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Viral metagenomic analysis of bushpigs (Potamochoerus larvatus) in Uganda identifies novel variants of Porcine parvovirus 4 and Torque teno sus virus 1 and 2

Anne-Lie Blomström1*, Karl Ståhl12, Charles Masembe3, Edward Okoth4, Ademun Rose Okurut5, Patrick Atmnedi6, Stephen Kemp4, Richard Bishop4, Sándor Belák12 and Mikael Berg1

Author Affiliations

1 Department of Biomedical Sciences and Veterinary Public Health, Section of Virology, Swedish University of Agricultural Sciences, Uppsala, Sweden

2 Department of Virology, Immunobiology and Parasitology (VIP), National Veterinary Institute (SVA), Uppsala, Sweden

3 Department of Biology, Makerere University, College of Natural Sciences. School of Biological Sciences, Box 7026, Kampala, Uganda

4 International Livestock Research Institute (ILRI), Nairobi, Kenya

5 National Animal Disease Diagnostics and Epidemiology Centre (NADDEC), Ministry of Agriculture Animal Industry and Fisheries, Entebbe, Uganda

6 Uganda Wildlife Authority, Kampala, Uganda

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Virology Journal 2012, 9:192  doi:10.1186/1743-422X-9-192

Published: 11 September 2012

Abstract

Background

As a result of rapidly growing human populations, intensification of livestock production and increasing exploitation of wildlife habitats for animal agriculture, the interface between wildlife, livestock and humans is expanding, with potential impacts on both domestic animal and human health. Wild animals serve as reservoirs for many viruses, which may occasionally result in novel infections of domestic animals and/or the human population. Given this background, we used metagenomics to investigate the presence of viral pathogens in sera collected from bushpigs (Potamochoerus larvatus), a nocturnal species of wild Suid known to move between national parks and farmland, in Uganda.

Results

Application of 454 pyrosequencing demonstrated the presence of Torque teno sus virus (TTSuV), porcine parvovirus 4 (PPV4), porcine endogenous retrovirus (PERV), a GB Hepatitis C–like virus, and a Sclerotinia hypovirulence-associated-like virus in sera from the bushpigs. PCR assays for each specific virus combined with Sanger sequencing revealed two TTSuV-1 variants, one TTSuV-2 variant as well as PPV4 in the serum samples and thereby confirming the findings from the 454 sequencing.

Conclusions

Using a viral metagenomic approach we have made an initial analysis of viruses present in bushpig sera and demonstrated for the first time the presence of PPV4 in a wild African Suid. In addition we identified novel variants of TTSuV-1 and 2 in bushpigs.