Survey and Associated Risk Factors for the Presence of Ruminant Pestiviruses in Domestic Ovine and Caprine Populations from Kazakhstan

Figures

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  Figure 1. Sampling sites prevalence of BVDV/BDV antibodies per localities and settlements where RT-qPCR-positive animals were identified. The gradient of the green background reflects the density of the sheep and goat population. Blue circles indicate settlements included in serological analysis. The size of the blue circles represents BVDV/BDV seroprevalence levels within each settlement. Red triangles represent the locations where pestivirus shedding was confirmed through RT-qPCR or sequencing. Orange triangles represent settlements with no RT-qPCR-positive animals. The map was created using the geographic information system ArcMap software ver. 10.5.1 (Esri Inc., Redlands, CA, USA). The number of cattle per district was obtained from the official website of the Bureau of National Statistics of the Republic of Kazakhstan [27].

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  Figure 2. Risk map for pestiviral infections.

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  Figure 3. Phylogenetic analysis based on partial 5′UTR sequences (291–295 nt) of pestiviruses. A maximum-likelihood phylogenetic tree was constructed in MEGA X from alignments of fourteen partial 5′UTR sequences generated in this study and 34 database sequences using Kimura’s two-parameter method (K2+G model) [57]. The tree is drawn to scale, with the branch lengths representing the number of substitutions per site (the scale bar is present at the bottom of the phylogenetic tree). The percentage of replicated trees in which the associated taxa were clustered together in the bootstrap test (1000 replicates) is indicated at the nodes. The GenBank accession numbers are shown in parentheses. The Kazakhstani BVDV2 isolates determined in this study (marked with black circles (●)) are shown in blue or green rectangles, depending on their grouping. The asterisk is the reference genomes of BVDV1 [46] (GenBank: M31182), BVDV2 [47] (GenBank: LC006970), BDV [49] (GenBank reference sequence: NC_003679). The Pestivirus D strain was used as an outgroup.