Elicitation of Broadly Neutralizing Antibodies against B.1.1.7, B.1.351, and B.1.617.1 SARS-CoV-2 Variants by Three Prototype Strain-Derived Recombinant Protein Vaccines

The ongoing coronavirus disease 2019 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Most of the currently approved SARS-CoV-2 vaccines use the prototype strain-derived spike (S) protein or its receptor-binding domain (RBD) as the vaccine antigen. The emergence of several novel SARS-CoV-2 variants has raised concerns about potential immune escape. In this study, we performed an immunogenicity comparison of prototype strain-derived RBD, S1, and S ectodomain trimer (S-trimer) antigens and evaluated their induction of neutralizing antibodies against three circulating SARS-CoV-2 variants, including B.1.1.7, B.1.351, and B.1.617.1. We found that, at the same antigen dose, the RBD and S-trimer vaccines were more potent than the S1 vaccine in eliciting long-lasting, high-titer broadly neutralizing antibodies in mice. The RBD immune sera remained highly effective against the B.1.1.7, B.1.351, and B.1.617.1 variants despite the corresponding neutralizing titers decreasing by 1.2-, 2.8-, and 3.5-fold relative to that against the wild-type strain. Significantly, the S-trimer immune sera exhibited comparable neutralization potency (less than twofold variation in neutralizing GMTs) towards the prototype strain and all three variants tested. These findings provide valuable information for further development of recombinant protein-based SARS-CoV-2 vaccines and support the continued use of currently approved SARS-CoV-2 vaccines in the regions/countries where variant viruses circulate.

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Yeast-produced RBD-based recombinant protein vaccines elicit broadly neutralizing antibodies and durable protective immunity against SARS-CoV-2 infection

Cell Discovery ◽

10.1038/s41421-021-00315-9 ◽

2021 ◽

Vol 7 (1) ◽

Cited By ~ 1

Author(s):

Jinkai Zang ◽

Yuanfei Zhu ◽

Yu Zhou ◽

Chenjian Gu ◽

Yufang Yi ◽

...

Keyword(s):

Recombinant Protein ◽

Neutralizing Antibodies ◽

Protective Immunity ◽

Vaccine Dose ◽

Cost Effective ◽

Prototype Strain ◽

Broadly Neutralizing Antibodies ◽

Preclinical Development ◽

Virus Challenge ◽

Opening Up

AbstractMassive production of efficacious SARS-CoV-2 vaccines is essential for controlling the ongoing COVID-19 pandemic. We report here the preclinical development of yeast-produced receptor-binding domain (RBD)-based recombinant protein SARS-CoV-2 vaccines. We found that monomeric RBD of SARS-CoV-2 could be efficiently produced as a secreted protein from transformed Pichia pastoris (P. pastoris) yeast. Yeast-derived RBD-monomer possessed functional conformation and was able to elicit protective level of neutralizing antibodies in mice. We further designed and expressed a genetically linked dimeric RBD protein in yeast. The engineered dimeric RBD was more potent than the monomeric RBD in inducing long-lasting neutralizing antibodies. Mice immunized with either monomeric RBD or dimeric RBD were effectively protected from live SARS-CoV-2 virus challenge even at 18 weeks after the last vaccine dose. Importantly, we found that the antisera raised against the RBD of a single SARS-CoV-2 prototype strain could effectively neutralize the two predominant circulating variants B.1.1.7 and B.1.351, implying broad-spectrum protective potential of the RBD-based vaccines. Our data demonstrate that yeast-derived RBD-based recombinant SARS-CoV-2 vaccines are feasible and efficacious, opening up a new avenue for rapid and cost-effective production of SARS-CoV-2 vaccines to achieve global immunization.

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Immunogenicity of a Prefusion HIV-1 Envelope Trimer in Complex with a Quaternary-Structure-Specific Antibody

Journal of Virology ◽

10.1128/jvi.02380-15 ◽

2015 ◽

Vol 90 (6) ◽

pp. 2740-2755 ◽

Cited By ~ 40

Author(s):

Cheng Cheng ◽

Marie Pancera ◽

Adam Bossert ◽

Stephen D. Schmidt ◽

Rita E. Chen ◽

...

Keyword(s):

Guinea Pigs ◽

Neutralizing Antibodies ◽

Quaternary Structure ◽

High Titer ◽

Antigen Binding ◽

Broadly Neutralizing Antibodies ◽

Closed Conformation ◽

Ligand Free ◽

V3 Region ◽

Hiv 1

ABSTRACTThe HIV-1 envelope trimer (Env) is the target of broadly neutralizing antibodies and is being explored as a vaccine candidate to elicit protective antibodies. One of the most promising antigenic and structural mimics of HIV-1 Env is the SOSIP.664-stabilized soluble trimer from the clade A strain BG505, which is preferentially recognized by broadly neutralizing antibodies. Trimer immunization elicits high-titer neutralization of the autologous tier 2 BG505 strain; however, breadth is limited, and substantial interest has focused on understanding and improving trimer immunogenicity. We sought to improve the antigenic specificity of BG505 SOSIP.664 by reducing recognition of the variable loop 3 (V3) region, which elicits only weakly neutralizing antibodies. To stabilize the trimer in its prefusion closed conformation, we complexed trimeric BG505 SOSIP.664 with the antigen-binding fragment (Fab) of PGT145, a broadly neutralizing quaternary-structure-specific antibody. Compared to the ligand-free trimer, the PGT145 Fab-BG505 SOSIP.664 complex displayed increased melting temperature stability and reduced V3 recognition. In guinea pigs, immunization with the PGT145 Fab-BG505 SOSIP.664 complex elicited ∼100-fold lower V3-directed binding and neutralization titers than those obtained with ligand-free BG505 SOSIP.664. Both complexed and ligand-free BG505 SOSIP.664 elicited comparable neutralization of the autologous BG505 virus, and in both cases, BG505 neutralization mapped to the outer domain of gp120 for some guinea pigs. Our results indicate that it is possible to reduce immune recognition of the V3 region of the trimer while maintaining the antigenic profile needed to induce autologous neutralizing antibodies. These data suggest that appropriate modifications of trimer immunogens could further focus the immune response on key neutralization epitopes.IMPORTANCEHIV-1 Env trimers have been proposed as preferred HIV-1 vaccine immunogens. One version, BG505 SOSIP.664, a soluble stabilized trimer, was recently shown to elicit high-titer autologous neutralizing antibodies (NAbs) in rabbits. Here we compared two immunogens: the ligand-free BG505 SOSIP.664 trimer and the same trimer bound to the antigen-binding fragment (Fab) of the PGT145 antibody, a broadly neutralizing antibody which recognizes the trimer at its membrane-distal apex. We hypothesized that the Fab-bound complex would stabilize BG505 SOSIP.664 in its prefusion closed conformation and limit reactivity to weakly neutralizing antibodies targeting the variable loop 3 (V3) region. In guinea pigs, the Fab-complexed trimer induced 100-fold lower responses to the V3 region, while both ligand-free and Fab-complexed trimers elicited similar levels of autologous NAbs. Our findings demonstrate the potential to reduce “off-target” immunogenicity while maintaining the capacity to generate autologous NAbs.

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Glycan-masking spike antigen in NTD and RBD elicits broadly neutralizing antibodies against SARS-CoV-2 variants

10.1101/2021.11.01.466834 ◽

2021 ◽

Author(s):

Wei-Shuo Lin ◽

I-Chen Chen ◽

Hui-Chen Chen ◽

Yi-Chien Lee ◽

Suh-Chin Wu

Keyword(s):

Neutralizing Antibodies ◽

Neutralizing Antibody ◽

Fold Increase ◽

Vaccine Antigen ◽

Broadly Neutralizing Antibodies ◽

Neutralization Titer ◽

Cell Responses ◽

Folded Structure ◽

Antibody Titers ◽

The Impact

Glycan-masking the vaccine antigen by mutating the undesired antigenic sites with an additional N-linked glycosylation motif can refocus B-cell responses to desired/undesired epitopes, without affecting the antigen overall-folded structure. This study examine the impact of glycan-masking mutants of the N-terminal domain (NTD) and receptor-binding domain (RBD) of SARS-CoV-2, and found that the antigenic design of the S protein increases the neutralizing antibody titers against the Wuhan-Hu-1 ancestral strain and the recently emerged SARS-CoV-2 variants Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2). Our results demonstrated that the use of glycan-masking Ad-S-R158N-Y160T in the NTD elicited a 2.8-fold, 6.5-fold, and 4.6-fold increase in the IC-50 NT titer against the Alpha (B.1.1.7), Beta (B.1.351) and Delta (B.1.617.2) variants, respectively. Glycan-masking of Ad-S-D428N in the RBD resulted in a 3.0-fold and 2.0-fold increase in the IC50 neutralization titer against the Alpha (B.1.1.7) and Beta (B.1.351) variants, respectively. The use of glycan-masking in Ad-S-R158N-Y160T and Ad-S-D428N antigen design may help develop universal COVID-19 vaccines against current and future emerging SARS-CoV-2 variants.

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Neutralizing Antibody Responses Induced by HIV-1 Envelope Glycoprotein SOSIP Trimers Derived from Elite Neutralizers

Journal of Virology ◽

10.1128/jvi.01214-20 ◽

2020 ◽

Vol 94 (24) ◽

Author(s):

Anna Schorcht ◽

Tom L. G. M. van den Kerkhof ◽

Christopher A. Cottrell ◽

Joel D. Allen ◽

Jonathan L. Torres ◽

...

Keyword(s):

Envelope Glycoprotein ◽

Neutralizing Antibodies ◽

High Titer ◽

Vaccine Design ◽

Neutralizing Antibody ◽

Antibody Responses ◽

Tier 2 ◽

Broadly Neutralizing Antibodies ◽

Subtype B ◽

Hiv 1

ABSTRACT The induction of broadly neutralizing antibodies (bNAbs) is a major goal in vaccine research. HIV-1-infected individuals that develop exceptionally strong bNAb responses, termed elite neutralizers, can inform vaccine design by providing blueprints for the induction of similar bNAb responses. We describe a new recombinant native-like envelope glycoprotein (Env) SOSIP trimer, termed AMC009, based on the viral founder sequences of an elite neutralizer. The subtype B AMC009 SOSIP protein formed stable native-like trimers that displayed multiple bNAb epitopes. Overall, its structure at 4.3-Å resolution was similar to that of BG505 SOSIP.664. The AMC009 trimer resembled one from a second elite neutralizer, AMC011, in having a dense and complete glycan shield. When tested as immunogens in rabbits, the AMC009 trimers did not induce autologous neutralizing antibody (NAb) responses efficiently while the AMC011 trimers did so very weakly, outcomes that may reflect the completeness of their glycan shields. The AMC011 trimer induced antibodies that occasionally cross-neutralized heterologous tier 2 viruses, sometimes at high titer. Cross-neutralizing antibodies were more frequently elicited by a trivalent combination of AMC008, AMC009, and AMC011 trimers, all derived from subtype B viruses. Each of these three individual trimers could deplete the NAb activity from the rabbit sera. Mapping the polyclonal sera by electron microscopy revealed that antibodies of multiple specificities could bind to sites on both autologous and heterologous trimers. These results advance our understanding of how to use Env trimers in multivalent vaccination regimens and the immunogenicity of trimers derived from elite neutralizers. IMPORTANCE Elite neutralizers, i.e., individuals who developed unusually broad and potent neutralizing antibody responses, might serve as blueprints for HIV-1 vaccine design. Here, we studied the immunogenicity of native-like recombinant envelope glycoprotein (Env) trimers based on viral sequences from elite neutralizers. While immunization with single trimers from elite neutralization did not recapitulate the breadth and potency of neutralization observed in these infected individuals, a combination of three subtype B Env trimers from elite neutralizers resulted in some neutralization breadth within subtype B viruses. These results should guide future efforts to design vaccines to induce broadly neutralizing antibodies.

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Chinks in the armor of the HIV-1 Envelope glycan shield: Implications for immune escape from anti-glycan broadly neutralizing antibodies

Virology ◽

10.1016/j.virol.2016.10.026 ◽

2017 ◽

Vol 501 ◽

pp. 12-24 ◽

Cited By ~ 6

Author(s):

Thandeka Moyo ◽

Roux-Cil Ferreira ◽

Reyaaz Davids ◽

Zarinah Sonday ◽

Penny L. Moore ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Immune Escape ◽

Broadly Neutralizing Antibodies ◽

Hiv 1

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Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants

Frontiers in Immunology ◽

10.3389/fimmu.2021.795741 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wei-Shuo Lin ◽

I-Chen Chen ◽

Hui-Chen Chen ◽

Yi-Chien Lee ◽

Suh-Chin Wu

Keyword(s):

Neutralizing Antibodies ◽

Neutralizing Antibody ◽

Fold Increase ◽

Vaccine Antigen ◽

Broadly Neutralizing Antibodies ◽

Neutralization Titer ◽

Cell Responses ◽

Folded Structure ◽

Antibody Titers ◽

The Impact

Glycan-masking the vaccine antigen by mutating the undesired antigenic sites with an additional N-linked glycosylation motif can refocus B-cell responses to desired epitopes, without affecting the antigen’s overall-folded structure. This study examined the impact of glycan-masking mutants of the N-terminal domain (NTD) and receptor-binding domain (RBD) of SARS-CoV-2, and found that the antigenic design of the S protein increases the neutralizing antibody titers against the Wuhan-Hu-1 ancestral strain and the recently emerged SARS-CoV-2 variants Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2). Our results demonstrated that the use of glycan-masking Ad-S-R158N/Y160T in the NTD elicited a 2.8-fold, 6.5-fold, and 4.6-fold increase in the IC-50 NT titer against the Alpha (B.1.1.7), Beta (B.1.351) and Delta (B.1.617.2) variants, respectively. Glycan-masking of Ad-S-D428N in the RBD resulted in a 3.0-fold and 2.0-fold increase in the IC-50 neutralization titer against the Alpha (B.1.1.7) and Beta (B.1.351) variants, respectively. The use of glycan-masking in Ad-S-R158N/Y160T and Ad-S-D428N antigen design may help develop universal COVID-19 vaccines against current and future emerging SARS-CoV-2 variants.

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Public broadly neutralizing antibodies against hepatitis B virus in individuals with elite serologic activity

10.1101/2020.03.04.976159 ◽

2020 ◽

Author(s):

Qiao Wang ◽

Eleftherios Michailidis ◽

Yingpu Yu ◽

Zijun Wang ◽

Arlene M. Hurley ◽

...

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Neutralizing Antibodies ◽

Immune Escape ◽

Hbv Infection ◽

Resistance Mutations ◽

Broadly Neutralizing Antibodies ◽

Peptide Epitope ◽

Chronic Hepatitis B Virus ◽

B Virus

SUMMARYAlthough there is no effective cure for chronic hepatitis B virus (HBV) infection, antibodies are protective and constitute clinical correlates of recovery from infection. To examine the human neutralizing antibody response to HBV in elite neutralizers we screened 144 individuals. The top individuals produced shared clones of broadly neutralizing antibodies (bNAbs) that targeted 3 non-overlapping epitopes on the HBV S antigen (HBsAg). Single bNAbs protected humanized mice against infection, but selected for resistance mutations in mice with established infection. In contrast, infection was controlled by a combination of bNAbs targeting non-overlapping epitopes with complementary sensitivity to mutations that commonly emerge during human infection. The co-crystal structure of one of the bNAbs with a peptide epitope containing residues frequently mutated in human immune escape variants revealed a loop anchored by oppositely charged residues. The structure provides a molecular explanation for why immunotherapy for HBV infection may require combinations of complementary bNAbs.

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An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies

10.1101/406355 ◽

2018 ◽

Cited By ~ 1

Author(s):

Adam S. Dingens ◽

Dana Arenz ◽

Haidyn Weight ◽

Julie Overbaugh ◽

Jesse D. Bloom

Keyword(s):

Neutralizing Antibodies ◽

Immune Escape ◽

Single Amino Acid ◽

Structural Studies ◽

Broadly Neutralizing Antibodies ◽

Functional Studies ◽

Amino Acid Mutations ◽

Env Protein ◽

Anti Hiv ◽

Hiv 1

SummaryAnti-HIV broadly neutralizing antibodies (bnAbs) have revealed vaccine targets on the virus’s Env protein and are themselves promising immunotherapeutics. The efficacy of bnAb-based therapies and vaccines depends in part on how readily the virus can escape neutralization. While structural studies can define contacts between bnAbs and Env, only functional studies can define mutations that confer escape. Here we map how all single amino-acid mutations to Env affect neutralization of HIV by nine bnAbs targeting five epitopes. For most bnAbs, mutations at only a small fraction of structurally defined contact sites mediated escape, and most escape occurred at sites that are near but do not directly contact the antibody. The mutations selected by two pooled bnAbs were similar to those expected from the combination of the bnAbs’ independent action. Overall, our mutation-level antigenic atlas provides a comprehensive dataset for understanding viral immune escape and refining therapies and vaccines.

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