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.

Phylogenetic analysis of SHFV-krc1 and SHFV-krc2 demonstrate the diversity of SHFV to be higher than has been documented for any other arterivirus. Indeed, the degree of phylogenetic divergence between the two new SHFV strains and the type strain is approximately equivalent to the degree of divergence between PRRSV and LDV, which are considered different viral species. We caution, however, that phylogenetic diversity within the other arteriviruses may be underestimated due to small numbers of currently available full genome sequences. For example, divergent EAV strains have been documented [23, 24] but, at the time of this writing, full genomes of such EAV isolates were not available. Unfortunately, our attempts to align the available hypervariable partial ORF5 sequences of these divergent EAV strains with homologous regions from other arteriviruses failed due to low sequence similarity. Future studies of EAV and other as-yet undiscovered arteriviruses may demonstrate levels of within-species diversity that match or even exceed what we have documented for SHFV.