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Phylogenetic diversity and genotypic complexity of H1N1 subtype swine influenza viruses isolated in mainland China - PubMed

  • ️Sun Jan 01 2012

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

Yizhi Liu et al. Virol J. 2012.

Abstract

Background: 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.

Results: 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.

Conclusions: 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.

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Figures

Figure 1
Figure 1

Phylogenetic tree of the HA gene of the H1N1 subtype swine influenza viruses. The unrooted phylogenetic trees were generated by the neighbor-joining method using MEGA 5.0 software. Bootstrap values were calculated out of 1000 replicates and only bootstrap values of ≥70% were shown. Different lineages were indicated by different colors.

Figure 2
Figure 2

Phylogenetic tree of the NA genes of the H1N1 subtype swine influenza viruses. The unrooted phylogenetic trees were generated by the neighbor-joining method using MEGA 5.0 software. Bootstrap values were calculated out of 1000 replicates and only bootstrap values of ≥70% were shown. Different lineages were indicated by different colors.

Figure 3
Figure 3

Phylogenetic tree of the PB2 genes of the H1N1 subtype swine influenza viruses. The unrooted phylogenetic trees were generated by the neighbor-joining method using MEGA 5.0 software. Bootstrap values were calculated out of 1000 replicates and only bootstrap values of ≥70% were shown. Different lineages were indicated by different colors.

Figure 4
Figure 4

Phylogenetic tree of the PA genes of the H1N1 subtype swine influenza viruses. The unrooted phylogenetic trees were generated by the neighbor-joining method using MEGA 5.0 software. Bootstrap values were calculated out of 1000 replicates and only bootstrap values of ≥70% were shown. Different lineages were indicated by different colors.

Figure 5
Figure 5

Phylogenetic tree of the NP genes of the H1N1 subtype swine influenza viruses. The unrooted phylogenetic trees were generated by the neighbor-joining method using MEGA 5.0 software. Bootstrap values were calculated out of 1000 replicates and only bootstrap values of ≥70% were shown. Different lineages were indicated by different colors.

Figure 6
Figure 6

Phylogenetic tree of the M genes of the H1N1 subtype swine influenza viruses. The unrooted phylogenetic trees were generated by the neighbor-joining method using MEGA 5.0 software. Bootstrap values were calculated out of 1000 replicates and only bootstrap values of ≥70% were shown. Different lineages were indicated by different colors.

Figure 7
Figure 7

Phylogenetic tree of the NS genes of the H1N1 subtype swine influenza viruses. The unrooted phylogenetic trees were generated by the neighbor-joining method using MEGA 5.0 software. Bootstrap values were calculated out of 1000 replicates and only bootstrap values of ≥70% were shown. Different lineages were indicated by different colors.

Figure 8
Figure 8

Phylogenetic tree of the PB1 genes of the H1N1 subtype swine influenza viruses. The unrooted phylogenetic trees were generated by the neighbor-joining method using MEGA 5.0 software. Bootstrap values were calculated out of 1000 replicates and only bootstrap values of ≥70% were shown. Different lineages were indicated by different colors.

Figure 9
Figure 9

The genotypes of H1N1 subtype swine influenza viruses in China mainland from 1992 to 2011. The eight gene segments (horizontal bars staring from the top) were PB2, PB1, PA, HA, NP, NA, M and NS genes, and were indicated in same color with representative viruses for each lineage.

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