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

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.

FIG. 1.

Complete genome scheme of the genotype E Roccaverano strain (top panel) and the B1 prototype CAEV Cork strain (bottom panel), with deletions highlighted. A similarity plot (SimPlot software) of complete SRLV reference sequences (black line, accession number M33677; gray line, accession number M51543; light gray line, accession number AF322109) and the Roccaverano strain (accession number EU293537) is shown. Each plotted point represents the percentage of identity within a sliding window 100 bp wide centered on the plot position as shown, with a 20-bp step size between points.

FIG. 2.

Bayesian tree based on concatenate genes of six reference strains and genotype E. Accession numbers of reference sequences are shown in parentheses. The newly described Italian genotype E is shown in boldface. The gag-, pol-, and env-based trees showed the same topology (not shown).