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

TL;DR

This study applies principal component analysis to influenza A hemagglutinin sequences, revealing significant hydrophobicity pattern changes associated with the 2009 pandemic and highlighting variability in swine viruses.

Contribution

It introduces a data-driven method to encode sequences using amino acid properties, enabling advanced analysis of large sequence alignments.

Findings

Hydrophobicity pattern changed after 2009 pandemic

Sequences from humans show distinct hydrophobicity shifts

High variability observed in swine influenza sequences

Abstract

A principal component analysis of a multiple sequence alignement of hemagglutinin sequences of subtype H1 has been performed, the sequences being encoded using the amino-acid property that maximizes the weight of the major component. In the case of this alignment, it happens to be a well-known hydrophobicity scale. Interestingly, sequences coming from human have large positive amplitudes along the major component before 2009, and large negative ones afterwards. This means that the 2009 pandemic was associated to a major change in the hydrophobicity pattern of hemagglutinin. The present analysis also highlights the high variability of viral sequences coming from swine. At a more general level, the method proposed in this paper allows to describe a sequence coming from an alignment with a set of numbers, the original point being that the choice of the corresponding property is driven by the data. This approach should allow the application of numerous methods to the study of large multiple sequence alignments.