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Stromberg ZR, Fischer W, Bradfute SB, Kubicek-Sutherland JZ, Hraber P. Vaccine Advances against Venezuelan, Eastern, and Western Equine Encephalitis Viruses. Vaccines (Basel) 2020; 8:vaccines8020273. [PMID: 32503232 PMCID: PMC7350001 DOI: 10.3390/vaccines8020273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 01/21/2023] Open
Abstract
Vaccinations are a crucial intervention in combating infectious diseases. The three neurotropic Alphaviruses, Eastern (EEEV), Venezuelan (VEEV), and Western (WEEV) equine encephalitis viruses, are pathogens of interest for animal health, public health, and biological defense. In both equines and humans, these viruses can cause febrile illness that may progress to encephalitis. Currently, there are no licensed treatments or vaccines available for these viruses in humans. Experimental vaccines have shown variable efficacy and may cause severe adverse effects. Here, we outline recent strategies used to generate vaccines against EEEV, VEEV, and WEEV with an emphasis on virus-vectored and plasmid DNA delivery. Despite candidate vaccines protecting against one of the three viruses, few studies have demonstrated an effective trivalent vaccine. We evaluated the potential of published vaccines to generate cross-reactive protective responses by comparing DNA vaccine sequences to a set of EEEV, VEEV, and WEEV genomes and determining the vaccine coverages of potential epitopes. Finally, we discuss future directions in the development of vaccines to combat EEEV, VEEV, and WEEV.
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Affiliation(s)
- Zachary R. Stromberg
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 505, USA; (Z.R.S.); (J.Z.K.-S.)
| | - Will Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 505, USA;
| | - Steven B. Bradfute
- Center for Global Health, Division of Infectious Diseases, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 505, USA;
| | - Jessica Z. Kubicek-Sutherland
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 505, USA; (Z.R.S.); (J.Z.K.-S.)
| | - Peter Hraber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 505, USA;
- Correspondence:
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2
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Zhang X, Huang Y, Li X, Wang Y, Yuan Y, Li M. Preparation of a new combination nanoemulsion-encapsulated MAGE1-MAGE3-MAGEn/HSP70 vaccine and study of its immunotherapeutic effect. Pathol Res Pract 2020; 216:152954. [PMID: 32321658 DOI: 10.1016/j.prp.2020.152954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/31/2020] [Accepted: 04/07/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND MAGE family genes have been studied as targets for tumor immunotherapy for a long time. Here, we combined MAGE1-, MAGE3- and MAGEn-derived peptides as a cancer vaccine and tested whether a new combination nanoemulsion-encapsulated vaccine could be used to inhibit the growth of tumor cells in humanized SCID mice. METHODS The nanoemulsion-encapsulated complex protein vaccine (MAGE1, MAGE3, and MAGEn/HSP70 fusion protein; M1M3MnH) was prepared using a magnetic ultrasonic technique. After screening, human PBMCs were injected into SCID mice to mimic the human immune system. Then, the humanized SCID mice were challenged with M3-HHCC cells and immunized with nanoemulsion-encapsulated MAGE1-MAGE3-MAGEn/HSP70 [NE(M1M3MnH)] or M1M3MnH. The cellular immune responses were detected by IFN-γ ELISPOT and cytotoxicity assays. Therapeutic and tumor challenge experiments were also performed. RESULTS The results showed that the immune responses elicited by NE(M1M3MnH) were apparently stronger than those elicited by M1M3MnH, NE(-) or PBS, suggesting that this novel nanoemulsion carrier induces potent antitumor immunity against the encapsulated antigens. The results of the therapeutic and tumor challenge experiments also indicated that the new vaccine had a definite effect on SCID mice bearing human hepatic cancer. CONCLUSION Our study indicated that the combination of several tumor antigen-derived peptides may be a relatively good strategy for peptide-based cancer immunotherapy. These results suggest that the complex nanoemulsion vaccine could have broader applications for both therapy and prevention mediated by antitumor effects in the future.
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Affiliation(s)
- Xiumin Zhang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Air Force Medical University, Xi'an, 710032, China
| | - Yang Huang
- Department of Emergency, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China
| | - Xia Li
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Air Force Medical University, Xi'an, 710032, China
| | - Yanxia Wang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Air Force Medical University, Xi'an, 710032, China
| | - Yuan Yuan
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Air Force Medical University, Xi'an, 710032, China
| | - Mingyang Li
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Air Force Medical University, Xi'an, 710032, China.
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3
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Theiler J, Korber B. Graph-based optimization of epitope coverage for vaccine antigen design. Stat Med 2018; 37:181-194. [PMID: 28132437 PMCID: PMC5763320 DOI: 10.1002/sim.7203] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 11/10/2016] [Accepted: 11/18/2016] [Indexed: 11/23/2022]
Abstract
Epigraph is a recently developed algorithm that enables the computationally efficient design of single or multi-antigen vaccines to maximize the potential epitope coverage for a diverse pathogen population. Potential epitopes are defined as short contiguous stretches of proteins, comparable in length to T-cell epitopes. This optimal coverage problem can be formulated in terms of a directed graph, with candidate antigens represented as paths that traverse this graph. Epigraph protein sequences can also be used as the basis for designing peptides for experimental evaluation of immune responses in natural infections to highly variable proteins. The epigraph tool suite also enables rapid characterization of populations of diverse sequences from an immunological perspective. Fundamental distance measures are based on immunologically relevant shared potential epitope frequencies, rather than simple Hamming or phylogenetic distances. Here, we provide a mathematical description of the epigraph algorithm, include a comparison of different heuristics that can be used when graphs are not acyclic, and we describe an additional tool we have added to the web-based epigraph tool suite that provides frequency summaries of all distinct potential epitopes in a population. We also show examples of the graphical output and summary tables that can be generated using the epigraph tool suite and explain their content and applications. Published 2017. This article is a U.S. Government work and is in the public domain in the USA. Statistics in Medicine published by John Wiley & Sons Ltd.
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Affiliation(s)
- James Theiler
- Los Alamos National LaboratoryLos Alamos87545NMU.S.A
- New Mexico ConsortiumLos Alamos87545NMU.S.A
| | - Bette Korber
- Los Alamos National LaboratoryLos Alamos87545NMU.S.A
- New Mexico ConsortiumLos Alamos87545NMU.S.A
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4
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Wang X, Zhou D, Wang G, Huang L, Zheng Q, Li C, Cheng Z. A novel multi-variant epitope ensemble vaccine against avian leukosis virus subgroup J. Vaccine 2017; 35:6685-6690. [DOI: 10.1016/j.vaccine.2017.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/22/2017] [Accepted: 10/10/2017] [Indexed: 12/12/2022]
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Abstract
A key unresolved challenge for developing an effective HIV‐1 vaccine is the discovery of strategies to elicit immune responses that are able to cross‐protect against a significant fraction of the diverse viruses that are circulating worldwide. Here, we summarize some of the immunological implications of HIV‐1 diversity, and outline the rationale behind several polyvalent vaccine design strategies that are currently under evaluation. Vaccine‐elicited T‐cell responses, which contribute to the control of HIV‐1 in natural infections, are currently being considered in both prevention and treatment settings. Approaches now in preclinical and human trials include full proteins in novel vectors, concatenated conserved protein regions, and polyvalent strategies that improve coverage of epitope diversity and enhance the cross‐reactivity of responses. While many barriers to vaccine induction of broadly neutralizing antibody (bNAb) responses remain, epitope diversification has emerged as both a challenge and an opportunity. Recent longitudinal studies have traced the emergence of bNAbs in HIV‐1 infection, inspiring novel approaches to recapitulate and accelerate the events that give rise to potent bNAb in vivo. In this review, we have selected two such lineage‐based design strategies to illustrate how such in‐depth analysis can offer conceptual improvements that may bring us closer to an effective vaccine.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, T6, Los Alamos National Laboratory, Los Alamos, NM, USA.,New Mexico Consortium, Los Alamos, NM, USA
| | - Peter Hraber
- Theoretical Biology and Biophysics, T6, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, T6, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
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6
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Sheikh QM, Gatherer D, Reche PA, Flower DR. Towards the knowledge-based design of universal influenza epitope ensemble vaccines. Bioinformatics 2016; 32:3233-3239. [PMID: 27402904 PMCID: PMC5079473 DOI: 10.1093/bioinformatics/btw399] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/14/2016] [Accepted: 06/18/2016] [Indexed: 12/14/2022] Open
Abstract
MOTIVATION Influenza A viral heterogeneity remains a significant threat due to unpredictable antigenic drift in seasonal influenza and antigenic shifts caused by the emergence of novel subtypes. Annual review of multivalent influenza vaccines targets strains of influenza A and B likely to be predominant in future influenza seasons. This does not induce broad, cross protective immunity against emergent subtypes. Better strategies are needed to prevent future pandemics. Cross-protection can be achieved by activating CD8+ and CD4+ T cells against highly conserved regions of the influenza genome. We combine available experimental data with informatics-based immunological predictions to help design vaccines potentially able to induce cross-protective T-cells against multiple influenza subtypes. RESULTS To exemplify our approach we designed two epitope ensemble vaccines comprising highly conserved and experimentally verified immunogenic influenza A epitopes as putative non-seasonal influenza vaccines; one specifically targets the US population and the other is a universal vaccine. The USA-specific vaccine comprised 6 CD8+ T cell epitopes (GILGFVFTL, FMYSDFHFI, GMDPRMCSL, SVKEKDMTK, FYIQMCTEL, DTVNRTHQY) and 3 CD4+ epitopes (KGILGFVFTLTVPSE, EYIMKGVYINTALLN, ILGFVFTLTVPSERG). The universal vaccine comprised 8 CD8+ epitopes: (FMYSDFHFI, GILGFVFTL, ILRGSVAHK, FYIQMCTEL, ILKGKFQTA, YYLEKANKI, VSDGGPNLY, YSHGTGTGY) and the same 3 CD4+ epitopes. Our USA-specific vaccine has a population protection coverage (portion of the population potentially responsive to one or more component epitopes of the vaccine, PPC) of over 96 and 95% coverage of observed influenza subtypes. The universal vaccine has a PPC value of over 97 and 88% coverage of observed subtypes. AVAILABILITY AND IMPLEMENTATION http://imed.med.ucm.es/Tools/episopt.html CONTACT: d.r.flower@aston.ac.uk.
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Affiliation(s)
- Qamar M Sheikh
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Derek Gatherer
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster LA1 4YW, UK
| | - Pedro A Reche
- Facultad de Medicina, Departamento de Microbiologia I, Universidad Complutense de Madrid, Madrid, Spain
| | - Darren R Flower
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
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Theiler J, Yoon H, Yusim K, Picker LJ, Fruh K, Korber B. Epigraph: A Vaccine Design Tool Applied to an HIV Therapeutic Vaccine and a Pan-Filovirus Vaccine. Sci Rep 2016; 6:33987. [PMID: 27703185 PMCID: PMC5050445 DOI: 10.1038/srep33987] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/01/2016] [Indexed: 11/09/2022] Open
Abstract
Epigraph is an efficient graph-based algorithm for designing vaccine antigens to optimize potential T-cell epitope (PTE) coverage. Epigraph vaccine antigens are functionally similar to Mosaic vaccines, which have demonstrated effectiveness in preliminary HIV non-human primate studies. In contrast to the Mosaic algorithm, Epigraph is substantially faster, and in restricted cases, provides a mathematically optimal solution. Epigraph furthermore has new features that enable enhanced vaccine design flexibility. These features include the ability to exclude rare epitopes from a design, to optimize population coverage based on inexact epitope matches, and to apply the code to both aligned and unaligned input sequences. Epigraph was developed to provide practical design solutions for two outstanding vaccine problems. The first of these is a personalized approach to a therapeutic T-cell HIV vaccine that would provide antigens with an excellent match to an individual’s infecting strain, intended to contain or clear a chronic infection. The second is a pan-filovirus vaccine, with the potential to protect against all known viruses in the Filoviradae family, including ebolaviruses. A web-based interface to run the Epigraph tool suite is available (http://www.hiv.lanl.gov/content/sequence/EPIGRAPH/epigraph.html).
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Affiliation(s)
- James Theiler
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Hyejin Yoon
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Karina Yusim
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Louis J Picker
- Oregon Health and Science University, Portland, OR 97239, USA
| | - Klaus Fruh
- Oregon Health and Science University, Portland, OR 97239, USA
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,New Mexico Consortium, Los Alamos, NM 87544, USA
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Jongwe TI, Chapman R, Douglass N, Chetty S, Chege G, Williamson AL. HIV-1 Subtype C Mosaic Gag Expressed by BCG and MVA Elicits Persistent Effector T Cell Responses in a Prime-Boost Regimen in Mice. PLoS One 2016; 11:e0159141. [PMID: 27427967 PMCID: PMC4948879 DOI: 10.1371/journal.pone.0159141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/28/2016] [Indexed: 11/18/2022] Open
Abstract
Over 90% of HIV/AIDS positive individuals in sub-Saharan Africa are infected with highly heterogeneous HIV-1 subtype C (HIV-1C) viruses. One of the best ways to reduce the burden of this disease is the development of an affordable and effective prophylactic vaccine. Mosaic immunogens are computationally designed to overcome the hurdle of HIV diversity by maximizing the expression of potential T cell epitopes. Mycobacterium bovis BCG ΔpanCD auxotroph and modified vaccinia Ankara (MVA) vaccines expressing HIV-1C mosaic Gag (GagM) were tested in a prime-boost regimen to demonstrate immunogenicity in a mouse study. The BCG-GagM vaccine was stable and persisted 11.5 weeks post vaccination in BALB/c mice. Priming with BCG-GagM and boosting with MVA-GagM elicited higher Gag-specific IFN-γ ELISPOT responses than the BCG-GagM only and MVA-GagM only homologous vaccination regimens. The heterologous vaccination also generated a more balanced and persistent CD4+ and CD8+ T cell Gag-specific IFN-γ ELISPOT response with a predominant effector memory phenotype. A Th1 bias was induced by the vaccines as determined by the predominant secretion of IFN-γ, TNF-α, and IL-2. This study shows that a low dose of MVA (104 pfu) can effectively boost a BCG prime expressing the same mosaic immunogen, generating strong, cellular immune responses against Gag in mice. Our data warrants further evaluation in non-human primates. A low dose vaccine would be an advantage in the resource limited countries of sub-Saharan Africa and India (where the predominating virus is HIV-1 subtype C).
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Affiliation(s)
- Tsungai Ivai Jongwe
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ros Chapman
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nicola Douglass
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shivan Chetty
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gerald Chege
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Anna-Lise Williamson
- Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Services, Groote Schuur Hospital, Cape Town, South Africa
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9
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Burk R, Bollinger L, Johnson JC, Wada J, Radoshitzky SR, Palacios G, Bavari S, Jahrling PB, Kuhn JH. Neglected filoviruses. FEMS Microbiol Rev 2016; 40:494-519. [PMID: 27268907 PMCID: PMC4931228 DOI: 10.1093/femsre/fuw010] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/06/2016] [Accepted: 05/04/2016] [Indexed: 12/22/2022] Open
Abstract
Eight viruses are currently assigned to the family Filoviridae Marburg virus, Sudan virus and, in particular, Ebola virus have received the most attention both by researchers and the public from 1967 to 2013. During this period, natural human filovirus disease outbreaks occurred sporadically in Equatorial Africa and, despite high case-fatality rates, never included more than several dozen to a few hundred infections per outbreak. Research emphasis shifted almost exclusively to Ebola virus in 2014, when this virus was identified as the cause of an outbreak that has thus far involved more than 28 646 people and caused more than 11 323 deaths in Western Africa. Consequently, major efforts are currently underway to develop licensed medical countermeasures against Ebola virus infection. However, the ecology of and mechanisms behind Ebola virus emergence are as little understood as they are for all other filoviruses. Consequently, the possibility of the future occurrence of a large disease outbreak caused by other less characterized filoviruses (i.e. Bundibugyo virus, Lloviu virus, Ravn virus, Reston virus and Taï Forest virus) is impossible to rule out. Yet, for many of these viruses, not even rudimentary research tools are available, let alone medical countermeasures. This review summarizes the current knowledge on these less well-characterized filoviruses.
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Affiliation(s)
- Robin Burk
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Baden-Württemberg, Germany
| | - Laura Bollinger
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Joshua C. Johnson
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Sheli R. Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Peter B. Jahrling
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
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Yusim K, Yoon H, Foley B, Feng S, Macke J, Dimitrijevic M, Abfalterer W, Szinger J, Fischer W, Kuiken C, Korber B. Integrated sequence and immunology filovirus database at Los Alamos. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw047. [PMID: 27103629 PMCID: PMC4839628 DOI: 10.1093/database/baw047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 03/14/2016] [Indexed: 12/11/2022]
Abstract
The Ebola outbreak of 2013–15 infected more than 28 000 people and claimed more lives than all previous filovirus outbreaks combined. Governmental agencies, clinical teams, and the world scientific community pulled together in a multifaceted response ranging from prevention and disease control, to evaluating vaccines and therapeutics in human trials. As this epidemic is finally coming to a close, refocusing on long-term prevention strategies becomes paramount. Given the very real threat of future filovirus outbreaks, and the inherent uncertainty of the next outbreak virus and geographic location, it is prudent to consider the extent and implications of known natural diversity in advancing vaccines and therapeutic approaches. To facilitate such consideration, we have updated and enhanced the content of the filovirus portion of Los Alamos Hemorrhagic Fever Viruses Database. We have integrated and performed baseline analysis of all family Filoviridae sequences deposited into GenBank, with associated immune response data, and metadata, and we have added new computational tools with web-interfaces to assist users with analysis. Here, we (i) describe the main features of updated database, (ii) provide integrated views and some basic analyses summarizing evolutionary patterns as they relate to geo-temporal data captured in the database and (iii) highlight the most conserved regions in the proteome that may be useful for a T cell vaccine strategy. Database URL: www.hfv.lanl.gov
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Affiliation(s)
- Karina Yusim
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Hyejin Yoon
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Brian Foley
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Shihai Feng
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | | | | | | | - Will Fischer
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Carla Kuiken
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM, USA
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11
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Abdul-Jawad S, Ondondo B, van Hateren A, Gardner A, Elliott T, Korber B, Hanke T. Increased Valency of Conserved-mosaic Vaccines Enhances the Breadth and Depth of Epitope Recognition. Mol Ther 2016; 24:375-384. [PMID: 26581160 PMCID: PMC4817818 DOI: 10.1038/mt.2015.210] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/09/2015] [Indexed: 12/19/2022] Open
Abstract
The biggest roadblock in development of effective vaccines against human immunodeficiency virus type 1 (HIV-1) is the virus genetic diversity. For T-cell vaccine, this can be tackled by focusing the vaccine-elicited T-cells on the highly functionally conserved regions of HIV-1 proteins, mutations in which typically cause a replicative fitness loss, and by computing multivalent mosaic proteins, which maximize the coverage of potential 9-mer T-cell epitopes of the input viral sequences. Our first conserved region vaccines HIVconsv employed clade alternating consensus sequences and showed promise in the initial clinical trials in terms of magnitude and breadth of elicited CD8(+) T-cells. Here, monitoring T-cells restricted by HLA-A*02:01 in transgenic mice, we assessed whether or not the tHIVconsv design (HIVconsv with a tissue plasminogen activator leader sequence) benefits from combining with a complementing conserved mosaic immunogen tHIVcmo, and compared the bivalent immunization to that with trivalent conserved mosaic vaccines. A hierarchy of tHIVconsv ≤ tHIVconsv+tHIVcmo < tCmo1+tCmo2+tCmo3 vaccinations for induction of CD8(+) T-cell responses was observed in terms of recognition of tested peptide variants. Thus, our HLA-A*02:01-restricted epitope data concur with previously published mouse and macaque observations and suggest that even conserved region vaccines benefit from oligovalent mosaic design.
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Affiliation(s)
| | | | - Andy van Hateren
- Faculty of Medicine and Institute for Life Science, University of Southampton, Southampton, UK
| | | | - Tim Elliott
- Faculty of Medicine and Institute for Life Science, University of Southampton, Southampton, UK
| | - Bette Korber
- Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, USA; The New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford, UK; International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.
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12
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Brannan JM, Froude JW, Prugar LI, Bakken RR, Zak SE, Daye SP, Wilhelmsen CE, Dye JM. Interferon α/β Receptor-Deficient Mice as a Model for Ebola Virus Disease. J Infect Dis 2015; 212 Suppl 2:S282-94. [PMID: 25943199 DOI: 10.1093/infdis/jiv215] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A major obstacle in ebolavirus research is the lack of a small-animal model for Sudan virus (SUDV), as well as other wild-type (WT) ebolaviruses. Here, we expand on research by Bray and by Lever et al suggesting that WT ebolaviruses are pathogenic in mice deficient for the type 1 interferon (IFN) α/β receptor (IFNα/βR-/-). We examined the disease course of several WT ebolaviruses: Boneface (SUDV/Bon) and Gulu variants of SUDV, Ebola virus (EBOV), Bundibugyo virus (BDBV), Taï Forest virus, and Reston virus (RESTV). We determined that exposure to WT SUDV or EBOV results in reproducible signs of disease in IFNα/βR-/- mice, as measured by weight loss and partial lethality. Vaccination with the SUDV or EBOV glycoprotein (GP)-expressing Venezuelan equine encephalitis viral replicon particle vaccine protected these mice from SUDV/Bon and EBOV challenge, respectively. Treatment with SUDV- or EBOV-specific anti-GP antibodies protected mice from challenge when delivered 1-3 days after infection. Serial sampling experiments revealed evidence of disseminated intravascular coagulation in the livers of mice infected with the Boneface variant of SUDV, EBOV, and BDBV. Taken together, these data solidify the IFNα/βR-/- mouse as an important and useful model for the study of WT EBOV disease.
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Affiliation(s)
- Jennifer M Brannan
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland
| | - Jeffery W Froude
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland
| | - Laura I Prugar
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland
| | - Russell R Bakken
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland
| | - Samantha E Zak
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland
| | - Sharon P Daye
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland
| | - Catherine E Wilhelmsen
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland
| | - John M Dye
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland
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13
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Choi JH, Schafer SC, Freiberg AN, Croyle MA. Bolstering Components of the Immune Response Compromised by Prior Exposure to Adenovirus: Guided Formulation Development for a Nasal Ebola Vaccine. Mol Pharm 2015; 12:2697-711. [PMID: 25549696 PMCID: PMC4525322 DOI: 10.1021/mp5006454] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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The
severity and longevity of the current Ebola outbreak highlight
the need for a fast-acting yet long-lasting vaccine for at-risk populations
(medical personnel and rural villagers) where repeated prime-boost
regimens are not feasible. While recombinant adenovirus (rAd)-based
vaccines have conferred full protection against multiple strains of
Ebola after a single immunization, their efficacy is impaired by pre-existing
immunity (PEI) to adenovirus. To address this important issue, a panel
of formulations was evaluated by an in vitro assay
for their ability to protect rAd from neutralization. An amphiphilic
polymer (F16, FW ∼39,000) significantly improved transgene
expression in the presence of anti-Ad neutralizing antibodies (NAB)
at concentrations of 5 times the 50% neutralizing dose (ND50). In vivo performance of rAd in F16 was compared
with unformulated virus, virus modified with poly(ethylene) glycol
(PEG), and virus incorporated into poly(lactic-co-glycolic) acid (PLGA) polymeric beads. Histochemical analysis of
lung tissue revealed that F16 promoted strong levels of transgene
expression in naive mice and those that were exposed to adenovirus
in the nasal cavity 28 days prior to immunization. Multiparameter
flow cytometry revealed that F16 induced significantly more polyfunctional
antigen-specific CD8+ T cells simultaneously producing
IFN-γ, IL-2, and TNF-α than other test formulations. These
effects were not compromised by PEI. Data from formulations that provided
partial protection from challenge consistently identified specific
immunological requirements necessary for protection. This approach
may be useful for development of formulations for other vaccine platforms
that also employ ubiquitous pathogens as carriers like the influenza
virus.
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Affiliation(s)
- Jin Huk Choi
- †Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Stephen C Schafer
- †Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Alexander N Freiberg
- ‡Department of Pathology, The University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Maria A Croyle
- †Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States.,§Center for Infectious Disease, The University of Texas at Austin, Austin, Texas 78712, United States
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14
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Roederer M, Keele BF, Schmidt SD, Mason RD, Welles HC, Fischer W, Labranche C, Foulds KE, Louder MK, Yang ZY, Todd JPM, Buzby AP, Mach LV, Shen L, Seaton KE, Ward BM, Bailer RT, Gottardo R, Gu W, Ferrari G, Alam SM, Denny TN, Montefiori DC, Tomaras GD, Korber BT, Nason MC, Seder RA, Koup RA, Letvin NL, Rao SS, Nabel GJ, Mascola JR. Immunological and virological mechanisms of vaccine-mediated protection against SIV and HIV. Nature 2014; 505:502-8. [PMID: 24352234 PMCID: PMC3946913 DOI: 10.1038/nature12893] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 11/21/2013] [Indexed: 02/07/2023]
Abstract
A major challenge for the development of a highly effective AIDS vaccine is the identification of mechanisms of protective immunity. To address this question, we used a nonhuman primate challenge model with simian immunodeficiency virus (SIV). We show that antibodies to the SIV envelope are necessary and sufficient to prevent infection. Moreover, sequencing of viruses from breakthrough infections revealed selective pressure against neutralization-sensitive viruses; we identified a two-amino-acid signature that alters antigenicity and confers neutralization resistance. A similar signature confers resistance of human immunodeficiency virus (HIV)-1 to neutralization by monoclonal antibodies against variable regions 1 and 2 (V1V2), suggesting that SIV and HIV share a fundamental mechanism of immune escape from vaccine-elicited or naturally elicited antibodies. These analyses provide insight into the limited efficacy seen in HIV vaccine trials.
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Affiliation(s)
- Mario Roederer
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Brandon F Keele
- SAIC-Frederick, Frederick National Laboratory, NIH, Frederick, Maryland 21702, USA
| | | | | | - Hugh C Welles
- 1] Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA [2] George Washington University, Washington DC 20052, USA
| | - Will Fischer
- Los Alamos National Laboratories, Los Alamos, New Mexico 87545, USA
| | - Celia Labranche
- Department of Surgery, Duke University, Durham, North Carolina 27710, USA
| | - Kathryn E Foulds
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Mark K Louder
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Zhi-Yong Yang
- 1] Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA [2] Sanofi-Pasteur, Cambridge, Massachusetts 02139, USA
| | - John-Paul M Todd
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Adam P Buzby
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
| | - Linh V Mach
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
| | - Ling Shen
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
| | - Kelly E Seaton
- Human Vaccine Institute, Duke University, Durham, North Carolina 27710, USA
| | - Brandy M Ward
- Department of Surgery, Duke University, Durham, North Carolina 27710, USA
| | - Robert T Bailer
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Raphael Gottardo
- Fred Hutchison Cancer Research Center, Seattle, Washington 98109, USA
| | - Wenjuan Gu
- Biostatistics Research Branch, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Guido Ferrari
- Department of Surgery, Duke University, Durham, North Carolina 27710, USA
| | - S Munir Alam
- Human Vaccine Institute, Duke University, Durham, North Carolina 27710, USA
| | - Thomas N Denny
- Human Vaccine Institute, Duke University, Durham, North Carolina 27710, USA
| | - David C Montefiori
- Department of Surgery, Duke University, Durham, North Carolina 27710, USA
| | - Georgia D Tomaras
- Human Vaccine Institute, Duke University, Durham, North Carolina 27710, USA
| | - Bette T Korber
- Los Alamos National Laboratories, Los Alamos, New Mexico 87545, USA
| | - Martha C Nason
- Biostatistics Research Branch, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Robert A Seder
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Richard A Koup
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Norman L Letvin
- 1] Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA [2]
| | - Srinivas S Rao
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA
| | - Gary J Nabel
- 1] Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA [2] Sanofi-Pasteur, Cambridge, Massachusetts 02139, USA
| | - John R Mascola
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA
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15
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Abstract
Ebola is a highly virulent pathogen causing severe hemorrhagic fever with a high case fatality rate in humans and non-human primates (NHPs). Although safe and effective vaccines or other medicinal agents to block Ebola infection are currently unavailable, a significant effort has been put forth to identify several promising candidates for the treatment and prevention of Ebola hemorrhagic fever. Among these, recombinant adenovirus-based vectors have been identified as potent vaccine candidates, with some affording both pre- and post-exposure protection from the virus. Recently, Investigational New Drug (IND) applications have been approved by the US Food and Drug Administration (FDA) and phase I clinical trials have been initiated for two small-molecule therapeutics: anti-sense phosphorodiamidate morpholino oligomers (PMOs: AVI-6002, AVI-6003) and lipid nanoparticle/small interfering RNA (LNP/siRNA: TKM-Ebola). These potential alternatives to vector-based vaccines require multiple doses to achieve therapeutic efficacy, which is not ideal with regard to patient compliance and outbreak scenarios. These concerns have fueled a quest for even better vaccination and treatment strategies. Here, we summarize recent advances in vaccines or post-exposure therapeutics for prevention of Ebola hemorrhagic fever. The utility of novel pharmaceutical approaches to refine and overcome barriers associated with the most promising therapeutic platforms are also discussed.
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Affiliation(s)
- Jin Huk Choi
- Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, U.S.A
| | - Maria A. Croyle
- Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, U.S.A
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, U.S.A
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16
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Induction of broad cytotoxic T cells by protective DNA vaccination against Marburg and Ebola. Mol Ther 2013; 21:1432-44. [PMID: 23670573 DOI: 10.1038/mt.2013.61] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 02/12/2013] [Indexed: 12/24/2022] Open
Abstract
Marburg and Ebola hemorrhagic fevers have been described as the most virulent viral diseases known to man due to associative lethality rates of up to 90%. Death can occur within days to weeks of exposure and there is currently no licensed vaccine or therapeutic. Recent evidence suggests an important role for antiviral T cells in conferring protection, but little detailed analysis of this response as driven by a protective vaccine has been reported. We developed a synthetic polyvalent-filovirus DNA vaccine against Marburg marburgvirus (MARV), Zaire ebolavirus (ZEBOV), and Sudan ebolavirus (SUDV). Preclinical efficacy studies were performed in guinea pigs and mice using rodent-adapted viruses, whereas murine T-cell responses were extensively analyzed using a novel modified assay described herein. Vaccination was highly potent, elicited robust neutralizing antibodies, and completely protected against MARV and ZEBOV challenge. Comprehensive T-cell analysis revealed cytotoxic T lymphocytes (CTLs) of great magnitude, epitopic breadth, and Th1-type marker expression. This model provides an important preclinical tool for studying protective immune correlates that could be applied to existing platforms. Data herein support further evaluation of this enhanced gene-based approach in nonhuman primate studies for in depth analyses of T-cell epitopes in understanding protective efficacy.
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17
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Grimm SK, Ackerman ME. Vaccine design: emerging concepts and renewed optimism. Curr Opin Biotechnol 2013; 24:1078-88. [PMID: 23474232 DOI: 10.1016/j.copbio.2013.02.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/29/2013] [Accepted: 02/15/2013] [Indexed: 01/15/2023]
Abstract
Arguably, vaccination represents the single most effective medical intervention ever developed. Yet, vaccines have failed to provide any or adequate protection against some of the most significant global diseases. The pathogens responsible for these vaccine-recalcitrant diseases have properties that allow them to evade immune surveillance and misdirect or eliminate the immune response. However, genomic and systems biology tools, novel adjuvants and delivery systems, and refined molecular insight into protective immunity have started to redefine the landscape, and results from recent efficacy trials of HIV and malaria vaccines have instilled hope that another golden age of vaccines may be on the horizon.
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18
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Hepatitis C genotype 1 mosaic vaccines are immunogenic in mice and induce stronger T-cell responses than natural strains. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2012; 20:302-5. [PMID: 23221002 DOI: 10.1128/cvi.00605-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Despite improved hepatitis C virus (HCV) treatments, vaccines remain an effective and economic option for curtailing the epidemic. Mosaic protein HCV genotype 1 vaccine candidates designed to address HCV diversity were immunogenic in mice. They elicited stronger T-cell responses to NS3-NS4a and E1-E2 proteins than did natural strains, as assessed with vaccine-matched peptides.
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