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. 2015 Sep 21:16:302.
doi: 10.1186/s12859-015-0738-2.

Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2

Hui-Wen Huang  1   2 , Yao-Shen Chen  3   4   5 , Jeff Yi-Fu Chen  6 , Po-Liang Lu  7   8 , Yung-Cheng Lin  9 , Bao-Chen Chen  10 , Li-Chiu Chou  11 , Chu-Feng Wang  12 , Hui-Ju Su  13 , Yi-Chien Huang  14 , Yong-Ying Shi  15 , Hsiu-Lin Chen  16   17 , Bintou Sanno-Duanda  18   19 , Tsi-Shu Huang  20 , Kuei-Hsiang Lin  21 , Yu-Chang Tyan  22   23 , Pei-Yu Chu  24   25
Affiliations

Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2

Hui-Wen Huang et al. BMC Bioinformatics. .

Abstract

Background: Studies regarding coxsackievirus (CV) tend to focus on epidemic outbreaks, an imbalanced topology is considered to be an indication of acute infection with partial cross-immunity. In enteroviruses, a clear understanding of the characteristics of tree topology, transmission, and its demographic dynamics in viral succession and circulation are essential for identifying prevalence trends in endemic pathogens such as coxsackievirus B2 (CV-B2). This study applied a novel Bayesian evolutionary approach to elucidate the phylodynamic characteristics of CV-B2. A dataset containing 51 VP1 sequences and a dataset containing 34 partial 3D(pol) sequencing were analyzed, where each dataset included Taiwan sequences isolated during 1988-2013.

Results: Four and five genotypes were determined based on the 846-nucleotide VP1 and 441-nucleotide 3D(pol) (6641-7087) regions, respectively, with spatiotemporally structured topologies in both trees. Some strains with tree discordance indicated the occurrence of recombination in the region between the VP1 and 3D(pol) genes. The similarities of VP1 and 3D(pol) gene were 80.0%-96.8% and 74.7%-91.9%, respectively. Analyses of population dynamics using VP1 dataset indicated that the endemic CV-B2 has a small effective population size. The balance indices, high similarity, and low evolutionary rate in the VP1 region indicated mild herd immunity selection in the major capsid region.

Conclusions: Phylodynamic analysis can reveal demographic trends and herd immunity in endemic pathogens.

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Figures

Fig. 1
Fig. 1
Maximum clade credibility (MCC) phylogeny of 51 VP1 sequences of coxsackievirus B2. For each branch, the thickness indicates the state probability, and the color indicates the most probable location. Support values are indicated on the major nodes. The genotypes and nucleotide/amino acid similarity within genotypes are shown on the right. For each strain name, the VP1 genotypes are differentiated by colors (Cluster I: purple, Genotype II: green, Genotype III: orange, Genotype IV: blue, and Genotype V: grey), whereas the 3Dpol genotypes are differentiated by shading (Genotype A: purple, Genotype B: green, Genotype C: orange, Genotype D: blue, and Genotype E: gray). The branch length is proportional to the evolutionary time, and the scale bar is proportional to calendar time
Fig. 2
Fig. 2
Maximum clade credibility (MCC) phylogeny of 34 3Dpol sequences coxsackievirus B2. For each branch, the thickness indicates the state probability and the color indicates the most probable location. Support values are indicated on the major nodes. The genotypes and nucleotide/amino acid similarity within genotypes are shown on the right. For each strain name, the VP1 genotypes are differentiated by colors (Cluster I: purple, Genotype II: green, Genotype III: orange, Genotype IV: blue, and Genotype V: grey), whereas the 3Dpol genotypes are differentiated by shading (Genotype A: purple, Genotype B: green, Genotype C: orange, Genotype D: blue, and Genotype E: gray). The branch length is proportional to the evolutionary time, and the scale bar is proportional to calendar time
Fig. 3
Fig. 3
Bayesian skyline plot of (a) 51 VP1 sequences and (b) 34 3Dpol sequences. The x-axis is the time scale (years) and the y-axis is the logarithmic Neτ scale (Ne is the effective population size and τ is the generation time). The thick solid line indicates the median estimates and the shaded area indicates the 95% highest posterior density
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