title: Whole genome sequencing and evolutionary analysis of human respiratory syncytial virus A and B from Milwaukee, WI 1998-2010.
abstract: BACKGROUND
  Respiratory Syncytial Virus (RSV) is the leading cause of lower respiratory-tract infections in infants and young children worldwide. Despite this, only six complete genome sequences of original strains have been previously published, the most recent of which dates back 35 and 26 years for RSV group A and group B respectively.
  
  
  RESULTS
  We present a semi-automated sequencing method allowing for the sequencing of four RSV whole genomes simultaneously. We were able to sequence the complete coding sequences of 13 RSV A and 4 RSV B strains from Milwaukee collected from 1998-2010. Another 12 RSV A and 5 RSV B strains sequenced in this study cover the majority of the genome. All RSV A and RSV B sequences were analyzed by neighbor-joining, maximum parsimony and Bayesian phylogeny methods. Genetic diversity was high among RSV A viruses in Milwaukee including the circulation of multiple genotypes (GA1, GA2, GA5, GA7) with GA2 persisting throughout the 13 years of the study. However, RSV B genomes showed little variation with all belonging to the BA genotype. For RSV A, the same evolutionary patterns and clades were seen consistently across the whole genome including all intergenic, coding, and non-coding regions sequences.
  
  
  CONCLUSIONS
  The sequencing strategy presented in this work allows for RSV A and B genomes to be sequenced simultaneously in two working days and with a low cost. We have significantly increased the amount of genomic data that is available for both RSV A and B, providing the basic molecular characteristics of RSV strains circulating in Milwaukee over the last 13 years. This information can be used for comparative analysis with strains circulating in other communities around the world which should also help with the development of new strategies for control of RSV, specifically vaccine development and improvement of RSV diagnostics.
authors: Midwest Respiratory Virus Program, Milwaukee, Wisconsin, United States of America.
authors: Cecilia
authors: C
authors: Rebuffo-Scheer
authors: Michael
authors: M
authors: Bose
authors: Jie
authors: J
authors: He
authors: Shamim
authors: S
authors: Khaja
authors: Michael
authors: M
authors: Ulatowski
authors: Eric T
authors: ET
authors: Beck
authors: Jiang
authors: J
authors: Fan
authors: Swati
authors: S
authors: Kumar
authors: Martha I
authors: MI
authors: Nelson
authors: Kelly J
authors: KJ
authors: Henrickson
mesh_terms: D002460:Cell Line; D018387:Codon, Initiator / Q000235:genetics; D018388:Codon, Terminator / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D019143:Evolution, Molecular; D016679:Genome, Viral / Q000235:genetics*; D005838:Genotype; D006023:Glycoproteins / Q000235:genetics; D006801:Humans; D054643:INDEL Mutation; D010802:Phylogeny; D018357:Respiratory Syncytial Virus Infections / Q000517:prevention & control / Q000821:virology*; D018113:Respiratory Syncytial Virus, Human / Q000235:genetics* / Q000276:immunology / Q000302:isolation & purification*; D017421:Sequence Analysis / Q000191:economics / Q000379:methods*; D013997:Time Factors; D014765:Viral Vaccines / Q000276:immunology; D014922:Wisconsin
chemical_list: D018387:Codon, Initiator; D018388:Codon, Terminator; D021901:DNA, Intergenic; D006023:Glycoproteins; D014765:Viral Vaccines