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Colom MS, Vučinić J, Adolf‐Bryfogle J, Bowman JW, Verel S, Moczygemba I, Schiex T, Simoncini D, Bahl CD. Complete combinatorial mutational enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity. Protein Sci 2024; 33:e5109. [PMID: 38989563 PMCID: PMC11237556 DOI: 10.1002/pro.5109] [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: 02/17/2024] [Revised: 05/20/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024]
Abstract
Understanding how proteins evolve under selective pressure is a longstanding challenge. The immensity of the search space has limited efforts to systematically evaluate the impact of multiple simultaneous mutations, so mutations have typically been assessed individually. However, epistasis, or the way in which mutations interact, prevents accurate prediction of combinatorial mutations based on measurements of individual mutations. Here, we use artificial intelligence to define the entire functional sequence landscape of a protein binding site in silico, and we call this approach Complete Combinatorial Mutational Enumeration (CCME). By leveraging CCME, we are able to construct a comprehensive map of the evolutionary connectivity within this functional sequence landscape. As a proof of concept, we applied CCME to the ACE2 binding site of the SARS-CoV-2 spike protein receptor binding domain. We selected representative variants from across the functional sequence landscape for testing in the laboratory. We identified variants that retained functionality to bind ACE2 despite changing over 40% of evaluated residue positions, and the variants now escape binding and neutralization by monoclonal antibodies. This work represents a crucial initial stride toward achieving precise predictions of pathogen evolution, opening avenues for proactive mitigation.
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Affiliation(s)
- Mireia Solà Colom
- Institute for Protein InnovationBostonMassachusettsUSA
- Division of Hematology/OncologyBoston Children's Hospital, Harvard Medical SchoolBostonMassachusettsUSA
- Present address:
AI ProteinsBostonMassachusettsUSA
| | - Jelena Vučinić
- Université Fédérale de Toulouse, IRIT UMR 5505, ANITI, Université Toulouse CapitoleToulouseFrance
| | - Jared Adolf‐Bryfogle
- Institute for Protein InnovationBostonMassachusettsUSA
- Division of Hematology/OncologyBoston Children's Hospital, Harvard Medical SchoolBostonMassachusettsUSA
| | - James W. Bowman
- Institute for Protein InnovationBostonMassachusettsUSA
- Division of Hematology/OncologyBoston Children's Hospital, Harvard Medical SchoolBostonMassachusettsUSA
- Present address:
AI ProteinsBostonMassachusettsUSA
| | | | - Isabelle Moczygemba
- Institute for Protein InnovationBostonMassachusettsUSA
- Division of Hematology/OncologyBoston Children's Hospital, Harvard Medical SchoolBostonMassachusettsUSA
- Present address:
AI ProteinsBostonMassachusettsUSA
| | - Thomas Schiex
- MIAT, Université Fédérale de Toulouse, ANITI, INRAE UR 875ToulouseFrance
| | - David Simoncini
- Université Fédérale de Toulouse, IRIT UMR 5505, ANITI, Université Toulouse CapitoleToulouseFrance
| | - Christopher D. Bahl
- Institute for Protein InnovationBostonMassachusettsUSA
- Division of Hematology/OncologyBoston Children's Hospital, Harvard Medical SchoolBostonMassachusettsUSA
- Present address:
AI ProteinsBostonMassachusettsUSA
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Buynak R, Cannon K, DeAtkine D, Kirby J, Usdan L, Bhavsar A, Gérard C, Kuznetsova A, Jayadev A, Amare H, Valenciano S, Meyer N. Randomized, Open-Label Phase 3 Study Evaluating Immunogenicity, Safety, and Reactogenicity of RSVPreF3 OA Coadministered with FLU-QIV-HD in Adults Aged ≥ 65. Infect Dis Ther 2024; 13:1789-1805. [PMID: 38981954 PMCID: PMC11266338 DOI: 10.1007/s40121-024-00985-4] [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: 02/01/2024] [Accepted: 04/30/2024] [Indexed: 07/11/2024] Open
Abstract
INTRODUCTION Respiratory syncytial virus (RSV) and influenza pose major disease burdens in older adults due to an aging immune system and comorbidities; seasonal overlap exists between these infections. In 2023, the RSV prefusion protein F3 older adult (RSVPreF3 OA) vaccine was first approved in the USA as a single dose for prevention of lower respiratory tract disease due to RSV in adults aged ≥ 60 years. The vaccine has since been approved in the European Union and elsewhere. RSVPreF3 OA and FLU-QIV-HD could be coadministered if immunogenicity, safety, and reactogenicity are not affected. METHODS This open-label, randomized (1:1), controlled, phase 3 study in 1029 adults aged ≥ 65 years in the USA evaluated the immunogenicity (up to 1 month after last vaccine dose) and safety (up to 6 months after last vaccine dose) of RSVPreF3 OA coadministered with FLU-QIV-HD (co-ad group) versus FLU-QIV-HD alone followed by RSVPreF3 OA at a separate visit 1 month later (control group). Non-inferiority criterion was defined as an upper limit of the two-sided 95% confidence interval of the geometric mean titer (GMT) group ratio (control/co-ad) ≤ 1.5. Secondary endpoints included safety and reactogenicity. RESULTS Proportions of participants across age categories between groups and proportions of male (50.4%) and female (49.6%) participants were well balanced; most participants were white (68.7%). Group GMT ratios for RSV-A neutralizing titers, hemagglutination inhibition titers for four influenza vaccine strains, and RSV-B neutralizing titers were non-inferior in the co-ad group versus the control group. No clinically meaningful differences in local or systemic solicited and unsolicited adverse events (AEs), serious AEs, and potential immune-mediated diseases were identified. The most common solicited AEs in both groups were injection-site pain and myalgia. CONCLUSION In adults aged ≥ 65 years, coadministration of RSVPreF3 OA and FLU-QIV-HD was immunogenically non-inferior to the sequential administration of both vaccines 1 month apart, and had clinically acceptable safety and reactogenicity profile. TRIAL REGISTRATION ClinicalTrials.gov identifier, NCT05559476.
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Affiliation(s)
| | - Kevin Cannon
- Accellacare Clinical Research, Wilmington, NC, USA
| | | | - John Kirby
- Summit Medical Group, Jefferson City, TN, USA
| | - Lisa Usdan
- Clinical Neuroscience Solution Healthcare, Memphis, TN, USA
| | - Amit Bhavsar
- GSK Vaccines, Avenue Fleming 20, 1300, Wavre, Belgium
| | | | | | | | - Hiwot Amare
- GSK Vaccines, Avenue Fleming 20, 1300, Wavre, Belgium
| | | | - Nadia Meyer
- GSK Vaccines, Avenue Fleming 20, 1300, Wavre, Belgium
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3
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Colom MS, Vucinic J, Adolf-Bryfogle J, Bowman JW, Verel S, Moczygemba I, Schiex T, Simoncini D, Bahl CD. Complete Combinatorial Mutational Enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity. RESEARCH SQUARE 2023:rs.3.rs-2248327. [PMID: 36482980 PMCID: PMC9727770 DOI: 10.21203/rs.3.rs-2248327/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Understanding how proteins evolve under selective pressure is a longstanding challenge. The immensity of the search space has limited efforts to systematically evaluate the impact of multiple simultaneous mutations, so mutations have typically been assessed individually. However, epistasis, or the way in which mutations interact, prevents accurate prediction of combinatorial mutations based on measurements of individual mutations. Here, we use artificial intelligence to define the entire functional sequence landscape of a protein binding site in silico, and we call this approach Complete Combinatorial Mutational Enumeration (CCME). By leveraging CCME, we are able to construct a comprehensive map of the evolutionary connectivity within this functional sequence landscape. As a proof of concept, we applied CCME to the ACE2 binding site of the SARS-CoV-2 spike protein receptor binding domain. We selected representative variants from across the functional sequence landscape for testing in the laboratory. We identified variants that retained functionality to bind ACE2 despite changing over 40% of evaluated residue positions, and the variants now escape binding and neutralization by monoclonal antibodies. This work represents a crucial initial stride towards achieving precise predictions of pathogen evolution, opening avenues for proactive mitigation.
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Affiliation(s)
- Mireia Solà Colom
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- current address: AI Proteins; Boston, Massachusetts, 02215, USA
| | - Jelena Vucinic
- Université Fédérale de Toulouse; ANITI, IRIT-CNRS UMR 5505, Université Toulouse Capitole, 31000 Toulouse, France
| | - Jared Adolf-Bryfogle
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - James W. Bowman
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- current address: AI Proteins; Boston, Massachusetts, 02215, USA
| | - Sébastien Verel
- Université Littoral Côte d’Opale; UR 4491, LISIC, F-62100 Calais, France
| | - Isabelle Moczygemba
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- current address: AI Proteins; Boston, Massachusetts, 02215, USA
| | - Thomas Schiex
- Université Fédérale de Toulouse; ANITI, INRAE-UR 875, 31000 Toulouse, France
| | - David Simoncini
- Université Fédérale de Toulouse; ANITI, IRIT-CNRS UMR 5505, Université Toulouse Capitole, 31000 Toulouse, France
| | - Christopher D. Bahl
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- current address: AI Proteins; Boston, Massachusetts, 02215, USA
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4
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Zhao F, Yuan M, Keating C, Shaabani N, Limbo O, Joyce C, Woehl J, Barman S, Burns A, Tran Q, Zhu X, Ricciardi M, Peng L, Smith J, Huang D, Briney B, Sok D, Nemazee D, Teijaro JR, Wilson IA, Burton DR, Jardine JG. Broadening a SARS-CoV-1-neutralizing antibody for potent SARS-CoV-2 neutralization through directed evolution. Sci Signal 2023; 16:eabk3516. [PMID: 37582161 DOI: 10.1126/scisignal.abk3516] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 07/27/2023] [Indexed: 08/17/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for strategies to rapidly develop neutralizing monoclonal antibodies that can function as prophylactic and therapeutic agents and to help guide vaccine design. Here, we demonstrate that engineering approaches can be used to refocus an existing antibody that neutralizes one virus but not a related virus. Through a rapid affinity maturation strategy, we engineered CR3022, a SARS-CoV-1-neutralizing antibody, to bind to the receptor binding domain of SARS-CoV-2 with >1000-fold increased affinity. The engineered CR3022 neutralized SARS-CoV-2 and provided prophylactic protection from viral challenge in a small animal model of SARS-CoV-2 infection. Deep sequencing throughout the engineering process paired with crystallographic analysis of engineered CR3022 elucidated the molecular mechanisms by which the antibody can accommodate sequence differences in the epitopes between SARS-CoV-1 and SARS-CoV-2. This workflow provides a blueprint for the rapid broadening of neutralization of an antibody from one virus to closely related but resistant viruses.
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Affiliation(s)
- Fangzhu Zhao
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Celina Keating
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Namir Shaabani
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oliver Limbo
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Collin Joyce
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jordan Woehl
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Shawn Barman
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alison Burns
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
| | - Quoc Tran
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Ricciardi
- Department of Pathology, George Washington University, Washington, DC 20052, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jessica Smith
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Deli Huang
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
- Center for Viral Systems Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - David Nemazee
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Teijaro
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Joseph G Jardine
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
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5
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Diethelm-Varela B, Soto JA, Riedel CA, Bueno SM, Kalergis AM. New Developments and Challenges in Antibody-Based Therapies for the Respiratory Syncytial Virus. Infect Drug Resist 2023; 16:2061-2074. [PMID: 37063935 PMCID: PMC10094422 DOI: 10.2147/idr.s379660] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/29/2023] [Indexed: 04/18/2023] Open
Abstract
Since the discovery of the human respiratory syncytial virus (hRSV), multiple research efforts have been conducted to develop vaccines and treatments capable of reducing the risk of severe disease, hospitalization, long-term sequelae, and death from this pathogen in susceptible populations. In this sense, therapies specifically directed against hRSV are mainly based on monoclonal and polyclonal antibodies such as intravenous IgG (IVIG)-RSV and the monoclonal antibody palivizumab. However, these therapies are associated with significant limitations, including the need for the recruitment of a high number of convalescent volunteers who donate blood to procure IVIG-RSV and the costs associated with the need for repeated administrations of palivizumab. These limitations render this product not cost-effective for populations other than high-risk patients. These problems have underscored that it is still necessary to identify new safe and effective therapies for human use. However, these new therapies must benefit from a comparatively cheap production cost and the opportunity to be available to the high-risk population and anyone who requires treatment. Here, we review the different antibodies used to prevent the pathology caused by hRSV infection, highlighting therapies currently approved for human use and their clinical value. Also, the new, most promising candidates based on preclinical studies and clinical trial results are revised.
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Affiliation(s)
- Benjamín Diethelm-Varela
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jorge A Soto
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Claudia A Riedel
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Susan M Bueno
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M Kalergis
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Correspondence: Alexis M Kalergis, Email
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6
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Brady T, Zhang T, Tuffy KM, Haskins N, Du Q, Lin J, Kaplan G, Novick S, Roe TL, Ren K, Rosenthal K, McTamney PM, Abram ME, Streicher K, Kelly EJ. Qualification of a Biolayer Interferometry Assay to Support AZD7442 Resistance Monitoring. Microbiol Spectr 2022; 10:e0103422. [PMID: 35993765 PMCID: PMC9704045 DOI: 10.1128/spectrum.01034-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/28/2022] [Indexed: 12/30/2022] Open
Abstract
AZD7442, a combination of two long-acting monoclonal antibodies (tixagevimab [AZD8895] and cilgavimab [AZD1061]), has been authorized for the prevention and treatment of coronavirus disease 2019 (COVID-19). The rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants requires methods capable of quickly characterizing resistance to AZD7442. To support AZD7442 resistance monitoring, a biolayer interferometry (BLI) assay was developed to screen the binding of tixagevimab and cilgavimab to SARS-CoV-2 spike proteins to reduce the number of viral variants for neutralization susceptibility verification. Six spike variants were chosen to assess the assay's performance: four with decreased affinity for tixagevimab (F486S:D614G and F486W:D614G proteins) or cilgavimab (S494L:D614G and K444R:D614G proteins) and two reference proteins (wild-type HexaPro and D614G protein). Equilibrium dissociation constant (KD) values from each spike protein were used to determine shifts in binding affinity. The assay's precision, range, linearity, and limits of quantitation were established. Qualification acceptance criteria determined whether the assay was fit for purpose. By bypassing protein purification, the BLI assay provided increased screening throughput. Although limited correlation between pseudotype neutralization and BLI data (50% inhibitory concentration versus KD) was observed for full immunoglobulins (IgGs), the correlations for antibody fragments (Fabs) were stronger and reflected a better comparison of antibody binding kinetics with neutralization potency. Therefore, despite strong assay performance characteristics, the use of full IgGs limited the screening utility of the assay; however, the Fab approach warrants further exploration as a rapid, high-throughput variant-screening method for future resistance-monitoring programs. IMPORTANCE SARS-CoV-2 variants harbor multiple substitutions in their spike trimers, potentially leading to breakthrough infections and clinical resistance to immune therapies. For this reason, a BLI assay was developed and qualified to evaluate the reliability of screening SARS-CoV-2 spike trimer variants against anti-SARS-CoV-2 monoclonal antibodies (MAbs) tixagevimab and cilgavimab, the components of AZD7442, prior to in vitro pseudovirus neutralization susceptibility verification testing. The assay bypasses protein purification with rapid assessment of the binding affinity of each MAb for each recombinant protein, potentially providing an efficient preliminary selection step, thus allowing a reduced testing burden in the more technically complex viral neutralization assays. Despite precise and specific measures, an avidity effect associated with MAb binding to the trimer confounded correlation with neutralization potency, negating the assay's utility as a surrogate for neutralizing antibody potency. Improved correlation with Fabs suggests that assay optimization could overcome any avidity limitation, warranting further exploration to support future resistance-monitoring programs.
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Affiliation(s)
- Tyler Brady
- Translational Medicine, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Tianhui Zhang
- Data Sciences and Quantitative Biology, AstraZeneca, Gaithersburg, Maryland, USA
| | - Kevin M. Tuffy
- Translational Medicine, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Nantaporn Haskins
- Biologics Engineering, R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Qun Du
- Biologics Engineering, R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Jia Lin
- Biologics Engineering, R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Gilad Kaplan
- Biologics Engineering, R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Steven Novick
- Data Sciences and Quantitative Biology, AstraZeneca, Gaithersburg, Maryland, USA
| | - Tiffany L. Roe
- Translational Medicine, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Kuishu Ren
- Virology and Vaccine Discovery, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Kim Rosenthal
- Virology and Vaccine Discovery, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Patrick M. McTamney
- Virology and Vaccine Discovery, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Michael E. Abram
- Translational Medicine, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Katie Streicher
- Translational Medicine, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Elizabeth J. Kelly
- Translational Medicine, Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
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7
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Beach SS, Hull MA, Ytreberg FM, Patel JS, Miura TA. Molecular Modeling Predicts Novel Antibody Escape Mutations in the Respiratory Syncytial Virus Fusion Glycoprotein. J Virol 2022; 96:e0035322. [PMID: 35678603 PMCID: PMC9278155 DOI: 10.1128/jvi.00353-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Monoclonal antibodies are increasingly used for the prevention and/or treatment of viral infections. One caveat of their use is the ability of viruses to evolve resistance to antibody binding and neutralization. Computational strategies to identify viral mutations that may disrupt antibody binding would leverage the wealth of viral genomic sequence data to monitor for potential antibody-resistant mutations. The respiratory syncytial virus is an important pathogen for which monoclonal antibodies against the fusion (F) protein are used to prevent severe disease in high-risk infants. In this study, we used an approach that combines molecular dynamics simulations with FoldX to estimate changes in free energy in F protein folding and binding to the motavizumab antibody upon each possible amino acid change. We systematically selected 8 predicted escape mutations and tested them in an infectious clone. Consistent with our F protein stability predictions, replication-effective viruses were observed for each selected mutation. Six of the eight variants showed increased resistance to neutralization by motavizumab. Flow cytometry was used to validate the estimated (model-predicted) effects on antibody binding to F. Using surface plasmon resonance, we determined that changes in the on-rate of motavizumab binding were associated with the reduced affinity for two novel escape mutations. Our study empirically validated the accuracy of our molecular modeling approach and emphasized the role of biophysical protein modeling in predicting viral resistance to antibody-based therapeutics that can be used to monitor the emergence of resistant viruses and to design improved therapeutic antibodies. IMPORTANCE Respiratory syncytial virus (RSV) causes severe disease in young infants, particularly those with heart or lung diseases or born prematurely. Because no vaccine is currently available, monoclonal antibodies are used to prevent severe RSV disease in high-risk infants. While it is known that RSV evolves to avoid recognition by antibodies, screening tools that can predict which changes to the virus may lead to antibody resistance are greatly needed.
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Affiliation(s)
- Sierra S. Beach
- Department of Biological Sciences, University of Idahogrid.266456.5, Moscow, Idaho, USA
| | - McKenna A. Hull
- Department of Biological Sciences, University of Idahogrid.266456.5, Moscow, Idaho, USA
| | - F. Marty Ytreberg
- Department of Physics, University of Idahogrid.266456.5, Moscow, Idaho, USA
- Institute for Modeling Collaboration and Innovation, University of Idahogrid.266456.5, Moscow, Idaho, USA
| | - Jagdish Suresh Patel
- Department of Biological Sciences, University of Idahogrid.266456.5, Moscow, Idaho, USA
- Institute for Modeling Collaboration and Innovation, University of Idahogrid.266456.5, Moscow, Idaho, USA
| | - Tanya A. Miura
- Department of Biological Sciences, University of Idahogrid.266456.5, Moscow, Idaho, USA
- Institute for Modeling Collaboration and Innovation, University of Idahogrid.266456.5, Moscow, Idaho, USA
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8
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Challenges in Maximizing Impacts of Preventive Strategies against Respiratory Syncytial Virus (RSV) Disease in Young Children. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2022; 95:293-300. [PMID: 35782467 PMCID: PMC9235255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract illness in infants and young children. It causes substantial morbidity and mortality in young children and older adults. As few therapeutic and prophylaxis options against RSV illness are currently available, there is a great need for effective RSV vaccines and immune-prophylaxis. Encouragingly, multiple vaccines and immuno-prophylaxis aiming to protect pediatric populations have shown promising progress in clinical trials. The three major preventive strategies include RSV F-protein-based vaccines for pregnant women, extended half-life monoclonal antibodies for neonates, and live-attenuated vaccines for infants. Each preventive strategy has its own merits and challenges yet to be overcome. Challenges also exist in maximizing vaccine impacts in the post-implementation era. This perspectives piece focuses on RSV preventive strategies in young children and highlights the remaining questions in current development of RSV immunization products and design of immunization programs.
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Zuniga A, Rassek O, Vrohlings M, Marrero-Nodarse A, Moehle K, Robinson JA, Ghasparian A. An epitope-specific chemically defined nanoparticle vaccine for respiratory syncytial virus. NPJ Vaccines 2021; 6:85. [PMID: 34145291 PMCID: PMC8213762 DOI: 10.1038/s41541-021-00347-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 06/02/2021] [Indexed: 12/05/2022] Open
Abstract
Respiratory syncytial virus (RSV) can cause severe respiratory disease in humans, particularly in infants and the elderly. However, attempts to develop a safe and effective vaccine have so far been unsuccessful. Atomic-level structures of epitopes targeted by RSV-neutralizing antibodies are now known, including that bound by Motavizumab and its clinically used progenitor Palivizumab. We developed a chemically defined approach to RSV vaccine design, that allows control of both immunogenicity and safety features of the vaccine. Structure-guided antigen design and a synthetic nanoparticle delivery platform led to a vaccine candidate that elicits high titers of palivizumab-like, epitope-specific neutralizing antibodies. The vaccine protects preclinical animal models from RSV infection and lung pathology typical of vaccine-derived disease enhancement. The results suggest that the development of a safe and effective synthetic epitope-specific RSV vaccine may be feasible by combining this conformationally stabilized peptide and synthetic nanoparticle delivery system.
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Affiliation(s)
- Armando Zuniga
- Virometix AG, Schlieren, Switzerland
- Shape Biopharmaceuticals Inc, Cambridge, MA, USA
| | | | - Melissa Vrohlings
- Virometix AG, Schlieren, Switzerland
- CDR-Life, Schlieren, Switzerland
| | | | - Kerstin Moehle
- Chemistry Department, University of Zurich, Zurich, Switzerland
| | - John A Robinson
- Chemistry Department, University of Zurich, Zurich, Switzerland.
| | - Arin Ghasparian
- Virometix AG, Schlieren, Switzerland.
- Shape Biopharmaceuticals Inc, Cambridge, MA, USA.
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Bhat R, Farrag MA, Almajhdi FN. Double-edged role of natural killer cells during RSV infection. Int Rev Immunol 2020; 39:233-244. [PMID: 32469615 DOI: 10.1080/08830185.2020.1770748] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Natural killer cells play a vital role in the rejection of tumors and pathogen-infected cells. NK cells are indispensable in the early immune response against viral infections by directly targeting infected cells. Furthermore, NK cells influence adaptive immunity by driving virus-specific T-cell responses. Respiratory syncytial virus, a highly contagious virus that causes bronchiolitis, is the main reason for mortality in infants and elderly patients. RSV infection triggers both innate and adaptive immune responses. However, immunity against RSV is ephemeral due to the impaired development of immunological memory. The role of NK cells during RSV infection remains ambiguous. NK cells play a dual role in RSV infection; initially, their role is a protective one as they utilize their intrinsic cytotoxicity, followed by a detrimental one that induces lung injury due to the inhibition of antibody responses and the secretion of pro-inflammatory factors. Noteworthy, IFN-γ released from NK cells play a critical role in promoting a shift to adaptive responses and inhibiting antibody responses in neonates. Indeed, NK cells have a pro-inflammatory and inhibitory role rather than a cytotoxic one that contributes to the severity of the disease. Therapeutic options, including DNA-protein-based vaccines, synthetic peptides, and attenuated strains, are presently under tests. However, there is a need for effective strategies to augment NK cell activity and circumvent the pro-inflammatory activity to benefit the host. In this review, we focused on the role played by NK cells in the immune response and its outcome on the immunopathogenesis of RSV disease.
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Affiliation(s)
- Rauf Bhat
- Virology Research Group, Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed A Farrag
- Virology Research Group, Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fahad N Almajhdi
- Virology Research Group, Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Huang J, Diaz D, Mousa JJ. Antibody Epitopes of Pneumovirus Fusion Proteins. Front Immunol 2019; 10:2778. [PMID: 31849961 PMCID: PMC6895023 DOI: 10.3389/fimmu.2019.02778] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/13/2019] [Indexed: 11/13/2022] Open
Abstract
The pneumoviruses respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are two widespread human pathogens that can cause severe disease in the young, the elderly, and the immunocompromised. Despite the discovery of RSV over 60 years ago, and hMPV nearly 20 years ago, there are no approved vaccines for either virus. Antibody-mediated immunity is critical for protection from RSV and hMPV, and, until recently, knowledge of the antibody epitopes on the surface glycoproteins of RSV and hMPV was very limited. However, recent breakthroughs in the recombinant expression and stabilization of pneumovirus fusion proteins have facilitated in-depth characterization of antibody responses and structural epitopes, and have provided an enormous diversity of new monoclonal antibody candidates for therapeutic development. These new data have primarily focused on the RSV F protein, and have led to a wealth of new vaccine candidates in preclinical and clinical trials. In contrast, the major structural antibody epitopes remain unclear for the hMPV F protein. Overall, this review will cover recent advances in characterizing the antigenic sites on the RSV and hMPV F proteins.
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Affiliation(s)
- Jiachen Huang
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Darren Diaz
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Jarrod J. Mousa
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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Zhu Q, Lu B, McTamney P, Palaszynski S, Diallo S, Ren K, Ulbrandt ND, Kallewaard N, Wang W, Fernandes F, Wong S, Svabek C, Moldt B, Esser MT, Jing H, Suzich JA. Prevalence and Significance of Substitutions in the Fusion Protein of Respiratory Syncytial Virus Resulting in Neutralization Escape From Antibody MEDI8897. J Infect Dis 2019; 218:572-580. [PMID: 29617879 DOI: 10.1093/infdis/jiy189] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/28/2018] [Indexed: 11/13/2022] Open
Abstract
Background Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection among infants and young children. To date, no vaccine is approved for the broad population of healthy infants. MEDI8897, a potent anti-RSV fusion antibody with extended serum half-life, is currently under clinical investigation as a potential passive RSV vaccine for all infants. As a ribonucleic acid virus, RSV is prone to mutation, and the possibility of viral escape from MEDI8897 neutralization is a potential concern. Methods We generated RSV monoclonal antibody (mAb)-resistant mutants (MARMs) in vitro and studied the effect of the amino acid substitutions identified on binding and viral neutralization susceptibility to MEDI8897. The impact of resistance-associated mutations on in vitro growth kinetics and the prevalence of these mutations in currently circulating strains of RSV in the United States was assessed. Results Critical residues identified in MARMs for MEDI8897 neutralization were located in the MEDI8897 binding site defined by crystallographic analysis. Substitutions in these residues affected the binding of mAb to virus, without significant impact on viral replication in vitro. The frequency of natural resistance-associated polymorphisms was low. Conclusions Results from this study provide insights into the mechanism of MEDI8897 escape and the complexity of monitoring for emergence of resistance.
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Affiliation(s)
- Qing Zhu
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Bin Lu
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Patrick McTamney
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Susan Palaszynski
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Seme Diallo
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Kuishu Ren
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Nancy D Ulbrandt
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Nicole Kallewaard
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Weijia Wang
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Fiona Fernandes
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Steve Wong
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Catherine Svabek
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Brian Moldt
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Mark T Esser
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - Hong Jing
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
| | - JoAnn A Suzich
- Department of Infectious Diseases-Vaccines, MedImmune, LLC, Gaithersburg, Maryland
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Alanine DGW, Quinkert D, Kumarasingha R, Mehmood S, Donnellan FR, Minkah NK, Dadonaite B, Diouf A, Galaway F, Silk SE, Jamwal A, Marshall JM, Miura K, Foquet L, Elias SC, Labbé GM, Douglas AD, Jin J, Payne RO, Illingworth JJ, Pattinson DJ, Pulido D, Williams BG, de Jongh WA, Wright GJ, Kappe SHI, Robinson CV, Long CA, Crabb BS, Gilson PR, Higgins MK, Draper SJ. Human Antibodies that Slow Erythrocyte Invasion Potentiate Malaria-Neutralizing Antibodies. Cell 2019; 178:216-228.e21. [PMID: 31204103 PMCID: PMC6602525 DOI: 10.1016/j.cell.2019.05.025] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 03/05/2019] [Accepted: 05/13/2019] [Indexed: 12/30/2022]
Abstract
The Plasmodium falciparum reticulocyte-binding protein homolog 5 (PfRH5) is the leading target for next-generation vaccines against the disease-causing blood-stage of malaria. However, little is known about how human antibodies confer functional immunity against this antigen. We isolated a panel of human monoclonal antibodies (mAbs) against PfRH5 from peripheral blood B cells from vaccinees in the first clinical trial of a PfRH5-based vaccine. We identified a subset of mAbs with neutralizing activity that bind to three distinct sites and another subset of mAbs that are non-functional, or even antagonistic to neutralizing antibodies. We also identify the epitope of a novel group of non-neutralizing antibodies that significantly reduce the speed of red blood cell invasion by the merozoite, thereby potentiating the effect of all neutralizing PfRH5 antibodies as well as synergizing with antibodies targeting other malaria invasion proteins. Our results provide a roadmap for structure-guided vaccine development to maximize antibody efficacy against blood-stage malaria.
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Affiliation(s)
- Daniel G W Alanine
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Doris Quinkert
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | | | - Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Francesca R Donnellan
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Nana K Minkah
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Ave. N., #500, Seattle, WA 98109, USA
| | - Bernadeta Dadonaite
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Ababacar Diouf
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD 20852, USA
| | - Francis Galaway
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Sarah E Silk
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Abhishek Jamwal
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jennifer M Marshall
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD 20852, USA
| | - Lander Foquet
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Ave. N., #500, Seattle, WA 98109, USA
| | - Sean C Elias
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Geneviève M Labbé
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Alexander D Douglas
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Jing Jin
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Ruth O Payne
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Joseph J Illingworth
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - David J Pattinson
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - David Pulido
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Barnabas G Williams
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Willem A de Jongh
- ExpreS(2)ion Biotechnologies, SCION-DTU Science Park, Agern Allé 1, Hørsholm 2970, Denmark
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Stefan H I Kappe
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Ave. N., #500, Seattle, WA 98109, USA
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Carole A Long
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD 20852, USA
| | - Brendan S Crabb
- Burnet Institute, 85 Commercial Road, Melbourne, VIC 3004, Australia
| | - Paul R Gilson
- Burnet Institute, 85 Commercial Road, Melbourne, VIC 3004, Australia
| | - Matthew K Higgins
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Simon J Draper
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK.
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Hijano DR, Vu LD, Kauvar LM, Tripp RA, Polack FP, Cormier SA. Role of Type I Interferon (IFN) in the Respiratory Syncytial Virus (RSV) Immune Response and Disease Severity. Front Immunol 2019; 10:566. [PMID: 30972063 PMCID: PMC6443902 DOI: 10.3389/fimmu.2019.00566] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/04/2019] [Indexed: 12/22/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract disease in children <2 years of age. Increased morbidity and mortality have been reported in high-risk patients, such as premature infants, patients with cardiac disease, and severely immune compromised patients. Severe disease is associated with the virulence of the virus as well as host factors specifically including the innate immune response. The role of type I interferons (IFNs) in the response to RSV infection is important in regulating the rate of virus clearance and in directing the character of the immune response, which is normally associated with protection and less severe disease. Two RSV non-structural proteins, NS1 and NS2, as well as the envelope G glycoprotein are known to suppress type I IFN production and a robust type I IFN response to RSV does not occur in human infants or neonatal mouse models of RSV infection. Additionally, presence of type I IFNs are associated with mild symptoms in infants and administration of IFN-α prior to infection of neonatal mice with RSV reduces immunopathology. This evidence has driven RSV prophylaxis and therapeutic efforts to consider strategies for enhancing type I IFN production.
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Affiliation(s)
- Diego R Hijano
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, United States
| | - Luan D Vu
- Department of Biological Sciences, Louisiana State University and School of Veterinary Medicine, Baton Rouge, LA, United States.,Department of Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, United States
| | | | - Ralph A Tripp
- Department of Infectious Disease, University of Georgia, Athens, GA, United States
| | | | - Stephania A Cormier
- Department of Biological Sciences, Louisiana State University and School of Veterinary Medicine, Baton Rouge, LA, United States.,Department of Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, United States
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15
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The resistance against Trichinella spiralis infection induced by primary infection with respiratory syncytial virus. Parasitology 2018; 146:634-642. [PMID: 30394235 DOI: 10.1017/s0031182018001889] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human infections with Trichinella spiralis and respiratory syncytial virus (RSV) are common, as T. spiralis infections are re-emerging in various parts of the world and RSV infections remain a threat for infants. Yet, studies investigating the relationship pertaining to the two are severely lacking. In particular, immune response induction via RSV and T. spiralis remain largely elusive. Here, we investigated the resistance against T. spiralis infection induced upon primary infection with RSV. RSV, notorious for causing severe inflammatory reaction in the lungs, were intranasally infected, followed with a T. spiralis infection in mice. Our results revealed that primary RSV infection in mice significantly raised T. spiralis-specific and total IgE, IgG and its subclass antibody responses upon T. spiralis challenge infection (RSV-Ts). Blood eosinophil levels were decreased in RSV-Ts, accompanied with significant increase in both Th1 and Th2 cytokines. Antibodies generated against RSV in RSV-infected mice were found to react with T. spiralis excretory/secretory antigen, showing several bands determined through immunoblotting. RSV-Ts also had a marked reduction of T. spiralis worm burden in diaphragm. These results indicate that immune responses induced by RSV infection contribute to resistance against subsequent T. spiralis infection.
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Gilbert BE, Patel N, Lu H, Liu Y, Guebre-Xabier M, Piedra PA, Glenn G, Ellingsworth L, Smith G. Respiratory syncytial virus fusion nanoparticle vaccine immune responses target multiple neutralizing epitopes that contribute to protection against wild-type and palivizumab-resistant mutant virus challenge. Vaccine 2018; 36:8069-8078. [PMID: 30389195 DOI: 10.1016/j.vaccine.2018.10.073] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/26/2022]
Abstract
Human respiratory syncytial virus (RSV) is the leading cause of severe lower respiratory tract infections in newborns, young children, elderly, and immune-compromised. The RSV fusion (F) glycoprotein is a major focus of vaccine development and the target of palivizumab (Synagis®) which is licensed as an immuno-prophylactic for use in newborn children at high risk of infection. However, clinical use of a narrowly targeted monoclonal antibodies leads to the generation of escape mutant strains that are fully resistant to neutralization by the antibody. Herein, we evaluated the RSV F nanoparticle vaccine (RSV F vaccine), produced as near-full-length, pre-fusogenic F trimers that form stable protein-detergent nanoparticles. The RSV F vaccine induces polyclonal antibodies that bind to antigenic site II as well as other epitopes known to be broadly neutralizing. Cotton rats immunized with the RSV F vaccine produced antibodies that were both neutralizing and protected against wild-type RSV infection, as well as against a palivizumab-resistant mutant virus. Use of aluminum phosphate adjuvant with the RSV F vaccine increased site II antibody avidity 100 to 1000-fold, which correlated with enhanced protection against challenge. The breadth of the vaccine-induced antibody response was demonstrated using competitive binding with monoclonal antibodies targeting antigenic sites Ø, II, IV, and VIII found on pre-fusion and post-fusion conformations of RSV F. In summary, we found the RSV F vaccine induced antibodies that bind to conserved epitopes including those defined as pre-fusion F specific; that use of adjuvant increased antibody avidity that correlated with enhanced protection in the cotton rat challenge model; and the polyclonal, high-avidity antibodies neutralized and protected against both wild-type and palivizumab-resistant mutant virus. These data support the ongoing clinical development of the aluminum phosphate adjuvanted RSV F nanoparticle vaccine.
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Affiliation(s)
- Brian E Gilbert
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| | | | - Hanxin Lu
- Novavax, Inc., Gaithersburg, MD, USA.
| | - Ye Liu
- Regenxbio, Inc., Rockville, MD, USA(1).
| | | | - Pedro A Piedra
- Department of Molecular Virology and Microbiology and Pediatrics, Baylor College of Medicine, Houston, TX, USA.
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Complete Genome Sequence of an ON1 Human Respiratory Syncytial Virus Strain Isolated in Lebanon in 2015. GENOME ANNOUNCEMENTS 2018; 6:6/16/e00316-18. [PMID: 29674556 PMCID: PMC5908921 DOI: 10.1128/genomea.00316-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We report here the complete genome sequence of a human respiratory syncytial virus (HRSV) strain obtained from an infant who presented to the emergency room with an acute respiratory illness during the 2014/2015 HRSV season in Lebanon. Analysis revealed that this virus belongs to the ON1 genotype that has recently emerged worldwide.
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Human antibody recognition of antigenic site IV on Pneumovirus fusion proteins. PLoS Pathog 2018; 14:e1006837. [PMID: 29470533 PMCID: PMC5823459 DOI: 10.1371/journal.ppat.1006837] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/21/2017] [Indexed: 11/19/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a major human pathogen that infects the majority of children by two years of age. The RSV fusion (F) protein is a primary target of human antibodies, and it has several antigenic regions capable of inducing neutralizing antibodies. Antigenic site IV is preserved in both the pre-fusion and post-fusion conformations of RSV F. Antibodies to antigenic site IV have been described that bind and neutralize both RSV and human metapneumovirus (hMPV). To explore the diversity of binding modes at antigenic site IV, we generated a panel of four new human monoclonal antibodies (mAbs) and competition-binding suggested the mAbs bind at antigenic site IV. Mutagenesis experiments revealed that binding and neutralization of two mAbs (3M3 and 6F18) depended on arginine (R) residue R429. We discovered two R429-independent mAbs (17E10 and 2N6) at this site that neutralized an RSV R429A mutant strain, and one of these mAbs (17E10) neutralized both RSV and hMPV. To determine the mechanism of cross-reactivity, we performed competition-binding, recombinant protein mutagenesis, peptide binding, and electron microscopy experiments. It was determined that the human cross-reactive mAb 17E10 binds to RSV F with a binding pose similar to 101F, which may be indicative of cross-reactivity with hMPV F. The data presented provide new concepts in RSV immune recognition and vaccine design, as we describe the novel idea that binding pose may influence mAb cross-reactivity between RSV and hMPV. Characterization of the site IV epitope bound by human antibodies may inform the design of a pan-Pneumovirus vaccine.
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Respiratory Syncytial Virus: Targeting the G Protein Provides a New Approach for an Old Problem. J Virol 2018; 92:JVI.01302-17. [PMID: 29118126 DOI: 10.1128/jvi.01302-17] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infection (LRTI) annually affecting >2 million children in the United States <5 years old. In the elderly (>65 years old), RSV results in ∼175,000 hospitalizations annually in the United States with a worldwide incidence of ∼34 million. There is no approved RSV vaccine, and treatments are limited. Recently, a phase 3 trial in the elderly using a recombinant RSV F protein vaccine failed to meet its efficacy objectives, namely, prevention of moderate-to-severe RSV-associated LRTI and reduced incidence of acute respiratory disease. Moreover, a recent phase 3 trial evaluating suptavumab (REGN2222), an antibody to RSV F protein, did not meet its primary endpoint of preventing medically attended RSV infections in preterm infants. Despite these setbacks, numerous efforts targeting the RSV F protein with vaccines, antibodies, and small molecules continue based on the commercial success of a monoclonal antibody (MAb) against the RSV F protein (palivizumab). As the understanding of RSV biology has improved, the other major coat protein, the RSV G protein, has reemerged as an alternative target reflecting progress in understanding its roles in infecting bronchial epithelial cells and in altering the host immune response. In mouse models, a high-affinity, strain-independent human MAb to the RSV G protein has shown potent direct antiviral activity combined with the alleviation of virus-induced immune system effects that contribute to disease pathology. This MAb, being prepared for clinical trials, provides a qualitatively new approach to managing RSV for populations not eligible for prophylaxis with palivizumab.
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Tang JW, Lam TT, Zaraket H, Lipkin WI, Drews SJ, Hatchette TF, Heraud JM, Koopmans MP. Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance. THE LANCET. INFECTIOUS DISEASES 2017; 17:e320-e326. [PMID: 28457597 PMCID: PMC7164797 DOI: 10.1016/s1473-3099(17)30238-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 01/06/2017] [Accepted: 02/07/2017] [Indexed: 01/13/2023]
Abstract
Together with influenza, the non-influenza RNA respiratory viruses (NIRVs), which include respiratory syncytial virus, parainfluenza viruses, coronavirus, rhinovirus, and human metapneumovirus, represent a considerable global health burden, as recognised by WHO's Battle against Respiratory Viruses initiative. By contrast with influenza viruses, little is known about the contemporaneous global diversity of these viruses, and the relevance of such for development of pharmaceutical interventions. Although far less advanced than for influenza, antiviral drugs and vaccines are in different stages of development for several of these viruses, but no interventions have been licensed. This scarcity of global genetic data represents a substantial knowledge gap and impediment to the eventual licensing of new antiviral drugs and vaccines for NIRVs. Enhanced genetic surveillance will assist and boost research and development into new antiviral drugs and vaccines for these viruses. Additionally, understanding the global diversity of respiratory viruses is also part of emerging disease preparedness, because non-human coronaviruses and paramyxoviruses have been listed as priority concerns in a recent WHO research and development blueprint initiative for emerging infectious diseases. In this Personal View, we explain further the rationale for expanding the genetic database of NIRVs and emphasise the need for greater investment in this area of research.
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Affiliation(s)
- Julian W Tang
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, UK; Department of Infection, Inflammation and Immunity, University of Leicester, Leicester, UK.
| | - Tommy T Lam
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hassan Zaraket
- Department of Experimental Pathology, Immunology, and Microbiology, American University of Beirut, Beirut, Lebanon
| | - W Ian Lipkin
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Steven J Drews
- Alberta Provincial Laboratory for Public Health, University of Alberta, Edmonton, AB, Canada
| | - Todd F Hatchette
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | | | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, Netherlands
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21
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Muñoz-Alía MA, Casasnovas JM, Celma ML, Carabaña J, Liton PB, Fernandez-Muñoz R. Measles Virus Hemagglutinin epitopes immunogenic in natural infection and vaccination are targeted by broad or genotype-specific neutralizing monoclonal antibodies. Virus Res 2017; 236:30-43. [PMID: 28465158 DOI: 10.1016/j.virusres.2017.04.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/24/2017] [Accepted: 04/24/2017] [Indexed: 11/27/2022]
Abstract
Measles virus (MV) remains a leading cause of vaccine-preventable deaths in children. Protection against MV is associated with neutralizing antibodies that preferentially recognize the viral hemagglutinin (MV-H), and to a lesser extent, the fusion protein (MV-F). Although MV is serologically monotypic, 24 genotypes have been identified. Here we report three neutralization epitopes conserved in the more prevalent circulating MV genotypes, two located in the MV-H receptor binding site (RBS) (antigenic site III) and a third in MV-H/MV-F interphase (antigenic site Ia) which are essential for MV multiplication. In contrast, two MV-H neutralization epitopes, showed a genotype-specific neutralization escape due to a single amino acid change, that we mapped in the "noose" antigenic site, or an enhanced neutralization epitope (antigenic site IIa). The monoclonal antibody (mAb) neutralization potency correlated with its binding affinity and was mainly driven by kinetic dissociation rate (koff). We developed an immunoassay for mAb binding to MV-H in its native hetero-oligomeric structure with MV-F on the surface of a MV productive steady-state persistently infected (p.i.) human cell lines, and a competitive-binding assay with serum from individuals with past infection by different MV genotypes. Binding assays revealed that a broad neutralization epitope, in RBS antigenic site, a genotype specific neutralization epitopes, in noose and IIa sites, were immunogenic in natural infection and vaccination and may elicit long-lasting humoral immunity that might contribute to explain MV immunogenic stability. These results support the design of improved measles vaccines, broad-spectrum prophylactic or therapeutic antibodies and MV-used in oncolytic therapies.
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Affiliation(s)
| | | | | | - Juan Carabaña
- Virology Unit, Ramón y Cajal Hospital, Madrid, Spain
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22
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Kimura H, Nagasawa K, Kimura R, Tsukagoshi H, Matsushima Y, Fujita K, Hirano E, Ishiwada N, Misaki T, Oishi K, Kuroda M, Ryo A. Molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B. INFECTION GENETICS AND EVOLUTION 2017; 52:1-9. [PMID: 28414106 DOI: 10.1016/j.meegid.2017.04.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/09/2017] [Accepted: 04/12/2017] [Indexed: 11/19/2022]
Abstract
In this study, we examined the molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B (HRSV-B). First, we performed time-scale evolution analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. Next, we performed genetic distance, linear B-cell epitope prediction, N-glycosylation, positive/negative selection site, and Bayesian skyline plot analyses. We also constructed a structural model of the F protein and mapped the amino acid substitutions and the predicted B-cell epitopes. The MCMC-constructed phylogenetic tree indicated that the HRSV F gene diverged from the bovine respiratory syncytial virus gene approximately 580years ago and had a relatively low evolutionary rate (7.14×10-4substitutions/site/year). Furthermore, a common ancestor of HRSV-A and -B diverged approximately 290years ago, while HRSV-B diverged into three clusters for approximately 60years. The genetic similarity of the present strains was very high. Although a maximum of 11 amino acid substitutions were observed in the structural model of the F protein, only one strain possessed an amino acid substitution located within the palivizumab epitope. Four epitopes were predicted, although these did not correspond to the neutralization sites of the F protein including the palivizumab epitope. In addition, five N-glycosylation sites of the present HRSV-B strains were inferred. No positive selection sites were identified; however, many sites were found to be under negative selection. The effective population size of the gene has remained almost constant. On the basis of these results, it can be concluded that the HRSV-B F gene is highly conserved, as is the F protein of HRSV-A. Moreover, our prediction of B-cell epitopes does not show that the palivizumab reaction site may be recognized as an epitope during naturally occurring infections.
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Affiliation(s)
- Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan; Department of Microbiology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanagawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan.
| | - Koo Nagasawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Ryusuke Kimura
- Faculty of Pharmacy, Takasaki University of Health and Welfare, 37-1 Nakaoruimachi, Takasaki-shi, Gunma 370-0033, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Yuki Matsushima
- Kawasaki City Institute for Public Health, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-0821, Japan
| | - Kiyotaka Fujita
- School of Medical Technology, Faculty of Health Science, Gumma Paz College, 1-7-1 Tonyamachi, Takasaki-shi, Gunma 370-0006, Japan
| | - Eiko Hirano
- Fukui Prefectural Institute of Public Health and Environmental Science, 39-4 Harame-cho, Fukui-shi, Fukui 910-8851, Japan
| | - Naruhiko Ishiwada
- Division of Infection Control and Prevention, Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8677, Japan
| | - Takako Misaki
- Kawasaki City Institute for Public Health, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-0821, Japan
| | - Kazunori Oishi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanagawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan
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23
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Abstract
Monoclonal antibodies (MAbs) have become a substantial part of many pharmaceutical company portfolios. However, the development process of MAbs for clinical use is quite different than for small-molecule drugs. MAb development programs require careful interdisciplinary evaluations to ensure the pharmacology of both the MAb and the target antigen are well-understood. Selection of appropriate preclinical species must be carefully considered and the potential development of anti-drug antibodies (ADA) during these early studies can limit the value and complicate the performance and possible duration of preclinical studies. In human studies, many of the typical pharmacology studies such as renal or hepatic impairment evaluations may not be needed but the pharmacokinetics and pharmacodynamics of these agents is complex, often necessitating more comprehensive evaluation of clinical data and more complex bioanalytical assays than might be used for small molecules. This paper outlines concerns and strategies for development of MAbs from the early in vitro assessments needed through preclinical and clinical development. This review focuses on how to develop, submit, and comply with regulatory requirements for MAb therapeutics.
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24
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Trivalency of a Nanobody Specific for the Human Respiratory Syncytial Virus Fusion Glycoprotein Drastically Enhances Virus Neutralization and Impacts Escape Mutant Selection. Antimicrob Agents Chemother 2016; 60:6498-6509. [PMID: 27550346 DOI: 10.1128/aac.00842-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/05/2016] [Indexed: 12/26/2022] Open
Abstract
ALX-0171 is a trivalent Nanobody derived from monovalent Nb017 that binds to antigenic site II of the human respiratory syncytial virus (hRSV) fusion (F) glycoprotein. ALX-0171 is about 6,000 to 10,000 times more potent than Nb017 in neutralization tests with strains of hRSV antigenic groups A and B. To explore the effect of this enhanced neutralization on escape mutant selection, viruses resistant to either ALX-0171 or Nb017 were isolated after serial passage of the hRSV Long strain in the presence of suboptimal concentrations of the respective Nanobodies. Resistant viruses emerged notably faster with Nb017 than with ALX-0171 and in both cases contained amino acid changes in antigenic site II of hRSV F. Detailed binding and neutralization analyses of these escape mutants as well as previously described mutants resistant to certain monoclonal antibodies (MAbs) offered a comprehensive description of site II mutations which are relevant for neutralization by MAbs and Nanobodies. Notably, ALX-0171 showed a sizeable neutralization potency with most escape mutants, even with some of those selected with the Nanobody, and these findings make ALX-0171 an attractive antiviral for treatment of hRSV infections.
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25
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A Rough Energy Landscape to Describe Surface-Linked Antibody and Antigen Bond Formation. Sci Rep 2016; 6:35193. [PMID: 27731375 PMCID: PMC5059681 DOI: 10.1038/srep35193] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/27/2016] [Indexed: 11/08/2022] Open
Abstract
Antibodies and B cell receptors often bind their antigen at cell-cell interface while both molecular species are surface-bound, which impacts bond kinetics and function. Despite the description of complex energy landscapes for dissociation kinetics which may also result in significantly different association kinetics, surface-bound molecule (2D) association kinetics usually remain described by an on-rate due to crossing of a single free energy barrier, and few experimental works have measured association kinetics under conditions implying force and two-dimensional relative ligand-receptor motion. We use a new laminar flow chamber to measure 2D bond formation with systematic variation of the distribution of encounter durations between antigen and antibody, in a range from 0.1 to 10 ms. Under physiologically relevant forces, 2D association is 100-fold slower than 3D association as studied by surface plasmon resonance assays. Supported by brownian dynamics simulations, our results show that a minimal encounter duration is required for 2D association; an energy landscape featuring a rough initial part might be a reasonable way of accounting for this. By systematically varying the temperature of our experiments, we evaluate roughness at 2kBT, in the range of previously proposed rough parts of landscapes models during dissociation.
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26
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Molecular evolution of the fusion protein gene in human respiratory syncytial virus subgroup A. INFECTION GENETICS AND EVOLUTION 2016; 43:398-406. [PMID: 27291709 DOI: 10.1016/j.meegid.2016.06.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/01/2016] [Accepted: 06/07/2016] [Indexed: 12/18/2022]
Abstract
We studied the molecular evolution of the fusion protein (F) gene in the human respiratory syncytial virus subgroup A (HRSV-A). We performed time-scaled phylogenetic analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. We also conducted genetic distance (p-distance), positive/negative selection, and Bayesian skyline plot analyses. Furthermore, we mapped the amino acid substitutions of the protein. The MCMC-constructed tree indicated that the HRSV F gene diverged from the bovine RSV (BRSV) gene approximately 550years ago and had a relatively low substitution rate (7.59×10(-4) substitutions/site/year). Moreover, a common ancestor of HRSV-A and -B diverged approximately 280years ago, which has since formed four distinct clusters. The present HRSV-A strains were assigned six genotypes based on F gene sequences and attachment glycoprotein gene sequences. The present strains exhibited high F gene sequence similarity values and low genetic divergence. No positive selection sites were identified; however, 50 negative selection sites were identified. F protein amino acid substitutions at 17 sites were distributed in the F protein. The effective population size of the gene has remained relatively constant, but the population size of the prevalent genotype (GA2) has increased in the last 10years. These results suggest that the HRSV-AF gene has evolved independently and formed some genotypes.
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27
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Dai K, Khan SN, Wang Y, He L, Guenaga J, Ingale J, Sundling C, O'Dell S, McKee K, Phad G, Corcoran M, Wilson R, Mascola JR, Zhu J, Li Y, Karlsson Hedestam GB, Wyatt RT. HIV-1 Vaccine-elicited Antibodies Reverted to Their Inferred Naive Germline Reveal Associations between Binding Affinity and in vivo Activation. Sci Rep 2016; 6:20987. [PMID: 26879974 PMCID: PMC4754655 DOI: 10.1038/srep20987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 01/14/2016] [Indexed: 11/10/2022] Open
Abstract
The elicitation of HIV-1 broadly neutralizing antibodies following envelope glycoprotein (Env) vaccination is exceedingly difficult. Suboptimal engagement of naïve B cells is suggested to limit these low frequency events, especially at the conserved CD4bs. Here, we analyzed CD4bs-directed monoclonal antibodies (mAbs) elicited by YU2 gp140-foldon trimers in a non-human primate by selective sorting using CD4bs “knock out” trimers. Following two inoculations, the CD4bs-directed mAbs efficiently recognized the eliciting immunogen in their affinity-maturing state but did not recognize CD4bs-defective probes. We reverted these mAbs to their most likely inferred germline (igL) state, leaving the HCDR3 unaltered, to establish correlates of in vitro affinity to in vivo activation. Most igL-reverted mAbs bound the eliciting gp140 immunogen, indicating that CD4bs-directed B cells possessing reasonable affinity existed in the naïve repertoire. We detected relatively high affinities for the majority of the igL mAbs to gp120 and of Fabs to gp140, which, as expected, increased when the antibodies ‘matured’ following vaccination. Affinity increases were associated with slower off-rates as well as with acquisition of neutralizing capacity. These data reveal in vitro binding properties associated with in vivo activation that result in functional archiving of antigen-specific B cells elicited by a complex glycoprotein antigen following immunization.
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Affiliation(s)
- Kaifan Dai
- IAVI Neutralizing Antibody Center at TSRI, La Jolla CA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA
| | - Salar N Khan
- IAVI Neutralizing Antibody Center at TSRI, La Jolla CA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA
| | - Yimeng Wang
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA
| | - Linling He
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA
| | - Javier Guenaga
- IAVI Neutralizing Antibody Center at TSRI, La Jolla CA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA
| | - Jidnyasa Ingale
- IAVI Neutralizing Antibody Center at TSRI, La Jolla CA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA.,The Scripps CHAVI-ID, The Scripps Research Institute, La Jolla CA
| | - Christopher Sundling
- Department of Microbiology, and Tumor Cell Biology Karolinska Institutet, Stockholm SE
| | | | | | - Ganesh Phad
- Department of Microbiology, and Tumor Cell Biology Karolinska Institutet, Stockholm SE
| | - Martin Corcoran
- Department of Microbiology, and Tumor Cell Biology Karolinska Institutet, Stockholm SE
| | - Richard Wilson
- IAVI Neutralizing Antibody Center at TSRI, La Jolla CA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA
| | | | - Jiang Zhu
- IAVI Neutralizing Antibody Center at TSRI, La Jolla CA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA.,The Scripps CHAVI-ID, The Scripps Research Institute, La Jolla CA
| | - Yuxing Li
- IAVI Neutralizing Antibody Center at TSRI, La Jolla CA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA
| | | | - Richard T Wyatt
- IAVI Neutralizing Antibody Center at TSRI, La Jolla CA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla CA.,The Scripps CHAVI-ID, The Scripps Research Institute, La Jolla CA
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28
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Bates JT, Pickens JA, Schuster JE, Johnson M, Tollefson SJ, Williams JV, Davis NL, Johnston RE, Schultz-Darken N, Slaughter JC, Smith-House F, Crowe JE. Immunogenicity and efficacy of alphavirus-derived replicon vaccines for respiratory syncytial virus and human metapneumovirus in nonhuman primates. Vaccine 2016; 34:950-6. [PMID: 26772634 DOI: 10.1016/j.vaccine.2015.12.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 12/15/2015] [Accepted: 12/18/2015] [Indexed: 12/14/2022]
Abstract
Human respiratory syncytial virus (hRSV) and human metapneumovirus (hMPV) are major causes of illness among children, the elderly, and the immunocompromised. No vaccine has been licensed for protection against either of these viruses. We tested the ability of two Venezuelan equine encephalitis virus-based viral replicon particle (VEE-VRP) vaccines that express the hRSV or hMPV fusion (F) protein to confer protection against hRSV or hMPV in African green monkeys. Animals immunized with VEE-VRP vaccines developed RSV or MPV F-specific antibodies and serum neutralizing activity. Compared to control animals, immunized animals were better able to control viral load in the respiratory mucosa following challenge and had lower levels of viral genome in nasopharyngeal and bronchoalveolar lavage fluids. The high level of immunogenicity and protective efficacy induced by these vaccine candidates in nonhuman primates suggest that they hold promise for further development.
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Affiliation(s)
- John T Bates
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jennifer A Pickens
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jennifer E Schuster
- The Department of Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Monika Johnson
- The Department of Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sharon J Tollefson
- The Department of Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - John V Williams
- The Department of Vanderbilt University Medical Center, Nashville, TN 37232, USA; The Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nancy L Davis
- The Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Nancy Schultz-Darken
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - James C Slaughter
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; The Department of Biostatistics of Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Frances Smith-House
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; The Department of Vanderbilt University Medical Center, Nashville, TN 37232, USA; The Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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29
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Garaicoechea L, Aguilar A, Parra GI, Bok M, Sosnovtsev SV, Canziani G, Green KY, Bok K, Parreño V. Llama nanoantibodies with therapeutic potential against human norovirus diarrhea. PLoS One 2015; 10:e0133665. [PMID: 26267898 PMCID: PMC4534396 DOI: 10.1371/journal.pone.0133665] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/30/2015] [Indexed: 11/24/2022] Open
Abstract
Noroviruses are a major cause of acute gastroenteritis, but no vaccines or therapeutic drugs are available. Llama-derived single chain antibody fragments (also called VHH) are small, recombinant monoclonal antibodies of 15 kDa with several advantages over conventional antibodies. The aim of this study was to generate recombinant monoclonal VHH specific for the two major norovirus (NoV) genogroups (GI and GII) in order to investigate their potential as immunotherapy for the treatment of NoV diarrhea. To accomplish this objective, two llamas were immunized with either GI.1 (Norwalk-1968) or GII.4 (MD2004) VLPs. After immunization, peripheral blood lymphocytes were collected and used to generate two VHH libraries. Using phage display technology, 10 VHH clones specific for GI.1, and 8 specific for GII.4 were selected for further characterization. All VHH recognized conformational epitopes in the P domain of the immunizing VP1 capsid protein, with the exception of one GII.4 VHH that recognized a linear P domain epitope. The GI.1 VHHs were highly specific for the immunizing GI.1 genotype, with only one VHH cross-reacting with GI.3 genotype. The GII.4 VHHs reacted with the immunizing GII.4 strain and showed a varying reactivity profile among different GII genotypes. One VHH specific for GI.1 and three specific for GII.4 could block the binding of homologous VLPs to synthetic HBGA carbohydrates, saliva, and pig gastric mucin, and in addition, could inhibit the hemagglutination of red blood cells by homologous VLPs. The ability of Nov-specific VHHs to perform well in these surrogate neutralization assays supports their further development as immunotherapy for NoV treatment and immunoprophylaxis.
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Affiliation(s)
| | - Andrea Aguilar
- Instituto de Virología, INTA, Castelar, Buenos Aires, Argentina
| | - Gabriel I. Parra
- Laboratory of Infectious Diseases, NIAID, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marina Bok
- Instituto de Virología, INTA, Castelar, Buenos Aires, Argentina
| | - Stanislav V. Sosnovtsev
- Laboratory of Infectious Diseases, NIAID, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Kim Y. Green
- Laboratory of Infectious Diseases, NIAID, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Karin Bok
- Laboratory of Infectious Diseases, NIAID, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Viviana Parreño
- Instituto de Virología, INTA, Castelar, Buenos Aires, Argentina
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30
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Molecular epidemiology and molecular characterization of respiratory syncytial viruses at a tertiary care university hospital in Catalonia (Spain) during the 2013–2014 season. J Clin Virol 2015; 66:27-32. [DOI: 10.1016/j.jcv.2015.02.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/22/2015] [Accepted: 02/25/2015] [Indexed: 01/22/2023]
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31
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Kim YI, DeVincenzo JP, Jones BG, Rudraraju R, Harrison L, Meyers R, Cehelsky J, Alvarez R, Hurwitz JL. Respiratory syncytial virus human experimental infection model: provenance, production, and sequence of low-passaged memphis-37 challenge virus. PLoS One 2014; 9:e113100. [PMID: 25415360 PMCID: PMC4240712 DOI: 10.1371/journal.pone.0113100] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 10/19/2014] [Indexed: 01/11/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in children and is responsible for as many as 199,000 childhood deaths annually worldwide. To support the development of viral therapeutics and vaccines for RSV, a human adult experimental infection model has been established. In this report, we describe the provenance and sequence of RSV Memphis-37, the low-passage clinical isolate used for the model's reproducible, safe, experimental infections of healthy, adult volunteers. The predicted amino acid sequences for major proteins of Memphis-37 are compared to nine other RSV A and B amino acid sequences to examine sites of vaccine, therapeutic, and pathophysiologic interest. Human T- cell epitope sequences previously defined by in vitro studies were observed to be closely matched between Memphis-37 and the laboratory strain RSV A2. Memphis-37 sequences provide baseline data with which to assess: (i) virus heterogeneity that may be evident following virus infection/transmission, (ii) the efficacy of candidate RSV vaccines and therapeutics in the experimental infection model, and (iii) the potential emergence of escape mutants as a consequence of experimental drug treatments. Memphis-37 is a valuable tool for pre-clinical research, and to expedite the clinical development of vaccines, therapeutic immunomodulatory agents, and other antiviral drug strategies for the protection of vulnerable populations against RSV disease.
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Affiliation(s)
- Young-In Kim
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Children's Foundation Research Institute of Le Bonheur Children's Hospital, Memphis, Tennessee, United States of America
| | - John P. DeVincenzo
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Children's Foundation Research Institute of Le Bonheur Children's Hospital, Memphis, Tennessee, United States of America
| | - Bart G. Jones
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Rajeev Rudraraju
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Lisa Harrison
- Children's Foundation Research Institute of Le Bonheur Children's Hospital, Memphis, Tennessee, United States of America
| | - Rachel Meyers
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Jeff Cehelsky
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Rene Alvarez
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Julia L. Hurwitz
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
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