Phylogenetic analysis of Small Ruminant Lentiviruses originating from naturally infected sheep and goats from Poland based on the LTR sequences

Abstract

Introduction: Previous studies on the basis of gag and env sequences revealed that Polish small ruminant lentiviruses (SRLVs) isolated from sheep and goats belonged to subtypes B1, B2, A1, A5, A12, A13, A16-A18, A23, A24, and A27. The aim of this study was to extend genetic/phylogenetic analysis of previously identified SRLV Polish strains by analysis of LTR sequences. Material and Methods: A total of 112 samples were analyzed in this study. The phylogenetic analyses were carried out on the LTR fragment using three methods: neighbor-joining (NJ), maximum likelihood (ML) method, and the unweighted pair group method with arithmetic mean (UPGMA). Results: Our results revealed that Polish caprine and ovine LTR sequence clustered within group A and grouped in at least 10 clusters (subtype A1, A5, A12, A13, A16-A18, A23, A24, and A27). Our results revealed that most of Polish strains (78%) analyzed in this study belonged to the same subtype based on gag, env and LTR genomic regions. Discrepancies in affiliation were observed in 24 (21%) Polish strains most of which came from mixed-species flocks where circulation of more than one SRLVs genotype was observed. Our results showed also that LTR sequence reflected the subtype-specific patterns. Several subtype-specific markers were identified. Strains representing subtype A17, A27, A20, and B3 had unique substitution of T to A in the fifth position of TATA box. Conclusion: This study provides additional insights into the genetic diversity of SRLV field strains in Poland, their phylogenetic relationships and their position in the recently established SRLVs classification. Our results confirmed existence of subtypes A1, A5, A12, A13, A16-A18, A23, A24, and A27, and fact that mixed-species flocks favor the emergence of new SRLV variants.