Heterologous sarbecovirus receptor binding domains as scaffolds for SARS-CoV-2 receptor binding motif presentation (preprint)

Structure-guided rational immunogen design can generate optimized immunogens that elicit a desired humoral response. Design strategies often center upon targeting conserved sites on viral glycoproteins that will ultimately confer potent neutralization. For SARS-CoV-2 (SARS-2), the surface-exposed spike glycoprotein includes a broadly conserved portion, the receptor binding motif (RBM), that is required to engage the host cellular receptor, ACE2. Expanding humoral responses to this site may result in a more potently neutralizing antibody response against diverse sarbecoviruses. Here, we used a "resurfacing" approach and iterative design cycles to graft the SARS-2 RBM onto heterologous sarbecovirus scaffolds. The scaffolds were selected to vary the antigenic distance relative to SARS-2 to potentially focus responses to RBM. Multimerized versions of these immunogens elicited broad neutralization against sarbecoviruses in the context of preexisting SARS-2 immunity. These validated engineering approaches can help inform future immunogen design efforts for sarbecoviruses and are generally applicable to other viruses.

Rationally Designed Immunogens Enable Immune Focusing Following SARS-CoV-2 Spike Imprinting (preprint)

Eliciting antibodies to surface-exposed viral glycoproteins can generate protective responses that control and prevent future infections. Targeting conserved sites may reduce the likelihood of viral escape and limit spread of related viruses with pandemic potential. Here, we leveraged rational immunogen design to focus humoral responses on conserved epitopes. Using glycan engineering and epitope scaffolding, we directed murine serum antibody responses to conserved receptor binding motif (RBM) and domain (RBD) epitopes in the context of SARS-CoV-2 spike imprinting. Whereas all engineered immunogens elicited a robust SARS-CoV-2-neutralizing serum response, the RBM-focusing immunogens exhibited increased potency against related sarbecoviruses, SARS-CoV, WIV1-CoV, RaTG13-CoV, and SHC014-CoV; structural characterization of representative antibodies defined a conserved epitope. Furthermore, the RBM-focused sera conferred protection against SARS-CoV-2 challenge. Thus, RBM focusing is a promising strategy to elicit breadth across emerging sarbecoviruses without compromising SARS-CoV-2 protection. Broadly, these engineering strategies are adaptable to other viral glycoproteins for targeting conserved epitopes.Funding: We acknowledge funding from NIH R01s AI146779 (AGS), AI124378, AI137057 and AI153098 (DL), R01 AI157155 (MSD) and a Massachusetts Consortium on Pathogenesis Readiness (MassCPR) grant (AGS); training grants: NIGMS T32 GM007753 (BMH, TMC); T32 AI007245 (JF); F31 Al138368 (MS); F30 AI160908 (BMH). ABB is supported by the National Institutes for Drug Abuse (NIDA) Avenir New Innovator Award DP2DA040254, the MGH Transformative Scholars Program as well as funding from the Charles H. Hood Foundation (ABB). This independent research was supported by the Gilead Sciences Research Scholars Program in HIV (ABB). JBC is supported by a Helen Hay Whitney Foundation postdoctoral fellowship.Declaration of Interests: BMH, TMC, and AGS have filed a provisional patent for the described immunogens. MSD is a consultant for Inbios, Vir Biotechnology, and Carnival Corporation, and on the Scientific Advisory Boards of Moderna and Immunome. The Diamond laboratory has received unrelated funding support in sponsored research agreements from Vir Biotechnology, Moderna, and Emergent BioSolutions.Ethics Approval Statement: All experiments were conducted with institutional IACUC approval (MGH protocol 2014N000252). Animal studies were carried out in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. The protocols were approved by the Institutional Animal Care and Use Committee at the Washington University School of Medicine (assurance number A3381–01).

Rationally designed immunogens enable immune focusing to the SARS-CoV-2 receptor binding motif (preprint)

Eliciting antibodies to surface-exposed viral glycoproteins can lead to protective responses that ultimately control and prevent future infections. Targeting functionally conserved epitopes may help reduce the likelihood of viral escape and aid in preventing the spread of related viruses with pandemic potential. One such functionally conserved viral epitope is the site to which a receptor must bind to facilitate viral entry. Here, we leveraged rational immunogen design strategies to focus humoral responses to the receptor binding motif (RBM) on the SARS-CoV-2 spike. Using glycan engineering and epitope scaffolding, we find an improved targeting of the serum response to the RBM in context of SARS-CoV-2 spike imprinting. Furthermore, we observed a robust SARS-CoV-2-neutralizing serum response with increased potency against related sarbecoviruses, SARS-CoV and WIV1-CoV. Thus, RBM focusing is a promising strategy to elicit breadth across emerging sarbecoviruses and represents an adaptable design approach for targeting conserved epitopes on other viral glycoproteins.

Naive human B cells can neutralize SARS-CoV-2 through recognition of its receptor binding domain (preprint)

Exposure to a pathogen elicits an adaptive immune response aimed to control and eradicate. This initial exposure is imprinted on the immune system, so that a subsequent encounter to the same pathogen or a variant will result in a memory recall response that is often protective. Interrogating the naive B cell repertoire in terms of both abundance and specificity to said pathogen may contribute to an understanding of how to potentially elicit protective responses. Here, we isolated naive B cells across 8 human donors, targeting the SARS-CoV-2 receptor-binding domain (RBD). Single B cell sorting, and subsequent sequence analysis, showed diverse gene usage and pairing with no apparent restriction on complementarity determining region length in either the heavy or light chains. We show that recombinantly expressed IgGs and Fabs of these germline precursors bind SARS-CoV-2 RBD. Importantly, a subset of these naive antibodies also bind SARS-CoV, an emergent variant (501Y.V2) and a potential pandemic (WIV-1) coronavirus. Furthermore, naive antibodies can also neutralize SARS-CoV-2 pseudoviruses in the absence of any somatic hypermutation, suggesting that protective immunity to coronaviruses, more broadly, may be genetically encoded. Future studies aimed at understanding the naive repertoire to other coronaviruses may ultimately reveal shared specificities that could be leveraged to develop pan-coronavirus vaccines aimed at priming encoded germline responses.

Engineered Receptor Binding Domain Immunogens Elicit Pan-Coronavirus Neutralizing Antibodies Outside the Receptor Binding Motif (preprint)

Effective countermeasures are needed against emerging coronaviruses of pandemic potential, similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Designing immunogens that elicit broadly neutralizing antibodies to conserved viral epitopes on the major surface glycoprotein, spike, such as the receptor binding domain (RBD) is one potential approach. Here, we report the generation of homotrimeric RBD immunogens from different sarbecoviruses using a stabilized, immune-silent trimerization tag. We find that a cocktail of these homotrimeric sarbecovirus RBDs elicit antibodies to conserved viral epitopes outside of the ACE-2 receptor binding motif. Importantly, these responses neutralize all sarbecovirus components even in context of prior SARS-CoV-2 imprinting. This may be an effective strategy for eliciting broadly neutralizing responses leading to a pan-sarbecovirus vaccine.Funding: We acknowledge funding from NIH R01s AI146779 (AGS), AI124378,AI137057 and AI153098 (DL), and a Massachusetts Consortium on Pathogenesis Readiness (MassCPR) grant (AGS); training grants: NIGMS T32 GM007753 (BMH and TMC); T32AI007245 (JF); F31 Al138368 (MS). A.B.B. is supported by the National Institutes for Drug Abuse (NIDA) Avenir New Innovator Award DP2DA040254, the MGH Transformative Scholars Program as well as funding from the Charles H. Hood Foundation. This independent research was supported by the Gilead Sciences Research Scholars Program in HIV.Conflict of Interest: Authors declare no competing interests.Ethical Approval: All experiments were conducted with institutional IACUC approval (MGH protocol 2014N000252).

Engineered receptor binding domain immunogens elicit pan-coronavirus neutralizing antibodies (preprint)

Effective countermeasures are needed against emerging coronaviruses of pandemic potential, similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Designing immunogens that elicit broadly neutralizing antibodies to conserved viral epitopes on the major surface glycoprotein, spike, such as the receptor binding domain (RBD) is one potential approach. Here, we report the generation of homotrimeric RBD immunogens from different sarbecoviruses using a stabilized, immune-silent trimerization tag. We find that that a cocktail of homotrimeric sarbecovirus RBDs can elicit a neutralizing response to all components even in context of prior SARS-CoV-2 imprinting. Importantly, the cross-neutralizing antibody responses are focused towards conserved RBD epitopes outside of the ACE-2 receptor-binding motif. This may be an effective strategy for eliciting broadly neutralizing responses leading to a pan-sarbecovirus vaccine.