A Bioinformatics Study of Complete Amino Acid Sequence's Changes of Hemagglutinin Antigen of H1N1 Influenza Viruses in GenBank From Year 2006 to 2013 in Iran

Influenza is a major cause of morbidity and mortality worldwide. Each year, influenza viruses cause epidemics by evading pre-existing immunity through mutations in major surface glycoprotein hemagglutinin, which helps in attachment of the viral strain on the host cell surface. Due to high mutation rate, only currently circulating strains should be used in the vaccines.
The present study aimed at analyzing a dataset of complete amino acid sequences of HA to assess the extent of diversity among circulating strains of Iran, during years 2006 to 2013, and studying important amino acid changes as well as changes in predicted ligand binding sites that could enhance viral performance.
110 sequences from 17 provinces were downloaded, edited, and classified. The alignment of sequences and creation of phylogenetic trees and similarity matrices were done using bioinformatics software, such as MEGA6.0, BioEdit, DNAsisMAX, and DNAstar. Web-based analyses including SWISS- MODEL, Phyre2, and 3DLigandSite were used for evaluation of the second and third protein structures and prediction of ligand binding sites.
The results showed that 2009 was an important transition year, which classified the selected isolates into two different distinct groups. This shows the importance of changes made during possible mutations in the genomic structure of the virus, which have made it antigenically different from the previous years. This pandemic strain became dominant in the next years, and has been used as a standard vaccine strain from 2010 onwards.
The results of this study can shed further light on better understanding of the antigenic evolution of H1N1 influenza viruses and can be useful for epidemiological studies.