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1.
Sci Rep ; 12(1): 19087, 2022 Nov 09.
Article in English | MEDLINE | ID: covidwho-2106475

ABSTRACT

The World Health Organization categorized SARS-CoV-2 as a variant of concern, having numerous mutations in spike protein, which have been found to evade the effect of antibodies stimulated by the COVID-19 vaccine. The susceptibility to omicron variant by immunization-induced antibodies are direly required for risk evaluation. To avoid the risk of arising viral illness, the construction of a specific vaccine that triggers the production of targeted antibodies to combat infection remains highly imperative. The aim of the present study is to develop a particular vaccine exploiting bioinformatics approaches which can target B- and T-cells epitopes. Through this approach, novel epitopes of the S protein-SARS-CoV-2 were predicted for the development of a multiple epitope vaccine. Multiple epitopes were selected on the basis of toxicity, immunogenicity and antigenicity, and vaccine subunit was constructed having potential immunogenic properties. The epitopes were linked with 3 types of linker EAAAK, AAY and GPGPG for vaccine construction. Subsequently, vaccine structure was docked with the receptor and cloned in a pET-28a (+) vector. The constructed vaccine was ligated in pET-28a (+) vector in E. coli using the SnapGene tool for the expression study and a good immune response was observed. Several computational tools were used to predict and analyze the vaccine constructed by using spike protein sequence of omicrons. The current study identified a Multi-Epitope Vaccine (MEV) as a significant vaccine candidate that could potentially help the global world to combat SARS-CoV-2 infections.


Subject(s)
COVID-19 , Viral Vaccines , Humans , SARS-CoV-2/genetics , COVID-19 Vaccines/genetics , Spike Glycoprotein, Coronavirus/chemistry , COVID-19/prevention & control , Computational Biology , Escherichia coli , Epitopes, B-Lymphocyte , Immunogenicity, Vaccine , Epitopes, T-Lymphocyte
2.
Frontiers in immunology ; 13, 2022.
Article in English | EuropePMC | ID: covidwho-1989332

ABSTRACT

Neo-Coronavirus (NeoCoV) is a novel Betacoronavirus (β-CoVs or Beta-CoVs) discovered in bat specimens in South Africa during 2011. The viral sequence is highly similar to Middle East Respiratory Syndrome, particularly that of structural proteins. Thus, scientists have emphasized the threat posed by NeoCoV associated with human angiotensin-converting enzyme 2 (ACE2) usage, which could lead to a high death rate and faster transmission rate in humans. The development of a NeoCoV vaccine could provide a promising option for the future control of the virus in case of human infection. In silico predictions can decrease the number of experiments required, making the immunoinformatics approaches cost-effective and convenient. Herein, with the aid of immunoinformatics and reverse vaccinology, we aimed to formulate a multi-epitope vaccine that may be used to prevent and treat NeoCoV infection. Based on the NeoCoV proteins, B-cell, cytotoxic T lymphocyte (CTL), and helper T lymphocyte (HTL) epitopes were shortlisted. Four vaccines (Neo-1–4) were devised by fusing shortlisted epitopes with appropriate adjuvants and linkers. The secondary and three-dimensional structures of final vaccines were then predicted. The binding interactions of these potential vaccines with toll-like immune receptors (TLR-2, TLR-3, and TLR-4) and major histocompatibility complex molecules (MHC-I and II) reveal that they properly fit into the receptors’ binding domains. Besides, Neo-1 and Neo-4 vaccines exhibited better docking energies of -101.08 kcal/mol and -114.47 kcal/mol, respectively, with TLR-3 as compared to other vaccine constructs. The constructed vaccines are highly antigenic, non-allergenic, soluble, non-toxic, and topologically assessable with good physiochemical characteristics. Codon optimization and in-silico cloning confirmed efficient expression of the designed vaccines in Escherichia coli strain K12. In-silico immune simulation indicated that Neo-1 and Neo-4 vaccines could induce a strong immune response against NeoCoV. Lastly, the binding stability and strong binding affinity of Neo-1 and Neo-4 with TLR-3 receptor were validated using molecular dynamics simulations and free energy calculations (Molecular Mechanics/Generalized Born Surface Area method). The final vaccines require experimental validation to establish their safety and effectiveness in preventing NeoCoV infections.

3.
Environ Sci Pollut Res Int ; 29(45): 67685-67703, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-1982295

ABSTRACT

The 2019 outbreak of corona virus disease began from Wuhan (China), transforming into a leading pandemic, posing an immense threat to the global population. The WHO coined the term nCOVID-19 for the disease on 11th February, 2020 and the International Committee of Taxonomy of Viruses named it SARS-CoV-2, on account of its similarity with SARS-CoV-1 of 2003. The infection is associated with fever, cough, pneumonia, lung damage, and ARDS along with clinical implications of lung opacities. Brief understanding of the entry target of virus, i.e., ACE2 receptors has enabled numerous treatment options as discussed in this review. The manuscript provides a holistic picture of treatment options in COVID-19, such as non-specific anti-viral drugs, immunosuppressive agents, anti-inflammatory candidates, anti-HCV, nucleotide inhibitors, antibodies and anti-parasitic, RNA-dependent RNA polymerase inhibitors, anti-retroviral, vitamins and hormones, JAK inhibitors, and blood plasma therapy. The text targets to enlist the investigations conducted on all the above categories of drugs, with respect to the COVID-19 pandemic, to accelerate their significance in hindering the disease progression. The data collected primarily targets recently published articles and most recent records of clinical trials, focusing on the last 10-year database. The current review provides a comprehensive view on the critical need of finding a suitable treatment for the currently prevalent COVID-19 disease, and an opportunity for the researchers to investigate the varying possibilities to find and optimized treatment approach to mitigate and ameliorate the chaos created by the pandemic worldwide.


Subject(s)
COVID-19 , Janus Kinase Inhibitors , Angiotensin-Converting Enzyme 2 , Anti-Inflammatory Agents , Hormones , Humans , Nucleotides , Pandemics , RNA-Dependent RNA Polymerase , SARS-CoV-2 , Vitamins
4.
Biomolecules ; 12(7)2022 07 11.
Article in English | MEDLINE | ID: covidwho-1928474

ABSTRACT

The number of deaths has been increased due to COVID-19 infections and uncertain neurological complications associated with the central nervous system. Post-infections and neurological manifestations in neuronal tissues caused by COVID-19 are still unknown and there is a need to explore how brainstorming promoted congenital impairment, dementia, and Alzheimer's disease. SARS-CoV-2 neuro-invasion studies in vivo are still rare, despite the fact that other beta-coronaviruses have shown similar properties. Neural (olfactory or vagal) and hematogenous (crossing the blood-brain barrier) pathways have been hypothesized in light of new evidence showing the existence of SARS-CoV-2 host cell entry receptors into the specific components of human nerve and vascular tissue. Spike proteins are the primary key and structural component of the COVID-19 that promotes the infection into brain cells. Neurological manifestations and serious neurodegeneration occur through the binding of spike proteins to ACE2 receptor. The emerging evidence reported that, due to the high rate in the immediate wake of viral infection, the olfactory bulb, thalamus, and brain stem are intensely infected through a trans-synaptic transfer of the virus. It also instructs the release of chemokines, cytokines, and inflammatory signals immensely to the blood-brain barrier and infects the astrocytes, which causes neuroinflammation and neuron death; and this induction of excessive inflammation and immune response developed in more neurodegeneration complications. The present review revealed the pathophysiological effects, molecular, and cellular mechanisms of possible entry routes into the brain, pathogenicity of autoantibodies and emerging immunotherapies against COVID-19.


Subject(s)
COVID-19 , SARS-CoV-2 , Blood-Brain Barrier/metabolism , Brain/metabolism , Humans , Spike Glycoprotein, Coronavirus/chemistry
5.
Environ Sci Pollut Res Int ; 29(28): 42404-42432, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1872658

ABSTRACT

The human coronavirus disease (COVID-19) pandemic is caused by a novel coronavirus; the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2). Natural products, secondary metabolites show positive leads with antiviral and immunotherapy treatments using genomic studies in silico docking. In addition, it includes the action of a mechanism targeting the SARS-CoV-2. In this literature, we aimed to evaluate the antiviral movement of the NT-VRL-1 unique terpene definition to Human coronavirus (HCoV-229E). The effects of 19 hydrolysable tannins on the SARS-CoV-2 were therefore theoretically reviewed and analyzed utilising the molecular operating surroundings for their C-Like protease 3CLpro catalytic dyad residues Angiotensin converting enzyme-2 (MOE 09). Pedunculagin, tercatan, and castalin were detected as interacting strongly with SARS-receptor Cov-2's binding site and catalytic dyad (Cys145 and His41). SARS-CoV-2 methods of subunit S1 (ACE2) inhibit the interaction of the receiver with the s-protein once a drug molecule is coupled to the s-protein and prevent it from infecting the target cells in alkaloids. Our review strongly demonstrates the evidence that natural compounds and their derivatives can be used against the human coronavirus and serves as an area of research for future perspective.


Subject(s)
Biological Products , COVID-19 , Antiviral Agents/pharmacology , Biological Products/pharmacology , Humans , Pandemics , SARS-CoV-2
6.
Molecules ; 27(7)2022 Apr 04.
Article in English | MEDLINE | ID: covidwho-1776291

ABSTRACT

Following the spread of the COVID-19 pandemic crisis, a race was initiated to find a successful regimen for postinfections. Among those trials, a recent study declared the efficacy of an antiviral combination of favipiravir (FAV) and molnupiravir (MLP). The combined regimen helped in a successful 60% eradication of the SARS-CoV-2 virus from the lungs of studied hamster models. Moreover, it prevented viral transmission to cohosted sentinels. Because both medications are orally bioavailable, the coformulation of FAV and MLP can be predicted. The developed study is aimed at developing new green and simple methods for the simultaneous determination of FAV and MLP and then at their application in the study of their dissolution behavior if coformulated together. A green micellar HPLC method was validated using an RP-C18 core-shell column (5 µm, 150 × 4.6 mm) and an isocratic mixed micellar mobile phase composed of 0.1 M SDS, 0.01 M Brij-35, and 0.02 M monobasic potassium phosphate mixture and adjusted to pH 3.1 at 1.0 mL min-1 flow rate. The analytes were detected at 230 nm. The run time was less than five minutes under the optimized chromatographic conditions. Four other multivariate chemometric model methods were developed and validated, namely, classical least square (CLS), principal component regression (PCR), partial least squares (PLS-1), and genetic algorithm-partial least squares (GA-PLS-1). The developed models succeeded in resolving the great similarity and overlapping in the FAV and MLP UV spectra unlike the traditional univariate methods. All methods were organic solvent-free, did not require extraction or derivatization steps, and were applied for the construction of the simultaneous dissolution profile for FAV tablets and MLP capsules. The methods revealed that the amount of the simultaneously released cited drugs increases up until reaching a plateau after 15 and 20 min for FAV and MLP, respectively. The greenness was assessed on GAPI and found to be in harmony with green analytical chemistry concepts.


Subject(s)
COVID-19 , Amides , Antiviral Agents/therapeutic use , COVID-19/drug therapy , Chromatography, High Pressure Liquid/methods , Cytidine/analogs & derivatives , Humans , Hydroxylamines , Micelles , Pandemics , Pyrazines , Reproducibility of Results , SARS-CoV-2 , Spectrophotometry, Ultraviolet/methods
7.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-317247

ABSTRACT

The Severe acute respiratory syndrome (SARS) corona virus (CoV) 2 SARS-CoV-2 mediated epidemic is a global pandemic. The first genome sequence data of SARS-CoV-2 (CoVid19) concluded that it has a bat reservoir and bat was the immediate donor. Andersen et al., (2020) has reported that it is improbable to do laboratory manipulation of SARS CoV [1]. But, Lau et al., (2010) has already reported the generation of recombinant bat SARS CoV and they had reported three recombinant genotypes. Hence laboratory based manipulation has already completed long before[2]. A deep comparative study of bat SARS CoV with other SARS CoVs (including human SARS CoV of German isolate) revealed, human SARS CoV-2 genomes (isolates of China, India, Italy, Nepal, and the United States of America) had sequence similarity of 79-80% only with bat SARS CoV and it has sequence similarity of approximately 60% with the human SARS CoV (German isolate). The presence of large genomic dissimilarity of bat SARS CoV genome with human SARS CoV-2 cannot be considered as an immediate donor to human SARS CoV-2. However, the genomic sequence similarity within the SARS CoV-2 isolates of China, India, Italy, Nepal, and USA shared 99-100% similarity. This suggests that human SARS CoV-2 did not undergo heavy mutation to generate immediate new genotype. If the SARS CoV-2 infection happened to the human through the SARS CoV of bat from Wuhan meat market, it should have sequence similarity of more than 99% which was not found in the study. Phylogenetic analysis revealed, bat SARS CoV did not fall with the group of SARS CoV-2 of China, India, Italy, Nepal, and USA isolates. This suggests that bat SARS CoV has genomic and evolutionary dissimilarity and cannot be considered as immediate and direct donor of human SARS CoV-2. The natural selection of bat genome before transfer to the zoonotic organism is a time-consuming process and natural selection in human post zoonotic transfer is also time-consuming event. Therefore, concept mentioned by Andersen et al., (2020)[1] regarding its transfer from a bat of Wuhan meat market is irrefutably incorrect. Sequence alignment revealed the presence of inserted codons in human SARS CoV-2 and synteny analysis corroborated with the presence of extra nucleotides/codons in the human SARS CoV-2. Relative time tree analysis revealed it origin before 0.00 million year ago, suggesting its recent synthetic/modified origin.

8.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-307305

ABSTRACT

In times of health crisis, including the current COVID-19 pandemic, the potential benefit of botanical drugs and supplements emerges as a focus of attention, although controversial efficacy claims are rightly a concern. Phytotherapy has an established role in everyday selfcare and health care, and since botanical preparations contain many chemical constituents rather than single compounds, challenges arise in demonstrating efficacy and safety. However, there is ample traditional, empirical and clinical evidence that botanicals can offer some protection and alleviation of disease symptoms as well as promoting general well-being. Newly emerging viral infections, specifically COVID-19, represent a unique challenge in their novelty and absence of established antiviral treatment or immunization. We discuss here the roles and limitations of phytotherapy in helping to prevent and address viral infections, and specifically regarding their effects on immune response. Botanicals with a documented immunomodulatory, immunostimulatory, and anti-inflammatory effect include adaptogens, Boswellia spp., Curcuma longa, Echinacea spp., Glycyrrhiza spp., medicinal fungi, Pelargonium sidoides, salicylate-yielding herbs, and Sambucus spp. We further provide a clinical perspective on applications and safety of these herbs in prevention, onset, progression, and convalescence from respiratory viral infections.

9.
Separations ; 8(12):243, 2021.
Article in English | MDPI | ID: covidwho-1572597

ABSTRACT

A green liquid chromatographic method is considered in this work to minimize the environmental impact of waste solvents. One important principle is to replace or eliminate the use of hazardous organic solvents. Organic impurities in any active pharmaceutical ingredient could arise either during the process of its synthesis, or as degradation products developed throughout the shelf-life. Remdesivir (RDS) is an antiviral drug, approved by the US Food and Drug Adminstration (-FDA), to treat SARS-Cov-2 virus during its pandemic crisis. We studied the stability of remdesivir against several degradation pathways using the organic solvent-free liquid chromatographic technique. Separation was performed on RP-C18 stationary phase using mixed-micellar mobile phase composed of a mixture of 0.025 M Brij-35, 0.1 M sodium lauryl sulfate (SLS), and 0.02 M disodium hydrogen phosphate, adjusted to pH 6.0. The mobile phase flow rate was 1 mL min−1, and detection was carried out at a wavelength of 244 nm. We profiled the impurities that originated in mild to drastic degradation conditions. The method was then validated according to International Conference of Harmonization (ICH) guidelines within a linearity range of 5–100 μg mL−1 and applied successfully for the determination of the drug in its marketed dosage form. A brief comparison was established with reported chromatographic methods, including a greenness assessment on two new metrics (GAPI and AGREE). This study is the first to be reported as eco-friendly, solvent-free, and stability indicating LC methodology for RDS determination and impurity profiling.

10.
Sci Total Environ ; 808: 152072, 2022 Feb 20.
Article in English | MEDLINE | ID: covidwho-1550061

ABSTRACT

The combat against the Corona virus disease of 2019 (COVID-19), has created a chaos among the healthcare institutions and researchers, in turn accelerating the dire need to curtail the infection spread. The already established entry mechanism, via ACE2 has not yet successfully aided in the development of a suitable and reliable therapy. Taking in account the constant progression and deterioration of the cases worldwide, a different perspective and mechanistic approach is required, which has thrown light onto the cluster of differentiation 147 (CD147) transmembrane protein, as a novel route for SARS-CoV-2 entry. Despite lesser affinity towards COVID-19 virus, as compared to ACE2, this receptor provides a suitable justification behind elevated blood glucose levels in infected patients, retarded COVID-19 risk in women, enhanced susceptibility in geriatrics, greater infection susceptibility of T cells, infection prevalence in non-susceptible human cardiac pericytes and so on. The manuscript invokes the title role and distribution of CD147 in COVID-19 as an entry receptor and mediator of endocytosis-promoted entry of the virus, along with the "catch and clump" hypothesis, thereby presenting its Fundamental significance as a therapeutic target for potential candidates, such as Azithromycin, melatonin, statins, beta adrenergic blockers, ivermectin, Meplazumab etc. Thus, the authors provide a comprehensive review of a different perspective in COVID-19 infection, aiming to aid the researchers and virologists in considering all aspects of viral entry, in order to develop a sustainable and potential cure for the 2019 COVID-19 disease.


Subject(s)
Basigin , COVID-19 , Spike Glycoprotein, Coronavirus , Antibodies, Monoclonal, Humanized , Cell Differentiation , Female , Humans , SARS-CoV-2
11.
J Biomol Struct Dyn ; : 1-18, 2021 Nov 23.
Article in English | MEDLINE | ID: covidwho-1541375

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which causes COVID-19 disease has been exponentially increasing throughout the world. The mortality rate is increasing gradually as effective treatment is unavailable to date. In silico based screening for novel testable hypotheses on SARS-CoV-2 Mpro protein to discover the potential lead drug candidate is an emerging area along with the discovery of a vaccine. Administration of NO-releasing agents, NO inducers or the NO gas itself may be useful as therapeutics in the treatment of SARS-CoV-2. In the present study, a 3D structure of SARS-CoV-2 Mpro protein was used for the rational setting of inhibitors to the binding pocket of enzyme which proposed that phenyl furoxan derivative gets efficiently dock in the target pocket. Molecular docking and molecular dynamics simulations helped to investigate possible effective inhibitor candidates bound to SARS-CoV-2 Mpro substrate binding pocket. Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations revealed energetic contributions of active site residues of Mpro in binding with most stable proposed NO donor heterocyclic vasodilator inhibitor molecules. Furthermore, principal component analysis (PCA) showed that the NO donor heterocyclic inhibitor molecules 14, 16, 18 and 19 was strongly bound to catalytic core of SARS-CoV-2 Mpro protein, limiting its movement to form stable complex as like control. Thus, overall in silico investigations revealed that 5-oxopiperazine-2-carboxylic acid coupled furoxan derivatives was found to be key pharmacophore in drug design for the treatment of SARS-CoV-2, a global pandemic disease with a dual mechanism of action as NO donor and a worthwhile ligand to act as SARS-CoV-2 Mpro protein inhibitor.Communicated by Ramaswamy H. Sarma.

12.
Pharmaceuticals (Basel) ; 14(9)2021 Sep 03.
Article in English | MEDLINE | ID: covidwho-1390721

ABSTRACT

The unprecedented pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is threatening global health. SARS-CoV-2 has caused severe disease with significant mortality since December 2019. The enzyme chymotrypsin-like protease (3CLpro) or main protease (Mpro) of the virus is considered to be a promising drug target due to its crucial role in viral replication and its genomic dissimilarity to human proteases. In this study, we implemented a structure-based virtual screening (VS) protocol in search of compounds that could inhibit the viral Mpro. A library of >eight hundred compounds was screened by molecular docking into multiple structures of Mpro, and the result was analyzed by consensus strategy. Those compounds that were ranked mutually in the 'Top-100' position in at least 50% of the structures were selected and their analogous binding modes predicted simultaneously in all the structures were considered as bioactive poses. Subsequently, based on the predicted physiological and pharmacokinetic behavior and interaction analysis, eleven compounds were identified as 'Hits' against SARS-CoV-2 Mpro. Those eleven compounds, along with the apo form of Mpro and one reference inhibitor (X77), were subjected to molecular dynamic simulation to explore the ligand-induced structural and dynamic behavior of Mpro. The MM-GBSA calculations reflect that eight out of eleven compounds specifically possess high to good binding affinities for Mpro. This study provides valuable insights to design more potent and selective inhibitors of SARS-CoV-2 Mpro.

13.
Vaccines (Basel) ; 9(8)2021 Jul 29.
Article in English | MEDLINE | ID: covidwho-1335263

ABSTRACT

As per the World Health Organization (WHO), more than 288 vaccines against COVID-19 are being developed, with an estimated 184 being presently investigated in the pre-clinical phases, while 104 of these vaccine candidates are at various stages of clinical trials. Twelve of these are in the advanced stages of clinical investigation, and promising results in the phase 3 trials have already paved the way for their regulatory approval and subsequent dissemination for global use. Preliminary and interim results of some of these candidate vaccines are being analyzed for public dissemination. Some of these vaccines have already been rolled out to immunize not only the highest risk individuals but also the general population in several countries. Once their safety and efficacy are established, the next limiting step would be their mass manufacturing by the pharmaceutical companies to fulfill the global demand. The challenge of manufacturing billions of doses of high-quality vaccines is under-appreciated at the moment. A massive vaccination drive would be needed to protect people of all ages. The timely and coordinated execution of the vaccination effort would require unprecedented coordination at the national and international levels for generating funds to purchase the required doses of vaccines, fair distribution of doses and managing the mechanics of delivering vaccines throughout the world.

14.
Molecules ; 26(12)2021 Jun 16.
Article in English | MEDLINE | ID: covidwho-1282539

ABSTRACT

Furan-2-carboxylic acid was used as a starting material for the synthesis of dehydro-homopilopic acid. Esterification, hydrogenation and enzymatic hydrolysis followed by the reduction of Weinreb amides and a single-step attachment of a 1-methyl-imidazole residue allowed for the concise synthesis of both enantiomers of pilocarpine.


Subject(s)
4-Butyrolactone/analogs & derivatives , Furans/chemistry , Pilocarpine/chemical synthesis , 4-Butyrolactone/chemical synthesis , Amides/chemistry , Carboxylic Acids/chemistry , Esterification , Hydrogenation , Hydrolysis , Pilocarpine/chemistry , Stereoisomerism
15.
Int J Mol Sci ; 22(12)2021 Jun 08.
Article in English | MEDLINE | ID: covidwho-1266745

ABSTRACT

With advanced technology and its development, bioinformatics is one of the avant-garde fields that has managed to make amazing progress in the pharmaceutical-medical field by modeling the infrastructural dimensions of healthcare and integrating computing tools in drug innovation, facilitating prevention, detection/more accurate diagnosis, and treatment of disorders, while saving time and money. By association, bioinformatics and pharmacovigilance promoted both sample analyzes and interpretation of drug side effects, also focusing on drug discovery and development (DDD), in which systems biology, a personalized approach, and drug repositioning were considered together with translational medicine. The role of bioinformatics has been highlighted in DDD, proteomics, genetics, modeling, miRNA discovery and assessment, and clinical genome sequencing. The authors have collated significant data from the most known online databases and publishers, also narrowing the diversified applications, in order to target four major areas (tetrad): DDD, anti-microbial research, genomic sequencing, and miRNA research and its significance in the management of current pandemic context. Our analysis aims to provide optimal data in the field by stratification of the information related to the published data in key sectors and to capture the attention of researchers interested in bioinformatics, a field that has succeeded in advancing the healthcare paradigm by introducing developing techniques and multiple database platforms, addressed in the manuscript.


Subject(s)
Computational Biology , Drug Development , Drug Discovery , MicroRNAs , Microbiological Techniques/methods , Whole Genome Sequencing , Animals , COVID-19 , Drug Industry , Genome-Wide Association Study , Humans , Pharmacovigilance , Public Health
16.
J Infect Public Health ; 14(7): 938-946, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1213376

ABSTRACT

BACKGROUND: Since the SARS-CoV-2 outbreak in December 2019 in Wuhan, China, the virus has infected more than 153 million individuals across the world due to its human-to-human transmission. The USA is the most affected country having more than 32-million cases till date. Sudden high fever, pneumonia and organ failure have been observed in infected individuals. OBJECTIVES: In the current situation of emerging viral disease, there is no specific vaccine, or any therapeutics available for SARS-CoV-2, thus there is a dire need to design a potential vaccine to combat the virus by developing immunity in the population. The purpose of present study was to develop a potential vaccine by targeting B and T-cell epitopes using bioinformatics approaches. METHODS: B- and T-cell epitopes are predicted from novel M protein-SARS-CoV-2 for the development of a unique multiple epitope vaccine by applying bioinformatics approaches. These epitopes were analyzed and selected for their immunogenicity, antigenicity scores, and toxicity in correspondence to their ability to trigger immune response. In combination to epitopes, best multi-epitope of potential immunogenic property was constructed. The epitopes were joined using EAAAK, AAY and GPGPG linkers. RESULTS: The constructed vaccine showed good results of worldwide population coverage and promising immune response. This constructed vaccine was subjected to in-silico immune simulations by C-ImmSim. Chimeric protein construct was cloned into PET28a (+) vector for expression study in Escherichia coli using snapgene. CONCLUSION: This vaccine design proved effective in various computer-based immune response analysis as well as showed good population coverage. This study is solely dependent on developing M protein-based vaccine, and these in silico findings would be a breakthrough in the development of an effective vaccine to eradicate SARS-CoV-2 globally.


Subject(s)
COVID-19 , SARS-CoV-2 , China , Computational Biology , Epitopes, B-Lymphocyte , Humans , Molecular Docking Simulation , Spike Glycoprotein, Coronavirus
17.
Int J Infect Dis ; 104: 139-149, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-997022

ABSTRACT

BACKGROUND: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been proven to be lethal to human health, which affects almost every corner of the world. The objectives of this study were to add context to the global data and international genomic consortiums, and to give insight into the efficiency of the contact tracing system in Oman. METHODS: We combined epidemiological data and whole-genome sequence data from 94 samples of SARS-CoV-2 in Oman to understand the origins, genetic variation, and transmissibility. The whole-genome size of sequence data was obtained through a customized SARS-COV-2 research panel. Amplifier methods ranged from 26 Kbp to 30 Kbp and were submitted to GISAID. FINDINGS: The study found that P323L (94.7%) is the most common mutation, followed by D614G (92.6%) Spike protein mutation. A unique mutation, I280V, was first reported in Oman and was associated with a rare lineage, B.1.113 (10.6%). In addition, the study revealed a good agreement between genetic and epidemiological data. INTERPRETATION: Oman's robust surveillance system was very efficient in guiding the outbreak investigation processes in the country, the study illustrates the future importance of molecular epidemiology in leading the national response to outbreaks and pandemics.


Subject(s)
COVID-19/epidemiology , Genome, Viral/genetics , Pandemics , SARS-CoV-2/genetics , Adolescent , Adult , COVID-19/transmission , COVID-19/virology , Child , Child, Preschool , Epidemiological Monitoring , Female , Humans , Infant , Male , Middle Aged , Molecular Epidemiology , Mutation , Oman/epidemiology , Phylogeny , SARS-CoV-2/isolation & purification , Whole Genome Sequencing , Young Adult
18.
Phytother Res ; 35(6): 3013-3031, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-996303

ABSTRACT

In times of health crisis, including the current COVID-19 pandemic, the potential benefit of botanical drugs and supplements emerges as a focus of attention, although controversial efficacy claims are rightly a concern. Phytotherapy has an established role in everyday self-care and health care, but, since botanical preparations contain many chemical constituents rather than single compounds, challenges arise in demonstrating efficacy and safety. However, there is ample traditional, empirical, and clinical evidence that botanicals can offer some protection and alleviation of disease symptoms as well as promoting general well-being. Newly emerging viral infections, specifically COVID-19, represent a unique challenge in their novelty and absence of established antiviral treatment or immunization. We discuss here the roles and limitations of phytotherapy in helping to prevent and address viral infections, especially regarding their effects on immune response. Botanicals with a documented immunomodulatory, immunostimulatory, and antiinflammatory effects include adaptogens, Boswellia spp., Curcuma longa, Echinacea spp., Glycyrrhiza spp., medicinal fungi, Pelargonium sidoides, salicylate-yielding herbs, and Sambucus spp. We further provide a clinical perspective on applications and safety of these herbs in prevention, onset, progression, and convalescence from respiratory viral infections.


Subject(s)
COVID-19/drug therapy , Plant Preparations/pharmacology , Plants, Medicinal/chemistry , Dietary Supplements , Humans , Immunity/drug effects , Phytotherapy/methods , SARS-CoV-2/drug effects
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