Sus scrofa domesticus Viral Metagenome

The rising demand for pork has resulted in a massive expansion of pig production in Uganda. This has resulted in increased contact between humans and pigs. Pigs can act as reservoirs for many emerging infectious diseases. Therefore identification of potential zoonotic pathogens is important for public health surveillance. In this study, we screened domestic pigs from Uganda for the presence of RNA and DNA viruses using a high-throughput pyrosequencing method. Serum samples from 19 domestic pigs were collected from six regions in Uganda and pooled accordingly. Genomic DNA and RNA were extracted and sequenced on the 454 GS-FLX platform. Among the sequences assigned to a taxon, 38%, mapped to the domestic pig (Sus scrofa). African swine fever virus, Torque Tenoviruses (TTVs), and porcine endogenous retroviruses were identified. Interestingly, two pools of RNA origin had sequences that showed 98% sequence identity to Ndumu virus (NDUV). This is the first report of the domestic pig as a vertebrate host for Ndumu virus. NDUV had been previously isolated only from culicine mosquitos. NDUV therefore represents a potential zoonotic pathogen, given the increasing risk of human-livestock-mosquito contact.