Molecular epidemiology and evolution of influenza viruses circulating within European swine between 2009 and 2013

Title: Molecular epidemiology and evolution of influenza viruses circulating within European swine between 2009 and 2013
Authors: Watson, SJ
Langat, P
Reid, SM
Lam, TT-Y
Cotten, M
Kelly, M
Van Reeth, K
Qiu, Y
Simon, G
Bonin, E
Foni, E
Chiapponi, C
Larsen, L
Hjulsager, C
Markowska-Daniel, I
Urbaniak, K
Duerrwald, R
Schlegel, M
Huovilainen, A
Davidson, I
Dan, A
Loeffen, W
Edwards, S
Bublot, M
Vila, T
Maldonado, J
Valls, L
Brown, IH
Pybus, OG
Kellam, P
Item Type: Journal Article
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.
Issue Date: 1-Oct-2015
Date of Acceptance: 14-Jul-2015
ISSN: 1098-5514
Publisher: American Society for Microbiology
Start Page: 9920
End Page: 9931
Journal / Book Title: Journal of Virology
Volume: 89
Issue: 19
Copyright Statement: © 2015 Watson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license (
Keywords: Science & Technology
Life Sciences & Biomedicine
Epidemiological Monitoring
Evolution, Molecular
Influenza A Virus, H1N1 Subtype
Influenza A Virus, H1N2 Subtype
Influenza A Virus, H3N2 Subtype
Influenza A virus
Influenza, Human
Molecular Epidemiology
Orthomyxoviridae Infections
Reassortant Viruses
Sus scrofa
Swine Diseases
ESNIP3 Consortium
06 Biological Sciences
07 Agricultural and Veterinary Sciences
11 Medical and Health Sciences
Publication Status: Published
Online Publication Date: 2015-09-01
Appears in Collections:Department of Medicine
Faculty of Medicine

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