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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Virus and Prion Research » Research » Publications at this Location » Publication #341611
Research Project: Intervention Strategies to Control Influenza A Virus Infection in Swine

Location: Virus and Prion Research

Title: The genomic evolution of H1 influenza A viruses from swine detected in the United States between 2009 and 2016

Author
item GAO, SHIBO - Iowa State University
item Anderson, Tavis
item WALIA, RASNA - Orise Fellow
item DORMAN, KARIN - Iowa State University
item JANAS-MARTINDALE, ALICIA - Animal And Plant Health Inspection Service (APHIS)
item Baker, Amy

Submitted to: Journal of General Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/6/2017
Publication Date: 8/1/2017
Citation: Gao, S., Anderson, T.K., Walia, R.R., Dorman, K.S., Janas-Martindale, A., Vincent, A.L. 2017. The genomic evolution of H1 influenza A viruses from swine detected in the United States between 2009 and 2016. Journal of General Virology. 98(8):2001-2010.

Interpretive Summary: The 2009 H1N1 swine-origin pandemic virus spread rapidly among humans, causing the first pandemic in over 40 years. Although the immediate origin of this virus was swine populations, it contained genes derived from avian, human, and swine influenza A virus (IAV) lineages. The H1N1pdm09 replaced the previous human seasonal H1N1, but in US swine populations, it is detected only at low levels mainly through repeated human-to-swine transmission. Despite seemingly low prevalence in swine, we provide evidence that the pandemic virus shared its genetic material with swine H1 IAV, generating many new genetic variants of viruses and novel gene segment combinations. The detection of genotypes was dynamic from year to year; some of the genotypes increased in frequency, whereas others decreased or ceased to be detected. We identified important changes in swine IAV diversity, which are important for control strategies for swine and for human pandemic preparedness.

Technical Abstract: Transmission of influenza A virus (IAV) from humans to swine occurs with relative frequency and is a critical contributor to swine IAV diversity. Subsequent to the introduction of these human seasonal lineages, there is often reassortment with endemic viruses and antigenic drift. To address whether particular genome constellations contributed to viral persistence following the introduction of the 2009 H1N1 human pandemic virus to swine in the USA, we collated and analyzed 616 whole genomes of swine H1 isolates. For each gene, sequences were aligned, the best-known maximum likelihood phylogeny was inferred, and each virus was assigned a clade based upon its evolutionary history. A time-scaled Bayesian approach was implemented for the hemagglutinin (HA) gene to determine the patterns of genetic diversity over time. From these analyses, we observed an increase in genome diversity across all H1 lineages and clades, with the H1-gamma and H1-delta1 genetic clades containing the greatest number of unique genome patterns. We documented 74 genome patterns from 2009 to 2016, of which 3 genome patterns were consistently detected at a significantly higher level than others across the entire time period. Eight genome patterns increased significantly while 5 genome patterns were shown to decline in detection over time. Viruses with genome patterns identified as persisting in the U.S. swine population may possess a greater capacity to infect and transmit in swine. This study highlights the emerging genetic diversity of U.S. swine IAV from 2009 to 2016 with implications for swine and public health and vaccine control efforts.