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United States Department of Agriculture

Agricultural Research Service

Research Project: USDA SWINE INFLUENZA VIRUS SURVEILLANCE SYSTEM: COMPUTATIONAL EVOLUTIONARY BIOLOGY OF WHOLE GENOME SEQUENCES Title: Population dynamics of co-circulating swine influenza A viruses in the United States from 2009-2012

Authors
item Anderson, Tavis -
item Nelson, Martha -
item Kitikoon, Pravina
item Swenson, Sabrina -
item Korslund, John -
item Vincent, Amy

Submitted to: Influenza and Other Respiratory Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 2, 2013
Publication Date: December 1, 2013
Citation: Anderson, T.K., Nelson, M.I., Kitikoon, P., Swenson, S.L., Korslund, J.A., Vincent, A.L. 2013. Population dynamics of cocirculating swine influenza A viruses in the United States from 2009 to 2012. Influenza and Other Respiratory Viruses. 7(Suppl. 4):42-51.

Interpretive Summary: Understanding the dynamics of influenza A viruses (IAV) in the swine population is critical to understanding the evolution of influenza viruses overall. IAV genetic makeup continually changes and documenting the patterns of swine IAV genetic change is needed to monitor for possible emerging influenza threats. Our data provide a baseline characterization of swine IAV genetic diversity in the United States for 2009-2012. This paper aids in improving agricultural production and pandemic preparedness by allowing for the identification and a benchmark from which to measure success of better intervention strategies. These interventions include timely vaccine and diagnostic updates for use in swine and humans, as well as factors to prevent infection and transmission, such as changes in production practices or farm management.

Technical Abstract: Understanding the ecology and evolution of influenza A viruses (IAV) in mammalian hosts is critical to reduce disease burden in production animals and lower zoonotic infection risk in humans. Recent advances in influenza surveillance in United States swine populations allow for timely epidemiological, phylogenetic, and virological analyses that monitor emergence of novel viruses, and assess changes in viral population dynamics. To better understand IAV in the North American swine population, we undertook a phylogenetic analysis of 1075 HA, 1049 NA and 1040 M sequences of IAV isolated from U.S. swine during 2009-2012 through voluntary and anonymous submissions into the U.S. Department of Agriculture IAV swine surveillance system. Analyses revealed changes in population dynamics among multiple clades of A/H1N1, A/H3N2, and A/H1N2 co-circulating in U.S. swine populations during 2009-2012. Viral isolates were categorized into one of seven genetically and antigenically distinct hemagglutinin lineages: H1alpha, H1beta, H1gamma, H1delta1, H1delta2, H1pdm09 and H3 cluster IV. Over this period there was a dramatic increase in occurrence of H1delta1 in samples submitted, with a concurrent decrease in H1pdm09. H3 cluster-IV exhibited increasing diversification, warranting a re-evaluation of phylogenetic nomenclature criteria. Although H3N2 represented 25% of identified viruses, this subtype was reported in increasing proportion of sequenced isolates since late 2011. Surveillance of IAV in U.S. swine has progressed substantially since 2009, providing timely insight into co-circulating viral diversity, which may be used to inform intervention strategies.

Last Modified: 11/27/2014
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