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

David Kalenzi Atuhaire,Mathias Afayoa,Sylvester Ochwo,Lonzy Ojok,Savannah Mwesigwa,Julius Boniface Okuni,William Olaho-Mukani

doi:10.1186/1743-422x-10-247

David Kalenzi Atuhaire, Mathias Afayoa + Show 5 more

Open Access

https://doi.org/10.1186/1743-422x-10-247

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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.

Highlights

African swine fever (ASF) is a highly lethal and economically significant disease of domestic pigs in Eastern Africa in Uganda where outbreaks regularly occur
By combining p72, P54 and pB602L (CVR), a high level resolution approach is achieved for viral discrimination [7,14]
Out of the 30 outbreaks, 21 tissue samples tested positive with the Office International des Epizooties (OIE) diagnostic polymerase chain reaction amplification (PCR)

Summary

Introduction

African swine fever (ASF) is a highly lethal and economically significant disease of domestic pigs in Eastern Africa in Uganda where outbreaks regularly occur. African swine fever virus (ASFV) is a large double stranded DNA virus with 170–190 kb, classified as sole member of Asfarviridae family [1]. It is responsible for a highly contagious and fatal disease of domestic pigs, representing a serious threat to swine industry in East. Though first isolated in domestic pigs in 1921 in Kenya, the virus occurs naturally in both vertebrate and invertebrate sylvatic hosts throughout sub-Saharan Africa and is transmitted to domestic pigs when infected ticks of the Ornithodoros moubata complex feed on them [2]. In 2007, it was introduced into Georgia, most probably through infected pig-meat that was unloaded from a ship, recycled and fed to local pigs and has since spread throughout the Caucasus and into southern Russia [3]

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