Based on available sequence data, a phylogeny of small ruminant lentiviruses (SRLV) was established for env, pol, gag and LTR fragments using maximum likelihood, neighbour-joining and minimum evolution reconstruction techniques. To reconstruct topologies as accurately as possible, phylogenetic parameters like base composition, percentage divergences, kappa, the gamma shape parameter alpha and codon position-specific rates were estimated prior to the reconstruction of trees. Divergences between fragments of SRLV ranged from 16% in gag and pol to 22% in env and 35% in LTR. The codon position bias found and the ratios of synonymous to nonsynonymous substitutions were inversely related to overall divergence, indicating the existence of both negative and positive Darwinian selection in SRLV genes. The phylogenetic trees reconstructed with relative substitution rates assigned to the codon positions revealed an interesting relationship between lentiviruses from sheep and goats. Overall, at least six different clades could be differentiated, with no clear separation of SRLV strains derived from goats (caprine arthritis-encephalitis virus) or sheep (maedi-visna virus). Trees generated with fragments from different coding regions were in good agreement with each other as well as with trees generated with different phylogeny reconstruction methods. In this work, clear indications of the existence and epidemiological importance of cross-species transmission were found.


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