Genetic Characterization of Small Ruminant Lentiviruses (SRLVs) Circulating in Naturally Infected Sheep in Central Italy

Abstract

Small ruminant lentiviruses (SRLVs) represent a very heterogeneous group of ss-RNA viruses that infect sheep and goats worldwide. They cause important, deleterious effects on animal production and limit the animal trade. SRLVs show a high genetic variability due to high mutation rate and frequent recombination events. Indeed, five genotypes (A-E) and several subtypes have been detected. The aim of this work was to genetically characterize SRLVs circulating in central Italy. On this basis, a phylogenetic study on the gag-pol genetic region of 133 sheep, collected from 19 naturally infected flocks, was conducted. In addition, to evaluate the frequency of mutation and the selective pressure on this region, a WebLogo 3 analysis was performed, and the dN/dS ratio was computed. The results showed that 26 samples out of 133 were clustered in genotype A and 106 samples belonged to genotype B, as follows: A9 (n = 8), A11 (n = 10), A24 (n = 7), B1 (n = 2), B2 (n = 59), and B3 (n = 45). No recombination events were found. Mutations were localized mainly in the VR-2 region, and the dN/dS ratio of 0.028 indicated the existence of purifying selection. Since the genetic diversity of SRLVs could make serological identification difficult, it is important to perform molecular characterization to ensure a more reliable diagnosis, to maintain flock health status, and for the application of local and national control programs.

Keywords: WebLogo analysis; dN/dS ratio; genotypes; pairwise distance; phylogenetic analysis; sheep; small ruminant lentivirus (SRLV).

Figure 1

Maximum likelihood phylogenetic tree based on the alignment of 642 nt from gag-pol region of 287 sequences: 133 analysed in this study (labeled by a different color for each subtype) and 154 reference strains available in GenBank (labeled by black color). Bar: number of substitutions per site. Correspondence between sample names and accession numbers are reported in Table S1.

Figure 2

Amino acid sequence multiple alignment of SRLVs deduced from the gag-pol fragment. Each subtype has been aligned with the respective reference sequence. Immunodominant epitopes 2 and 3, major homology region (MHR) and variable region 2 (VR-2) are reported. Dots represent the same amino acid residue. Correspondence between sample names and accession numbers are reported in Table S1. (a) Subtypes A9, A11, A24, B1, B2; (b) Subtype B3.

Figure 2

Amino acid sequence multiple alignment of SRLVs deduced from the gag-pol fragment. Each subtype has been aligned with the respective reference sequence. Immunodominant epitopes 2 and 3, major homology region (MHR) and variable region 2 (VR-2) are reported. Dots represent the same amino acid residue. Correspondence between sample names and accession numbers are reported in Table S1. (a) Subtypes A9, A11, A24, B1, B2; (b) Subtype B3.

Figure 3

Graphical representation of the relative amino acid frequency of the partial SRLV gag-pol protein obtained by WebLogo 3 software. The height of the letter corresponding to each amino acid indicates its relative frequency at that specific position. Different colors indicate the physiochemical characteristics of the amino acid (black: non-polar, green: polar, red: aromatic, blue: positively charged, purple: negatively charged).