title: Early co-circulation of different clades of influenza A/H1N1v pandemic virus in northern Italy.
abstract: BACKGROUND
  The spatial diffusion over time of pandemic influenza A/HINI virus (A/HIN1v) was surveyed in Northern Italy (nearly 10 million inhabitants)from April to December 2009, and the molecular characteristics of circulating viruses were analyzed to identify the appearance of drift variants. About 45% of analyzed samples were laboratory-confirmed cases of A/HINlv. Sporadic cases occurred until the middle of June 2009, then, case numbers began to increase delineating distinct epidemiological phases of viral circulation.
  
  
  METHODS
  RNA was extracted using RNeasy Mini kit (QIAGEN GmbH, Germany). Virological diagnosis of A/HINlv infection was carried out by real-time RT-PCR assay. Sequence analysis of hemagglutinin (HA) gene was performed through a RT-PCR assay specific for a 995 bp fragment (nt. 64-1,058) in the HAl domain. The nucleotide sequences were obtained by automated DNA sequencing. The HAl sequences were aligned with other sequences collected from GenBank database by ClustalX software. The multiple sequence alignment was used to perform a basic phylogenetic analysis and a phylogenetic tree from HA sequences was constructed.
  
  
  RESULTS
  The HA gene sequences ofA/HINlv analyzed segregated into three genetically distinct clades and were characterized by the appearance of amino acid variations that were progressively fixed in the field viral population under scrutiny.
  
  
  CONCLUSIONS
  These data suggest an early co-circulation of genetically distinct A/HNINv variants and emphasize the importance of a close molecular surveillance to detect rapidly the spread of new viral variants and to define their epidemiological impact.
authors.affiliation: Department of Public Health-Microbiology-Virology, University of Milan, Italy.
authors.forename: E
authors.initials: E
authors.lastname: Pariani
authors.forename: A
authors.initials: A
authors.lastname: Piralla
authors.forename: E
authors.initials: E
authors.lastname: Frati
authors.forename: G
authors.initials: G
authors.lastname: Anselmi
authors.forename: G
authors.initials: G
authors.lastname: Campanini
authors.forename: F
authors.initials: F
authors.lastname: Rovida
authors.forename: A
authors.initials: A
authors.lastname: Ranghiero
authors.forename: E
authors.initials: E
authors.lastname: Percivalle
authors.forename: A
authors.initials: A
authors.lastname: Amendola
authors.forename: F
authors.initials: F
authors.lastname: Baldanti
authors.forename: A R
authors.initials: AR
authors.lastname: Zanetti
mesh_terms: D004196:Disease Outbreaks; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics* / Q000302:isolation & purification; D007251:Influenza, Human / Q000453:epidemiology* / Q000821:virology*; D007558:Italy / Q000453:epidemiology; D017720:Molecular Epidemiology; D011159:Population Surveillance / Q000379:methods; D012367:RNA, Viral / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data*
chemical_list: D012367:RNA, Viral