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Sun Y, Zhu Y, Zhang P, Sheng S, Guan Z, Cong Y. Hemagglutinin glycosylation pattern-specific effects: implications for the fitness of H9.4.2.5-branched H9N2 avian influenza viruses. Emerg Microbes Infect 2024; 13:2364736. [PMID: 38847071 PMCID: PMC11182062 DOI: 10.1080/22221751.2024.2364736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/02/2024] [Indexed: 06/16/2024]
Abstract
Since 2007, h9.4.2.5 has emerged as the most predominant branch of H9N2 avian influenza viruses (AIVs) that affects the majority of the global poultry population. The spread of this viral branch in vaccinated chicken flocks has not been considerably curbed despite numerous efforts. The evolutionary fitness of h9.4.2.5-branched AIVs must consequently be taken into consideration. The glycosylation modifications of hemagglutinin (HA) play a pivotal role in regulating the balance between receptor affinity and immune evasion for influenza viruses. Sequence alignment showed that five major HA glycosylation patterns have evolved over time in h9.4.2.5-branched AIVs. Here, we compared the adaptive phenotypes of five virus mutants with different HA glycosylation patterns. According to the results, the mutant with 6 N-linked glycans displayed the best acid and thermal stability and a better capacity for multiplication, although having a relatively lower receptor affinity than 7 glycans. The antigenic profile between the five mutants revealed a distinct antigenic distance, indicating that variations in glycosylation level have an impact on antigenic drift. These findings suggest that changes in the number of glycans on HA can not only modulate the receptor affinity and antigenicity of H9N2 AIVs, but also affect their stability and multiplication. These adaptive phenotypes may underlie the biological basis for the dominant strain switchover of h9.4.2.5-branched AIVs. Overall, our study provides a systematic insight into how changes in HA glycosylation patterns regulate the evolutionary fitness and epidemiological dominance drift of h9.4.2.5-branched H9N2 AIVs, which will be of great benefit for the glycosylation-dependent vaccine design.
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Affiliation(s)
- Yixue Sun
- Department of Policies and Regulations, Changchun University, Changchun, People’s Republic of China
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yanting Zhu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Pengju Zhang
- Institute of Animal Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, People’s Republic of China
| | - Shouzhi Sheng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhenhong Guan
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yanlong Cong
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, and College of Veterinary Medicine, Jilin University, Changchun, China
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2
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Peter AS, Hoffmann DS, Klier J, Lange CM, Moeller J, Most V, Wüst CK, Beining M, Gülesen S, Junker H, Brumme B, Schiffner T, Meiler J, Schoeder CT. Strategies of rational and structure-driven vaccine design for Arenaviruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105626. [PMID: 38908736 DOI: 10.1016/j.meegid.2024.105626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/16/2024] [Accepted: 06/18/2024] [Indexed: 06/24/2024]
Abstract
The COVID-19 outbreak has highlighted the importance of pandemic preparedness for the prevention of future health crises. One virus family with high pandemic potential are Arenaviruses, which have been detected almost worldwide, particularly in Africa and the Americas. These viruses are highly understudied and many questions regarding their structure, replication and tropism remain unanswered, making the design of an efficacious and molecularly-defined vaccine challenging. We propose that structure-driven computational vaccine design will contribute to overcome these challenges. Computational methods for stabilization of viral glycoproteins or epitope focusing have made progress during the last decades and particularly during the COVID-19 pandemic, and have proven useful for rational vaccine design and the establishment of novel diagnostic tools. In this review, we summarize gaps in our understanding of Arenavirus molecular biology, highlight challenges in vaccine design and discuss how structure-driven and computationally informed strategies will aid in overcoming these obstacles.
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Affiliation(s)
- Antonia Sophia Peter
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Dieter S Hoffmann
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Johannes Klier
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Christina M Lange
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Johanna Moeller
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany
| | - Victoria Most
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Christina K Wüst
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; Molecular Medicine Studies, Faculty for Biology and Preclinical Medicine, University of Regensburg, Regensburg, Germany
| | - Max Beining
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; SECAI, School of Embedded Composite Artificial Intelligence, Dresden/Leipzig, Germany
| | - Sevilay Gülesen
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Hannes Junker
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Birke Brumme
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | - Torben Schiffner
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; The Scripps Research Institute, Department for Immunology and Microbiology, La Jolla, CA, United States
| | - Jens Meiler
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany; Department of Chemistry, Vanderbilt University, Nashville, TN, United States; Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Clara T Schoeder
- Institute for Drug Discovery, Leipzig University, Faculty of Medicine, Leipzig, Germany; Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany.
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3
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Hill BD, Zak AJ, Raja S, Bugada LF, Rizvi SM, Roslan SB, Nguyen HN, Chen J, Jiang H, Ono A, Goldstein DR, Wen F. iGATE analysis improves the interpretability of single-cell immune landscape of influenza infection. JCI Insight 2024; 9:e172140. [PMID: 38814732 DOI: 10.1172/jci.insight.172140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024] Open
Abstract
Influenza poses a persistent health burden worldwide. To design equitable vaccines effective across all demographics, it is essential to better understand how host factors such as genetic background and aging affect the single-cell immune landscape of influenza infection. Cytometry by time-of-flight (CyTOF) represents a promising technique in this pursuit, but interpreting its large, high-dimensional data remains difficult. We have developed a new analytical approach, in silico gating annotating training elucidating (iGATE), based on probabilistic support vector machine classification. By rapidly and accurately "gating" tens of millions of cells in silico into user-defined types, iGATE enabled us to track 25 canonical immune cell types in mouse lung over the course of influenza infection. Applying iGATE to study effects of host genetic background, we show that the lower survival of C57BL/6 mice compared with BALB/c was associated with a more rapid accumulation of inflammatory cell types and decreased IL-10 expression. Furthermore, we demonstrate that the most prominent effect of aging is a defective T cell response, reducing survival of aged mice. Finally, iGATE reveals that the 25 canonical immune cell types exhibited differential influenza infection susceptibility and replication permissiveness in vivo, but neither property varied with host genotype or aging. The software is available at https://github.com/UmichWenLab/iGATE.
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Affiliation(s)
| | | | | | | | | | | | | | - Judy Chen
- Program in Immunology
- Department of Internal Medicine
| | | | - Akira Ono
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Fei Wen
- Department of Chemical Engineering
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4
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Luo Z, Miranda HA, Burke KN, Spurrier MA, Berry M, Stover EL, Spreng RL, Waitt G, Soderblom EJ, Macintyre AN, Wiehe K, Heaton NS. Vaccination with antigenically complex hemagglutinin mixtures confers broad protection from influenza disease. Sci Transl Med 2024; 16:eadj4685. [PMID: 38691617 DOI: 10.1126/scitranslmed.adj4685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 03/06/2024] [Indexed: 05/03/2024]
Abstract
Current seasonal influenza virus vaccines induce responses primarily against immunodominant but highly plastic epitopes in the globular head of the hemagglutinin (HA) glycoprotein. Because of viral antigenic drift at these sites, vaccines need to be updated and readministered annually. To increase the breadth of influenza vaccine-mediated protection, we developed an antigenically complex mixture of recombinant HAs designed to redirect immune responses to more conserved domains of the protein. Vaccine-induced antibodies were disproportionally redistributed to the more conserved stalk of the HA without hindering, and in some cases improving, antibody responses against the head domain. These improved responses led to increased protection against homologous and heterologous viral challenges in both mice and ferrets compared with conventional vaccine approaches. Thus, antigenically complex protein mixtures can at least partially overcome HA head domain antigenic immunodominance and may represent a step toward a more universal influenza vaccine.
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Affiliation(s)
- Zhaochen Luo
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hector A Miranda
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kaitlyn N Burke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - M Ariel Spurrier
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Madison Berry
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Erica L Stover
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rachel L Spreng
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Greg Waitt
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC 27710, USA
| | - Erik J Soderblom
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC 27710, USA
| | - Andrew N Macintyre
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
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5
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Ertelt M, Mulligan VK, Maguire JB, Lyskov S, Moretti R, Schiffner T, Meiler J, Schoeder CT. Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins. PLoS Comput Biol 2024; 20:e1011939. [PMID: 38484014 DOI: 10.1371/journal.pcbi.1011939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 03/26/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024] Open
Abstract
Post-translational modifications (PTMs) of proteins play a vital role in their function and stability. These modifications influence protein folding, signaling, protein-protein interactions, enzyme activity, binding affinity, aggregation, degradation, and much more. To date, over 400 types of PTMs have been described, representing chemical diversity well beyond the genetically encoded amino acids. Such modifications pose a challenge to the successful design of proteins, but also represent a major opportunity to diversify the protein engineering toolbox. To this end, we first trained artificial neural networks (ANNs) to predict eighteen of the most abundant PTMs, including protein glycosylation, phosphorylation, methylation, and deamidation. In a second step, these models were implemented inside the computational protein modeling suite Rosetta, which allows flexible combination with existing protocols to model the modified sites and understand their impact on protein stability as well as function. Lastly, we developed a new design protocol that either maximizes or minimizes the predicted probability of a particular site being modified. We find that this combination of ANN prediction and structure-based design can enable the modification of existing, as well as the introduction of novel, PTMs. The potential applications of our work include, but are not limited to, glycan masking of epitopes, strengthening protein-protein interactions through phosphorylation, as well as protecting proteins from deamidation liabilities. These applications are especially important for the design of new protein therapeutics where PTMs can drastically change the therapeutic properties of a protein. Our work adds novel tools to Rosetta's protein engineering toolbox that allow for the rational design of PTMs.
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Affiliation(s)
- Moritz Ertelt
- Institute for Drug Discovery, Leipzig University Medical Faculty, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany
| | - Vikram Khipple Mulligan
- Center for Computational Biology, Flatiron Institute, New York, New York, United States of America
| | - Jack B Maguire
- Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Rocco Moretti
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Torben Schiffner
- Institute for Drug Discovery, Leipzig University Medical Faculty, Leipzig, Germany
| | - Jens Meiler
- Institute for Drug Discovery, Leipzig University Medical Faculty, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Clara T Schoeder
- Institute for Drug Discovery, Leipzig University Medical Faculty, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence ScaDS.AI, Dresden/Leipzig, Germany
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6
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Xu D, Powell AE, Utz A, Sanyal M, Do J, Patten JJ, Moliva JI, Sullivan NJ, Davey RA, Kim PS. Design of universal Ebola virus vaccine candidates via immunofocusing. Proc Natl Acad Sci U S A 2024; 121:e2316960121. [PMID: 38319964 PMCID: PMC10873634 DOI: 10.1073/pnas.2316960121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/19/2023] [Indexed: 02/08/2024] Open
Abstract
The Ebola virus causes hemorrhagic fever in humans and poses a significant threat to global public health. Although two viral vector vaccines have been approved to prevent Ebola virus disease, they are distributed in the limited ring vaccination setting and only indicated for prevention of infection from orthoebolavirus zairense (EBOV)-one of three orthoebolavirus species that have caused previous outbreaks. Ebola virus glycoprotein GP mediates viral infection and serves as the primary target of neutralizing antibodies. Here, we describe a universal Ebola virus vaccine approach using a structure-guided design of candidates with hyperglycosylation that aims to direct antibody responses away from variable regions and toward conserved epitopes of GP. We first determined the hyperglycosylation landscape on Ebola virus GP and used that to generate hyperglycosylated GP variants with two to four additional glycosylation sites to mask the highly variable glycan cap region. We then created vaccine candidates by displaying wild-type or hyperglycosylated GP variants on ferritin nanoparticles (Fer). Immunization with these antigens elicited potent neutralizing antisera against EBOV in mice. Importantly, we observed consistent cross-neutralizing activity against Bundibugyo virus and Sudan virus from hyperglycosylated GP-Fer with two or three additional glycans. In comparison, elicitation of cross-neutralizing antisera was rare in mice immunized with wild-type GP-Fer. These results demonstrate a potential strategy to develop universal Ebola virus vaccines that confer cross-protective immunity against existing and emerging filovirus species.
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Affiliation(s)
- Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Abigail E. Powell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Ashley Utz
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA94305
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA94305
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Jonathan Do
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - J. J. Patten
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
| | - Juan I. Moliva
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
| | - Nancy J. Sullivan
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
- Department of Biology, Boston University, Boston, MA02118
| | - Robert A. Davey
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Chan Zuckerberg Biohub, San Francisco, CA94158
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7
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Xu D, Carter JJ, Li C, Utz A, Weidenbacher PAB, Tang S, Sanyal M, Pulendran B, Barnes CO, Kim PS. Vaccine design via antigen reorientation. Nat Chem Biol 2024:10.1038/s41589-023-01529-6. [PMID: 38225471 DOI: 10.1038/s41589-023-01529-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024]
Abstract
A major challenge in creating universal influenza vaccines is to focus immune responses away from the immunodominant, variable head region of hemagglutinin (HA-head) and toward the evolutionarily conserved stem region (HA-stem). Here we introduce an approach to control antigen orientation via site-specific insertion of aspartate residues that facilitates antigen binding to alum. We demonstrate the generalizability of this approach with antigens from Ebola, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses and observe enhanced neutralizing antibody responses in all cases. We then reorient an H2 HA in an 'upside-down' configuration to increase the exposure and immunogenicity of HA-stem. The reoriented H2 HA (reoH2HA) on alum induced stem-directed antibodies that cross-react with both group 1 and group 2 influenza A subtypes. Electron microscopy polyclonal epitope mapping (EMPEM) revealed that reoH2HA (group 1) elicits cross-reactive antibodies targeting group 2 HA-stems. Our results highlight antigen reorientation as a generalizable approach for designing epitope-focused vaccines.
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Affiliation(s)
- Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Joshua J Carter
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Ashley Utz
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Payton A B Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Shaogeng Tang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher O Barnes
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter S Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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8
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Musunuri S, Weidenbacher PAB, Kim PS. Bringing immunofocusing into focus. NPJ Vaccines 2024; 9:11. [PMID: 38195562 PMCID: PMC10776678 DOI: 10.1038/s41541-023-00792-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
Immunofocusing is a strategy to create immunogens that redirect humoral immune responses towards a targeted epitope and away from non-desirable epitopes. Immunofocusing methods often aim to develop "universal" vaccines that provide broad protection against highly variant viruses such as influenza virus, human immunodeficiency virus (HIV-1), and most recently, severe acute respiratory syndrome coronavirus (SARS-CoV-2). We use existing examples to illustrate five main immunofocusing strategies-cross-strain boosting, mosaic display, protein dissection, epitope scaffolding, and epitope masking. We also discuss obstacles for immunofocusing like immune imprinting. A thorough understanding, advancement, and application of the methods we outline here will enable the design of high-resolution vaccines that protect against future viral outbreaks.
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Affiliation(s)
- Sriharshita Musunuri
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Payton A B Weidenbacher
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Peter S Kim
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA.
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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9
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Wu NC, Ellebedy AH. Targeting neuraminidase: the next frontier for broadly protective influenza vaccines. Trends Immunol 2024; 45:11-19. [PMID: 38103991 PMCID: PMC10841738 DOI: 10.1016/j.it.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 12/19/2023]
Abstract
Current seasonal influenza vaccines, which mainly target hemagglutinin (HA), require annual updates due to the continuous antigenic drift of the influenza virus. Developing an influenza vaccine with increased breadth of protection will have significant public health benefits. The recent discovery of broadly protective antibodies to neuraminidase (NA) has provided important insights into developing a universal influenza vaccine, either by improving seasonal influenza vaccines or designing novel immunogens. However, further in-depth molecular characterizations of NA antibody responses are warranted to fully leverage broadly protective NA antibodies for influenza vaccine designs. Overall, we posit that focusing on NA for influenza vaccine development is synergistic with existing efforts targeting HA, and may represent a cost-effective approach to generating a broadly protective influenza vaccine.
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Affiliation(s)
- Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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10
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Dosey A, Ellis D, Boyoglu-Barnum S, Syeda H, Saunders M, Watson MJ, Kraft JC, Pham MN, Guttman M, Lee KK, Kanekiyo M, King NP. Combinatorial immune refocusing within the influenza hemagglutinin RBD improves cross-neutralizing antibody responses. Cell Rep 2023; 42:113553. [PMID: 38096052 PMCID: PMC10801708 DOI: 10.1016/j.celrep.2023.113553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/28/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
The receptor-binding domain (RBD) of influenza virus hemagglutinin (HA) elicits potently neutralizing yet mostly strain-specific antibodies. Here, we evaluate the ability of several immunofocusing techniques to enhance the functional breadth of vaccine-elicited immune responses against the HA RBD. We present a series of "trihead" nanoparticle immunogens that display native-like closed trimeric RBDs from the HAs of several H1N1 influenza viruses. The series includes hyperglycosylated and hypervariable variants that incorporate natural and designed sequence diversity at key positions in the receptor-binding site periphery. Nanoparticle immunogens displaying triheads or hyperglycosylated triheads elicit higher hemagglutination inhibition (HAI) and neutralizing activity than the corresponding immunogens lacking either trimer-stabilizing mutations or hyperglycosylation. By contrast, mosaic nanoparticle display and antigen hypervariation do not significantly alter the magnitude or breadth of vaccine-elicited antibodies. Our results yield important insights into antibody responses against the RBD and the ability of several structure-based immunofocusing techniques to influence vaccine-elicited antibody responses.
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Affiliation(s)
- Annie Dosey
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hubza Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mason Saunders
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Michael J Watson
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - John C Kraft
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Minh N Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
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11
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Hulbert SW, Desai P, Jewett MC, DeLisa MP, Williams AJ. Glycovaccinology: The design and engineering of carbohydrate-based vaccine components. Biotechnol Adv 2023; 68:108234. [PMID: 37558188 DOI: 10.1016/j.biotechadv.2023.108234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/12/2023] [Accepted: 08/05/2023] [Indexed: 08/11/2023]
Abstract
Vaccines remain one of the most important pillars in preventative medicine, providing protection against a wide array of diseases by inducing humoral and/or cellular immunity. Of the many possible candidate antigens for subunit vaccine development, carbohydrates are particularly appealing because of their ubiquitous presence on the surface of all living cells, viruses, and parasites as well as their known interactions with both innate and adaptive immune cells. Indeed, several licensed vaccines leverage bacterial cell-surface carbohydrates as antigens for inducing antigen-specific plasma cells secreting protective antibodies and the development of memory T and B cells. Carbohydrates have also garnered attention in other aspects of vaccine development, for example, as adjuvants that enhance the immune response by either activating innate immune responses or targeting specific immune cells. Additionally, carbohydrates can function as immunomodulators that dampen undesired humoral immune responses to entire protein antigens or specific, conserved regions on antigenic proteins. In this review, we highlight how the interplay between carbohydrates and the adaptive and innate arms of the immune response is guiding the development of glycans as vaccine components that act as antigens, adjuvants, and immunomodulators. We also discuss how advances in the field of synthetic glycobiology are enabling the design, engineering, and production of this new generation of carbohydrate-containing vaccine formulations with the potential to prevent infectious diseases, malignancies, and complex immune disorders.
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Affiliation(s)
- Sophia W Hulbert
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Primit Desai
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Matthew P DeLisa
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA; Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Cornell Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA.
| | - Asher J Williams
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.
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12
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Huang CQ, Vishwanath S, Carnell GW, Chan ACY, Heeney JL. Immune imprinting and next-generation coronavirus vaccines. Nat Microbiol 2023; 8:1971-1985. [PMID: 37932355 DOI: 10.1038/s41564-023-01505-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/13/2023] [Indexed: 11/08/2023]
Abstract
Vaccines based on historical virus isolates provide limited protection from continuously evolving RNA viruses, such as influenza viruses or coronaviruses, which occasionally spill over between animals and humans. Despite repeated booster immunizations, population-wide declines in the neutralization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have occurred. This has been compared to seasonal influenza vaccinations in humans, where the breadth of immune responses induced by repeat exposures to antigenically distinct influenza viruses is confounded by pre-existing immunity-a mechanism known as imprinting. Since its emergence, SARS-CoV-2 has evolved in a population with partial immunity, acquired by infection, vaccination or both. Here we critically examine the evidence for and against immune imprinting in host humoral responses to SARS-CoV-2 and its implications for coronavirus disease 2019 (COVID-19) booster vaccine programmes.
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Affiliation(s)
- Chloe Qingzhou Huang
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sneha Vishwanath
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - George William Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Andrew Chun Yue Chan
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jonathan Luke Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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13
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Xu D, Powell AE, Utz A, Sanyal M, Do J, Patten J, Moliva JI, Sullivan NJ, Davey RA, Kim PS. Design of universal Ebola virus vaccine candidates via immunofocusing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.14.562364. [PMID: 37904982 PMCID: PMC10614775 DOI: 10.1101/2023.10.14.562364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Ebola virus causes hemorrhagic fever in humans and poses a significant threat to global public health. Although two viral vector vaccines have been approved to prevent Ebola virus disease, they are distributed in the limited ring vaccination setting and only indicated for prevention of infection from orthoebolavirus zairense (EBOV) - one of three orthoebolavirus species that have caused previous outbreaks. Ebola virus glycoprotein GP mediates viral infection and serves as the primary target of neutralizing antibodies. Here we describe a universal Ebola virus vaccine approach using structure-guided design of candidates with hyperglycosylation that aims to direct antibody responses away from variable regions and toward conserved epitopes of GP. We first determined the hyperglycosylation landscape on Ebola virus GP and used that to generate hyperglycosylated GP variants with two to four additional glycosylation sites to mask the highly variable glycan cap region. We then created vaccine candidates by displaying wild-type or hyperglycosylated GP variants on ferritin nanoparticles (Fer). Immunization with these antigens elicited potent neutralizing antisera against EBOV in mice. Importantly, we observed consistent cross-neutralizing activity against Bundibugyo virus and Sudan virus from hyperglycosylated GP-Fer with two or three additional glycans. In comparison, elicitation of cross-neutralizing antisera was rare in mice immunized with wild-type GP-Fer. These results demonstrate a potential strategy to develop universal Ebola virus vaccines that confer cross-protective immunity against existing and emerging filovirus species.
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Affiliation(s)
- Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Abigail E. Powell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Ashley Utz
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Jonathan Do
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - J.J. Patten
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Juan I. Moliva
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Nancy J. Sullivan
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Biology, Boston University, Boston, MA 02118, USA
| | - Robert A. Davey
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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14
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Vishwanath S, Carnell GW, Ferrari M, Asbach B, Billmeier M, George C, Sans MS, Nadesalingam A, Huang CQ, Paloniemi M, Stewart H, Chan A, Wells DA, Neckermann P, Peterhoff D, Einhauser S, Cantoni D, Neto MM, Jordan I, Sandig V, Tonks P, Temperton N, Frost S, Sohr K, Ballesteros MTL, Arbabi F, Geiger J, Dohmen C, Plank C, Kinsley R, Wagner R, Heeney JL. A computationally designed antigen eliciting broad humoral responses against SARS-CoV-2 and related sarbecoviruses. Nat Biomed Eng 2023:10.1038/s41551-023-01094-2. [PMID: 37749309 DOI: 10.1038/s41551-023-01094-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 08/23/2023] [Indexed: 09/27/2023]
Abstract
The threat of spillovers of coronaviruses associated with the severe acute respiratory syndrome (SARS) from animals to humans necessitates vaccines that offer broader protection from sarbecoviruses. By leveraging a viral-genome-informed computational method for selecting immune-optimized and structurally engineered antigens, here we show that a single antigen based on the receptor binding domain of the spike protein of sarbecoviruses elicits broad humoral responses against SARS-CoV-1, SARS-CoV-2, WIV16 and RaTG13 in mice, rabbits and guinea pigs. When administered as a DNA immunogen or by a vector based on a modified vaccinia virus Ankara, the optimized antigen induced vaccine protection from the Delta variant of SARS-CoV-2 in mice genetically engineered to express angiotensin-converting enzyme 2 and primed by a viral-vector vaccine (AZD1222) against SARS-CoV-2. A vaccine formulation incorporating mRNA coding for the optimized antigen further validated its broad immunogenicity. Vaccines that elicit broad immune responses across subgroups of coronaviruses may counteract the threat of zoonotic spillovers of betacoronaviruses.
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Affiliation(s)
- Sneha Vishwanath
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - George William Carnell
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Benedikt Asbach
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Martina Billmeier
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Charlotte George
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Maria Suau Sans
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Angalee Nadesalingam
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Chloe Qingzhou Huang
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Minna Paloniemi
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Hazel Stewart
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Andrew Chan
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Patrick Neckermann
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Sebastian Einhauser
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, UK
| | - Martin Mayora Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, UK
| | | | | | - Paul Tonks
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, UK
| | - Simon Frost
- DIOSynVax Ltd, University of Cambridge, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
- Microsoft Health Futures, Redmond, WA, USA
| | | | | | | | | | | | | | - Rebecca Kinsley
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- DIOSynVax Ltd, University of Cambridge, Cambridge, UK
| | - Ralf Wagner
- DIOSynVax Ltd, University of Cambridge, Cambridge, UK
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Jonathan Luke Heeney
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
- DIOSynVax Ltd, University of Cambridge, Cambridge, UK.
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15
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Puente-Massaguer E, Vasilev K, Beyer A, Loganathan M, Francis B, Scherm MJ, Arunkumar GA, González-Domínguez I, Zhu X, Wilson IA, Coughlan L, Sun W, Palese P, Krammer F. Chimeric hemagglutinin split vaccines elicit broadly cross-reactive antibodies and protection against group 2 influenza viruses in mice. SCIENCE ADVANCES 2023; 9:eadi4753. [PMID: 37703367 PMCID: PMC10499326 DOI: 10.1126/sciadv.adi4753] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/11/2023] [Indexed: 09/15/2023]
Abstract
Seasonal influenza virus vaccines are effective when they are well matched to circulating strains. Because of antigenic drift/change in the immunodominant hemagglutinin (HA) head domain, annual vaccine reformulations are necessary to maintain a match with circulating strains. In addition, seasonal vaccines provide little to no protection against newly emerging pandemic strains. Sequential vaccination with chimeric HA (cHA) constructs has been proven to direct the immune response toward the immunosubdominant but more conserved HA stalk domain. In this study, we show that immunization with group 2 cHA split vaccines in combination with the CpG 1018 adjuvant elicits broadly cross-reactive antibodies against all group 2 HAs, as well as systemic and local antigen-specific T cell responses. Antibodies elicited after sequential vaccination are directed to conserved regions of the HA such as the stalk and the trimer interface and also to the N2 neuraminidase (NA). Immunized mice were fully protected from challenge with a broad panel of influenza A viruses.
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Affiliation(s)
- Eduard Puente-Massaguer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kirill Vasilev
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Annika Beyer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Madhumathi Loganathan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin Francis
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael J. Scherm
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lynda Coughlan
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Weina Sun
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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16
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Li Y, Wang X, Zeng X, Ren W, Liao P, Zhu B. Protective efficacy of a universal influenza mRNA vaccine against the challenge of H1 and H5 influenza A viruses in mice. MLIFE 2023; 2:308-316. [PMID: 38817814 PMCID: PMC10989953 DOI: 10.1002/mlf2.12085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/02/2023] [Accepted: 06/29/2023] [Indexed: 06/01/2024]
Abstract
Current influenza vaccines need to be updated annually owing to constant antigenic drift in the globular head of the viral surface hemagglutinin (HA) glycoprotein. The immunogenic subdominant stem domain of HA is highly conserved and can be recognized by antibodies capable of binding multiple HA subtypes. Therefore, the HA stem antigen is a promising target for the design of universal influenza vaccines. On the basis of an established lipid nanoparticle-encapsulated mRNA vaccine platform, we designed and developed a novel universal influenza mRNA vaccine (mHAs) encoding the HA stem antigen of the influenza A (H1N1) virus. We tested the efficacy of the mHAs vaccine using a mouse model. The vaccine induced robust humoral and specific cellular immune responses against the stem region of HA. Importantly, two doses of the mHAs vaccine fully protected mice from lethal challenges of the heterologous H1N1 and heterosubtypic H5N8 influenza viruses. Vaccinated mice had less pathological lung damage and lower viral titers than control mice. These results suggest that an mRNA vaccine using the conserved stem region of HA may provide effective protection against seasonal and other possible influenza variants.
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Affiliation(s)
- Yulei Li
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
- The Key Laboratory of Molecular Pathology (Hepatobiliary Diseases) of Guangxi, Department of PathologyThe Affiliated Hospital of Youjiang Medical University for NationalitiesBaiseChina
| | - Xi Wang
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyChinese Academy of SciencesBeijingChina
| | - Xi Zeng
- Beijing Children's HospitalCapital Medical UniversityBeijingChina
| | - Wenbo Ren
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Pu Liao
- Department of Clinical LaboratoryChongqing General HospitalChongqingChina
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Department of Pathogenic Biology, School of Basic Medical SciencesSouthwest Medical UniversityLuzhouChina
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17
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Chiba S, Kong H, Neumann G, Kawaoka Y. Influenza H3 hemagglutinin vaccine with scrambled immunodominant epitopes elicits antibodies directed toward immunosubdominant head epitopes. mBio 2023; 14:e0062223. [PMID: 37466314 PMCID: PMC10470489 DOI: 10.1128/mbio.00622-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/13/2023] [Indexed: 07/20/2023] Open
Abstract
Vaccination is the most effective countermeasure to reduce the severity of influenza. Current seasonal influenza vaccines mainly elicit humoral immunity targeting hemagglutinin (HA). In particular, the amino acid residues around the receptor-binding site in the HA head domain are predominantly targeted by humoral immunity as "immunodominant" epitopes. However, mutations readily accumulate in the head domain due to high plasticity, resulting in antigenic drift and vaccine mismatch, particularly with influenza A (H3N2) viruses. A vaccine strategy that targets more conserved immunosubdominant epitopes is required to attain a universal vaccine. Here, we designed an H3 HA vaccine antigen with various amino acids at immunodominant epitopes of the HA head domain, termed scrambled HA (scrHA). In ferrets, scrHA vaccination induced lower serum neutralizing antibody levels against homologous virus compared with wild-type (WT) HA vaccination; however, similar levels of moderately neutralizing titers against antigenically distinct H3N2 viruses were observed. Ferrets vaccinated with scrHA twice and then challenged with homologous or heterologous virus showed the same level of reduced virus shedding in nasal swabs as WT HA-vaccinated animals but reduced body temperature increase, whereas WT HA-vaccinated ferrets exhibited body temperature increases similar to those of mock-vaccinated animals. scrHA elicited antibodies against HA immunodominant and -subdominant epitopes at lower and higher levels, respectively, than WT HA vaccination, whereas antistalk antibodies were induced at the same level for both groups, suggesting scrHA-induced redirection from immunodominant to immunosubdominant head epitopes. scrHA vaccination thus induced broader coverage than WT HA vaccination by diluting out the immunodominancy of HA head epitopes. IMPORTANCE Current influenza vaccines mainly elicit antibodies that target the immunodominant head domain, where strain-specific mutations rapidly accumulate, resulting in frequent antigenic drift and vaccine mismatch. Targeting conserved immunosubdominant epitopes is essential to attain a universal vaccine. Our findings with the scrHA developed in this study suggest that designing vaccine antigens that "dilute out" the immunodominancy of the head epitopes may be an effective strategy to induce conserved immunosubdominant epitope-based immune responses.
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Affiliation(s)
- Shiho Chiba
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Huihui Kong
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), The University of Tokyo, Tokyo, Japan
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18
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Zhang X, Zhou Z. The Mechanism of bnAb Production and Its Application in Mutable Virus Broad-Spectrum Vaccines: Inspiration from HIV-1 Broad Neutralization Research. Vaccines (Basel) 2023; 11:1143. [PMID: 37514959 PMCID: PMC10384589 DOI: 10.3390/vaccines11071143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Elite controllers among HIV-1-infected individuals have demonstrated a stronger ability to control the viral load in their bodies. Scientists have isolated antibodies with strong neutralizing ability from these individuals, which can neutralize HIV-1 variations; these are known as broadly neutralizing antibodies. The nucleic acid of some viruses will constantly mutate during replication (such as SARS-CoV-2), which will reduce the protective ability of the corresponding vaccines. The immune escape caused by this mutation is the most severe challenge faced by humans in the battle against the virus. Therefore, developing broad-spectrum vaccines that can induce broadly neutralizing antibodies against various viruses and their mutated strains is the best way to combat virus mutations. Exploring the mechanism by which the human immune system produces broadly neutralizing antibodies and its induction strategies is crucial in the design process of broad-spectrum vaccines.
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Affiliation(s)
- Xinyu Zhang
- Research Center for Infectious Diseases, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
- College of Life Science, Jilin University, Changchun 130012, China
| | - Zehua Zhou
- Research Center for Infectious Diseases, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
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19
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Dosey A, Ellis D, Boyoglu-Barnum S, Syeda H, Saunders M, Watson M, Kraft JC, Pham MN, Guttman M, Lee KK, Kanekiyo M, King NP. Combinatorial immune refocusing within the influenza hemagglutinin head elicits cross-neutralizing antibody responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541996. [PMID: 37292967 PMCID: PMC10245820 DOI: 10.1101/2023.05.23.541996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The head domain of influenza hemagglutinin (HA) elicits potently neutralizing yet mostly strain-specific antibodies during infection and vaccination. Here we evaluated a series of immunogens that combined several immunofocusing techniques for their ability to enhance the functional breadth of vaccine-elicited immune responses. We designed a series of "trihead" nanoparticle immunogens that display native-like closed trimeric heads from the HAs of several H1N1 influenza viruses, including hyperglycosylated variants and hypervariable variants that incorporate natural and designed sequence diversity at key positions in the periphery of the receptor binding site (RBS). Nanoparticle immunogens displaying triheads or hyperglycosylated triheads elicited higher HAI and neutralizing activity against vaccine-matched and -mismatched H1 viruses than corresponding immunogens lacking either trimer-stabilizing mutations or hyperglycosylation, indicating that both of these engineering strategies contributed to improved immunogenicity. By contrast, mosaic nanoparticle display and antigen hypervariation did not significantly alter the magnitude or breadth of vaccine-elicited antibodies. Serum competition assays and electron microscopy polyclonal epitope mapping revealed that the trihead immunogens, especially when hyperglycosylated, elicited a high proportion of antibodies targeting the RBS, as well as cross-reactive antibodies targeting a conserved epitope on the side of the head. Our results yield important insights into antibody responses against the HA head and the ability of several structure-based immunofocusing techniques to influence vaccine-elicited antibody responses.
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Affiliation(s)
- Annie Dosey
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hubza Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mason Saunders
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Michael Watson
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - John C. Kraft
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Minh N. Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
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20
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Frey SJ, Carreño JM, Bielak D, Arsiwala A, Altomare CG, Varner C, Rosen-Cheriyan T, Bajic G, Krammer F, Kane RS. Nanovaccines Displaying the Influenza Virus Hemagglutinin in an Inverted Orientation Elicit an Enhanced Stalk-Directed Antibody Response. Adv Healthc Mater 2023; 12:e2202729. [PMID: 36689343 PMCID: PMC10386890 DOI: 10.1002/adhm.202202729] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 01/18/2023] [Indexed: 01/24/2023]
Abstract
Despite the availability of licensed vaccines, influenza causes considerable morbidity and mortality worldwide. Current influenza vaccines elicit an immune response that primarily targets the head domain of the viral glycoprotein hemagglutinin (HA). Influenza viruses, however, readily evade this response by acquiring mutations in the head domain. While vaccines that target the more conserved HA stalk may circumvent this problem, low levels of antistalk antibodies are elicited by vaccination, possibly due to the poor accessibility of the stalk domain to B cell receptors. In this work, it is demonstrated that nanoparticles presenting HA in an inverted orientation generate tenfold higher antistalk antibody titers after a prime immunization and fivefold higher antistalk titers after a boost than nanoparticles displaying HA in its regular orientation. Moreover, nanoparticles presenting HA in an inverted orientation elicit a broader antistalk response that reduces mouse weight loss and improves survival after challenge to a greater extent than nanoparticles displaying HA in a regular orientation. Refocusing the antibody response toward conserved epitopes by controlling antigen orientation may enable the design of broadly protective nanovaccines targeting influenza viruses and other pathogens with pandemic potential.
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Affiliation(s)
- Steven J Frey
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dominika Bielak
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ammar Arsiwala
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Clara G Altomare
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chad Varner
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Tania Rosen-Cheriyan
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ravi S Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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21
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Dzimianski JV, Han J, Sautto GA, O'Rourke SM, Cruz JM, Pierce SR, Ecker JW, Carlock MA, Nagashima KA, Mousa JJ, Ross TM, Ward AB, DuBois RM. Structural insights into the broad protection against H1 influenza viruses by a computationally optimized hemagglutinin vaccine. Commun Biol 2023; 6:454. [PMID: 37185989 PMCID: PMC10126545 DOI: 10.1038/s42003-023-04793-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 03/31/2023] [Indexed: 05/17/2023] Open
Abstract
Influenza virus poses an ongoing human health threat with pandemic potential. Due to mutations in circulating strains, formulating effective vaccines remains a challenge. The use of computationally optimized broadly reactive antigen (COBRA) hemagglutinin (HA) proteins is a promising vaccine strategy to protect against a wide range of current and future influenza viruses. Though effective in preclinical studies, the mechanistic basis driving the broad reactivity of COBRA proteins remains to be elucidated. Here, we report the crystal structure of the COBRA HA termed P1 and identify antigenic and glycosylation properties that contribute to its immunogenicity. We further report the cryo-EM structure of the P1-elicited broadly neutralizing antibody 1F8 bound to COBRA P1, revealing 1F8 to recognize an atypical receptor binding site epitope via an unexpected mode of binding.
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Affiliation(s)
- John V Dzimianski
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Giuseppe A Sautto
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Sara M O'Rourke
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Joseph M Cruz
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Spencer R Pierce
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Jeffrey W Ecker
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Michael A Carlock
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Kaito A Nagashima
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Jarrod J Mousa
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
| | - Ted M Ross
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rebecca M DuBois
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
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22
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Martina CE, Crowe JE, Meiler J. Glycan masking in vaccine design: Targets, immunogens and applications. Front Immunol 2023; 14:1126034. [PMID: 37033915 PMCID: PMC10076883 DOI: 10.3389/fimmu.2023.1126034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 02/28/2023] [Indexed: 04/11/2023] Open
Abstract
Glycan masking is a novel technique in reverse vaccinology in which sugar chains (glycans) are added on the surface of immunogen candidates to hide regions of low interest and thus focus the immune system on highly therapeutic epitopes. This shielding strategy is inspired by viruses such as influenza and HIV, which are able to escape the immune system by incorporating additional glycosylation and preventing the binding of therapeutic antibodies. Interestingly, the glycan masking technique is mainly used in vaccine design to fight the same viruses that naturally use glycans to evade the immune system. In this review we report the major successes obtained with the glycan masking technique in epitope-focused vaccine design. We focus on the choice of the target antigen, the strategy for immunogen design and the relevance of the carrier vector to induce a strong immune response. Moreover, we will elucidate the different applications that can be accomplished with glycan masking, such as shifting the immune response from hyper-variable epitopes to more conserved ones, focusing the response on known therapeutic epitopes, broadening the response to different viral strains/sub-types and altering the antigen immunogenicity to elicit higher or lower immune response, as desired.
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Affiliation(s)
- Cristina E. Martina
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
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23
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Ivanochko D, Fabra-García A, Teelen K, van de Vegte-Bolmer M, van Gemert GJ, Newton J, Semesi A, de Bruijni M, Bolscher J, Ramjith J, Szabat M, Vogt S, Kraft L, Duncan S, Lee SM, Kamya MR, Feeney ME, Jagannathan P, Greenhouse B, Sauerwein RW, Richter King C, MacGill RS, Bousema T, Jore MM, Julien JP. Potent transmission-blocking monoclonal antibodies from naturally exposed individuals target a conserved epitope on Plasmodium falciparum Pfs230. Immunity 2023; 56:420-432.e7. [PMID: 36792575 PMCID: PMC9942874 DOI: 10.1016/j.immuni.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/04/2022] [Accepted: 01/12/2023] [Indexed: 02/16/2023]
Abstract
Pfs230 is essential for Plasmodium falciparum transmission to mosquitoes and is the protein targeted by the most advanced malaria-transmission-blocking vaccine candidate. Prior understanding of functional epitopes on Pfs230 is based on two monoclonal antibodies (mAbs) with moderate transmission-reducing activity (TRA), elicited from subunit immunization. Here, we screened the B cell repertoire of two naturally exposed individuals possessing serum TRA and identified five potent mAbs from sixteen Pfs230 domain-1-specific mAbs. Structures of three potent and three low-activity antibodies bound to Pfs230 domain 1 revealed four distinct epitopes. Highly potent mAbs from natural infection recognized a common conformational epitope that is highly conserved across P. falciparum field isolates, while antibodies with negligible TRA derived from natural infection or immunization recognized three distinct sites. Our study provides molecular blueprints describing P. falciparum TRA, informed by contrasting potent and non-functional epitopes elicited by natural exposure and vaccination.
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Affiliation(s)
- Danton Ivanochko
- Program in Molecular Medicine, the Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | | | - Karina Teelen
- Department of Medical Microbiology, Radboudumc, Nijmegen, the Netherlands
| | | | | | - Jocelyn Newton
- Program in Molecular Medicine, the Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Anthony Semesi
- Program in Molecular Medicine, the Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | | | | | - Jordache Ramjith
- Radboud Institute for Health Sciences, Department for Health Evidence, Biostatistics Section, Radboudumc, Nijmegen, the Netherlands
| | | | | | - Lucas Kraft
- AbCellera Biologics Inc., Vancouver, BC, Canada
| | | | - Shwu-Maan Lee
- PATH's Malaria Vaccine Initiative, Washington, DC 20001, USA
| | - Moses R Kamya
- Infectious Disease Research Collaboration, Kampala, Uganda
| | - Margaret E Feeney
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Prasanna Jagannathan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Bryan Greenhouse
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - C Richter King
- PATH's Malaria Vaccine Initiative, Washington, DC 20001, USA
| | | | - Teun Bousema
- Department of Medical Microbiology, Radboudumc, Nijmegen, the Netherlands.
| | - Matthijs M Jore
- Department of Medical Microbiology, Radboudumc, Nijmegen, the Netherlands.
| | - Jean-Philippe Julien
- Program in Molecular Medicine, the Hospital for Sick Children Research Institute, Toronto, ON, Canada; Departments of Biochemistry and Immunology, University of Toronto, Toronto, ON, Canada.
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24
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Inoue T, Shinnakasu R, Kawai C, Yamamoto H, Sakakibara S, Ono C, Itoh Y, Terooatea T, Yamashita K, Okamoto T, Hashii N, Ishii-Watabe A, Butler NS, Matsuura Y, Matsumoto H, Otsuka S, Hiraoka K, Teshima T, Murakami M, Kurosaki T. Antibody feedback contributes to facilitating the development of Omicron-reactive memory B cells in SARS-CoV-2 mRNA vaccinees. J Exp Med 2023; 220:213745. [PMID: 36512034 PMCID: PMC9750191 DOI: 10.1084/jem.20221786] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
In contrast to a second dose of the SARS-CoV-2 mRNA vaccine, a third dose elicits potent neutralizing activity against the Omicron variant. To address the underlying mechanism for this differential antibody response, we examined spike receptor-binding domain (RBD)-specific memory B cells in vaccinated individuals. Frequency of Omicron-reactive memory B cells increased ∼9 mo after the second vaccine dose. These memory B cells show an altered distribution of epitopes from pre-second memory B cells, presumably due to an antibody feedback mechanism. This hypothesis was tested using mouse models, showing that an addition or a depletion of RBD-induced serum antibodies results in a concomitant increase or decrease, respectively, of Omicron-reactive germinal center (GC) and memory B cells. Our data suggest that pre-generated antibodies modulate the selection of GC and subsequent memory B cells after the second vaccine dose, accumulating more Omicron-reactive memory B cells over time, which contributes to the generation of Omicron-neutralizing antibodies elicited by the third vaccine dose.
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Affiliation(s)
- Takeshi Inoue
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Ryo Shinnakasu
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Division of Medical Research Support, Advanced Research Support Center, Ehime University, Ehime, Japan.,Translational Research Center, Ehime University Hospital, Ehime, Japan
| | - Chie Kawai
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Hiromi Yamamoto
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Shuhei Sakakibara
- Laboratory of Immune Regulation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Chikako Ono
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | | | | | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Noritaka Hashii
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Kanagawa, Japan
| | - Akiko Ishii-Watabe
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Kanagawa, Japan
| | - Noah S Butler
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA, USA
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
| | - Hisatake Matsumoto
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Shinya Otsuka
- Department of Surgery, National Hospital Organization Hakodate National Hospital, Hokkaido, Japan
| | - Kei Hiraoka
- Department of Surgery, National Hospital Organization Hakodate National Hospital, Hokkaido, Japan
| | - Takanori Teshima
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan.,Department of Hematology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Masaaki Murakami
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan.,Team of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology, Chiba, Japan.,Division of Molecular Neuroimmunology, Department of Homeostatic Regulation, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Aichi, Japan
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan.,Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
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25
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King SM, Bryan SP, Hilchey SP, Wang J, Zand MS. First Impressions Matter: Immune Imprinting and Antibody Cross-Reactivity in Influenza and SARS-CoV-2. Pathogens 2023; 12:169. [PMID: 36839441 PMCID: PMC9967769 DOI: 10.3390/pathogens12020169] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/24/2023] Open
Abstract
Many rigorous studies have shown that early childhood infections leave a lasting imprint on the immune system. The understanding of this phenomenon has expanded significantly since 1960, when Dr. Thomas Francis Jr first coined the term "original antigenic sin", to account for all previous pathogen exposures, rather than only the first. Now more commonly referred to as "immune imprinting", this effect most often focuses on how memory B-cell responses are shaped by prior antigen exposure, and the resultant antibodies produced after subsequent exposure to antigenically similar pathogens. Although imprinting was originally observed within the context of influenza viral infection, it has since been applied to the pandemic coronavirus SARS-CoV-2. To fully comprehend how imprinting affects the evolution of antibody responses, it is necessary to compare responses elicited by pathogenic strains that are both antigenically similar and dissimilar to strains encountered previously. To accomplish this, we must be able to measure the antigenic distance between strains, which can be easily accomplished using data from multidimensional immunological assays. The knowledge of imprinting, combined with antigenic distance measures, may allow for improvements in vaccine design and development for both influenza and SARS-CoV-2 viruses.
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Affiliation(s)
- Samantha M. King
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Shane P. Bryan
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Shannon P. Hilchey
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jiong Wang
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Martin S. Zand
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
- Clinical and Translational Science Institute, University of Rochester Medical Center, Rochester, NY 14618, USA
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26
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Carnell GW, Billmeier M, Vishwanath S, Suau Sans M, Wein H, George CL, Neckermann P, Del Rosario JMM, Sampson AT, Einhauser S, Aguinam ET, Ferrari M, Tonks P, Nadesalingam A, Schütz A, Huang CQ, Wells DA, Paloniemi M, Jordan I, Cantoni D, Peterhoff D, Asbach B, Sandig V, Temperton N, Kinsley R, Wagner R, Heeney JL. Glycan masking of a non-neutralising epitope enhances neutralising antibodies targeting the RBD of SARS-CoV-2 and its variants. Front Immunol 2023; 14:1118523. [PMID: 36911730 PMCID: PMC9995963 DOI: 10.3389/fimmu.2023.1118523] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
The accelerated development of the first generation COVID-19 vaccines has saved millions of lives, and potentially more from the long-term sequelae of SARS-CoV-2 infection. The most successful vaccine candidates have used the full-length SARS-CoV-2 spike protein as an immunogen. As expected of RNA viruses, new variants have evolved and quickly replaced the original wild-type SARS-CoV-2, leading to escape from natural infection or vaccine induced immunity provided by the original SARS-CoV-2 spike sequence. Next generation vaccines that confer specific and targeted immunity to broadly neutralising epitopes on the SARS-CoV-2 spike protein against different variants of concern (VOC) offer an advance on current booster shots of previously used vaccines. Here, we present a targeted approach to elicit antibodies that neutralise both the ancestral SARS-CoV-2, and the VOCs, by introducing a specific glycosylation site on a non-neutralising epitope of the RBD. The addition of a specific glycosylation site in the RBD based vaccine candidate focused the immune response towards other broadly neutralising epitopes on the RBD. We further observed enhanced cross-neutralisation and cross-binding using a DNA-MVA CR19 prime-boost regime, thus demonstrating the superiority of the glycan engineered RBD vaccine candidate across two platforms and a promising candidate as a broad variant booster vaccine.
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Affiliation(s)
- George W Carnell
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Martina Billmeier
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Sneha Vishwanath
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Maria Suau Sans
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Hannah Wein
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Charlotte L George
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Patrick Neckermann
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | | | - Alexander T Sampson
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sebastian Einhauser
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Ernest T Aguinam
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Paul Tonks
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Angalee Nadesalingam
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Anja Schütz
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Chloe Qingzhou Huang
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Minna Paloniemi
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ingo Jordan
- Applied Science & Technologies, ProBioGen AG, Berlin, Germany
| | - Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, United Kingdom
| | - David Peterhoff
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany.,Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Benedikt Asbach
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Volker Sandig
- Applied Science & Technologies, ProBioGen AG, Berlin, Germany
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, United Kingdom
| | - Rebecca Kinsley
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.,DIOSynVax, Ltd., Cambridge, United Kingdom
| | - Ralf Wagner
- Institute of Medical Microbiology & Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany.,Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Jonathan L Heeney
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.,DIOSynVax, Ltd., Cambridge, United Kingdom
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27
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Xu D, Li C, Utz A, Weidenbacher PA, Tang S, Sanyal M, Pulendran B, Kim PS. Designing epitope-focused vaccines via antigen reorientation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.20.521291. [PMID: 36597536 PMCID: PMC9810212 DOI: 10.1101/2022.12.20.521291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A major challenge in vaccine development, especially against rapidly evolving viruses, is the ability to focus the immune response toward evolutionarily conserved antigenic regions to confer broad protection. For example, while many broadly neutralizing antibodies against influenza have been found to target the highly conserved stem region of hemagglutinin (HA-stem), the immune response to seasonal influenza vaccines is predominantly directed to the immunodominant but variable head region (HA-head), leading to narrow-spectrum efficacy. Here, we first introduce an approach to controlling antigen orientation based on the site-specific insertion of short stretches of aspartate residues (oligoD) that facilitates antigen-binding to alum adjuvants. We demonstrate the generalizability of this approach to antigens from the Ebola virus, SARS-CoV-2, and influenza and observe enhanced antibody responses following immunization in all cases. Next, we use this approach to reorient HA in an "upside down" configuration, which we envision increases HA-stem exposure, therefore also improving its immunogenicity compared to HA-head. When applied to HA of H2N2 A/Japan/305/1957, the reoriented H2 HA (reoH2HA) on alum induced a stem-directed antibody response that cross-reacted with both group 1 and 2 influenza A HAs. Our results demonstrate the possibility and benefits of antigen reorientation via oligoD insertion, which represents a generalizable immunofocusing approach readily applicable for designing epitope-focused vaccine candidates.
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Affiliation(s)
- Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Ashley Utz
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Payton A.B. Weidenbacher
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Shaogeng Tang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Bali Pulendran
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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28
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Xu D, Li C, Utz A, Weidenbacher PAB, Tang S, Sanyal M, Pulendran B, Kim PS. Designing epitope-focused vaccines via antigen reorientation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 36597536 DOI: 10.1101/2022.09.08.507187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
UNLABELLED A major challenge in vaccine development, especially against rapidly evolving viruses, is the ability to focus the immune response toward evolutionarily conserved antigenic regions to confer broad protection. For example, while many broadly neutralizing antibodies against influenza have been found to target the highly conserved stem region of hemagglutinin (HA-stem), the immune response to seasonal influenza vaccines is predominantly directed to the immunodominant but variable head region (HA-head), leading to narrow-spectrum efficacy. Here, we first introduce an approach to controlling antigen orientation based on the site-specific insertion of short stretches of aspartate residues (oligoD) that facilitates antigen-binding to alum adjuvants. We demonstrate the generalizability of this approach to antigens from the Ebola virus, SARS-CoV-2, and influenza and observe enhanced antibody responses following immunization in all cases. Next, we use this approach to reorient HA in an "upside down" configuration, which we envision increases HA-stem exposure, therefore also improving its immunogenicity compared to HA-head. When applied to HA of H2N2 A/Japan/305/1957, the reoriented H2 HA (reoH2HA) on alum induced a stem-directed antibody response that cross-reacted with both group 1 and 2 influenza A HAs. Our results demonstrate the possibility and benefits of antigen reorientation via oligoD insertion, which represents a generalizable immunofocusing approach readily applicable for designing epitope-focused vaccine candidates. GRAPHICAL ABSTRACT Seasonal influenza vaccines induce a biased antibody response against the variable head of hemagglutinin, whereas conserved epitopes on the stem are a target for universal vaccines. Here we show that reorienting HA in an "upside-down" configuration sterically occludes the head and redirects the antibody response to the more exposed stem, thereby inducing broad cross-reactivity against hemagglutinins from diverse influenza strains.
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Shafqat A, Omer MH, Ahmad O, Niaz M, Abdulkader HS, Shafqat S, Mushtaq AH, Shaik A, Elshaer AN, Kashir J, Alkattan K, Yaqinuddin A. SARS-CoV-2 epitopes inform future vaccination strategies. Front Immunol 2022; 13:1041185. [PMID: 36505475 PMCID: PMC9732895 DOI: 10.3389/fimmu.2022.1041185] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022] Open
Abstract
All currently approved COVID-19 vaccines utilize the spike protein as their immunogen. SARS-CoV-2 variants of concern (VOCs) contain mutations in the spike protein, enabling them to escape infection- and vaccination-induced immune responses to cause reinfection. New vaccines are hence being researched intensively. Studying SARS-CoV-2 epitopes is essential for vaccine design, as identifying targets of broadly neutralizing antibody responses and immunodominant T-cell epitopes reveal candidates for inclusion in next-generation COVID-19 vaccines. We summarize the major studies which have reported on SARS-CoV-2 antibody and T-cell epitopes thus far. These results suggest that a future of pan-coronavirus vaccines, which not only protect against SARS-CoV-2 but numerous other coronaviruses, may be possible. The T-cell epitopes of SARS-CoV-2 have gotten less attention than neutralizing antibody epitopes but may provide new strategies to control SARS-CoV-2 infection. T-cells target many SARS-CoV-2 antigens other than spike, recognizing numerous epitopes within these antigens, thereby limiting the chance of immune escape by VOCs that mainly possess spike protein mutations. Therefore, augmenting vaccination-induced T-cell responses against SARS-CoV-2 may provide adequate protection despite broad antibody escape by VOCs.
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Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia,*Correspondence: Areez Shafqat,
| | - Mohamed H. Omer
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Omar Ahmad
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Mahnoor Niaz
- Medical College, Aga Khan University, Karachi, Pakistan
| | | | | | | | - Abdullah Shaik
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | - Junaid Kashir
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia,Department of Comparative Medicine, King Faisal Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Khaled Alkattan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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30
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Caradonna TM, Ronsard L, Yousif AS, Windsor IW, Hecht R, Bracamonte-Moreno T, Roffler AA, Maron MJ, Maurer DP, Feldman J, Marchiori E, Barnes RM, Rohrer D, Lonberg N, Oguin TH, Sempowski GD, Kepler TB, Kuraoka M, Lingwood D, Schmidt AG. An epitope-enriched immunogen expands responses to a conserved viral site. Cell Rep 2022; 41:111628. [PMID: 36351401 PMCID: PMC9883670 DOI: 10.1016/j.celrep.2022.111628] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/22/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting these conserved epitopes are often broadly protective but remain minor components of the repertoire. Rational immunogen design leverages a structural understanding of viral antigens to modulate humoral responses to favor these responses. Here, we report an epitope-enriched immunogen presenting a higher copy number of the influenza hemagglutinin (HA) receptor-binding site (RBS) epitope relative to other B cell epitopes. Immunization in a partially humanized murine model imprinted with an H1 influenza shows H1-specific serum and >99% H1-specific B cells being RBS-directed. Single B cell analyses show a genetically restricted response that structural analysis defines as RBS-directed antibodies engaging the RBS with germline-encoded contacts. These data show how epitope enrichment expands B cell responses toward conserved epitopes and advances immunogen design approaches for next-generation viral vaccines.
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Affiliation(s)
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ashraf S Yousif
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Rachel Hecht
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Anne A Roffler
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Max J Maron
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Daniel P Maurer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Elisa Marchiori
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Thomas H Oguin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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31
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Kraft JC, Pham MN, Shehata L, Brinkkemper M, Boyoglu-Barnum S, Sprouse KR, Walls AC, Cheng S, Murphy M, Pettie D, Ahlrichs M, Sydeman C, Johnson M, Blackstone A, Ellis D, Ravichandran R, Fiala B, Wrenn S, Miranda M, Sliepen K, Brouwer PJM, Antanasijevic A, Veesler D, Ward AB, Kanekiyo M, Pepper M, Sanders RW, King NP. Antigen- and scaffold-specific antibody responses to protein nanoparticle immunogens. Cell Rep Med 2022; 3:100780. [PMID: 36206752 PMCID: PMC9589121 DOI: 10.1016/j.xcrm.2022.100780] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/27/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022]
Abstract
Protein nanoparticle scaffolds are increasingly used in next-generation vaccine designs, and several have established records of clinical safety and efficacy. Yet the rules for how immune responses specific to nanoparticle scaffolds affect the immunogenicity of displayed antigens have not been established. Here we define relationships between anti-scaffold and antigen-specific antibody responses elicited by protein nanoparticle immunogens. We report that dampening anti-scaffold responses by physical masking does not enhance antigen-specific antibody responses. In a series of immunogens that all use the same nanoparticle scaffold but display four different antigens, only HIV-1 envelope glycoprotein (Env) is subdominant to the scaffold. However, we also demonstrate that scaffold-specific antibody responses can competitively inhibit antigen-specific responses when the scaffold is provided in excess. Overall, our results suggest that anti-scaffold antibody responses are unlikely to suppress antigen-specific antibody responses for protein nanoparticle immunogens in which the antigen is immunodominant over the scaffold.
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Affiliation(s)
- John C Kraft
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Minh N Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Laila Shehata
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Mitch Brinkkemper
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection and Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Suna Cheng
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Mike Murphy
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Maggie Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Max Johnson
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Blackstone
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Samuel Wrenn
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Marcos Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection and Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Philip J M Brouwer
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection and Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marion Pepper
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection and Immunity Institute, 1105 AZ Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
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32
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Vaccination with Deglycosylated Modified Hemagglutinin Broadly Protects against Influenza Virus Infection in Mice and Ferrets. Vaccines (Basel) 2022; 10:vaccines10081304. [PMID: 36016191 PMCID: PMC9414581 DOI: 10.3390/vaccines10081304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022] Open
Abstract
Recent efforts have been directed toward the development of universal influenza vaccines inducing broadly neutralizing antibodies to conserved antigenic supersites of Hemagglutinin (HA). Although several studies raise the importance of glycosylation in HA antigen design, whether this theory can be widely confirmed remains unclear; which influenza HA with an altered glycosylation profile could impact the amplitude and focus of the host immune response. Here, we evaluated the characteristics and efficacy of deglycosylated modified HA proteins, including monoglycosylated HA (HAmg), unglycosylated HA (HAug), and fully glycosylated HA (HAfg), without treatment with H3N2 Wisconsin/67/2005. Our results showed that HAug could induce a cross-strain protective immune response in mice against both H3N2 and H7N9 subtypes with better antibody-dependent cellular cytotoxicity (ADCC) than the HAmg- and HAfg-immunized groups, which suggested that highly conserved epitopes that were masked by surface glycosylation may be exposed and thus promote the induction of broad antibodies that recognize the hidden epitopes. This strategy may also supplement the direction of deglycosylated modified HA for universal influenza vaccines.
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33
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Wang WC, Sayedahmed EE, Sambhara S, Mittal SK. Progress towards the Development of a Universal Influenza Vaccine. Viruses 2022; 14:v14081684. [PMID: 36016306 PMCID: PMC9415875 DOI: 10.3390/v14081684] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 11/21/2022] Open
Abstract
Influenza viruses are responsible for millions of cases globally and significantly threaten public health. Since pandemic and zoonotic influenza viruses have emerged in the last 20 years and some of the viruses have resulted in high mortality in humans, a universal influenza vaccine is needed to provide comprehensive protection against a wide range of influenza viruses. Current seasonal influenza vaccines provide strain-specific protection and are less effective against mismatched strains. The rapid antigenic drift and shift in influenza viruses resulted in time-consuming surveillance and uncertainty in the vaccine protection efficacy. Most recent universal influenza vaccine studies target the conserved antigen domains of the viral surface glycoproteins and internal proteins to provide broader protection. Following the development of advanced vaccine technologies, several innovative strategies and vaccine platforms are being explored to generate robust cross-protective immunity. This review provides the latest progress in the development of universal influenza vaccines.
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Affiliation(s)
- Wen-Chien Wang
- Department of Comparative Pathobiology, Purdue Institute for Immunology, Inflammation and Infectious Disease, and Purdue University Center for Cancer Research, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA; (W.-C.W.); (E.E.S.)
| | - Ekramy E. Sayedahmed
- Department of Comparative Pathobiology, Purdue Institute for Immunology, Inflammation and Infectious Disease, and Purdue University Center for Cancer Research, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA; (W.-C.W.); (E.E.S.)
| | - Suryaprakash Sambhara
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Correspondence: (S.S.); (S.K.M.)
| | - Suresh K. Mittal
- Department of Comparative Pathobiology, Purdue Institute for Immunology, Inflammation and Infectious Disease, and Purdue University Center for Cancer Research, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA; (W.-C.W.); (E.E.S.)
- Correspondence: (S.S.); (S.K.M.)
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34
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Antibodies to combat viral infections: development strategies and progress. Nat Rev Drug Discov 2022; 21:676-696. [PMID: 35725925 PMCID: PMC9207876 DOI: 10.1038/s41573-022-00495-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 12/11/2022]
Abstract
Monoclonal antibodies (mAbs) are appealing as potential therapeutics and prophylactics for viral infections owing to characteristics such as their high specificity and their ability to enhance immune responses. Furthermore, antibody engineering can be used to strengthen effector function and prolong mAb half-life, and advances in structural biology have enabled the selection and optimization of potent neutralizing mAbs through identification of vulnerable regions in viral proteins, which can also be relevant for vaccine design. The COVID-19 pandemic has stimulated extensive efforts to develop neutralizing mAbs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with several mAbs now having received authorization for emergency use, providing not just an important component of strategies to combat COVID-19 but also a boost to efforts to harness mAbs in therapeutic and preventive settings for other infectious diseases. Here, we describe advances in antibody discovery and engineering that have led to the development of mAbs for use against infections caused by viruses including SARS-CoV-2, respiratory syncytial virus (RSV), Ebola virus (EBOV), human cytomegalovirus (HCMV) and influenza. We also discuss the rationale for moving from empirical to structure-guided strategies in vaccine development, based on identifying optimal candidate antigens and vulnerable regions within them that can be targeted by antibodies to result in a strong protective immune response. Monoclonal antibodies (mAbs) are appealing as potential therapeutics and prophylactics for viral infections. This Review describes advances in antibody discovery and engineering that have led to the development of mAbs that target viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respiratory syncytial virus and Ebola virus, and also considers the implications for vaccine development.
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35
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A Hemagglutinin Stem Vaccine Designed Rationally by AlphaFold2 Confers Broad Protection against Influenza B Infection. Viruses 2022; 14:v14061305. [PMID: 35746776 PMCID: PMC9229588 DOI: 10.3390/v14061305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 12/04/2022] Open
Abstract
Two lineages of influenza B viruses (IBV) co-circulating in human beings have been posing a significant public health burden worldwide. A substantial number of broadly neutralizing antibodies (bnAbs) have been identified targeting conserved epitopes on hemagglutinin (HA) stem domain, posing great interest for universal influenza vaccine development. Various strategies to design immunogens that selectively present these conserved epitopes are being explored. However, it has been a challenge to retain native conformation of the HA stem region, especially for soluble expression in prokaryotic systems. Here, using a structure prediction tool AlphaFold2, we rationally designed a stable stem antigen “B60-Stem-8071”, an HA stem vaccine derived from B/Brisbane/60/2006 grafted with a CR8071 epitope as a linker. The B60-Stem-8071 exhibited better solubility and more stable expression in the E. coli system compared to the naïve HA stem antigen. Immunization with B60-Stem-8071 in mice generated cross-reactive antibodies and protected mice broadly against lethal challenge with Yamagata and Victoria lineages of influenza B virus. Notably, soluble expression of B60-stem-8071 in the E. coli system showed the potential to produce the influenza B vaccine in a low-cost way. This study represents a proof of concept for the rational design of HA stem antigen based on structure prediction and analysis.
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36
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Carascal MB, Pavon RDN, Rivera WL. Recent Progress in Recombinant Influenza Vaccine Development Toward Heterosubtypic Immune Response. Front Immunol 2022; 13:878943. [PMID: 35663997 PMCID: PMC9162156 DOI: 10.3389/fimmu.2022.878943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/20/2022] [Indexed: 12/15/2022] Open
Abstract
Flu, a viral infection caused by the influenza virus, is still a global public health concern with potential to cause seasonal epidemics and pandemics. Vaccination is considered the most effective protective strategy against the infection. However, given the high plasticity of the virus and the suboptimal immunogenicity of existing influenza vaccines, scientists are moving toward the development of universal vaccines. An important property of universal vaccines is their ability to induce heterosubtypic immunity, i.e., a wide immune response coverage toward different influenza subtypes. With the increasing number of studies and mounting evidence on the safety and efficacy of recombinant influenza vaccines (RIVs), they have been proposed as promising platforms for the development of universal vaccines. This review highlights the current progress and advances in the development of RIVs in the context of heterosubtypic immunity induction toward universal vaccine production. In particular, this review discussed existing knowledge on influenza and vaccine development, current hemagglutinin-based RIVs in the market and in the pipeline, other potential vaccine targets for RIVs (neuraminidase, matrix 1 and 2, nucleoprotein, polymerase acidic, and basic 1 and 2 antigens), and deantigenization process. This review also provided discussion points and future perspectives in looking at RIVs as potential universal vaccine candidates for influenza.
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Affiliation(s)
- Mark B Carascal
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines.,Clinical and Translational Research Institute, The Medical City, Pasig City, Philippines
| | - Rance Derrick N Pavon
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Windell L Rivera
- Pathogen-Host-Environment Interactions Research Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
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37
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Zhu X, Han J, Sun W, Puente-Massaguer E, Yu W, Palese P, Krammer F, Ward AB, Wilson IA. Influenza chimeric hemagglutinin structures in complex with broadly protective antibodies to the stem and trimer interface. Proc Natl Acad Sci U S A 2022; 119:e2200821119. [PMID: 35594401 PMCID: PMC9173763 DOI: 10.1073/pnas.2200821119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/13/2022] [Indexed: 11/18/2022] Open
Abstract
Influenza virus hemagglutinin (HA) has been the primary target for influenza vaccine development. Broadly protective antibodies targeting conserved regions of the HA unlock the possibility of generating universal influenza immunity. Two group 2 influenza A chimeric HAs, cH4/3 and cH15/3, were previously designed to elicit antibodies to the conserved HA stem. Here, we show by X-ray crystallography and negative-stain electron microscopy that a broadly protective antistem antibody can stably bind to cH4/3 and cH15/3 HAs, thereby validating their potential as universal vaccine immunogens. Furthermore, flexibility was observed in the head domain of the chimeric HA structures, suggesting that antibodies could also potentially interact with the head interface epitope. Our structural and binding studies demonstrated that a broadly protective antihead trimeric interface antibody could indeed target the more open head domain of the cH15/3 HA trimer. Thus, in addition to inducing broadly protective antibodies against the conserved HA stem, chimeric HAs may also be able to elicit antibodies against the conserved trimer interface in the HA head domain, thereby increasing the vaccine efficacy.
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Affiliation(s)
- Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Weina Sun
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | | | - Wenli Yu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
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38
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Ovchinnikov V, Karplus M. A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell Receptor Avidity in Epitope Subdominance. Front Immunol 2022; 13:816634. [PMID: 35371013 PMCID: PMC8971376 DOI: 10.3389/fimmu.2022.816634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/24/2022] [Indexed: 12/02/2022] Open
Abstract
The elicitation of broadly neutralizing antibodies (bnAbs) is a major goal in the design of vaccines against rapidly-mutating viruses. In the case of influenza, many bnAbs that target conserved epitopes on the stem of the hemagglutinin protein (HA) have been discovered. However, these antibodies are rare, are not boosted well upon reinfection, and often have low neutralization potency, compared to strain-specific antibodies directed to the HA head. Different hypotheses have been proposed to explain this phenomenon. We use a coarse-grained computational model of the germinal center reaction to investigate how B-cell receptor binding valency affects the growth and affinity maturation of competing B-cells. We find that receptors that are unable to bind antigen bivalently, and also those that do not bind antigen cooperatively, have significantly slower rates of growth, memory B-cell production, and, under certain conditions, rates of affinity maturation. The corresponding B-cells are predicted to be outcompeted by B-cells that bind bivalently and cooperatively. We use the model to explore strategies for a universal influenza vaccine, e.g., how to boost the concentrations of the slower growing cross-reactive antibodies directed to the stem. The results suggest that, upon natural reinfections subsequent to vaccination, the protectiveness of such vaccines would erode, possibly requiring regular boosts. Collectively, our results strongly support the importance of bivalent antibody binding in immunodominance, and suggest guidelines for developing a universal influenza vaccine.
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Affiliation(s)
- Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, United States
- *Correspondence: Victor Ovchinnikov, ; ; Martin Karplus,
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, United States
- Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, Strasbourg, France
- *Correspondence: Victor Ovchinnikov, ; ; Martin Karplus,
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Doelger J, Kardar M, Chakraborty AK. Inferring the intrinsic mutational fitness landscape of influenzalike evolving antigens from temporally ordered sequence data. Phys Rev E 2022; 105:024401. [PMID: 35291059 DOI: 10.1103/physreve.105.024401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
There still are no effective long-term protective vaccines against viruses that continuously evolve under immune pressure such as seasonal influenza, which has caused, and can cause, devastating epidemics in the human population. To find such a broadly protective immunization strategy, it is useful to know how easily the virus can escape via mutation from specific antibody responses. This information is encoded in the fitness landscape of the viral proteins (i.e., knowledge of the viral fitness as a function of sequence). Here we present a computational method to infer the intrinsic mutational fitness landscape of influenzalike evolving antigens from yearly sequence data. We test inference performance with computer-generated sequence data that are based on stochastic simulations mimicking basic features of immune-driven viral evolution. Although the numerically simulated model does create a phylogeny based on the allowed mutations, the inference scheme does not use this information. This provides a contrast to other methods that rely on reconstruction of phylogenetic trees. Our method just needs a sufficient number of samples over multiple years. With our method, we are able to infer single as well as pairwise mutational fitness effects from the simulated sequence time series for short antigenic proteins. Our fitness inference approach may have potential future use for the design of immunization protocols by identifying intrinsically vulnerable immune target combinations on antigens that evolve under immune-driven selection. In the future, this approach may be applied to influenza and other novel viruses such as SARS-CoV-2, which evolves and, like influenza, might continue to escape the natural and vaccine-mediated immune pressures.
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Affiliation(s)
- Julia Doelger
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Mehran Kardar
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Arup K Chakraborty
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; and Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts 02139, USA
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40
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Abstract
Human noroviruses are the most common viral cause of acute gastroenteritis worldwide. Currently, there are no approved vaccines or specific therapeutics to treat the disease. Some obstacles delaying the development of a norovirus vaccine are: (i) the extreme diversity presented by noroviruses; (ii) our incomplete understanding of immunity to noroviruses; and (iii) the lack of a robust cell culture system or animal model for human noroviruses. Recent advances in in vitro cultivation of norovirus, novel approaches applied to viral genomics and immunity, and completion of vaccine trials and birth cohort studies have provided new information toward a better understanding of norovirus immunity. Here, we will discuss the complex relationship between norovirus diversity and correlates of protection for human noroviruses, and how this information could be used to guide the development of cross-protective vaccines.
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Affiliation(s)
- Lauren A. Ford-Siltz
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
| | - Kentaro Tohma
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States
| | - Gabriel I. Parra
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States,CONTACT Gabriel I. Parra Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Building 52/72, Room 1308, Silver Spring, MD20993, United States
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41
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Abstract
The germinal centre (GC) response is critical for the generation of affinity-matured plasma cells and memory B cells capable of mediating long-term protective immunity. Understanding whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or vaccination elicits a GC response has profound implications for the capacity of responding B cells to contribute to protection against infection. However, direct assessment of the GC response in humans remains a major challenge. Here we summarize emerging evidence for the importance of the GC response in the establishment of durable and broad immunity against SARS-CoV-2 and discuss new approaches to modulate the GC response to better protect against newly emerging SARS-CoV-2 variants. We also discuss new findings showing that the GC B cell response persists in the draining lymph nodes for at least 6 months in some individuals following vaccination with SARS-CoV-2 mRNA-based vaccines.
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Affiliation(s)
- Brian J Laidlaw
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA.
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42
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Universal influenza vaccine technologies and recombinant virosome production. METHODS IN MICROBIOLOGY 2022. [DOI: 10.1016/bs.mim.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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43
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Shinnakasu R, Sakakibara S, Yamamoto H, Wang PH, Moriyama S, Sax N, Ono C, Yamanaka A, Adachi Y, Onodera T, Sato T, Shinkai M, Suzuki R, Matsuura Y, Hashii N, Takahashi Y, Inoue T, Yamashita K, Kurosaki T. Glycan engineering of the SARS-CoV-2 receptor-binding domain elicits cross-neutralizing antibodies for SARS-related viruses. J Exp Med 2021; 218:212688. [PMID: 34623376 PMCID: PMC8641255 DOI: 10.1084/jem.20211003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/24/2021] [Accepted: 09/22/2021] [Indexed: 11/21/2022] Open
Abstract
Broadly protective vaccines against SARS-related coronaviruses that may cause future outbreaks are urgently needed. The SARS-CoV-2 spike receptor-binding domain (RBD) comprises two regions, the core-RBD and the receptor-binding motif (RBM); the former is structurally conserved between SARS-CoV-2 and SARS-CoV. Here, in order to elicit humoral responses to the more conserved core-RBD, we introduced N-linked glycans onto RBM surfaces of the SARS-CoV-2 RBD and used them as immunogens in a mouse model. We found that glycan addition elicited higher proportions of the core-RBD–specific germinal center (GC) B cells and antibody responses, thereby manifesting significant neutralizing activity for SARS-CoV, SARS-CoV-2, and the bat WIV1-CoV. These results have implications for the design of SARS-like virus vaccines.
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Affiliation(s)
- Ryo Shinnakasu
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Shuhei Sakakibara
- Laboratory of Immune Regulation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Hiromi Yamamoto
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Po-Hung Wang
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Saya Moriyama
- Reseach Center for Drug and Vaccine Development, National Institute of Infection Diseases, Tokyo, Japan
| | | | - Chikako Ono
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Virus Control, Center for Infectious Diseases Education and Research, Osaka University, Osaka, Japan
| | - Atsushi Yamanaka
- Mahidol-Osaka Center for Infectious Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Mahidol-Osaka Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yu Adachi
- Reseach Center for Drug and Vaccine Development, National Institute of Infection Diseases, Tokyo, Japan
| | - Taishi Onodera
- Reseach Center for Drug and Vaccine Development, National Institute of Infection Diseases, Tokyo, Japan
| | | | | | - Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Virus Control, Center for Infectious Diseases Education and Research, Osaka University, Osaka, Japan
| | - Noritaka Hashii
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Kawasaki, Japan
| | - Yoshimasa Takahashi
- Reseach Center for Drug and Vaccine Development, National Institute of Infection Diseases, Tokyo, Japan
| | - Takeshi Inoue
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | | | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Laboratory for Lymphocyte Differentiation, Research Center for Allergy and Immunology, RIKEN, Yokohama, Japan.,Center for Infectious Diseases Education and Research, Osaka University, Osaka, Japan
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44
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Chen Z, Du R, Galvan Achi JM, Rong L, Cui Q. SARS-CoV-2 cell entry and targeted antiviral development. Acta Pharm Sin B 2021; 11:3879-3888. [PMID: 34002130 PMCID: PMC8117542 DOI: 10.1016/j.apsb.2021.05.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 12/25/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the pandemic coronavirus disease 2019 (COVID-19), which threatens human health and public safety. In the urgent campaign to develop anti-SARS-CoV-2 therapies, the initial entry step is one of the most appealing targets. In this review, we summarize the current understanding of SARS-CoV-2 cell entry, and the development of targeted antiviral strategies. Moreover, we speculate upon future directions toward next-generation of SARS-CoV-2 entry inhibitors during the upcoming post-pandemic era.
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Affiliation(s)
- Zinuo Chen
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Ruikun Du
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
- Qingdao Academy of Chinese Medicinal Sciences, Shandong University of Traditional Chinese Medicine, Qingdao 266122, China
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Jazmin M. Galvan Achi
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Qinghua Cui
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
- Qingdao Academy of Chinese Medicinal Sciences, Shandong University of Traditional Chinese Medicine, Qingdao 266122, China
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
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45
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McMillan CLD, Cheung STM, Modhiran N, Barnes J, Amarilla AA, Bielefeldt-Ohmann H, Lee LYY, Guilfoyle K, van Amerongen G, Stittelaar K, Jakon V, Lebas C, Reading P, Short KR, Young PR, Watterson D, Chappell KJ. Development of molecular clamp stabilized hemagglutinin vaccines for Influenza A viruses. NPJ Vaccines 2021; 6:135. [PMID: 34750396 PMCID: PMC8575991 DOI: 10.1038/s41541-021-00395-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 10/01/2021] [Indexed: 11/25/2022] Open
Abstract
Influenza viruses cause a significant number of infections and deaths annually. In addition to seasonal infections, the risk of an influenza virus pandemic emerging is extremely high owing to the large reservoir of diverse influenza viruses found in animals and the co-circulation of many influenza subtypes which can reassort into novel strains. Development of a universal influenza vaccine has proven extremely challenging. In the absence of such a vaccine, rapid response technologies provide the best potential to counter a novel influenza outbreak. Here, we demonstrate that a modular trimerization domain known as the molecular clamp allows the efficient production and purification of conformationally stabilised prefusion hemagglutinin (HA) from a diverse range of influenza A subtypes. These clamp-stabilised HA proteins provided robust protection from homologous virus challenge in mouse and ferret models and some cross protection against heterologous virus challenge. This work provides a proof-of-concept for clamp-stabilised HA vaccines as a tool for rapid response vaccine development against future influenza A virus pandemics.
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Affiliation(s)
- Christopher L D McMillan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Stacey T M Cheung
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - James Barnes
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Alberto A Amarilla
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Helle Bielefeldt-Ohmann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, 4072 and 4029, Australia.,School of Veterinary Science, The University of Queensland Gatton Campus, Gatton, QLD, 4343, Australia
| | - Leo Yi Yang Lee
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Kate Guilfoyle
- Viroclinics Xplore, Landerd Campus, Nistelrooise Baan 3, 5374 RE, Schaijk, The Netherlands
| | - Geert van Amerongen
- Viroclinics Xplore, Landerd Campus, Nistelrooise Baan 3, 5374 RE, Schaijk, The Netherlands
| | - Koert Stittelaar
- Viroclinics Xplore, Landerd Campus, Nistelrooise Baan 3, 5374 RE, Schaijk, The Netherlands
| | - Virginie Jakon
- Vaccine Formulation Institute, Chemin des Aulx 14, 1228 Plan-Les-Ouates, Geneva, Switzerland
| | - Celia Lebas
- Vaccine Formulation Institute, Chemin des Aulx 14, 1228 Plan-Les-Ouates, Geneva, Switzerland
| | - Patrick Reading
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia.,Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, 3000, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, 4072 and 4029, Australia
| | - Paul R Young
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia. .,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, 4072 and 4029, Australia. .,The Australian Institute of Biotechnology and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia. .,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, 4072 and 4029, Australia. .,The Australian Institute of Biotechnology and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Keith J Chappell
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia. .,Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, 4072 and 4029, Australia. .,The Australian Institute of Biotechnology and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia.
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46
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Wessel AW, Doyle MP, Engdahl TB, Rodriguez J, Crowe JE, Diamond MS. Human Monoclonal Antibodies against NS1 Protein Protect against Lethal West Nile Virus Infection. mBio 2021; 12:e0244021. [PMID: 34634945 PMCID: PMC8510529 DOI: 10.1128/mbio.02440-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 08/31/2021] [Indexed: 11/20/2022] Open
Abstract
Envelope protein-targeted vaccines for flaviviruses are limited by concerns of antibody-dependent enhancement (ADE) of infections. Nonstructural protein 1 (NS1) provides an alternative vaccine target that avoids this risk since this protein is absent from the virion. Beyond its intracellular role in virus replication, extracellular forms of NS1 function in immune modulation and are recognized by host-derived antibodies. The rational design of NS1-based vaccines requires an extensive understanding of the antigenic sites on NS1, especially those targeted by protective antibodies. Here, we isolated human monoclonal antibodies (MAbs) from individuals previously naturally infected with WNV, mapped their epitopes using structure-guided mutagenesis, and evaluated their efficacy in vivo against lethal WNV challenge. The most protective epitopes clustered at three antigenic sites that are exposed on cell surface forms of NS1: (i) the wing flexible loop, (ii) the outer, electrostatic surface of the wing, and (iii) the spaghetti loop face of the β-ladder. One additional MAb mapped to the distal tip of the β-ladder and conferred a lower level of protection against WNV despite not binding to NS1 on the surface of infected cells. Our study defines the epitopes and modes of binding of protective anti-NS1 MAb antibodies following WNV infection, which may inform the development of NS1-based countermeasures against flaviviruses. IMPORTANCE Therapeutic antibodies against flaviviruses often promote neutralization by targeting the envelope protein of the virion. However, this approach is hindered by a possible concern for antibody-dependent enhancement of infection and paradoxical worsening of disease. As an alternative strategy, antibodies targeting flavivirus nonstructural protein 1 (NS1), which is absent from the virion, can protect against disease and do not cause enhanced infection. Here, we evaluate the structure-function relationships and protective activity of West Nile virus (WNV) NS1-specific monoclonal antibodies (MAbs) isolated from the memory B cells of a naturally infected human donor. We identify several anti-NS1 MAbs that protect mice against lethal WNV challenge and map their epitopes using charge reversal mutagenesis. Antibodies targeting specific regions in the NS1 structure could serve as the basis for countermeasures that control WNV infection in humans.
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Affiliation(s)
- Alex W. Wessel
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael P. Doyle
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Taylor B. Engdahl
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jessica Rodriguez
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Michael S. Diamond
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, Missouri, USA
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Freyn AW, Pine M, Rosado VC, Benz M, Muramatsu H, Beattie M, Tam YK, Krammer F, Palese P, Nachbagauer R, McMahon M, Pardi N. Antigen modifications improve nucleoside-modified mRNA-based influenza virus vaccines in mice. Mol Ther Methods Clin Dev 2021; 22:84-95. [PMID: 34485597 PMCID: PMC8390451 DOI: 10.1016/j.omtm.2021.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 06/04/2021] [Indexed: 11/26/2022]
Abstract
Nucleoside-modified, lipid nanoparticle-encapsulated mRNAs have recently emerged as suitable vaccines for influenza viruses and other pathogens in part because the platform allows delivery of multiple antigens in a single immunization. mRNA vaccines allow for easy antigen modification, enabling rapid iterative design. We studied protein modifications such as mutating functional sites, changing secretion potential, and altering protein conformation, which could improve the safety and/or potency of mRNA-based influenza virus vaccines. Mice were vaccinated intradermally with wild-type or mutant constructs of influenza virus hemagglutinin (HA), neuraminidase (NA), matrix protein 2 (M2), nucleoprotein (NP), or matrix protein 1 (M1). Membrane-bound HA constructs elicited more potent and protective antibody responses than secreted forms. Altering the catalytic site of NA to reduce enzymatic activity decreased reactogenicity while protective immunity was maintained. Disruption of M2 ion channel activity improved immunogenicity and protective efficacy. A comparison of internal proteins NP and M1 revealed the superiority of NP in conferring protection from influenza virus challenge. These findings support the use of the nucleoside-modified mRNA platform for guided antigen design for influenza virus with extension to other pathogens.
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Affiliation(s)
- Alec W Freyn
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew Pine
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Victoria C Rosado
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marcel Benz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hiromi Muramatsu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Ying K Tam
- Acuitas Therapeutics, Vancouver, BC V6T 1Z3, Canada
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Meagan McMahon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Norbert Pardi
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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48
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Isakova-Sivak I, Stepanova E, Mezhenskaya D, Matyushenko V, Prokopenko P, Sychev I, Wong PF, Rudenko L. Influenza vaccine: progress in a vaccine that elicits a broad immune response. Expert Rev Vaccines 2021; 20:1097-1112. [PMID: 34348561 DOI: 10.1080/14760584.2021.1964961] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION The licensed seasonal influenza vaccines predominantly induce neutralizing antibodies against immunodominant hypervariable epitopes of viral surface proteins, with limited protection against antigenically distant influenza viruses. Strategies have been developed to improve vaccines' performance in terms of broadly reactive and long-lasting immune response induction. AREAS COVERED We have summarized the advancements in the development of cross-protective influenza vaccines and discussed the challenges in evaluating them in preclinical and clinical trials. Here, the literature regarding the current stage of development of universal influenza vaccine candidates was reviewed. EXPERT OPINION Although various strategies aim to redirect adaptive immune responses from variable immunodominant to immunosubdominant antigens, more conserved epitopes are being investigated. Approaches that improve antibody responses to conserved B cell epitopes have increased the protective efficacy of vaccines within a subtype or phylogenetic group of influenza viruses. Vaccines that elicit significant levels of T cells recognizing highly conserved viral epitopes possess a high cross-protective potential and may cover most circulating influenza viruses. However, the development of T cell-based universal influenza vaccines is challenging owing to the diversity of MHCs in the population, unpredictable degree of immunodominance, lack of adequate animal models, and difficulty in establishing T cell immunity in humans. ABBREVIATIONS cHA: chimeric HA; HBc: hepatitis B virus core protein; HA: hemagglutinin; HLA: human leucocyte antigen; IIV: inactivated influenza vaccine; KLH: keyhole limpet hemocyanin; LAH: long alpha helix; LAIV: live attenuated influenza vaccine; M2e: extracellular domain of matrix 2 protein; MHC: major histocompatibility complex; mRNA: messenger ribonucleic acid; NA: neuraminidase; NS1: non-structural protein 1; qNIV: quadrivalent nanoparticle influenza vaccine; TRM: tissue-resident memory T cells; VE: vaccine effectiveness; VLP: virus-like particles; VSV: vesicular stomatitis virus.
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Affiliation(s)
- Irina Isakova-Sivak
- Department Of Virology, Institute Of Experimental Medicine, Saint Petersburg, Russia
| | - Ekaterina Stepanova
- Department Of Virology, Institute Of Experimental Medicine, Saint Petersburg, Russia
| | - Daria Mezhenskaya
- Department Of Virology, Institute Of Experimental Medicine, Saint Petersburg, Russia
| | - Victoria Matyushenko
- Department Of Virology, Institute Of Experimental Medicine, Saint Petersburg, Russia
| | - Polina Prokopenko
- Department Of Virology, Institute Of Experimental Medicine, Saint Petersburg, Russia
| | - Ivan Sychev
- Department Of Virology, Institute Of Experimental Medicine, Saint Petersburg, Russia
| | - Pei-Fong Wong
- Department Of Virology, Institute Of Experimental Medicine, Saint Petersburg, Russia
| | - Larisa Rudenko
- Department Of Virology, Institute Of Experimental Medicine, Saint Petersburg, Russia
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A non-neutralizing antibody broadly protects against influenza virus infection by engaging effector cells. PLoS Pathog 2021; 17:e1009724. [PMID: 34352041 PMCID: PMC8341508 DOI: 10.1371/journal.ppat.1009724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 06/18/2021] [Indexed: 12/30/2022] Open
Abstract
Hemagglutinin (HA) is the immunodominant protein of the influenza virus. We previously showed that mice injected with a monoglycosylated influenza A HA (HAmg) produced cross-strain-reactive antibodies and were better protected than mice injected with a fully glycosylated HA (HAfg) during lethal dose challenge. We employed a single B-cell screening platform to isolate the cross-protective monoclonal antibody (mAb) 651 from mice immunized with the HAmg of A/Brisbane/59/2007 (H1N1) influenza virus (Bris/07). The mAb 651 recognized the head domain of a broad spectrum of HAs from groups 1 and 2 influenza A viruses and offered prophylactic and therapeutic efficacy against A/California/07/2009 (H1N1) (Cal/09) and Bris/07 infections in mice. The antibody did not possess neutralizing activity; however, antibody-dependent cellular cytotoxicity and antibody-dependent cellular phagocytosis mediated by natural killer cells and alveolar macrophages were important in the protective efficacy of mAb 651. Together, this study highlighted the significance of effector functions for non-neutralizing antibodies to exhibit protection against influenza virus infection. The protective efficacy of antibodies is generally related to their neutralization potency. Here, we isolated a monoclonal antibody from mice injected with monoglycosylated hemagglutinin protein-based universal influenza vaccine, and demonstrated a head-domain recognizing, but non-neutralizing, monoclonal antibody carried prophylactic and therapeutic efficacy against a broad spectrum of influenza virus infections in vivo via effector functions.
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Narkhede YB, Gonzalez KJ, Strauch EM. Targeting Viral Surface Proteins through Structure-Based Design. Viruses 2021; 13:v13071320. [PMID: 34372526 PMCID: PMC8310314 DOI: 10.3390/v13071320] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/28/2022] Open
Abstract
The emergence of novel viral infections of zoonotic origin and mutations of existing human pathogenic viruses represent a serious concern for public health. It warrants the establishment of better interventions and protective therapies to combat the virus and prevent its spread. Surface glycoproteins catalyzing the fusion of viral particles and host cells have proven to be an excellent target for antivirals as well as vaccines. This review focuses on recent advances for computational structure-based design of antivirals and vaccines targeting viral fusion machinery to control seasonal and emerging respiratory viruses.
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Affiliation(s)
- Yogesh B Narkhede
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, USA;
| | - Karen J Gonzalez
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA;
| | - Eva-Maria Strauch
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, USA;
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA;
- Correspondence:
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