Cocirculation of Swine H1N1 Influenza A Virus Lineages in Germany

Figures

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  Figure 1. Distribution of swH1N1 isolates. Year of isolation of H1N1 strains sequenced in this study. Different clades are indicated.

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  Figure 2. Phylogenetic analyses of hemagglutinin (HA) and neuraminidase (NA) genes using Bayesian tree inference. Relevant lineages and sublineages are indicated. The scale bars indicate substitutions per site. The Wachtum/2014-like swH1pdmN1pdm are boxed. (a) Analysis of 950 HAH1 sequences of lineages 1A, 1B and 1C (Anderson-2016 nomenclature). Details are presented in Supplementary Figure S1. (b) Analysis of 577 NAN1 sequences. Details are presented in Supplementary Figure S2. Color code: green, EA swH1N1; light green, seasonal H1N1; olive, Schneiderkrug/2013-like swH1N1; purple, H1pdmN1pdm; magenta, H1pdmN2 reassortants; blue, swH1N2; light blue, Diepholz/2008-like swH1N2; black, classical swine H1N1; ochre, avian H1.

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  Figure 3. Distribution of Schneiderkrug/2013-like swH1N1 in Germany. Place and collection date of the first isolate is indicated.

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  Figure 4. Incursion of Wachtum/2014-like swH1pdmN1pdm into the German pig population. Dark squares indicate the places where isolates were collected; the place and sampling date of the first German isolate is printed in red. The inset presents the pig population density in Germany (gray shades correspond to the numbers of pigs per administrative district). The data were retrieved from the 2017-yearbooks of the 16 State Statistical Offices in Germany.

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  Figure 5. Evolution of German S-IAVs. Reassortment events leading to the main S-IAV lineages and the novel swH1N1 virus (presented in gray box) are shown. The Wachtum/2014-like swH1N1 are not shown here. Pictograms denote anthroponotic and spill-over infections. Asteriscs (*) indicate isolates with partial sequences.