Genetic Characterization of Human Influenza Viruses in the Pandemic (2009–2010) and Post-Pandemic (2010–2011) Periods in Japan

Isolde C Dapat,Hiroki Kondo,Tatiana Baranovich,Yasushi Suzuki,Reiko Saito,Clyde Dapat,Yugo Shobugawa,Hiroshi Suzuki,Man-Seong Park

doi:10.1371/journal.pone.0036455

Isolde C Dapat, Hiroki Kondo + Show 7 more

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https://doi.org/10.1371/journal.pone.0036455

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Journal: PloS one	Publication Date: Jun 27, 2012
Citations: 114	License type: CC BY 4.0

Affiliation: Niigata University, Niigata Seiryo University

Abstract

BackgroundPandemic 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.MethodsRespiratory 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.Results and ConclusionIn 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.

Highlights

In late March to early April of 2009, a novel influenza virus of swine origin emerged in humans in Mexico and the USA and rapidly spread worldwide, prompting the WHO to declare an influenza pandemic [1,2,3]
A(H1N1)pdm09 influenza virus activity peaked in November 2009 (Figure 1) which was 2–3 months earlier than in previous years
In the course of the surveillance study we conducted during the pandemic period, A(H1N1)pdm09 viruses were the only circulating strains detected

Summary

Introduction

In late March to early April of 2009, a novel influenza virus of swine origin emerged in humans in Mexico and the USA and rapidly spread worldwide, prompting the WHO to declare an influenza pandemic [1,2,3]. This is the first influenza pandemic since the A(H3N2) Hong Kong pandemic of 1968. 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

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