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Displacement of the Gent/1999 human-like swine H1N2 influenza A virus lineage by novel H1N2 reassortants in Germany

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Abstract

A swine influenza survey was conducted between 2003 and 2015 in Germany. During this period, 8122 snout swabs or other respiratory specimens from pigs of 5178 herds, mainly from Germany, were investigated for the presence of swine influenza A virus (S-IAV). In total, 1310 S-IAV isolates were collected. Of this collection, the complete genome of 267 H1N2 S-IAV isolates was sequenced and phylogenetically analyzed. The data demonstrate the incursion of human-like swine H1N2 viruses (Gent/1999-like) in 2000 and prevalent circulation until 2010. From 2008 onward, a sustained and broad change of the genetic constellation of the swine H1N2 subtype commenced. The Gent/1999-like swine H1N2 viruses ceased and several new swine H1N2 reassortants emerged and became prevalent in Germany. Of these, the upsurge of the Diepholz/2008-like, Emmelsbuell/2009-like and Papenburg/2010-like viruses is notable. The data reveal the importance of reassortment events in S-IAV evolution. The strong circulation of S-IAV of different lineages in the swine population throughout the year underlines that pigs are important reservoir hosts.

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Acknowledgements

The authors thank M. Müller, I. Heinze and I. Görlich for technical assistance, and S. Bergmann, S. Motzke and C. Steglich for their contributions. Further, we are indebted to I. Brown, M. Büttner, R. Heckler, L. Larsen, C. Linne-Jonas, I. Markowska-Daniel, S. Pleschka, G. Simon, K. van Reeth, J. Süß, O. Werner and members of FluResearchNet for providing influenza virus isolates, and all veterinarians and swine holders who submitted samples to the partner laboratories.

Funding

This study was funded by the German Federal Ministry of Education and Research within the framework of the FluResearchNet (grant nos. 01KI7142, 01KI07143 awarded to R.Z. and 01KI1006J awarded to R.D.) and by the European Union FP7-INFLUENZA-2010 ESNIP3 programme (grant #259949 awarded to R.D.). The sponsors had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Author notes

  1. Andi Krumbholz

    Present address: Institute of Infection Medicine, Kiel University and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany

  2. Jeannette Lange

    Present address: Paul-Ehrlich-Institut, 63225, Langen, Germany

  3. Anja Philipps

    Present address: Thermo Fisher Scientific GENEART GmbH, 93059, Regensburg, Germany

  4. Ralf Dürrwald

    Present address: Robert Koch Institute, 13353, Berlin, Germany

  5. Roland Zell and Ralf Dürrwald contributed equally.

Authors and Affiliations

  1. Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University Jena, 07745, Jena, Germany

    Roland Zell, Andi Krumbholz, Jeannette Lange, Anja Philipps & Ralf Dürrwald

  2. CF DNA Sequencing, Leibniz Institute on Aging, Fritz Lipmann Institute, 07745, Jena, Germany

    Marco Groth

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  1. Roland Zell
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Contributions

R.D. designed surveillance and conducted serological investigations, PCR diagnostics and virus isolation; M.G., A.P., J.L., A.K., R.Z. sequenced virus strains; R.Z. conducted phylogenetic analyses; R.Z., A.K., R.D. drafted the manuscript. All authors read the final manuscript.

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Correspondence to Roland Zell.

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Zell, R., Groth, M., Krumbholz, A. et al. Displacement of the Gent/1999 human-like swine H1N2 influenza A virus lineage by novel H1N2 reassortants in Germany. Arch Virol 165, 55–67 (2020). https://doi.org/10.1007/s00705-019-04457-w

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