A panel of rabies virus isolates (RABV) endemic within Botswana between 1988 and 1992 have been typed by anti-nucleocapsid monoclonal antibodies (MAb) into two dominant groups. The first associated with the domestic dog (Canis familiaris) and the second associated with a range of wildlife species. Using nucleoprotein coding sequence data, we have applied molecular phylogenetic techniques to the same panel of 35 well-characterised rabies virus isolates from throughout Botswana in an attempt to compare both techniques and to further investigate the virus/host species relationships within this African country. The results confirm that there are indeed two major groups and that these are related primarily to biotype. The wildlife-associated biotype appeared more phylogenetically diverse and was more commonly isolated in the southeast of the country, with the canine-associated group dominating the north of the country. In addition, molecular phylogeny identified further groupings within both biotypes and a small number of isolates, which were not classified by MAb typing, could be assigned to a group. During the study period (4 years) there appeared to be little sequence variation within groups suggesting that distinct lineages persisted throughout the study and that there appears to be little evolutionary pressure on the nucleoprotein coding region of the viral genome.
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