African swine fever (ASF) which is caused by the African swine fever virus (ASFV) has infected domestic pigs in Uganda and several African countries. Recent events in the country where the disease is endemic show that it is progressing unabated at epidemic rates associated with a range of factors and drivers of infection.
In this study, we evaluated the drivers and risk factors, serological patterns and molecular identification of ASF in Uganda. A cross-sectional survey was conducted in seven districts of Uganda from December 2012 to April 2013, viz. in Pallisa, Lira, Abim, Nebbi, Kabarole, Kibaale, and Mukono which were selected to ensure wide geographic representation, had reported outbreaks in the recent past areas and were in close proximity to potentially high-risk locations associated with ASF epidemiology. A total of 196 farmers were involved in the questionnaire survey, while 190 sera samples were used for the serological assay, and 59 tissue samples were finally used for the molecular phylogenetic study.
The observed drivers, risk factors and socio-anthropological factors that were associated with ASF virus epidemiology in Uganda obtained from carefully selected representative sub-populations of pig farms and statistics in a case-control model of ASF infection on pig farms in Uganda were: the indiscriminate disposal of pig viscera and waste materials post-slaughter, farm-gate buyers collecting pigs and pig products from within the farm, retention of survivor pigs on the farm, and the disposal into an open refuse dump, of pig viscera and products following slaughter. The possession of wire mesh windows in pig houses was protective against ASF infection while the sighting of engorged ticks on the pigs, possession of a lock for each pig pen and having a gate at the farm entrance were significant.
The second component of this study cautioned against serological determination of ASF status as the sole diagnostic method with an 88 % chance of missing an on-going infection with 6 out of 25 sera collected from Abim district testing positive while all sera from other locations were negative giving an overall prevalence of 3.1 %, and a regional prevalence of 24 %.
This work shows for the first time the use of the TK gene region for ASF diagnosis in Uganda. Four gene regions were successfully amplified and characterised, producing a total of 41 genomic sequences from viruses in domestic pigs in Uganda. A combination of TK, p72, p54 and CVR-ORF gene regions were characterised for 10 PCR-positive domestic pigs. The TK gene sequencing detected four additional PCR positive individuals initially assigned a negative status on the basis of two independent p72 assays, the OIE diagnostic PCR and C-terminal genotyping PCRs.