Genome and phylogenetic analyses of Chinese pepper mottle virus isolates from chili pepper plants

In 2013, a chili pepper (Capsicum annuum cv. ‘Favorite’) sample displaying crinkled and mottled leaves was collected from a field in the Hunan Province, China. Small RNA (sRNA) sequencing identified the putative virus as pepper mottle virus (PepMoV), which was confirmed by RT-PCR analysis. Full length sequence of this virus strain (designated as HN) was obtained and shown to be typical of a potyvirus. Coat protein (CP) genes of nine PepMoV isolates obtained from south China were sequenced and they shared 89 to 99% sequence identity with PepMoV CP sequences retrieved from GenBank. Phylogenetic analysis, and the level of recombination, gene flow and genetic differention revealed that the PepMoV isolates of Chinese lineage clustered within the south-east group. PepMoV has now been detected in three different provinces of southern part of China.