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

  • Roland ZellEmail author
  • Marco Groth
  • Andi Krumbholz
  • Jeannette Lange
  • Anja Philipps
  • Ralf Dürrwald
Original Article


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.



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.

Author 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.


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.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

705_2019_4457_MOESM1_ESM.pdf (7.3 mb)
Supplementary material 1 (PDF 7505 kb)


  1. 1.
    McCauley JW, Hongo S, Kaverin NV, Kochs G, Lanb RA, Matrosovich MN, Perez DR, Palese P, Presti RM, Rimstad E, Smith GJD (2012) Family Orthomyxoviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus Taxonomy. Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, Amsterdam, pp 749–761Google Scholar
  2. 2.
    Zell R, Scholtissek C, Ludwig S (2013) Genetics, evolution, and the zoonotic capacity of European swine influenza viruses. Curr Top Microbiol Immunol 370:29–55PubMedGoogle Scholar
  3. 3.
    Wu Y, Wu Y, Tefsen B, Shi Y, Gao GF (2014) Bat-derived influenza-like viruses H17N10 and H18N11. Trends Microbiol 22:183–191PubMedCrossRefGoogle Scholar
  4. 4.
    Webster RG, Bean WJ, Gorman WT, Chambers TM, Kawaoka Y (1992) Evolution and ecology of influenza A viruses. Microbiol Rev 56(1):152–179PubMedPubMedCentralGoogle Scholar
  5. 5.
    Lu G, Rowley T, Garten R, Donis RO (2007) FluGenome: a web tool for genotyping influenza A virus. Nucl Acids Res 35:W275–W279PubMedCrossRefGoogle Scholar
  6. 6.
    Zhou NN, Senne DA, Landgraf JS, Swenson SL, Erickson G, Rossow K, Liu L, Yoon KJ, Krauss S, Webster RG (1999) Genetic reassortment of avian, swine, and human influenza A viruses in American pigs. J Virol 73:8851–8856PubMedPubMedCentralGoogle Scholar
  7. 7.
    Olsen CW (2002) The emergence of novel swine influenza viruses in North America. Virus Res 85:199–210PubMedCrossRefPubMedCentralGoogle Scholar
  8. 8.
    Brown IH, Harris PA, McCauley JW, Alexander DJ (1998) Multiple genetic reassortment of avian and human influenza A viruses in European pigs, resulting in the emergence of an H1N2 virus of novel genotype. J Gen Virol 79:2947–2955PubMedCrossRefPubMedCentralGoogle Scholar
  9. 9.
    Van Reeth K, Brown IH, Pensaert M (2000) Isolations of H1N2 influenza A virus from pigs in Belgium. Vet Rec 146:588–589PubMedCrossRefPubMedCentralGoogle Scholar
  10. 10.
    Schrader C, Suss J (2003) Genetic characterization of a porcine H1N2 influenza virus strain isolated in Germany. Intervirology 46:66–70PubMedCrossRefPubMedCentralGoogle Scholar
  11. 11.
    Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, Okomo-Adhiambo M, Gubareva L, Barnes J, Smith CB, Emery SL, Hillman MJ, Rivailler P, Smagala J, de Graaf M, Burke DF, Foucher RAM, Pappas C, Alpuche-Aranda CM, Lopez-Gatell H, Olivera H, Lopez I, Myers CA, Faix D, Blair PJ, Yu C, Keene KM, Dotson PD Jr, Boxrud D, Sambol AR, Abid SH, St George K, Bannerman T, Moore AL, Stringer DJ, Blevins P, Demmler-Harrison GJ, Ginsberg M, Kriner P, Waterman S, Smole S, Guevara HF, Belongia EA, Clark PA, Beatrice ST, Donis R, Katz J, Finelli L, Bridges CB, Shaw M, Jernigan DB, Uyeki TM, Smith DJ, Klimov AI, Cox N (2009) Antigenic and genetic characterization of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 325:197–201PubMedPubMedCentralCrossRefGoogle Scholar
  12. 12.
    Smith GJD, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, Peiris JSM, Guan Y, Rambaut A (2009) Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459:1122–1125CrossRefGoogle Scholar
  13. 13.
    Moreno A, Di Trani L, Alborali L, Vaccari G, Barbieri I, Falcone E, Sozzi E, Puzelli S, Ferri G, Cordioli P (2010) First pandemic H1N1 outbreak from a pig farm in Italy. Open Virol J 4:52–56PubMedPubMedCentralCrossRefGoogle Scholar
  14. 14.
    Vijaykrishna D, Poon LLM, Zhu HC, Ma SK, Li OTW, Cheung CL, Smith GJD, Peiris JSM, Guan Y (2010) Reassortment of pandemic H1N1/2009 influenza A virus in swine. Science 328:1529PubMedPubMedCentralCrossRefGoogle Scholar
  15. 15.
    Welsh MD, Baird PM, Guelbenzu-Gonzalo MP, Hanna A, Reid SM, Essen S, Russell C, Thomas S, Barrass L, McNeilly F, McKillen J, Todd D, Harkin V, McDowell S, Choudhury B, Irvine RM, Borobia J, Grant J, Brown IH (2010) Initial incursion of pandemic (H1N1) 2009 influenza A virus into European pigs. Vet Rec 166:642–645PubMedCrossRefPubMedCentralGoogle Scholar
  16. 16.
    Ducatez MF, Hause B, Stigger-Rosser E, Darnell D, Corzo C, Juleen K, Simonson R, Brockwell-Staats C, Rubrum A, Wang D, Webb A, Crumpton JC, Lowe J, Gramer M, Webby RJ (2011) Multiple reassortment between pandemic (H1N1) 2009 and endemic influenza viruses in pigs, United States. Emerg Infect Dis 17:1624–1629PubMedPubMedCentralCrossRefGoogle Scholar
  17. 17.
    Hoen SC, Strugnell BW, Russell C, Barrass L, Reid SM, Brown IH (2011) Reassortant pandemic (H1N1) 2009 virus in pigs, United Kingdom. Emerg Infect Dis 17(6):1049–1052CrossRefGoogle Scholar
  18. 18.
    Moreno A, Di Trani L, Faccini S, Vaccari G, Nigrelli D, Boniotti MB, Falcone E, Boni A, Chiapponi C, Sozzi E, Cordioli P (2011) Novel H1N2 swine influenza reassortant strain in pigs derived from the pandemic H1N1/2009 virus. Vet Microbiol 149:472–477PubMedCrossRefGoogle Scholar
  19. 19.
    Starick E, Lange E, Fereidouni S, Bunzenthal C, Höveler R, Kuczka A, Grosse Beilage E, Hamann HP, Klingelhöfer I, Steinhauer D, Vahlenkamp T, Beer M, Harder T (2011) Reassorted pandemic (H1N1) 2009 influenza A viruses discovered from pigs in Germany. J Gen Virol 92:1184–1188PubMedCrossRefGoogle Scholar
  20. 20.
    Liang H, Lam TTY, Fan X, Chen X, Zeng Y, Zhou J, Duan L, Tse M, Chan CH, Li L, Leung TY, Yip CH, Cheung CL, Zhou B, Smith DK, Poon LLM, Peiris M, Guan Y, Zhu H (2014) Expansion of genotypic diversity and establishment of 2009 H1N1 pandemic-origin internal genes in pigs in China. J Virol 88:19864–19874Google Scholar
  21. 21.
    Lange J, Groth M, Schlegel M, Krumbholz A, Wieczorek K, Ulrich R, Köppen S, Schulz K, Appl D, Selbitz HJ, Sauerbrei A, Platzer M, Zell R, Dürrwald R (2013) Reassortment of the pandemic (H1N1) 2009 virus and establishment of a novel porcine H1N2 influenza virus lineage in Germany. Vet Microbiol 167:345–356PubMedCrossRefPubMedCentralGoogle Scholar
  22. 22.
    Zell R, Bergmann S, Krumbholz A, Wutzler P, Dürrwald R (2008) Ongoing evolution of swine influenza viruses: a novel reassortant. Arch Virol 153:2085–2092PubMedCrossRefPubMedCentralGoogle Scholar
  23. 23.
    Zell R, Motzke S, Krumbholz A, Wutzler P, Herwig V, Dürrwald R (2008) Novel reassortant of swine influenza H1N2 virus in Germany. J Gen Virol 89:271–276PubMedCrossRefPubMedCentralGoogle Scholar
  24. 24.
    Krumbholz A, Schmidtke M, Bergmann S, Motzke S, Bauer K, Stech J, Dürrwald R, Wutzler P, Zell R (2009) High prevalence of amantadine resistance among circulating European porcine influenza A viruses. J Gen Virol 90:900–908PubMedCrossRefPubMedCentralGoogle Scholar
  25. 25.
    Lange J, Groth M, Kanrai P, Pleschka S, Scholtissek C, Dürrwald R, Platzer M, Sauerbrei A, Zell R (2014) Circulation of classical swine influenza virus in Europe between the wars? Arch Virol 159:1467–1473PubMedCrossRefPubMedCentralGoogle Scholar
  26. 26.
    Stech J, Stech O, Herwig A, Altmeppen H, Hundt J, Gohrbandt S, Kreibich A, Weber S, Klenk HD, Mettenleiter TC (2008) Rapid and reliable universal cloning of influenza A virus genes by target-primed plasmid amplification. Nucl Acids Res 36:e139PubMedCrossRefPubMedCentralGoogle Scholar
  27. 27.
    Groth M, Lange J, Kanrai P, Pleschka S, Scholtissek C, Krumbholz A, Platzer M, Sauerbrei A, Zell R (2014) The genome of an influenza virus from a pilot whale: Relation to influenza viruses of gulls and marine mammals. Infect Genet Evol 24:183–186PubMedCrossRefPubMedCentralGoogle Scholar
  28. 28.
    Tamura K, Peterson D, Peterson N (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574PubMedCrossRefPubMedCentralGoogle Scholar
  30. 30.
    Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUTi and the BEAST 1.7. Mol Biol Evol 29:1969–1973PubMedPubMedCentralCrossRefGoogle Scholar
  31. 31.
    Rozas J, Sanches-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497PubMedCrossRefGoogle Scholar
  32. 32.
    Anderson TK, Macken CA, Lewis NS, Scheuermann RH, Van Reeth K, Brown IH, Swenson SL, Simon G, Saito T, Berhane Y, Ciacci-Zanella J, Pereda A, Davis CT, Donis RO, Webby RJ, Vincent AL (2016) A phylogeny-based global nomenclature system and automated annotation tool for H1 hemagglutinin genes from swine influenza A viruses. mSphere 1(6):e00275–16PubMedPubMedCentralCrossRefGoogle Scholar
  33. 33.
    Watson SJ, Langat P, Reid SM, Lam TTY, 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, Dürrwald R, Schlegel M, Huovilainen A, Davidson I, Dan A, Loeffen W, Edwards S, Bublot M, Vila T, Maldonado J, Valls L, ESNIP3 Consortium, Brown IH, Pybus OG, Kellam P (2015) Molecular epidemiology and evolution of influenza viruses circulating within European swine between 2009 and 2013. J Virol 89(19):9920–9931PubMedPubMedCentralCrossRefGoogle Scholar
  34. 34.
    Moreno A, Chiapponi C, Boniotti MB, Sozzi E, Foni E, Barbieri I, Zanoni MG, Faccini S, Lelli D, Cordioli P (2012) Genomic characterization of H1N2 swine influenza viruses in Italy. Vet Microbiol 156(3–4):265–276PubMedCrossRefPubMedCentralGoogle Scholar
  35. 35.
    Campitelli L, Donatelli I, Foni E, Castrucci MR, Fabiani C, Kawaoka Y, Krauss S, Webster RG (1997) Continued evolution of H1N1 and H3N2 influenza viruses in pigs in Italy. Virology 232:310–318PubMedCrossRefGoogle Scholar
  36. 36.
    Harder TC, Grosse Beilage E, Lange E, Meiners C, Döhring S, Pesch S, Noe T, Grund C, Beer M, Starick E (2013) Expanded cocirculation of stable subtypes, emerging lineages, and new sporadic reassortants of porcine influenza viruses in swine populations in Northwest Germany. J Virol 87(19):10460–10476PubMedPubMedCentralCrossRefGoogle Scholar
  37. 37.
    Krumbholz A, Philipps A, Oehring H, Schwarzer K, Eitner A, Wutzler P, Zell R (2011) Current knowledge on PB1-F2 of influenza A viruses. Med Microbiol Immunol 200:69–75PubMedCrossRefPubMedCentralGoogle Scholar
  38. 38.
    Bálint A, Metreveli G, Widén F, Zohari S, Berg M, Isaksson M, Renström LH, Wallgren P, Belák S, Segall T, Kiss I (2009) The first Swedish H1N2 swine influenza virus isolate represents an uncommon reassortant. Virol J 6:180PubMedPubMedCentralCrossRefGoogle Scholar
  39. 39.
    Metreveli G, Emmoth E, Zohari S, Bálint A, Widén F, Muradrasoli S, Wallgren P, Belák S, Leblanc N, Berg M, Kiss I (2011) Comparison of two H1N2 swine influenza A viruses from disease outbreaks in pigs in Sweden during 2009 and 2010. Virus Genes 42(2):236–244PubMedCrossRefPubMedCentralGoogle Scholar
  40. 40.
    Brown IH (2013) History and epidemiology of swine influenza in Europe. Curr Top Microbiol Immunol 370:133–146PubMedPubMedCentralGoogle Scholar
  41. 41.
    Bhatt S, Lam TT, Lycett SJ, Leigh Brown AJ, Bowden TA, Holmes EC, Guan Y, Wood JLN, Brown IH, Kellam P, Combating Swine Influenza Consortium, Pybus OG (2013) The evolutionary dynamics of influenza A virus adaptation to mammalian hosts. Phil Trans R Soc B 368:20120382PubMedCrossRefPubMedCentralGoogle Scholar
  42. 42.
    Bedford T, Riley S, Barr IG, Broor S, Chadha M, Cox NJ, Daniels RS, Gunasekaran CP, Hurt AC, Kelso A, Klimov A, Lewis NS, Li Y, McCauley JW, Odagiri T, Potdar V, Rambaut A, Shu Y, Skepner E, Smith DJ, Suchard MA, Tashiro M, Wang D, Xu X, Lemey P, Russell CA (2015) Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nature 523:217–220PubMedPubMedCentralCrossRefGoogle Scholar
  43. 43.
    Lyons DM, Lauring AS (2018) Mutation and epistasis in influenza virus evolution. Viruses 10:407PubMedCentralCrossRefGoogle Scholar
  44. 44.
    Krumbholz A, Lange J, Dürrwald R, Walther M, Müller TH, Kühnel D, Wutzler P, Sauerbrei A, Zell R (2014) Prevalence of antibodies to European porcine influenza viruses in humans living in high pig density areas of Germany. Med Microbiol Immunol 203(1):13–24PubMedCrossRefPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Section of Experimental Virology, Institute for Medical Microbiology, Jena University HospitalFriedrich Schiller University JenaJenaGermany
  2. 2.CF DNA Sequencing, Leibniz Institute on Aging, Fritz Lipmann InstituteJenaGermany
  3. 3.Institute of Infection MedicineKiel University and University Medical Center Schleswig-HolsteinKielGermany
  4. 4.Paul-Ehrlich-InstitutLangenGermany
  5. 5.Thermo Fisher Scientific GENEART GmbHRegensburgGermany
  6. 6.Robert Koch InstituteBerlinGermany

Personalised recommendations