  Influenza has been circulating in the human population and has caused three
pandemics in the last century (1918 H1N1, 1957 H2N2, 1968 H3N2). The 2009
A(H1N1) was classified by the World Health Organization (WHO) as the fourth
pandemic. Influenza has a high evolution rate, which makes vaccine design
challenging. We here consider an approach for early detection of new dominant
strains. By clustering the 2009 A(H1N1) sequence data, we found two main
clusters. We then define a metric to detect the emergence of dominant strains.
We show on historical H3N2 data that this method is able to identify a cluster
around an incipient dominant strain before it becomes dominant. For example,
for H3N2 as of March 30, 2009, the method detects the cluster for the new
A/British Columbia/RV1222/2009 strain. This strain detection tool would appear
to be useful for annual influenza vaccine selection.
