Emerging infectious diseases pose a constant threat to the U.S. pork industry. Given that vaccines are usually not available for emerging diseases, early and rapid pathogen detection and is the most critical step for adequate and effective control of disease outbreaks. The overarching goal of the proposed study is to enhance diagnostic capabilities and emerging disease preparedness of the swine industry through the development of improved next-generation sequencing (NGS) assays with increased sensitivity for the detection, identification, and genomic characterization of newly emerging or re-emerging viral pathogens of swine.