Infectious diseases pose a constant threat to the U.S. livestock and poultry industries. Given that vaccines are usually not available, or used for most foreign animal diseases (FADs) or for emerging diseases, early and rapid pathogen detection and identification is the most critical step for adequate and effective control of disease outbreaks. The overarching goal of the proposed study is to enhance the National Animal Health Laboratory Network (NAHLN) diagnostic capabilities and emerging disease preparedness through the development of targeted and random next-generation sequencing (NGS) assays and bioinformatics analysis pipelines for the detection and characterization of important infectious diseases of swine.

Rapid methods for pathogen detection such as real-time PCR are widely utilized in diagnostic laboratories in the U.S. However, as these assays are highly specific to previously known and characterized pathogens, they may fail to detect new variants that are constantly emerging throughout the world. These challenges could be overcome with the use of NGS technologies, which provide means for rapid and simultaneous detection, identification and genetic characterization of pathogens. The major bottlenecks that currently hinder the wide use of NGS in routine pathogen diagnostics are: i. the lack of standardized NGS protocols and procedures that can be used across different laboratories; and ii. the need for highly specialized bioinformatics capabilities for NGS data analysis, interpretation and reporting.

To address these issues, we assembled a broad network of collaborating laboratories, including five NALHN laboratories (the Animal Health Diagnostic Center [AHDC] at Cornell University, the Veterinary Diagnostic Laboratory (VDL) at University of Georgia, the VDL at Kansas State University, California Animal Health and Food Safety Laboratory at UC Davis, and the Texas A&M Veterinary Medical Diagnostic Laboratory [TVMDL]), two government laboratories including the Foreign Animal Disease Research Unit (FADRU) ARS/USDA at Plum Island Animal Disease Center (PIADC) and the Southeast Poultry Research Laboratory (SEPRL), and a bioinformatics service company (BASE2BIO). These partner institutions will work collaboratively to develop and optimize NGS procedures for key NAHLN-scope and emerging diseases and to establish automated bioinformatics pipelines for fast and accurate data processing and reporting.