The pre-existing human antibody repertoire to computationally optimized influenza H1 hemagglutinin vaccines

Abstract

The computationally optimized broadly reactive antigen (COBRA) approach has previously been used to generate hemagglutinin (HA) immunogens for several influenza subtypes that expand vaccine-elicited antibody breadth. As nearly all individuals have pre-existing immunity to influenza viruses, influenza-specific memory B cells will likely be recalled upon COBRA HA vaccination. We determined the epitope specificity and repertoire characteristics of pre-existing human B cells to H1 COBRA HA antigens. Cross-reactivity between wild type HA and H1 COBRA HA proteins were observed at both the oligoclonal B cell level and for a subset of isolated monoclonal antibodies (mAbs). The mAbs bound five distinct epitopes on the pandemic A/California/04/2009 head and stem domains, and the majority of the mAbs had HAI and neutralizing activity against pandemic H1 strains. Two head-directed mAbs, CA09-26 and CA09-45, had HAI and neutralizing activity against a pre-pandemic H1 strain. One mAb, P1-05, targets the stem region of H1 HA proteins, but does not compete with known stem-targeting H1 mAbs. We determined that mAb P1-05 recognizes a recently discovered membrane proximal epitope on HA, the anchor epitope, and we identified similar mAbs using B cell repertoire sequencing. In addition, the trimerization domain distance from HA was critical to recognition of this epitope by P1-05. Overall, these data indicate that seasonally vaccinated individuals possess a population of functional H1 COBRA HA- reactive B cells that target head, central stalk, and anchor epitopes, and demonstrate the importance of structure-based assessment of subunit protein vaccine candidates to ensure accessibility of optimal protein epitopes. SignificanceInfluenza imposes significant human and economic costs every year. The current seasonal vaccine elicits primarily strain-specific antibodies, and year to year vaccine effectiveness is variable. The COBRA approach could provide longer protection and obviate the requirement for annual vaccination. Whereas COBRA HAs have previously been evaluated in animal models, the pre-existing COBRA HA-reactive human B cell population has yet to be elucidated, and is important to identify specific B cells that may be recalled by H1 HA COBRA vaccination. This work demonstrates that seasonally vaccinated individuals possess a functional B cell population targeting both head and stem domains that could be recalled with COBRA HA immunogens.