Expanded Strain-Specific RT-PCR Assay for Differential Detection of Currently Known Citrus Tristeza Virus Strains: a Useful Screening Tool

Genotypic characterization of Citrus tristeza virus (CTV) strains has progressed significantly, but their phenotypic expression is poorly established as CTV naturally occurs as mixed-strain populations. A screening system for the analysis of mixed-strain populations is required for population studies and the correlation with symptom expression. In this study, a published CTV strain-specific detection assay was expanded and improved to facilitate detection of currently known CTV strains. Supplementary RT-PCR assays were developed for two variant groups of the RB strain and the HA16-5 strain, and assays for the T36 strain and generic CTV detection were improved. The value of the strain-specific assays was shown by the ability to identify the strain components of two CTV cross-protecting sources, GFMS35 and LMS6, used in the South African budwood certification scheme and to demonstrate the segregation of strains in budwood source trees.