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Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2
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 demog...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578604/ https://www.ncbi.nlm.nih.gov/pubmed/26390997 http://dx.doi.org/10.1186/s12859-015-0738-2 |
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author | Huang, Hui-Wen Chen, Yao-Shen Chen, Jeff Yi-Fu Lu, Po-Liang Lin, Yung-Cheng Chen, Bao-Chen Chou, Li-Chiu Wang, Chu-Feng Su, Hui-Ju Huang, Yi-Chien Shi, Yong-Ying Chen, Hsiu-Lin Sanno-Duanda, Bintou Huang, Tsi-Shu Lin, Kuei-Hsiang Tyan, Yu-Chang Chu, Pei-Yu |
author_facet | Huang, Hui-Wen Chen, Yao-Shen Chen, Jeff Yi-Fu Lu, Po-Liang Lin, Yung-Cheng Chen, Bao-Chen Chou, Li-Chiu Wang, Chu-Feng Su, Hui-Ju Huang, Yi-Chien Shi, Yong-Ying Chen, Hsiu-Lin Sanno-Duanda, Bintou Huang, Tsi-Shu Lin, Kuei-Hsiang Tyan, Yu-Chang Chu, Pei-Yu |
author_sort | Huang, Hui-Wen |
collection | PubMed |
description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0738-2) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4578604 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-45786042015-09-23 Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2 Huang, Hui-Wen Chen, Yao-Shen Chen, Jeff Yi-Fu Lu, Po-Liang Lin, Yung-Cheng Chen, Bao-Chen Chou, Li-Chiu Wang, Chu-Feng Su, Hui-Ju Huang, Yi-Chien Shi, Yong-Ying Chen, Hsiu-Lin Sanno-Duanda, Bintou Huang, Tsi-Shu Lin, Kuei-Hsiang Tyan, Yu-Chang Chu, Pei-Yu BMC Bioinformatics Research Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0738-2) contains supplementary material, which is available to authorized users. BioMed Central 2015-09-21 /pmc/articles/PMC4578604/ /pubmed/26390997 http://dx.doi.org/10.1186/s12859-015-0738-2 Text en © Huang et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Huang, Hui-Wen Chen, Yao-Shen Chen, Jeff Yi-Fu Lu, Po-Liang Lin, Yung-Cheng Chen, Bao-Chen Chou, Li-Chiu Wang, Chu-Feng Su, Hui-Ju Huang, Yi-Chien Shi, Yong-Ying Chen, Hsiu-Lin Sanno-Duanda, Bintou Huang, Tsi-Shu Lin, Kuei-Hsiang Tyan, Yu-Chang Chu, Pei-Yu Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2 |
title | Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2 |
title_full | Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2 |
title_fullStr | Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2 |
title_full_unstemmed | Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2 |
title_short | Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2 |
title_sort | phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus b2 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578604/ https://www.ncbi.nlm.nih.gov/pubmed/26390997 http://dx.doi.org/10.1186/s12859-015-0738-2 |
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