@article{fdi:010062542,
  title = {{A}daptive evolution and environmental durability jointly structure phylodynamic patterns in avian {I}nfluenza viruses},
  author = {{R}oche, {B}enjamin and {D}rake, {J}. {M}. and {B}rown, {J}. and {S}tallknecht, {D}. {E}. and {B}edford, {T}. and {R}ohani, {P}.},
  editor = {},
  language = {{ENG}},
  abstract = {{A}vian influenza viruses ({AIV}s) have been pivotal to the origination of human pandemic strains. {D}espite their scientific and public health significance, however, there remains much to be understood about the ecology and evolution of {AIV}s in wild birds, where major pools of genetic diversity are generated and maintained. {H}ere, we present comparative phylodynamic analyses of human and {AIV}s in {N}orth {A}merica, demonstrating (i) significantly higher standing genetic diversity and (ii) phylogenetic trees with a weaker signature of immune escape in {AIV}s than in human viruses. {T}o explain these differences, we performed statistical analyses to quantify the relative contribution of several potential explanations. {W}e 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). {E}xtending 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. {F}urther 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. {T}he 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.},
  keywords = {},
  booktitle = {},
  journal = {{P}los {B}iology},
  volume = {12},
  numero = {8},
  pages = {e1001931},
  ISSN = {1545-7885},
  year = {2014},
  DOI = {10.1371/journal.pbio.1001931},
  URL = {https://www.documentation.ird.fr/hor/fdi:010062542},
}