Design of Antigenically-Specific Probes for Sera Analysis and MAb Isolation

National Institute Of Allergy And Infectious Diseases

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Abstract

An understanding of the serum responses of virus-infected individuals and vaccinees is critical for the development of effective vaccines against HIV-1, SARS-CoV-2 and other viral pathogens. Antigenically specific molecular probes produced based on viral protein structures and computational biology allow for sera analysis and isolation of B-cells so that their antibody gene loci can be sequenced, which leads to in-depth characterization of secreted antibodies. Although the primary two-dose mRNA vaccine against SARS-CoV-2 elicit a robust and prolonged immune responses that lead to protection, the effectiveness of boosters has been dampened by rapidly evolving variants. Accordingly, bivalent SARS-CoV-2 vaccines have been deployed, in hope that these updated vaccines will provide better protection against emergent variants. To study the effectiveness of bivalent vaccines and to compare the routes of administration, we developed SARS-CoV-2 WA1, BA.5 and XBB.1.16 spike probes to measure the specificity and frequency of mucosal and circulating memory B cells following intramuscular boosting with bivalent mRNA encoding WA1 and BA.5 spike proteins or mucosal boosting with a WA1–BA.5 bivalent chimpanzee adenoviral-vectored vaccine delivered by intranasal or aerosol device. We observed that B cell specificity established by the initial mRNA vaccination remained consistent following any of the boosts. B cells were predominately cross-reactive to multiple variants or were specific for the priming immunogen WA1. Nevertheless, when we assessed protection against heterologous XBB.1.16 challenge in nonhuman primates (NHPs) five months after boosting, those boosted by either mucosal route showed minimal virus replication in the nose and lungs. In contrast, intramuscular mRNA boosting provided protection primarily confined to the lower airways. This study showed that even though there was immune imprinting to the original viral strain, the antibody repertoire was still cross-reactive and WA1/BA.5 bivalent boosters were protective against XBB.1.16. In a separate study, we immunized NHPs with fusion-peptide site of vulnerability and boosted with prefusion-closed Env trimers. The animals were then infected with SHIVs encoding FP8v1 sequences identical to their prime immunizations. To search for potent and broad HIV-1-neutralizing antibodies, antigen-specific B cells that bound to at least two of three probes (FP8, BG505 trimer, or ConC trimer) were isolated and sequenced. We further analyzed 16 pairs of antibody sequences from the sort and found 15 of these broadly neutralizing antibody lineages recognized the fusion-peptide site of vulnerability.