Stevens Kristian A, Al Rwahnih Maher
Department of Computer Science, University of California-Davis, Davis, CA 95616, USA.
Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA.
Viruses. 2024 Dec 20;16(12):1957. doi: 10.3390/v16121957.
Among the cultivated crop species, the economically and culturally important grapevine plays host to the greatest number of distinctly characterized viruses. A critical component of the management and containment of these viral diseases in grapevine is both the identification of infected vines and the characterization of new pathogens. Next-generation high-throughput sequencing technologies, i.e., HTS technologies, have been widely adopted for their ability to quickly, broadly and directly characterize molecular sequences associated with potential pathogens. We empirically analyze the performance of HTS as a diagnostic tool in a phytosanitary context and make recommendations on its deployment for detecting known and novel viruses in grapevine. Three popular and widely used modalities for analyzing HTS data are characterized and compared using the standard diagnostic performance criteria of sensitivity (the true positive rate), specificity (the true negative rate) and analytical sensitivity (dilution series).
在栽培作物品种中，经济和文化意义重大的葡萄藤携带的具有明显特征的病毒数量最多。对葡萄藤中这些病毒病进行管理和控制的一个关键要素是识别受感染的葡萄藤以及鉴定新的病原体。新一代高通量测序技术，即HTS技术，因其能够快速、广泛且直接地表征与潜在病原体相关的分子序列而被广泛采用。我们通过实证分析了HTS作为植物检疫背景下诊断工具的性能，并就其用于检测葡萄藤中已知和新型病毒的部署提出建议。使用灵敏度（真阳性率）、特异性（真阴性率）和分析灵敏度（稀释系列）等标准诊断性能标准，对三种常用且广泛使用的HTS数据分析模式进行了表征和比较。
