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A synchronized global sweep of the internal genes of modern avian influenza virus
Published: 16 February 2014 by Nature Publishing Group in Nature
Nature Publishing Group, Volume 508; 10.1038/nature13016
Abstract: 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.
Keywords: Influenza Virus, birds, avian influenza, genomic segments, phylogenies, Equine, synchronized, pandemic, synchrony

Comments on this paper Get comment updates
Guenter Stertenbrink
I can't verify that European and American PB2 may have a common ancester in ~1888.
Looks more like ~1800 to me. Maybe there is no clear "clock" in mallards with waterborne transmission
and possible survival in the environment for prolonged time. (see the slow evolution thread ...)
[but that picture confirms the American origin of the 1918-PB2 and the
Eurasian origin of the 1925-PB2]
[also the special role of the Alaska viruses (Eurasian or slow evolution i.e. murres from 1976)]

Creative Peptides
It can cause a disease of high economic importance for poultry production worldwide. Aviptadil Acetate

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