Molecular characterization and phylogenetic study of African swine fever virus isolates from recent outbreaks in Uganda (2010–2013)

Abstract

BackgroundAfrican swine fever (ASF) is a highly lethal and economically significant disease of domestic pigs in Eastern Africa particularly in Uganda where outbreaks regularly occur. Sequence analysis of variable genome regions have been extensively used for molecular epidemiological studies of African swine fever virus (ASFV) isolates. By combining p72, P54 and pB602L (CVR), a high level resolution approach is achieved for viral discrimination. The major aim of this study therefore, was to investigate the genetic relatedness of ASF outbreaks that occurred between 2010 and 2013 in Uganda to contribute to the clarification of the epidemiological situation over a four year period.MethodsTissue samples from infected domestic pigs associated with an ASF outbreak from 15 districts in Uganda were confirmed as being infected with ASFV using a p72 gene-based polymerase chain reaction amplification (PCR) assay recommended by OIE. The analysis was conducted by genotyping based on sequence data from three single copy ASFV genes. The E183L gene encoding the structural protein P54 and part of the gene encoding the p72 protein was used to delineate genotypes. Intra-genotypic resolution of viral relationships was achieved by analysis of tetramer amino acid repeats within the hypervariable CVR of the B602L gene.ResultsTwenty one (21) ASF outbreaks were confirmed by the p72 ASF diagnostic PCR, however; only 17 isolates were successfully aligned after sequencing. Our entire isolates cluster with previous ASF viruses in genotype IX isolated in Uganda and Kenya using p72 and P54 genes. Analysis of the CVR gene generated three sub-groups one with 23 tetrameric amino acid repeats (TRS) with an additional CAST sequence, the second with 22 TRS while one isolate Ug13. Kampala1 had 13 TRS.ConclusionWe identified two new CVR subgroups different from previous studies. This study constitutes the first detailed assessment of the molecular epidemiology of ASFV in domestic pigs in the different regions of Uganda.

Genetic Characterization of Circulating African Swine Fever Viruses in Nigeria (2007-2015)

“…Sequence analysis also suggests that the circulating viruses do not undergo rapid genetic changes and reaffirms genotype I as the only circulating genotype in Nigeria. Our data appear to be in agreement with other studies (Owolodun et al, 2010a), but differ from reports from East and southern Africa where high levels of heterogeneity are associated with the presence of Ornithodoros ticks (Boshoff et al, 2007;Atuhaire et al, 2013). This study attempted to resolve the intragenotypic relationships of genotype I ASFV circulating in Nigeria for over 9 years using ASFV central variable region of B602L gene.…”

Identification of a New Genotype of African Swine Fever Virus in Domestic Pigs from Ethiopia

“…The highest nucleotide identity of the Ethiopia viruses was found with p72 genotype IX (Table ). This genotype comprises ASFV isolates obtained mainly from domestic pig outbreaks in Kenya, Uganda and the Republic of Congo since 2003 until 2013 (Lubisi et al., ; Gallardo et al., , ,b; Atuhaire et al., ). Kenya and Uganda share borders to the south of Ethiopia suggesting that the ASFV Ethiopia strains might have evolved from the same origin although the mechanisms of the evolution of the viruses are yet unknown.…”

“…This rich genetic diversity is promoted through the sylvatic cycle and extended by the domestic cycle with open borders and unrestricted movement of swine in conflict areas. Several studies have assessed the role of cross border pig movements and related them to the occurrence of ASF outbreaks within the borders of several countries such as Zambia, South Africa, Mozambique, Tanzania, Kenya and Uganda (Lubisi et al., ; Boshoff et al., ; Gallardo et al., , ,b; Misinzo et al., ; Atuhaire et al., ). Thus, genotypes that were once thought to be specific to one country are now being detected in neighbouring countries.…”

African swine fever outbreak on a medium-sized farm in Uganda: biosecurity breaches and within-farm virus contamination

“…The presence of ASFV in the sylvatic cycle is probably as ancient as in other areas of the region (Montgomery 1921; Plowright et al 1994), but with a growing domestic pig population, numerous outbreaks are now described every year (Gallardo et al 2011; Muwonge et al 2012; Atuhaire et al 2013; Barongo et al 2015; Chenais et al 2015b; Muhangi et al 2015). The Ugandan pig population is the largest in East Africa (FAOSTAT 2013), but larger-scale enterprises are rare and most of the pigs are still kept in smallholder family farms in the rural areas (NEPAD and FAO 2004; Dione et al 2014).…”