Kansas Biosciences Authority /National Pork Board Joint Call Funded Projects
African Swine Fever Virus: a bioinformatics resource to support comparative genomics for vaccine and virulence studies
University of Victoria PI: Chris Upton
Kansas State University Co-PI: Juergen Richt
07/01/2015 – 06/30/2016
The benefits of this proposal will be significant and wide ranging. The project will create a powerful Bioinformatics Resource for the annotation, management and analysis (comparative genomics) of African Swine Fever Virus (ASFV) genomes. This Bioinformatics Resource will increase the efficiency and effectiveness of molecular virologists by providing them access to a large variety of novel analyses that cannot be performed without such specialized tools and properly managed genomics data. These comparative genomics analyses are part of standard day-to-day “experiments” performed by researchers working on the development of viral vaccines and diagnostics. Currently, there are no competing bioinformatics resources available to ASFV researchers.
This new resource will make genome annotation much easier (much quicker) and more accurate. This will be achieved in part by the software, but an important component will be the creation of Standard Operating Procedures (SOPs) for genome annotation. Once a series of genomes, representative of the various genotypes, have been annotated to established rules, then the annotation of new genomes will be much more efficient and effective. Accuracy in genome annotation is critical if genome comparisons are to be at all meaningful.
Another key objective is to give all ASFV researchers, regardless of their physical location in the world, full access to this Bioinformatics Resource. This will also enhance the effectiveness of those research labs that have limited bioinformatics resources.
Characterizing a U.S. swine movement network to enhance epidemiological modeling and response to transboundary animal disease
University of Minnesota PI: Tim Boyer
PIC USA Inc Co-I: Tim Snider
07/01/2015 – 06/30/2016
The goal of this project is to improve the emergency preparedness of the U.S. pork industry for a potential transboundary animal disease (TAD) outbreak by providing more accurate and effective epidemiological models upon which to base preparation activities and emergency response plans. It provides Novel and Cross Cutting research directly addressing the call for proposals’ research priorities of advancing pork industry preparedness with practical applications for response to TAD of swine. The project will include the following objectives: 1) to collect data on the movements of swine and people, vehicle, or other potential carriers of pathogens (fomites) among swine premises in a major U.S. swine-producing region; 2) to characterize the structure of integrated swine systems in the United States and their supply chains; and 3) to use the data collected for Objectives 1 and 2 to develop direct and indirect contact parameters for use in epidemiologic models of TADs of swine.