Host shifts and molecular evolution of H7 avian influenza virus hemagglutinin

Abstract

Evolutionary consequences of host shifts represent a challenge to identify the mechanisms involved in the emergence of influenza A (IA) viruses. In this study we focused on the evolutionary history of H7 IA virus in wild and domestic birds, with a particular emphasis on host shifts consequences on the molecular evolution of the hemagglutinin (HA) gene. Based on a dataset of 414 HA nucleotide sequences, we performed an extensive phylogeographic analysis in order to identify the overall genetic structure of H7 IA viruses. We then identified host shift events and investigated viral population dynamics in wild and domestic birds, independently. Finally, we estimated changes in nucleotide substitution rates and tested for positive selection in the HA gene. A strong association between the geographic origin and the genetic structure was observed, with four main clades including viruses isolated in North America, South America, Australia and Eurasia-Africa. We identified ten potential events of virus introduction from wild to domestic birds, but little evidence for spillover of viruses from poultry to wild waterbirds. Several sites involved in host specificity (addition of a glycosylation site in the receptor binding domain) and virulence (insertion of amino acids in the cleavage site) were found to be positively selected in HA nucleotide sequences, in genetically unrelated lineages, suggesting parallel evolution for the HA gene of IA viruses in domestic birds. These results highlight that evolutionary consequences of bird host shifts would need to be further studied to understand the ecological and molecular mechanisms involved in the emergence of domestic bird-adapted viruses.

Figure 1

Maximum likelihood consensus tree derived from 414 H7 HA nucleotide sequences. Computations were realized with the GTR+I+Г evolutionary model and 100 bootstrap replications (I = 0.27; α = 0.85). Tip colors represent the geographic origin of viruses: dark blue: Europe; light blue: Australia; green: Asia; yellow: Africa; purple: South America; orange: North America. Internal branches were also colored for monophyletic groups (i.e., same continent). Tips were annotated with red stars for HP viruses. A detailed phylogenetic tree including virus strain names is available in Figure S3.

Figure 2

Maximum clade credibility tree for the Eurasian-African-Australian genetic lineage. Tip and branch colors represent host origin (wild in green, domestic in orange). Tips were annotated with red stars for HP viruses. Blue letters (A to H) represent host shift events. Main genetic lineages, with information related to virus origin, are highlighted in the right part of the trees. Except for the ones identified with dashed lines, these lineages were monophyletic and supported by posterior probability values equal to 1. A detailed tree, including strain names, posterior probability values and 95% highest posterior density for time of the most recent common ancestors, is available in Figure S4.

Figure 3

Maximum clade credibility tree for the North-South American genetic lineage. Tip and branch colors represent host origin (wild in green, domestic in orange). Tips were annotated with red stars for HP viruses. Blue letters (I to N) represent host shift events. Main genetic lineages, with information related to virus origin, are highlighted in the right part of the trees. Except for the ones identified with dashed lines, these lineages were monophyletic and supported by posterior probability values equal to 1. A detailed tree, including strain names, posterior probability values and 95% highest posterior density for time of the most recent common ancestors, is available in Figure S5.

Figure 4

Relative genetic diversity over time for the H7 HA of IA viruses circulating in wild (A, B) and domestic (C-G) birds. A: wild birds Eurasia-Africa-Australia; B: North and South America; C: Australia; D: Italy (1999-2001); E: Italy (2002-2007); F: Pakistan; G: USA. Dashed lines represent 95% highest posterior density.