title: Viral genetic sequence variations in pandemic H1N1/2009 and seasonal H3N2 influenza viruses within an individual, a household and a community.
abstract: BACKGROUND
  There are few data in the literature on viral sequence variation between host generations/successive transmission events. Relatively little is known about the sequence heterogeneity of the influenza viruses transmitted within families.
  
  
  OBJECTIVE
  To study the molecular epidemiology of influenza virus and to determine the sequence variation within an individual, a household and a community during the first wave of influenza pandemic in 2009.
  
  
  METHODS
  A prospective study of household transmission of influenza A in Hong Kong was conducted during the pandemic in 2009. The HA and NA sequences of pandemic and seasonal influenza A viral isolates identified in this household transmission study were sequences and analyzed.
  
  
  RESULTS
  Our results indicated that there were multiple introductions of influenza viruses into Hong Kong. Sequence analysis of these isolates suggested that members of these family clusters acquired the infection by household transmissions. Interestingly, unlike those concluded from previous household transmission studies, we observed sequence variations between sequential samples from the same person and also within the same household.
  
  
  CONCLUSIONS
  Family clusters of influenza A viral infection are predominantly the result of secondary transmission within a household. Our results also suggested that the intra-host viral sequence variation might be more common that than previously thought.
authors.affiliation: State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology and the Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, China. llmpoon@hkucc.hku.hk
authors.forename: Leo L M
authors.initials: LL
authors.lastname: Poon
authors.forename: Kowk H
authors.initials: KH
authors.lastname: Chan
authors.forename: Daniel K W
authors.initials: DK
authors.lastname: Chu
authors.forename: Cherry C Y
authors.initials: CC
authors.lastname: Fung
authors.forename: Calvin K Y
authors.initials: CK
authors.lastname: Cheng
authors.forename: Dennis K M
authors.initials: DK
authors.lastname: Ip
authors.forename: Gabriel M
authors.initials: GM
authors.lastname: Leung
authors.forename: Joseph S M
authors.initials: JS
authors.lastname: Peiris
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Cowling
mesh_terms: D005191:Family Characteristics; D014644:Genetic Variation; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D006723:Hong Kong / Q000453:epidemiology; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D053122:Influenza A Virus, H3N2 Subtype / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D007251:Influenza, Human / Q000453:epidemiology* / Q000821:virology*; D008969:Molecular Sequence Data; D009439:Neuraminidase / Q000235:genetics; D058873:Pandemics; D010802:Phylogeny; D011446:Prospective Studies; D012111:Residence Characteristics; D012621:Seasons; D014764:Viral Proteins / Q000235:genetics
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus; D014764:Viral Proteins; C487630:NA protein, influenza A virus; D009439:Neuraminidase