title: Molecular epidemiology and phylodynamics of the human respiratory syncytial virus fusion protein in northern Taiwan.
abstract: OBJECTIVE
  The glycoprotein (G protein) and fusion protein (F protein) of respiratory syncytial virus (RSV) both show genetic variability, but few studies have examined the F protein gene. This study aimed to characterize the molecular epidemiology and phylodynamics of the F protein gene in clinical RSV strains isolated in northern Taiwan from 2000-2011.
  
  
  METHODS
  RSV isolates from children presenting with acute respiratory symptoms between July 2000 and June 2011 were typed based on F protein gene sequences. Phylogeny construction and evaluation were performed using the neighbor-joining (NJ) and maximum likelihood (ML) methods. Phylodynamic patterns in RSV F protein genes were analyzed using the Bayesian Markov Chain Monte Carlo framework. Selection pressure on the F protein gene was detected using the Datamonkey website interface.
  
  
  RESULTS
  From a total of 325 clinical RSV strains studied, phylogenetic analysis showed that 83 subgroup A strains (RSV-A) could be further divided into three clusters, whereas 58 subgroup B strains (RSV-B) had no significant clustering. Three amino acids were observed to differ between RSV-A and -B (positions 111, 113, and 114) in CTL HLA-B*57- and HLA-A*01-restricted epitopes. One positive selection site was observed in RSV-B, while none was observed in RSV-A. The evolution rate of the virus had very little change before 2000, then slowed down between 2000 and 2005, and evolved significantly faster after 2005. The dominant subtypes of RSV-A in each epidemic were replaced by different subtypes in the subsequent epidemic.
  
  
  CONCLUSIONS
  Before 2004, RSV-A infections were involved in several small epidemics and only very limited numbers of strains evolved and re-emerged in subsequent years. After 2005, the circulating RSV-A strains were different from those of the previous years and continued evolving through 2010. Phylodynamic pattern showed the evolutionary divergence of RSV increased significantly in the recent 5 years in northern Taiwan.
authors.affiliation: Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan.
authors.forename: Hsin
authors.initials: H
authors.lastname: Chi
authors.forename: Hsin-Fu
authors.initials: HF
authors.lastname: Liu
authors.forename: Li-Chuan
authors.initials: LC
authors.lastname: Weng
authors.forename: Nai-Yu
authors.initials: NY
authors.lastname: Wang
authors.forename: Nan-Chang
authors.initials: NC
authors.lastname: Chiu
authors.forename: Mei-Ju
authors.initials: MJ
authors.lastname: Lai
authors.forename: Yung-Cheng
authors.initials: YC
authors.lastname: Lin
authors.forename: Yu-Ying
authors.initials: YY
authors.lastname: Chiu
authors.forename: Wen-Shyang
authors.initials: WS
authors.lastname: Hsieh
authors.forename: Li-Min
authors.initials: LM
authors.lastname: Huang
mesh_terms: D001499:Bayes Theorem; D002460:Cell Line; D045744:Cell Line, Tumor; D002648:Child; D002675:Child, Preschool; D018984:Epitopes, T-Lymphocyte / Q000276:immunology / Q000378:metabolism; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D015788:HLA-A1 Antigen / Q000276:immunology / Q000378:metabolism; D015235:HLA-B Antigens / Q000276:immunology / Q000378:metabolism; D056945:Hep G2 Cells; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D010802:Phylogeny; D018357:Respiratory Syncytial Virus Infections / Q000453:epidemiology / Q000276:immunology / Q000821:virology*; D018113:Respiratory Syncytial Virus, Human / Q000145:classification* / Q000235:genetics; D013602:T-Lymphocytes, Cytotoxic / Q000276:immunology / Q000378:metabolism; D013624:Taiwan / Q000453:epidemiology; D014760:Viral Fusion Proteins / Q000145:classification* / Q000235:genetics
chemical_list: D018984:Epitopes, T-Lymphocyte; C526850:F protein, human respiratory syncytial virus; C506470:HLA-A*01:01 antigen; D015788:HLA-A1 Antigen; D015235:HLA-B Antigens; C103707:HLA-B57 antigen; D014760:Viral Fusion Proteins