ArticleViruses2021
HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection.
Article in Viruses, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 34 citations in OpenAlex.
- CRISPR-Cas13-based amplification-free detection of three quarantine-significant sugarcane viruses.Plant cell reports · 2026Article
- Molecular and Biological Characterization of a Newly Identified Virus Representing a Novel Taxon ofInternational journal of molecular sciences · 2026Article
- Host-dependent virus accumulation dynamics of blackberry chlorotic ringspot virus in two Rubus species.Virology journal · 2026Article
- A ribodepletion and tagging protocol to multiplex samples for RNA-seq based virus detection: application to the cassava virome.Virology journal · 2025Article
- A comparative template-switching cDNA approach for HTS-based multiplex detection of three viruses and one viroid commonly found in apple trees.Scientific reports · 2025Article
- Article
- Comprehensive virome profiling of sugarcane and simplified duplex OneStep RT-PCR assay reveals the prevalence of sugarcane streak mosaic virus along with sugarcane yellow leaf virus in India.Journal, genetic engineering & biotechnology · 2024Article
- PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data.BMC bioinformatics · 2023Article
- Thermotherapy Followed by Shoot Tip Cryotherapy Eradicates Latent Viruses and Apple Hammerhead Viroid from In Vitro Apple Rootstocks.Plants (Basel, Switzerland) · 2022Article
- Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage.Frontiers in microbiology · 2022Article
- High-throughput detection of a large set of viruses and viroids of pome and stone fruit trees by multiplex PCR-based amplicon sequencing.Frontiers in plant science · 2022Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rapid global germplasm trade has increased concern about the spread of plant pathogens and pests across borders that could become established, affecting agriculture and environment systems. Viral pathogens are of particular concern due to their difficulty to control once established. A comprehensive diagnostic platform that accurately detects both known and unknown virus species, as well as unreported variants, is playing a pivotal role across plant germplasm quarantine programs. Here we propose the addition of high-throughput sequencing (HTS) from total RNA to the routine quarantine diagnostic workflow of sugarcane viruses. We evaluated the impact of sequencing depth needed for the HTS-based identification of seven regulated sugarcane RNA/DNA viruses across two different growing seasons (spring and fall). Our HTS analysis revealed that viral normalized read counts (RPKM) was up to 23-times higher in spring than in the fall season for six out of the seven viruses. Random read subsampling analyses suggested that the minimum number of reads required for reliable detection of RNA viruses was 0.5 million, with a viral genome coverage of at least 92%. Using an HTS-based total RNA metagenomics approach, we identified all targeted viruses independent of the time of the year, highlighting that higher sequencing depth is needed for the identification of DNA viruses.
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