title: Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2.
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.
authors.affiliation: Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, ROC, Taiwan. july25wen@gmail.com.|Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, ROC, Taiwan. july25wen@gmail.com.
authors.forename: Hui-Wen
authors.initials: HW
authors.lastname: Huang
authors.affiliation: Division of Infectious Diseases, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan. yschen@isca.vghks.gov.tw.|Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan. yschen@isca.vghks.gov.tw.|Department of Internal Medicine, National Yang-Ming Medical University, Taipei, ROC, Taiwan. yschen@isca.vghks.gov.tw.
authors.forename: Yao-Shen
authors.initials: YS
authors.lastname: Chen
authors.affiliation: Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. yifuc@kmu.edu.tw.
authors.forename: Jeff Yi-Fu
authors.initials: JY
authors.lastname: Chen
authors.affiliation: School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. idpaul@gmail.com.|Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. idpaul@gmail.com.
authors.forename: Po-Liang
authors.initials: PL
authors.lastname: Lu
authors.affiliation: Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, ROC, Taiwan. lin65mt@gmail.com.
authors.forename: Yung-Cheng
authors.initials: YC
authors.lastname: Lin
authors.affiliation: Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan. metapneumonvirus83@gmail.com.
authors.forename: Bao-Chen
authors.initials: BC
authors.lastname: Chen
authors.affiliation: Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. chou9566@yahoo.com.tw.
authors.forename: Li-Chiu
authors.initials: LC
authors.lastname: Chou
authors.affiliation: Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. virus7047@yahoo.com.tw.
authors.forename: Chu-Feng
authors.initials: CF
authors.lastname: Wang
authors.affiliation: Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. ruth780124@yahoo.com.tw.
authors.forename: Hui-Ju
authors.initials: HJ
authors.lastname: Su
authors.affiliation: Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. kimo21835@yahoo.com.tw.
authors.forename: Yi-Chien
authors.initials: YC
authors.lastname: Huang
authors.affiliation: Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. wing_282@hotmail.com.
authors.forename: Yong-Ying
authors.initials: YY
authors.lastname: Shi
authors.affiliation: Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. 840062@ms.kmuh.org.tw.|Department of Respiratory Therapy, College of Medicine, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. 840062@ms.kmuh.org.tw.
authors.forename: Hsiu-Lin
authors.initials: HL
authors.lastname: Chen
authors.affiliation: Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. nenneht@gmail.com.|Department of laboratory medicine, Edward Francis Small Teaching Hospital, Banjul, Gambia. nenneht@gmail.com.
authors.forename: Bintou
authors.initials: B
authors.lastname: Sanno-Duanda
authors.affiliation: Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan. tsishuhuang@gmail.com.
authors.forename: Tsi-Shu
authors.initials: TS
authors.lastname: Huang
authors.affiliation: School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. kuhsli@gmail.com.
authors.forename: Kuei-Hsiang
authors.initials: KH
authors.lastname: Lin
authors.affiliation: Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan. yctyan@cc.kmu.edu.tw.|Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan. yctyan@cc.kmu.edu.tw.
authors.forename: Yu-Chang
authors.initials: YC
authors.lastname: Tyan
authors.affiliation: Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. peiyuchu@kmu.edu.tw.|Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. peiyuchu@kmu.edu.tw.
authors.forename: Pei-Yu
authors.initials: PY
authors.lastname: Chu
mesh_terms: D001499:Bayes Theorem; D002648:Child; D002675:Child, Preschool; D003384:Coxsackievirus Infections / Q000453:epidemiology / Q000635:transmission* / Q000821:virology*; D003710:Demography; D004196:Disease Outbreaks; D004770:Enterovirus / Q000302:isolation & purification / Q000502:physiology*; D005838:Genotype; D006801:Humans; D007223:Infant; D010802:Phylogeny; D058974:Phylogeography; D012367:RNA, Viral / Q000235:genetics; D013624:Taiwan / Q000453:epidemiology; D014764:Viral Proteins / Q000235:genetics
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins