Novel, Divergent Simian Hemorrhagic Fever Viruses in a Wild Ugandan Red Colobus Monkey Discovered Using Direct Pyrosequencing

Lauck, Michael; Hyeroba, David; Tumukunde, Alex; Weny, Geoffrey; Lank, Simon M.; Chapman, Colin A.; O'Connor, David H.; Friedrich, Thomas C.; Goldberg, Tony L.

Because we generated near full-length viral genome sequences, we were able to reconstruct the genomic architecture of SHFV-krc1 and SHFV-krc2 (Figure 1 ). SHFV-krc1 and SHFV-krc2 both possess two large putative replicase-encoding ORFs and several smaller downstream ORFs, all comparable in size to the published ORFs of type strain LVR 42-0/M6941 but all highly divergent at the amino acid level from the type strain (Table 1 ). Consistent with previously described arteriviruses, the putative ORF1a and ORF1b coding regions in both new SHFV variants contain a canonical heptanucleotide ''slippery sequence'' (UUUAAAC) and predicted downstream pseudoknot structure [7] . Importantly, both new viral genomes contain homologs of the type strain SHFV ORFs 2a, 2b, and 3 in the same genomic positions, indicating conservation of the unusual 39 genomic architecture of SHFV even among highly divergent variants.