Sequences and coding strategies of the S RNAs of Toscana and Rift Valley fever viruses compared to those of Punta Toro, Sicilian Sandfly fever, and Uukuniemi viruses

Abstract

The sequences and coding strategies of the S RNAs of two viruses, Toscana (TOS) and the M12 derivative of Rift Valley fever ZH-548 (RVF, Phlebovirus genus, Bunyaviridae) have been determined from cDNA clones and compared to the previously published sequences of Punta Toro (PT), Sandfly fever Sicilian (SFS), and Uukuniemi (UUK) viruses. All five viruses exhibit an ambisense coding strategy for their small (S) RNA species, i.e., one gene product (the NSs protein) is encoded in the 5' half of the viral RNA, a second (the N protein) is encoded in the sequence complementary to the 3' half. The terminal nucleotides of the S RNAs of the five viruses are comparable through 13-14 residues. The 3' and 5' ends of these S RNAs have inverted complementary compositions. Three phleboviruses (TOS, SFS, and RVFV) exhibit comparable G-rich, centrally located intergenic sequences, albeit of different lengths. These sequences have a number of similar motifs at, or immediately following, the end of the coding regions, motifs that may be involved in their S mRNA transcription termination processes. The other two viruses (UUK, PT) have AT-rich intergenic sequences that have the potential to form secondary structure. They lack the G-rich sequences or particular sequence motifs recognized in the other three virus RNAs. The deduced sizes of the TOS and RVFV N proteins are 27,704 and 27,430 kDa (respectively). Their NSS proteins are 36,677 and 29,903 kDa (respectively). When aligned, the deduced sequences of the N proteins of the five viruses exhibit homologies ranging from 54 to 30%. The order of homology to RVFV N protein is PT greater than TOS greater than SFS greater than UUK; to TOS N protein it is PT greater than or equal to RVF greater than SFS greater than UUK. The sequences of the NSS proteins are less similar, with values ranging from 30 to less than 17%. The order of homology to RVFV NSS is SFS greater than PT greater than TOS greater than UUK. Due to these more distant relationships, the homologies to TOS NSS protein are less clear.