Nucleotide sequence survey of perilla mosaic virus isolates in Japan unveils complex genetic structure and conserved RNA segments encoding homologous protein groups

Perilla mosaic virus (PerMV) is a fimovirus that harbors ten RNA segments (RNAs 1, 2, 3a, 3b, 4, 5, 6a, 6b, 6c, and 7). The presence of PerMV was first reported in Kochi, followed by Ibaraki, Aichi, and Oita prefectures in Japan, and most recently from South Korea. To understand the genetic diversity of these PerMV isolates, partial nucleotide sequences of RNAs 1 to 4 from 21 Japanese isolates were determined. Phylogenetic analysis revealed that the segments of the isolates are divided into two clades: the Eastern clade (isolates in Ibaraki) and the Western clade (isolates in Kochi, Oita, and South Korea). Isolates in Aichi appeared to be reassortants of both; RNAs 1 and 3b belonged to the Eastern clade, while the others were of the Western clade. Isolates lacking RNA2, found in four prefectures, suggest RNA2 is not essential for plant infection. Near-complete nucleotide sequences from four isolates in Ibaraki, Aichi, and Oita were determined. They maintained ten RNA segments, including RNAs encoding proteins of P3s, P6s, and P7. This indicates that these proteins, encoded by an apparently redundant segment, are crucial for PerMV’s infection and transmission cycles.