Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701.
U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97330.
Plant Dis. 2022 Feb;106(2):518-525. doi: 10.1094/PDIS-05-21-0949-RE. Epub 2022 Feb 2.
We completed a comprehensive study comparing virus detection between high throughput sequencing (HTS) and standard protocols in 30 berry selections (12 , 10 , and eight ) with known virus profiles. The study examined temporal detection of viruses at four sampling times encompassing two growing seasons. Within the standard protocols, reverse transcription (RT) PCR proved better than biological indexing. Detection of known viruses by HTS and RT-PCR nearly mirrored each other. HTS provided superior detection compared with RT-PCR on a wide spectrum of variants and discovery of novel viruses. More importantly, in most cases in which the two protocols showed parallel virus detection, 11 viruses in 16 selections were not consistently detected by both methods at all sampling points. Based on these data, we propose a testing requirement of four sampling times over two growing seasons for berry and potentially other crops, to ensure that no virus remains undetected independent of titer, distribution, or other virus-virus or virus-host interactions.
我们完成了一项综合研究，比较了高通量测序 (HTS) 和标准方案在 30 个浆果品种（12 个、10 个和 8 个）中的病毒检测，这些品种具有已知的病毒特征。该研究在两个生长季节的四个采样时间内检测了病毒的时间动态。在标准方案中，逆转录 (RT) PCR 比生物指标法更好。HTS 和 RT-PCR 对已知病毒的检测几乎相互匹配。HTS 在检测广泛的变体和发现新病毒方面优于 RT-PCR。更重要的是，在两种方法在所有采样点平行检测病毒的大多数情况下，16 个品种中的 11 种病毒并非始终能被两种方法同时检测到。基于这些数据，我们建议对浆果和可能的其他作物进行两次生长季节的四次采样时间的测试要求，以确保无论病毒滴度、分布或其他病毒-病毒或病毒-宿主相互作用如何，都不会有病毒未被检测到。
