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Article

Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing

1
Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
2
Citrus Research International, P.O. Box 28, Nelspruit 1200, South Africa
3
Citrus Research International, Stellenbosch, P.O. Box 2201, Matieland 7602, South Africa
*
Author to whom correspondence should be addressed.
Academic Editors: Olivier Lemaire and Etienne Herrbach
Viruses 2021, 13(2), 168; https://doi.org/10.3390/v13020168
Received: 18 December 2020 / Revised: 5 January 2021 / Accepted: 11 January 2021 / Published: 23 January 2021
(This article belongs to the Special Issue Closteroviridae)
The 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. View Full-Text
Keywords: CTV; HTS; next-generation sequencing; variants CTV; HTS; next-generation sequencing; variants
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MDPI and ACS Style

Bester, R.; Cook, G.; Maree, H.J. Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing. Viruses 2021, 13, 168. https://doi.org/10.3390/v13020168

AMA Style

Bester R, Cook G, Maree HJ. Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing. Viruses. 2021; 13(2):168. https://doi.org/10.3390/v13020168

Chicago/Turabian Style

Bester, Rachelle, Glynnis Cook, and Hans J. Maree. 2021. "Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing" Viruses 13, no. 2: 168. https://doi.org/10.3390/v13020168

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