Population coverage analysis of T-Cell epitopes of Neisseria meningitidis serogroup B from Iron acquisition proteins for vaccine design

Misra, Namrata; Panda, Prasanna Kumar; Shah, Kavita; Sukla, Lala Behari; Chaubey, Priyanka

doi:10.6026/97320630006255

Cited by 24 publications

(21 citation statements)

References 19 publications

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“…Currently, commercial inactivated whole‐virus vaccines are produced by exposing the virus of interest to a cross‐linking agent such as formaldehyde or an alkylating agent such as beta‐propiolactone. Incorporating the diversity of predicted epitopes may be useful for computationally optimized design of broadly cross‐reactive vaccine candidates including the development of T‐cell epitope‐based vaccines . With experimental confirmation of true immunogenic CD8+ T‐cell epitopes, the spatial and phylogenetic distribution of conserved and variable epitopes should be integrated into pre‐pandemic planning and vaccine selection to ensure broad reactivity and potential effectiveness.…”

Section: Discussionmentioning

confidence: 99%

Lineage‐specific epitope profiles for HPAI H5 pre‐pandemic vaccine selection and evaluation

Qiu

Duvvuri

Gubbay

et al. 2017

Influenza Resp Viruses

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BackgroundMultiple highly pathogenic avian influenza (HPAI) H5 viruses continue to co‐circulate. This has complicated pandemic preparedness and confounded effective vaccine candidate selection and evaluation.ObjectivesIn this study, we aimed to predict and map the diversity of CD8+ T‐cell epitopes among H5 hemagglutinin (HA) gene lineages to estimate CD8+ T‐cell immunity in humans induced by vaccine candidates.MethodsA dataset consisting of 1125 H5 HA sequences collected between 1996 and 2017 from avian and humans was assembled for phylogenetic and lineage‐specific epitope analyses. Conserved epitopes were predicted from WHO‐endorsed vaccine candidates and representative clade‐defining strains by pairwise comparison with Immune Epitope Database (IEDB). The distribution of predicted epitopes was mapped to each HPAI H5 lineage. We assume that high similarity and conservancy of predicted epitopes from vaccine candidates among all circulating HPAI H5 lineages is correlated with high immunity.ResultsA total of 49 conserved CD8+ T‐cell epitopes were predicted at 28 different amino acid positions of the HA protein. Mapping these epitopes to the phylogenetic tree allowed us to develop epitope profiles, or “fingerprints,” for each HPAI H5 lineage. Vaccine epitope percentage analyses showed some epitope profiles were highly conserved for all H5 isolates and may be valuable for universal vaccine design. However, the positions with low coverage may explain why the vaccine candidates do not always function well.ConclusionsThese findings demonstrate that our analytical approach to evaluate conserved CD8+ T‐cell epitope prediction in a phylogenetic framework may provide important insights for computational design of vaccine selection and future epitope‐based design.

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Section: Discussionmentioning

confidence: 99%

Lineage‐specific epitope profiles for HPAI H5 pre‐pandemic vaccine selection and evaluation

Qiu

Duvvuri

Gubbay

et al. 2017

Influenza Resp Viruses

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“…The conservancy values of selected BCL and CTL epitopes were more than 80%, a standard value to generate broad-spectrum antigenicity, and welldesired criteria for any predicted epitopes (17,37). A potential binder (epitope) should have three characteristics in order to generate strong immunogenicity, (i) an IC50 value of less than 500nM, (ii) percentile rank of below 1.5%, and (iii) population coverage of more than 80% (35,38). We found satisfactory IC50 value and percentile rank in our predicted epitope and population coverage of more than 98%, therefore, could be a potential immunogen against hRSV.…”

Section: Discussionmentioning

confidence: 61%

“…Population coverage is usually used to check whether the predicted final epitope and its HLA alleles can cover a significant percent of the world population or not. The IEDB population coverage tool (http://tools.immuneepitope.org/tools/pop ulation/iedb) was used to calculate the cumulative percent of world wide population coverage for the final predicted epitope for both MHC classes, as described previously (35).…”

Section: Population Coveragementioning

confidence: 99%

An immunoinformatic approach to design a novel vaccine against the human respiratory syncytial virus (hRSV) by targeting M2-1 protein

Momtaz¹,

Foysal²

2019

Af J Clin Exp Micro

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Background: Human respiratory syncytial virus (hRSV) is the leading cause of upper and lower respiratory infection in infants, adults and immunocompromised persons. The matrix protein, M2-1 of hRSV is a cofactor of viral RNA polymerase that plays a crucial role during replication. This programmed study was designed to scrutinize potential immunogens from the M2-1 protein characterized from four different continents. Methods: Sequence data obtained from NCBI databases were analysed by using a series of web and software based bioinformatics tools to find out the best epitope against hRSV. Results: The phylogenetic data revealed a homogenized clustering of M2-1 protein for the African, European, and Asian clades while proteins from North American collections found to have a significant evolutionary detachment compared to three other clusters. Using various web-based bioinformatics tools, the study identified four common B-cell epitopes present in all the M2-1 proteins from four different clusters with higher antigenicity and conservancy. Among the 17 M2-1 protein investigated for T-cell epitopes, "VLQNLDVGL" peptide from A2 super-type, and "QSACVAMSK" and "CLNGRRCHY" from A3 super-type showed the highest antigenicity at >0.80 conservancy cutoff value. After evaluation of all antigenic properties, only "CLNGRRCHY" peptide qualified as a potential vaccine candidate against hRSV. Molecular docking revealed strong and stable binding of the epitope to major histocompatibility complexes (MHC) molecules in terms of hydrogen bonding. Conclusion: The designed epitope could be used as a possible vaccine candidate against hRSV.

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“…Immunome‐derived vaccines approach is well suited only when there is sequence conservation within species variants . Identification and selection of T‐cell epitopes for cytolytic and regulatory responses to pathogen thus form an important part of vaccine development . Epitope‐based vaccines for HIV, tuberculosis, and malaria have proved promising in clinical trials supporting thereby the importance of T‐cell epitope selection as useful vaccine targets …”

Section: Introductionmentioning

confidence: 99%

“…3,4 Identification and selection of T-cell epitopes for cytolytic and regulatory responses to pathogen thus form an important part of vaccine development. [5][6][7][8] Epitope-based vaccines for HIV, tuberculosis, and malaria have proved promising in clinical trials supporting thereby the importance of T-cell epitope selection as useful vaccine targets. 9,10 Neisseria meningitidis, a human-specific bacterial pathogen causes bacterial meningitis (brain fever) by invading the meninges (outer lining) of central nervous system through bloodstream 11 ( Figure S1 in the Supporting Information).…”

Section: Introductionmentioning

confidence: 99%

An epitope‐imprinted piezoelectric diagnostic tool for Neisseria meningitidis detection

Gupta

Shah

Singh

2016

J of Molecular Recognition

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Neisseria meningitidis, a human-specific bacterial pathogen causes bacterial meningitis by invading the meninges (outer lining) of central nervous system. It is the polysaccharide present on the bacterial capsid that distinguishes various serogroups of N. meningitidis and can be utilized as antigens to elicit immune response. A computational approach identified candidate T-cell epitopes from outer membrane proteins Por B of N. meningitidis (MC58): ( KGLVDDADI in loop VII and GRHNSESYH in loop IV) present on the exposed surface of immunogenic loops of class 3 outer membrane proteins allele of N. meningitidis. One of them, KGLVDDADI is used here for designing a diagnostic tool via molecularly imprinted piezoelectric sensor (molecularly imprinted polymer-quartz crystal microbalance) for N. meningitidis strain MC58. Methacrylic acid, ethylene glycol dimethacrylate and azoisobutyronitrile were used as functional monomer, cross-linker and initiator, respectively. The epitope can be simultaneously bound to methacrylic acid and fitted into the shape-selective cavities. On extraction of epitope sequence from thus grafted polymeric film, shape-selective and sensitive sites were generated on electrochemical quartz crystal microbalance crystal, ie, known as epitope imprinted polymers. Imprinting was characterized by atomic force microscopy images. The epitope-imprinted sensor was able to selectively bind N. meningitidis proteins present in blood serum of patients suffering from brain fever. Thus, fabricated sensor can be used as a diagnostic tool for meningitis disease.

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Population coverage analysis of T-Cell epitopes of Neisseria meningitidis serogroup B from Iron acquisition proteins for vaccine design

Cited by 24 publications

References 19 publications

Lineage‐specific epitope profiles for HPAI H5 pre‐pandemic vaccine selection and evaluation

Lineage‐specific epitope profiles for HPAI H5 pre‐pandemic vaccine selection and evaluation

An immunoinformatic approach to design a novel vaccine against the human respiratory syncytial virus (hRSV) by targeting M2-1 protein

An epitope‐imprinted piezoelectric diagnostic tool for Neisseria meningitidis detection

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