Population dynamics of cocirculating swine influenza A viruses in the United States from 2009 to 2012

Abstract

BackgroundUnderstanding 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 US swine populations allow for timely epidemiological, phylogenetic, and virological analyses that monitor emergence of novel viruses and assess changes in viral population dynamics.MethodsTo 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 US swine during 2009–2012 through voluntary and anonymous submissions to the US Department of Agriculture IAV swine surveillance system.ResultsAnalyses revealed changes in population dynamics among multiple clades of A/H1N1, A/H3N2, and A/H1N2 cocirculating in US swine populations during 2009–2012. Viral isolates were categorized into one of seven genetically and antigenically distinct hemagglutinin lineages: H1α, H1β, H1γ, H1δ1, H1δ2, H1pdm09, and H3 cluster IV. There was an increase in occurrence of H1δ1 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.ConclusionsSurveillance and reporting of IAV in US swine have increased since 2009, and we demonstrate a period of expanded viral diversity. These data may be used to inform intervention strategies of vaccine and diagnostic updates and changes in swine health management.

Viable influenza A virus in airborne particles expelled during coughs versus exhalations

“…Although influenza is known to be transmitted through respiratory secretions containing the virus, infectious material can be passed from person to person in many different ways. The relative importance of the different pathways is uncertain and probably varies depending upon the setting, the severity of the illness, the characteristics of the viral strain, environmental conditions, and other factors 1. In order to choose the appropriate interventions to block the spread of the virus, it is necessary to understand which routes of transmission occur and when they are likely to be important.…”

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

“…Vaccines against IAV are routinely used in swine in the US; however, the continued presence of such a diverse population of swine H1 IAV may limit the effectiveness of these vaccines [19,[31][32][33]. Although we have no vaccination history corresponding with our virus genome data, it is plausible to suggest that the increase in the number of H1 clades plus varying genome patterns will further confound vaccine control efforts.…”

“…North Carolina in the southeast and Oklahoma in the southwest were shown to be sources of viruses of human seasonal H1-d lineages in a previous study [12], and these areas continue to have higher detections of the H1-d2 HA lineage, but there was no apparent trend for particular NA+internal gene combinations. However, the majority of the data used in this study rely upon passive surveillance conducted by the USDA [9,19], and consequently may reflect participation in that programme rather than the true number of genome patterns in circulation.…”

“…These data provide the opportunity to study evolutionary trends and variation of swine H1 IAV whole genomes. Prior studies have reported reassortment between endemic swine viruses and H1N1pdm09 [19][20][21][22]. In this work, we extended those analyses by collating and analysing publicly available whole-genome data from 2009 to 2016.…”

“…In 2009, the United States Department of Agriculture (USDA) initiated a national surveillance system for swine IAV, collecting virus isolates and sequencing HA, NA and M genes [19]. A subset of viruses maintained in the USDA IAV repository were also selected for whole-genome sequencing.…”