Reproducibility and Sensitivity of High-Throughput Sequencing (HTS)-Based Detection of Citrus Tristeza Virus and Three Citrus Viroids

The credibility of a pathogen detection assay is measured using specific parameters including repeatability, specificity, sensitivity, and reproducibility. The use of high-throughput sequencing (HTS) as a routine detection assay for viruses and viroids in citrus was previously evaluated and, in this...

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Bibliographic Details
Published in:Plants (Basel) 2022-07, Vol.11 (15), p.1939
Main Authors: Bester, Rachelle, Steyn, Chanel, Breytenbach, Johannes H. J., de Bruyn, Rochelle, Cook, Glynnis, Maree, Hans J.
Format: Article
Language:English
Subjects:
Assaying
citrus dwarfing viroid (CDVd)
citrus exocortis viroid (CEVd)
Citrus fruits
CTV
Evaluation
Fruits
Genes
Genomes
Genotype & phenotype
hop stunt viroid (HSVd)
Next-generation sequencing
Parameter sensitivity
Pathogens
Polymerase chain reaction
repeatability
Reproducibility
Viroids
Viruses
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Summary:The credibility of a pathogen detection assay is measured using specific parameters including repeatability, specificity, sensitivity, and reproducibility. The use of high-throughput sequencing (HTS) as a routine detection assay for viruses and viroids in citrus was previously evaluated and, in this study, the reproducibility and sensitivity of the HTS assay were assessed. To evaluate the reproducibility of HTS, the same plants assayed in a previous study were sampled again, one year later, and assessed in triplicate using the same analyses to construct the virome profile. The sensitivity of the HTS assay was compared to routinely used RT-PCR assays in a time course experiment, to compensate for natural pathogen accumulation in plants over time. The HTS pipeline applied in this study produced reproducible and comparable results to standard RT-PCR assays for the detection of CTV and three viroid species in citrus. Even though the limit of detection of HTS can be influenced by pathogen concentration, sample processing method and sequencing depth, detection with HTS was found to be either equivalent or more sensitive than RT-PCR in this study.
ISSN:2223-7747
2223-7747
DOI:10.3390/plants11151939