title: Sequencing and analysis of globally obtained human respiratory syncytial virus A and B genomes.
abstract: BACKGROUND
  Human respiratory syncytial virus (RSV) is the leading cause of respiratory tract infections in children globally, with nearly all children experiencing at least one infection by the age of two. Partial sequencing of the attachment glycoprotein gene is conducted routinely for genotyping, but relatively few whole genome sequences are available for RSV. The goal of our study was to sequence the genomes of RSV strains collected from multiple countries to further understand the global diversity of RSV at a whole-genome level.
  
  
  METHODS
  We collected RSV samples and isolates from Mexico, Argentina, Belgium, Italy, Germany, Australia, South Africa, and the USA from the years 1998-2010. Both Sanger and next-generation sequencing with the Illumina and 454 platforms were used to sequence the whole genomes of RSV A and B. Phylogenetic analyses were performed using the Bayesian and maximum likelihood methods of phylogenetic inference.
  
  
  RESULTS
  We sequenced the genomes of 34 RSVA and 23 RSVB viruses. Phylogenetic analysis showed that the RSVA genome evolves at an estimated rate of 6.72 × 10(-4) substitutions/site/year (95% HPD 5.61 × 10(-4) to 7.6 × 10(-4)) and for RSVB the evolutionary rate was 7.69 × 10(-4) substitutions/site/year (95% HPD 6.81 × 10(-4) to 8.62 × 10(-4)). We found multiple clades co-circulating globally for both RSV A and B. The predominant clades were GA2 and GA5 for RSVA and BA for RSVB.
  
  
  CONCLUSIONS
  Our analyses showed that RSV circulates on a global scale with the same predominant clades of viruses being found in countries around the world. However, the distribution of clades can change rapidly as new strains emerge. We did not observe a strong spatial structure in our trees, with the same three main clades of RSV co-circulating globally, suggesting that the evolution of RSV is not strongly regionalized.
authors: Midwest Respiratory Virus Program, Medical College of Wisconsin, Milwaukee, WI, USA.
authors: Michael E
authors: ME
authors: Bose
authors: Midwest Respiratory Virus Program, Medical College of Wisconsin, Milwaukee, WI, USA.
authors: Jie
authors: J
authors: He
authors: J. Craig Venter Institute, Rockville, MD, United States of America.
authors: Susmita
authors: S
authors: Shrivastava
authors: Fogarty International Center, National Institutes of Health, Bethesda, MD, United States of America.
authors: Martha I
authors: MI
authors: Nelson
authors: J. Craig Venter Institute, Rockville, MD, United States of America.
authors: Jayati
authors: J
authors: Bera
authors: J. Craig Venter Institute, Rockville, MD, United States of America.
authors: Rebecca A
authors: RA
authors: Halpin
authors: J. Craig Venter Institute, Rockville, MD, United States of America.
authors: Christopher D
authors: CD
authors: Town
authors: J. Craig Venter Institute, Rockville, MD, United States of America.
authors: Hernan A
authors: HA
authors: Lorenzi
authors: Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico.
authors: Daniel E
authors: DE
authors: Noyola
authors: Department of Virology, Institute for Medical Microbiology and Hygiene, University Medical Center Freiburg, Freiburg, Germany.
authors: Valeria
authors: V
authors: Falcone
authors: Laboratori Sperimentali di Ricerca, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
authors: Giuseppe
authors: G
authors: Gerna
authors: Department of Microbiology, OLV Hospital Aalst, Aalst, Belgium.
authors: Hans
authors: H
authors: De Beenhouwer
authors: Clinical Virology Laboratory, Centro de Educación Médica e Investigaciones Clínicas University Hospital, Buenos Aires, Argentina.
authors: Cristina
authors: C
authors: Videla
authors: School of Molecular and Biomedical Science, University of Adelaide, Adelaide, Australia.
authors: Tuckweng
authors: T
authors: Kok
authors: Zoonoses Research Unit, Department Medical Virology, University of Pretoria, Pretoria, South Africa.
authors: Marietjie
authors: M
authors: Venter
authors: Departments of Pediatrics and Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States of America.
authors: John V
authors: JV
authors: Williams
authors: Midwest Respiratory Virus Program, Medical College of Wisconsin, Milwaukee, WI, USA.
authors: Kelly J
authors: KJ
authors: Henrickson
mesh_terms: D001483:Base Sequence; D019143:Evolution, Molecular; D016679:Genome, Viral; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D018357:Respiratory Syncytial Virus Infections / Q000821:virology*; D018113:Respiratory Syncytial Virus, Human / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification