Genetic analysis of influenza A/H3N2 and A/H1N1 viruses circulating in Vietnam from 2001 to 2006

Abstract

Influenza A virus has the ability to overcome immunity from previous infections through the acquisition of genetic changes. Thus, understanding the evolution of the viruses in humans is important for the surveillance and the selection of vaccine strains. A total of 30 influenza A/H3N2 viruses and 35 influenza A/H1N1 viruses that were collected in Vietnam from 2001 to 2006 were used to analyze the evolution of the hemagglutinin (HA), neuraminidase (NA), and matrix protein (M) genes. Phylogenetic analysis of individual gene segments revealed that the HA and the NA genes of the influenza A viruses evolved in a sequential way. However, the evolutionary pattern of the M gene proved to be nonlinear and was not linked with that of the HA and NA genes. Genetic drift in HA1 segments, especially in the antigenic sites of A/H3N2 viruses, occurred more frequently in A/H3N2 viruses than it did in A/H1N1 viruses. Two reassortants, one influenza A/H3N2 strain and one A/H1N1 strain, were found on the basis of the phylogenetic analysis of the three genes. While both genetic mutation and reassortment contributed to their evolution, the frequency of genetic changes and reassortment events differs between the two subtypes. As influenza viruses circulate throughout the year, we emphasize the importance of surveillance in tropical and subtropical zones, where the emergence of new strains may be detected earlier than it is in temperate zones.

FIG. 1.

Phylogenetic analysis of the HA1 domain of HA gene nucleotide sequences (906 bp), NA gene nucleotide sequences (1,363 bp), and M gene (with regions of the overlapping reading frames of M1-M2) nucleotide sequences (923 bp) of influenza A/H3N2 viruses circulating in Vietnam from 2002 to 2005. Reference strains shown in black were obtained from the genetic database. The isolates were assigned to group I (orange), group II (green), group III (purple), or group IV (red) in the phylogenetic tree of the HA gene (A). The grouping of the NA and the M genes was made in accordance with the branching in each tree. The colors of the strains in the phylogenetic trees of the NA gene (B) and the M gene (C) comply with those for the HA gene. Sequence data for the reference strains were obtained from the GenBank database. The asterisks denote the amantadine-resistant strain with the amino acid change S31N in the M2 protein. Bootstrap values of >70% are shown for the main groups.

FIG. 2.

Phylogenetic analysis of the HA1 domain of HA gene nucleotide sequences (829 bp), NA gene nucleotide sequences (1,363 bp), and M gene (with regions of the overlapping reading frames of M1-M2) nucleotide sequences (938 bp) of influenza A/H1N1 viruses circulating in Vietnam from 2001 to 2006. Reference strains shown in black were obtained from the genetic database. The isolates were assigned to group I (orange), group II (dark red), group III (purple), or group IV (red) in the phylogenetic tree of HA gene (Fig. 1A). The grouping of the NA and M genes was made in accordance with the branching in each tree. The colors of the strains in the phylogenetic trees of the NA gene (B) and the M gene (C) comply with those for the HA gene. The asterisks denote the amantadine-resistant strain with the amino acid change S31N in the M2 protein. Bootstrap values of >70% are shown for the main groups.