Genetic variability in the coat protein genes of Cymbidium mosaic virus isolates from orchids

The variability in the nucleotide (nt) and amino acid (aa) sequences of the coat protein (CP) of Cymbidium mosaic virus (CymMV), which naturally infects orchids worldwide, was investigated. The CP genes of 55 CymMV isolates originating from different locations in Korea were amplified using RT-PCR and sequenced. The encoded CP consists of 223 aa. The CP sequences of the Korean isolates were compared with those of previously published CymMV isolates originating from different countries at both nt and aa levels. The Korean isolates shared 74.9-98.3 and 52.7-100% CP homology with CymMV isolates from other countries at the nt and aa levels, respectively. No particular region of variability could be found in either grouping of viruses. In the deduced CymMV CP aa sequence, the C-terminal region was more divergent than the N-terminal. The phylogenetic tree analysis based on nt sequence diversity of CP genes of CymMV isolates supported the hypothesis that CymMV isolates were divided into two subgroups. However, these subgroups were not formed by phylogenetic tree analysis of CP aa sequences. There was no distinct correlation between geographical locations and specific sequence identity, while recombination analysis revealed that there were no intra-specific recombination events among CymMV isolates.