Complete nucleotide sequence and transcriptional analysis of the snakehead fish retrovirus

The complete genome of the snakehead fish retrovirus has been cloned and sequenced, and its transcriptional profile in cell culture has been determined. The 11.2-kb provirus displays a complex expression pattern capable of encoding accessory proteins and is unique in the predicted location of the env initiation codon and signal peptide upstream of gag and the common splice donor site, The virus is distinguishable from all known retrovirus groups by the presence of an arginine tRNA primer binding site, The coding regions are highly divergent and show a number of unusual characteristics, including a large Gag coiled-coil region, a Pot domain of unknown function, and a long, lentiviral-like, Env cytoplasmic domain. Phylogenetic analysis of the Pol sequence emphasizes the divergent nature of the virus from the avian and mammalian retroviruses. The snakehead virus is also distinct from a previously characterized complex fish retrovirus, suggesting that discrete groups of these viruses have yet to be identified in the lower vertebrates.