Viroscope™: a universal solution for plant virus and viroid diagnostics using HTS and cloud-based analysis

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 h...

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Published in:Frontiers in microbiology Vol. 16; p. 1609663
Main Authors: Morgante, Verónica, Jiménez, Juan Cristóbal, Ponce, Claudio, Urrutia, Cristóbal, Vera, Fernanda, Farías, Camila, Camps de la Maza, Rocío, Caro, Valentina, Muñoz, Marco, Pollak, Bernardo
Format: Journal Article
Language:English
Published: Switzerland Frontiers Media S.A 03.07.2025
Subjects:
border security
genome assembly coverage
high-throughput sequencing (HTS)
Microbiology
phytosanitary quarantine
plant health
RT-qPCR
border security
phytosanitary quarantine
plant health
Viroscope
high-throughput sequencing (HTS)
genome assembly coverage
replicase identification
RT-qPCR
ISSN:1664-302X, 1664-302X
Online Access:Get full text
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Summary: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 ( n = 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.
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Wen-Shi Tsai, National Chiayi University, Taiwan
Despoina Beris, Benaki Phytopathological Institute, Greece
Edited by: Chellappan Padmanabhan, USDA APHIS PPQ Science and Technology, United States
These authors have contributed equally to this work
Reviewed by: Vijayanandraj Selvaraj, National Botanical Research Institute (CSIR), India
ISSN:1664-302X
1664-302X
DOI:10.3389/fmicb.2025.1609663