Résumé
Avian influenza viruses (AIVs) have been pivotal to the origination of
human pandemic strains. Despite their scientific and public health
significance, however, there remains much to be understood about the
ecology and evolution of AIVs in wild birds, where major pools of genetic
diversity are generated and maintained. Here, we present comparative
phylodynamic analyses of human and AIVs in North America, demonstrating
(i) significantly higher standing genetic diversity and (ii) phylogenetic
trees with a weaker signature of immune escape in AIVs than in human
viruses. To explain these differences, we performed statistical analyses
to quantify the relative contribution of several potential explanations.
We found that HA genetic diversity in avian viruses is determined by a
combination of factors, predominantly subtype-specific differences in host
immune selective pressure and the ecology of transmission (in particular,
the durability of subtypes in aquatic environments). Extending this
analysis using a computational model demonstrated that virus durability
may lead to long-term, indirect chains of transmission that, when coupled
with a short host lifespan, can generate and maintain the observed high
levels of genetic diversity. Further evidence in support of this novel
finding was found by demonstrating an association between subtype-specific
environmental durability and predicted phylogenetic signatures: genetic
diversity, variation in phylogenetic tree branch lengths, and tree height.
The conclusion that environmental transmission plays an important role in
the evolutionary biology of avian influenza viruses—a manifestation of the
“storage effect”—highlights the potentially unpredictable impact of
wildlife reservoirs for future human pandemics and the need for improved
understanding of the natural ecology of these viruses.