Insights gained from influenza genomic sequence data: viral diversity within human populations

The advent of large amounts of influenza genomic sequence data produced by the Influenza Genome Sequencing Project (IGSP) has led to new concepts regarding influenza viral diversity.  It was previously believed that a single influenza lineage entered a human population at the start of an influenza season and gradually spread over time; however, recent analyses of influenza genomes revealed that multiple viral lineages co-circulate within individual populations throughout an influenza season.  These different lineages appear to be continuously introduced which provides the opportunity for frequent intra-subtype reassortment.  Interestingly, similar levels of influenza diversity exist within populations of both large metropolitan cities and small towns (E.C. Holmes, 2009).  Multiple, diverse viral lineages of the same subtype have been observed co-circulating in urban locations comprised of expansive travel networks and rural locations that are geographically isolated.

Additional analyses of complete influenza genomes have led to a 'source-sink' model of influenza seasonality.  In this model, a global, human 'source' population of influenza viruses is thought to be responsible for the antigenic variants that ignite seasonal epidemics in the 'sink' populations of the Northern and Southern hemispheres (A. Rambaut, 2008; E. C. Holmes, 2009).  The geographic regions of East and Southeast Asia have been hypothesized as potential sources of influenza due to the large, dense human populations which would allow influenza viruses to antigenically evolve with maximum efficiency.  These locales may be the focus of future surveillance efforts aimed at identifying emergent influenza viruses that have evolved mechanisms to evade current vaccines.