1
|
Chen J, Tan S, Avadhanula V, Moise L, Piedra PA, De Groot AS, Bahl J. Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus. PLoS Comput Biol 2023; 19:e1010360. [PMID: 36626370 PMCID: PMC9870173 DOI: 10.1371/journal.pcbi.1010360] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 01/23/2023] [Accepted: 12/07/2022] [Indexed: 01/11/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is a major cause of lower respiratory infection. Despite more than 60 years of research, there is no licensed vaccine. While B cell response is a major focus for vaccine design, the T cell epitope profile of RSV is also important for vaccine development. Here, we computationally predicted putative T cell epitopes in the Fusion protein (F) and Glycoprotein (G) of RSV wild circulating strains by predicting Major Histocompatibility Complex (MHC) class I and class II binding affinity. We limited our inferences to conserved epitopes in both F and G proteins that have been experimentally validated. We applied multidimensional scaling (MDS) to construct T cell epitope landscapes to investigate the diversity and evolution of T cell profiles across different RSV strains. We find the RSV strains are clustered into three RSV-A groups and two RSV-B groups on this T epitope landscape. These clusters represent divergent RSV strains with potentially different immunogenic profiles. In addition, our results show a greater proportion of F protein T cell epitope content conservation among recent epidemic strains, whereas the G protein T cell epitope content was decreased. Importantly, our results suggest that RSV-A and RSV-B have different patterns of epitope drift and replacement and that RSV-B vaccines may need more frequent updates. Our study provides a novel framework to study RSV T cell epitope evolution. Understanding the patterns of T cell epitope conservation and change may be valuable for vaccine design and assessment.
Collapse
Affiliation(s)
- Jiani Chen
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- Center for Influenza Disease and Emergence Response, University of Georgia, Athens, Georgia, United States of America
| | - Swan Tan
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- Center for Influenza Disease and Emergence Response, University of Georgia, Athens, Georgia, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Leonard Moise
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- EpiVax Inc., Providence, Rhode Island, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anne S. De Groot
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- EpiVax Inc., Providence, Rhode Island, United States of America
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, United States of America
- Center for Influenza Disease and Emergence Response, University of Georgia, Athens, Georgia, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, United States of America
| |
Collapse
|
2
|
Tan S, Moise L, Pearce DS, Kyriakis CS, Gutiérrez AH, Ross TM, Bahl J, De Groot AS. H1N1 G4 swine influenza T cell epitope analysis in swine and human vaccines and circulating strains uncovers potential risk to swine and humans. Influenza Other Respir Viruses 2022; 17:e13058. [PMID: 36285342 PMCID: PMC9835423 DOI: 10.1111/irv.13058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Pandemic influenza viruses may emerge from animal reservoirs and spread among humans in the absence of cross-reactive antibodies in the human population. Immune response to highly conserved T cell epitopes in vaccines may still reduce morbidity and limit the spread of the new virus even when cross-protective antibody responses are lacking. METHODS We used an established epitope content prediction and comparison tool, Epitope Content Comparison (EpiCC), to assess the potential for emergent H1N1 G4 swine influenza A virus (G4) to impact swine and human populations. We identified and computed the total cross-conserved T cell epitope content in HA sequences of human seasonal and experimental influenza vaccines, swine influenza vaccines from Europe and the United States (US) against G4. RESULTS The overall T cell epitope content of US commercial swine vaccines was poorly conserved with G4, with an average T cell epitope coverage of 35.7%. EpiCC scores for the comparison between current human influenza vaccines and circulating human influenza strains were also very low. In contrast, the T cell epitope coverage of a recent European swine influenza vaccine (HL03) was 65.8% against G4. CONCLUSIONS Poor T cell epitope cross-conservation between emergent G4 and swine and human influenza vaccines in the US may enable G4 to spread in swine and spillover to human populations in the absence of protective antibody response. One European influenza vaccine, HL03, may protect against emergent G4. This study illustrates the use of the EpiCC tool for prospective assessment of existing vaccine strains against emergent viruses in swine and human populations.
Collapse
Affiliation(s)
- Swan Tan
- Department of Infectious Diseases, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,Center for Vaccines and Immunology, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA
| | - Lenny Moise
- Center for Vaccines and Immunology, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,EpiVax Inc.ProvidenceRhode IslandUSA
| | - Douglas S. Pearce
- Zoetis Inc., Veterinary Medicine Research and DevelopmentKalamazooMichiganUSA
| | - Constantinos S. Kyriakis
- Center for Vaccines and Immunology, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,Department of Pathobiology, College of Veterinary MedicineAuburn UniversityAuburnAlabamaUSA
| | | | - Ted M. Ross
- Department of Infectious Diseases, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,Center for Vaccines and Immunology, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA
| | - Justin Bahl
- Department of Infectious Diseases, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,Center for Vaccines and Immunology, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,Institute of BioinformaticsUniversity of GeorgiaAthensGeorgiaUSA,Department of Epidemiology and BiostatisticsUniversity of GeorgiaAthensGeorgiaUSA
| | - Anne S. De Groot
- Center for Vaccines and Immunology, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgiaUSA,EpiVax Inc.ProvidenceRhode IslandUSA
| |
Collapse
|
3
|
Tan S, Gutiérrez AH, Gauger PC, Opriessnig T, Bahl J, Moise L, De Groot AS. Quantifying the Persistence of Vaccine-Related T Cell Epitopes in Circulating Swine Influenza A Strains from 2013-2017. Vaccines (Basel) 2021; 9:vaccines9050468. [PMID: 34066605 PMCID: PMC8148565 DOI: 10.3390/vaccines9050468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 12/02/2022] Open
Abstract
When swine flu vaccines and circulating influenza A virus (IAV) strains are poorly matched, vaccine-induced antibodies may not protect from infection. Highly conserved T cell epitopes may, however, have a disease-mitigating effect. The degree of T cell epitope conservation among circulating strains and vaccine strains can vary, which may also explain differences in vaccine efficacy. Here, we evaluate a previously developed conserved T cell epitope-based vaccine and determine the persistence of T cell epitope conservation over time. We used a pair-wise homology score to define the conservation between the vaccine’s swine leukocyte antigen (SLA) class I and II-restricted epitopes and T cell epitopes found in 1272 swine IAV strains sequenced between 2013 and 2017. Twenty-four of the 48 total T cell epitopes included in the epitope-based vaccine were highly conserved and found in >1000 circulating swine IAV strains over the 5-year period. In contrast, commercial swine IAV vaccines developed in 2013 exhibited a declining conservation with the circulating IAV strains over the same 5-year period. Conserved T cell epitope vaccines may be a useful adjunct for commercial swine flu vaccines and to improve protection against influenza when antibodies are not cross-reactive.
Collapse
Affiliation(s)
- Swan Tan
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (S.T.); (J.B.)
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; or
| | | | - Phillip Charles Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (P.C.G.); or (T.O.)
| | - Tanja Opriessnig
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (P.C.G.); or (T.O.)
- Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Justin Bahl
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA; (S.T.); (J.B.)
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; or
| | - Leonard Moise
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; or
- EpiVax Inc., Providence, RI 02909, USA;
| | - Anne Searls De Groot
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; or
- EpiVax Inc., Providence, RI 02909, USA;
- Correspondence: or or ; Tel.: +1-401-952-4227
| |
Collapse
|
4
|
Moise L, Gutiérrez AH, Khan S, Tan S, Ardito M, Martin WD, De Groot AS. New Immunoinformatics Tools for Swine: Designing Epitope-Driven Vaccines, Predicting Vaccine Efficacy, and Making Vaccines on Demand. Front Immunol 2020; 11:563362. [PMID: 33123135 PMCID: PMC7571332 DOI: 10.3389/fimmu.2020.563362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/10/2020] [Indexed: 12/16/2022] Open
Abstract
Novel computational tools for swine vaccine development can expand the range of immunization approaches available to prevent economically devastating swine diseases and spillover events between pigs and humans. PigMatrix and EpiCC are two new tools for swine T cell epitope identification and vaccine efficacy analysis that have been integrated into an existing computational vaccine design platform named iVAX. The iVAX platform is already in use for the development of human vaccines, thus integration of these tools into iVAX improves and expands the utility of the platform overall by making previously validated immunoinformatics tools, developed for humans, available for use in the design and analysis of swine vaccines. PigMatrix predicts T cell epitopes for a broad array of class I and class II swine leukocyte antigen (SLA) using matrices that enable the scoring of sequences for likelihood of binding to SLA. PigMatrix facilitates the prospective selection of T cell epitopes from the sequences of swine pathogens for vaccines and permits the comparison of those predicted epitopes with "self" (the swine proteome) and with sequences from other strains. Use of PigMatrix with additional tools in the iVAX toolkit also enables the computational design of vaccines in silico, for testing in vivo. EpiCC uses PigMatrix to analyze existing or proposed vaccines for their potential to protect, based on a comparison between T cell epitopes in the vaccine and circulating strains of the same pathogen. Performing an analysis of T cell epitope relatedness analysis using EpiCC may facilitate vaccine selection when a novel strain emerges in a herd and also permits analysis of evolutionary drift as a means of immune escape. This review of novel computational immunology tools for swine describes the application of PigMatrix and EpiCC in case studies, such as the design of cross-conserved T cell epitopes for swine influenza vaccine or for African Swine Fever. We also describe the application of EpiCC for determination of the best vaccine strains to use against circulating viral variants of swine influenza, swine rotavirus, and porcine circovirus type 2. The availability of these computational tools accelerates infectious disease research for swine and enable swine vaccine developers to strategically advance their vaccines to market.
Collapse
Affiliation(s)
- Lenny Moise
- EpiVax, Inc., Providence, RI, United States.,Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | | | | | - Swan Tan
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | | | | | - Anne S De Groot
- EpiVax, Inc., Providence, RI, United States.,Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| |
Collapse
|
5
|
De Groot AS, Moise L, Terry F, Gutierrez AH, Hindocha P, Richard G, Hoft DF, Ross TM, Noe AR, Takahashi Y, Kotraiah V, Silk SE, Nielsen CM, Minassian AM, Ashfield R, Ardito M, Draper SJ, Martin WD. Better Epitope Discovery, Precision Immune Engineering, and Accelerated Vaccine Design Using Immunoinformatics Tools. Front Immunol 2020; 11:442. [PMID: 32318055 PMCID: PMC7154102 DOI: 10.3389/fimmu.2020.00442] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/26/2020] [Indexed: 12/19/2022] Open
Abstract
Computational vaccinology includes epitope mapping, antigen selection, and immunogen design using computational tools. Tools that facilitate the in silico prediction of immune response to biothreats, emerging infectious diseases, and cancers can accelerate the design of novel and next generation vaccines and their delivery to the clinic. Over the past 20 years, vaccinologists, bioinformatics experts, and advanced programmers based in Providence, Rhode Island, USA have advanced the development of an integrated toolkit for vaccine design called iVAX, that is secure and user-accessible by internet. This integrated set of immunoinformatic tools comprises algorithms for scoring and triaging candidate antigens, selecting immunogenic and conserved T cell epitopes, re-engineering or eliminating regulatory T cell epitopes, and re-designing antigens to induce immunogenicity and protection against disease for humans and livestock. Commercial and academic applications of iVAX have included identifying immunogenic T cell epitopes in the development of a T-cell based human multi-epitope Q fever vaccine, designing novel influenza vaccines, identifying cross-conserved T cell epitopes for a malaria vaccine, and analyzing immune responses in clinical vaccine studies. Animal vaccine applications to date have included viral infections of pigs such as swine influenza A, PCV2, and African Swine Fever. “Rapid-Fire” applications for biodefense have included a demonstration project for Lassa Fever and Q fever. As recent infectious disease outbreaks underscore the significance of vaccine-driven preparedness, the integrated set of tools available on the iVAX toolkit stand ready to help vaccine developers deliver genome-derived, epitope-driven vaccines.
Collapse
Affiliation(s)
- Anne S De Groot
- EpiVax, Inc., Providence, RI, United States.,Institute for Immunology and Informatics, Providence, RI, United States
| | - Leonard Moise
- EpiVax, Inc., Providence, RI, United States.,Institute for Immunology and Informatics, Providence, RI, United States
| | | | - Andres H Gutierrez
- EpiVax, Inc., Providence, RI, United States.,Institute for Immunology and Informatics, Providence, RI, United States
| | | | | | - Daniel Fredric Hoft
- Departments of Molecular Microbiology & Immunology and Internal Medicine, Division of Infectious Diseases, Allergy & Immunology, Saint Louis University, St. Louis, MO, United States
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Amy R Noe
- Leidos Life Sciences, Frederick, MD, United States
| | | | | | - Sarah E Silk
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | | | | | | | - Simon J Draper
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | |
Collapse
|
6
|
Balz K, Trassl L, Härtel V, Nelson PP, Skevaki C. Virus-Induced T Cell-Mediated Heterologous Immunity and Vaccine Development. Front Immunol 2020; 11:513. [PMID: 32296430 PMCID: PMC7137989 DOI: 10.3389/fimmu.2020.00513] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/06/2020] [Indexed: 12/15/2022] Open
Abstract
Heterologous immunity (H.I.) is a consequence of an encounter with a specific antigen, which can alter the subsequent immune response to a different antigen. This can happen at the innate immune system level—often called trained immunity or innate immune memory—and/or at the adaptive immune system level involving T memory cells and antibodies. Viruses may also induce T cell-mediated H.I., which can confer protection or drive immunopathology against other virus subtypes, related or unrelated viruses, other pathogens, auto- or allo-antigens. It is important to understand the underlying mechanisms for the development of antiviral “universal” vaccines and broader T cell responses rather than just subtype-specific antibody responses as in the case of influenza. Furthermore, knowledge about determinants of vaccine-mediated H.I. may inform public health policies and provide suggestions for repurposing existing vaccines. Here, we introduce H.I. and provide an overview of evidence on virus- and antiviral vaccine-induced T cell-mediated cross-reactive responses. We also discuss the factors influencing final clinical outcome of virus-mediated H.I. as well as non-specific beneficial effects of live attenuated antiviral vaccines such as measles and vaccinia. Available epidemiological and mechanistic data have implications both for the development of new vaccines and for personalized vaccinology, which are presented. Finally, we formulate future research priorities and opportunities.
Collapse
Affiliation(s)
- Kathrin Balz
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
| | - Lilith Trassl
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
| | - Valerie Härtel
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
| | - Philipp P Nelson
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
| | - Chrysanthi Skevaki
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
| |
Collapse
|
7
|
Bandrick M, Gutiérrez AH, Desai P, Rincon G, Martin WD, Terry FE, De Groot AS, Foss DL. T cell epitope content comparison (EpiCC) analysis demonstrates a bivalent PCV2 vaccine has greater T cell epitope overlap with field strains than monovalent PCV2 vaccines. Vet Immunol Immunopathol 2020; 223:110034. [PMID: 32278900 DOI: 10.1016/j.vetimm.2020.110034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/17/2020] [Accepted: 03/03/2020] [Indexed: 01/14/2023]
Abstract
Porcine circovirus type 2 (PCV2) has one of the highest evolutionary rates among DNA viruses. Traditionally, PCV2 vaccines have been based on the 2a genotype as this was the first genotype discovered. Today, eight genotypes of PCV2 viruses have been identified, and, taken together with the rapid evolutionary rate, propensity to recombine, and high rate of vaccination, further variation in PCV2 is expected. For these reasons, there is a growing genetic gap between available vaccines and field strains. When selecting vaccines, it is important to consider vaccines that contain T cell epitopes that are well-matched to the circulating strains. To quantify the relatedness between PCV2 vaccines and field strains, we predicted and compared their T cell epitope content and calculated Epitope Content Comparison (EpiCC) scores using established in silico tools. T cell epitopes predicted to bind common class I and class II swine leukocyte antigen (SLA) alleles were identified from two major structural proteins, the capsid (encoded by ORF2) and the replicase (encoded by ORF1). The T cell epitope content of three commercial PCV2a-based vaccines (a baculovirus expressed PCV2a ORF2 [VacAlt], a PCV1-PCV2a chimeric virus vaccine [VacA] and a combination cPCV2a-cPCV2b chimeric virus vaccine [VacAB]) and an experimental PCV2b ORF2-based chimeric virus vaccine [VacB] (Table 1), were compared to that of 161 PCV2 field strains (representing genotypes a-f). The T cell epitope content and conservation between vaccine and field strains varied. While all vaccine strains provided broad coverage of the field strains including heterologous genotypes, none of the vaccines covered all the putative T cell epitopes identified in the field strains. PCV2a-based vaccine strains generally scored higher in terms of conserved epitope content against PCV2a field isolates but were not identical. The PCV2b-based vaccine strain had higher scores against PCV2b and PCV2d field strains. The combination PCV2a-PCV2b vaccine (VacAB) had, on average, the highest EpiCC score. PCV2 continues to evolve and EpiCC analysis provides a new tool to assess the possible impact of virus genetic divergence on T cell epitope coverage of vaccine strains. Given that multiple genotypes are currently found and may co-exist on farms, this analysis suggests that a combination of PCV2a and PCV2b vaccine strains may be required to provide optimal coverage of current and future field isolates.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Anne S De Groot
- EpiVax, Inc., Providence, RI, United States; Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | | |
Collapse
|
8
|
Singh G, Pritam M, Banerjee M, Singh AK, Singh SP. Genome based screening of epitope ensemble vaccine candidates against dreadful visceral leishmaniasis using immunoinformatics approach. Microb Pathog 2019; 136:103704. [PMID: 31479726 DOI: 10.1016/j.micpath.2019.103704] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/12/2019] [Accepted: 08/31/2019] [Indexed: 01/09/2023]
Abstract
Visceral leishmaniasis (VL) is a dreadful protozoan disease caused by Leishmania donovani that severely affects huge populations in tropical and sub-tropical regions. The present study reports an unbiased genome based screening of 4 potent vaccine antigens against 8023 L. donovani proteins by following the criteria of presence of signal peptides, GPI-anchors and ≤1 transmembrane helix using advanced bioinformatics tools viz. SignalP4.0, PredGPI and TMHMM2.0, respectively. They are designated as genome based predicted signal peptide antigens (GBPSPA). The antigenicity/immunogenicity of chosen vaccine antigens (GBPSPA) with 4 randomly selected known leishmanial antigens (RSKLA) was compared by simulation study employing C-ImmSim software for human immune responses. This revealed better immunological responses. These antigens were further evaluated for the presence of B- and T-cell epitopes using immune epitope database (IEDB) based recommended consensus method of MHC class I and II tools. It was found to forecast CD4+ and CD8+ T-cell responses in genetically diverse human population worldwide as well as different endemic regions through IEDB based predicted population coverage (PPC) analysis tool. The worldwide percent PPC value of combined (HLA class I and II) epitope ensemble forecast was found to be 99.98, 99.96 and 50.04, respectively for GBPSPA, RSKLA and experimentally known epitopes (EKE) of L. donovani. Therefore, these potential antigens/epitope ensembles could favor the design of prospective and novel vaccine constructs like self-assembled epitopes as nano vaccine formulations against VL. Overall, the present study will serve as a model framework that might improve the effectiveness of designed vaccine against L. donovani and other related pathogens.
Collapse
Affiliation(s)
- Garima Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow-226028, India.
| | - Manisha Pritam
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow-226028, India.
| | - Monisha Banerjee
- Molecular and Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow- 226007, India.
| | - Akhilesh Kumar Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow-226028, India.
| | - Satarudra Prakash Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow-226028, India; Department of Biotech and Genome, School of Life Sciences, Mahatma Gandhi Central University, Motihari-845401, India.
| |
Collapse
|
9
|
Hewitt JS, Karuppannan AK, Tan S, Gauger P, Halbur PG, Gerber PF, De Groot AS, Moise L, Opriessnig T. A prime-boost concept using a T-cell epitope-driven DNA vaccine followed by a whole virus vaccine effectively protected pigs in the pandemic H1N1 pig challenge model. Vaccine 2019; 37:4302-4309. [PMID: 31248687 DOI: 10.1016/j.vaccine.2019.06.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 01/08/2023]
Abstract
Influenza A virus (IAV) vaccines in pigs generally provide homosubtypic protection but fail to prevent heterologous infections. In this pilot study, the efficacy of an intradermal pDNA vaccine composed of conserved SLA class I and class II T cell epitopes (EPITOPE) against a homosubtypic challenge was compared to an intramuscular commercial inactivated whole virus vaccine (INACT) and a heterologous prime boost approach using both vaccines. Thirty-nine IAV-free, 3-week-old pigs were randomly assigned to one of five groups including NEG-CONTROL (unvaccinated, sham-challenged), INACT-INACT-IAV (vaccinated with FluSure XP® at 4 and 7 weeks, pH1N1 challenged), EPITOPE-INACT-IAV (vaccinated with PigMatrix EDV at 4 and FluSure XP® at 7 weeks, pH1N1 challenged), EPITOPE-EPITOPE-IAV (vaccinated with PigMatrix EDV at 4 and 7 weeks, pH1N1 challenged), and a POS-CONTROL group (unvaccinated, pH1N1 challenged). The challenge was done at 9 weeks of age and pigs were necropsied at day post challenge (dpc) 5. At the time of challenge, all INACT-INACT-IAV pigs, and by dpc 5 all EPITOPE-INACT-IAV pigs were IAV seropositive. IFNγ secreting cells, recognizing vaccine epitope-specific peptides and pH1N1 challenge virus were highest in the EPITOPE-INACT-IAV pigs at challenge. Macroscopic lung lesion scores were reduced in all EPITOPE-INACT-IAV pigs while INACT-INACT-IAV pigs exhibited a bimodal distribution of low and high scores akin to naïve challenged animals. No IAV antigen in lung tissues was detected at necropsy in the EPITOPE-INACT-IAV group, which was similar to naïve unchallenged pigs and different from all other challenged groups. Results suggest that the heterologous prime boost approach using an epitope-driven DNA vaccine followed by an inactivated vaccine was effective against a homosubtypic challenge, and further exploration of this vaccine approach as a practical control measure against heterosubtypic IAV infections is warranted.
Collapse
Affiliation(s)
- Joshua S Hewitt
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Anbu K Karuppannan
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Swan Tan
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | - Phillip Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Patrick G Halbur
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Priscilla F Gerber
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, Australia
| | - Anne S De Groot
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA; EpiVax Inc., Providence, RI, USA
| | - Leonard Moise
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA; EpiVax Inc., Providence, RI, USA
| | - Tanja Opriessnig
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA; The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK.
| |
Collapse
|
10
|
Bazmara S, Shadmani M, Ghasemnejad A, Aghazadeh H, Pooshang Bagheri K. In silico rational design of a novel tetra-epitope tetanus vaccine with complete population coverage using developed immunoinformatics and surface epitope mapping approaches. Med Hypotheses 2019; 130:109267. [PMID: 31383332 DOI: 10.1016/j.mehy.2019.109267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 06/03/2019] [Accepted: 06/08/2019] [Indexed: 01/01/2023]
Abstract
Presentation of many unwanted epitopes within tetanus toxoid vaccine to lymphocyte clones may lead to production of many unwanted antibodies. Moreover an ideal vaccine must cover all individuals in a population that is dependent to the kinds of human leukocyte antigen alleles. Concerning these issues, our study was aimed to in silico design of a multi-epitope tetanus vaccine (METV) in order to improve population coverage and protectivity of tetanus vaccine as well as reduction of complications. Concerning these issues, a novel rational filtration was implemented to design a novel METV using immunoinformatics and surface epitope mapping approaches. Prediction of epitopes for tetanus toxin was performed in the candidate country in which the frequency had been gathered from almost all geographical distributions. The most strong binder epitopes for major histocompatibility complex class II were selected and among them the surface epitopes of native toxin were selected. The population coverage of the selected epitopes was estimated. The final candidate epitopes had highly population coverage. Molecular docking was performed to prediction of binding affinity of our candidate epitopes to the HLA-DRB1 alleles. At first, 680 strong binder epitopes were predicted. Among them 11 epitopes were selected. Finally, 4 epitopes had the most population coverage and suggested as a tetra-epitope tetanus vaccine. 99.41% of inessential strong binders were deleted using our tree steps filtration. HLA-DP had the most roles in epitope presentation. Molecular docking analysis proved the strong binding affinity of candidate epitopes to the HLA-DRB1 alleles. In conclusion, we theoretically reduced 99.41% of unwanted antibodies using our novel filtration strategies. Our tetra-epitope tetanus vaccine showed 100% population coverage in the candidate country. Furthermore, it was demonstrated that HLA-DP and HLA-DQ had more potential in epitope presentation in comparison to HLA-DRB1.
Collapse
Affiliation(s)
- Samira Bazmara
- Venom and Biotherapeutics Molecules Lab., Biotechnology Dept., Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mahsa Shadmani
- Venom and Biotherapeutics Molecules Lab., Biotechnology Dept., Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Atefeh Ghasemnejad
- Venom and Biotherapeutics Molecules Lab., Biotechnology Dept., Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Hossein Aghazadeh
- Venom and Biotherapeutics Molecules Lab., Biotechnology Dept., Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Kamran Pooshang Bagheri
- Venom and Biotherapeutics Molecules Lab., Biotechnology Dept., Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
11
|
Khan S, Parrillo M, Gutierrez AH, Terry FE, Moise L, Martin WD, De Groot AS. Immune escape and immune camouflage may reduce the efficacy of RTS,S vaccine in Malawi. Hum Vaccin Immunother 2019; 16:214-227. [PMID: 30614773 PMCID: PMC7062414 DOI: 10.1080/21645515.2018.1560772] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The RTS,S/AS01 malaria vaccine will undergo a pilot vaccination study in sub-Saharan Africa beginning in 2019. RTS,S/AS01 Phase III trials reported an efficacy of 28.3% (children 5–17 months) and 18.3% (infants 6–12 weeks), with substantial variability across study sites. We postulated that the relatively low efficacy of the RTS,S vaccine and variability across sites may be due to lack of T-cell epitopes in the vaccine antigen, and due to the HLA distribution of the vaccinated population, and/or due to ‘immune camouflage’, an immune escape mechanism. To examine these hypotheses, we used immunoinformatics tools to compare T helper epitopes contained in RTS,S vaccine antigens with Plasmodium falciparum circumsporozoite protein (CSP) variants isolated from infected individuals in Malawi. The prevalence of epitopes restricted by specific HLA-DRB1 alleles was inversely associated with prevalence of the HLA-DRB1 allele in the Malawi study population, suggesting immune escape. In addition, T-cell epitopes in the CSP of strains circulating in Malawi were more often restricted by low-frequency HLA-DRB1 alleles in the population. Furthermore, T-cell epitopes that were highly conserved across CSP variants in Malawi possessed TCR-facing residues that were highly conserved in the human proteome, potentially reducing T-cell help through tolerance. The CSP component of the RTS,S vaccine also exhibited a low degree of T-cell epitope relatedness to circulating variants. These results suggest that RTS,S vaccine efficacy may be impacted by low T-cell epitope content, reduced presentation of T-cell epitopes by prevalent HLA-DRB1, high potential for human-cross-reactivity, and limited conservation with the CSP of circulating malaria strains.
Collapse
Affiliation(s)
- Sundos Khan
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | - Matthew Parrillo
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | | | | | - Leonard Moise
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA.,EpiVax, Inc., Providence, RI, USA
| | | | - Anne S De Groot
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA.,EpiVax, Inc., Providence, RI, USA
| |
Collapse
|
12
|
Gutiérrez AH, Rapp-Gabrielson VJ, Terry FE, Loving CL, Moise L, Martin WD, De Groot AS. T-cell epitope content comparison (EpiCC) of swine H1 influenza A virus hemagglutinin. Influenza Other Respir Viruses 2018; 11:531-542. [PMID: 29054116 PMCID: PMC5705686 DOI: 10.1111/irv.12513] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2017] [Indexed: 02/03/2023] Open
Abstract
Background Predicting vaccine efficacy against emerging pathogen strains is a significant problem in human and animal vaccine design. T‐cell epitope cross‐conservation may play an important role in cross‐strain vaccine efficacy. While influenza A virus (IAV) hemagglutination inhibition (HI) antibody titers are widely used to predict protective efficacy of 1 IAV vaccine against new strains, no similar correlate of protection has been identified for T‐cell epitopes. Objective We developed a computational method (EpiCC) that facilitates pairwise comparison of protein sequences based on an immunological property—T‐cell epitope content—rather than sequence identity, and evaluated its ability to classify swine IAV strain relatedness to estimate cross‐protective potential of a vaccine strain for circulating viruses. Methods T‐cell epitope relatedness scores were assessed for 23 IAV HA sequences representing the major H1 swine IAV phylo‐clusters circulating in North American swine and HA sequences in a commercial inactivated vaccine (FluSure XP®). Scores were compared to experimental data from previous efficacy studies. Results Higher EpiCC scores were associated with greater protection by the vaccine against strains for 23 field IAV strain vaccine comparisons. A threshold for EpiCC relatedness associated with full or partial protection in the absence of cross‐reactive HI antibodies was identified. EpiCC scores for field strains for which FluSure protective efficacy is not yet available were also calculated. Conclusion EpiCC thresholds can be evaluated for predictive accuracy of protection in future efficacy studies. EpiCC may also complement HI cross‐reactivity and phylogeny for selection of influenza strains in vaccine development.
Collapse
Affiliation(s)
- Andres H Gutiérrez
- Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, USA
| | | | | | - Crystal L Loving
- Virus and Prion Diseases Research Unit, NADC, USDA ARS, Ames, IA, USA
| | - Leonard Moise
- Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, USA.,EpiVax Inc., Providence, RI, USA
| | | | - Anne S De Groot
- Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, USA.,EpiVax Inc., Providence, RI, USA
| |
Collapse
|