Antigenic and genetic evolution of swine influenza A (H3N2) viruses in Europe

Abstract

In the early 1970s, a human influenza A/Port Chalmers/1/73 (H3N2)-like virus colonized the European swine population. Analyses of swine influenza A (H3N2) viruses isolated in The Netherlands and Belgium revealed that in the early 1990s, antigenic drift had occurred, away from A/Port Chalmers/1/73, the strain commonly used in influenza vaccines for pigs. Here we show that Italian swine influenza A (H3N2) viruses displayed antigenic and genetic changes similar to those observed in Northern European viruses in the same period. We used antigenic cartography methods for quantitative analyses of the antigenic evolution of European swine H3N2 viruses and observed a clustered virus evolution as seen for human viruses. Although the antigenic drift of swine and human H3N2 viruses has followed distinct evolutionary paths, potential cluster-differentiating amino acid substitutions in the influenza virus surface protein hemagglutinin (HA) were in part the same. The antigenic evolution of swine viruses occurred at a rate approximately six times slower than the rate in human viruses, even though the rates of genetic evolution of the HA at the nucleotide and amino acid level were similar for human and swine H3N2 viruses. Continuous monitoring of antigenic changes is recommended to give a first indication as to whether vaccine strains may need updating. Our data suggest that humoral immunity in the population plays a smaller role in the evolutionary selection processes of swine H3N2 viruses than in human H3N2 viruses.

FIG. 1.

Phylogenetic tree for HA1 of swine influenza A(H3N2) viruses and human reference strains. HA1 nucleotide sequences, 987 nucleotides in length, which were sequenced for the current study or collected from public databases were aligned and bootstrapped 100 times, after which trees were constructed with a maximum-likelihood algorithm, using A/Duck/Hokkaido/33/80 as the outgroup. The consensus tree was generated, for which the branch lengths were subsequently recalculated. Strains in bold were used for antigenic characterization, and the antigenic cluster to which they belong (see Fig. 2) is indicated. The underlined swine strains did not belong to the swine PCh lineage. The scale bar represents approximately 10% nucleotide change between close relatives.

FIG. 2.

Antigenic and genetic maps of swine and human H3N2 viruses. The relative positions of strains (colored spheres) and antisera (not shown) in the maps were computed such that the distances between strains and antisera in the map represent the corresponding HI measurements with the least error. Because only the relative positions of antigens can be determined, the orientation of the map within the axes is free. A two-dimensional map was generated on the basis of 20 HI tables, which included 30 ferret antisera and 48 influenza H3N2 viruses (A). The same analysis was repeated for the same strains to allow antigens and antisera to be positioned in a three-dimensional space (B). For the strains shown in panels A and B for which the HA1 amino acid sequence had been determined, a genetic map was generated based on an amino acid Hamming distance matrix (C). The color-coding of the viruses is the same in the three maps, and these colors are explained in the lower right panel.

FIG. 3.

Rates of genetic and antigenic evolution of swine and human H3N2 viruses. For all swine PCh-lineage strains shown in Fig. 1, the genetic distance to A/Port Chalmers/1/73 was calculated from the phylogenetic tree and was plotted as a function of time (A). The same was done for the post-1982 subset of human H3N2 strains from an earlier study (23) (B). The regression lines for panels A (R² = 0.88) and B (R² = 0.95) had similar slopes, of 0.0047 and 0.006, respectively. For the same strains, the antigenic distance to A/Port Chalmers/1/73 was computed from the two-dimensional antigenic maps as described previously (23). The antigenic distances from A/Port Chalmers/1/73 through antigenic cluster centroids (23), as a function of time, were plotted both for the swine strains (C) and the human strains (D). The regression lines for panels C (R² = 0.64) and D (R² = 0.86) had different slopes, of 0.3 and 2.0, respectively.