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. 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.

本研究对所有可获得的委内瑞拉马脑炎（Venezuelan equine encephalitis, VEE）病毒抗原复合体基因组开展了全基因组单核苷酸多态性（single nucleotide polymorphism, SNP）分析，并开发了一款高分辨率全基因组SNP微阵列。本研究利用该SNP微阵列对多株VEE病毒分离株进行分析，结果显示，针对已完成全基因组测序的毒株，微阵列检测结果与基于测序的基因型分型结果具有极佳的一致性，同时完成了未测序毒株的基因型分型。本研究利用该SNP微阵列共分析了134株VEE病毒及VEE抗原复合体分离株，其中81株已具备全基因组测序数据，被用于评估微阵列分型与测序分型结果的一致性。另有4株毒株进行了微阵列重复检测。此外，本研究还针对感染VEE病毒TC-83毒株2天的小鼠脑组织样本完成了3次微阵列检测。