Molecular epidemiology of rabies virus in South Africa: evidence for two distinct virus groups.

In order to derive phylogenetic relationships between rabies virus isolates from different geographical locations and host species in South Africa, two genome regions of the virus, viz. the cytoplasmic domain of the glycoprotein and the G-L intergenic region (pseudogene), were sequenced. A high level of nucleic acid sequence conservation indicated a close phylogenetic relationship between virus isolates from domestic dogs, jackals and bat-eared foxes, i.e. Canidae. These isolates appeared to be distinct from but closely related to European strains of rabies virus. However, a phylogenetically distinguishable and distant group, which contained isolates from mongooses (i.e. Viverridae) was identifiable. The latter group appears to be distantly related to European and vaccine strains of rabies virus and may have evolved uniquely on the central plateau of South Africa. Our data also indicate that spillover from mongooses (or other viverrids) to canid hosts occurs occasionally.