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Open AccessReview
A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics
by
Thomas Farrall
Thomas Farrall 1,2,
Jeremy Brawner
Jeremy Brawner 2,3,*,
Adrian Dinsdale
Adrian Dinsdale 1 and
Monica Kehoe
Monica Kehoe 4
1
Plant Innovation Centre, Australian Government, Department of Agriculture, Fisheries and Forestry (DAFF), Canberra 2601, Australia
2
Forest Research Institute, School of Science, Technology and Engineering, University of the Sunshine Coast, Queensland 4556, Australia
3
Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA
4
Diagnostic Laboratory Services, Biosecurity and Sustainability, Department of Primary Industries and Regional Development (DPIRD), Perth, WA 6151, Australia
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2024, 25(15), 8348; https://doi.org/10.3390/ijms25158348 (registering DOI)
Submission received: 6 June 2024
/
Revised: 20 July 2024
/
Accepted: 28 July 2024
/
Published: 30 July 2024
Abstract
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.
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MDPI and ACS Style
Farrall, T.; Brawner, J.; Dinsdale, A.; Kehoe, M.
A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics. Int. J. Mol. Sci. 2024, 25, 8348.
https://doi.org/10.3390/ijms25158348
AMA Style
Farrall T, Brawner J, Dinsdale A, Kehoe M.
A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics. International Journal of Molecular Sciences. 2024; 25(15):8348.
https://doi.org/10.3390/ijms25158348
Chicago/Turabian Style
Farrall, Thomas, Jeremy Brawner, Adrian Dinsdale, and Monica Kehoe.
2024. "A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics" International Journal of Molecular Sciences 25, no. 15: 8348.
https://doi.org/10.3390/ijms25158348
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