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A principal component analysis of a multiple sequence alignement ofhemagglutinin sequences of subtype H1 has been performed, the sequences beingencoded using the amino-acid property that maximizes the weight of the majorcomponent. In the case of this alignment, it happens to be a well-knownhydrophobicity scale. Interestingly, sequences coming from human have largepositive amplitudes along the major component before 2009, and large negativeones afterwards. This means that the 2009 pandemic was associated to a majorchange in the hydrophobicity pattern of hemagglutinin.  The present analysis also highlights the high variability of viral sequencescoming from swine. At a more general level, the method proposed in this paperallows to describe a sequence coming from an alignment with a set of numbers,the original point being that the choice of the corresponding property isdriven by the data. This approach should allow the application of numerousmethods to the study of large multiple sequence alignments.

Mutational dynamics of influenza A viruses: a principal component analysis of hemagglutinin sequences of subtype H1