Organization of the simian hemorrhagic fever virus genome and identification of the sgRNA junction sequences.

SHFV is a member of the Arteriviridae family. Viruses within this family encode eight open reading frames (ORFs), two of which are translated from the full-length genome RNA. The remaining six ORFs are translated from a nested set of six or seven 3' co-terminal, subgenomic RNAs (sgRNAs). We have cloned and sequenced approximately 6000 nucleotides (nt) from the 3' end of the SHFV genome. Eleven ORFs, numbered ORFs 1a, 1b, 2a, 2b, 3, 4, 5, 6, 7, 8, and 9, were identified, three more than the other arteriviruses. The characteristics of the peptides encoded by ORFs 2a through 9 were determined from their computer-generated amino acid sequences. We also amplified the junction sequences from each of the SHFV subgenomic RNAs (sgRNAs) using RT-PCR analysis. Eight separate junction sequences were found which suggests that SHFV produces eight sgRNAs during replication. ORFs 2a and 2b appear to be encoded on the same sgRNA implying that RNA 2 is polycistronic. Sequence analysis identified the conserved SHFV junction sequence as 5'-(U/C)(C/U)N(U/C)(U/C)(A/C/G)AC(C/U)-3'. Since SHFV encodes additional ORFs and produces additional sgRNAs during replication, these data suggest that SHFV may be more complex than the other arteriviruses.