title: Molecular monitoring of causative viruses in child acute respiratory infection in endemo-epidemic situations in Shanghai.
abstract: BACKGROUND
  Numerous viruses are responsible for respiratory infections; however, both their distribution and genetic diversity, in a limited area and a population subgroup, have been studied only rarely during a sustained period of time.
  
  
  METHODS
  A 2-year surveillance program of children presenting with acute respiratory infections (ARIs) was carried out to characterize the viral etiology and to assess whether using gene amplification and sequencing could be a reliable approach to monitor virus introduction and spread in a population subgroup.
  
  
  RESULTS
  Using multiplex RT-PCR, 15 different respiratory viruses were detected within the 486 nasopharyngeal positive samples collected among 817 children aged <9-year old who presented with ARI during October 2006 to September 2008. A single virus was detected in 373 patients (45.7%), and two to four viruses in 113 patients (13.8%). The most frequent causative viruses were respiratory syncytial virus (RSV) (24.7%), human bocavirus (24.5%), and human rhinovirus (HRV) (15%). RSV was more prevalent in winter and among young infants. Cases of seasonal influenza A and B viruses were reported mainly in January and August. An increase in adenovirus infection was observed during the spring of the second year of the study. Sequence analyses showed multiple introductions of different virus subtypes and identified a high prevalence of the newly defined HRV-C species. A higher viral incidence was observed during the winter of 2008, which was unusually cold.
  
  
  CONCLUSIONS
  This study supports the usefulness of multiplex RT-PCR for virus detection and co-infection, and for implementation of a molecular monitoring system for endemic and epidemic viral respiratory infections.
authors.affiliation: Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Unit of Emerging Viruses, Shanghai, PR China.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.forename: Philippe
authors.initials: P
authors.lastname: Cavailler
authors.forename: Peijun
authors.initials: P
authors.lastname: Ren
authors.forename: Jing
authors.initials: J
authors.lastname: Zhang
authors.forename: Wei
authors.initials: W
authors.lastname: Dong
authors.forename: Huajie
authors.initials: H
authors.lastname: Yan
authors.forename: Sek
authors.initials: S
authors.lastname: Mardy
authors.forename: Johann
authors.initials: J
authors.lastname: Cailhol
authors.forename: Philippe
authors.initials: P
authors.lastname: Buchy
authors.forename: Jun
authors.initials: J
authors.lastname: Sheng
authors.forename: Arnaud
authors.initials: A
authors.lastname: Fontanet
authors.forename: Vincent
authors.initials: V
authors.lastname: Deubel
mesh_terms: D002648:Child; D002675:Child, Preschool; D002681:China / Q000453:epidemiology; D004196:Disease Outbreaks; D019353:Endemic Diseases; D006801:Humans; D007223:Infant; D017720:Molecular Epidemiology / Q000379:methods; D012141:Respiratory Tract Infections / Q000453:epidemiology* / Q000821:virology*; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D017422:Sequence Analysis, DNA; D014777:Virus Diseases / Q000453:epidemiology* / Q000821:virology*; D014780:Viruses / Q000145:classification / Q000302:isolation & purification*