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

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

Huang HW1,2, Chen YS3,4,5, Chen JY6, Lu PL7,8, Lin YC9, Chen BC10, Chou LC11, Wang CF12, Su HJ13, Huang YC14, Shi YY15, Chen HL16,17, Sanno-Duanda B18,19, Huang TS20, Lin KH21, Tyan YC22,23, Chu PY24,25.

Author information

1
Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, ROC, Taiwan. july25wen@gmail.com.
2
Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, ROC, Taiwan. july25wen@gmail.com.
3
Division of Infectious Diseases, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan. yschen@isca.vghks.gov.tw.
4
Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan. yschen@isca.vghks.gov.tw.
5
Department of Internal Medicine, National Yang-Ming Medical University, Taipei, ROC, Taiwan. yschen@isca.vghks.gov.tw.
6
Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. yifuc@kmu.edu.tw.
7
School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. idpaul@gmail.com.
8
Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. idpaul@gmail.com.
9
Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, ROC, Taiwan. lin65mt@gmail.com.
10
Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan. metapneumonvirus83@gmail.com.
11
Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. chou9566@yahoo.com.tw.
12
Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. virus7047@yahoo.com.tw.
13
Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. ruth780124@yahoo.com.tw.
14
Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. kimo21835@yahoo.com.tw.
15
Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. wing_282@hotmail.com.
16
Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. 840062@ms.kmuh.org.tw.
17
Department of Respiratory Therapy, College of Medicine, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. 840062@ms.kmuh.org.tw.
18
Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. nenneht@gmail.com.
19
Department of laboratory medicine, Edward Francis Small Teaching Hospital, Banjul, Gambia. nenneht@gmail.com.
20
Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan. tsishuhuang@gmail.com.
21
School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. kuhsli@gmail.com.
22
Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan. yctyan@cc.kmu.edu.tw.
23
Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan. yctyan@cc.kmu.edu.tw.
24
Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. peiyuchu@kmu.edu.tw.
25
Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. peiyuchu@kmu.edu.tw.

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.

PMID:
26390997
PMCID:
PMC4578604
DOI:
10.1186/s12859-015-0738-2
[Indexed for MEDLINE]
Free PMC Article

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