Peptide-based epitope design on non-structural proteins of SARS-CoV-2

The SARS-CoV-2 virus has caused the severe pandemic, COVID19 and since then its been critical to produce a potent vaccine to prevent the quick transmission and also to avoid alarming deaths. Among all type of vaccines peptide based epitope design tend to outshine with respect to low cost production and more efficacy. Therefore, we started with obtaining the necessary protein sequences from NCBI database of SARS-CoV-2 virus and filtered with respect to antigenicity, virulency, pathogenicity and non- homologous nature with human proteome using different available online tools and servers. The promising proteins was checked for containing common B and T- cell epitopes. The structure for these proteins were modeled from I-TASSER server followed by its refinement and validation. The predicted common epitopes were mapped on modeled structures of proteins by using Pepitope server. The surface exposed epitopes were docked with the most common allele DRB1*0101 using the GalaxyPepDock server. The epitopes, ELEGIQYGRS from Leader protein (NSP1), YGPFVDRQTA from 3c-like proteinase (nsp5), DLKWARFPKS from NSP9 and YQDVNCTEVP from Surface glycoprotein (spike protein) are the epitopes which has more hydrogen bonds. Hence these four epitopes could be considered as a more promising epitopes and these epitopes can be used for future studies.

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Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2

Infectious Diseases of Poverty ◽

10.1186/s40249-020-00752-w ◽

2020 ◽

Vol 9 (1) ◽

Author(s):

Muhammad Tahir ul Qamar ◽

Farah Shahid ◽

Sadia Aslam ◽

Usman Ali Ashfaq ◽

Sidra Aslam ◽

...

Keyword(s):

In Silico ◽

Subunit Vaccine ◽

Human Leukocyte ◽

Surface Glycoprotein ◽

Structural Proteins ◽

Effective Vaccine ◽

Severe Illness ◽

T Cell Epitopes ◽

Hla Binding ◽

K 12

Abstract Background Coronavirus disease 2019 (COVID-19) linked with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause severe illness and life-threatening pneumonia in humans. The current COVID-19 pandemic demands an effective vaccine to acquire protection against the infection. Therefore, the present study was aimed to design a multiepitope-based subunit vaccine (MESV) against COVID-19. Methods Structural proteins (Surface glycoprotein, Envelope protein, and Membrane glycoprotein) of SARS-CoV-2 are responsible for its prime functions. Sequences of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast B- and T- cell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective MESV. Results Predicted epitopes suggested high antigenicity, conserveness, substantial interactions with the human leukocyte antigen (HLA) binding alleles, and collective global population coverage of 88.40%. Taken together, 276 amino acids long MESV was designed by connecting 3 cytotoxic T lymphocytes (CTL), 6 helper T lymphocyte (HTL) and 4 B-cell epitopes with suitable adjuvant and linkers. The MESV construct was non-allergenic, stable, and highly antigenic. Molecular docking showed a stable and high binding affinity of MESV with human pathogenic toll-like receptors-3 (TLR3). Furthermore, in silico immune simulation revealed significant immunogenic response of MESV. Finally, MEV codons were optimized for its in silico cloning into the Escherichia coli K-12 system, to ensure its increased expression. Conclusion The MESV developed in this study is capable of generating immune response against COVID-19. Therefore, if designed MESV further investigated experimentally, it would be an effective vaccine candidate against SARS-CoV-2 to control and prevent COVID-19.

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Estimation of the Inhaled Dose of Pollutants in Different Micro-Environments: A Systematic Review of the Literature

Toxics ◽

10.3390/toxics9060140 ◽

2021 ◽

Vol 9 (6) ◽

pp. 140

Author(s):

Francesca Borghi ◽

Andrea Spinazzè ◽

Simone Mandaglio ◽

Giacomo Fanti ◽

Davide Campagnolo ◽

...

Keyword(s):

Systematic Review ◽

Residence Time ◽

Low Cost ◽

Pulmonary Ventilation ◽

Personal Exposure ◽

Ventilation Rate ◽

Atmospheric Pollutants ◽

Active Commuting ◽

Review Of The Literature ◽

Future Studies

Recently, the need to assess personal exposure in different micro-environments has been highlighted. Further, estimating the inhaled dose of pollutants is considerably one of the most interesting parameters to be explored to complete the fundamental information obtained through exposure assessment, especially if associated with a dose-response approach. To analyze the main results obtained from the studies related to the estimation of the inhaled dose of pollutants in different micro-environments (environments in which an individual spends a part of his day), and to identify the influence of different parameters on it, a systematic review of the literature was performed. The principal outcomes from the considered studies outlined that (i) exposure concentration and residence time are among the most important parameters to be evaluated in the estimation of the inhaled dose, especially in transport environments. Further, (ii) the pulmonary ventilation rate can be of particular interest during active commuting because of its increase, which increases the inhalation of pollutants. From a methodological point of view, the advent of increasingly miniaturized, portable and low-cost technologies could favor these kinds of studies, both for the measurement of atmospheric pollutants and the real-time evaluation of physiological parameters used for estimation of the inhaled dose. The main results of this review also show some knowledge gaps. In particular, numerous studies have been conducted for the evaluation (in terms of personal exposure and estimation of the inhaled dose) of different PM fractions: other airborne pollutants, although harmful to human health, are less represented in studies of this type: for this reason, future studies should be conducted, also considering other air pollutants, not neglecting the assessment of exposure to PM. Moreover, many studies have been conducted indoors, where the population spends most of their daily time. However, it has been highlighted how particular environments, even if characterized by a shorter residence time, can contribute significantly to the dose of inhaled pollutants. These environments are, therefore, of particular importance and should be better evaluated in future studies, as well as occupational environments, where the work results in a high pulmonary ventilation rate. The attention of future studies should also be focused on these categories of subjects and occupational studies.

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Immunodominant T-Cell Epitopes in the VP1 Capsid Protein of Rhinovirus Species A and C

Journal of Virology ◽

10.1128/jvi.01701-16 ◽

2016 ◽

Vol 90 (23) ◽

pp. 10459-10471 ◽

Cited By ~ 13

Author(s):

Cibele M. Gaido ◽

Shane Stone ◽

Abha Chopra ◽

Wayne R. Thomas ◽

Peter N. Le Souëf ◽

...

Keyword(s):

T Cell ◽

T Cell Responses ◽

Antibody Responses ◽

T Cell Proliferation ◽

T Cell Epitopes ◽

Future Studies ◽

Cell Responses ◽

Asthma Exacerbations ◽

Antibody Titers ◽

Vp1 Capsid Protein

ABSTRACTRhinovirus (RV) species A and C are the most frequent cause of respiratory viral illness worldwide, and RV-C has been linked to more severe exacerbations of asthma in young children. Little is known about the immune responses to the different RV species, although studies comparing IgG1 antibody titers found impaired antibody responses to RV-C. Therefore, the aim of this study was to assess whether T-cell immunity to RV-C is similarly impaired. We measured T-cell proliferation to overlapping synthetic peptides covering the entire VP1 capsid protein of an RV-A and RV-C genotype for 20 healthy adult donors. Human leukocyte antigen (HLA) was typed in all the donors in order to investigate possible associations between the HLA type and RV peptide recognition. Total and specific IgG1 antibody titers to the VP1 proteins of both RV-A and RV-C were also measured to examine associations between the antibody and T-cell responses. We identified T-cell epitopes that are specific to and representative of each RV-A and RV-C species. These epitopes stimulated CD4+-specific T-cell proliferation, with similar magnitudes of response for both RV species. All the donors, independent of their HLA-DR or -DQ type, were able to recognize the immunodominant RV-A and -C regions of VP1. Furthermore, the presence or absence of specific antibody titers was not related to changes in T-cell recognition. Our results indicate a dissociation between the antibody and T-cell responses to rhinoviruses. The species-representative T-cell epitopes identified in this study are valuable tools for future studies investigating T-cell responses to the different RV species.IMPORTANCERhinoviruses (RVs) are mostly associated with the common cold and asthma exacerbations, although their contributions to most upper and lower respiratory tract diseases have increasingly been reported. Species C (RV-C) has been associated with more frequent and severe asthma exacerbations in young children and, along with RV-A, is the most clinically relevant species. Little is known about how our immune system responds to rhinoviruses, and there are limited tools to study specific adaptive immunity against each rhinovirus species. In this study, we identified immunodominant T-cell epitopes of the VP1 proteins of RV-A and RV-C, which are representative of each species. The study found that T-cell responses to RV-A and RV-C were of similar magnitudes, in contrast with previous findings showing RV-C-specific antibody responses were low. These findings will provide the basis for future studies on the immune response to rhinoviruses and can help elucidate the mechanisms of severity of rhinovirus-induced infections.

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Computational Approaches and Challenges to Developing Universal Influenza Vaccines

Vaccines ◽

10.3390/vaccines7020045 ◽

2019 ◽

Vol 7 (2) ◽

pp. 45 ◽

Cited By ~ 4

Author(s):

Xueting Qiu ◽

Venkata R. Duvvuri ◽

Justin Bahl

Keyword(s):

Influenza Vaccine ◽

Influenza A ◽

Low Cost ◽

T Cell Epitopes ◽

Computational Approaches ◽

Novel Technologies ◽

Consensus Sequences ◽

Computational Optimization ◽

Sequence Reconstruction ◽

Universal Influenza Vaccine

The traditional design of effective vaccines for rapidly-evolving pathogens, such as influenza A virus, has failed to provide broad spectrum and long-lasting protection. With low cost whole genome sequencing technology and powerful computing capabilities, novel computational approaches have demonstrated the potential to facilitate the design of a universal influenza vaccine. However, few studies have integrated computational optimization in the design and discovery of new vaccines. Understanding the potential of computational vaccine design is necessary before these approaches can be implemented on a broad scale. This review summarizes some promising computational approaches under current development, including computationally optimized broadly reactive antigens with consensus sequences, phylogenetic model-based ancestral sequence reconstruction, and immunomics to compute conserved cross-reactive T-cell epitopes. Interactions between virus-host-environment determine the evolvability of the influenza population. We propose that with the development of novel technologies that allow the integration of data sources such as protein structural modeling, host antibody repertoire analysis and advanced phylodynamic modeling, computational approaches will be crucial for the development of a long-lasting universal influenza vaccine. Taken together, computational approaches are powerful and promising tools for the development of a universal influenza vaccine with durable and broad protection.

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Detection and Characterization of Functional T-Cell Epitopes on the Structural Proteins VP2, VP3, and VP4 of Foot and Mouth Disease Virus O1 Campos

Virology ◽

10.1006/viro.2000.0281 ◽

2000 ◽

Vol 271 (2) ◽

pp. 234-239 ◽

Cited By ~ 14

Author(s):

M. Pérez Filgueira ◽

A. Wigdorovitz ◽

A. Romera ◽

P. Zamorano ◽

M.V. Borca ◽

...

Keyword(s):

T Cell ◽

Disease Virus ◽

Foot And Mouth Disease ◽

Mouth Disease ◽

Structural Proteins ◽

T Cell Epitopes ◽

Mouth Disease Virus ◽

Foot And Mouth

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Identification of porcine reproductive and respiratory syndrome virus ORF1a-encoded non-structural proteins in virus-infected cells

Journal of General Virology ◽

10.1099/vir.0.039289-0 ◽

2012 ◽

Vol 93 (4) ◽

pp. 829-839 ◽

Cited By ~ 53

Author(s):

Yanhua Li ◽

Ali Tas ◽

Eric J. Snijder ◽

Ying Fang

Keyword(s):

Rna Synthesis ◽

Immunofluorescence Microscopy ◽

Polyclonal Antibodies ◽

Structural Proteins ◽

Respiratory Syndrome Virus ◽

Replicase Gene ◽

Future Studies ◽

Swine Pathogen ◽

Infected Cells

The porcine reproductive and respiratory syndrome virus (PRRSV) replicase gene consists of two large ORFs, ORF1a and ORF1b, the latter of which is expressed by ribosomal frameshifting. The ORF1a-encoded part of the resulting replicase polyproteins (pp1a and pp1ab) is predicted to be processed proteolytically into ten non-structural proteins (nsps), known as nsp1–8, with both the nsp1 and nsp7 regions being cleaved internally (yielding nsp1α and nsp1β, and nsp7α and nsp7β, respectively). The experimental verification of these predictions depends strongly on the ability to identify individual cleavage products with specific antibodies. In this study, a panel of monoclonal and polyclonal antibodies was generated, which together were able to recognize eight ORF1a-encoded PRRSV nsps. Using these reagents, replicase cleavage products were detected in PRRSV-infected MARC-145 cells using a variety of immunoassays. By immunofluorescence microscopy, most nsps could be detected by 6 h post-infection. During the early stages of infection, nsp1β, nsp2, nsp4, nsp7α, nsp7β and nsp8 co-localized in distinct punctate foci in the perinuclear region of the cell, which were determined to be the site of viral RNA synthesis by in situ labelling. Western blot and immunoprecipitation analysis identified most individual nsps and several long-lived processing intermediates (nsp3–4, nsp5–7, nsp5–8 and nsp3–8). The identification and subcellular localization of PRRSV nsps in virus-infected cells documented here provides a basis for the further structure–function studies. Thus, this PRRSV antibody panel will be an important tool for future studies on the replication and pathogenesis of this major swine pathogen.

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SubMito-PSPCP: Predicting Protein Submitochondrial Locations by Hybridizing Positional Specific Physicochemical Properties with Pseudoamino Acid Compositions

BioMed Research International ◽

10.1155/2013/263829 ◽

2013 ◽

Vol 2013 ◽

pp. 1-7 ◽

Cited By ~ 13

Author(s):

Pufeng Du ◽

Yuan Yu

Keyword(s):

Physicochemical Properties ◽

Outer Membrane ◽

Acid Composition ◽

State Of The Art ◽

Mitochondrial Protein ◽

Protein Sequences ◽

Online Service ◽

Inner Membrane ◽

Future Studies ◽

General Method

Knowing the submitochondrial location of a mitochondrial protein is an important step in understanding its function. We developed a new method for predicting protein submitochondrial locations by introducing a new concept: positional specific physicochemical properties. With the framework of general form pseudoamino acid compositions, our method used only about 100 features to represent protein sequences, which is much simpler than the existing methods. On the dataset of SubMito, our method achieved over 93% overall accuracy, with 98.60% for inner membrane, 93.90% for matrix, and 70.70% for outer membrane, which are comparable to all state-of-the-art methods. As our method can be used as a general method to upgrade all pseudoamino-acid-composition-based methods, it should be very useful in future studies. We implement our method as an online service: SubMito-PSPCP.

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Immunoinformatic Approach for the identification of T Cell and B Cell Epitopes in the Surface Glycoprotein and Designing a Potent Multiepitope Vaccine Construct Against SARS-CoV-2 including the new UK variant

10.1101/2021.03.15.435391 ◽

2021 ◽

Author(s):

Kaveri Krishnasamy ◽

Gracy Fathima Selvaraj ◽

Kiruba Ramesh ◽

Padmaoriya Padmanabhan ◽

Vidya Gopalan ◽

...

Keyword(s):

T Cell ◽

Immune Responses ◽

B Cell ◽

T Lymphocyte ◽

Vaccine Candidate ◽

Surface Glycoprotein ◽

T Cell Epitopes ◽

B Cell Epitopes ◽

New Variant

The emergence of a novel coronavirus in China in late 2019 has turned into a SARS-CoV-2 pandemic affecting several millions of people worldwide in a short span of time with high fatality. The crisis is further aggravated by the emergence and evolution of new variant SARS-CoV-2 strains in UK during December, 2020 followed by their transmission to other countries. A major concern is that prophylaxis and therapeutics are not available yet to control and prevent the virus which is spreading at an alarming rate, though several vaccine trials are in the final stage. As vaccines are developed through various strategies, their immunogenic potential may drastically vary and thus pose several challenges in offering both arms of immunity such as humoral and cell-mediated immune responses against the virus. In this study, we adopted an immunoinformatics-aided identification of B cell and T cell epitopes in the Spike protein, which is a surface glycoprotein of SARS-CoV-2, for developing a new Multiepitope vaccine construct (MEVC). MEVC has 575 amino acids and comprises adjuvants and various cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and B-cell epitopes that possess the highest affinity for the respective HLA alleles, assembled and joined by linkers. The computational data suggest that the MEVC is non-toxic, non-allergenic and thermostable with the capability to elicit both humoral and cell-mediated immune responses. The population coverage of various countries affected by COVID-19 with respect to the selected B and T cell epitopes in MEVC was also investigated. Subsequently, the biological activity of MEVC was assessed by bioinformatic tools using the interaction between the vaccine candidate and the innate immune system receptors TLR3 and TLR4. The epitopes of the construct were analyzed with that of the strains belonging to various clades including the new variant UK strain having multiple unique mutations in S protein. Due to the advantageous features, the MEVC can be tested in vitro for more practical validation and the study offers immense scope for developing a potential vaccine candidate against SARS-CoV-2 in view of the public health emergency associated with COVID-19 disease caused by SARS-CoV-2.

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T Cell Epitope-Based Vaccine Design for Pandemic Novel Coronavirus 2019-nCoV

10.26434/chemrxiv.12029523.v2 ◽

2020 ◽

Author(s):

Dr. Seema Mishra

Keyword(s):

T Cell ◽

Cell Epitope ◽

Structural Proteins ◽

T Cell Epitope ◽

T Cell Epitopes ◽

Consensus Sequences ◽

Tight Cluster ◽

Cell Assays ◽

Novel Coronavirus

Immunoinformatics approach has been used to identify potential T cell epitopes from structural and non-structural proteins for immunotherapy against novel coronavirus 2019-nCoV across populations Two different prediction algorithms, NetCTLpan and Pickpocket were used to generate consensus epitopes against HLA supertypes. All of the 57 epitopes identified had no similarity/identity with the human proteome thus preventing crossreactivity. Many of these epitopes formed a tight cluster around consensus sequences MGYINVFAFPFTIYSLLLC and KVSIWNLDYIINLI across proteins and alleles. These should be urgently tested in in-vitro MHC binding and T cell assays before being tried as vaccines to further prevent pandemic due to this lethal coronavirus.

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Geographical Distribution of Amino Acid Mutations in Human SARS-CoV-2 Orf1ab Poly-Proteins Compared to the Equivalent Reference Proteins from China

10.26434/chemrxiv.12951617.v1 ◽

2020 ◽

Author(s):

Kunchur Guruprasad

Keyword(s):

Amino Acid ◽

North America ◽

South America ◽

Protein Sequences ◽

Sequence Length ◽

Amino Acid Residues ◽

Deletion Mutations ◽

Leader Protein ◽

Amino Acid Mutations ◽

Geographical Locations

Mutations in orf1ab poly-protein sequences from human SARS-CoV-2 isolates representing six geographical locations were identified by comparing with the equivalent reference sequences from the Wuhan-Hu-1, China isolate, epicentre of the current COVID-19 pandemic disease. The orf1ab poly-proteins of sequence length 7096 amino acid residues representing 10,929 genomes from six geographical locations comprised a total of 27,895 mutations that corresponded to 2,095 distinct mutation sites. The percentage of mutations was significantly high for RdRp (33.47%), nsp2 (20.04%), helicase (15.95%) and nsp3 (12.61%) proteins, compared to rest of the proteins which ranged between (0.14%) for nsp10 to (2.79%) for nsp6 proteins. A total of 2715 mutations were observed for the unique mutation sites identified for each of the six geographical locations. The distribution of the mutations was; Africa (87), Asia (605), Europe (134), North America (1677), Oceania (200) and South America (12). The RdRp protein contained significantly high mutation percentage (>31%) that varied among the different geographical locations. The nsp2 proteins from Asia, North America, Oceania and South America, the nsp3 proteins from Africa and Europe and the helicase proteins from North America showed high mutation percentage next to the RdRp proteins. The P4715L mutation in RdRp, T265I in nsp2 and L3606F in nsp6 were observed in all the geographical locations with the RdRp P4715L mutation being predominant among the orf1ab poly-proteins. In another dataset comprising 158 genomes in which the orf1ab poly-proteins comprised sequences of variable length between 7084-7095 amino acid residues, 88 additional distinct mutations were observed for the six geographical locations that included deletion mutations. The proteins containing deletion mutations were; leader protein, nsp2, nsp3, nsp4, nsp6, RdRp, 3’ -to-5’ exonuclease and endoRNAse. In this work, all the mutations observed in 11,087 orf1ab poly-proteins of human SARS CoV-2 comprising between 7084-7096 amino acid residues with reference to the human SARS-CoV-2 orf1ab poly-protein sequences from Wuhan-Hu-1, China and representing the six geographical locations; Africa, Asia, Europe, North America, Oceania and South America are presented.

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