Dataset Information

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

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

SUBMITTER: Huang HW

PROVIDER: S-EPMC4578604 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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

Huang Hui-Wen HW Chen Yao-Shen YS Chen Jeff Yi-Fu JY Lu Po-Liang PL Lin Yung-Cheng YC Chen Bao-Chen BC Chou Li-Chiu LC Wang Chu-Feng CF Su Hui-Ju HJ Huang Yi-Chien YC Shi Yong-Ying YY Chen Hsiu-Lin HL Sanno-Duanda Bintou B Huang Tsi-Shu TS Lin Kuei-Hsiang KH Tyan Yu-Chang YC Chu Pei-Yu PY

BMC bioinformatics 20150921

<h4>Background</h4>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 e ...[more]

PMID: 26390997

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Dataset Information

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

Publications

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

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