Epidemiologic and Genomic Characterizations of Porcine Kobuviruses in Diarrheic and Healthy Pigs

Figure 1. PKV genome amplification. The PCR amplicons of GDCZ2202-1606 sample covering the PKV genome using primers in Table 1 are presented. The PKV genome was divided into seven overlapping fragments. The size of each amplicon is shown.

Figure 2. Geographical distribution of PKV in China. Retrospective evaluation indicated that PKV has been detected in at least 26 provinces/cities of China. The six provinces with PKV-positive samples detected in this study are highlighted in dark blue, while the other provinces/cities with PKV sequences from GenBank are marked in light blue.

Figure 3. Multiple sequence alignment of PKV polyproteins. The aligned sequences include representative S-1-HUN and SH-W-CHN isolates and three PKV strains identified in this study. The aa insertion in VP1 is highlighted in yellow, while the 30 aa deletion in 3B is marked in pink. The proteins derived from the polyprotein are presented in distinct colors.

Figure 4. Phylogenetic tree based on 36 polyprotein-encoding sequences. The three species of kobuviruses are shown in distinct colors. Chinese PKV strains were clustered into three groups: SH-W-CHN-like, S-1-HUN-like and JXAT2015-like strains, respectively. All three PKV strains identified in this study are highlighted with blue squares. Each virus is shown by its name, GenBank accession number, country and year of isolation.

Figure 5. Recombination event detected in JSYZ1806-158 using SimPlot. The cross-over region is shown in the dashed line box, which is consistent with the result from RDP4. JX-2 is the major parental virus, while AH-42 is the minor parental virus for JSYZ1806-158. The y axis shows the percentage of permutated trees employing a sliding window of 500 bp and a step size of 20 bp. Other options, including Kimura (2-parameter) distance model, 2.0 Ts/Tv ratio, neighbor-joining tree model and 1000 Bootstrap replicates, are used.