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

Highlilghts•Phylogenetic analyses using long consensus sequences confirm the existence of B1 subtype SRLV in Canadian goats•Phylogenetic analyses using long consensus sequences confirm the existence of A2 subtype SRLV in Canadian sheep•An emerging circulating recombinant form (CRF) SRLV was identified and characterized in several Canadian goat flocks.

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 3 kb 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.