Tracing movement of African buffalo in southern Africa Introduction The use of techniques that enable analysis of the genomes of infectious agents combined with statistical methods for deriving relationships between them is being used increasingly to advance the understanding of the epidemiologies of a number of important livestock diseases (13, 22, 27, 29, 34, 48, 61, 66). The previously painstaking and often unreliable process of determining the origin of infections such as foot and mouth disease (FMD) and classical swine fever (CSF) that suddenly appeared in new locations can now be a rapid and reliable process, if adequate background data are available (28). Infectious agents, and ribonucleic acid (RNA)-containing viruses in particular, are able to mutate rapidly. This can result in geographically separated populations evolving independently, allowing representatives of such separated microbial populations to be identified (so-called topotypes) (7, 12, 25, 42, 53, 65). Subsequent spread of these topotypes to new locations can therefore be traced by genome analysis. Thus, for example, the recent intra- and intercontinental spread of the pan-Asian O topotype of FMD virus, which has caused serious epidemics in locations as far apart as the Indian subcontinent, South-East Asia, South Africa and the United Kingdom, is well known (40, 54). This approach is being used increasingly for other important infections of animals, some of which are discussed here. However, these techniques provide another possibility that was not originally anticipated, namely the use of genome analysis of infectious agents to identify the origin of animals that harbour them. The rate at which the genomes of infectious agents mutate is several orders of magnitude faster than the rate of mutation of mammalian genomes (33). This means that differentiable mutations occur much faster than in the mammalian hosts. Therefore, the identification of the probable origin of animals may be possible by studying the infectious agents harboured by animals where more usual methods for animal identification have failed. This method is particularly useful where particular populations of animals have been isolated for relatively long periods of time, e.g. within wildlife reserves or on closed-herd farms. So far, the infectious agents that have been used are principally those that are potentially pathogenic, because information on these agents is usually more detailed than that on non-pathogenic agents. However, Rev. sci. tech. Off. int. Epiz., 2001, 20 (2), 630-639 W. Vosloo (1) , A.D.S. Bastos (2) , A. Michel (1) & G.R. Thomson (3) (1) Onderstepoort Veterinary Institute, Private Bag X05, Onderstepoort 0110, South Africa (2) Department of Zoology and Entomology, University of Pretoria, Pretoria 0002, South Africa (3) Onderstepoort Veterinary Institute, Private Bag X05, Onderstepoort 0110, South Africa; present address: Organisation of African Unity/Inter-African Bureau for Animal Resources (OAU-IBAR), P.O. Box 30786, Nairobi, Kenya Summary Genetic characterisation of two pathogens, namely foot and mouth disease (FMD) virus and Mycobacterium bovis, isolated from African buffalo (Syncerus caffer) in southern Africa was used to determine the origin of buffalo in situations where the source of infection was obscure. By determining the phylogenetic relatedness of various FMD virus isolates using partial sequencing of the main antigenic determinant, VP1, the origin of buffalo moved illegally to the non-endemic region of South Africa was traced to the Kruger National Park (KNP) where FMD is endemic in the buffalo population. Comparative analysis of the ‘genetic fingerprints’ of bovine tuberculosis isolates from buffalo and cattle has aided in tracing the original source of infection of buffalo populations in the KNP. Furthermore, these analyses have assisted in tracing the origin of infected animals that have been moved to other parts of South Africa. Keywords African buffalo – Bovine tuberculosis – Foot and mouth disease virus – Southern Africa – Traceability.