The molecular-level characterization of the serum antibody repertoire to influenza

Abstract

Vaccination is the most effective means to protect populations against infectious viruses by eliciting a diverse repertoire of antibodies. For influenza, a rapidly mutating virus posing a constant threat of a pandemic, seasonal vaccination is considered the best prophylactics, but it has limited efficacy and requires annual vaccination. To develop more effective influenza vaccine strategies, a comprehensive understanding of serum antibodies elicited by vaccination is essential, yet it has been confounded by the complexity of the antibody response. In this work, we used the high-resolution proteomics analysis of immunoglobulin (Ig-seq) coupled with the high-throughput sequencing of B cell receptor transcripts (BCR-seq) to quantitatively delineate the serum antibody repertoire to influenza. In Chapter 2, we analyzed the sera collected from four young adults before and after receiving trivalent seasonal influenza vaccine, which contains hemagglutinins from two influenza A virus strains (H1 and H3) and one influenza B strain. The serum repertoire comprised between 40-147 clonotypes specific to each of the three monovalent components of the vaccine, with ~60% of the vaccine response consisting of antibodies that were already present in serum before vaccination. We also observed a surprisingly high fraction of serum antibodies recognizing both the H1 and H3 monovalent vaccines (H1 + H3 cross-reactive antibodies). For subsequent analysis, in Chapter 3, we recombinantly expressed representative serum antibodies, and the H1 + H3 cross-reactive antibodies displayed a broad range of binding specificities to hemagglutinins from historic viral strains. We identified a group of antibodies recognizing the same conserved epitope in the hemagglutinin head domain that is only exposed in its monomeric form. These antibodies protected mice in challenging with H1N1 and H3N2 virus strains. In Chapter 4, we performed a longitudinal analysis of an individual’s serological repertoire specific to pandemic A/California/04/2009 (CA09pdm) viral strain across 6 years. Through multiple exposures to CA09pdm from infection and vaccination, our analysis revealed that the immediate antibody response to CA09pdm differed for each instance of exposure, but the antibody repertoire returned back to the pre-exposure state. This observation was due to the persistent antibodies comprising about half of the serum antibodies, while the intermittent antibodies were elicited following exposures but decayed soon after. The subsequent analysis on their binding specificities revealed that the persistent antibodies were likely to be targeting the stem region of the hemagglutinin while the intermittent antibodies tended to be head-specific. Collectively, our data provide unprecedented insights on the serological responses to influenza with direct implications for engineering a future influenza vaccine endowed with higher and broader protective efficacy