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Zilch TJ, Lee JJ, Bressan GC, McDonough SP, Mohammed HO, Divers TJ, Chang YF. Evaluation of new leptospiral antigens for the diagnosis of equine leptospirosis: An approach using pan-genomic analysis, reverse vaccinology and antigenic selection. Equine Vet J 2020; 53:1025-1035. [PMID: 33135163 DOI: 10.1111/evj.13380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/10/2020] [Accepted: 10/23/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND The current gold standard diagnostic test for leptospirosis is the microscopic agglutination test (MAT), which has many drawbacks; therefore, the development of a better and easier serological test for leptospirosis is needed. OBJECTIVES To apply reverse vaccinology (RV) and antigenic selection on the assortment of leptospiral targets and evaluate their potential for use as reagents for the diagnosis of equine leptospirosis. STUDY DESIGN Cross-sectional study. METHODS The antigenic selection parameters were: proteins with antigenicity score ≥0.5 (VaxiJen), at least one B cell epitope and size between 10 and 275 KDa. New leptospiral proteins were cloned, expressed and serologically screened against equine sera (n = 128) on a single analysis and comparative combinations. Sensitivity (Se) and specificity (Sp), accuracy, positive predictive value (PPV) and negative predictive value (NPV) were calculated. A BLAST with nucleotide and protein sequences was used to identify the serovar or species specificity. MAIN LIMITATIONS This cross-sectional analysis had three main limitations: (a) The equine sera used in these tests were limited to sera submitted to the Animal Health Diagnosis Center and were only tested against seven serovars; (b) MAT results were considered being 'perfect', and the highest titre presented was considered being the infecting serovar, which may not hold true; (c) The strains used to represent the serovars and the limited number of different serovars and species included in the genetic analysis, which leads to the possibility that these proteins might be present in different species or serovars that perhaps would be seroprevalent in another geographic region. CONCLUSIONS The new leptospiral antigens described in this research could increase the sensitivity and specificity of ELISA for detection of Leptospira exposure and the detection of leptospirosis in horses along with support from other clinical signs. Some of these new antigens might be used to improve the detection of infecting serovar.
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Affiliation(s)
- Tiago J Zilch
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jen-Jie Lee
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gustavo C Bressan
- Department of Biochemistry and Molecular Biology, Federal University of Viçosa, Viçosa, MG, Brazil
| | - Sean P McDonough
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Hussni O Mohammed
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Thomas J Divers
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Kardani K, Bolhassani A, Namvar A. An overview of in silico vaccine design against different pathogens and cancer. Expert Rev Vaccines 2020; 19:699-726. [PMID: 32648830 DOI: 10.1080/14760584.2020.1794832] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Due to overcome the hardness of the vaccine design, computational vaccinology is emerging widely. Prediction of T cell and B cell epitopes, antigen processing analysis, antigenicity analysis, population coverage, conservancy analysis, allergenicity assessment, toxicity prediction, and protein-peptide docking are important steps in the process of designing and developing potent vaccines against various viruses and cancers. In order to perform all of the analyses, several bioinformatics tools and online web servers have been developed. Scientists must take the decision to apply more suitable and precise servers for each part based on their accuracy. AREAS COVERED In this review, a wide-range list of different bioinformatics tools and online web servers has been provided. Moreover, some studies were proposed to show the importance of various bioinformatics tools for predicting and developing efficient vaccines against different pathogens including viruses, bacteria, parasites, and fungi as well as cancer. EXPERT OPINION Immunoinformatics is the best way to find potential vaccine candidates against different pathogens. Thus, the selection of the most accurate tools is necessary to predict and develop potent preventive and therapeutic vaccines. To further evaluation of the computational and in silico vaccine design, in vitro/in vivo analyses are required to develop vaccine candidates.
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Affiliation(s)
- Kimia Kardani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences , Tehran, Iran.,Department of Hepatitis and AIDS, Pasteur Institute of Iran , Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran , Tehran, Iran
| | - Ali Namvar
- Iranian Comprehensive Hemophilia Care Center , Tehran, Iran
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Bhattacharya M, Malick RC, Mondal N, Patra P, Pal BB, Patra BC, Kumar Das B. Computational characterization of epitopic region within the outer membrane protein candidate in Flavobacterium columnare for vaccine development. J Biomol Struct Dyn 2019; 38:450-459. [PMID: 30744535 DOI: 10.1080/07391102.2019.1580222] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Gram-negative bacteria is the main causative agents for columnaris disease outbreak to finfishes. The outer membrane proteins (OMPs) candidate of Flavobacterium columnare bacterial cell served a critical component for cellular invasion targeted to the eukaryotic cell and survival inside the macrophages. Therefore, OMPs considered as the supreme element for the development of promising vaccine against F. columnare. Implies advanced in silico approaches, the predicted 3-D model of targeted OMPs were characterized by the Swiss model server and validated through Procheck programs and Protein Structure Analysis (ProSA) web server. The protein sequences having B-cell binding sites were preferred from sequence alignment; afterwards the B cell epitopes prediction was prepared using the BCPred and amino acid pairs (AAP) prediction algorithms modules of BCPreds. Consequently, the selected antigenic amino acids sequences (B-cell epitopic regions) were analyzed for T-cell epitopes determination (MHC I and MHC II alleles binding sequence) performing the ProPred 1 and ProPred server respectively. The epitopes (9 mer: IKKYEPAPV, YGPNYKWKF and YRGLNVGTS) within the OMPs binds to both of the MHC classes (MHC I and MHC II) and covered highest number of MHC alleles are characterized. OMPs of F. columnare being conserved across serotypes and highly immunogenic for their exposed epitopes on the cell surface as a potent candidate focus to vaccine development for combating the disease problems in commercial aquaculture. The portrayed epitopes might be beneficial for practical designing of abundant peptide-based vaccine development against the columnaris through boosting up the advantageous immune responses.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manojit Bhattacharya
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
| | - Ramesh Chandra Malick
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India.,bMicrobiology Division, Regional Medical Research Centre, (ICMR), Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Niladri Mondal
- cCentre For Aquaculture Research, Extension & Livelihood, Department of Aquaculture Management & Technology, Vidyasagar University, Midnapore, West Bengal, India
| | - Prasanta Patra
- Centre For Aquaculture Research, Extension & Livelihood, Department of Aquaculture Management & Technology, Vidyasagar University, Midnapore, West Bengal, India
| | - Bibhuti Bhusan Pal
- Microbiology Division, Regional Medical Research Centre, (ICMR), Chandrasekharpur, Bhubaneswar, Odisha, India
| | - Bidhan Chandra Patra
- Centre For Aquaculture Research, Extension & Livelihood, Department of Aquaculture Management & Technology, Vidyasagar University, Midnapore, West Bengal, India
| | - Basanta Kumar Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, India
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Pasala C, Chilamakuri CSR, Katari SK, Nalamolu RM, Bitla AR, Amineni U. Epitope-driven common subunit vaccine design against H. pylori strains. J Biomol Struct Dyn 2018; 37:3740-3750. [DOI: 10.1080/07391102.2018.1526714] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chiranjeevi Pasala
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, AP, India
| | | | - Sudheer Kumar Katari
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, AP, India
| | | | - Aparna R. Bitla
- Department of Biochemistry, SVIMS University, Tirupati, AP, India
| | - Umamaheswari Amineni
- Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati, AP, India
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Pradhan D, Yadav M, Verma R, Khan NS, Jena L, Jain AK. Discovery of T-cell Driven Subunit Vaccines from Zika Virus Genome: An Immunoinformatics Approach. Interdiscip Sci 2017; 9:468-477. [PMID: 29094318 PMCID: PMC7091030 DOI: 10.1007/s12539-017-0238-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/26/2017] [Accepted: 05/09/2017] [Indexed: 11/16/2022]
Abstract
The recent outbreaks of Zika virus and the absence of a specific therapy have necessitated to identify T-cell-stimulating antigenic peptides as potential subunit vaccine candidates. The translated ssRNA (+) genome of Zika virus was explored in EMBOSS antigenic and VaxiJen to predict 63 peptides as potential antigens. Three MHC-II binding peptide prediction tools, viz. NetMHCIIpan, PREDIVAC and immune epitope database (IEDB) were employed in consensus on 63 antigenic peptides to propose 14 T-helper cell epitopes. Similarly, analysis on 63 antigenic peptides through NetMHC, NetCTL and IEDB MHC-I binding peptide prediction tool led to identification of 14 CTL epitopes. Seven T-cell epitopes, C:44-66, M:135-149, NS2A:124-144, NS3:421-453, NS3:540-554, NS4B:90-134 and NS4B:171-188, are observed to share overlapping MHC-I and MHC-II binding motifs and hence, are being proposed to constitute minimum T-cell antigens to elicit protective T-cell immune response against Zika. Three of them, C:44-66, NS3:421-453 and NS3:540-554 are identified to be conserved across all the selected strains of Zika virus. Moreover, the 21 T-cell epitopes are non-self to humans and exhibited good coverage in variable populations of 14 geographical locations. Therefore, 21 T-cell epitopes are proposed as potential subunit vaccines against Zika virus.
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Affiliation(s)
- Dibyabhaba Pradhan
- Biomedical Informatics Centre, National Institute of Pathology-ICMR, New Delhi, 110029, India
| | - Monika Yadav
- Biomedical Informatics Centre, National Institute of Pathology-ICMR, New Delhi, 110029, India
| | - Rashi Verma
- Biomedical Informatics Centre, National Institute of Pathology-ICMR, New Delhi, 110029, India
| | - Noor Saba Khan
- Biomedical Informatics Centre, National Institute of Pathology-ICMR, New Delhi, 110029, India
| | - Lingaraja Jena
- Bioinformatics Centre, Mahatma Gandhi Institute of Medical Sciences, Sevagram, Wardha, 442102, India
| | - Arun Kumar Jain
- Biomedical Informatics Centre, National Institute of Pathology-ICMR, New Delhi, 110029, India.
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Dellagostin OA, Grassmann AA, Rizzi C, Schuch RA, Jorge S, Oliveira TL, McBride AJA, Hartwig DD. Reverse Vaccinology: An Approach for Identifying Leptospiral Vaccine Candidates. Int J Mol Sci 2017; 18:ijms18010158. [PMID: 28098813 PMCID: PMC5297791 DOI: 10.3390/ijms18010158] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 12/01/2022] Open
Abstract
Leptospirosis is a major public health problem with an incidence of over one million human cases each year. It is a globally distributed, zoonotic disease and is associated with significant economic losses in farm animals. Leptospirosis is caused by pathogenic Leptospira spp. that can infect a wide range of domestic and wild animals. Given the inability to control the cycle of transmission among animals and humans, there is an urgent demand for a new vaccine. Inactivated whole-cell vaccines (bacterins) are routinely used in livestock and domestic animals, however, protection is serovar-restricted and short-term only. To overcome these limitations, efforts have focused on the development of recombinant vaccines, with partial success. Reverse vaccinology (RV) has been successfully applied to many infectious diseases. A growing number of leptospiral genome sequences are now available in public databases, providing an opportunity to search for prospective vaccine antigens using RV. Several promising leptospiral antigens were identified using this approach, although only a few have been characterized and evaluated in animal models. In this review, we summarize the use of RV for leptospirosis and discuss the need for potential improvements for the successful development of a new vaccine towards reducing the burden of human and animal leptospirosis.
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Affiliation(s)
- Odir A Dellagostin
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas RS 96100-000, Brazil.
| | - André A Grassmann
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas RS 96100-000, Brazil.
| | - Caroline Rizzi
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas RS 96100-000, Brazil.
| | - Rodrigo A Schuch
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas RS 96100-000, Brazil.
| | - Sérgio Jorge
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas RS 96100-000, Brazil.
| | - Thais L Oliveira
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas RS 96100-000, Brazil.
| | - Alan J A McBride
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas RS 96100-000, Brazil.
| | - Daiane D Hartwig
- Departamento de Microbiologia e Parasitologia, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas RS 96100-000, Brazil.
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In silico identification of outer membrane protein (Omp) and subunit vaccine design against pathogenic Vibrio cholerae. Comput Biol Chem 2016; 65:61-68. [DOI: 10.1016/j.compbiolchem.2016.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 08/11/2016] [Accepted: 10/05/2016] [Indexed: 11/22/2022]
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Expansion of the in vitro assay for Leptospira potency testing to other serovars: case study with Leptospira Hardjo. Biologicals 2013; 41:323-4. [PMID: 23838569 DOI: 10.1016/j.biologicals.2013.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 06/17/2013] [Indexed: 11/21/2022] Open
Abstract
Evaluation of leptospiral vaccines for potency against Leptospira interrogans serovars Pomona, Icterohaemorrhagiae, Canicola, and Grippotyphosa is accomplished using the hamster potency test method described in 9 CFR 113.101-104. Applicability of this method to evaluation of bacterins developed for immunization against infection with L. interrogans serovar Hardjo or Leptospira borgpetersenii serovar Hardjo is complicated by several issues. Information from research on target host animal efficacy studies and evaluation of the immune response elicited using effective whole-cell bacterin formulations have revealed problems in relating these studies to either hamster-based or other potency testing methods. Future work on serovar Hardjo vaccines employing recombinant proteins will require preliminary testing methods in models other than the host animal. These models may also prove applicable to evaluation of potency for protein-based vaccines. Both an acute lethal infection model and a chronic infection model have been developed using two different strains of serovar Hardjo and will be described.
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Munikumar M, Priyadarshini IV, Pradhan D, Umamaheswari A, Vengamma B. Computational approaches to identify common subunit vaccine candidates against bacterial meningitis. Interdiscip Sci 2013; 5:155-64. [PMID: 23740398 DOI: 10.1007/s12539-013-0161-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 04/05/2012] [Accepted: 05/15/2012] [Indexed: 11/29/2022]
Abstract
Bacterial meningitis, an infection of the membranes (meninges) and cerebrospinal fluid (CSF) surrounding the brain and spinal cord, is a major cause of death and disability all over the world. From perinatal period to adult, four common organisms responsible for most of the bacterial meningitis are Streptococcus pneumonia, Neisseria meningitidis, Haemophilus influenza and Staphylococcus aureus. As the disease is caused by more organisms, currently available vaccines for bacterial meningitis are specific and restricted to some of the serogroups or serotypes of each bacterium. In an effort to design common vaccine against bacterial meningitis, proteomes of the four pathogens were compared to extract seven common surface exposed ABC transporter proteins. Pro-Pred server was used to investigate the seven surface exposed proteins for promiscuous T-cell epitopes prediction. Predicted 22 T-cell epitopes were validated through published positive control, SYFPEITHI and immune epitope database to reduce the epitope dataset into seven. T-cell epitope 162-FMILPIFNV-170 of spermidine/putrescine ABC transporter permease (potH) protein was conserved across the four selected pathogens of bacterial meningitis. Hence, structural analysis was extended for epitope 162-FMILPIFNV-170. Crystal structures of HLA-DRB alleles were retrieved and structure of potH was modeled using Prime v3.0 for structural analysis. Computational docking of HLA-DRB alleles and epitope 162-FMILPIFNV-170 of potH was performed using Glide v5.7. RMSD and RMSF of simulation studies were analyzed by Desmond v3.2. The docking and simulation results revealed that the HLA-DRB-epitope complex was stable with interaction repressive function of HLA. Thus, the epitope would be ideal candidate for T-cell driven subunit vaccine design against bacterial meningitis.
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Affiliation(s)
- Manne Munikumar
- SVIMS Bioinformatics Centre, Department of Bioinformatics, SVIMS University, Tirupati 517507, AP, India
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Munikumar M, Priyadarshini V, Pradhan D, Swargam S, Umamaheswari A. 177 T-cell vaccine design forStreptococcus pneumoniae: anin silicoapproach. J Biomol Struct Dyn 2013. [DOI: 10.1080/07391102.2013.786419] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Patent Highlights. Pharm Pat Anal 2013. [DOI: 10.4155/ppa.12.79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A snapshot of recent key developments in the patent literature of relevance to the advancement of pharmaceutical and medical R&D
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Verma AK, Kumar A, Dhama K, Deb R, Rahal A, Chakraborty S. Leptospirosis-persistence of a dilemma: an overview with particular emphasis on trends and recent advances in vaccines and vaccination strategies. Pak J Biol Sci 2012; 15:954-963. [PMID: 24199473 DOI: 10.3923/pjbs.2012.954.963] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Leptospirosis, caused by pathogenic spirochetes of the genus Leptospira, affects both humans and animals and is among the most common but neglected direct zoonotic disease in the world, particularly in untreated or undiagnosed animals as well as humans. Now, it has been considered as a re-emerging disease causing global health problem due to its increasing incidences in developing as well as developed nations. It is a multisystemic disease leading to death. Diagnostic tests of importance are Latex Agglutination Test (LAT), lateral flow and immunoglobulin M (IgM) based ELISA, PCR based assays, Multiple-microscopic Agglutination Test (MAT), Loop-mediated Isothermal Amplification (LAMP) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Molecular tools like PCR-RFLP, real-time PCR, multiplex PCR, qPCR and immunocapture PCR have all been found useful for rapid and confirmatory detection and differentiation of pathogenic and non-pathogenic leptospires. Inactivated/killed and attenuated vaccines are always attempted, since the beginning of vaccine and vaccination story, against all emerging pathogens with mixed success stories. The advanced tools and techniques like recombinant DNA technology, reverse genetics, DNA vaccination, molecular genetics and proteomics approaches are being explored for search of novel antigens, proteins and genes as potential candidates to discover safer, efficient and better vaccines for leptospirosis. The present review highlights the leptospirosis, susceptible population, disease transmission and epidemiology, treatment, trends and advances in diagnosis, vaccines and vaccination strategies in humans and animals with a view to combat this organism having public health significance.
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Affiliation(s)
- Amit Kumar Verma
- Department of Veterinary Epidemiology and Preventive Medicine, Uttar Pradesh Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishvidhyalaya Ewam Go-Anusandhan Sansthan (DUVASU), Mathura (U.P.), India
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