Abstract
The central variable region (CVR) within the B602L gene of the African swine fever virus (ASFV) is highly polymorphic within the 23 ASFV genotypes defined by sequencing of the C-terminal end of the p72 locus. Sequencing the p54 gene further discriminates ASFV genotypes that are conserved at the p72 locus. Variation in the thymidine kinase locus is a novel additional tool for ASFV genotyping whose application for this purpose is described for the first time herein. We evaluated genetic variation at these four polymorphic loci in 39 ASFV isolates obtained from outbreaks in Kenya and a region of Eastern Uganda between 2011 and 2013. Analysis of the p72 and p54 loci revealed high genetic conservation among these isolates; all clustered within p72 genotype IX and were similar to isolates associated with earlier outbreaks in East Africa. The thymidine kinase gene of the Kenyan isolates in this study were distinct relative to Southern African isolates and synonymous substitutions were observed among viruses from central Kenya. Analysis of the CVR within the B602L gene revealed two previously unknown polymorphisms that were restricted to Western Kenya and Eastern Uganda. A novel variant was revealed within CVR subgroup XXIV and a novel CVR subgroup XXIVa that contains tetrameric repeat F which has previously only been associated with p72 genotype I, was also identified for the first time in East Africa. Phylogeographic analysis of isolates based on CVR polymorphisms revealed rapid evolution and dissemination of variants present within ASFV genotype IX in East Africa.
Highlights
African swine fever (ASF) is a highly contagious and frequently fatal hemorrhagic disease of swine that typically results in high mortality in domestic pigs and European wild boar
A total of 39 domestic pigs tested African swine fever virus (ASFV) positive by both conventional and Universal probe library (UPL) PCR and an additional 2 pigs were confirmed to be positive by UPL PCR (Table 1)
This study confirmed the endemic status of African swine fever virus in Western Kenya and Eastern Uganda and that the majority of outbreaks in the region occur as a result of ASFV genotype IX
Summary
African swine fever (ASF) is a highly contagious and frequently fatal hemorrhagic disease of swine that typically results in high mortality in domestic pigs and European wild boar. The disease is caused by the African swine fever virus (ASFV); a large virus that replicates within the cell’s cytoplasm and is the sole member of the family Asfarviridae, genus Asfivirus [1] and the only currently known DNA. The epidemiology of ASF is complex and differs across countries, regions, and continents depending on the presence or absence of wild suids, arthropod vectors, and pig production systems [5]. Transmission occurs through three distinct cycles, an ancestral sylvatic cycle involving African wild suids and soft ticks (genus Ornithodoros), a domestic pig to pig cycle, which is probably the most frequent current mode of transmission in the majority of African pig production systems, and transmission between domestic pigs via Ornithodoros ticks, which has rarely been confirmed [6]
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