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.The small-ruminant lentiviruses (SRLVs) are a genetically and antigenically heterogeneous group of viruses infecting sheep and goats, leading to persistent infection and chronic debilitating diseases. The majority of SRLV isolates can be classified into two main phylogenetic clusters: genotype A, involving maedi-visna virus-like strains, and genotype B, including caprine arthritis-encephalitis virus (CAEV)-like isolates, originally isolated from sheep and goats, respectively. Additional genotypes include Norwegian (genotype C) (4) and Swiss and Spanish (genotype D) (15, 18) isolates and the recently described Italian caprine isolates (genotype E) identified in flocks in which the local Roccaverano goat breed was prevalent (5). Interestingly, as for other indigenous goat breeds, typical clinical signs of lentiviral infection had never been observed in Italy before the introduction of imported breeds carrying the B1 subtype in the early 1980s.SRLVs possess a complex genome comprising the gag, pol, and env structural genes and the vif, tat, and rev accessory genes. The low-pathogenicity SRLVs characterized so far have shown that deletions or mutations in the long terminal repeat (LTR) may be associated with variations in virulence, likely due to the presence of replication enhancer elements such as AP1, AML, tumor necrosis factor-␣, and gamma interferon response elements (1, 11). Additional information about virulence factors has been produced in in vitro and in vivo studies by using genetic manipulation of infectious molecular clones (7,8,10,19,23). The dUTPase subunit, encoded by the pol gene, has been found to be dispensable for viral replication (12); however, dUTPase-negative strains produce less-severe lesions, restricted to the injection site (20). The tat gene of SRLV has been recently designated vpr-like, based on its primary protein structure and some functional similarities to human immunodeficiency virus type 1 Vpr protein (21). The CAEV tat (hereafter named vpr-like) gene increases the viral load, tissue distribution, and inflammatory lesion severity over that of the vpr deletion counterpart (9).In ...