Transboundary and emerging infectious diseases pose a constant threat to the U.S. livestock industry. Early, reliable, and rapid pathogen detection and identification are the most critical steps for timely, adequate, and effective control of disease outbreaks. The overarching goal of this integrated project is to enhance the National Animal Health Laboratory Network diagnostic capabilities and emerging disease preparedness through the development of next-generation sequencing (NGS) and rapid bioinformatics analysis pipelines for the detection and characterization of current, transboundary, and emerging pathogens of cattle. The objectives of the proposed study are: (1) To develop and optimize NGS-based diagnostic assays that will allow early detection of current, transboundary and/or emerging diseases of cattle; (2) To develop and optimize streamlined bioinformatics pipelines for targeted and random NGS diagnostic applications for cattle; and (3) To establish NGS-based diagnostic capability in several NAHLN laboratories.

The proposed study will leverage on our team’s extensive experience with animal diagnostics and the use of next generation sequencing as a tool to diagnose infectious diseases in livestock and poultry. The objectives of the proposed study align with the priorities of the Tactical Sciences for Agricultural Biosecurity (A1181) program. Availability of these diagnostic tools will enhance the capacity of the NAHLN and strengthen the capability of the US food and agricultural industry to combat and prevent transboundary and/or emerging disease outbreaks in cattle, one of the major livestock industries in the US.