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Phylogenetic diversity and genotypic complexity of H1N1 subtype swine influenza viruses isolated in Mainland China

Yizhi Liu12, Jing Wang12, Jun Ji1, Shuang Chang3, Chunyi Xue4, Jingyun Ma1, Yingzuo Bi1 and Qingmei Xie1*

  • * Corresponding author: Qingmei Xie

  • † Equal contributors

Author Affiliations

1 College of Animal Science, South China Agricultural University, Guangzhou, 510642, China

2 Guangdong Wen’s Foodstuffs Group Co. Ltd, Yunfu, 527439, China

3 Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA

4 State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China

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Virology Journal 2012, 9:289  doi:10.1186/1743-422X-9-289

Published: 26 November 2012



After the occurrence of 2009 pandemic H1N1, close attention has been paid to the H1N1 subtype swine influenza viruses (H1N1 SIV) by scientific communities in many countries. A large-scale sequence analysis of the NCBI Influenza Virus Resource Database on H1N1 SIVs submitted primarily by scientists in China during 1992 to 2011 was performed. The aims of this study were to elucidate the genetic and evolutionary characteristics of H1N1 SIVs, to identify and unify the lineages and genetic characteristics of the H1N1 SIVs isolated in mainland China.


Most of the strains were isolated during the period of 2008 to 2010 from Guangdong and Shandong provinces, China. Based on the phylogenetic and genotypic analyses, all of the H1N1 SIV strains can be classified into 8 lineages and 10 genotypes. All strains were of the characteristics of low pathogenic influenza viruses. The viruses of different lineage are characterized with different amino acid residues at the receptor-binding sites. Viruses containing PB2 genes of the classical swine, early seasonal human and recent seasonal human lineage might be more infectious to human. Some genotypes were directly related with human influenza viruses, which include strains that harbored genes derived from human influenza viruses.


Phylogenetic diversity and complexity existed in H1N1 SIVs isolated in mainland China. These H1N1 SIV strains were closely related to other subtype influenza viruses, especially to human influenza viruses. Moreover, it was shown that, novel lineages and genotypes of H1N1 SIVs emerged recently in mainland China. These findings provided new and essential information for further understanding of the genetic and evolutionary characteristics and monitoring the H1N1 SIVs in mainland China.