title: Avian influenza virus exhibits distinct evolutionary dynamics in wild birds and poultry.
abstract: BACKGROUND
  Wild birds are the major reservoir hosts for influenza A viruses, occasionally transmitting to other species such as domesticated poultry. Despite an abundance of genomic data from avian influenza virus (AIV), little is known about whether AIV evolves differently in wild birds and poultry, although this is critical to revealing the dynamics and time-scale of viral evolution. In particular, because environmental (water-borne) transmission is more common in wild birds, which may reduce the number of replications per unit time, it is possible that evolutionary rates are systematically lower in wild birds than in poultry.
  
  
  RESULTS
  We estimated rates of nucleotide substitution in two AIV subtypes that are strongly associated with infections in wild birds - H4 and H6 - and compared these to rates in the H5N1 subtype that has circulated in poultry for almost two decades. Our analyses of three internal genes confirm that H4 and H6 viruses are evolving significantly more slowly than H5N1 viruses, suggesting that evolutionary rates of AIV are reduced in wild birds. This result was verified by the analysis of a poultry-associated H6 lineage that exhibited a markedly higher substitution rate than those H6 viruses circulating in wild birds. Interestingly, we also observed a significant difference in evolutionary rate between H4 and H6, despite frequent reassortment rate among them.
  
  
  CONCLUSIONS
  AIV experiences markedly different evolutionary dynamics between wild birds and poultry. These results suggest that rate heterogeneity among viral subtypes and ecological groupings should be taken into account when estimating evolutionary rates and divergence times.
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia. mfourment@sydney.edu.au.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Fourment
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia. edward.holmes@sydney.edu.au.
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
mesh_terms: D000818:Animals; D000835:Animals, Wild; D005075:Biological Evolution; D001717:Birds; D053124:Influenza A Virus, H5N1 Subtype / Q000235:genetics*; D009980:Influenza A virus / Q000145:classification / Q000235:genetics*; D005585:Influenza in Birds / Q000821:virology*; D011200:Poultry; D011201:Poultry Diseases / Q000821:virology*