title: Genetic characterization of human influenza viruses in the pandemic (2009-2010) and post-pandemic (2010-2011) periods in Japan.
abstract: BACKGROUND
  Pandemic influenza A(H1N1) 2009 virus was first detected in Japan in May 2009 and continued to circulate in the 2010-2011 season. This study aims to characterize human influenza viruses circulating in Japan in the pandemic and post-pandemic periods and to determine the prevalence of antiviral-resistant viruses.
  
  
  METHODS
  Respiratory specimens were collected from patients with influenza-like illness on their first visit at outpatient clinics during the 2009-2010 and 2010-2011 influenza seasons. Cycling probe real-time PCR assays were performed to screen for antiviral-resistant strains. Sequencing and phylogenetic analysis of the HA and NA genes were done to characterize circulating strains.
  
  
  CONCLUSIONS
  In the pandemic period (2009-2010), the pandemic influenza A(H1N1) 2009 virus was the only circulating strain isolated. None of the 601 A(H1N1)pdm09 virus isolates had the H275Y substitution in NA (oseltamivir resistance) while 599/601 isolates (99.7%) had the S31N substitution in M2 (amantadine resistance). In the post-pandemic period (2010-2011), cocirculation of different types and subtypes of influenza viruses was observed. Of the 1,278 samples analyzed, 414 (42.6%) were A(H1N1)pdm09, 525 (54.0%) were A(H3N2) and 33 (3.4%) were type-B viruses. Among A(H1N1)pdm09 isolates, 2 (0.5%) were oseltamivir-resistant and all were amantadine-resistant. Among A(H3N2) viruses, 520 (99.0%) were amantadine-resistant. Sequence and phylogenetic analyses of A(H1N1)pdm09 viruses from the post-pandemic period showed further evolution from the pandemic period viruses. For viruses that circulated in 2010-2011, strain predominance varied among prefectures. In Hokkaido, Niigata, Gunma and Nagasaki, A(H3N2) viruses (A/Perth/16/2009-like) were predominant whereas, in Kyoto, Hyogo and Osaka, A(H1N1)pdm09 viruses (A/New_York/10/2009-like) were predominant. Influenza B Victoria(HA)-Yamagata(NA) reassortant viruses (B/Brisbane/60/2008-like) were predominant while a small proportion was in Yamagata lineage. Genetic variants with mutations at antigenic sites were identified in A(H1N1)pdm09, A(H3N2) and type-B viruses in the 2010-2011 season but did not show a change in antigenicity when compared with respective vaccine strains.
authors: Division of International Health, Public Health, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.
authors: Isolde C
authors: IC
authors: Dapat
authors: Clyde
authors: C
authors: Dapat
authors: Tatiana
authors: T
authors: Baranovich
authors: Yasushi
authors: Y
authors: Suzuki
authors: Hiroki
authors: H
authors: Kondo
authors: Yugo
authors: Y
authors: Shobugawa
authors: Reiko
authors: R
authors: Saito
authors: Hiroshi
authors: H
authors: Suzuki
mesh_terms: D000998:Antiviral Agents / Q000627:therapeutic use; D024882:Drug Resistance, Viral; D006801:Humans; D007251:Influenza, Human / Q000188:drug therapy / Q000453:epidemiology / Q000821:virology*; D007564:Japan / Q000453:epidemiology; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D009975:Orthomyxoviridae / Q000145:classification / Q000235:genetics* / Q000276:immunology; D058873:Pandemics; D010802:Phylogeny; D012333:RNA, Messenger / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012621:Seasons
chemical_list: D000998:Antiviral Agents; D012333:RNA, Messenger; D012367:RNA, Viral