Diversity of viruses detected by deep sequencing in pigs from a common background

Although advances in nucleic acid sequencing have enabled the discovery of many infectious agents, challenges remain for scientists and veterinary diagnosticians trying to design animal studies with a minimum of variables and to interpret laboratory results. To evaluate pyrosequencing technology as a potential screening method to estimate the virome in pigs, fecal samples were collected from 4 pigs out of a group of 175 that had been raised together since birth. A number of viruses were detected, demonstrating the application of this technology to determine the background noise in the pigs. However, pyrosequencing also demonstrated the diversity of viruses within a group of animals and how that can confound experimental design and obscure a definitive diagnosis.