Genotype classification and molecular evidence for the presence of mixed infections in Indian Citrus tristeza virus isolates

Citrus tristeza virus (CTV) is usually present in field trees as a mixture or complex of isolates. Different biological types of CTV exist in India and this affects disease incidence and yield in the various citrus growing areas. Genotypic profiles were determined for 21 Indian CTV isolates. Of the 21 isolates, 15 contained only the VT genotype. The other isolates contained mixtures of either T30 or T3 with VT or T30, T3 and VT genotypes. One exception was isolate BAN-1, which contained a mixture of T36, T30 and T3 genotypes. Sequence diversity of Indian CTV isolates was determined by characterization in the k17 region of ORF 1a and the overlapping region of RdRp, gene p33, and sequence differences were utilized to identify group-specific genome features. A phylogenetic analysis of these regions divided the isolates into five distinct groups. There was a general trend for severe isolates to cluster into one of four groups and mild isolates into the fifth group. All the sequences from the two different regions of the CTV genome showed nucleotide identity to either VT, T30 or T36 isolates and confirmed the mixed infection of mild isolates with severe CTV isolates from three distinct geographical citrus growing regions in India.