Molecular Characterization of Small Ruminant Lentiviruses in Polish Mixed Flocks Supports Evidence of Cross Species Transmission, Dual Infection, a Recombination Event, and Reveals the Existence of New Subtypes within Group A

Abstract

Small ruminant lentiviruses (SRLVs) are a group of highly divergent viruses responsible for global infection in sheep and goats. In a previous study we showed that SRLV strains found in mixed flocks in Poland belonged to subtype A13 and A18, but this study was restricted only to the few flocks from Małopolska region. The present work aimed at extending earlier findings with the analysis of SRLVs in mixed flocks including larger numbers of animals and flocks from different part of Poland. On the basis of gag and env sequences, Polish SRLVs were assigned to the subtypes B2, A5, A12, and A17. Furthermore, the existence of a new subtypes, tentatively designed as A23 and A24, were described for the first time. Subtypes A5 and A17 were only found in goats, subtype A24 has been detected only in sheep while subtypes A12, A23, and B2 have been found in both sheep and goats. Co-infection with strains belonging to different subtypes was evidenced in three sheep and two goats originating from two flocks. Furthermore, three putative recombination events were identified within gag and env SRLVs sequences derived from three sheep. Amino acid (aa) sequences of immunodominant epitopes in CA protein were well conserved while Major Homology Region (MHR) had more alteration showing unique mutations in sequences of subtypes A5 and A17. In contrast, aa sequences of surface glycoprotein exhibited higher variability confirming type-specific variation in the SU5 epitope. The number of potential N-linked glycosylation sites (PNGS) ranged from 3 to 6 in respective sequences and were located in different positions. The analysis of LTR sequences revealed that sequences corresponding to the TATA box, AP-4, AML-vis, and polyadenylation signal (poly A) were quite conserved, while considerable alteration was observed in AP-1 sites. Interestingly, our results revealed that all sequences belonging to subtype A17 had unique substitution T to A in the fifth position of TATA box and did not have a 11 nt deletion in the R region which was noted in other sequences from Poland. These data revealed a complex picture of SRLVs population with ovine and caprine strains belonging to group A and B. We present strong and multiple evidence of dually infected sheep and goats in mixed flocks and present evidence that these viruses can recombine in vivo.

Phylogenetic analysis of small ruminant lentiviruses originating from naturally infected sheep and goats from Poland based on the long terminal repeat sequences

“…Previous studies on the genetic diversity of SRLVs from Poland provided evidence for the presence of two groups (A and B) and 12 subtypes within SRLVs. Polish SRLVs isolated from sheep and goats belonged to subtypes B1, B2, A1, A5, A12, A13, A16–A18, A23, A24 and A27 ( 17 ). The phylogenetic analysis of Polish strains has so far been performed based on gag gene or gag and env gene sequences; however, phylogenetic analysis of the LTR has never been performed.…”

Longitudinal study on seroreactivity of goats exposed to colostrum and milk of small ruminant lentivirus–infected dams

“…The diagnosis of CAE was also confirmed by SRLV isolation (29). The virus in this herd belonged to the MVV-like genotype A subtype A17 as demonstrated in several genetic studies (47,48,49). A harem mating system was practiced in this herd.…”

Genetic Diversity of the LTR Region of Polish SRLVs and Its Impact on the Transcriptional Activity of Viral Promoters

“…The 22 blood samples analyzed in this study originated from sheep and goats that were naturally infected with an SRLVs from 5 herds within different regions in Poland. All samples were tested previously and were PCR-positive for an SRLVs [ 11 , 30 ]. Sample animals were clinically healthy, without any clinical signs of SRLVs.…”

“…SRLVs are characterized by high genetic variations leading to a variety of divergent strains and quasi-species. SRLVs are phylogenetically divided into five groups (A–E), which include different subtypes [ 11 , 12 ]. The majority of subtypes are able to cross the species barrier between sheep and goats under field conditions.…”

“…The majority of subtypes are able to cross the species barrier between sheep and goats under field conditions. To date, group A has 27 recognized subtypes (A1–A27), group B has 5 subtypes (B1–B5) and group E has 2 subtypes (E1 and E2) [ 11 , 13 , 14 , 15 , 16 , 17 , 18 , 19 ]. The transcription of the lentivirus genome depends on the presence of appropriate cellular transcription factors.…”