scholarly journals In silico Vaccine Design against Dengue Virus Type 2 Envelope Glycoprotein

2020 ◽  
Vol 27 (3) ◽  
pp. 228
Author(s):  
Muhammad Adnan ◽  
Matin Nuhamunada ◽  
Lisna Hidayati ◽  
Nastiti Wijayanti
Keyword(s):  
T Cell ◽  
B Cell ◽  
Envelope Glycoprotein ◽  
In Silico ◽  
Vaccine Development ◽  
Severe Infection ◽  
Cell Types ◽  
Peptide Region ◽  
Dengue Virus Type 2

Dengue fever is caused by the mosquito-borne virus termed (DENV). However, DENV-2 has been identified as the most prevalent amongst the Indonesian pediatric urban population, in contrast with the other four serotypes. Therefore, it is important to reduce severe infection risk by adopting preventive measures, including through vaccine development. The aim of this study, therefore is to use various in silico tools in the design of epitope-based peptide vaccines (T-cell and B-cell types), based on the DENV-2 envelope glycoprotein sequences available. Therefore, in silico methods were adopted in the analysis of the retrieved protein sequences. This technique was required to determine the most immunogenic protein, and is achieved through conservancy analysis, epitope identification, molecular simulation, and allergenicity assessment. Furthermore, B4XPM1, and KAWLVHRQW were identified from positions 204-212, while the 77 to 85 peptide region was considered the most potent T-cell and B-cell epitopes. The interaction between KAWLVHRQW and HLA-C*12:03 occurs with maximum population coverage, alongside high conservancy (96.98%) and binding affinity. These results indicated a potential for the designed epitopes to demonstrate high immunity against DENV-2.

scholarly journals In-silico Design of Multi-epitope Vaccine against Nipah Virus using Immunoinformatics Approach

2021 ◽  
Vol 15 (1) ◽  
pp. 212-231
Author(s):  
Suraj Raju ◽  
Debasish Sahoo ◽  
Vikas Kumar Bhari
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Vaccine Development ◽  
Homology Modelling ◽  
Nipah Virus ◽  
Docking Simulation ◽  
Dynamics Simulation ◽  
Cytotoxic T Cell ◽  
Viral Spread

Nipah virus is a pleomorphic virus that causes high mortality with unpredictable outbreaks. The virus also shows high zoonotic potential with long term neurological damage after recovery further adding to the disease burden. An in-silico epitope-based vaccine offers a promising solution to supplement wider efforts to control the viral spread. This is achieved through immunoinformatics approach using a plethora of servers available. We derived cytotoxic T-cell, T-Helper, B-cell and IFN-γ targeting epitopes from surface glycoprotein G. Cytotoxic T-cell specific epitopes, HLA-B*4402, chimeric multiepitope vaccine structures were prepared using homology modelling method. The structures were validated using various methods and docking simulation was performed between epitopes and HLA-B*4402. Similarly, the vaccine construct was docked to Toll like receptor-4 and a molecular dynamics simulation was performed to assess stability of interaction. Both the docking simulations showed stable interactions with their respective receptors. Immune-simulation was carried out to validate the efficacy of vaccine candidate which showed elevated levels of antibodies such as IgM and IgG due to increase in active B cell population. Both in-vitro and in-vivo serological analysis is required for confirmation of vaccine potency. To facilitate this effort, codon optimization was undertaken to remove existing codon bias. The optimized gene sequence was cloned into the PUC19 vector to express in Escherichia coli K12 strain. Additionally, a poly histidine (6xHis) tag was added at the C-terminal end to ease the purification step. The immune-informatics approach hopes to accelerate vaccine development process to reduce the risk of attenuation while increasing the success rates of pre-clinical trials.

In silico prediction of T‐cell and B‐cell epitopes of human papillomavirus type 16 L1 protein

2021 ◽  
Author(s):  
Shahab Mahmoudvand ◽  
Somayeh Shokri ◽  
Manoochehr Makvandi ◽  
Reza Taherkhani ◽  
Mohammad Rashno ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
T Cell ◽  
B Cell ◽  
In Silico ◽  
In Silico Prediction ◽  
B Cell Epitopes ◽  
Human Papillomavirus Type 16 ◽  
L1 Protein

scholarly journals Evolution of immune responses to SARS-CoV-2 in mild-moderate COVID-19

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Adam K. Wheatley ◽  
Jennifer A. Juno ◽  
Jing J. Wang ◽  
Kevin J. Selva ◽  
Arnold Reynaldi ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Vaccine Development ◽  
Natural Infection ◽  
Population Level ◽  
Cell Dynamics ◽  
Follicular Helper ◽  
Cell Immunity ◽  
Specific Igg ◽  
Over Time

AbstractThe durability of infection-induced SARS-CoV-2 immunity has major implications for reinfection and vaccine development. Here, we show a comprehensive profile of antibody, B cell and T cell dynamics over time in a cohort of patients who have recovered from mild-moderate COVID-19. Binding and neutralising antibody responses, together with individual serum clonotypes, decay over the first 4 months post-infection. A similar decline in Spike-specific CD4+ and circulating T follicular helper frequencies occurs. By contrast, S-specific IgG+ memory B cells consistently accumulate over time, eventually comprising a substantial fraction of circulating the memory B cell pool. Modelling of the concomitant immune kinetics predicts maintenance of serological neutralising activity above a titre of 1:40 in 50% of convalescent participants to 74 days, although there is probably additive protection from B cell and T cell immunity. This study indicates that SARS-CoV-2 immunity after infection might be transiently protective at a population level. Therefore, SARS-CoV-2 vaccines might require greater immunogenicity and durability than natural infection to drive long-term protection.

scholarly journals A single antigen-specific B cell can conjugate to either a type 1 or a type 2 helper T cell.

1988 ◽  
Vol 85 (20) ◽  
pp. 7724-7728 ◽  
Author(s):  
V. M. Sanders ◽  
R. Fernandez-Botran ◽  
R. L. Coffman ◽  
T. R. Mosmann ◽  
E. S. Vitetta
Keyword(s):  
T Cell ◽  
B Cell ◽  
Helper T Cell ◽  
Single Antigen

Composite lymphoma of follicular B-cell and peripheral T-cell types with distinct zone distribution in a 75-year-old male patient: a case study

2018 ◽  
Vol 76 ◽  
pp. 110-116 ◽  
Author(s):  
John Tanaka ◽  
Pu Su ◽  
Catherine Luedke ◽  
Rachel Jug ◽  
Lian-He Yang ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Male Patient ◽  
Cell Types ◽  
Composite Lymphoma

scholarly journals Phenotype of recovering lymphoid cell populations after marrow transplantation.

1985 ◽  
Vol 161 (6) ◽  
pp. 1483-1502 ◽  
Author(s):  
K A Ault ◽  
J H Antin ◽  
D Ginsburg ◽  
S H Orkin ◽  
J M Rappeport ◽  
...  
Keyword(s):  
T Cell ◽  
B Cells ◽  
B Cell ◽  
Nk Cells ◽  
Cell Types ◽  
Lymphoid Cells ◽  
The Other ◽  
Hla Dr ◽  
T Cell Antigens ◽  
Leu 7

Four patients who received bone marrow transplants were studied sequentially during the posttransplant period to define the pattern of recovering lymphoid cell types. Three patients received T cell-depleted, HLA-matched marrow, and one received untreated marrow from an identical twin. Blood lymphoid cells were labeled with 25 different pairs of monoclonal antibodies. In each sample, one antibody was conjugated to fluorescein and one to phycoerythrin, thus allowing simultaneous assessment of the expression of the two markers using the fluorescence activated cell sorter. A total of 14 antibodies were used, routinely including HLE, Leu-M3, Leu-4, Leu-1, Leu-5, Leu-9, Leu-6, Leu-2, Leu-3, HLA-DR, Leu-7, Leu-11, Leu-15, and Leu-12. Other antibodies were used to further define some populations. This study has allowed us to define six distinct cell types that have appeared in all four patients by day 90 posttransplantation, and which account for 90-100% of all circulating lymphoid cells. These cell types are (a) T helper cells expressing Leu-1, Leu-4, Leu-9, Leu-5, Leu-3, and variable amounts of HLA-DR; (b) T suppressor cells expressing Leu-1, Leu-4, Leu-9, Leu-5, Leu-2, and variable amounts of HLA-DR; (c) B cells expressing Leu-12, B1, HLA-DR, IgD, and IgM, but none of the T cell antigens; (d) an unusual B cell phenotype (Leu-1 B) expressing all of the B cell markers, and also having low amounts of Leu-1, but none of the other T cell antigens; (e) natural killer (NK) cells expressing Leu-11, Leu-15, Leu-5 but none of the other T cell or B cell markers; (f) NK cells expressing Leu-11, Leu-15, Leu-5, and low levels of Leu-2. Both NK types also express Leu-7 on some, but not all cells. The relative frequencies of these cell types varied among the patients and with time, but the striking findings were the presence of relatively few mature T cells, large numbers of NK cells, and the preponderance of the unusual Leu-1 B cell over conventional B cells in all three patients who developed B cells. Sorting experiments confirmed the NK activity of the major NK cell phenotypes, and DNA analysis confirmed that all of the cells studied were of donor origin. In addition, analysis of Ig genes in one patient showed that the Leu-1 B cells were not clonally rearranged.(ABSTRACT TRUNCATED AT 400 WORDS)

scholarly journals In silico identification of vaccine targets for 2019-nCoV

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 145 ◽  
Author(s):  
Chloe Hyun-Jung Lee ◽  
Hashem Koohy
Keyword(s):  
T Cell ◽  
In Silico ◽  
Vaccine Development ◽  
De Novo ◽  
Cell Receptor ◽  
Binding Potential ◽  
Hla Alleles ◽  
Immunogenic Peptides ◽  
Novel Coronavirus ◽  
Positional Weight

Background: The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China. Methods: The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0. Results: We report in silico identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a de novo search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential. Conclusions: Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline.

Selection and identification of B-cell epitope on NS1 protein of dengue virus type 2

2010 ◽  
Vol 150 (1-2) ◽  
pp. 49-55 ◽  
Author(s):  
Lan Jiang ◽  
Jun-Mei Zhou ◽  
Yue Yin ◽  
Dan-Yun Fang ◽  
Yun-Xia Tang ◽  
...  
Keyword(s):  
Dengue Virus ◽  
B Cell ◽  
Virus Type ◽  
Cell Epitope ◽  
Ns1 Protein ◽  
B Cell Epitope ◽  
Dengue Virus Type 2

Establishment and characterization of dengue virus type 2 nonstructural protein 1 specific T cell lines

2010 ◽  
Vol 33 (6) ◽  
pp. e75-e80 ◽  
Author(s):  
Yang Xiao-meng ◽  
Jiang Li-fang ◽  
Tang Yun-xia ◽  
Yin Yue ◽  
Liu Wen-quan ◽  
...  
Keyword(s):  
T Cell ◽  
Dengue Virus ◽  
Cell Lines ◽  
Virus Type ◽  
Nonstructural Protein ◽  
Nonstructural Protein 1 ◽  
T Cell Lines ◽  
Dengue Virus Type 2
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