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MBE Advance Access published online on August 31, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl102
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted August 24, 2006

Research Article

Avian Influenza Virus Exhibits Rapid Evolutionary Dynamics

Rubing Chen 1 and Edward C. Holmes 2 *

1 Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802. USA
2 Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802. USA; Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA

* To whom correspondence should be addressed.
Edward C. Holmes, E-mail: ech15{at}psu.edu


  Abstract

Influenza A viruses from wild aquatic birds, their natural reservoir species, are thought to have reached a form of stasis, characterized by low rates of evolutionary change. We tested this hypothesis by estimating rates of nucleotide substitution in a diverse array of avian influenza viruses (AIV) and allowing for rate variation among lineages. The rates observed were extremely high, at >10-3 substitutions per site, per year, with little difference among wild and domestic host species or viral subtypes, and were similar to those seen in mammalian influenza A viruses. Influenza A virus therefore exhibits rapid evolutionary dynamics across its host range, consistent with a high background mutation rate and rapid replication. Using the same approach, we also estimated that the common ancestors of the hemagglutinin and neuraminidase sequences of AIV arose within the last 3000 years, with most intra-subtype diversity emerging within the last 100 years, and suggestive of a continual selective turnover.

Keywords: avian influenza virus; relaxed molecular clock; emerging virus; H5N1; coalescent.
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