Avian influenza virus exhibits rapid evolutionary dynamics

Rubing Chen, Edward C. Holmes

Research output: Contribution to journalArticlepeer-review

181 Scopus citations


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 3,000 years, with most intrasubtype diversity emerging within the last 100 years and suggestive of a continual selective turnover.

Original languageEnglish (US)
Pages (from-to)2336-2341
Number of pages6
JournalMolecular biology and evolution
Issue number12
StatePublished - Dec 2006
Externally publishedYes


  • Avian influenza virus
  • Coalescent
  • Emerging virus
  • H5N1
  • Relaxed molecular clock

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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