The evolutionary interaction between influenza A virus and the human immune system, manifest as 'antigenic drift' of the viral haemagglutinin, is one of the best described patterns in molecular evolution. However, little is known about the genome-scale evolutionary dynamics of this pathogen. Similarly, how genomic processes relate to global influenza epidemiology, in which the A/H3N2 and A/H1N1 subtypes co-circulate, is poorly understood. Here through an analysis of 1,302 complete viral genomes sampled from temperate populations in both hemispheres, we show that the genomic evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective sweeps. The A/H3N2 and A/H1N1 subtypes exhibit different evolutionary dynamics, with diverse lineages circulating in A/H1N1, indicative of weaker antigenic drift. These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions.

Original publication

DOI

10.1038/nature06945

Type

Journal article

Journal

Nature

Publication Date

05/2008

Volume

453

Pages

615 - 619

Addresses

Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK. a.rambaut@ed.ac.uk

Keywords

Humans, Reassortant Viruses, Neuraminidase, Hemagglutinin Glycoproteins, Influenza Virus, Evolution, Molecular, Phylogeny, Genetic Drift, Genome, Viral, Models, Biological, New York, New Zealand, Influenza, Human, Influenza A Virus, H3N2 Subtype, Influenza A Virus, H1N1 Subtype, Genetic Variation