title: Molecular characterization and phylogenetic analysis of human influenza A viruses in three consecutive seasons with different epidemiological profiles.
abstract: BACKGROUND
  Influenza activity and influenza virus circulation were observed in Lombardy (northern Italy) during three consecutive seasons and the molecular characteristics of circulating viruses analysed to control for introduction of new variants.
  
  
  METHODS
  The molecular characterization of 38 isolates, namely 20 A/H3N2 and 18 A/H1N1 influenza strains from the 2005/06, 2006/07 and 2007/08 seasons, was performed by sequence analysis of the globular head region of the HA protein (HA1 subunit), specific for influenza virus A/H3 and A/H1.
  
  
  CONCLUSIONS
  The last three influenza seasons in the study region were characterized by medium-low activity. A typical co-circulation of several variants was shown for A/H3 viruses for approximately two years and were subsequently almost entirely substituted by new emerging variants. Vice versa, A/H1 viruses had a more homogeneous circulation with a single lineage clearly dominating each season. The HA sequences of the A/H3 and the A/H1 viruses isolated in the last three seasons fell into 4 and 3 principal phylogenetic groups, respectively. No evidence of positive or negative selection in the sequence alignments was observed.
  
  
  CONCLUSIONS
  Molecular characterization of the influenza viruses in three consecutive seasons highlighted considerable heterogeneity in their HA sequences. A careful surveillance of genetic changes in the HA1 domain during seasonal influenza epidemics may reveal immune escape and provide early information on newly emerging strains with epidemiologic inference.
authors.affiliation: Department of Public Health-Microbiology-Virology, University of Milan, Italy. elena.pariani@unimi.it
authors.forename: E
authors.initials: E
authors.lastname: Pariani
authors.forename: E R
authors.initials: ER
authors.lastname: Frati
authors.forename: A
authors.initials: A
authors.lastname: Amendola
authors.forename: A
authors.initials: A
authors.lastname: Zappa
authors.forename: S
authors.initials: S
authors.lastname: Bianchi
authors.forename: D
authors.initials: D
authors.lastname: Colzani
authors.forename: M
authors.initials: M
authors.lastname: Canuti
authors.forename: D
authors.initials: D
authors.lastname: Brambilla
authors.forename: A
authors.initials: A
authors.lastname: Zanetti
authors.forename: E
authors.initials: E
authors.lastname: Tanzi
mesh_terms: D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics* / Q000302:isolation & purification; D053122:Influenza A Virus, H3N2 Subtype / Q000235:genetics* / Q000302:isolation & purification; D009980:Influenza A virus / Q000145:classification / Q000235:genetics; D007251:Influenza, Human / Q000453:epidemiology* / Q000517:prevention & control / Q000821:virology*; D007558:Italy / Q000453:epidemiology; D017720:Molecular Epidemiology / Q000379:methods; D011159:Population Surveillance / Q000379:methods; D017422:Sequence Analysis, DNA