One of the most serious diseases of citrus worldwide is caused by the viral pathogen Citrus tristeza virus (CTV) (family: Closteroviridae, genus: Closterovrius). This RNA virus is known to cause several economically important syndromes, namely quick decline , stem pitting and seedling yellows . The natural hosts for CTV include nearly all citrus species and cultivars, various citrus relatives such as Aeglopsis, Afraegle, Fortunella and Pamburus, and some intergeneric hybrids (Yokomi, 2009). The movement of CTV between different regions is mainly due to the dispersal of infected budwood (Bertolini et al., 2008). However, natural transmission and spread of CTV can also occur with the help of several aphid species of which the most effective vector is the Brown citrus aphid (Kirkaldy) Toxoptera citricida (Tsai et al., 2009). The severity of a CTV infection may vary depending on various contributing factors, such as environmental conditions, the rootstock combination used and lastly the presence of the CTV genotype predominating within the mixed infection. Currently, there are eight known and published CTV genotypes, each with their own degree of virulence, and up to date, forty-seven CTV genomes have been fully sequenced. It has been observed in numerous CTV population diversity studies, that a host is normally infected with a mixture of genotypic strains (Read and Pietersen, 2015; Roy et al., 2010; Roy and Brlansky, 2004). This complicates biological indexing as well as diagnostic procedures in identifying homogenous genotypic sources. This pathogen is endemic to the citrus producing areas in South Africa; hence, a mild strain cross-protection scheme has been initiated during the year 1973; aiming to control the viral disease.