ArticleMethods in molecular biology (Clifton, N.J.)2024
Validation of High-Throughput Sequencing (HTS) for Routine Detection of Citrus Viruses and Viroids.
Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 6 citations in OpenAlex.
- From reads to results: comparing Oxford Nanopore to Illumina sequencing for citrus virus surveillance.BMC genomics · 2026Article
- Evaluation of the influence of RNA extraction methods on the detection of citrus viruses and viroids.Virology journal · 2025Article
- Molecular characterisation of a novel citrus-infecting emaravirus, citrus emaravirus 1.Archives of virology · 2025Article
- Complete genome sequence of fig leaf mottle-associated virus 2.Archives of virology · 2025Article
- Viroscope™: a universal solution for plant virus and viroid diagnostics using HTS and cloud-based analysis.Frontiers in microbiology · 2025Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The management of plant diseases relies on the accurate identification of pathogens that requires a robust and validated tool in terms of specificity, sensitivity, repeatability, and reproducibility. High-throughput sequencing (HTS) has become the method of choice for virus detection when either a complete viral status of a plant is required in a single assay or if an unknown viral agent is expected. To ensure that the most accurate diagnosis is made from an HTS data analysis, a standardized protocol per pathosystem is required. This chapter presents a detailed protocol for the detection of viruses and viroids infecting citrus using HTS. The protocol describes all the steps from sample processing, nucleic acid extraction, and bioinformatic analyses validated to be an efficient method for detection in this pathosystem. The protocol also includes a section on citrus tristeza virus (CTV) genotype differentiation using HTS data.
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