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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Virus and Prion Research » Research » Research Project #442620

Research Project: Algorithms to Identify Novel Influenza A Viruses in Genomic Surveillance Data

Location: Virus and Prion Research

Project Number: 5030-32000-231-095-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2022
End Date: Aug 31, 2024

Develop computational algorithms and improve data analysis and reporting on the genetic and antigenic diversity of influenza A viruses. Algorithms will be generated that can be applied to predict inter-species pathogen transmission potential of influenza A virus in swine.

The publicly available influenza A virus (IAV) 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. Phylogenetic network analyses will be conducted to identify linked evolution within and between gene segments. The effect of evolutionary rate, genome constellation diversity, and structural novelty on IAV clade detection frequency will be determined using statistical modeling. General models predicting antigenic drift of influenza A virus in swine will be developed and parameterized by empirical HI antibody cross-reactivity data. 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. These algorithms will be integrated in interactive genomic epidemiological websites (octoFLUshow) and databases (US Swine Pathogen Database).