Comparison of HA, NA amino acid sequences of novel influenza virus A/H1N1 and prediction of related B cell epitopes

Objective: To compare the amino acid sequences of HA, NA from novel influenza virus A/H1N1 isolates, and decipher possible B cell epitopes of HA, NA proteins. Methods: The amino acid sequences of 28 novel influenza A/H1N1 virus isolates around the world were downloaded from Genbank. Phylogenetic trees were constructed based on the amino acid sequences of HA and NA by using software Clustal X and MEGA 2.0. B cell epitopes were predicted with Protean software. Results: HA protein sequences showed a relatively larger variation comparing to NA protein sequences. Nevertheless both of them each have very less divergent amino acid residues. Software prediction results revealed the presence of 8 putative antigenic regions randomly distributed throughout HA sequence and 12 throughout NA sequence. Conclusion: the antigenicity of HA, NA protein is relatively stable in certain regions which can be used as the target regions in diagnosis and vaccine manufacturing.