Morgante Verónica, Jiménez Juan Cristóbal, Ponce Claudio, Urrutia Cristóbal, Vera Fernanda, Farías Camila, Camps de la Maza Rocío, Caro Valentina, Muñoz Marco, Pollak Bernardo
Multiplex SpA, Santiago, Chile.
Servicio Agrícola y Ganadero (SAG), Santiago, Chile.
Front Microbiol. 2025 Jul 3;16:1609663. doi: 10.3389/fmicb.2025.1609663. eCollection 2025.
Border biosecurity and food supply face significant global challenges due to the increasing threat of plant viruses, exacerbated by international plant trade. While high-throughput sequencing (HTS) -based virus diagnosis offers promising applications, challenges in data analysis and implementation have limited widespread adoption. Viroscope™ addresses these limitations through an advanced cloud service that leverages HTS for high-certainty virus and viroid identification. A field study was conducted on plants in post-entry quarantines using the Viroscope™ algorithm to evaluate its performance for phytosanitary diagnostics of virus and viroids. Tissue samples provided by the Chilean phytosanitary agency were processed and deep-sequenced ( = 144) using the Illumina® platform, with parallel analysis using conventional and RT-qPCR methods. The results demonstrated the enhanced detection capabilities and biological insights by Viroscope algorithm, even in cases of low viral abundance. From the tested plants in post-entry quarantine programs, 28.5% contained regulated and/or emergent viruses and viroids. No viral pathogens from the quarantine list were detected, in agreement with RT-qPCR results. Notably, 25% of plants harbored emergent viruses with functional evidence, highlighting potential risks undetected by traditional procedures. Comparative analysis with RT-qPCR confirmed that Viroscope™ results exhibited a high degree of correlation with current methods and furthermore, Viroscope™ was able to detect viruses in samples which yielded negative RT-qPCR results. Universally applicable across plant tissue, Viroscope™ detects all known viruses and viroids in public databases while employing innovative metrics for functional assessment. The cloud-based platform facilitates global adoption of HTS technology by phytosanitary agencies through user-friendly reports that enable rapid and informed decision-making.
由于植物病毒威胁不断增加，边境生物安全和食品供应面临重大全球挑战，国际植物贸易加剧了这一情况。虽然基于高通量测序（HTS）的病毒诊断提供了有前景的应用，但数据分析和实施方面的挑战限制了其广泛采用。Viroscope™通过先进的云服务解决了这些限制，该服务利用HTS进行高确定性病毒和类病毒鉴定。使用Viroscope™算法对入境后检疫的植物进行了实地研究，以评估其在病毒和类病毒植物检疫诊断中的性能。智利植物检疫机构提供的组织样本使用Illumina®平台进行处理和深度测序（ = 144），并使用传统方法和RT-qPCR方法进行平行分析。结果表明，即使在病毒丰度较低的情况下，Viroscope算法也具有增强的检测能力和生物学见解。在入境后检疫计划中测试的植物中，28.5%含有受管制和/或新出现的病毒和类病毒。未检测到检疫清单中的病毒病原体，这与RT-qPCR结果一致。值得注意的是，25%的植物携带具有功能证据的新出现病毒，突出了传统程序未检测到的潜在风险。与RT-qPCR的比较分析证实，Viroscope™结果与当前方法具有高度相关性，此外，Viroscope™能够在RT-qPCR结果为阴性的样本中检测到病毒。Viroscope™普遍适用于植物组织，可检测公共数据库中的所有已知病毒和类病毒，同时采用创新指标进行功能评估。基于云的平台通过用户友好的报告促进植物检疫机构全球采用HTS技术，这些报告能够实现快速和明智的决策。
