Characterization of genetic variability of Venezuelan equine encephalitis viruses. Characterization of genetic variability of Venezuelan equine encephalitis viruses

We performed whole genome single nucleotide polymorphism (SNP) based analysis of all available Venezuelan equine encephalitis (VEE) virus antigenic complex genomes and developed a high resolution genome-wide SNP microarray. We used the SNP microarray to analyze a broad panel of VEEV isolates, found excellent concordance between array and sequence based genotypes for previously sequenced strains, and genotyped unsequenced strains. Overall design: We analyzed 134 VEEV and VEE antigenic complex isolates with the SNP microarray. 81 of these had genome sequences available and were used to assess concordance between array- and sequence-based genotypes. 4 strains were analyzed with duplicate arrays. In addition, 3 arrays were run on samples of brain tissue from mice that had been infected with VEEV strain TC-83 2 days previously.