Detection and identification of Cymbidium mosaic virus infecting vanilla (Vanilla planifolia Andrews) in India based on coat protein gene sequence relationships

Sixty five diseased vanilla (Vanilla planifolia Andrews) plants showing different kinds of symptoms were collected from different regions of Karnataka and Kerala. They were subjected to reverse transcription (RT) PCR using primers designed for coat protein (CP) gene of Cymbidium mosaic virus (CymMV). A -650 bp RT-PCR amplified fragment was consistently seen in only those plants of vanilla showing mild chlorotic mottle or streaks on leaves. The amplicon obtained from one infected vanilla plant was cloned and sequenced. Sequenced region contained a single open reading frame of 672 nucleotides potentially coding for 223 amino acids. Sequence analyses confirmed the identity of the virus as a strain of CymMV. The CP gene of the virus showed the greatest identity with a CymMV isolate from Singapore (99.1%). An identity of 92.3 to 97.3% was seen with different CymMV isolates from India while with available partial CP sequences of CymMV isolates infecting vanilla identity ranged from 98.2 to 99.4%. Phylogenetic analyses confirmed the results of sequence alignment and showed no clear cut clustering of isolates either based on host they infect or geographical origin. This is the first report of occurrence of CymMV on V. planifolia from India.