Identification and characterization of an emerging small ruminant lentivirus circulating recombinant form (CRF).

The molecular epidemiology of small ruminant lentiviruses (SRLVs) is constantly changing due to animal movements, cross species transmission and because of their rapid evolutionary rate. This study reports a comprehensive genetic and phylogenetic analysis based on consensus gag and pol sequences covering 3kb of the SRLV genome from small ruminants in Québec, Canada. A group of strains obtained from goats originating from different flocks, segregated in a unique clade distinct from currently known SRLV groups. Genetic dissection of the gag gene from these strains revealed that it originated as a result of a recombination event between parental strains currently circulating in small ruminants of the country. Following HIV nomenclature, we propose to call this group of strains, circulating recombinant form 1 SRLV, or CRF01_AB SRLV. In addition, the study confirms the existence of genetically distinct and homogeneous populations of SRLVs infecting sheep and goats housed in single species flocks.

Phylogenetic analysis of small ruminant lentiviruses in mixed flocks: multiple evidence of dual infection and natural transmission of types A2 and B1 between sheep and goats.

Previous molecular analyses of small ruminant lentivirus (SRLV) populations in single species herds in Quebec, Canada, have revealed a relatively simple structure where goats and sheep appeared exclusively infected with B1 and A2 subtypes respectively. The present work aimed at extending these earlier findings with the analysis of SRLVs in mixed flocks. Molecular analyses revealed a more complex picture of SRLV population structure in mixed herds compared to single species herds. Notably, phylogenetic analyses of long gag sequences strongly support transmission of A2 subtype from sheep to goats as well as transmission of B1 subtype from goats to sheep. Hence, this work uncovered for the first time natural transmission between sheep and goats of North American subtype A2. In addition, multiple evidences of mixed infection of sheep and goats with A2 and B1 subtypes were found. The data reported in this study reinforces the concept of a genetic continuum of SRLVs where strains are exchanged between sheep and goats under favourable conditions and in the absence of specific species barriers. Most interestingly, this study suggests that dual infection, which is a hallmark of the lentivirus paradigm HIV, may not be such rare events in small ruminants but may simply be understudied and underreported. Overall, the present data shows that sheep and goats in Canada can be infected with both SRLV A and B types, sometimes simultaneously, and that mixed flocks may represent a breeding ground for their evolution.