Genome Analysis of Small-Ruminant Lentivirus Genotype E: a Caprine Lentivirus with Natural Deletions of the dUTPase Subunit, vpr -Like Accessory Gene, and 70-Base-Pair Repeat of the U3 Region

Abstract

ABSTRACT The nucleotide sequence of the highly divergent small-ruminant lentivirus genotype E has been determined. The full genome consists of 8,418 nucleotides and lacks two large portions corresponding nearly to the entire dUTPase subunit of the pol and vpr -like accessory genes. Moreover, the 70-bp repeat of the U3 region of the long terminal repeat was observed to be deleted. Interestingly, this lentivirus genotype is able to persist in a local breed population, and retrospective analysis revealed its presence in milk samples collected in 1999. gag sequences obtained from a flock coinfected with the B1 and E genotypes revealed that the evolutionary rates of the two viruses were quite similar. Since a reduced viral load and/or disease progression was observed for viruses with artificially deleted dUTPase and vpr -like genes, it is proposed that this viral cluster be designated a low-pathogenicity caprine lentivirus.