Insilico study of COVID-19 ORF1ab protein allergenicity

Introduction: Vaccination has become a main tool in combat against coronavirus disease 2019 (COVID-19). ORF1ab (open reading frame1ab) is biggest ORF of severe acute respiratory disease coronavirus 2 (SARS-CoV-2) genome. Moreover ORF1ab protein is early translated in infected cells. Besides ORF1ab is genetically stable and could be a valuable source of conserved epitopes appropriate to prepare effective protein vaccines for control of many SARS-CoV-2 variants. Hypersensitivity responses to SARS-CoV-2 vaccines have been reported by numerous studies. Objective(s): In this study SARS-CoV-2 ORF1ab protein allergenicity was predicted by bioinformatic. Method(s): The amino acid sequences of SARS-CoV-2 ORF1ab protein were obtained in NCBI database at www.ncbi.nlm.nih.gov in FASTA format. Next, allergenicity of the SARS-CoV-2 ORF1ab protein was evaluated with Allergen FP server V.1. Result(s): ORF1ab protein of SARS-CoV-2 was found to be an allergen as was confirmed by allergen FP server V.1. Conclusion(s): According to our data, ORF1ab protein of COVID-19 was potentially allergenic. Hypersensitivity reactions to some SARS-CoV-2 vaccines reported by various studies may be partly due to ORF1ab protein allergenicity. Meanwhile ORF1ab protein being a valuable source of conserved epitopes is suitable to make efficient protein vaccines for control of many SARS-CoV-2 variants. For preparation of safe and effective anti- SARS-CoV-2 vaccines from ORF1ab protein, recognition and elimination of its allergenic epitope (s) is necessary. Altogether immunization with an allergenically engineered ORF1ab protein might have potential implication in fighting the virus.

Allergenic Effect of Facemasks Used Due To Covid-19 Pandemic

We aim to discuss the prevalence of adverse skin reactions to facemask among the community admitted to our hospital during the SARS outbreak. Between 2019 and 2020, 97 patients who developed an allergic reaction on their face in the SARS-CoV-2 pandemic were discussed. The average age of the patients was 37.7 (range 18-78), while the average age was 35.2 for males and 40.04 for females. While 13 (27.7%) of the male patients were using cloth masks, 34 (72.3%) of them were using surgical masks, 11 (22%) of the female patients were using cloth masks and 39 (78%) of them were using surgical masks.The combination of the female gender, additional disease, and surgical mask contributes to the development of allergic reactions on the face.Copyright © 2022 International Journal of Academic Medicine and Pharmacy. All rights reserved.

An Immunoinformatics Approach to Design Novel and Potent Multi-Epitope-Based Vaccine to Target Lumpy Skin Disease

The lumpy skin disease (LSD) virus of the Poxviridae family is a serious threat that mostly affects cattle and causes significant economic loss. LSD has the potential to spread widely and its rapidly across borders. Despite the availability of information, there is still no competitive vaccine available for LSD. Therefore, the current study was conducted to develop an epitope-based LSD vaccine that is efficient, secure, and biocompatible and stimulates both innate and adaptive immune responses using immunoinformatics techniques. Initially, putative virion core proteins were manipulated;B-cell and T-cell epitopes have been predicted and connected with the help of adjuvants and linkers. Numerous bioinformatics methods, including antigenicity testing, transmembrane topology screening, allergenicity assessment, conservancy analysis, and toxicity evaluation, were employed to find superior epitopes. Based on promising vaccine candidates and immunogenic potential, the vaccine design was selected. Strong interactions between TLR4 and TLR9 and the anticipated vaccine design were revealed by molecular docking. Finally, based on the high docking score, computer simulations were performed in order to assess the stability, efficacy, and compactness of the constructed vaccine. The simulation outcomes showed that the polypeptide vaccine design was remarkably stable, with high expression, stability, immunogenic qualities, and considerable solubility. Additionally, computer-based research shows that the constructed vaccine provides adequate population coverage, making it a promising candidate for use in the design of vaccines against other viruses within the Poxviridae family and potentially other virus families as well. These outcomes suggest that the epitope-based vaccine developed in this study will be a significant candidate against LSD to control and prevent LSDV-related disorders if further investigated experimentally.

Molecular characterization and prediction of B-cell epitopes for the development of SARS-CoV-2 vaccine through bioinformatics approach

Context: The SARS-CoV-2 virus is the cause of the COVID-19 pandemic, which is a severe public health crisis worldwide. Aims: To analyze the SARS-CoV-2 isolates of Surabaya and predict ORF1ab polyprotein epitopes through the bioinformatics approach for vaccine candidate development. Methods: Three genomic sequences of Surabaya isolates were obtained from the GISAID, NCBI and PDB Gen-bank databases and MEGA-11 software were used to understand the transformations in the isolates. The IEDB and VaxiJen, AllerTop, and ToxinPred web servers were used to predict B-cell epitopes and analyze their antigenicity, non-allergenicity, non-toxicity, respectively. Moreover, these epitopes were linked by EAAAK for 3D modeling, refinement, and validation through Swiss- Model, Galaxy Refine, and RAMPAGE web tools. Results: The Surabaya isolates, RSDS-RCVTD-UNAIR-49-A, 54-A, and 42-A, had 10, 20, and 16 mutations in nucleotides and depicted a phylogenetically close relationship to isolates of Egypt, Pakistan, and Bangladesh, respectively. A total of 71 sequential Orf1ab B-cell epitopes were predicted, and only three peptides were found to be antigenic, non-allergenic, and non-toxic. These epitopes were linked with the EAAAK linker to develop a 3D refined and validated structure. This construct was docked with TLR-3 receptor by the Cluspro webserver and found a high affinity of ORF1ab+TLR3 due to 15 hydrogen bonds. The construct demonstrated good humoral and cellular immune responses in the C-ImmSim server, and cloning in the expression vector pET28a (+) yielded a colon of 846bp. Conclusions: ORF1ab B-cell epitopes could be useful for developing effective vaccines to combat SARS-CoV-2 infection.

Climate change and allergies.

The climate crisis poses a major challenge to human health as well as the healthcare system and threatens to jeopardize the medical progress made in recent decades. However, addressing climate change may also be the greatest opportunity for global health in the 21st century. The climate crisis and its consequences, such as rising temperatures, forest fires, floods, droughts, and changes in the quality and quantity of food and water, directly and indirectly affect human physical and mental health. More intense and frequent heat waves and declining air quality have been shown to increase all-cause mortality, especially among the most vulnerable. Climate warming alters existing ecosystems and favors biological invasions by species that better tolerate heat and drought. Pathogen profiles are changing, and the transmission and spread of vector-borne diseases are increasing. The spread of neophytes in Europe, such as ragweed, is creating new pollen sources that increase allergen exposure for allergy sufferers. In addition, the overall milder weather, especially in combination with air pollution and increased CO2 levels, is changing the production and allergenicity of pollen. The phenomenon of thunderstorm asthma is also occurring more frequently. In view of the increasing prevalence of allergic diseases due to climate change, early causal immunomodulatory therapy is therefore all the more important. During a climate consultation, patients can receive individual advice on climate adaptation and resilience and the benefits of CO2 reduction-for their own and the planet's health. Almost 5% of all greenhouse gas emissions in Europe come from the healthcare sector. It thus has a central responsibility for a climate-neutral and sustainable transformation.

Immunogenic Epitope-Based Vaccine Prediction from Surface Glycoprotein of MERS-CoV by Deploying Immunoinformatics Approach.

Middle East respiratory syndrome coronavirus (MERS-CoV) has caused a high mortality rate since its emergence in 2012 in the Middle East. Currently, no effective drug or vaccine is available for MERS-CoV. Supportive care and prevention are the only ways to manage infection. In this study, we identified an epitope-based vaccine that could be an optimal solution for the prevention of MERS-CoV infection. By deploying an immunoinformatics approach, we predicted a subunit vaccine based on the surface glycoprotein (S protein) of MERS-CoV. For this purpose, the proteome of the MERS-CoV spike protein was obtained from the NCBI GenBank database. Then, it was subjected to a check for allergenicity using the Allergen FP v.1.0 tool. The Vaxijen v.2.0 tool was used to conduct antigenicity tests for binding with major histocompatibility complex class I and II molecules. The solidity of the predicted epitope-allele docked complex was evaluated by a molecular dynamics simulation. After docking a total of eight epitopes from the MERS-CoV S protein, further analyses predicted their non-toxicity and therapeutic immunogenic properties. These epitopes have potential utility as vaccine candidates against MERS-CoV, to be validated by wet-lab testing. Supplementary Information: The online version contains supplementary material available at 10.1007/s10989-022-10382-5.

Design of a multi-epitope-based peptide vaccine against the S and N proteins of SARS-COV-2 using immunoinformatics approach

Background: As the new pandemic created by COVID-19 virus created the need of rapid acquisition of a suitable vaccine against SARS-CoV-2 to develop Immunity and to reduce the mortality, the aim of this study was to identify SARS-CoV-2 S protein and N antigenic epitopes by using immunoinformatic methods to design a vaccine against SARS-CoV-2, for which S and N protein-dependent epitopes are predicted. B cell, CTL and HTL were determined based on antigenicity, allergenicity and toxicity that were non-allergenic, non-toxic, and antigenic and were selected for the design of a multi-epitope vaccine structure. Then, in order to increase the safety of Hbd-3 and Hbd-2 as adjuvants, they were connected to the N and C terminals of the vaccine construct, respectively, with a linker. The three-dimensional structure of the structure was predicted and optimized, and its quality was evaluated. The vaccine construct was ligated to MHCI. Finally, after optimizing the codon to increase expression in E. coli K12, the vaccine construct was cloned into pET28a (+) vector. Results: Epitopes which were used in our survey were based on non-allergenic, non-toxic and antigenic. Therefore, 543-amino-acid-long multi-epitope vaccine formation was invented through linking 9 cytotoxic CTL, 5 HTL and 14 B cell epitopes with appropriate adjuvants and connectors that can control the SARS coronavirus 2 infection and could be more assessed in medical scientific researches. Conclusion: We believe that the proposed multi-epitope vaccine can effectively evoke an immune response toward SARS-CoV-2.

Allergenic Effect of Facemasks Used Due To Covid-19 Pandemic

We aim to discuss the prevalence of adverse skin reactions to facemask among the community admitted to our hospital during the SARS outbreak. Between 2019 and 2020, 97 patients who developed an allergic reaction on their face in the SARS-CoV-2 pandemic were discussed. The average age of the patients was 37.7 (range 18-78), while the average age was 35.2 for males and 40.04 for females. While 13 (27.7%) of the male patients were using cloth masks, 34 (72.3%) of them were using surgical masks, 11 (22%) of the female patients were using cloth masks and 39 (78%) of them were using surgical masks.The combination of the female gender, additional disease, and surgical mask contributes to the development of allergic reactions on the face.

Targeting mucormycosis polyprotein (RVT_1 region) through antifungal phytochemicals: An in-silico perspective

Mucormycosis has become a global issue due to its potential to infect and destroy organs, as well as its high fatality rate. Co-infecting with Covid 19 or when infecting after Covid 19, it becomes more lethal. Several antifungal medicines have been utilized to treat this illness, but they come with a slew of dangerous side effects. Hence, using various computational tools;the current study was attempted to determine several antifungal plant metabolites that can act as inhibitory agents of Rhizopus oryzae, which is responsible for 70% of mucormycosis cases. In total, 56 antifungal plant metabolites were evaluated against Rhizopus oryzae polyprotein (RVT_1 region). Four metabolites, i.e., emetine, jatrorrhizine, isoboldine, and 6-a-hydroxymedicarpin showed maximum binding affinity with the targeted polyprotein (RVT_1 region) according to the lowest global binding energy and binding energy. The fungal protein's critical binding sites and drug surface hotspots were uncovered. The best candidates were gone through an ADME (absorption, distribution, metabolism, and excretion) analysis to observe their drug profiles. According to the findings, none have any side effects that could interfere with their drug likeness efficiency as well as no significant toxic effects and allergenicity were found. The majority of the target classes for proposed drug candidates were enzyme groups (e.g., oxidoreductase, family a g protein-coupled receptor, enzyme, protease). Furthermore, emetine and jatrorrhizine have been proposed to have inhibitory potency against covid 19 in several studies. Hence, we strongly propose additional in vivo trials in order to experimentally validate our findings, based on the optimistic results.

The effect of atmospheric pollutants on the grass pollen allergenicity

Background: Grass pollen is one of the most important allergen sources inducing respiratory allergies and Phl p 5 allergen of timothy pollen is considered one of the major parts of the allergenic activity of grass pollen. In this study, we evaluated seasonal variation in the concentration of both grass pollen and Phl p 5 allergens as well as the ratio allergen/pollen (pollen potency) in the air of Bratislava, Slovakia during two consecutive years, 2019-2020. These two years differed in terms of air pollution, as COVID-19 lockdown in 2020 improved air quality in a very emphatic manner in the study area. Therefore, the goal of this research was also to determine how environmental factors affect airborne pollen and aeroallergen levels and pollen potency. Method: Pollen sampling was performed using a Hirst-type sampler, while a cyclone sampler was used for the aeroallergen capturing. Allergenic molecules were quantified by ELISA assay. Results: In 2020, the year characterised by a less polluted atmosphere due to COVID-19 lockdown, we observed significantly higher Seasonal Poaceae Pollen Integral, the mean daily pollen value and even peak pollen value, while the mean daily pollen potency, the mean daily allergen concentration and peak allergen value were significantly lower than in 2019. Raised pollen concentrations were accompanied by increased ozone and carbon monoxide levels in 2020, whereas increased rainfall or relative humidity led to the reduction of pollen in the atmosphere. In 2020, the aeroallergen levels were associated mainly with pollen, but nitrogen dioxide in the air could increase the number of allergens per pollen. In contrast, the aeroallergen levels were associated with carbon monoxide in 2019. Conclusion: Based on our results it is evident that air pollutants can influence grass plants to produce pollen with altered allergenic content.

Viroinformatics investigation of B-cell epitope conserved region in SARSCoV-2 lineage B.1.1.7 isolates originated from Indonesia to develop vaccine candidate against COVID-19

Context: SARS-CoV-2, a member of family Coronaviridae and the causative agent of COVID-19, is a virus which is transmitted to human and other mammals. Aims: To analyze the B-cell epitope conserved region and viroinformatics-based study of the SARS-CoV-2 lineage from Indonesian B.1.1.7 isolates to invent a vaccine nominee for overcoming COVID-19. Methods: The sequences of seven Indonesian B.1.1.7 isolates, Wuhan-Hu- 1 isolate, and WIV04 isolate were extracted from the GISAID EpiCoV and GenBank, NCBI. MEGA X was employed to understand the transformations of amino acid in the S protein and to develop a molecular phylogenetic tree. The IEDB was implemented to reveal the linear B-cell epitopes. In addition, PEP-FOLD3 web server was utilized to perform peptide modeling, while docking was performed using PatchDock, FireDock, and the PyMOL software. Moreover, in silico cloning was developed by using SnapGene v.3.2.1 software. Results: In this study, the changes of amino acid in all seven Indonesian B.1.1.7 isolates were uncovered. Furthermore, various peptides based on the B-cell epitope prediction, allergenicity prediction, toxicity prediction from S protein to generate a vaccine contrary to SARS-CoV-2 were identified. Furthermore, the development of in silico cloning using pET plasmid was successfully achieved. Conclusions: This study exhibits the transformations of amino acid in Indonesian B.1.1.7 isolates, and proposes four peptides ("LTPGDSSSGWTAG", "VRQIAPGQTGKIAD", "ILPDPSKPSKRS", and "KNHTSPDVDLG") from S protein as the candidate for a peptide-based vaccine. However, further advance trials such as in vitro and in vivo testing are involved for validation.

SARS-CoV-2: Origin, Intermediate Host and Allergenicity Features and Hypotheses.

The goal of this study is to investigate the probable intermediate hosts and the allergenicity of the notorious virus SARS-CoV-2 to understand how this virus emerged. The phylogenetic analysis of the virus spike proteins indicates that SARS-CoV-2 falls into various small subclades that include a bat coronavirus RaTG13, suggesting bats as a likely natural origin. Refined alignment of the spike protein in NCBI found several fragments that are specific to SARS-CoV-2 and/or SARS-CoV are specific to Rattus norvegicus and/or Mus musculus, suggesting that rodents are the intermediate reservoir of SARS-CoV-2 and SARS-CoV. To evaluate the allergenicity values, the binding affinities of human leukocyte antigen (HLA) class I or II molecules with the spike proteins were calculated, and the results showed that both SARS-CoV-2 and SARS-CoV are predicted to bind to fourteen HLA class I and II molecules with super-high HLA allele-peptide affinities. The infection rate of individuals who have HLA alleles with very high binding affinities who might become infected and develop into refractory patients if there were no medical or non-medical interventions is about 7.36% and 4.78% of Chinese and Americans, respectively. Extremely high temperature and exceptionally low precipitation, the common climate factors between the outbreak sites of COVID-19 in Wuhan in 2019 and SARS in Guangdong in 2002, might have promoted coronavirus evolution into more virulent forms. Our hypothesis suggests that early immunization with an allergenically-engineered virus, in combination with continued surveillance of meteorological factors and viral mutations, may be one of the most powerful prophylactic modalities to fight this virus.

Design of an epitope-based peptide vaccine against the SARS-CoV-2: a vaccine-informatics approach.

The recurrent and recent global outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has turned into a global concern which has infected more than 42 million people all over the globe, and this number is increasing in hours. Unfortunately, no vaccine or specific treatment is available, which makes it more deadly. A vaccine-informatics approach has shown significant breakthrough in peptide-based epitope mapping and opens the new horizon in vaccine development. In this study, we have identified a total of 15 antigenic peptides [including thymus cells (T-cells) and bone marrow or bursa-derived cells] in the surface glycoprotein (SG) of SARS-CoV-2 which is nontoxic and nonallergenic in nature, nonallergenic, highly antigenic and non-mutated in other SARS-CoV-2 virus strains. The population coverage analysis has found that cluster of differentiation 4 (CD4+) T-cell peptides showed higher cumulative population coverage over cluster of differentiation 8 (CD8+) peptides in the 16 different geographical regions of the world. We identified 12 peptides ((LTDEMIAQY, WTAGAAAYY, WMESEFRVY, IRASANLAA, FGAISSVLN, VKQLSSNFG, FAMQMAYRF, FGAGAALQI, YGFQPTNGVGYQ, LPDPSKPSKR, QTQTNSPRRARS and VITPGTNTSN) that are $80\hbox{--} 90\%$ identical with experimentally determined epitopes of SARS-CoV, and this will likely be beneficial for a quick progression of the vaccine design. Moreover, docking analysis suggested that the identified peptides are tightly bound in the groove of human leukocyte antigen molecules which can induce the T-cell response. Overall, this study allows us to determine potent peptide antigen targets in the SG on intuitive grounds, which opens up a new horizon in the coronavirus disease (COVID-19) research. However, this study needs experimental validation by in vitro and in vivo.

In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives.

Growing evidence suggests that T cells may play a critical role in combating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Hence, COVID-19 vaccines that can elicit a robust T cell response may be particularly important. The design, development and experimental evaluation of such vaccines is aided by an understanding of the landscape of T cell epitopes of SARS-CoV-2, which is largely unknown. Due to the challenges of identifying epitopes experimentally, many studies have proposed the use of in silico methods. Here, we present a review of the in silico methods that have been used for the prediction of SARS-CoV-2 T cell epitopes. These methods employ a diverse set of technical approaches, often rooted in machine learning. A performance comparison is provided based on the ability to identify a specific set of immunogenic epitopes that have been determined experimentally to be targeted by T cells in convalescent COVID-19 patients, shedding light on the relative performance merits of the different approaches adopted by the in silico studies. The review also puts forward perspectives for future research directions.

Vaccine Design from the Ensemble of Surface Glycoprotein Epitopes of SARS-CoV-2: An Immunoinformatics Approach.

The present study aimed to work out a peptide-based multi-epitope vaccine against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We predicted different B-cell and T-cell epitopes by using the Immune Epitopes Database (IEDB). Homology modeling of the construct was done using SWISS-MODEL and then docked with different toll-like-receptors (TLR4, TLR7, and TLR8) using PatchDock, HADDOCK, and FireDock, respectively. From the overlapped epitopes, we designed five vaccine constructs C1-C5. Based on antigenicity, allergenicity, solubility, different physiochemical properties, and molecular docking scores, we selected the vaccine construct 1 (C1) for further processing. Docking of C1 with TLR4, TLR7, and TLR8 showed striking interactions with global binding energy of -43.48, -65.88, and -60.24 Kcal/mol, respectively. The docked complex was further simulated, which revealed that both molecules remain stable with minimum RMSF. Activation of TLRs induces downstream pathways to produce pro-inflammatory cytokines against viruses and immune system simulation shows enhanced antibody production after the booster dose. In conclusion, C1 was the best vaccine candidate among all designed constructs to elicit an immune response SARS-CoV-2 and combat the coronavirus disease (COVID-19).

A SARS-CoV-2 vaccine candidate: In-silico cloning and validation.

SARS-CoV-2 is spreading globally at a rapid pace. To contain its spread and prevent further fatalities, the development of a vaccine against SARS-CoV-2 is an urgent prerequisite. Thus, in this article, by utilizing the in-silico approach, a vaccine candidate for SARS-CoV-2 has been proposed. Moreover, the effectiveness and safety measures of our proposed epitopic vaccine candidate have been evaluated by in-silico tools and servers (AllerTOP and AllergenFP servers). We observed that the vaccine candidate has no allergenicity and successfully combined with Toll-like receptor (TLR) protein to elicit an inflammatory immune response. Stable, functional mobility of the vaccine-TLR protein binding interface was confirmed by the Normal Mode Analysis. The in-silico cloning model demonstrated the efficacy of the construct vaccine along with the identified epitopes against SARS-CoV-2. Taken together, our proposed in-silico vaccine candidate has potent efficacy against COVID-19 infection, and successive research work might validate its effectiveness in in vitro and in vivo models.