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United States Department of Agriculture

Agricultural Research Service

Research Project: INTERVENTION STRATEGIES TO CONTROL VIRAL DISEASES OF SWINE

Location: Virus and Prion Research

Title: Current trends from the USDA influenza a virus in swine surveillance system

Author
item Walia, Rasna
item Anderson, Tavis
item Kassari, Ellen
item Janas-martindale, Alicia
item Schlitz, John
item Vincent, Amy

Submitted to: Pig Veterinary Society International Congress Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 3/1/2016
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: A U.S. national surveillance system for influenza A viruses (IAV) in swine was initiated in 2009 with increasing participation to the present day. The objectives are to monitor genetic evolution of IAV in swine, make isolates available for research, diagnostic reagents, and vaccine development through an IAV repository, and provide publically available sequence data for animal and human health purposes. These data can be used to investigate patterns of virus evolution or movement, regional differences, and temporal changes. We report analyses of IAV isolated from fiscal years 2014-15 (FY14-15) since earlier data were reported previously. Materials and Methods: Routine samples submitted for diagnostic investigation of respiratory disease are included in the USDA system through the National Animal Health Laboratory Network. Testing includes RT-PCR screening for IAV, subtyping RT-PCR, virus isolation, and sequencing of the HA, NA, and M genes. Whole genome sequencing is conducted on a subset of viruses each month. Sequences are deposited into GenBank and phylogenetic analyses of available HA, NA, and M genes from viruses isolated in FY14-15 were performed. Results: Approximately 15,000 accessions were submitted during FY14-15 and approximately 1600 viruses isolated with sequences available in GenBank. Phylogenetic analyses revealed changes in dynamics among multiple clades of H1N1, H3N2, and H1N2 co-circulating in U.S. swine. Sequences were categorized into clades based on the HA genes: H1alpha, H1beta, H1gamma, H1delta1, H1delta2, H1pdm09, H3 IVA-F or human seasonal H3; and NA genes: classical N1, H1pdm09 N1, 1998-N2, 2002-N2, or human seasonal N2. The predominant HA and NA clade combinations during this period were H1'/classical N1, H3 IVA/ 2002-N2, H1d1/2002-N2. However, the major genotypes did not replace the minor genotypes that continued to persist at low or sporadic levels. The H1N1pdm09 M gene was exclusively detected in all genotypes. Notable was the continued detection of an emerging IAV with a contemporary human seasonal H3 and swine classical N1 or 2002-N2. Some differences between regions were observed which suggest that regional decisions on vaccine components could be considered. Conclusion: Surveillance and reporting of IAV in U.S. swine has increased dramatically since 2009, and we demonstrated continued genetic diversity, regional trends, and detection of emerging lineages in FY14-15. These results can inform vaccine strain selection and potential need for diagnostic updates. Furthermore, monitoring viral temporal and spatial patterns may indicate a need for changes in production practices that facilitate viral migration between and within U.S. states and regions.

Last Modified: 10/19/2017
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