Comparative analysis of evolutionary mechanisms of the hemagglutinin and three internal protein genes of influenza B virus: multiple cocirculating lineages and frequent reassortment of the NP, M, and NS genes

Abstract

Phylogenetic profiles of the genes coding for the hemagglutinin (HA) protein, nucleoprotein (NP), matrix (M) protein, and nonstructural (NS) proteins of influenza B viruses isolated from 1940 to 1998 were analyzed in a parallel manner in order to understand the evolutionary mechanisms of these viruses. Unlike human influenza A (H3N2) viruses, the evolutionary pathways of all four genes of recent influenza B viruses revealed similar patterns of genetic divergence into two major lineages. Although evolutionary rates of the HA, NP, M, and NS genes of influenza B viruses were estimated to be generally lower than those of human influenza A viruses, genes of influenza B viruses demonstrated complex phylogenetic patterns, indicating alternative mechanisms for generation of virus variability. Topologies of the evolutionary trees of each gene were determined to be quite distinct from one another, showing that these genes were evolving in an independent manner. Furthermore, variable topologies were apparently the result of frequent genetic exchange among cocirculating epidemic viruses. Evolutionary analysis done in the present study provided further evidence for cocirculation of multiple lineages as well as sequestering and reemergence of phylogenetic lineages of the internal genes. In addition, comparison of deduced amino acid sequences revealed a novel amino acid deletion in the HA1 domain of the HA protein of recent isolates from 1998 belonging to the B/Yamagata/16/88-like lineage. It thus became apparent that, despite lower evolutionary rates, influenza B viruses were able to generate genetic diversity among circulating viruses through a combination of evolutionary mechanisms involving cocirculating lineages and genetic reassortment by which new variants with distinct gene constellations emerged.

FIG. 1

Evolutionary tree based on the total number of nucleotide substitutions of the HA1 domain of the HA gene of human influenza B viruses constructed by neighbor-joining analysis. Isolates indicated in blue represent viruses belonging to lineage II, whereas those indicated in red represent viruses belonging to lineage III.

FIG. 2

Evolutionary tree of the NP gene of human influenza B viruses based on the total number of nucleotide substitutions in the complete protein coding region constructed by neighbor-joining analysis. Isolates indicated in red represent viruses whose HA gene belonged to lineage I, while isolates indicated in blue represent those whose HA gene belonged to lineage II.

FIG. 3

Evolutionary tree of the M gene of human influenza B viruses based on the total number of nucleotide substitutions in the complete protein coding region constructed by neighbor-joining analysis. Isolates indicated in red represent viruses whose HA gene belonged to lineage I, while isolates indicated in blue represent those whose HA gene belonged to lineage II.

FIG. 4

Evolutionary tree of the NS gene of human influenza B viruses based on the total number of nucleotide substitutions in the complete protein coding region constructed by neighbor-joining analysis. Isolates indicated in red represent viruses whose HA gene belonged to lineage I, while isolates indicated in blue represent those whose HA gene belonged to lineage II.

FIG. 5

Proposed pattern for evolution and gene reassortment among influenza B viruses. Genome constellations of influenza B viruses are represented as follows. The HA genes of lineages II and III are represented by blue diamonds and red diamonds, respectively; NP genes of lineages of II and III are represented by blue squares and red squares, respectively; M genes of lineages II and III are represented by blue circles and red circles, respectively; the corresponding lineages of NS genes (lineages III and IV) are symbolized by blue triangles and red triangles, respectively.