Genetic characterization of human influenza viruses in the pandemic (2009-2010) and post-pandemic (2010-2011) periods in Japan

• Published in: PloS one 2012-06, Vol.7 (6), p.e36455-e36455
• Main Authors: Dapat, Isolde C, Dapat, Clyde, Baranovich, Tatiana, Suzuki, Yasushi, Kondo, Hiroki, Shobugawa, Yugo, Saito, Reiko, Suzuki, Hiroshi
• Format: Article
• Language: English
• Subjects: 20th century; Amantadine; Antigenicity; Antigens; Antiviral Agents - therapeutic use; Biology; Collaboration; Disease resistance; Drug resistance; Drug Resistance, Viral; Gene sequencing; Genetic diversity; Genetic variance; Humans; Influenza; Influenza A; Influenza B; Influenza, Human - drug therapy; Influenza, Human - epidemiology; Influenza, Human - virology; Japan - epidemiology; Medicine; Molecular Sequence Data; Mutation; Mutation - genetics; Orthomyxoviridae - classification; Orthomyxoviridae - genetics; Orthomyxoviridae - immunology; Oseltamivir; Pandemics; Phylogenetics; Phylogeny; Public health; Real-Time Polymerase Chain Reaction; Reverse Transcriptase Polymerase Chain Reaction; RNA, Messenger - genetics; RNA, Viral - genetics; Seasons; Strains (organisms); Viruses
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0036455

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. 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. 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.