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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Virus and Prion Research » Research » Research Project #444750

Research Project: USDA Influenza A Virus in Swine Surveillance System – Genomic Epidemiology and Evolution

Location: Virus and Prion Research

Project Number: 5030-32000-231-104-I
Project Type: Interagency Reimbursable Agreement

Start Date: Sep 1, 2023
End Date: Aug 31, 2025

Objective 1: Quantify USA swine influenza A virus genetic evolution through the analysis of the USDA influenza A virus in swine surveillance system data. Objective 2: Development and implementation of treeSORT as an online analysis platform to quantify and detect novel reassorted influenza A virus in swine. Objective 3: Determine global genetic and antigenic relationships of influenza A virus in swine.

A better understanding of the genetic evolution of influenza A viruses (IAV) in swine is warranted based on the tremendous diversity of IAV in the swine population. Through computational analyses of the surface proteins and select whole genomes of IAV, we will identify spatial and temporal trends in genetic diversity, and select viruses for in vitro and in vivo pathogenesis, transmission, and vaccine studies. National Animal Health Laboratory Network IAV sequence submissions will be accessed from NCBI Genbank and we will perform genomic epidemiology and evolutionary analyses where the fully assembled sequences are analyzed in the context of contemporary and historical IAV for determination of phylogenetic relationships, lineages, and reassortment. These analyses will be used to objectively select representative viruses and those with unique genetic characteristics for additional phenotypic testing. Avian or human IAV of potential risk to the swine population will be identified and IAV identified through public health investigations of zoonotic transmission events or from the animal health sector will be assessed for genetic signatures that may drive unique phenotypes. A novel software will be developed to analyze whole genome sequencing data in near real-time to determine evolutionary history and genetic novelty. Integrating the IAV-S data into global swine IAV genetic and antigenic analyses will occur biannually for the OFFLU WOAH/FAO Network of Expertise on Animal Influenza reports contributed to WHO Vaccine Consultation Meetings.