Molecular epidemiology of rabies virus in South Africa.

Nucleic acid sequence analysis was used to determine the phylogenetic relationships amongst rabies viruses isolated from typical canid hosts such as bat-eared fox, jackal and dog in South Africa (SA). Geographical factors were taken into account in the selection of isolates and three different regions within the genomes of the isolates were compared for their use as phylogenetic indicators. The three genome regions, being the cytoplasmic domain of the G-gene, the G-L intergenic pseudogene and the antigenic domain II of the N-gene were found to differ in terms of the of nucleic acid conservation, but produced similar results when analyzed phylogenetically. The SA canid isolates were found to be closely related and could clearly be distinguished from all other rabies virus groups for which sequence data is available. In addition four SA mongoose rabies isolates were studied which were shown to be distant from the SA canid rabies virus group as well as from any other rabies viruses (or group) for which sequence data is available. Our results also indicate that spillover between the distinct canid and viverrid host reservoirs may occur.