Sequence and phylogenetic analysis of the RNA1 and RNA2 segments of Korean Rice stripe virus isolates and comparison with those of China and Japan

Rice stripe virus (RSV) is one of the most destructive pathogens of rice plants in East Asia. The RSV genome consists of four single-stranded RNA segments. We have determined and compared the complete nucleotide sequences of the RNA1 and RNA2 segments and the deduced amino acid sequence of each ORF of the 13 Korean RSV isolates and established their relationships with reported RSV sequences from China and Japan. Our results showed that the average percent nucleotide divergence based on the full-length genome is higher in RNA2 (2.2%) than in RNA1 (2.0%). The average percent amino acid variation of the RNA-dependent RNA polymerase (RdRp), glycoprotein and NS2 genes encoded by viral complementary (vc) RNA1, viral RNA2 and vcRNA2, showed 2.8, 2.5 and 6.46%, respectively. On the other hand, the average percent nucleotide variation in the intergenic region (IGR) of RNA2 among the 13 Korean-RSV isolates was 3.5%. Phylogenetic analysis of the 13 Korean, 1 Japanese and 5 Chinese isolates based on their complete nucleotide sequences revealed two distinct types of RNA1 and three distinct types of RNA2. Most Chinese isolates grouped with one of the RNA1 types, but they were distributed among the three types when grouped by RNA2. Japanese isolate T was grouped with Korean isolates into one of the RNA1 and RNA2 genotypes. Taken together, our results suggest that the RSV population in Korea consists of mixtures of RNA1–RNA4 genome segments originating from distinctive ancestors, most likely due to either reassortment or recombination events among isolates.