Summary auto-generated
This study established a comprehensive phylogeny of small ruminant lentiviruses (SRLV), which includes caprine arthritis-encephalitis virus (CAEV) from goats and maedi-visna virus (MVV) from sheep. Researchers analyzed available DNA sequences from four genomic regions (env, pol, gag, and LTR) using maximum likelihood, neighbor-joining, and minimum evolution methods. The analysis revealed sequence divergences ranging from 16% in conserved regions (gag and pol) to 35% in the regulatory LTR domain. The phylogenetic trees identified at least six distinct clades without clear separation between goat and sheep lentiviruses, indicating substantial intermixing of strains from different host species and geographic origins. The study found evidence of both negative selection in conserved regions and positive selection in the envelope (env) region, consistent with other lentiviruses. Importantly, the research demonstrated clear indications of cross-species transmission between sheep and goats, challenging previous field observations suggesting this was rare. Trees generated from different genomic regions showed good agreement with each other and with different reconstruction methods, validating the phylogenetic framework. The work rejected a molecular clock model for SRLV evolution, indicating variable evolutionary rates across lineages.
Key findings
- At least six distinct SRLV clades were identified with no clear phylogenetic separation between caprine (CAEV) and ovine (MVV) strains, indicating frequent cross-species transmission
- Sequence divergence varied significantly by genomic region: pol (16.3%), env (22-24.8%), and LTR (35.1%), reflecting different selection pressures
- Evidence of both negative selection in gag/pol genes and positive selection in env gene, with synonymous-to-nonsynonymous substitution rate ratios of 20.8 (gag), 7.5 (pol), and 4.5 (env)
- Phylogenetic trees from different genomic regions (env, pol, gag, LTR) and different reconstruction methods showed strong agreement, validating the topology
- SRLV evolution does not follow a molecular clock, indicating variable evolutionary rates among different viral lineages
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Abstract
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.