Molecular Characterization of Highly Pathogenic Avian Influenza Viruses H5N6 Detected in Denmark in 2018-2019

Abstract

Beginning in late 2017, highly pathogenic avian influenza (HPAI) H5N6 viruses caused outbreaks in wild birds and poultry in several European countries. H5N6 viruses were detected in 43 wild birds found dead throughout Denmark. Most of the Danish virus-positive dead birds were found in the period from February to April 2018. However, unlike the rest of Europe, sporadic HPAI H5N6-positive dead wild birds were detected in Denmark in July, August, September, and December 2018, with the last positive bird being found in January 2019. HPAI viruses were not detected in active surveillance of apparently healthy wild birds. In this study, we use full genome sequencing and phylogenetic analysis to investigate the wild bird HPAI H5N6 viruses found in Denmark. The Danish viruses were found to be closely related to those of contemporary HPAI H5N6 viruses detected in Europe. Their sequences formed two clusters indicating that at least two or more introductions of H5N6 into Denmark occurred. Notably, all viruses detected in the latter half of 2018 and in 2019 grouped into the same cluster. The H5N6 viruses appeared to have been maintained undetected in the autumn 2018.

Keywords: Europa; H5N6 subtype; birds; disease outbreaks; highly pathogenic avian influenza; infectious disease outbreak; influenza A virus; phylogeny; surveillance; wild.

Figure 1

Geographic distribution of 2.3.4.4b H5N6 HPAIV detections in Denmark and sample locations of the cross-sectional study. Every white, pink, or red point represents one wild bird found dead and infected with H5N6. The gradient from white to red points represents when in the year the detections occurred. The blue points represent the locations where pheasants were collected for the cross-sectional study. Map made with QGIS [35]. Outline of Denmark from Kortforsyningen (www.kortforsyningen.dk, downloaded 26 April 2012).

Figure 2

BEAST analysis on concatenated dataset including all European clade 2.3.4.4b H5N6 HPAIV detected in 2017–2019. All gene segments of the influenza viruses included in the analysis were concatenated. The H5N6 viruses isolated in Denmark are in red with the rest being in black. The viruses within the clock tree can be divided into two major clusters, which have been denoted as cluster 1 (blue) and cluster 2 (orange). The scale bar depicts a timeline.