Novel reassortant swine H3N2 influenza A viruses in Germany

Roland Zell,Anja Philipps,Andi Krumbholz,Ralf Dürrwald,Jeannette Lange,Marco Groth

doi:10.1038/s41598-020-71275-5

Abstract

Analysis of 228 H3N2 swine influenza A virus isolates collected between 2003 and 2015 in Germany revealed important changes in molecular epidemiology. The data indicate that a novel reassortant, Rietberg/2014-like swine H3N2, emerged in February 2014 in Northern Germany. It is comprised of a hemagglutinin gene of seasonal H3N2 (A/Denmark/129/2005-like), a neuraminidase gene of Emmelsbuell/2009-like swine H1N2 and the internal gene cassette of pandemic H1N1 viruses. Together with Danish swine H3N2 strains of 2013–2015 with identical genome layout, the Rietberg/2014-like viruses represent a second swine H3N2 lineage which cocirculates with a variant of the Gent/1984-like swine H3N2 lineage. This variant, named Gent1984/Diepholz-like swine H3N2, has a Gent/1984-like HA and a Diepholz/2008-like NA; the origin of the internal gene cassette likely derived from avian-like swine H1N1. The first isolate of the Gent1984/Diepholz reassortant emerged in Northern Germany in September 2011 whereas the last German Gent/1984-like isolate was collected in October 2011.

Highlights

Analysis of 228 H3N2 swine influenza A virus isolates collected between 2003 and 2015 in Germany revealed important changes in molecular epidemiology
Adaptation to specific hosts and geographic isolation are the main drivers that led to the evolution of sublineages and alleles of all IAV gene segments, which have been described in a previous study by Lu et al.[4]
Our influenza A viruses (IAV-S) archive included 13 swH3N2 isolates that were obtained from other sources

Summary

Introduction

Analysis of 228 H3N2 swine influenza A virus isolates collected between 2003 and 2015 in Germany revealed important changes in molecular epidemiology. The data indicate that a novel reassortant, Rietberg/2014-like swine H3N2, emerged in February 2014 in Northern Germany It is comprised of a hemagglutinin gene of seasonal H3N2 (A/Denmark/129/2005-like), a neuraminidase gene of Emmelsbuell/2009-like swine H1N2 and the internal gene cassette of pandemic H1N1 viruses. A subsequent analysis of 290 IAV-S isolates collected from 14 European countries revealed a remarkable genetic diversity[2] This is the result of (i) reassortment events upon multiple infection, and (ii) ecological factors, e.g. a broad host range of IAV which allows a limited exchange of virus between aquatic fowl (main hosts), poultry, pigs, humans, and horses. Genome sequencing and genetic analysis of 267 swH1N2 isolates collected during a 13-year long-term swine influenza surveillance in Germany revealed the replacement of the previously prevalent European continental hu-like swH1N2 by four novel swH1N2 reassortants named Diepholz/2008-like, Emmelsbuell/2009-like, Papenburg/2010-like and Gladau/2012-like swH1N2. The continental hu-like swH3N2 viruses (Gent/1984-like) were replaced by a variant swH3N2 with a similar gene constellation in Germany

Methods

Results

Conclusion