title: Molecular characterization and phylogenetic study of African swine fever virus isolates from recent outbreaks in Uganda (2010-2013).
abstract: BACKGROUND
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: College of Veterinary Medicine, Animal resources and Biosecurity, Makerere University, P.O. BOX 7062, Kampala, Uganda. atuhaired@vetmed.mak.ac.ug
authors.forename: David Kalenzi
authors.initials: DK
authors.lastname: Atuhaire
authors.forename: Mathias
authors.initials: M
authors.lastname: Afayoa
authors.forename: Sylvester
authors.initials: S
authors.lastname: Ochwo
authors.forename: Savannah
authors.initials: S
authors.lastname: Mwesigwa
authors.forename: Julius Boniface
authors.initials: JB
authors.lastname: Okuni
authors.forename: William
authors.initials: W
authors.lastname: Olaho-Mukani
authors.forename: Lonzy
authors.initials: L
authors.lastname: Ojok
mesh_terms: D000357:African Swine Fever / Q000453:epidemiology*; D000358:African Swine Fever Virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D000818:Animals; D016000:Cluster Analysis; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D004196:Disease Outbreaks; D005838:Genotype; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013552:Swine; D014454:Uganda / Q000453:epidemiology
chemical_list: D004279:DNA, Viral
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