Genetic diversity of Chilli veinal mottle virus infecting different chilli landraces in North East India indicates the possibility of transboundary movement of virus.

Diverse chilli genetic resources of North East India occupy a unique niche in the Nation's chilli gene pool. Widely cultivated chilli landraces (King chilli: Capsicum chinense, bird eye chilli: Capsicum frutescens and Capsicum annuum) of North East India in general and Manipur in particular suffer from decline complex due to high incidence of viral diseases. With this background and the known prominent distribution of Chilli veinal mottle virus (ChiVMV) in Asian region, we studied its prevalence and association with diverse symptoms of chilli landraces. Molecular indexing of samples from 40 chilli plantation groves of Manipur using reverse transcription (RT)-PCR targeting the coat protein (CP) region of ChiVMV genome revealed a high incidence and wide prevalence. Out of a total of 127 chilli samples collected from different groves of Manipur, 81 chilli samples (63.78%) were positive for ChiVMV. Interestingly, ChiVMV infection rate was comparatively higher in the hilly groves (69.23% samples positive) compared to the valley groves (60% samples positive). Present study through the extensive surveys and molecular indexing work, conclusively reported the association of ChiVMV with diverse symptoms like cupping of leaf lamina with mottling, vein banding and puckering in different chilli landraces. Further, five representative ChiVMV isolates sampled from different groves of Manipur upon mechanical inoculation showed significant variation in symptom expression, indicating wide pathogenic diversity among them. Partial coat protein (CP) sequence analysis of five ChiVMV isolates from Manipur although indicated genetic homogeneity among them, but distinctiveness from ChiVMV isolates reported from the other parts of India. Phylogenetic clustering of ChiVMV isolates from Manipur near Chinese isolates rather than other Indian isolates suggested the possibility of transboundary movement.