Molecular taxonomy of a new potyvirus isolated from chilli pepper in Thailand

A virus isolated from chilli pepper plants in Kamphaengsaen, Nakorn Fathom, showing vein banding mottle symptoms was classified using sequence analysis and phylogeny of the coat protein gene and 3' noncoding region (3' NCR.). This virus was found to be a typical potyvirus on the basis of particle morphology, biological properties and cytopathology. The 3' terminus region of the genome of 1,309 nucleotides, representing the viral coat protein gene and 3' NCR was cloned and sequenced. Nucleotide sequence analysis indicated that the 3' region of the viral genome had a polyA tail of at least 12 nucleotides, a noncoding region of 272 nucleotides, a coat protein gene of 864 nucleotides and 161 nucleotides representing the 3' terminus of the polymerase gene. The amino acid sequence of the coat protein was compared with those of 23 distinct potyviruses, and 63.1% shown to be the highest homology. However the 3' NCR had, at most, 29.7% random homology, thus indicating that this virus is a distinct species in the genus Potyvirus in the family Potyviridae. The result is well supported by previous studies on the biology and biochemical properties of this virus.