scholarly journals In silico multi-epitope vaccine against covid19 showing effective interaction with HLA-B*15:03

2020 ◽  
Author(s):  
Muniba Faiza ◽  
Tariq Abdullah ◽  
Jose Franklin Calderon-Tantalean ◽  
Manish Ravindranath Upadhyay ◽  
Abdelrahman H. Abdelmoneim ◽  
...  
Keyword(s):  
Human Health ◽  
In Silico ◽  
Selection Pressure ◽  
Vaccine Candidate ◽  
Promising Result ◽  
Effective Interaction ◽  
Epitope Vaccine ◽  
Furin Cleavage Site ◽  
Viral Vaccine ◽  
Pressure Analysis

AbstractThe recent outbreak of severe acute respiratory syndrome (SARS) coronavirus (CoV)-2 (SARS-CoV-2) causing coronavirus disease (covid19) has posed a great threat to human health. Previous outbreaks of SARS-CoV and Middle East respiratory Syndrome CoV (MERS-CoV) from the same CoV family had posed similar threat to human health and economic growth. To date, not even a single drug specific to any of these CoVs has been developed nor any anti-viral vaccine is available for the treatment of diseases caused by CoVs. Subunits present in spike glycoproteins of SARS-CoV and SARS-CoV-2 are involved in binding to human ACE2 Receptor which is the primary method of viral invasion. As it has been observed in the previous studies that there are very minor differences in the spike glycoproteins of SARS-CoV and SARS-CoV-2. SARS-CoV-2 has an additional furin cleavage site that makes it different from SARS-CoV (Walls et al., 2020). In this study, we have analyzed spike glycoproteins of SARS-CoV-2 and SARS-CoV phylogenetically and subjected them to selection pressure analysis. Selection pressure analysis has revealed some important sites in SARS-CoV-2 and SARS-CoV spike glycoproteins that might be involved in their pathogenicity. Further, we have developed a potential multi-epitope vaccine candidate against SARS-CoV-2 by analyzing its interactions with HLA-B*15:03 subtype. This vaccine consists of multiple T-helper (TH) cells, B-cells, and Cytotoxic T-cells (CTL) epitopes joined by linkers and an adjuvant to increase its immunogenicity. Conservation of selected epitopes in SARS, MERS, and human hosts, suggests that the designed vaccine could provide cross-protection. The vaccine is designed in silico by following a reverse vaccinology method acknowledging its antigenicity, immunogenicity, toxicity, and allergenicity. The vaccine candidate that we have designed as a result of this work shows promising result indicating its potential capability of simulating an immune response.

scholarly journals In silico design of a T-cell epitope vaccine candidate for parasitic helminth infection

2020 ◽  
Vol 16 (3) ◽  
pp. e1008243 ◽  
Author(s):  
Ayat Zawawi ◽  
Ruth Forman ◽  
Hannah Smith ◽  
Iris Mair ◽  
Murtala Jibril ◽  
...  
Keyword(s):  
T Cell ◽  
In Silico ◽  
Helminth Infection ◽  
Vaccine Candidate ◽  
Cell Epitope ◽  
T Cell Epitope ◽  
Epitope Vaccine ◽  
Parasitic Helminth ◽  
In Silico Design

scholarly journals Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study

2020 ◽  
pp. 1-16 ◽  
Author(s):  
Maryam Enayatkhani ◽  
Mehdi Hasaniazad ◽  
Sobhan Faezi ◽  
Hamed Gouklani ◽  
Parivash Davoodian ◽  
...  
Keyword(s):  
In Silico ◽  
Vaccine Candidate ◽  
Reverse Vaccinology ◽  
Epitope Vaccine ◽  
In Silico Study

scholarly journals In-silico design of a multi-epitope vaccine candidate against onchocerciasis and related filarial diseases

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Robert Adamu Shey ◽  
Stephen Mbigha Ghogomu ◽  
Kevin Kum Esoh ◽  
Neba Derrick Nebangwa ◽  
Cabirou Mounchili Shintouo ◽  
...  
Keyword(s):  
In Silico ◽  
Vaccine Candidate ◽  
Epitope Vaccine ◽  
In Silico Design

Immunoinformatics approaches to design: A novel multi-epitope vaccine candidate against SARS-CoV-2 and it’s in silico expression (Preprint)

2021 ◽  
Author(s):  
Ravi Deval ◽  
Ayushi Saxena ◽  
Zeba Mueed ◽  
Dibyabhaba Pradhan ◽  
Pankaj Kumar Rai
Keyword(s):  
B Cell ◽  
In Silico ◽  
Vaccine Candidate ◽  
Rna Virus ◽  
Consensus Sequence ◽  
Structure Model ◽  
Epitope Vaccine ◽  
B Cell Epitopes ◽  
Epitope Vaccines ◽  
Further Development

BACKGROUND SARS-CoV-2, belonging to the Coronaviridae family, is a novel RNA virus, known for causing fatal disease in humans called COVID-19. Researchers all around the world are keen on developing a precise treatment or vaccine against this deadly disease. OBJECTIVE The main objective of this paper is to design a novel multi-epitope vaccine candidate against SARS-CoV-2 using immunoinformatics tools. METHODS A consensus sequence was generated from various genomes of SARS-Cov-2 available from various countries of the outbreak at the ViPR database using JalView software. T cell and B cell epitopes were predicted by restricting them to certain HLA alleles using various servers (nHLApred, NetMHCIIpan v.3.1, ABCpred) and were validated using IEDB tools. Using these epitopes and adjuvant, a multi-epitope vaccine was constructed in-silicoand was later subjected to allergenicity, antigenicity and physicochemical properties profiling along with identification of conformational B-cell epitopes. The designed vaccine was evaluated via codon optimization by the Jcat server and finally, it’s in-silicoexpression was done in pET-28a(+) vector using snap-gene software. RESULTS A total of 18 epitopes (both T and B cell) were predicted that constituted vaccine construct along with adjuvant and end tag. Vaccine construct was validated and its best structure model was successfully docked with human Toll-like receptors. In-silico expression of the designed vector was also seen in pET-28a(+) plasmid. CONCLUSIONS The designed novel vaccine candidate has been validated in-silico to elicit robust immune responses hence; it can be used as a potential model for further development of multi-epitope vaccines in the laboratory.

scholarly journals Design of multi-epitope vaccine candidate against SARS-CoV-2: a in-silico study

2020 ◽  
pp. 1-9 ◽  
Author(s):  
K. Abraham Peele ◽  
T. Srihansa ◽  
S. Krupanidhi ◽  
Vijaya Sai Ayyagari ◽  
T. C. Venkateswarulu
Keyword(s):  
In Silico ◽  
Vaccine Candidate ◽  
Epitope Vaccine ◽  
In Silico Study

scholarly journals Whole-Genome Sequence Analysis of Pseudorabies Virus Clinical Isolates from Pigs in China between 2012 and 2017 in China

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1322
Author(s):  
Ruiming Hu ◽  
Leyi Wang ◽  
Qingyun Liu ◽  
Lin Hua ◽  
Xi Huang ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Pseudorabies Virus ◽  
Viral Evolution ◽  
Infectious Agent ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Evolutionary Constraint ◽  
The Novel ◽  
Novel Variants ◽  
Pressure Analysis

Pseudorabies virus (PRV) is an economically significant swine infectious agent. A PRV outbreak took place in China in 2011 with novel virulent variants. Although the association of viral genomic variability with pathogenicity is not fully confirmed, the knowledge concerning PRV genomic diversity and evolution is still limited. Here, we sequenced 54 genomes of novel PRV variants isolated in China from 2012 to 2017. Phylogenetic analysis revealed that China strains and US/Europe strains were classified into two separate genotypes. PRV strains isolated from 2012 to 2017 in China are highly related to each other and genetically close to classic China strains such as Ea, Fa, and SC. RDP analysis revealed 23 recombination events within novel PRV variants, indicating that recombination contributes significantly to the viral evolution. The selection pressure analysis indicated that most ORFs were under evolutionary constraint, and 19 amino acid residue sites in 15 ORFs were identified under positive selection. Additionally, 37 unique mutations were identified in 19 ORFs, which distinguish the novel variants from classic strains. Overall, our study suggested that novel PRV variants might evolve from classical PRV strains through point mutation and recombination mechanisms.

scholarly journals In-silico design of envelope based multi-epitope vaccine candidate against Kyasanur forest disease virus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sathishkumar Arumugam ◽  
Prasad Varamballi
Keyword(s):  
Disease Virus ◽  
In Silico ◽  
Hemorrhagic Fever ◽  
Epitope Vaccine ◽  
Epitope Region ◽  
Vaccine Candidates ◽  
Forest Disease ◽  
In Silico Design ◽  
Antigenic Properties ◽  
Kyasanur Forest Disease

AbstractKyasanur forest disease virus (KFDV) causing tick-borne hemorrhagic fever which was earlier endemic to western Ghats, southern India, it is now encroaching into new geographic regions, but there is no approved medicine or effective vaccine against this deadly disease. In this study, we did in-silico design of multi-epitope subunit vaccine for KFDV. B-cell and T-cell epitopes were predicted from conserved regions of KFDV envelope protein and two vaccine candidates (VC1 and VC2) were constructed, those were found to be non-allergic and possess good antigenic properties, also gives cross-protection against Alkhurma hemorrhagic fever virus. The 3D structures of vaccine candidates were built and validated. Docking analysis of vaccine candidates with toll-like receptor-2 (TLR-2) by Cluspro and PatchDock revealed strong affinity between VC1 and TLR2. Ligplot tool was identified the intermolecular hydrogen bonds between vaccine candidates and TLR-2, iMOD server confirmed the stability of the docking complexes. JCAT sever ensured cloning efficiency of both vaccine constructs and in-silico cloning into pET30a (+) vector by SnapGene showed successful translation of epitope region. IMMSIM server was identified increased immunological responses. Finally, multi-epitope vaccine candidates were designed and validated their efficiency, it may pave the way for up-coming vaccine and diagnostic kit development.

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