Spatio-temporal distribution and international context of bovine viral diarrhoea virus genetic diversity in France

Figures

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  Figure 1. Geographical and temporal distribution of Bovine viral diarrhoea virus samples in this study and cattle density. A Map of France showing department administrative subdivision. The colour gradient indicates cattle density km−2 extracted from Robinson et al. [56]. B Spatial distribution of sample collection. Black circles represent the number of samples collected in each department. The map is coloured according to French administrative regions and was plotted using the R package sf [79]. C Temporal distribution of samples. The number of samples over time is presented in two panels, according to the level of precision of the metadata available for each sample: month and year of collection (top panel) or period only (bottom panel). Bar charts are coloured according to French administrative regions.

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  Figure 2. Phylogenetic relationships between French and international sequences of BVDV-1 genotypes 1e and 1b. Maximum likelihood phylogenetic trees inferred from French and international sequences of genotypes (A) 1e and (B) 1b. Tips are coloured according to the sample continent or country of origin and sizes represent the number of closely related publicly available sequences (99.5% identity) from the same location. European countries with less than ten sequences were grouped under the location “Europe” in 1e phylogeny.

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  Figure 3. Temporal and spatial distribution of BVDV-1 genotypes in France. A Proportion of genotypes over time in France. Genotyping data include current and previous studies (1994–1998: Vilček et al., 2001 [13], 2004–2005: Jackova et al., 2008 [12]; 2018–2020: Rivas et al., 2022 [10]). Rare genotypes (1r, 1s, 1k, 1i) were grouped. Numbers at the top of bar charts indicate the total number of samples for each period. B Proportion of each genotype per French department over the 2011–2023 period. Genotyping data includes current study and those from Rivas et al. [10]. Pie charts denote genotype proportions per department and sizes are proportional to the number of samples. Black boxes show the location of the three focused regions: Bretagne, Normandie and Auvergne-Rhône-Alpes.

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  Figure 4. Spatial distribution and local structure of BVDV-1 genotypes in three focused French regions. Proportions of BVDV-1 genotypes at local scale in (A) Bretagne, (B) Normandie (B) and (C) Auvergne-Rhône-Alpes. Pie charts denote genotype proportions per farm postal code and sizes are proportional to the number of samples. A small amount of random variation was added to each pie chart location to ensure anonymity. Grey lines outline department borders. D Mantel correlograms measuring correlations between phylogenetic and geographical distances for the three focused regions. Each dot is positioned in the middle of a distance class. Statistically significant correlations are indicated by a square.