A total of 171,466 reads were obtained from the 454sequencing run, and after assembly 4,441 contigs were created while 32,863 reads remained unmatched (singletons). Although blastn and blastx analysis showed that a majority of the sequences were non-viral, 35 contigs and singletons sequences were identified as viral sequences ( Table 1 ). The high percentage of host genetic sequences found despite of the nuclease treatment prior to sequencing demonstrates the difficulties of completely reducing the background of the host as discussed in the review by Blomström A-L 2011 [4] . Most viral hits showed closest similarity to known pig viruses such as, Torque teno virus (TTSuV) and porcine parvovirus 4 (PPV4). By design of primers based on the sequences obtained from the 454-sequencing run, PCR assays were established to verify the presence of these viruses. These PCR assays confirm the presence of TTSuV1, TTSuV2, PPV4, and the porcine endogenous retrovirus (PERV). The GB Hepatitis C-like, and the Sclerotinia hypovirulence associated like virus, on the other hand, were not detected by the PCR approach, possibly due to the low concentration of these viruses in the samples as only one sequencing read was found for each among the total 171,466 reads obtained from the 454-sequencing run. Also it is possible that in some cases sequencing errors led to primer mismatches.