Molecular epidemiology of African swine fever in East Africa

African swine fever (ASF), a hemorrhagic disease of domestic pigs, is caused by a large enveloped icosahedral arbovirus of the Asfivirus genus in the family Asfarviridae . It has a linear, covalently close-ended, double stranded DNA (dsDNA) genome, 170 – 190 kbp in size. Warthogs (Phaecochoerus aethiopicus ), bushpigs (Potamochoerus porcus ) and soft ticks of the Ornithodoros genus are natural reservoirs of ASF virus (ASFV) in Africa. Serological differentiation between field strains is not possible and as no vaccine is available, control relies on stamping out and strict zoosanitary practices. In order to identify possible sources of virus and prevent further introductions, ASFVs need to be differentiated on genotype basis. Genotyping of East African ASFV isolates was achieved in this study by characterization of the C-terminal region of the major capsid protein gene, p72 . Thirteen genotypes were identified among East African sylvatic and domestic hosts. Of significance was the recovery of an apparently geographically restricted homogenous domestic pig cycle in the region, as well as the presence of viruses of the ESACWA genotype, formerly believed to be confined to Europe, South America, the Caribbean Islands and West Africa. Due to the conserved nature of the p72 gene, intra-genotypic relationships of viruses recovered from a homogeneous domestic pig-associated lineage, genotype VIII, could not be resolved. In an attempt to address this short-coming, genetic characterization of the Central Variable Region (CVR) within the 9-RL open reading frame (ORF) of the central conserved region of ASFV genome was conducted. Eight groups were resolved, some of which confirmed prolonged periods of circulation of a particular virus type, whilst others confirmed transboundary transmission of the disease. The complexity of ASF epidemiology in East Africa exemplified by the presence of a sylvatic and domestic pig cycle, multiple genotypes within countries and identical genotypes shared by multiple countries, was revealed. The East African ASFV molecular epidemiological database created in this study will be of great assistance to veterinary officials implementing prevention and outbreak control strategies.