A paper has recently appeared in PLoS Currents describing the evolution of the pandemic H1N1 virus. It was written by Martha Nelson, David Spiro and David Wentworth. Samples were collected in New York and Wisconsin and sequenced at the J. Craig Venter Institute. The dataset included these sequences as well as the pandemic H1N1 sequences which have been deposited in GenBank. Sequences from GISAID were not included, presumably due to their restrictive policies on data analysis.
Influenza viruses mutate frequently. Despite some erroneous press reports, this applies to pandemic H1N1 just as much, if not more, than seasonal flu. In the PLoS paper, statistical techniques were applied to the sequence dataset described above to separate out the various pandemic flu isolates into 7 distinct groups called clades. The sequences contained within each clade are more closely related to each other than to the other clades. However, they are not necessarily identical. The paper describes the relationships between the different clades and outlines their geographical distribution.
One of the most striking results from this paper was that although six of the seven clades were found in multiple regions throughout the world, in the two areas that were extensively sampled, New York and Wisconsin, there was a clear founder effect. In other words, most of the people in each area were infected with the descendants of specific strains of virus. Most people in Wisconsin were infected with a different variant of the virus than most people in New York were infected with.
Although the authors of the PLoS Currents paper did not demonstrate any obviously functionally important changes in pandemic H1N1, they did clearly show that the virus is mutating and diversifying as it spreads. Further, they found that regionally distinct clades are evolving in different geographical areas. Since the sort of intensive sampling and sequencing conducted for this paper is rarely done, we can only guess at how the virus is evolving in thousands of regions around the world.
Although the WHO and the CDC frequently suggest that the pandemic H1N1 virus is an homogeneous entity, the reality is quite different. The virus is opening many different doors, simultaneously. We don’t know what the odds are that one of these doors will lead to higher virulence or Tamiflu resistance. But what we do know is that it will keep opening door after door, in city after city, month after month in a never ending search for optimal fitness.
Nelson et al. (2009) The early diversification of influenza A/H1N1pdm. PLoS Currents.