Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013

Abstract

The emergence in humans of the A(H1N1)pdm09 influenza virus, a complex reassortant virus of swine origin, highlighted the importance of worldwide influenza virus surveillance in swine. To date, large-scale surveillance studies have been reported for southern China and North America, but such data have not yet been described for Europe. We report the first large-scale genomic characterization of 290 swine influenza viruses collected from 14 European countries between 2009 and 2013. A total of 23 distinct genotypes were identified, with the 7 most common comprising 82% of the incidence. Contrasting epidemiological dynamics were observed for two of these genotypes, H1huN2 and H3N2, with the former showing multiple long-lived geographically isolated lineages, while the latter had short-lived geographically diffuse lineages. At least 32 human-swine transmission events have resulted in A(H1N1)pdm09 becoming established at a mean frequency of 8% across European countries. Notably, swine in the United Kingdom have largely had a replacement of the endemic Eurasian avian virus-like ("avian-like") genotypes with A(H1N1)pdm09-derived genotypes. The high number of reassortant genotypes observed in European swine, combined with the identification of a genotype similar to the A(H3N2)v genotype in North America, underlines the importance of continued swine surveillance in Europe for the purposes of maintaining public health. This report further reveals that the emergences and drivers of virus evolution in swine differ at the global level.

Importance: The influenza A(H1N1)pdm09 virus contains a reassortant genome with segments derived from separate virus lineages that evolved in different regions of the world. In particular, its neuraminidase and matrix segments were derived from the Eurasian avian virus-like ("avian-like") lineage that emerged in European swine in the 1970s. However, while large-scale genomic characterization of swine has been reported for southern China and North America, no equivalent study has yet been reported for Europe. Surveillance of swine herds across Europe between 2009 and 2013 revealed that the A(H1N1)pdm09 virus is established in European swine, increasing the number of circulating lineages in the region and increasing the possibility of the emergence of a genotype with human pandemic potential. It also has implications for veterinary health, making prevention through vaccination more challenging. The identification of a genotype similar to the A(H3N2)v genotype, causing zoonoses at North American agricultural fairs, underlines the importance of continued genomic characterization in European swine.

FIG 1

swIAV genotypes isolated from European swine between 2009 and 2013. The 23 distinct genetic constellations are labeled A to W, with the lineage of origin for each segment indicated by a colored block.

FIG 2

Frequencies of the swIAV genotypes across Europe. (Upper panel) Pie charts indicate the proportions of samples isolated in each country that were either EA H1N1 (dark green) or A(H1N1)pdm09 (dark red) or contained either an EA IGC (light green) or a pdm09 IGC (light red). Isolates whose IGC contained both EA and pdm09 segments are colored gray. The sizes of the pie charts reflect the number of samples used for analysis from each country as follows: Belgium, 24; Denmark, 17; Finland, 2; France, 47; Germany, 38; Hungary, 6; Italy, 42; The Netherlands, 30; Norway, 1; Poland, 11; Spain, 28; Sweden, 2; United Kingdom, 41. For clarity, the data for Israel [n = 1; A(H1N1)pdm09 (pdm09)] are not shown. IGC, internal gene cassette. (Panels A to R) Relative frequencies of the six most prevalent swIAV genotypes in countries across Europe. Each genotype is specified as described for Fig. 1. The intensity of the color in each panel reflects the relative frequency of the genotype in that country. Countries that provided no samples are not outlined. Numbers in parentheses indicate the number of countries each genotype was isolated from. Maps were created using Tableau version 9.0.0.

FIG 3

Comparison of swIAV genotypes isolated in the United Kingdom (A) and mainland Europe (B). Bar charts are colored according to the corresponding genotypes, with genotypes specified as given in Fig. 1. The six most prevalent genotypes are shown separately, with the remaining genotypes clustered according to the lineage of the corresponding internal gene cassettes.

FIG 4

Phylogeny of the Scot/94 lineage N2 gene inferred using Bayesian analysis. Taxa sequenced by members of the ESNIP3 consortium are highlighted in red, while those in black were obtained from the Influenza Virus Resource. Colored squares to the right of each taxon name indicate the corresponding genotypes, with coloring and segment order as described for Fig. 1. White squares indicate that no sequence was available for that segment. Posterior probabilities are given at selected nodes. Colored highlights indicate well-supported circulating clades. The scale bar is given in numbers of substitutions per site.

FIG 5

Phylogeny of the Gent/84 lineage N2 gene inferred using Bayesian analysis. Posterior probabilities are given at selected nodes, and the scale bar is given in numbers of substitutions per site. See Fig. 4 legend for other details.