Historical Evolutionary Dynamics and Phylogeography Analysis of Transmissible Gastroenteritis Virus and Porcine Deltacoronavirus: Findings from 59 Suspected Swine Viral Samples from China

Figures

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  Figure 1. Isolation and identification of TGEV and PDCoV. (a). RT-PCR was performed on the samples to ensure no other common viral contamination. (b). Isolation and passage of TGEV in ST cells (40×). (c). Isolation and passage of PDCoV in LLC-PK cells (40×).

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  Figure 2. Geographical distribution of TGEV and PDCoV around the world and in China. (a). Different colors characterize the distribution of TGEV in different countries. (b). Distribution of TGEV in China, different provinces were indicated by different colors. (c). Different colors characterize the distribution of PDCoV in different countries. (d). Distribution of PDCoV in China, different provinces were indicated by different colors.

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  Figure 3. ML tree and BI tree of TGEV and PDCoV. (a). ML tree of TGEV complete genome. (b). BI tree of TGEV complete genome. Different colors represented different genotypes. (c). ML tree of PDCoV complete genome. (d). BI tree of PDCoV complete genome. Different colors indicated different genotypes/lineages.

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  Figure 4. Demographic history of TGEV. (a). Demographic history was inferred via Bayesian skyline analysis. The median and 95% HPD intervals were plotted. (b). MCC tree of TGEV complete genome. Different colors represented different genotypes. The red dot indicates that the strain was sequenced in this study.

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  Figure 5. Demographic history of PDCoV. (a). Demographic history was inferred via Bayesian skyline analysis. The median and 95% HPD intervals were plotted. (b). MCC tree of PDCoV complete genome. Different colors represented different lineages (we merged early China lineage into China lineage). The red dot indicates that the strain was sequenced in this study.

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  Figure 6. BSSVS analysis of TGEV. (a). Phylogeographic reconstruction of estimated global spatial diffusion of TGEV. The curves and arrows indicate the direction and geographical location of TGEV migration (BF > 3, posterior probability > 0.5). The color and width of the curves represent the BF value and migration rate, respectively. (b). BF supports between the USA, China, and Mexico. (c). The histogram of TGEV migration changes for each location. (d). Migration rates for each supported migration route.

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  Figure 7. BSSVS analysis of PDCoV. (a). Phylogeographic reconstruction of estimated global spatial diffusion of PDCoV. The curves and arrows indicate the direction and geographical location of PDCoV migration (BF > 3, posterior probability > 0.5). The color and width of the curves represent the BF value and migration rate, respectively. (b). BF supports between China, Haiti, Japan, SK, Peru, and the USA. (c). The histogram of PDCoV migration changes for each location. (d). Migration rates for each supported migration route. South Korea, SK.

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  Figure 8. Structural display of the PDCoV S protein and the location of positive selection sites in the structure. (a). Surface representation of PDCoV S-trimer. (b). Cartoon representation of PDCoV S monomer. The S1 subunit is shown in red and S2 subunit in blue. Selected amino acids are presented as yellow spheres. (c). Hydrogen bond exists between Tyr 123 and nearby Ala 119 (shown in cyan). (d). Hydrogen bond exists between Ala 137 and Thr 136 (shown in cyan). (e). Ala 630 formed hydrogen bonds with Leu 626, Ser 634, and Gln 592, close to Leu 720 located in the fusion peptide (6.295 Å).