ArticlePloS one2020
Comparative study on three viral enrichment approaches based on RNA extraction for plant virus/viroid detection using high-throughput sequencing.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 54 citations in OpenAlex.
- Review
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- Nanopore Workflow for Grapevine Viroid Surveillance in Kazakhstan: Bypassing rRNA Depletion Through Non-Canonical Priming.Pathogens (Basel, Switzerland) · 2025Article
- A ribodepletion and tagging protocol to multiplex samples for RNA-seq based virus detection: application to the cassava virome.Virology journal · 2025Article
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- Diagnostics of viral infections using high-throughput genome sequencing data.Briefings in bioinformatics · 2024Article
- Simulated High Throughput Sequencing Datasets: A Crucial Tool for Validating Bioinformatic Pathogen Detection Pipelines.Biology · 2024Article
- Draft genome of neotropical Bacillus thuringiensis UFT038 and its potential against lepidopteran soybean pests.Folia microbiologica · 2024Article
- Application of Nanopore-Based Sequencing to Identify Virus Infections in Woody Plants.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community.Journal of virology · 2023Article
- Ecological Strategies for Resource Use by Three Bromoviruses in Anthropic and Wild Plant Communities.Viruses · 2023Article
- Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests.Plants (Basel, Switzerland) · 2023Article
- Green Synthesis of Iron Oxide (Hematite) Nanoparticles and Their Influence onPlants (Basel, Switzerland) · 2023Article
- NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection.Frontiers in microbiology · 2023Article
- Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly.Microbial genomics · 2022Article
- Targeted Whole Genome Sequencing (TWG-Seq) of Cucumber Green Mottle Mosaic Virus Using Tiled Amplicon Multiplex PCR and Nanopore Sequencing.Plants (Basel, Switzerland) · 2022Article
- Bacteriophages pass through candle-shaped porous ceramic filters: Application for the collection of viruses in soil water.MicrobiologyOpen · 2022Article
- Examination of the Virome of Taro Plants Affected by a Lethal Disease, the Alomae-Bobone Virus Complex, in Papua New Guinea.Viruses · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing (HTS) has become increasingly popular as virus diagnostic tool. It has been used to detect and identify plant viruses and viroids in different types of matrices and tissues. A viral sequence enrichment method prior to HTS is required to increase the viral reads in the generated data to ease the bioinformatic analysis of generated sequences. In this study, we compared the sensitivity of three viral enrichment approaches, i.e. double stranded RNA (dsRNA), ribosomal RNA depleted total RNA (ribo-depleted totRNA) and small RNA (sRNA) for plant virus/viroid detection, followed by sequencing on MiSeq and NextSeq Illumina platforms. The three viral enrichment approaches used here enabled the detection of all viruses/viroid used in this study. When the data was normalised, the recovered viral/viroid nucleotides and depths were depending on the viral genome and the enrichment method used. Both dsRNA and ribo-depleted totRNA approaches detected a divergent strain of Wuhan aphid virus 2 that was not expected in this sample. Additionally, Vicia cryptic virus was detected in the data of dsRNA and sRNA approaches only. The results suggest that dsRNA enrichment has the highest potential to detect and identify plant viruses and viroids. The dsRNA approach used here detected all viruses/viroid, consumed less time, was lower in cost, and required less starting material. Therefore, this approach appears to be suitable for diagnostics laboratories.
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