Data from: A synchronized global sweep of the internal genes of modern avian influenza virus

Zoonotic infectious diseases such as influenza continue to pose a grave
threat to human health. However, the factors that mediate the emergence of
RNA viruses such as influenza A virus (IAV) are still incompletely
understood. Phylogenetic inference is crucial to reconstructing the
origins and tracing the flow of IAV within and between hosts. Here we show
that explicitly allowing IAV host lineages to have independent rates of
molecular evolution is necessary for reliable phylogenetic inference of
IAV and that methods that do not do so, including ‘relaxed’ molecular
clock models, can be positively misleading. A phylogenomic analysis using
a host-specific local clock model recovers extremely consistent
evolutionary histories across all genomic segments and demonstrates that
the equine H7N7 lineage is a sister clade to strains from birds—as well as
those from humans, swine and the equine H3N8 lineage—sharing an ancestor
with them in the mid to late 1800s. Moreover, major western and eastern
hemisphere avian influenza lineages inferred for each gene coalesce in the
late 1800s. On the basis of these phylogenies and the synchrony of these
key nodes, we infer that the internal genes of avian influenza virus (AIV)
underwent a global selective sweep beginning in the late 1800s, a process
that continued throughout the twentieth century and up to the present. The
resulting western hemispheric AIV lineage subsequently contributed most of
the genomic segments to the 1918 pandemic virus and, independently, the
1963 equine H3N8 panzootic lineage. This approach provides a clear
resolution of evolutionary patterns and processes in IAV, including the
flow of viral genes and genomes within and between host lineages.