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.

Across the coding genome, the SHFV-krc1 and SHFV-krc2 showed only 51.9% nucleotide identity with each other and only 52.0% and 51.8% nucleotide identity, respectively, with type strain LVR 42-0/M6941, which is roughly equivalent to the nucleotide percent identity between the prototypical PRRSV and LDV strains (51.1%; Table 2 ). A maximum-likelihood phylogenetic tree constructed from concatenated nucleotide sequence alignments of homologous ORFs from representative arteriviruses is shown in Figure 2 . The tree is consistent with established phylogenetic relationships among the arteriviruses [21, 22] , supporting with high statistical confidence the close relationship between PRRSV and LDV relative to SHFV and EAV. Within the SHFV clade, SHFV-krc1 and SHFV-krc2 are highly divergent from each other and from the type strain SHFV LVR 42-0/ M6941. Although SHFV-krc1 and SHFV-krc2 cluster together, statistical support for this relationship is relatively weak even with near-complete genome sequences. Overall, the degree of phylogenetic diversity within SHFV is remarkably high and is approximately equal to that between PRRSV and LDV.