Molecular characterization and phylogenetic study of African swine fever virus isolates from recent outbreaks in Uganda (2010–2013)
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Date
2013
Journal Title
Journal ISSN
Volume Title
Publisher
Virology journal
Abstract
African 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.
Methods: Tissue 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.
Results: Twenty 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.
Conclusion: We 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.
Description
Keywords
African swine fever virus, Genotyping, P54, p72, pB602L (central variable region) sequencing
Citation
Atuhaire, D. K., Afayoa, M., Ochwo, S., Mwesigwa, S., Okuni, J. B., Olaho-Mukani, W., & Ojok, L. (2013). Molecular characterization and phylogenetic study of African swine fever virus isolates from recent outbreaks in Uganda (2010–2013). Virology journal, 10(1), 1-8. doi:10.1186/1743-422X-10-247