Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses

Abstract

Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2 influenza A viruses collected between 1999 and 2004 from New York State, United States, and observed multiple co-circulating clades with different population frequencies. Strikingly, phylogenies inferred for individual gene segments revealed that multiple reassortment events had occurred among these clades, such that one clade of H3N2 viruses present at least since 2000 had provided the hemagglutinin gene for all those H3N2 viruses sampled after the 2002-2003 influenza season. This reassortment event was the likely progenitor of the antigenically variant influenza strains that caused the A/Fujian/411/2002-like epidemic of the 2003-2004 influenza season. However, despite sharing the same hemagglutinin, these phylogenetically distinct lineages of viruses continue to co-circulate in the same population. These data, derived from the first large-scale analysis of H3N2 viruses, convincingly demonstrate that multiple lineages can co-circulate, persist, and reassort in epidemiologically significant ways, and underscore the importance of genomic analyses for future influenza surveillance.

Figure 1. Evolutionary Relationships of Concatenated Major Coding Regions of Influenza A Viruses Sampled in New York State during 1999–2004

The maximum likelihood phylogenetic tree is mid-point rooted for purposes of clarity, and all horizontal branch lengths are drawn to scale. Bootstrap values are shown for key nodes. Isolates assigned to clade A (light blue), clade B (yellow), and clade C (red) are indicated, as are those isolates involved in other reassortment events: A/New York/11/2003 (orange), A/New York/182/2000 (dark blue), and A/New York/137/1999 and A/New York/138/1999 (green).

Figure 2. Evolutionary Relationships of Individual Major Coding Regions from Influenza A Viruses Sampled in New York State during 1999–2004

All maximum likelihood phylogenetic trees are mid-point rooted for purposes of clarity only, and all horizontal branch lengths are drawn to scale. Bootstrap values are shown for clades A, B, and C. Colors are as in Figure 1.

Figure 3. Evolutionary Relationships of 197 NA Sequences Sampled from Mammalian Hosts during 1999–2005

The maximum likelihood phylogenetic tree is mid-point rooted for purposes of clarity only, and all horizontal branch lengths are drawn to scale. Bootstrap values are shown for clades A, B, and C. Colors are as in Figure 1.

Figure 4. Evolutionary Relationships of 256 Sequences of the HA1 Sequences Sampled from Mammalian Hosts during 1999–2004

The maximum likelihood phylogenetic tree is rooted on a divergent set of human and swine viruses for purposes of clarity only, and all horizontal branch lengths are drawn to scale. Bootstrap values are shown for key nodes. Colors are as in Figure 1, with yellow indicating all those viruses identified as clade B viruses from the analysis of the expanded NA dataset. The phylogenetic location of the reassortment event between clades A and B was set at the position of the most basal clade A virus, defined on the basis of the NA analysis, within the older clade B. The phylogenetic locations of the two critical antigenic mutations at sites 155 and 156 are also shown.