Barrette Roger W, Rowland Jessica M, Grau Frederic R, McIntosh Michael T
United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Orient, NY, United States of America.
Department of Environmental and Global Health, Emerging Pathogens Institute University of Florida, Gainesville, FL, United States of America.
PLoS One. 2017 Jan 3;12(1):e0166870. doi: 10.1371/journal.pone.0166870. eCollection 2017.
Several RT-PCR and genome sequencing strategies exist for the resolution of Foot-and-Mouth Disease virus (FMDV). While these approaches are relatively straightforward, they can be vulnerable to failure due to the unpredictable nature of FMDV genome sequence variations. Sequence independent single primer amplification (SISPA) followed by genotyping microarray offers an attractive unbiased approach to FMDV characterization. Here we describe a custom FMDV microarray and a companion feature and template-assisted assembler software (FAT-assembler) capable of resolving virus genome sequence using a moderate number of conserved microarray features. The results demonstrate that this approach may be used to rapidly characterize naturally occurring FMDV as well as an engineered chimeric strain of FMDV. The FAT-assembler, while applied to resolving FMDV genomes, represents a new bioinformatics approach that should be broadly applicable to interpreting microarray genotyping data for other viruses or target organisms.
目前有几种用于解析口蹄疫病毒（FMDV）的逆转录聚合酶链反应（RT-PCR）和基因组测序策略。虽然这些方法相对简单，但由于FMDV基因组序列变异的不可预测性，它们可能容易失败。序列独立单引物扩增（SISPA）随后进行基因分型微阵列提供了一种有吸引力的无偏方法来表征FMDV。在这里，我们描述了一种定制的FMDV微阵列以及一个配套的特征和模板辅助组装软件（FAT-assembler），该软件能够使用适量的保守微阵列特征来解析病毒基因组序列。结果表明，这种方法可用于快速表征天然存在的FMDV以及一种工程化的FMDV嵌合菌株。FAT-assembler虽然应用于解析FMDV基因组，但代表了一种新的生物信息学方法，应该广泛适用于解释其他病毒或目标生物体的微阵列基因分型数据。
