Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses.
Authors: Gardner Shea N, McLoughlin Kevin, Be Nicholas A, Allen Jonathan, Weaver Scott C, Forrester Naomi, Guerbois Mathilde, Jaing Crystal
Journal: PloS one
Summary
Venezuelan equine encephalitis virus (VEEV) presents a significant biosecurity concern for equine practitioners, given its capacity to cause severe disease outbreaks in both horses and humans; however, rapid identification and characterisation of newly emerging strains remains challenging. Gardner and colleagues developed a single nucleotide polymorphism (SNP) microarray platform to enable fast, high-resolution genetic analysis of VEEV isolates across the entire antigenic complex, validating their approach against traditional phylogenetic methods and demonstrating concordance between array-based and sequence-derived SNP calls. The microarray proved capable of genotyping virus directly from infected tissue samples without requiring viral isolation or culture—a significant practical advantage for outbreak response—and successfully placed previously unsequenced isolates within an established phylogenetic framework. Analysis of diverse VEEV strains revealed specific genomic variants associated with particular serotypes and host species, though the relationship between genotype and phenotype proved complex, suggesting that genetic markers alone cannot reliably predict virulence or epidemic potential. For equine professionals involved in disease surveillance or outbreak management, this work offers a rapid diagnostic tool to characterise emerging VEEV strains and contextualise them epidemiologically, whilst the identified genomic variants may eventually support prediction of which strains pose highest risk to horse populations.
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Practical Takeaways
- •Rapid SNP microarray genotyping could enable faster identification of VEEV strains during outbreaks, potentially improving outbreak response and epidemiological tracking
- •Direct genotyping from tissue samples bypasses lengthy culture and sequencing procedures, providing quicker assessment of epidemic potential and human virulence risk
- •Genomic variant characterization may eventually allow prediction of host amplification capacity and disease severity, informing preventive measures on at-risk equine operations
Key Findings
- •SNP-based phylogenetic analysis accurately captured evolutionary relationships of VEE antigenic complex genomes comparable to multiple sequence alignment methods
- •High-resolution genome-wide SNP microarray successfully genotyped VEEV isolates with excellent concordance to sequence-based SNP calls
- •SNP microarray enabled direct VEEV genotyping from infected tissue samples without requiring viral isolation, culture, or genomic sequencing
- •Identified genomic variants associated with different serotypes and host species, demonstrating complex genotype-phenotype relationships