Association for Public Health Labs 2015 Annual Meeting
Emerging virus discovery through meta-transcriptomics: a novel virus impacting Rainbow Trout (Oncorhynchus mykiss) farming in Chile
Viral pathogen discovery is critically important to clinical microbiology, infectious diseases, and public health. During 2012-13 there was an outbreak of unknown etiology affecting farmed rainbow trout (Oncorhynchus mykiss) in southern Chile. Clinical inspection and conventional diagnostic methods (PCR, cell and bacterial culture, immunofluorescence) failed to detect any known infectious agents, and transmission microscopy micrographs suggested the presence of viral particles in many organs. Here we present the results of a meta-transcriptomics analysis of two infected individuals and one control on spleen, muscle, heart, and brain tissues. Using high-throughput sequencing and our Absolute*Discovery pipeline on rRNA depleted Total RNA preparations, we found the presence of a new salmonid alphavirus described for the first time in Chile. This study demonstrates the utility of high-throughput sequencing and novel computational techniques to the study of emerging infectious agents in animal production.