Re: sequence evolution of H3N2 HA
These recurrent sweeps are mentioned in a recent Nature article:
The genomic and epidemiological dynamics of human influenza A virus. Andrew Rambaut, Oliver G. Pybus, Martha I. Nelson, Cecile Viboud, Jeffery K. Taubenberger & Edward C. Holmes. Nature 453, 615-619 (29 May 2008) | doi:10.1038/nature06945.
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 <b>periodic selective sweeps.</b> 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.
Periodic selective sweeps = influenza vaccine mismatch from previous serial (use) seasons in temperate climates??
Also, the authors seem to suggest that one subtype predominates in a season, although this seems to be in direct opposition to conclusions in several articles mapping *successive subtype waves* within seasons.
For instance, when Niman was chit-chatting about Hawaiian isolates, I visited the state public health site to view 2007-08 data and saw the same pattern as mentioned in a recent publication, of sequential rise and fall of Type AH1N1, H3N2 and Type B, with three overlapping peaks.
The publication that compared recent season-to-season variations in the three subtypes also noted that some countries experience overlapping waves of two of three subtypes.
