Phylogenetic Analysis of a Swine Influenza A(H3N2) Virus Isolated in Korea in 2012

Jin Il Kim,Jun Heo,Ilseob Lee,Man-Seong Park,Min-Woong Hwang,Seok-Il Jang,Kabsu Kim,Sehee Park,Sangmoo Lee,Joon-Yong Bae,Donghwan Kim,Todd Davis

doi:10.1371/journal.pone.0088782

Jin Il Kim, Jun Heo + Show 10 more

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https://doi.org/10.1371/journal.pone.0088782

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Abstract

Influenza A virus (IAV) can infect avian and mammalian species, including humans. The genome nature of IAVs may contribute to viral adaptation in different animal hosts, resulting in gene reassortment and the reproduction of variants with optimal fitness. As seen again in the 2009 swine-origin influenza A H1N1 pandemic, pigs are known to be susceptible to swine, avian, and human IAVs and can serve as a ‘mixing vessel’ for the generation of novel IAV variants. To this end, the emergence of swine influenza viruses must be kept under close surveillance. Herein, we report the isolation and phylogenetic study of a swine IAV, A/swine/Korea/PL01/2012 (swPL01, H3N2 subtype). After screening nasopharyngeal samples from pigs in the Gyeongsangnam-do region of Korea from December 2011 to May 2012, we isolated the swPL01 virus and sequenced its all of 8 genome segments (polymerase basic 2, PB2; polymerase basic 1, PB1; polymerase acidic, PA; hemagglutinin, HA; nucleocapsid protein, NP; neuraminidase, NA; matrix protein, M; and nonstructural protein, NS). The phylogenetic study, analyzed with reference strains registered in the National Center for Biotechnology Information (NCBI) database, indicated that the swPL01 virus was similar to the North American triple-reassortant swine strains and that the HA gene of the swPL01 virus was categorized into swine H3 cluster IV. The swPL01 virus had the M gene of the triple-reassortant swine H3N2 viruses, whereas that of other contemporary strains in Korea was transferred from the 2009 pandemic H1N1 virus. These data suggest the possibility that various swine H3N2 viruses may co-circulate in Korea, which underlines the importance of a sustained surveillance system against swine IAVs.

Highlights

Influenza A viruses (IAVs) are respiratory pathogens of a genus of the family Orthomyxoviridae and infect many animal species [1]
Considered together, these findings suggest that the swine/Korea/PL01/ 2012 (swPL01) virus retains polymerase genes that drifted from the swTx/98 virus but it is phylogenetically different from those of other contemporary Korean strains
Our results demonstrate the genetic diversity of the swine H3N2 viruses circulating in Korea and the necessity of epidemiological preparedness through comprehensive surveillance

Summary

Introduction

Influenza A viruses (IAVs) are respiratory pathogens of a genus of the family Orthomyxoviridae and infect many animal species [1]. Because NeuAc-a2,3-Gal- and NeuAc-a2,6-Gal-linked sialic acids are present in swine respiratory tracts, both human and avian IAVs can readily infect pigs [6] When these viruses co-infect a single cell, progeny virions may have more opportunities for their gene selection, and pigs can serve as a wonderful melting pot for genetic reassortment and adaptation of IAVs [7]. The triplereassortant virus has gone through multiple reassortment events and it diverged into various evolution routes of IAVs [12] During these reassortment events, the triple-reassortant internal genes (TRIG) have been a gene cassette for accepting different HA and/or NA genes from other contemporary human and swine IAVs [13]. These swine IAVs continue to circulate and to establish their individual evolution in pigs and in other susceptible hosts [14]

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