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.

SHFV is in the family Arteriviridae, which also contains equine arteritis virus (EAV), lactate dehydrogenase elevating virus of mice (LDV), and porcine reproductive and respiratory syndrome virus (PRRSV) [6] . Similar to the other arteriviruses, SHFV has a positive-sense RNA genome approximately 15 kb in length, consisting of a short 59 untranslated region, two large open reading frames (ORFs 1a and 1b) encoding the replicase plus various nonstructural proteins, a number of smaller downstream ORFs encoding structural proteins, and a short 39 untranslated region [7] . However, SHFV is unusual compared to the other arteriviruses in that it contains three additional ORFs (2a, 2b, and 3) immediately downstream of the replicase-encoding ORFs, perhaps as the result of a gene duplication event [8] . As of the time of this writing, only one full SHFV genome was available in GenBank (accession number NC_003092), representing prototype strain LVR 42-0/M6941, which was isolated on MA-104 cells from a moribund rhesus macaque during the original SHFV outbreak in 1964 [9] . Because the genome organization of SHFV was determined from this single strain, and because this sequence was generated from an isolate obtained from a macaque after growth in cells derived from embryonic rhesus macaque kidney tissue, it is unclear whether the unusual 39 genomic architecture of SHFV is typical or whether it might be an artifact of passage in a non-natural host or in cultured cells.