Molecular epidemiology and phylodynamic analysis of enterovirus 71 in Beijing, China, 2009–2019

Figures

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  Fig. 1. Time-scaled phylogeographic history of EV71 in Beijing from 2009 to 2019. A: The MCC phylogenetic tree was constructed base on the VP1 coding region in Beijing and colored according to the different years. B: Genetic diversity of EV71 VP1 sequences in Beijing. The x-axis represents the year, and the y-axis shows the measure of genetic diversity. The black line shows the median estimates of the EV71 population size, and the blue shading represents the 95% CI.

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  Fig. 2. Spatial diffusion of EV71 in China. A: Spatial transmission pathways of EV71 inferred using the Bayesian Stochastic Search Variable Selection method. The solid arrow shows decisive support for the diffusion pathway identified by the VP1 coding regions, with 90,000 > BF > 3,001 and indicator > 0.99. The dashed arrow represents very strong support for the diffusion pathway identified by VP1 coding regions, with 300 > BF > 101 and indicator > 0.98. B: The histogram of the average number of state transitions based on six geographic locations

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  Fig. 3. Tertiary structure of the P1 protein estimated with homology model. Four different amino acid residues on the viral capsid protein were labeled on the 3D structure of the EV71 capsid protein using Pymol software. VP1 (purple), VP2 (blue), VP3 (brown), and VP4 (yellow). Sites under positive selection were highlighted as cyan, pale cyan, red, and green, respectively. Letters and numbers refer to the amino acid residues and positions of VP1 in the prototype strain BrCr (U22521.1)

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  Fig. 4. Birth-death skyline plot of the EV71. The curve and the grey area show the mean Re values and their 95% confidence intervals. The y and x-axes represent Re values and time in years, respectively. HPD means the highest posterior density