National swine health statistics indicate a growing death rate due to respiratory disease in both the nursery and grower/finished phases in swine (Swine 2006, APHIS, USDA). In 2006, veterinary diagnostic testing revealed that Porcine Reproductive and Respiratory Syndrome was the most prevalent of the diagnosed diseases in breeding herd and nursery pigs (Swine 2006, APHIS, USDA). Additional diseases that contribute to the swine morbidity and mortality rate include Porcine Circovirus 2 associated diseases, swine influenza, foot and mouth disease, classic swine fever and swine vesicular disease. The proposed TessArray RPM assay is a simultaneously differential diagnosis platform for these and other targeted pathogens of the assay. The single test result can establish cause of infectious disease in individual animals as well as outbreaks of infectious disease in local herds or across swine production communities. No existing test other than RPM can enable rapid differential diagnosis, determine presence of multiple infectious agents co-infecting individual animals, or support epidemiological tracking in epidemic outbreaks to minimize effective response times. OBJECTIVES: We will design and develop a highly multiplexed gene sequencing based assay for the detection and identification of viral and bacterial pathogens causing agriculturally and economically significant disease of swine. This approach, using a high-density gene sequencing microarray offers significant advantages over conventional single-target, biomarker-based (e.g. antibody or PCR) testing. In addition to maximum sensitivity for detection of one or more multiple pathogens that may be present in a single specimen, the assay result represents one or more specimen-specific gene sequences, rather than a measured signal for a presence/absence report of only one targeted pathogen. The reported pathogen gene sequences enable forensic and epidemiological tracking of the same detected pathogens from one specimen to another, which no biomarker-based assay can support. Furthermore, the microarray assay is capable of detection and identification, through gene sequences, of emergent pathogen strains and variants that are at least 80% sequence-similar. Biomarkers are so constrained to perfect sequence matching of assay probes and intended target pathogens that natural variants often result in false negative or false positive assay results. TessArae will collaborate with the Kansas State University College of Veterinary Medicine for the selection of simultaneously targeted pathogens, to include at least 15 bacterial genera and at least 18 categories of virus
