Origins of a Humoral Immune Response: Characterizing Virus-specific Naive B cells

Abstract

Initial exposure to a pathogen elicits the production of pathogen-specific antibodies that may protect and eradicate the threat. The naive B cell repertoire is the starting material from which these protective antibodies arise, providing an enormously diverse substrate for the initial recognition of any pathogen or vaccine antigen. The composition of the naive repertoire, including frequency and binding strength for antigen, influences the quality of the initial pathogen response including the elicitation of immune memory. However, the human naive B cell repertoire remains largely undefined. Interrogating the abundance and specificity of this pre-immune repertoire can drive an understanding of how protective responses are mounted, especially for emerging pathogens to which we have no prior exposure. Here, we characterized naive B cell reactivity for viral antigens from SARS-CoV-2 and avian influenza virus. For SARS-CoV-2, we characterized naive B cells specific for the receptor binding domain (RBD) from seronegative donors to understand their relative abundance, intrinsic affinity, potential for activation, and putative maturation pathways. We identified genetically diverse naive B cell receptors (BCRs) targeting distinct RBD epitopes, including the identification of a conserved mode of recognition shared with infection-induced antibodies. For representative naive BCRs, higher-affinity RBD interactions could be engineered through a single amino acid change, which conferred potent SARS-CoV-2 neutralization and suggested a potentially low threshold for naive B cells to acquire protective capabilities. We also characterized avian influenza virus hemagglutinin (HA)-specific naive B cells with efforts focused on comparing the frequency, affinity, and neutralization potential between strain-specific B cells and those which cross-react to HAs circulating in the human population. We found that naive B cells targeting the HA head domain were at an elevated precursor frequency relative to cross-reactive clones. Further, a subset of HA head-specific antibodies neutralized H5 at germline and bound to HA at major antigenic sites previously characterized by H5 vaccine- and infection-elicited neutralizing antibodies. This work expands our understanding of human B cell specificities for emerging pathogens to support the prediction of potential responses made upon zoonotic infection and the design of next generation vaccines aimed at engaging protective germline responses.