A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics

Thomas Farrall; Jeremy Brawner; Adrian Dinsdale; Monica Kehoe

doi:10.3390/ijms25158348

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A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics

Journal article

Open access

Peer reviewed

A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics

Thomas Farrall, Jeremy Brawner, Adrian Dinsdale and Monica Kehoe

International Journal of Molecular Sciences, Vol.25(15), pp.1-14

2024

DOI: https://doi.org/10.3390/ijms25158348

PMCID: PMC11312432

PMID: 39125919

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Abstract

hybridisation capture

next-generation sequencing

viruses

Modern diagnostic techniques based on DNA sequence similarity are currently the gold standard for the detection of existing and emerging pathogens. Whilst individual assays are inexpensive to use, assay development is costly and carries risks of not being sensitive or specific enough to capture an increasingly diverse range of targets. Sequencing can provide the entire nucleic acid content of a sample and may be used to identify all pathogens present in the sample when the depth of coverage is sufficient. Targeted enrichment techniques have been used to increase sequence coverage and improve the sensitivity of detection within virus samples, specifically, to capture sequences for a range of different viruses or increase the number of reads from low-titre virus infections. Vertebrate viruses have been well characterised using in-solution hybridisation capture to target diverse virus families. The use of probes for genotyping and strain identification has been limited in plants, and uncertainty around sensitivity is an impediment to the development of a large-scale virus panel to use within regulatory settings and diagnostic pipelines. This review aims to compare significant studies that have used targeted enrichment of viruses to identify approaches to probe design and potential for use in plant virus detection and characterisation.

Details

Title: A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics
Authors: Thomas Farrall (Author) - University of the Sunshine Coast, Queensland, Forest Research Institute
Jeremy Brawner (Corresponding Author) - University of the Sunshine Coast, Queensland, Forest Research Institute
Adrian Dinsdale (Author) - Australian Government
Monica Kehoe (Author) - Department of Primary Industries and Regional Development
Publication details: International Journal of Molecular Sciences, Vol.25(15), pp.1-14
Publisher: MDPI AG
Date published: 2024
DOI: 10.3390/ijms25158348
ISSN: 1422-0067
PMID: 39125919; PMC11312432
Copyright note: © 2024 by the authors. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Data Availability: The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.
Grant note: RTC scholarship with additional funding from Australian Government, Department of Agriculture, Fisheries and Forestry
Organisation Unit: Forest Industries Research Centre; School of Science, Technology and Engineering; Forest Research Institute
Language: English
Record Identifier: 991060559702621
Output Type: Journal article

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