Sequence analysis of rice hoja blanca virus RNA 3

RNA 3 of rice hoja blanca tenuivirus (RHBV) has 2299 nucleotides and resembles RNA 3 of other tenuiviruses such as maize stripe (MStV) and rice stripe (RStV) viruses in potentially coding with an ambisense strategy for two proteins. Both the viral-sense protein of 23K and the complementary-sense protein of 35K have about 46% amino acid identity with the analogous proteins encoded by RNA 3 of MStV and RStV. As the proteins of MStV and RStV have about 65% identity between themselves, RHBV cannot be a South and Central American strain of the Asian RStV. The intergenic region resembles those of other tenuiviruses, being rich in A and U residues, but its predicted folding pattern is unlike those of other tenuiviruses. Instead, the predicted folding of the intergenic region was indistinguishable from that of the coding regions and there was no evidence for a distinct hairpin-loop structure. The significance to the evolution of tenuiviruses of the similarities that the two proteins have with their analogues in other tenuiviruses is discussed.