PhD Thesis
In recent decades, the growing domestic pig population in response to an increase in demand for meat in sub-Saharan Africa has been followed by the increase of African swine fever (ASF) outbreaks. African swine fever is a contagious viral disease that causes high mortality, approaching 100%, in domestic pigs and wild boars. The disease has neither cure nor a vaccine and it is caused by ASF virus (ASFV), the only member of the family Asfarviridae, genus Asfivirus, and the only known DNA arbovirus. Twenty four genotypes of ASFV have been described to date and all of them are present in Africa. Thirty three (33) African countries, South of the Sahara are known to have experienced ASF outbreaks and it continues to impact negatively on small-scale domestic pig farmers particularly in eastern and southern Africa where three ASFV transmission cycles are found and this area is believed to play an important role in the maintenance and spread of ASF. African swine fever, by its recent spread beyond its traditional geographic boundaries to Caucasus, European Union, Russia and Asia particularly to China, which is the major pork producing country, is threatening global food and nutritional security. African swine fever outbreaks are mandated to be reported to the World Organization for Animal Health (OIE) and despite the perceived increase of the reported ASF outbreaks in domestic pigs, our understanding of the process of ASFV maintenance and spread in eastern and southern Africa is quite limited. This study was conducted to investigate molecular epidemiology of the ASFV in selected countries of eastern and southern Africa. The overriding research question for this study was “How are the ASFV strains circulating and causing ASF outbreaks in eastern and southern Africa related in terms of genotypes as determined by molecular characterization, in time and space?” Phylogeographic approach applied to ASFV p72 (B646L) gene sequences dataset was used to assess the evolutionary history and the dispersal pattern of the ASFV strains circulating between Tanzania and its eight neighbouring countries. Furthermore, partial genetic characterization of the ASFV strains responsible for recent ASF outbreaks in Burundi and Malawi was carried out targeting specific genomic regions using standardized molecular approach. The whole genome sequencing of the ASFV strains responsible for the 2018 outbreak in Burundi and 2019 ASF outbreak in Malawi were performed using Illumina next-generation sequencing (NGS) platform. The sequencing data were subjected to bioinformatics analysis using appropriate softwares and tools. The results of this study indicate that from 2005 to 2019, a total of 1588 ASF outbreaks affecting 341 742 cases that led to 302 739 domestic pig deaths were reported to the World Organization for Animal Health (OIE) by Tanzania and its eight neighbouring countries. The case fatality rates (CFR) varied from 15.41 to 98.95% with an overall CFR of 88.58%. Fifteen different p72 ASFV genotypes were reported by Tanzania and its eight neighbouring countries and the time to the most recent common ancestor (TMRCA) for ASFV strains dated back to 1652.233 (1626.473, 1667.735) with an evolutionary rate of 4.805 x 10-5 (2.5857 x 10-5, 9.7789 x 10-5). Phylogeographic dispersal analysis revealed several transboundary spread events of ASFV strains between these countries. Phylogenetic analysis of the Burundian 2018 ASFV grouped the virus within p72 (B646L) genotype X and clustered together with those previously reported during the 1984 and 1990 ASF outbreaks in Burundi with high nucleotide identity to some ASFV strains previously reported in neighbouring east African countries, indicating a regional distribution of this ASFV genotype. The results of this study confirmed an ASF outbreak in Karonga district in northern Malawi in September 2019. The virus was closely related to other p72 (B646L) genotype II ASFV strains that caused outbreaks in neighbouring eastern and southern African countries, emphasizing the possible regional transboundary transmission of this ASFV genotype. Complete genome sequencing of ASFV that caused outbreak in 2018 in Burundi (BUR/18/Rutana) and the ASF outbreak during 2019 in Malawi (MAL/19/Karonga) was conducted during this study. The complete nucleotides sequence of the ASFV BUR/18/Rutana and MAL/19/Karonga were 176 564 and 183 325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with p72 genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). Analysis of the EP402R gene that encodes the CD2v major ASFV antigen protein revealed high nucleotide sequence variation and the serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study suggest persistent circulation of ASFV in countries involved in this study and provide important insights into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern and southern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread. The findings of this study advocate for more research on ASFV sylvatic cycle and more whole genome sequencing of ASFV to improve our understanding of the transmission dynamics of the virus, structural and antigenic diversity of ASFV. These findings call for a concerted regional and international effort to control the spread of ASF in order to improve nutritional and food security.
PASET and RSIF