Molecular Identification of Pre-Existing Immunityin Human against H9N2 Influenza Viruses Using HLA-A*0201 Binding Peptides

The contribution genetic and antigenic diversity of H9N2 influenza viruses in evading from immune responses, cytotoxic T lymphocytes (CTL) epitopes in hemagglutinin (HA) protein restricted by HLA binding peptides was identified. Phylogenetic analyses were carried out for all of full length HA and deduced amino acid sequences of H9N2 viruses available in GenBank from their emergence to now. The impact of amino acid substitutions on emergence of antigenic variants was evaluated by using in silico prediction of the HLA-A*0201 binding peptides within HA protein. Potentially changes in structure and antigenic function of HA protein were quantified. The viruses phylogenetically clustered in Middle East and China. HA protein of the Middle East viruses represented a single sublineage, G1-like, while China isolates grouped to various sublineages and genotypes. Despite Middle Eastern viruses, more variations found in CTL epitopes of China isolates correlated to phylogenic analysis. Quantify and scoring of HA epitopes revealed that structure and antigenic function of the protein was not changed within H9N2 viruses during the previous decades indicating viral recognition by host-specific CTL response was not affected. Using an evolutionary and immunological approach, we showed that substantial levels of immunogenic peptide conservation for H9N2 HA protein was presented by HLA-A*0201. The potentially pre-existing immunity to H9N2 viruses in human is important for determining the outcome of influenza infection and developing vaccine with a T cell–based component against the public health threat.