Characterization and complete nucleotide sequencing of Pepper Mild Mottle Virus infecting Bell Pepper in India

Capsicum (Capsicum annuum L var. grossum Sendt) commonly known as bell pepper or sweet pepper, is one of the most economical agricultural crop grown under both open and polyhouse conditions. The presence of Pepper mild mottle virus (PMMoV) from different districts of Himachal Pradesh was confirmed by double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) and RT-PCR using coat protein (CP) gene amplification. The first complete genome sequence of Indian isolate of PMMoV (HP-1) was elucidated and compared with other members of Virgaviridae family and PMMoV isolates. Sequence homology, multiple alignment and phylogenetic analysis on the basis of nucleotide and amino acid sequences showed that PMMoV-HP1 isolate is more closely related to the PMMoV-J, the Japanese isolate. Based on CP gene amino acid sequence analysis, the PMMoV-HP1 isolate showed 100 per cent identity with P12 pathotypes (capable of breaking L2 gene mediated resistance in capsicum). This is the first report of the PMMoV complete genome organization intercepted in India.