Quantitative, Molecular-Level Analysis of the Serum Antibody Repertoire Reveals Unanticipated Features of the Response to Influenza Vaccination

Vaccination is the most effective means to protect populations against infectious diseases, conferring protection by eliciting a diverse repertoire of virus-specific antibodies that circulate in blood and afford immunity by binding and neutralizing viruses. For influenza, which is a respiratory virus that poses a constant threat of a pandemic, seasonal vaccination is the best prophylactics; however, it leaves a large fraction of the population vulnerable, having less than 60% efficacy in young adults and substantially lower for at-risk groups. To design better vaccination strategies aimed at increasing its effectiveness, a molecular-level understanding of serological immunity to influenza is needed, but it has been confounded by the complexity of the polyclonal antibody response. Here, we used novel high-resolution proteomics coupled with high-throughput single B-cell sequencing technologies to quantitatively identify the antibodies elicited by 2011-2012 seasonal flu vaccination in four healthy donors and subsequently determined the biochemical and functional properties of prevalent serum antibodies. Following vaccination, we determined that the boosting of the antibodies pre-existing prior to vaccination accounted for ~60% of the vaccine response, indicating the substantial degree of antibody response being biased by the antibodies that were already existing prior to vaccination. We also observed a surprisingly high fraction of antibodies binding to both of the two highly diverse virus strains (group 1 and group 2). Characterization of these cross-reactive antibodies revealed broad recognition of historical virus strains and led to the discovery of a new class of antibodies that protect mice against H1N1 and H3N2 virus lethal challenges. This class of antibodies recognized the same conserved region in the head domain of hemagglutinin that is exposed only in its monomeric form. This is the first-ever report providing an extensive molecular-level description of the identities, dynamics and functions of the monoclonal antibodies that comprise the antibody response to seasonal flu vaccination. Collectively, our data provide unprecedented insights on the serological responses to influenza vaccination that have direct implications for the engineering of immunogens for a future vaccine for influenza.