Unrevealed genetic diversity of GII Norovirus in the swine population of North East Italy

Figures

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  Figure 1. Density map (Kernel Density) of Veneto swine farms and distribution of NoV positive swine farms: 2018–2019. Green crosses identify the NoV positive fattening farms, dark blue crosses the NoV positive farrow to finish farms. The Kernel Density tool calculates the density of features in a neighbourhood around those features. The input data was the industrial swine farms in Veneto region and the density was calculated considering the potential capacity of each farm. The parameter used to calculate the density was a radius of 500 m and the raster cell of the analysis was 10 km2.

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  Figure 2. Phylogenetic analysis based on the RdRp nucleotide sequence. Maximum likelihood phylogenetic tree was obtained using PhyML 3.0. The subgroups of the Italian viruses described in this paper were highlighted in different colours. Numbers at the nodes indicate the bootstrap support values. Bootstrap values lower than 60% were omitted.

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  Figure 3. Unique amino acid mutations of Italian GII. P11 RdRp sequences. The figure displays the unique aa mutations of the Italian GII.P11 RdRp sequences, not present in any other GII sequences. The reference sequence used for the aa and nt numbering was: HQ392821.1_Norovirus/pig/GII/Ch6/China/2009. Mutations are reported with the one letter amino acid code. Dots are used to indicate the presence of the same aa for each sequence maintaining the same colour, while dashes indicate that genetic information in that position is not available. The last two rows reported the codon entropy calculated for the Genbank available GII.P11 NoVs and for the Italian GII.P11 samples described in this study. Colour intensity reflects entropy values. Na = not attributable.