Characterization of cucumber mosaic virus (CMV) subgroup IB infecting chilli in Tamil Nadu, India

CMV (cucumber mosaic virus) is the most primitive virus infecting chilli (Capsicum annuum. L). The mosaic incidence with leaf filiformity, mosaic mottling and stunted growth was observed in major chilli growing regions of Tamil Nadu. CMV sap was inoculated on chilli, cowpea, bitter gourd, bottle gourd, ridge gourd, banana, cucumber, Nicotiana and Chenopodium plants. Host range studies revealed that CMV produced localized infection on Nicotiana and systemic symptoms on most of the test plants. The occurrence of CMV was confirmed through DAC-ELISA and RT-PCR analysis. Host plant samples tested with DAC-ELISA showed strong reaction with 1.7 optical density. For molecular characterization, total RNA isolated from infected plants used in RT-PCR with CMV specific primers. The specific amplicons were cloned and sequenced. The complete genome sequencing depicts CMV-RNA1 consist of 3339 nucleotides (nt), RNA2 and RNA3 with 3052nt and 2027nt respectively. Phylogenetic and nucleotide sequence analysis showed TN CMV isolates closely associated with subgroup IB rather than subgroup IA and II. Comparative sequence analysis indicates replicase protein to be more variable among five genes. CP sequence analysis showed 97-98 per cent identity with subgroup IB strains, 92-93 per cent identity with subgroup IA strains and 81-82 per cent identity with subgroup II strains. CMV-RNA3 was predicted to have recombination with Indian black pepper isolate (KU947031) between 165-505nt and Egyptian tomato isolate (KX014666) between 165-506nt positions.