sequence WEEV strains from the outbreak in Uruguay.
    • Analyze the genetic relationship of these strains with those from neighboring countries and past outbreaks.
    • Understand the viral evolutionary patterns that could explain the rapid spread.
    • Evaluate the molecular diagnostics currently in use for issues that could affect detection accuracy.

Methods: Virus Genome Sequencing and Analysis

  • Researchers obtained virus samples from 15 strains isolated during the outbreak in Uruguay.
  • A novel multiplex PCR assay was developed to amplify viral genomic material efficiently.
  • Next-generation sequencing technology (Illumina platform) was used to determine the full viral genomes.
  • Phylogenetic analysis was employed to compare these genomes with existing sequences from Brazil, Argentina, and North America.

Key Findings: Phylogenetics and Evolution

  • The genetic data showed that the Uruguayan and Brazilian outbreak strains formed a cluster with an Argentine strain from 1958, indicating a shared evolutionary lineage.
  • These South American strains were genetically distinct from North American WEEV strains, implying separate evolutionary histories.
  • Phylogenetic and epidemiological evidence suggested the outbreak likely began in Argentina and then spread to Uruguay and Brazil.
  • The spread pattern was consistent with movement of wild birds carrying the virus, which transmitted it to mosquitoes in new regions.

Implications for Diagnostics

  • Genomic analysis revealed mismatches in the sequences where diagnostic real-time PCR primers and probes bind.
  • These mismatches could reduce binding efficiency and diagnostic sensitivity.
  • The results highlight a potential risk that official diagnostic protocols may fail to accurately detect some outbreak strains.
  • Updating diagnostic primers and probes based on recent genomic data is essential for accurate detection and surveillance.

Conclusion

  • This study provided the first detailed genomic characterization of the largest WEEV outbreak in Uruguay.
  • It traced the virus’s evolutionary history and geographical spread within South America.
  • The work underscores the importance of continuous genomic surveillance to track arboviral outbreaks and improve diagnostic tools.

Cite This Article

APA
(2024). Diagnosis and genomic characterization of the largest western equine encephalitis virus outbreak in Uruguay during 2023-2024. Npj Viruses, 2(1), 70. https://doi.org/10.1038/s44298-024-00078-6

Publication

Npj viruses
ISSN: 2948-1767
NlmUniqueID: 9918716188906676
Country: England
Language: English
Volume: 2
Issue: 1
Pages: 70
PII: 70

Researcher Affiliations

Conflict of Interest Statement

Competing interests: The authors declare no competing interests. Institutional Review Board statement: The study does not require ethical approval because it was conducted by the Ministry of Livestock, Agriculture, and Fisheries of Uruguay (MGAP) as part of public health surveillance by official veterinary authorities (DILAVE) in response to equine encephalitis outbreaks.

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Citations

This article has been cited 1 times.
  1. Fan X, Li W, Oros J, Plante JA, Mitchell BM, Plung JS, Basu H, Nagappan-Chettiar S, Boeckers JM, Tjang LV, Mann CJ, Brusic V, Buck TK, Varnum H, Yang P, Malcolm LM, Choi SY, de Souza WM, Chiu IM, Umemori H, Weaver SC, Plante KS, Abraham J. Molecular basis for shifted receptor recognition by an encephalitic arbovirus.. Cell 2025 May 29;188(11):2957-2973.e28.
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