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De Groot AS, Terry F, Cousens L, Martin W. Beyond humanization and de-immunization: tolerization as a method for reducing the immunogenicity of biologics. Expert Rev Clin Pharmacol 2013; 6:651-62. [PMID: 24164613 PMCID: PMC4086238 DOI: 10.1586/17512433.2013.835698] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Immune responses to some monoclonal antibodies (mAbs) and biologic proteins interfere with their efficacy due to the development of anti-drug antibodies (ADA). In the case of mAbs, most ADA target 'foreign' sequences present in the complementarity determining regions (CDRs). Humanization of the mAb sequence is one approach that has been used to render biologics less foreign to the human immune system. However, fully human mAbs can also drive immunogenicity. De-immunization (removing epitopes) has been used to reduce biologic protein immunogenicity. Here, we discuss a third approach to reducing the immunogenicity of biologics: introduction of Treg epitopes that stimulate Treg function and induce tolerance to the biologic protein. Supplementing humanization (replacing xeno-sequences with human) and de-immunization (reducing T effector epitopes) with tolerization (introducing Treg epitopes) where feasible, as a means of improving biologics 'quality by design', may lead to the development of ever more clinically effective, but less immunogenic, biologics.
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Affiliation(s)
- Anne S De Groot
- Institute for Immunology and Informatics,University of Rhode Island, 80 Washington Street, Providence, RI 02903,USA
- EpiVax, Inc.,146 Clifford Street, Providence, RI 02903,USA
| | - Frances Terry
- EpiVax, Inc.,146 Clifford Street, Providence, RI 02903,USA
| | - Leslie Cousens
- EpiVax, Inc.,146 Clifford Street, Providence, RI 02903,USA
| | - William Martin
- EpiVax, Inc.,146 Clifford Street, Providence, RI 02903,USA
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De Groot AS, Einck L, Moise L, Chambers M, Ballantyne J, Malone RW, Ardito M, Martin W. Making vaccines "on demand": a potential solution for emerging pathogens and biodefense? Hum Vaccin Immunother 2013; 9:1877-84. [PMID: 23877094 PMCID: PMC3906351 DOI: 10.4161/hv.25611] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The integrated US Public Health Emergency Medical Countermeasures Enterprise (PHEMCE) has made great strides in strategic preparedness and response capabilities. There have been numerous advances in planning, biothreat countermeasure development, licensure, manufacturing, stockpiling and deployment. Increased biodefense surveillance capability has dramatically improved, while new tools and increased awareness have fostered rapid identification of new potential public health pathogens. Unfortunately, structural delays in vaccine design, development, manufacture, clinical testing and licensure processes remain significant obstacles to an effective national biodefense rapid response capability. This is particularly true for the very real threat of “novel pathogens” such as the avian-origin influenzas H7N9 and H5N1, and new coronaviruses such as hCoV-EMC. Conventional approaches to vaccine development, production, clinical testing and licensure are incompatible with the prompt deployment needed for an effective public health response. An alternative approach, proposed here, is to apply computational vaccine design tools and rapid production technologies that now make it possible to engineer vaccines for novel emerging pathogen and WMD biowarfare agent countermeasures in record time. These new tools have the potential to significantly reduce the time needed to design string-of-epitope vaccines for previously unknown pathogens. The design process—from genome to gene sequence, ready to insert in a DNA plasmid—can now be accomplished in less than 24 h. While these vaccines are by no means “standard,” the need for innovation in the vaccine design and production process is great. Should such vaccines be developed, their 60-d start-to-finish timeline would represent a 2-fold faster response than the current standard.
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Affiliation(s)
- Anne S De Groot
- EpiVax, Inc.; Providence, RI USA; Institute for Immunology and Informatics; University of Rhode Island; Providence, RI USA
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The contribution of rodent models to the pathological assessment of flaviviral infections of the central nervous system. Arch Virol 2012; 157:1423-40. [PMID: 22592957 DOI: 10.1007/s00705-012-1337-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 03/30/2012] [Indexed: 12/16/2022]
Abstract
Members of the genus Flavivirus are responsible for a spectrum of important neurological syndromes in humans and animals. Rodent models have been used extensively to model flavivirus neurological disease, to discover host-pathogen interactions that influence disease outcome, and as surrogates to determine the efficacy and safety of vaccines and therapeutics. In this review, we discuss the current understanding of flavivirus neuroinvasive disease and outline the host, viral and experimental factors that influence the outcome and reliability of virus infection of small-animal models.
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Immunogenicity of novel Dengue virus epitopes identified by bioinformatic analysis. Virus Res 2010; 153:113-20. [DOI: 10.1016/j.virusres.2010.07.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 07/06/2010] [Accepted: 07/08/2010] [Indexed: 11/17/2022]
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Larsen MV, Lelic A, Parsons R, Nielsen M, Hoof I, Lamberth K, Loeb MB, Buus S, Bramson J, Lund O. Identification of CD8+ T cell epitopes in the West Nile virus polyprotein by reverse-immunology using NetCTL. PLoS One 2010; 5:e12697. [PMID: 20856867 PMCID: PMC2939062 DOI: 10.1371/journal.pone.0012697] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 08/21/2010] [Indexed: 11/19/2022] Open
Abstract
Background West Nile virus (WNV) is a growing threat to public health and a greater understanding of the immune response raised against WNV is important for the development of prophylactic and therapeutic strategies. Methodology/Principal Findings In a reverse-immunology approach, we used bioinformatics methods to predict WNV-specific CD8+ T cell epitopes and selected a set of peptides that constitutes maximum coverage of 20 fully-sequenced WNV strains. We then tested these putative epitopes for cellular reactivity in a cohort of WNV-infected patients. We identified 26 new CD8+ T cell epitopes, which we propose are restricted by 11 different HLA class I alleles. Aiming for optimal coverage of human populations, we suggest that 11 of these new WNV epitopes would be sufficient to cover from 48% to 93% of ethnic populations in various areas of the World. Conclusions/Significance The 26 identified CD8+ T cell epitopes contribute to our knowledge of the immune response against WNV infection and greatly extend the list of known WNV CD8+ T cell epitopes. A polytope incorporating these and other epitopes could possibly serve as the basis for a WNV vaccine.
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Affiliation(s)
- Mette Voldby Larsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
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Koo QY, Khan AM, Jung KO, Ramdas S, Miotto O, Tan TW, Brusic V, Salmon J, August JT. Conservation and variability of West Nile virus proteins. PLoS One 2009; 4:e5352. [PMID: 19401763 PMCID: PMC2670515 DOI: 10.1371/journal.pone.0005352] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 03/10/2009] [Indexed: 12/02/2022] Open
Abstract
West Nile virus (WNV) has emerged globally as an increasingly important pathogen for humans and domestic animals. Studies of the evolutionary diversity of the virus over its known history will help to elucidate conserved sites, and characterize their correspondence to other pathogens and their relevance to the immune system. We describe a large-scale analysis of the entire WNV proteome, aimed at identifying and characterizing evolutionarily conserved amino acid sequences. This study, which used 2,746 WNV protein sequences collected from the NCBI GenPept database, focused on analysis of peptides of length 9 amino acids or more, which are immunologically relevant as potential T-cell epitopes. Entropy-based analysis of the diversity of WNV sequences, revealed the presence of numerous evolutionarily stable nonamer positions across the proteome (entropy value of ≤1). The representation (frequency) of nonamers variant to the predominant peptide at these stable positions was, generally, low (≤10% of the WNV sequences analyzed). Eighty-eight fragments of length 9–29 amino acids, representing ∼34% of the WNV polyprotein length, were identified to be identical and evolutionarily stable in all analyzed WNV sequences. Of the 88 completely conserved sequences, 67 are also present in other flaviviruses, and several have been associated with the functional and structural properties of viral proteins. Immunoinformatic analysis revealed that the majority (78/88) of conserved sequences are potentially immunogenic, while 44 contained experimentally confirmed human T-cell epitopes. This study identified a comprehensive catalogue of completely conserved WNV sequences, many of which are shared by other flaviviruses, and majority are potential epitopes. The complete conservation of these immunologically relevant sequences through the entire recorded WNV history suggests they will be valuable as components of peptide-specific vaccines or other therapeutic applications, for sequence-specific diagnosis of a wide-range of Flavivivirus infections, and for studies of homologous sequences among other flaviviruses.
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Affiliation(s)
- Qi Ying Koo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Asif M. Khan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Keun-Ok Jung
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Shweta Ramdas
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Olivo Miotto
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Vladimir Brusic
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Jerome Salmon
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - J. Thomas August
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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Recombinant vesicular stomatitis virus-based west Nile vaccine elicits strong humoral and cellular immune responses and protects mice against lethal challenge with the virulent west Nile virus strain LSU-AR01. Vaccine 2008; 27:893-903. [PMID: 19070640 PMCID: PMC7115407 DOI: 10.1016/j.vaccine.2008.11.087] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 11/11/2008] [Accepted: 11/20/2008] [Indexed: 11/24/2022]
Abstract
Vesicular stomatitis virus (VSV) has been extensively utilized as a viral vector system for the induction of protective immune responses against a variety of pathogens. We constructed recombinant VSVs specifying either the Indiana or Chandipura virus G glycoprotein and expressing the West Nile virus (WNV) envelope (E) glycoprotein. Mice were intranasally vaccinated using a prime (Indiana)-boost (Chandipura) immunization approach and challenged with the virulent WNV-LSU-AR01. Ninety-percent (9 of 10) of the vaccinated mice survived as compared to 10% of the mock-vaccinated mice after WNV lethal challenge. Histopathological examination of brain tissues revealed neuronal necrosis in mock-vaccinated mice but not in vaccinated mice, and vaccinated, but not mock-vaccinated mice developed a strong neutralizing antibody response against WNV. Extensive immunological analysis using polychromatic flow cytometry staining revealed that vaccinated, but not mock-vaccinated mice developed robust cellular immune responses as evidenced by up-regulation of CD4+ CD154+ IFNγ+ T cells in vaccinated, but not mock-vaccinated mice. Similarly, vaccinated mice developed robust E-glycoprotein-specific CD8+ T cell immune responses as evidenced by the presence of a high percentage of CD8+ CD62Llow IFNγ+ cells. In addition, a sizeable population of CD8+ CD69+ cells was detected indicating E-specific activation of mature T cells and CD4+ CD25+ CD127low T regulatory (T reg) cells were down-regulated. These results suggest that VSV-vectored vaccines administered intranasally can efficiently induce protective humoral and cellular immune responses against WNV infections.
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Purtha WE, Myers N, Mitaksov V, Sitati E, Connolly J, Fremont DH, Hansen TH, Diamond MS. Antigen-specific cytotoxic T lymphocytes protect against lethal West Nile virus encephalitis. Eur J Immunol 2007; 37:1845-54. [PMID: 17559174 DOI: 10.1002/eji.200737192] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Infection with West Nile virus (WNV) causes fatal encephalitis in immunocompromised animals. Previous studies in mice have established that T cell protection is required for clearance of WNV infection from tissues and preventing viral persistence. The current study assessed whether specific WNV peptide epitopes could elicit a cytotoxic T lymphocyte (CTL) response capable of protecting against virus infection. Hidden Markov model analysis was used to identify WNV-encoded peptides that bound the MHC class I proteins K(b) or D(b). Of the 35 peptides predicted to bind MHC class I molecules, one immunodominant CTL recognition peptide was identified in each of the envelope and non-structural protein 4B genes. Addition of these but not control peptides to CD8(+) T cells from WNV-infected mice induced IFN-gamma production. CTL clones that were generated ex vivo lysed peptide-pulsed or WNV-infected target cells in an antigen-specific manner. Finally, adoptive transfer of a mixture of envelope- and non-structural protein 4B-specific CTL to recipient mice protected against lethal WNV challenge. Based on this, we conclude that CTL responses against immundominant WNV epitopes confer protective immunity and thus should be targets for inclusion in new vaccines.
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Affiliation(s)
- Whitney E Purtha
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
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Ovsyannikova IG, Ryan JE, Vierkant RA, Pankratz VS, Jacobson RM, Poland GA. Immunologic significance of HLA class I genes in measles virus-specific IFN-gamma and IL-4 cytokine immune responses. Immunogenetics 2005; 57:828-36. [PMID: 16331510 DOI: 10.1007/s00251-005-0061-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Accepted: 10/25/2005] [Indexed: 01/30/2023]
Abstract
The variability of immune responses modulated by human leukocyte antigen (HLA) genes and secreted cytokines is a significant factor in the development of a protective effect of measles vaccine. We studied the association between type 1 helper T cells (Th1)- and Th2-like cytokine immune responses and HLA class I alleles among 339 schoolchildren who previously received two doses of the measles vaccine. Median values for measles-specific interferon gamma (IFN-gamma) and interleukin-4 (IL-4) cytokines were 40.7 pg/ml [interquartile range (IQR) 8.1-176.7] and 9.7 pg/ml (IQR 2.8-24.3), respectively. Class I HLA-A (*0101 and *3101) and HLA-Cw (*0303 and *0501) alleles were significantly associated with measles-virus-induced IFN-gamma secretion. HLA-A*3101 and Cw*0303 were associated with a higher median IFN-gamma response, while A*0101 and Cw*0501 were associated with lower measles-specific IFN-gamma response. We found limited associations between HLA class I gene polymorphisms and Th2-like (IL-4) immune responses after measles vaccination, indicating that HLA class I molecules may have a limited effect on measles-vaccine-induced IL-4 secretion. Understanding the genetic factors that influence variations in cytokine secretion following measles vaccination will provide insight into the factors that influence both cell-mediated and humoral immunity to measles.
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Affiliation(s)
- Inna G Ovsyannikova
- Mayo Vaccine Research Group, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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Zhang GL, Srinivasan KN, Veeramani A, August JT, Brusic V. PREDBALB/c: a system for the prediction of peptide binding to H2d molecules, a haplotype of the BALB/c mouse. Nucleic Acids Res 2005; 33:W180-3. [PMID: 15980450 PMCID: PMC1160239 DOI: 10.1093/nar/gki479] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
PREDBALB/c is a computational system that predicts peptides binding to the major histocompatibility complex-2 (H2d) of the BALB/c mouse, an important laboratory model organism. The predictions include the complete set of H2d class I (H2-Kd, H2-Ld and H2-Dd) and class II (I-Ed and I-Ad) molecules. The prediction system utilizes quantitative matrices, which were rigorously validated using experimentally determined binders and non-binders and also by in vivo studies using viral proteins. The prediction performance of PREDBALB/c is of very high accuracy. To our knowledge, this is the first online server for the prediction of peptides binding to a complete set of major histocompatibility complex molecules in a model organism (H2d haplotype). PREDBALB/c is available at .
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Affiliation(s)
- Guang Lan Zhang
- Institute for Infocomm Research21 Heng Mui Keng Terrace, Singapore 119613
- School of Computer Engineering, Nanyang Technological UniversitySingapore 6397984
| | - Kellathur N. Srinivasan
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of MedicineBaltimore, MD 21205, USA
- Division of Biomedical Sciences, Johns Hopkins in Singapore#02–01 The Nanos, 31 Biopolis Way, Singapore 138669
| | - Anitha Veeramani
- Institute for Infocomm Research21 Heng Mui Keng Terrace, Singapore 119613
| | - J. Thomas August
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of MedicineBaltimore, MD 21205, USA
| | - Vladimir Brusic
- Institute for Infocomm Research21 Heng Mui Keng Terrace, Singapore 119613
- School of Land and Food Sciences and the Institute for Molecular Bioscience, University of QueenslandBrisbane QLD 4072, Australia
- To whom correspondence should be addressed: Tel: +65 96 212 415; Fax: +65 6774 8056;
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Brusic V, Bajic VB, Petrovsky N. Computational methods for prediction of T-cell epitopes--a framework for modelling, testing, and applications. Methods 2005; 34:436-43. [PMID: 15542369 DOI: 10.1016/j.ymeth.2004.06.006] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2004] [Indexed: 11/20/2022] Open
Abstract
Computational models complement laboratory experimentation for efficient identification of MHC-binding peptides and T-cell epitopes. Methods for prediction of MHC-binding peptides include binding motifs, quantitative matrices, artificial neural networks, hidden Markov models, and molecular modelling. Models derived by these methods have been successfully used for prediction of T-cell epitopes in cancer, autoimmunity, infectious disease, and allergy. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures and performed according to strict standards. This requires careful selection of data for model building, and adequate testing and validation. A range of web-based databases and MHC-binding prediction programs are available. Although some available prediction programs for particular MHC alleles have reasonable accuracy, there is no guarantee that all models produce good quality predictions. In this article, we present and discuss a framework for modelling, testing, and applications of computational methods used in predictions of T-cell epitopes.
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Affiliation(s)
- Vladimir Brusic
- Laboratories for Information Technology, 21 Heng Mui Keng Terrace, 119613, Singapore.
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De Groot AS, Nene V, Hegde NR, Srikumaran S, Rayner J, Martin W. T cell epitope identification for bovine vaccines: an epitope mapping method for BoLA A-11. Int J Parasitol 2003; 33:641-53. [PMID: 12782061 DOI: 10.1016/s0020-7519(03)00051-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
T cell responses play an important role in immunity to parasites and other microbial agents of infectious diseases, therefore a number of T cell-directed vaccines are in development. Computer-driven algorithms that facilitate the discovery of T cell epitopes from protein and genome sequences are now being used to accelerate preclinical studies of human vaccines. Similar tools are not yet available for predicting T cell epitopes for animal vaccines, but there may be sufficient data available to begin the process of compiling the algorithms. We describe the construction of a novel mathematical 'matrix' that describes the properties of bovine major histocompatibility complex (BoLA) system antigen (BoLA) A-11 peptide ligands, developed for use with EpiMatrix, an existing T cell epitope-mapping algorithm. An alternative means of developing BoLA matrices, using the pocket profile method, is also discussed. Matrices such as the one described here may be used to develop T cell epitope-mapping tools for cattle and other ruminants. Epitope-mapping algorithms offer a significant advantage over other methods of epitope selection, such as the screening of synthetic overlapping peptides, because high throughput screening can be performed in silico, followed by ex vivo confirmatory studies. Furthermore, using epitope-mapping algorithms, putative T cell epitopes can be derived directly from genomic sequences, allowing researchers to circumvent labor-intensive cloning steps in the genome-to-vaccine discovery pathway.
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