Golyaev Victor, Dierickx Sam, Deforche Koen, Dumon Wim, Vanderschuren Hervé
Tropical Crop Improvement Laboratory, Crop Biotechnics, Department of Biosystems, KU Leuven, Leuven 3001, Belgium.
KU Leuven Plant Institute (LPI), KU Leuven, Leuven 3001, Belgium.
Nucleic Acids Res. 2025 Mar 20;53(6). doi: 10.1093/nar/gkaf221.
Severe epidemic outbreaks of diseases associated with newly emerging strains of single-stranded DNA (ssDNA) viruses have led to serious economic losses of numerous important food crops. While the current mitigation strategies are mostly relying on the deployment of genetic resistance in crop varieties, the constantly evolving virus populations have the potential to rapidly break virus resistance. Therefore, the development of diagnostic tools enabling early detection of virus variants associated with hypervirulence and/or expansion to new host species is urgently needed as an effective mitigation solution. Here, we introduce a novel approach by designing a pipeline that allows accurately identifying and characterizing the full-length sequence variants of viral circular DNA genomes utilizing Nanopore sequencing technology and the bioinformatics tool Genome Detective. We demonstrate that the pipeline is suitable to provide an accurate and in-depth analysis of monopartite Tomato yellow leaf curl Sardinia virus (TYLCSV) and multipartite Banana bunchy top virus (BBTV) ssDNA virus populations resulting in the profiling of high- and low-frequency virus variants with ≥1% relative abundance. The approach also enabled the unambiguous detection and characterization of four TYLCSV partial genomic sequences as well as several partial genomic sequences for each BBTV genomic component not previously reported and accumulating during infection.
与新出现的单链DNA（ssDNA）病毒株相关的严重疾病流行已给众多重要粮食作物造成了严重经济损失。虽然目前的缓解策略主要依赖于在作物品种中部署遗传抗性，但不断进化的病毒群体有可能迅速突破病毒抗性。因此，迫切需要开发能够早期检测与高毒力和/或向新宿主物种扩展相关的病毒变体的诊断工具，作为一种有效的缓解解决方案。在此，我们介绍一种新方法，通过设计一个流程，利用纳米孔测序技术和生物信息学工具Genome Detective，能够准确识别和表征病毒环状DNA基因组的全长序列变体。我们证明，该流程适用于对单分体番茄黄化曲叶撒丁岛病毒（TYLCSV）和多分体香蕉束顶病毒（BBTV）的ssDNA病毒群体进行准确而深入的分析，从而对相对丰度≥1%的高频和低频病毒变体进行分析。该方法还能够明确检测和表征四个TYLCSV部分基因组序列，以及每个BBTV基因组组分的几个此前未报道且在感染过程中积累的部分基因组序列。
