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Luo T, Xin C, Liu H, Li C, Chen H, Xia C, Gao C. Potential SLA Hp-4.0 haplotype-restricted CTL epitopes identified from the membrane protein of PRRSV induce cell immune responses. Front Microbiol 2024; 15:1404558. [PMID: 38841061 PMCID: PMC11150780 DOI: 10.3389/fmicb.2024.1404558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/03/2024] [Indexed: 06/07/2024] Open
Abstract
Swine leukocyte antigen (SLA) class I molecule-restricted T-cell epitopes, which induce cytotoxic T lymphocyte (CTL) responses, play a critical role in the clearance of porcine reproductive and respiratory syndrome virus (PRRSV) and the development of efficient protective vaccines. The SLA-1*04:01:01, SLA-2*04:01, and SLA-3*04:01 alleles, assigned the Hp-4.0 haplotype, are highly prevalent and usually present in all pig breeds. However, the SLA Hp-4.0 haplotype-restricted CTL epitopes in the structural membrane (M) protein of PRRSV are still unknown. In this study, we predicted 27 possible 9-mer epitope peptides in M protein with high binding scores for SLA-1*04:01:01 using CTL epitope prediction tools. In total, 45 SLA class I complexes, comprising the predicted peptide, extracellular region of the SLA-I molecules, and β2-microglobulin, were constructed in vitro to detect the specific binding of these peptides to SLA-1*04:01:01 (27 complexes), SLA-2*04:01 (9 complexes), and SLA-3*04:01 (9 complexes), respectively. Our results showed that the M27 (T91WKFITSRC), M39 (N130HAFVVRRP), and M49 (G158RKAVKQGV) peptides bind specifically to SLA-1*04:01:01, SLA-2*04:01, and SLA-3*04:01, respectively. Subsequently, using peripheral blood mononuclear cells (PBMCs) isolated from the homozygous Hp-4.0 and Hp-26.0 haplotype piglets vaccinated with commercial PRRSV HuN4-F112 strain, we determined the capacities of these 27 potential peptides to stimulate their proliferation with a Cell Counting Kit-8 and their secretion and expression of interferon gamma (IFN-γ) with an ELISpot assay and real-time qPCR, respectively. The immunological activities of M27, M39, and M49 were therefore confirmed when they efficiently induced PBMC proliferation and IFN-γ secretion in PBMCs from piglets with the prevalent SLA Hp-4.0 haplotype. The amino acid sequence alignment revealed that M27, M39, and M49 are highly conserved among 248 genotype II PRRSV strains collected between 1998 and 2019. These findings contribute to the understanding of the mechanisms of cell-mediated immune responses to PRRSV. Our study also provides a novel strategy for identifying and confirming potential SLA haplotype-restricted CTL epitopes that could be used to develop novel peptide-based vaccines against swine diseases.
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Affiliation(s)
| | | | | | | | | | - Changyou Xia
- State Key Laboratory for Animal Disease Control and Prevention, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, China
| | - Caixia Gao
- State Key Laboratory for Animal Disease Control and Prevention, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, China
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Calderon-Rico F, Bravo-Patiño A, Mendieta I, Perez-Duran F, Zamora-Aviles AG, Franco-Correa LE, Ortega-Flores R, Hernandez-Morales I, Nuñez-Anita RE. Glycoprotein 5-Derived Peptides Induce a Protective T-Cell Response in Swine against the Porcine Reproductive and Respiratory Syndrome Virus. Viruses 2023; 16:14. [PMID: 38275949 PMCID: PMC10819526 DOI: 10.3390/v16010014] [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: 11/22/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
We analyzed the T-cell responses induced by lineal epitopes of glycoprotein 5 (GP5) from PRRSV to explore the role of this protein in the immunological protection mediated by T-cells. The GP5 peptides were conjugated with a carrier protein for primary immunization and booster doses. Twenty-one-day-old pigs were allocated into four groups (seven pigs per group): control (PBS), vehicle (carrier), PTC1, and PTC2. Cytokine levels were measured at 2 days post-immunization (DPI) from serum samples. Cytotoxic T-lymphocytes (CTLs, CD8+) from peripheral blood were quantified via flow cytometry at 42 DPI. The cytotoxicity was evaluated by co-culturing primed lymphocytes with PRRSV derived from an infectious clone. The PTC2 peptide increased the serum concentrations of pro-inflammatory cytokines (i.e., TNF-α, IL-1β, IL-8) and cytokines that activate the adaptive cellular immunity associated with T-lymphocytes (i.e., IL-4, IL-6, IL-10, and IL-12). The concentration of CTLs (CD8+) was significantly higher in groups immunized with the peptides, which suggests a proliferative response in this cell population. Primed CTLs from immunized pigs showed cytolytic activity in PRRSV-infected cells in vitro. PTC1 and PTC2 peptides induced a protective T-cell-mediated response in pigs immunized against PRRSV, due to the presence of T epitopes in their sequences.
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Affiliation(s)
- Fernando Calderon-Rico
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolas de Hidalgo, Km. 9.5 S/N carretera Morelia-Zinapecuaro, La Palma, Tarimbaro PC 58893, Mexico; (F.C.-R.); (A.B.-P.); (F.P.-D.); (A.G.Z.-A.); (L.E.F.-C.); (R.O.-F.)
| | - Alejandro Bravo-Patiño
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolas de Hidalgo, Km. 9.5 S/N carretera Morelia-Zinapecuaro, La Palma, Tarimbaro PC 58893, Mexico; (F.C.-R.); (A.B.-P.); (F.P.-D.); (A.G.Z.-A.); (L.E.F.-C.); (R.O.-F.)
| | - Irasema Mendieta
- Posgrado en Ciencias Quimico-Biológicas, Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Querétaro PC 76010, Mexico;
| | - Francisco Perez-Duran
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolas de Hidalgo, Km. 9.5 S/N carretera Morelia-Zinapecuaro, La Palma, Tarimbaro PC 58893, Mexico; (F.C.-R.); (A.B.-P.); (F.P.-D.); (A.G.Z.-A.); (L.E.F.-C.); (R.O.-F.)
| | - Alicia Gabriela Zamora-Aviles
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolas de Hidalgo, Km. 9.5 S/N carretera Morelia-Zinapecuaro, La Palma, Tarimbaro PC 58893, Mexico; (F.C.-R.); (A.B.-P.); (F.P.-D.); (A.G.Z.-A.); (L.E.F.-C.); (R.O.-F.)
| | - Luis Enrique Franco-Correa
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolas de Hidalgo, Km. 9.5 S/N carretera Morelia-Zinapecuaro, La Palma, Tarimbaro PC 58893, Mexico; (F.C.-R.); (A.B.-P.); (F.P.-D.); (A.G.Z.-A.); (L.E.F.-C.); (R.O.-F.)
| | - Roberto Ortega-Flores
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolas de Hidalgo, Km. 9.5 S/N carretera Morelia-Zinapecuaro, La Palma, Tarimbaro PC 58893, Mexico; (F.C.-R.); (A.B.-P.); (F.P.-D.); (A.G.Z.-A.); (L.E.F.-C.); (R.O.-F.)
| | - Ilane Hernandez-Morales
- Escuela Nacional de Estudios Superiores Unidad Leon, Universidad Nacional Autonoma de Mexico, Blv. UNAM No. 2011, Leon PC 37684, Guanajuato, Mexico;
| | - Rosa Elvira Nuñez-Anita
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolas de Hidalgo, Km. 9.5 S/N carretera Morelia-Zinapecuaro, La Palma, Tarimbaro PC 58893, Mexico; (F.C.-R.); (A.B.-P.); (F.P.-D.); (A.G.Z.-A.); (L.E.F.-C.); (R.O.-F.)
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Zhao X, Wang X, Yuan M, Zhang X, Yang X, Guan X, Li S, Ma J, Qiu HJ, Li Y. Identification of two novel T cell epitopes on the E2 protein of classical swine fever virus C-strain. Vet Microbiol 2023; 284:109814. [PMID: 37356277 DOI: 10.1016/j.vetmic.2023.109814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023]
Abstract
C-strain, also known as the HCLV strain, is a well-known live attenuated vaccine against classical swine fever (CSF), a devastating disease caused by classical swine fever virus (CSFV). Vaccination with C-strain induces a rapid onset of protection, which is associated with virus-specific gamma interferon (IFN-γ)-secreting CD8+ T cell responses. The E2 protein of CSFV is a major protective antigen. However, the T cell epitopes on the E2 protein remain largely unknown. In this study, eight overlapping nonapeptides of the E2 protein were predicted and synthesized to screen for potential T cell epitopes on the CSFV C-strain E2 protein. Molecular docking was performed on the candidate epitopes with the swine leukocyte antigen-1*0401. The analysis obtained two highly conserved T cell epitopes, 90STEEMGDDF98 and 331ATDRHSDYF339, which were further identified by enzyme-linked immunospot assay. Interestingly, the mutants deleting or substituting the epitopes are nonviable. Further analysis demonstrated that 90STEEMGDDF98 is crucial for the E2 homodimerization, while CSFV infection is significantly inhibited by the 331ATDRHSDYF339 peptide treatment. The two novel T cell epitopes can be used to design new vaccines that are able to provide rapid-onset protection.
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Affiliation(s)
- Xiaotian Zhao
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China; Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China
| | - Xiao Wang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, China
| | - Mengqi Yuan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xin Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaoke Yang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiangyu Guan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Shuwen Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jifei Ma
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China.
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Yongfeng Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
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Feng L, Gao YY, Sun M, Li ZB, Zhang Q, Yang J, Qiao C, Jin H, Feng HS, Xian YH, Qi J, Gao GF, Liu WJ, Gao FS. The Parallel Presentation of Two Functional CTL Epitopes Derived from the O and Asia 1 Serotypes of Foot-and-Mouth Disease Virus and Swine SLA-2*HB01: Implications for Universal Vaccine Development. Cells 2022; 11:cells11244017. [PMID: 36552780 PMCID: PMC9777387 DOI: 10.3390/cells11244017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) poses a significant threat to the livestock industry. Through their recognition of the conserved epitopes presented by the swine leukocyte antigen (SLA), T cells play a pivotal role in the antiviral immunity of pigs. Herein, based on the peptide binding motif of SLA-2*HB01, from an original SLA-2 allele, a series of functional T-cell epitopes derived from the dominant antigen VP1 of FMDV with high binding capacity to SLA-2 were identified. Two parallel peptides, Hu64 and As64, from the O and Asia I serotypes, respectively, were both crystallized with SLA-2*HB01. Compared to SLA-1 and SLA-3, the SLA-2 structures showed the flexibility of residues in the P4, P6, and P8 positions and in their potential interface with TCR. Notably, the peptides Hu64 and As64 adopted quite similar overall conformation when bound to SLA-2*HB01. Hu64 has two different conformations, a more stable 'chair' conformation and an unstable 'boat' conformation observed in the two molecules of one asymmetric unit, whereas only a single 'chair' conformation was observed for As64. Both Hu64 and As64 could induce similar dominant T-cell activities. Our interdisciplinary study establishes a basis for the in-depth interpretation of the peptide presentation of SLA-I, which can be used toward the development of universal vaccines.
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Affiliation(s)
- Lei Feng
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Yong-Yu Gao
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
- College of Animal Medicine, Jilin Agricultural University, Changchun 130118, China
| | - Mingwei Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Zi-Bin Li
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, China
| | - Qiang Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Jie Yang
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Cui Qiao
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Hang Jin
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
| | - Hong-Sheng Feng
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
| | - Yu-Han Xian
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Correspondence: (G.F.G.); (W.J.L.); (F.-S.G.)
| | - William J. Liu
- NHC Key Laboratory of Biosafety, Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Correspondence: (G.F.G.); (W.J.L.); (F.-S.G.)
| | - Feng-Shan Gao
- Department of Bioengineering, College of Life and Health, Dalian University, Dalian 116622, China
- Correspondence: (G.F.G.); (W.J.L.); (F.-S.G.)
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Salaikumaran MR, Kasamuthu PS, Aathmanathan VS, Burra VLSP. An in silico approach to study the role of epitope order in the multi-epitope-based peptide (MEBP) vaccine design. Sci Rep 2022; 12:12584. [PMID: 35869117 PMCID: PMC9307121 DOI: 10.1038/s41598-022-16445-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractWith different countries facing multiple waves, with some SARS-CoV-2 variants more deadly and virulent, the COVID-19 pandemic is becoming more dangerous by the day and the world is facing an even more dreadful extended pandemic with exponential positive cases and increasing death rates. There is an urgent need for more efficient and faster methods of vaccine development against SARS-CoV-2. Compared to experimental protocols, the opportunities to innovate are very high in immunoinformatics/in silico approaches, especially with the recent adoption of structural bioinformatics in peptide vaccine design. In recent times, multi-epitope-based peptide vaccine candidates (MEBPVCs) have shown extraordinarily high humoral and cellular responses to immunization. Most of the publications claim that respective reported MEBPVC(s) assembled using a set of in silico predicted epitopes, to be the computationally validated potent vaccine candidate(s) ready for experimental validation. However, in this article, for a given set of predicted epitopes, it is shown that the published MEBPVC is one among the many possible variants and there is high likelihood of finding more potent MEBPVCs than the published candidates. To test the same, a methodology is developed where novel MEBP variants are derived by changing the epitope order of the published MEBPVC. Further, to overcome the limitations of current qualitative methods of assessment of MEBPVC, to enable quantitative comparison and ranking for the discovery of more potent MEBPVCs, novel predictors, Percent Epitope Accessibility (PEA), Receptor specific MEBP vaccine potency (RMVP), MEBP vaccine potency (MVP) are introduced. The MEBP variants indeed showed varied MVP scores indicating varied immunogenicity. Further, the MEBP variants with IDs, SPVC_446 and SPVC_537, had the highest MVP scores indicating these variants to be more potent MEBPVCs than the published MEBPVC and hence should be preferred candidates for immediate experimental testing and validation. The method enables quicker selection and high throughput experimental validation of vaccine candidates. This study also opens the opportunity to develop new software tools for designing more potent MEBPVCs in less time.
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Analysis of Foot and Mouth Disease Virus Polyprotein for Multi Peptides Vaccine Design: An In silico Strategy. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.3.63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) is small RNA virus from Picornaviridae family; genus Aphthovirus. FMDV causes maximum levels of infectivity in cattle and harmful socioeconomic effects. The present report attempted to design vaccine candidate from the polyprotein of FMDV to stimulate protective immune response. The IEDB server was used to predict B and T cells epitopes that were linked via GPGPG and YAA linkers, respectively. Mycobacterium tuberculosis 50S ribosomal protein was exploited as an adjuvant and a six histidine-tag sequence was linked to the carboxyl end of the vaccine for purification and identification. The predicted vaccine comprised 313aa and was antigenic and not allergic. Moreover, the vaccine was acidic and showed stability and hydrophilicity. Vaccine secondary and tertiary structures were predicted. The tertiary structure was refined to ameliorate the quality of the global and local structures of the vaccine. Vaccine model validation was performed and the final quality score of the structural model was computed. The validated model was used for molecular docking with bovine (N*01801-BoLA-A11) allele. Docking process in terms of binding free energy score was significant. Vaccine solubility was investigated based on the protein of E. coli and the stability was based on the disulfide bonding to lessen the entropic and mobile points in vaccine. Lastly, the in silico cloning ensured the proper cloning and best translation of the DNA of vaccine in molecular vectors.
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Gao Z, Chen L, Song T, Pan X, Li X, Lu G, Tang Y, Wu X, Zhao B, Zhang R. A candidate multi-epitope vaccine against porcine reproductive and respiratory syndrome virus and Mycoplasma hyopneumoniae induces robust humoral and cellular response in mice. Vaccine 2022; 40:2370-2378. [DOI: 10.1016/j.vaccine.2022.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022]
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Polyacrylate-GnRH Peptide Conjugate as an Oral Contraceptive Vaccine Candidate. Pharmaceutics 2021; 13:pharmaceutics13071081. [PMID: 34371772 PMCID: PMC8308917 DOI: 10.3390/pharmaceutics13071081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 01/30/2023] Open
Abstract
Contraceptive vaccines are designed to elicit immune responses against major components of animal reproductive systems. These vaccines, which are most commonly administered via injection, typically target gonadotropin-releasing hormone (GnRH). However, the need to restrain animals for treatment limits the field applications of injectable vaccines. Oral administration would broaden vaccine applicability. We explored contraceptive vaccine candidates composed of GnRH peptide hormone, universal T helper PADRE (P), and a poly(methylacrylate) (PMA)-based delivery system. When self-assembled into nanoparticles, PMA-P-GnRH induced the production of high IgG titers after subcutaneous and oral administration in mice. PADRE was then replaced with pig T helper derived from the swine flu virus, and the vaccine was tested in pigs. High levels of systemic antibodies were produced in pigs after both injection and oral administration of the vaccine. In conclusion, we developed a simple peptide–polymer conjugate that shows promise as an effective, adjuvant-free, oral GnRH-based contraceptive vaccine.
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Sangewar N, Waghela SD, Yao J, Sang H, Bray J, Mwangi W. Novel Potent IFN-γ-Inducing CD8 + T Cell Epitopes Conserved among Diverse Bovine Viral Diarrhea Virus Strains. THE JOURNAL OF IMMUNOLOGY 2021; 206:1709-1718. [PMID: 33762324 DOI: 10.4049/jimmunol.2001424] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/12/2021] [Indexed: 11/19/2022]
Abstract
Studies of immune responses elicited by bovine viral diarrhea virus (BVDV) vaccines have primarily focused on the characterization of neutralizing B cell and CD4+ T cell epitopes. Despite the availability of commercial vaccines for decades, BVDV prevalence in cattle has remained largely unaffected. There is limited knowledge regarding the role of BVDV-specific CD8+ T cells in immune protection, and indirect evidence suggests that they play a crucial role during BVDV infection. In this study, the presence of BVDV-specific CD8+ T cells that are highly cross-reactive in cattle was demonstrated. Most importantly, novel potent IFN-γ-inducing CD8+ T cell epitopes were identified from different regions of BVDV polyprotein. Eight CD8+ T cell epitopes were identified from the following structural BVDV Ags: Erns, E1, and E2 glycoproteins. In addition, from nonstructural BVDV Ags Npro, NS2-3, NS4A-B, and NS5A-B, 20 CD8+ T cell epitopes were identified. The majority of these IFN-γ-inducing CD8+ T cell epitopes were found to be highly conserved among more than 200 strains from BVDV-1 and -2 genotypes. These conserved epitopes were also validated as cross-reactive because they induced high recall IFN-γ+CD8+ T cell responses ex vivo in purified bovine CD8+ T cells isolated from BVDV-1- and -2-immunized cattle. Altogether, 28 bovine MHC class I-binding epitopes were identified from key BVDV Ags that can elicit broadly reactive CD8+ T cells against diverse BVDV strains. The data presented in this study will lay the groundwork for the development of a contemporary CD8+ T cell-based BVDV vaccine capable of addressing BVDV heterogeneity more effectively than current vaccines.
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Affiliation(s)
- Neha Sangewar
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506; and
| | - Suryakant D Waghela
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843
| | - Jianxiu Yao
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506; and
| | - Huldah Sang
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506; and
| | - Jocelyn Bray
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843
| | - Waithaka Mwangi
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506; and
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Coronado L, Perera CL, Rios L, Frías MT, Pérez LJ. A Critical Review about Different Vaccines against Classical Swine Fever Virus and Their Repercussions in Endemic Regions. Vaccines (Basel) 2021; 9:154. [PMID: 33671909 PMCID: PMC7918945 DOI: 10.3390/vaccines9020154] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/31/2021] [Accepted: 02/09/2021] [Indexed: 12/24/2022] Open
Abstract
Classical swine fever (CSF) is, without any doubt, one of the most devasting viral infectious diseases affecting the members of Suidae family, which causes a severe impact on the global economy. The reemergence of CSF virus (CSFV) in several countries in America, Asia, and sporadic outbreaks in Europe, sheds light about the serious concern that a potential global reemergence of this disease represents. The negative aspects related with the application of mass stamping out policies, including elevated costs and ethical issues, point out vaccination as the main control measure against future outbreaks. Hence, it is imperative for the scientific community to continue with the active investigations for more effective vaccines against CSFV. The current review pursues to gather all the available information about the vaccines in use or under developing stages against CSFV. From the perspective concerning the evolutionary viral process, this review also discusses the current problematic in CSF-endemic countries.
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Affiliation(s)
- Liani Coronado
- National Centre for Animal and Plant Health (CENSA), OIE Collaborating Centre for Disaster Risk Reduction in Animal Health, San José de las Lajas 32700, Cuba; (L.C.); (C.L.P.); (M.T.F.)
| | - Carmen L. Perera
- National Centre for Animal and Plant Health (CENSA), OIE Collaborating Centre for Disaster Risk Reduction in Animal Health, San José de las Lajas 32700, Cuba; (L.C.); (C.L.P.); (M.T.F.)
| | - Liliam Rios
- Reiman Cancer Research Laboratory, Faculty of Medicine, University of New Brunswick, Saint John, NB E2L 4L5, Canada;
| | - María T. Frías
- National Centre for Animal and Plant Health (CENSA), OIE Collaborating Centre for Disaster Risk Reduction in Animal Health, San José de las Lajas 32700, Cuba; (L.C.); (C.L.P.); (M.T.F.)
| | - Lester J. Pérez
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana–Champaign, Champaign, IL 61802, USA
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Defaus S, Forner M, Cañas-Arranz R, de León P, Bustos MJ, Rodríguez-Pulido M, Blanco E, Sobrino F, Andreu D. Designing Functionally Versatile, Highly Immunogenic Peptide-Based Multiepitopic Vaccines against Foot-and-Mouth Disease Virus. Vaccines (Basel) 2020; 8:vaccines8030406. [PMID: 32707834 PMCID: PMC7565419 DOI: 10.3390/vaccines8030406] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/02/2020] [Accepted: 07/16/2020] [Indexed: 11/23/2022] Open
Abstract
A broadly protective and biosafe vaccine against foot-and-mouth disease virus (FMDV) remains an unmet need in the animal health sector. We have previously reported solid protection against serotype O FMDV afforded by dendrimeric peptide structures harboring virus-specific B- and T-cell epitopes, and also shown such type of multivalent presentations to be advantageous over simple B-T-epitope linear juxtaposition. Chemically, our vaccine platforms are modular constructions readily made from specified B- and T-cell epitope precursor peptides that are conjugated in solution. With the aim of developing an improved version of our formulations to be used for on-demand vaccine applications, we evaluate in this study a novel design for epitope presentation to the immune system based on a multiple antigen peptide (MAP) containing six immunologically relevant motifs arranged in dendrimeric fashion (named B2T-TB2). Interestingly, two B2T units fused tail-to-tail into a single homodimer platform elicited higher B- and T-cell specific responses than former candidates, with immunization scores remaining stable even after 4 months. Moreover, this macromolecular assembly shows consistent immune response in swine, the natural FMDV host, at reduced dose. Thus, our versatile, immunogenic prototype can find application in the development of peptide-based vaccine candidates for various therapeutic uses using safer and more efficacious vaccination regimens.
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Affiliation(s)
- Sira Defaus
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu-Fabra, 08003 Barcelona, Spain; (S.D.); (M.F.)
| | - Mar Forner
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu-Fabra, 08003 Barcelona, Spain; (S.D.); (M.F.)
| | - Rodrigo Cañas-Arranz
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain; (R.C.-A.); (P.d.L.); (M.J.B.); (M.R.-P.)
| | - Patricia de León
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain; (R.C.-A.); (P.d.L.); (M.J.B.); (M.R.-P.)
| | - María J. Bustos
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain; (R.C.-A.); (P.d.L.); (M.J.B.); (M.R.-P.)
| | - Miguel Rodríguez-Pulido
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain; (R.C.-A.); (P.d.L.); (M.J.B.); (M.R.-P.)
| | - Esther Blanco
- Centro de Investigación en Sanidad Animal (CISA-INIA), Valdeolmos, 28130 Madrid, Spain;
| | - Francisco Sobrino
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain; (R.C.-A.); (P.d.L.); (M.J.B.); (M.R.-P.)
- Correspondence: (F.S.); (D.A.)
| | - David Andreu
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu-Fabra, 08003 Barcelona, Spain; (S.D.); (M.F.)
- Correspondence: (F.S.); (D.A.)
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12
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Pan X, Zhang N, Wei X, Jiang Y, Chen R, Li Q, Liang R, Zhang L, Ma L, Xia C. Illumination of PRRSV Cytotoxic T Lymphocyte Epitopes by the Three-Dimensional Structure and Peptidome of Swine Lymphocyte Antigen Class I (SLA-I). Front Immunol 2020; 10:2995. [PMID: 31969884 PMCID: PMC6960135 DOI: 10.3389/fimmu.2019.02995] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 12/05/2019] [Indexed: 01/03/2023] Open
Abstract
To investigate CTL epitope applications in swine, SLA-1*1502-restricted peptide epitopes matching porcine reproductive and respiratory syndrome virus (PRRSV) strains were explored by crystallography, biochemistry, and the specific pathogen-free (SPF) swine experiments. First, nine predicted PRRSV peptides were tested by assembly of the peptide-SLA-1*1502 (pSLA-1*1502) complexes, and the crystal structure of the SLA-1*1502 complex with one peptide (NSP9-TMP9) was determined. The NSP9-TMP9 peptide conformation presented by pSLA-1*1502 is different from that of the peptides presented by the known pSLA-1*0401 and pSLA-3*hs0202 complexes. Two consecutive Pro residues make the turn between P3 and P4 of NSP9-TMP9 much sharper. The D pocket of pSLA-1*1502 is unique and is important for peptide binding. Next, the potential SLA-1*1502-restricted peptide epitopes matching four typical genetic PRRSV strains were identified based on the peptide-binding motif of SLA-1*1502 determined by structural analysis and alanine scanning of the NSP9-TMP9 peptide. The tetrameric complex of SLA-1*1502 and NSP9-TMP9 was constructed and examined. Finally, taking NSP9-TMP9 as an example, the CTL immunogenicity of the identified PRRSV peptide epitope was evaluated. The SPF swine expressing the SLA-1*1502 alleles were divided into three groups: modified live vaccine (MLV), MLV+NSP9-TMP9, and the blank control group. NSP9-TMP9 was determined as a PRRSV CTL epitope with strong immunogenicity by flow cytometry and IFN-γ expression. Our study developed an integrated approach to identify SLA-I-restricted CTL epitopes from various important viruses and is helpful in designing and applying effective peptide-based vaccines for swine.
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Affiliation(s)
- Xiaocheng Pan
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei, China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaohui Wei
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yinan Jiang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Rong Chen
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qirun Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ruiying Liang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lijie Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, China Agricultural University, Beijing, China
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13
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Sankar S, Ramamurthy M, Nandagopal B, Sridharan G. Short peptide epitope design from hantaviruses causing HFRS. Bioinformation 2017; 13:231-236. [PMID: 28943728 PMCID: PMC5602290 DOI: 10.6026/97320630013231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/03/2017] [Accepted: 07/05/2017] [Indexed: 12/15/2022] Open
Abstract
Several genotypes of the hantavirus cause hemorrhagic fever with renal syndrome (HFRS) and is an important public health problem
worldwide. There is now growing interest to develop subunit vaccines especially focused to elicit cytotoxic T lymphocyte responses
which are important against viral infection. We identified candidate T-cell epitopes that bind to Class I HLA supertypes towards
identifying potential subunit vaccine entity. These epitopes are conserved in all 5 hantavirus genotypes of HFRS (Hantaan, Dobrava-
Belgrade, Seoul, Gou virus and Amur). The epitopes identified from S and M segment genomes were analyzed for human proteasome
cleavage, transporter associated antigen processing (TAP) efficiency and antigenicity using bioinformatic approaches. The epitope
MRNTIMASK which had the two characteristics of high proteasomal cleavage score and TAP score, also had high antigenicity score.
Our results indicate that this epitope from the nucleocapsid protein may be considered the most favorable moiety for the development
of subunit peptide vaccine.
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Affiliation(s)
- Sathish Sankar
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore 632 055, Tamil Nadu, India
| | - Mageshbabu Ramamurthy
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore 632 055, Tamil Nadu, India
| | - Balaji Nandagopal
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore 632 055, Tamil Nadu, India
| | - Gopalan Sridharan
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore 632 055, Tamil Nadu, India
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14
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Gao C, Quan J, Jiang X, Li C, Lu X, Chen H. Swine Leukocyte Antigen Diversity in Canadian Specific Pathogen-Free Yorkshire and Landrace Pigs. Front Immunol 2017; 8:282. [PMID: 28360911 PMCID: PMC5350106 DOI: 10.3389/fimmu.2017.00282] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 02/28/2017] [Indexed: 01/09/2023] Open
Abstract
The highly polymorphic swine major histocompatibility complex (MHC), termed swine leukocyte antigen (SLA), is associated with different levels of immunologic responses to infectious diseases, vaccines, and transplantation. Pig breeds with known SLA haplotypes are important genetic resources for biomedical research. Canadian Yorkshire and Landrace pigs represent the current specific pathogen-free (SPF) breeding stock maintained in the isolation environment at the Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences. In this study, we identified 61 alleles at five polymorphic SLA loci (SLA-1, SLA-2, SLA-3, DRB1, and DQB1) representing 17 class I haplotypes and 11 class II haplotypes using reverse transcription-polymerase chain reaction (RT-PCR) sequence-based typing and PCR-sequence specific primers methods in 367 Canadian SPF Yorkshire and Landrace pigs. The official designation of the alleles has been assigned by the SLA Nomenclature Committee of the International Society for Animal Genetics and released in updated Immuno Polymorphism Database-MHC SLA sequence database [Release 2.0.0.3 (2016-11-03)]. The submissions confirmed some unassigned alleles and standardized nomenclatures of many previously unconfirmed alleles in the GenBank database. Three class I haplotypes, Hp-37.0, 63.0, and 73.0, appeared to be novel and have not previously been reported in other pig populations. One crossover within the class I region and two between class I and class II regions were observed, resulting in three new recombinant haplotypes. The presence of the duplicated SLA-1 locus was confirmed in three class I haplotypes Hp-28.0, Hp-35.0, and Hp-63.0. Furthermore, we also analyzed the functional diversities of 19 identified frequent SLA class I molecules in this study and confirmed the existence of four supertypes using the MHCcluster method. These results will be useful for studying the adaptive immune response and immunological phenotypic differences in pigs, screening potential T-cell epitopes, and further developing the more effective vaccines.
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Affiliation(s)
- Caixia Gao
- Laboratory Animal and Comparative Medicine Team, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Harbin , China
| | - Jinqiang Quan
- Laboratory Animal and Comparative Medicine Team, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Harbin , China
| | - Xinjie Jiang
- Laboratory Animal and Comparative Medicine Team, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Harbin , China
| | - Changwen Li
- Laboratory Animal and Comparative Medicine Team, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Harbin , China
| | - Xiaoye Lu
- Laboratory Animal and Comparative Medicine Team, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Harbin , China
| | - Hongyan Chen
- Laboratory Animal and Comparative Medicine Team, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Harbin , China
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15
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Robinson L, Knight-Jones TJD, Charleston B, Rodriguez LL, Gay CG, Sumption KJ, Vosloo W. Global Foot-and-Mouth Disease Research Update and Gap Analysis: 3 - Vaccines. Transbound Emerg Dis 2017; 63 Suppl 1:30-41. [PMID: 27320164 DOI: 10.1111/tbed.12521] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Indexed: 11/28/2022]
Abstract
This study assessed research knowledge gaps in the field of FMDV (foot-and-mouth disease virus) vaccines. The study took the form of a literature review (2011-15) combined with research updates collected in 2014 from 33 institutes from across the world. Findings were used to identify priority areas for future FMD vaccine research. Vaccines play a vital role in FMD control, used both to limit the spread of the virus during epidemics in FMD-free countries and as the mainstay of disease management in endemic regions, particularly where sanitary controls are difficult to apply. Improvements in the performance or cost-effectiveness of FMD vaccines will allow more widespread and efficient disease control. FMD vaccines have changed little in recent decades, typically produced by inactivation of whole virus, the quantity and stability of the intact viral capsids in the final preparation being key for immunogenicity. However, these are exciting times and several promising novel FMD vaccine candidates have recently been developed. This includes the first FMD vaccine licensed for manufacture and use in the USA; this adenovirus-vectored FMD vaccine causes in vivo expression of viral capsids in vaccinated animals. Another promising vaccine candidate comprises stabilized empty FMDV capsids produced in vitro in a baculovirus expression system. Recombinant technologies are also being developed to improve otherwise conventionally produced inactivated vaccines, for example, by creating a chimeric vaccine virus to increase capsid stability and by inserting sequences into the vaccine virus for desired antigen expression. Other important areas of ongoing research include enhanced adjuvants, vaccine quality control procedures and predicting vaccine protection from immune correlates, thus reducing dependency on animal challenge studies. Globally, the degree of independent vaccine evaluation is highly variable, and this is essential for vaccine quality. Previously neglected, the importance of evaluating vaccination programme effectiveness and impact is increasingly being recognized.
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Affiliation(s)
| | | | | | - L L Rodriguez
- Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, USA
| | - C G Gay
- Agricultural Research Service, USDA, National Program 103-Animal Health, Beltsville, MD, USA
| | - K J Sumption
- European Commission for the Control of FMD (EuFMD), FAO, Rome, Italy
| | - W Vosloo
- Australian Animal Health Laboratory, CSIRO-Biosecurity Flagship, Geelong, Vic., Australia
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16
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Farrell D, Jones G, Pirson C, Malone K, Rue-Albrecht K, Chubb AJ, Vordermeier M, Gordon SV. Integrated computational prediction and experimental validation identifies promiscuous T cell epitopes in the proteome of Mycobacterium bovis. Microb Genom 2016; 2:e000071. [PMID: 28348866 PMCID: PMC5320590 DOI: 10.1099/mgen.0.000071] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/26/2016] [Indexed: 11/18/2022] Open
Abstract
The discovery of novel antigens is an essential requirement in devising new diagnostics or vaccines for use in control programmes against human tuberculosis (TB) and bovine tuberculosis (bTB). Identification of potential epitopes recognised by CD4+ T cells requires prediction of peptide binding to MHC class-II, an obligatory prerequisite for T cell recognition. To comprehensively prioritise potential MHC-II-binding epitopes from Mycobacterium bovis, the agent of bTB and zoonotic TB in humans, we integrated three binding prediction methods with the M. bovisproteome using a subset of human HLA alleles to approximate the binding of epitope-containing peptides to the bovine MHC class II molecule BoLA-DRB3. Two parallel strategies were then applied to filter the resulting set of binders: identification of the top-scoring binders or clusters of binders. Our approach was tested experimentally by assessing the capacity of predicted promiscuous peptides to drive interferon-γ secretion from T cells of M. bovis infected cattle. Thus, 376 20-mer peptides, were synthesised (270 predicted epitopes, 94 random peptides with low predictive scores and 12 positive controls of known epitopes). The results of this validation demonstrated significant enrichment (>24 %) of promiscuously recognised peptides predicted in our selection strategies, compared with randomly selected peptides with low prediction scores. Our strategy offers a general approach to the identification of promiscuous epitopes tailored to target populations where there is limited knowledge of MHC allelic diversity.
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Affiliation(s)
- Damien Farrell
- 1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland
| | - Gareth Jones
- 2Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK
| | - Christopher Pirson
- 2Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK
| | - Kerri Malone
- 1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland
| | - Kevin Rue-Albrecht
- 1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland.,3School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - Anthony J Chubb
- 4School of Medicine, University College Dublin, Dublin D4, Ireland
| | - Martin Vordermeier
- 2Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK
| | - Stephen V Gordon
- 6School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland.,5Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin D4, Ireland.,1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland.,4School of Medicine, University College Dublin, Dublin D4, Ireland
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17
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Abstract
Porcine reproductive and respiratory disease syndrome (PRRS) is a viral pandemic that especially affects neonates within the “critical window” of immunological development. PRRS was recognized in 1987 and within a few years became pandemic causing an estimated yearly $600,000 economic loss in the USA with comparative losses in most other countries. The causative agent is a single-stranded, positive-sense enveloped arterivirus (PRRSV) that infects macrophages and plasmacytoid dendritic cells. Despite the discovery of PRRSV in 1991 and the publication of >2,000 articles, the control of PRRS is problematic. Despite the large volume of literature on this disease, the cellular and molecular mechanisms describing how PRRSV dysregulates the host immune system are poorly understood. We know that PRRSV suppresses innate immunity and causes abnormal B cell proliferation and repertoire development, often lymphopenia and thymic atrophy. The PRRSV genome is highly diverse, rapidly evolving but amenable to the generation of many mutants and chimeric viruses for experimental studies. PRRSV only replicates in swine which adds to the experimental difficulty since no inbred well-defined animal models are available. In this article, we summarize current knowledge and apply it toward developing a series of provocative and testable hypotheses to explain how PRRSV immunomodulates the porcine immune system with the goal of adding new perspectives on this disease.
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18
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Abstract
Immunoinformatics focuses on modeling immune responses for better understanding of the immune system and in many cases for proposing agents able to modify the immune system. The most classical of these agents are vaccines derived from living organisms such as smallpox or polio. More modern vaccines comprise recombinant proteins, protein domains, and in some cases peptides. Generating a vaccine from peptides however requires technologies and concepts very different from classical vaccinology. Immunoinformatics therefore provides the computational tools to propose peptides suitable for formulation into vaccines. This chapter introduces the essential biological concepts affecting design and efficacy of peptide vaccines and discusses current methods and workflows applied to design successful peptide vaccines using computers.
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Affiliation(s)
- Johannes Söllner
- Emergentec Biodevelopment GmbH, Gersthofer Straße 29-31, 1180, Vienna, Austria,
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19
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Lu ZH, Archibald AL, Ait-Ali T. Beyond the whole genome consensus: unravelling of PRRSV phylogenomics using next generation sequencing technologies. Virus Res 2014; 194:167-74. [PMID: 25312450 PMCID: PMC4275598 DOI: 10.1016/j.virusres.2014.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/01/2014] [Accepted: 10/01/2014] [Indexed: 02/05/2023]
Abstract
NGS allows the whole genome sequencing of PRRSV without any prior knowledge. Low frequency variants within the co-evolving quasispecies can be detected. Both macro- and micro-evolutionary events can be followed using NGS.
The highly heterogeneous porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent responsible for an economically important pig disease with the characteristic symptoms of reproductive losses in breeding sows and respiratory illnesses in young piglets. The virus can be broadly divided into the European and North American-like genotype 1 and 2 respectively. In addition to this intra-strains variability, the impact of coexisting viral quasispecies on disease development has recently gained much attention; owing very much to the advent of the next-generation sequencing (NGS) technologies. Genomic data produced from the massive sequencing capacities of NGS have enabled the study of PRRSV at an unprecedented rate and details. Unlike conventional sequencing methods which require knowledge of conserved regions, NGS allows de novo assembly of the full viral genomes. Evolutionary variations gained from different genotypic strains provide valuable insights into functionally important regions of the virus. Together with the advancement of sophisticated bioinformatics tools, ultra-deep NGS technologies make the detection of low frequency co-evolving quasispecies possible. This short review gives an overview, including a proposed workflow, on the use of NGS to explore the genetic diversity of PRRSV at both macro- and micro-evolutionary levels.
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Affiliation(s)
- Zen H Lu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG Midlothian, United Kingdom.
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG Midlothian, United Kingdom
| | - Tahar Ait-Ali
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG Midlothian, United Kingdom.
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20
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Lu ZH, Brown A, Wilson AD, Calvert JG, Balasch M, Fuentes-Utrilla P, Loecherbach J, Turner F, Talbot R, Archibald AL, Ait-Ali T. Genomic variation in macrophage-cultured European porcine reproductive and respiratory syndrome virus Olot/91 revealed using ultra-deep next generation sequencing. Virol J 2014; 11:42. [PMID: 24588855 PMCID: PMC3945042 DOI: 10.1186/1743-422x-11-42] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/24/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Porcine Reproductive and Respiratory Syndrome (PRRS) is a disease of major economic impact worldwide. The etiologic agent of this disease is the PRRS virus (PRRSV). Increasing evidence suggest that microevolution within a coexisting quasispecies population can give rise to high sequence heterogeneity in PRRSV. FINDINGS We developed a pipeline based on the ultra-deep next generation sequencing approach to first construct the complete genome of a European PRRSV, strain Olot/9, cultured on macrophages and then capture the rare variants representative of the mixed quasispecies population. Olot/91 differs from the reference Lelystad strain by about 5% and a total of 88 variants, with frequencies as low as 1%, were detected in the mixed population. These variants included 16 non-synonymous variants concentrated in the genes encoding structural and nonstructural proteins; including Glycoprotein 2a and 5. CONCLUSION Using an ultra-deep sequencing methodology, the complete genome of Olot/91 was constructed without any prior knowledge of the sequence. Rare variants that constitute minor fractions of the heterogeneous PRRSV population could successfully be detected to allow further exploration of microevolutionary events.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Tahar Ait-Ali
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK.
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