{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T03:15:03Z","timestamp":1783307703133,"version":"3.54.6"},"reference-count":52,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T00:00:00Z","timestamp":1739404800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:p>Scrub typhus is a life-threatening, undifferentiated febrile illness caused by a gram-negative bacterium, <jats:italic>Orientia tsutsugamushi<\/jats:italic>. The bacterial strain is a global health concern that should be considered. Despite several years of effort for the development of an effective immunogenic vaccine, no successful licensed vaccine is available. The aim of the study is to construct an epitope response using a reverse vaccinology approach. The TSA56 and ScaA proteins combined can be the most promising subunit vaccine candidates against <jats:italic>O. tsutsugamushi<\/jats:italic>. B-cell, CTL, and HTL epitopes were predicted, and subsequently, all the epitopes were linked by KK, AAY, and GPGPG linkers, respectively, along with an adjuvant at the N-terminal region. Furthermore, molecular docking and MD simulations were performed that exhibited a higher affinity towards TLR-2. A total of 16 linear B-cells, 6 CTL, and 2 HTL epitopes were identified and validated. The final vaccine construct showed high antigenicity, stability, and solubility. Molecular docking and MD simulations indicated strong binding interactions with TLR-2 and a stable vaccine-receptor complex. The expression of the vaccine in pET28a (+) vector was successfully implemented via in silico cloning as well as significant results from immune simulation demonstrated the efficacy of the vaccine in the immune cell interaction during the innate and adaptive immune responses immune simulation. In conclusion, the outcome suggested that the newly developed vaccine will be a promising candidate for controlling and providing definitive preventive measures against scrub typhus if further investigation is conducted experimentally.<\/jats:p>","DOI":"10.3389\/fimmu.2025.1513245","type":"journal-article","created":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T07:08:51Z","timestamp":1739430531000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["Designing a potent multivalent epitope vaccine candidate against Orientia tsutsugamushi via reverse vaccinology technique - bioinformatics and immunoinformatic approach"],"prefix":"10.3389","volume":"16","author":[{"given":"Subhasmita","family":"Panda","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Subrat Kumar","family":"Swain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Basanta Pravas","family":"Sahu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soumya Ranjan","family":"Mahapatra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jyotirmayee","family":"Dey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachita","family":"Sarangi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anu Vinod","family":"Ranade","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Namrata","family":"Mishra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,2,13]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"e0006062","DOI":"10.1371\/journal.pntd.0006062","article-title":"A review of the global epidemiology of scrub typhus","volume":"11","author":"Xu","year":"2017","journal-title":"PloS Negl Trop Dis"},{"key":"B2","doi-asserted-by":"publisher","first-page":"e0003990","DOI":"10.1371\/journal.pntd.0003990","article-title":"Increased nucleosomes and neutrophil activation link to disease progression in patients with scrub typhus but not murine typhus in Laos","volume":"9","author":"Paris","year":"2015","journal-title":"PloS Negl Trop Dis"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1128\/CVI.00553-15","article-title":"Diagnostic accuracy of the InBios scrub typhus detect enzyme-linked immunoassay for the detection of IgM antibodies in northern Thailand","volume":"23","author":"Blacksell","year":"2016","journal-title":"Clin Vaccine Immunol"},{"key":"B4","doi-asserted-by":"publisher","first-page":"8","DOI":"10.3390\/tropicalmed3010008","article-title":"A review of scrub typhus (Orientia tsutsugamushi and related organisms): then, now, and tomorrow","volume":"3","author":"Luce-Fedrow","year":"2018","journal-title":"Trop Med Infect Dis"},{"key":"B5","doi-asserted-by":"publisher","first-page":"1619","DOI":"10.3390\/healthcare9121619","article-title":"Epidemiology and risk factors for notifiable scrub typhus in Taiwan during the period 2010-2019","volume":"9","author":"Lin","year":"2021","journal-title":"Healthc (Basel)"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.3389\/fpubh.2023.1177578","article-title":"Epidemiological analysis and risk prediction of scrub typhus from 2006 to 2021 in Sichuan, China","volume":"11","author":"Zhang","year":"2023","journal-title":"Front Public Health"},{"key":"B7","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1016\/j.bcp.2016.05.001","article-title":"Vaccine technologies: From whole organisms to rationally designed protein assemblies","volume":"15","author":"Karch","year":"2016","journal-title":"Biochem Pharmacol"},{"key":"B8","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1186\/s12864-024-10691-7","article-title":"A novel mRNA multi-epitope vaccine of Acinetobacter baumannii based on multi-target protein design in immunoinformatic approach","volume":"25","author":"Xu","year":"2024","journal-title":"BMC Genomics"},{"key":"B9","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1007\/s10989-021-10356-z","article-title":"Molecular characterization and designing of a novel multiepitope vaccine construct against Pseudomonas aeruginosa","volume":"28","author":"Dey","year":"2022","journal-title":"Int J Pept Res Ther"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1007\/s10989-018-9698-5","article-title":"Designing a novel multi-epitope peptide vaccine against pathogenic Shigella spp. based immunoinformatics approaches","volume":"25","author":"Farhani","year":"2019","journal-title":"Int J Pept Res Ther"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1007\/s10989-020-10157-w","article-title":"A novel multi-epitopic peptide vaccine candidate against Helicobacter pylori: in-silico identification, design, cloning and validation through molecular dynamics","volume":"27","author":"Ghosh","year":"2021","journal-title":"Int J Pept Res Ther"},{"key":"B12","doi-asserted-by":"publisher","first-page":"1249","DOI":"10.1038\/s41598-020-80899-6","article-title":"In silico analysis of epitope-based vaccine candidate against tuberculosis using reverse vaccinology","volume":"11","author":"Bibi","year":"2021","journal-title":"Sci Rep"},{"key":"B13","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1002\/rmv.v19:2","article-title":"An introduction to epitope prediction methods and software","volume":"19","author":"Yang","year":"2009","journal-title":"Rev Med Virol"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1093\/abbs\/36.9.589","article-title":"Recombinant bivalent vaccine against foot-and-mouth disease virus serotype O\/A infection in Guinea pig","volume":"36","author":"Yi","year":"2004","journal-title":"Acta Biochim Biophys Sinica"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.2174\/156652311798192815","article-title":"Novel strategies to improve DNA vaccine immunogenicity","volume":"11","author":"Coban","year":"2011","journal-title":"Curr Gene Ther"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1128\/CVI.00285-12","article-title":"Detection of antibodies against Orientia tsutsugamushi Sca proteins in scrub typhus patients and genetic variation of sca genes of different strains","volume":"19","author":"Ha","year":"2012","journal-title":"Clin Vaccine Immunol"},{"key":"B17","doi-asserted-by":"publisher","first-page":"e0003585","DOI":"10.1371\/journal.pntd.0003585","article-title":"Immunization with an autotransporter protein of Orientia tsutsugamushi provides protective immunity against scrub typhus","volume":"9","author":"Ha","year":"2015","journal-title":"PloS Negl Trop Dis"},{"key":"B18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12951-016-0229-2","article-title":"Generation of protective immunity against Orientia tsutsugamushi infection by immunization with a zinc oxide nanoparticle combined with ScaA antigen","volume":"14","author":"Ha","year":"2016","journal-title":"J Nanobiotechnol"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1002\/prot.21078","article-title":"Prediction of continuous B-cell epitopes in an antigen using recurrent neural network","volume":"65","author":"Saha","year":"2006","journal-title":"Proteins: Struct Funct Bioinf"},{"key":"B20","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaa379","article-title":"NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data","volume":"48","author":"Reynisson","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"B21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-8-4","article-title":"VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines","volume":"8","author":"Doytchinova","year":"2007","journal-title":"BMC Bioinf"},{"key":"B22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00894-014-2278-5","article-title":"AllerTOP v. 2\u2014a server for in silico prediction of allergens","volume":"20","author":"Dimitrov","year":"2014","journal-title":"J Mol Model"},{"key":"B23","doi-asserted-by":"publisher","first-page":"e73957","DOI":"10.1371\/journal.pone.0073957","article-title":"In silico approach for predicting toxicity of peptides and proteins","volume":"8","author":"Gupta","year":"2013","journal-title":"PloS One"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx345","article-title":"Protein\u2013Sol: a web tool for predicting protein solubility from sequence","volume":"33","author":"Hebditch","year":"2017","journal-title":"Bioinformatics"},{"key":"B25","doi-asserted-by":"crossref","DOI":"10.1385\/1-59259-890-0:571","volume-title":"Protein identification and analysis tools on the ExPASy server","author":"Gasteiger","year":"2005"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg595","article-title":"Mfold web server for nucleic acid folding and hybridization prediction","volume":"31","author":"Zuker","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1007\/s00251-013-0714-9","article-title":"MHCcluster, a method for functional clustering of MHC molecules","volume":"65","author":"Thomsen","year":"2013","journal-title":"Immunogenetics"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1006","article-title":"The immune epitope database (IEDB): 2018 update","volume":"47","author":"Vita","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"B29","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-7-153","article-title":"Predicting population coverage of T-cell epitope-based diagnostics and vaccines","volume":"7","author":"Bui","year":"2006","journal-title":"BMC Bioinf"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz297","article-title":"The PSIPRED protein analysis workbench: 20 years on","volume":"47","author":"Buchan","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh468","article-title":"Protein structure prediction and analysis using the Robetta server","volume":"32","author":"Kim","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz288","article-title":"GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure","volume":"47","author":"Lee","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK: a program to check the stereochemical quality of protein structures","volume":"26","author":"Laskowski","year":"1993","journal-title":"J Appl Crystallogr"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky427","article-title":"SWISS-MODEL: homology modelling of protein structures and complexes","volume":"46","author":"Waterhouse","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5560020916","article-title":"Verification of protein structures: patterns of nonbonded atomic interactions","volume":"2","author":"Colovos","year":"1993","journal-title":"Protein Sci"},{"key":"B36","first-page":"396","article-title":"[20] VERIFY3D: assessment of protein models with three-dimensional profiles","volume-title":"Methods in enzymology","author":"Eisenberg","year":"1997"},{"key":"B37","doi-asserted-by":"publisher","first-page":"514)","DOI":"10.1186\/1471-2105-9-514","article-title":"ElliPro: a new structure-based tool for the prediction of antibody epitopes","volume":"9","author":"Ponomarenko","year":"2008","journal-title":"BMC Bioinf"},{"key":"B38","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-14-S19-S1","article-title":"Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins","volume":"14","author":"Craig","year":"2013","journal-title":"BMC Bioinf"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2016.169","article-title":"The ClusPro web server for protein\u2013protein docking","volume":"12","author":"Kozakov","year":"2017","journal-title":"Nat Protoc"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1021\/ct700301q","article-title":"GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation","author":"Hess","year":"2008","journal-title":"J Chem Theory Comput"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki376","article-title":"JCat: a novel tool to adapt codon usage of a target gene to its potential expression host","volume":"33","author":"Grote","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"B42","doi-asserted-by":"publisher","first-page":"e9862","DOI":"10.1371\/journal.pone.0009862","article-title":"Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system","volume":"5","author":"Rapin","year":"2010","journal-title":"PloS One"},{"key":"B43","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.micpath.2019.02.023","article-title":"Reverse vaccinology approach to design a novel multi-epitope subunit vaccine against avian influenza A (H7N9) virus","volume":"130","author":"Hasan","year":"2019","journal-title":"Microb Pathogen"},{"key":"B44","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.1038\/s41598-018-19456-1","article-title":"Novel immunoinformatics approaches to design multi-epitope subunit vaccine for malaria by investigating anopheles salivary protein","volume":"8","author":"Pandey","year":"2018","journal-title":"Sci Rep"},{"key":"B45","first-page":"3","article-title":"The impact of bioinformatics on vaccine design and development","volume":"2","author":"Mar\u00eda","year":"2017","journal-title":"Vaccines"},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20151960","article-title":"Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design","volume":"213","author":"Rappuoli","year":"2016","journal-title":"J Exp Med"},{"key":"B47","doi-asserted-by":"publisher","DOI":"10.1038\/nrd2224","article-title":"More than one reason to rethink the use of peptides in vaccine design","volume":"6","author":"Purcell","year":"2007","journal-title":"Nat Rev Drug Discov"},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.iy.07.040189.001045","article-title":"TH1 and TH2 cells: different patterns of lymphokine secretion lead to different functional properties","volume":"7","author":"Mosmann","year":"1989","journal-title":"Annu Rev Immunol"},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.5661\/bger-28-147","article-title":"Production platforms for biotherapeutic glycoproteins. Occurrence, impact, and challenges of non-human sialylation","volume":"28","author":"Ghaderi","year":"2012","journal-title":"Biotechnol Genet Eng Rev"},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.29245\/2578-3009\/2018\/2.1118","article-title":"Advances and challenges in enveloped virus-like particle\u00a0(VLP)-based vaccines","volume":"2","author":"Dai","year":"2018","journal-title":"J Immunol Sci"},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1080\/21645515.2015.1016674","article-title":"Progress on adenovirus-vectored universal influenza vaccines","volume":"11","author":"Xiang","year":"2015","journal-title":"Hum Vaccines Immunother"},{"key":"B52","doi-asserted-by":"publisher","DOI":"10.1002\/biot.201400390","article-title":"Large-scale adenovirus and poxvirus-vectored vaccine manufacturing to enable clinical trials","volume":"10","author":"Kallel","year":"2015","journal-title":"Biotechnol J"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2025.1513245\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T07:09:01Z","timestamp":1739430541000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2025.1513245\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,13]]},"references-count":52,"alternative-id":["10.3389\/fimmu.2025.1513245"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2025.1513245","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,13]]},"article-number":"1513245"}}