The paper you cite by Chen & Holmes was published in 2006. The same group published a new article in 2015 that acknowledges evolutionary stasis of influenza in wild birds, it’s natural reservoir !
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.
A question that has been less frequently addressed is whether evolutionary patterns and processes also differ between wild birds and poultry? Indeed, there are a number of factors that could create important evolutionary differences between AIV in wild birds and poultry, notably reflecting differences in the mode of transmission and population structure. In particular, the transmission of AIV between wild birds largely occurs through an indirect faecal-oral route, in which, following excretion, the virus sits in an aquatic environment before infecting another host [2,7,8]. Importantly, there is growing evidence that AIV is able to remain in these water environments for several weeks, although this is dependent on the physico-chemical characteristics of the water source in question, and the presence of microorganisms which limit AIV infectiousness [7-11]. Critically, while present in the environment, AIV will effectively be in a “latent” state, such that there will be no viral replication and no mutational accumulation.
Conclusions
The estimates of nucleotide substitution rate presented here reveal a more complex picture of the evolutionary processes driving the evolution of avian influenza virus than previously thought. Most notably, it is clear that a single substitution rate cannot be applied to wild birds and poultry equally, as the evolutionary rates are consistently lower in the former and which may reflect a greater role for environmental transmission. Hence, it is evidently incorrect to impose a single substitution to AIV sampled from hosts as diverse as wild birds and poultry, and that molecular clock estimates based on a single rate may be erroneous. Similarly, rates differ significantly between the strict and relaxed clock models. It is therefore likely that the evolutionary dynamics of avian influenza virus can only be captured by new models that allow rates to vary in a more complex manner along lineages and which reflect changes in the underlying ecology.