The impact and complete genome characterisation of viruses involved in outbreaks of gastroenteritis in a farrow-to-finish holding

Figure 1. Histopathological and immunohistochemical findings in PEDV (A–C) and RVA (D–F) infected piglets. Shortening, blunting and fusion of villi in PEDV-infected pigs were most pronounced in the jejunum, accompanied by marked submucosal oedema (A, asterisk) (A). In RVA-infected animals, lesions were also present in the colon, characterised by a moderate increase in the number of lymphocytes in the lamina propria, necrosis of individual surface epithelial cells, and oedema of the mesocolon. (HE 10×) (D). Positive IHC reaction (brown colour) to PEDV and RVA antigens was detected in the intestinal mucosa (jejunum, B, C and colon, E, F) (IHC 10x). Intracytoplasmic brown granular staining was seen in superficial enterocytes in PEDV (C, arrow) (jejunum, IHC 40×) and in crypts of Lieberkűhn of RVA infected animals (F, arrow) (colon, IHC 40x).

Figure 2. Phylogenetic relationship between PEDV-SeCoV recombinant strain and selected reference strains. The phylogenetic analysis was based on the S gene (A) and the complete genome (B) nucleotide sequence. The strain described in the present study is bolded and marked in red, while the branch in red designates the cluster of PEDV-SeCoV recombinant strains. The GenBank accession numbers of referent strains are designated within taxa. Both trees were generated by the NJ method and maximum composite likelihood model in MEGA 11 software. The branching stability of each phylogenetic tree was assessed by 1000 bootstrap replicates (values indicated adjacent to the nodes if > 0.7). The scale bar represents the number of substitutions per site.

Figure 3. Phylogenetic relationship between RVA strains based on the VP7 (A) and VP4 (B) genomic segments. The strain described in the present study is bolded and marked in red. All sequences are representative of the genotypes G3 (A) and P[23] (B). Human G3 lineages (Lineages I and IX) are annotated. The GenBank accession numbers of referent strains are designated within taxa. Based on the complete CDS, both trees were generated by the ML method and T92 + G + I model in MEGA 11 software. The branching stability of each phylogenetic tree was assessed by 1000 bootstrap replicates (values indicated adjacent to the nodes if > 0.7). The scale bar represents the number of substitutions per site. In displaying RVA strain nomenclature within taxa, the brackets for the P genotype were omitted for the sake of simplicity.

Figure 4. Phylogenetic relationship between RVB strains based on the VP7 (A) and VP4 (B) genomic segments. The strain described in the present study is bolded and marked in red, and corresponding novel genotypes G27 and P[6] are annotated in blue. The GenBank accession numbers of referent strains are designated within taxa. Based on the complete CDS, both trees were generated by the ML method and T92 + G + I (VP7) or HKY + G + I (VP4) model in MEGA 11 software. The branching stability of each phylogenetic tree was assessed by 1000 bootstrap replicates (values indicated adjacent to the nodes if > 0.7). The scale bar represents the number of substitutions per site. In displaying RVB strain nomenclature within taxa, the brackets for the P genotype were omitted for the sake of simplicity.

Figure 5. Phylogenetic relationship between PKV strains based on the complete genome nucleotide sequence. The strain described in the present study is bolded and marked in red. The GenBank accession numbers of referent strains are designated within taxa. The tree was generated by the ML method and GTR + G + I model in MEGA 11 software. The branching stability of each phylogenetic tree was assessed by 1000 bootstrap replicates (values indicated adjacent to the nodes if > 0.7). The scale bar represents the number of substitutions per site.

Figure 6. Seasonal indices (SI) for the average number of weaned pigs per saw in 2017–2019 timeframe. The SI (%) was calculated by comparing the average number of weaned pigs for every saw in each week (A) or month (B) to the average number in the respective week for all months (A) or in the respective month for all three years (B). A significant decrease in the number of weaned pigs per sow is indicated with an asterisk. All months were divided into four weeks, and four additional weeks over the year were added to the nearest week, and the average was calculated.