Large-Scale Sequence Analysis of Hemagglutinin of Influenza A Virus Identifies Conserved Regions Suitable for Targeting an Anti-Viral Response

Abstract

BackgroundInfluenza A viral surface protein, hemagglutinin, is the major target of neutralizing antibody response and hence a main constituent of all vaccine formulations. But due to its marked evolutionary variability, vaccines have to be reformulated so as to include the hemagglutinin protein from the emerging new viral strain. With the constant fear of a pandemic, there is critical need for the development of anti-viral strategies that can provide wider protection against any Influenza A pathogen. An anti-viral approach that is directed against the conserved regions of the hemaggutinin protein has a potential to protect against any current and new Influenza A virus and provide a solution to this ever-present threat to public health.Methodology/Principal FindingsInfluenza A human hemagglutinin protein sequences available in the NCBI database, corresponding to H1, H2, H3 and H5 subtypes, were used to identify highly invariable regions of the protein. Nine such regions were identified and analyzed for structural properties like surface exposure, hydrophilicity and residue type to evaluate their suitability for targeting an anti-peptide antibody/anti-viral response.Conclusion/SignificanceThis study has identified nine conserved regions in the hemagglutinin protein, five of which have the structural characteristics suitable for an anti-viral/anti-peptide response. This is a critical step in the design of efficient anti-peptide antibodies as novel anti-viral agents against any Influenza A pathogen. In addition, these anti-peptide antibodies will provide broadly cross-reactive immunological reagents and aid the rapid development of vaccines against new and emerging Influenza A strains.

Eliciting unnatural immune responses by activating cryptic epitopes in viral antigens

“…The present analysis identified 9 conserved sites in the HA1 subunit of influenza HA (10). Then, each site was further evaluated for potential accessibility to specific antibodies.…”

“…The selection criteria included: 1 ) conservation among H1, H2, H3, and H5 subtypes; 2 ) sites containing ≥6 residues as a minimum length required for a peptide to elicit an antibody response; and 3 ) sites where >50% residues had a conservation score of 0.9–1.0 calculated from multiple sequence alignment. Previously, Sahini et al (10) used the monomer conformation of H3 (PDB: 1HGJ), but here, we used the trimer structure as a more-relevant conformation for the present purpose, considering that influenza HA is a homotrimeric membrane glycoprotein, and some antigenic sites require HA trimerization (39). To determine whether the predicted sites are suitable for binding to their specific antibodies, structural characteristics, such as accessible surface area and polarity, were analyzed in HA trimers ( Fig.…”

Evaluation of a conserved HA274–288 epitope to detect antibodies to highly pathogenic avian influenza virus H5N1 in Indonesian commercial poultry

“…The HA2 subunit forms the stem in the trimer and acts as a fusion peptide and anchor for the HA1 subunit (Wiley et al, 1981;Yoshida et al, 2009). The HA1 is the major antigen of the virus and contain most of antigenic epitopes that are involved in virus neutralisation, protection, subtype specificity and serological detection (Okuno et al, 1993;Sahini et al, 2010;Wang et al, 2010). Several ELISAs have been developed using HA1 subunit antigenic epitopes that are subtype-specific.…”

Recombinant Influenza Vaccines

“…The conformational epitopes of HA have been identified for various influenza A subtypes; broad-spectrum antibodies against these epitopes can be secreted both after the infection and after live virus vaccination [85]. Vaccination with recombinant adenoviral vectors imitates an infection of mucosal cells of the upper air passages, thus providing expression of antigens with a native tertiary structure, which allows to trigger the formation of these cross-reactive antibodies.…”