Citrus tristeza virus genotype detection using high-throughput sequencing

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dc.contributor.authorBester, Rachelleen_ZA
dc.contributor.authorCook, Glynnisen_ZA
dc.contributor.authorMaree, Hans J.en_ZA
dc.date.accessioned2021-02-02T10:49:56Z
dc.date.available2021-02-02T10:49:56Z
dc.date.issued2021-01-23
dc.descriptionCITATION: Bester, R., Cook, G. & Maree, H.H. 2021. Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing. Viruses, 13(2):1-17. https://doi.org/10.3390/v13020168en_ZA
dc.descriptionThe original publication is available at https://www.mdpi.com/journal/viruses/abouten_ZA
dc.description.abstractThe application of high-throughput sequencing (HTS) has successfully been used for virus discovery to resolve disease etiology in many agricultural crops. The greatest advantage of HTS is that it can provide a complete viral status of a plant, including information on mixed infections of viral species or virus variants. This provides insight into the virus population structure, ecology, or evolution and can be used to differentiate among virus variants that may contribute differently toward disease etiology. In this study, the use of HTS for citrus tristeza virus (CTV) genotype detection was evaluated. A bioinformatic pipeline for CTV genotype detection was constructed and evaluated using simulated and real data sets to determine the parameters to discriminate between false positive read mappings and true genotype-specific genome coverage. A 50% genome coverage cut-off was identified for non-target read mappings. HTS with the associated bioinformatic pipeline was validated and proposed as a CTV genotyping assay.en_ZA
dc.description.versionPublishers versionen_ZA
dc.identifier.citationBester, R., Cook, G. & Maree, H.H. 2021. Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing. Viruses, 13(2):1-17. https://doi.org/10.3390/v13020168en_ZA
dc.identifier.issn1999-4915 (online)
dc.identifier.otherdoi:10.3390/v13020168
dc.identifier.urihttp://hdl.handle.net/10019.1/109496
dc.language.isoen_ZAen_ZA
dc.publisherMDPIen_ZA
dc.rights.holderAuthors retain copyrighten_ZA
dc.subjectNext-generation sequencingen_ZA
dc.subjectCitrus tristeza virusen_ZA
dc.subjectCitrus -- Etiologyen_ZA
dc.subjectHigh-throughput nucleotide sequencingen_ZA
dc.titleCitrus tristeza virus genotype detection using high-throughput sequencingen_ZA
dc.typeArticleen_ZA
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