Location: Virus and Prion Research
Project Number: 5030-32000-231-103-A
Project Type: Cooperative Agreement
Start Date: Sep 1, 2023
End Date: Aug 31, 2025
Objective: To develop computational algorithms and improve data analysis and reporting on the genetic diversity and reassortment patterns of influenza A viruses in swine. Algorithms will be developed, which can rapidly assess reassortment of influenza A viruses in swine from genomic surveillance data and a system will be developed that can ingest and analyze data in near-real time to identify genetically novel influenza A virus.
The publicly available influenza A virus in swine genetic sequence data collected within the USDA influenza A virus in swine surveillance system stream will be analyzed using phylogenetic and genomic epidemiological methods. Genetic diversity of the surface proteins and whole genome diversity will be quantified. Fully assembled sequences will be analyzed in the context of contemporary and historical IAV for determination of phylogenetic relationships, lineages, and reassortment. Phylogenetic network analyses will be conducted to identify linked evolution within and between gene segments. Though sequence analysis approaches exist, we will develop novel algorithmic approaches that can analyze the high-dimensional and high-volume of data that are generated in the national surveillance system. A novel software will be developed to analyze whole genome sequencing data in near real-time to determine evolutionary history and genetic novelty. These algorithms will be integrated in interactive genomic epidemiological websites (octoFLUshow) and databases (US Swine Pathogen Database).