Applications of Viral Metagenomics in the Veterinary Field Looking for the Unknown

Viral metagenomics provide a powerful technology to investigate the viral flora of healthy and sick animals. Using these methodologies, we gain a better understanding in the etiology of diseases, as well as deepen our knowledge into the viruses circulating in nature and the complex interaction between virus and host. The aim of this thesis was to utilize viral metagenomics into different areas of interest for veterinary science. One multifactorial disease complex was studied, as were a disease of unknown etiology, where traditional methods had failed to identify a causative agent. The final study was on viruses in an arthropod vector. Postweaning multisystemic wasting syndrome (PMWS) was the multifactorial disease chosen here. Though, porcine circovirus type 2 (PCV-2) has been found the causative agent other factors, such as viruses, are believed to influence the disease. Using multiple displacement amplification followed by large-scale sequencing we discovered, apart from PCV-2 and torque teno virus, a novel porcine bocavirus in the background of PCV-2 in lymph nodes collected from pigs suffering from PMWS. This co-infection was seen in a high percentage (71%) of pigs suffering from PMWS compared to only 33% in pigs without PMWS. Shaking mink syndrome (SMS) was used to investigate a disease of unknown etiology. By random amplification and large-scale sequencing we found an astrovirus in the brain of minks experimentally infected with brain homogenate from diseased animals. Astrovirus was also detected in the brain of naturally infected minks. Vectors are important transmitters of disease, and in the final study, soft ticks (Ornithodoros) collected from a warthog burrow in Uganda were investigated for the presence of viruses. Among others, we discovered a possible novel RNA virus that showed a distant relationship to hepatitis E virus. In conclusion, viral metagenomics have successfully been applied to investigate three important areas for veterinary science and through these studies three novel viruses were discovered and genetically characterized.