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 NS s 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 NS s 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 > TOS > SFS > UUK; to TOS N protein it is PT ⩾ RVF > SFS > UUK. The sequences of the NS s proteins are less similar, with values ranging from 30 to <17%. The order of homology to RVFV NS s is SFS > PT . TOS > UUK. Due to these more distant relationships, the homologies to TOS NS s protein are less clear.