Abstract

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 (TM) 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 (TM) 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 (n = 144) using the Illumina (R) platform, with parallel analysis using conventional and RT-qPCR methods. The results demonstrated the enhanced detection capabilities and biological insights by Viroscope (TM) 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 (TM) results exhibited a high degree of correlation with current methods and furthermore, Viroscope (TM) was able to detect viruses in samples which yielded negative RT-qPCR results. Universally applicable across plant tissue, Viroscope (TM) 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.