Proteomics-based characterization of hemagglutinins in different strains of influenza virus

Infection with influenza A (subtypes H1N1 and H3N2) or B viruses results in over half a million deaths worldwide every year. Frequent antigenic changes (drift) in two major viral surface proteins hemagglutinin (HA) and neuraminidase lead to the constant emergence of antigenically distinct virus strains against which there is sub-optimal immunity in the population. Consequently the suitability of the viral strains included in the trivalent influenza vaccine (TIV) has to be re-evaluated annually. While virus seeds selected for vaccine manufacture are very well characterized, there is no assay in place to identify the source of HA in the formulated trivalent vaccine. Our study describes a proteomics-based method to identify the HA strain (not just subtype) and more fully characterize the final vaccine product. Unique and shared tryptic peptides of HAs were predicted by in silico tryptic digest of different influenza A and B virus strains. Recombinant HA and whole virus preparations of selected strains were then digested to identify the peptides detected by MS. Both subtype and strain-specific peptides were observed. The feasibility of this method to accurately identify HA strains in an inactivated TIV was tested using a 2006/2007 formulation. Each of the three HAs in the vaccine was identified in addition to a number of other viral and non-viral proteins. In summary, MS is a powerful method that is both specific and inclusive; in a single analysis, HAs of individual virus strains can be identified and the composition of the TIV fully characterized.