Analysis of highly frequent point mutations in glycoprotein C, glycoprotein N, and nucleoprotein of CCHFV

Crimean-Congo hemorrhagic fever virus (CCHFV) is classified among top 10 priority pathogens by World Health Organization. CCHFV belongs to Bunyaviridae family and negative sense ssRNA genome composed of three RNA segments: L, M, and S. RNA viruses show higher mutation rate as compared to DNA viruses. To gain deeper understanding of impact of point mutations in CCHFV M and S segment, mutation profiling, homology modeling, and molecular dynamic (MD) simulation were performed. Structural glycoproteins (glycoprotein C [Gc] and glycoprotein N [Gn]) of CCHFV are important for host-virus interaction and genome packaging, whereas CCHFV nucleoprotein (NP) is crucial for viral replication. Hence, current study is focused on evaluation of eight mutations in structural glycoproteins (Gc: 7 and Gn: 1) of M segment and seven mutations in NP of S segment. All these mutations were highly frequent, with mutation frequency between 0.81 and 1.0 and found to be persistent in the recent strains of CCHFV. Solubility analysis predicted that selected point mutations reduce solubility of Gc protein and increase solubility of Gn and NP proteins. MD simulation study deciphered that A1046V and G1158E in Gc protein, I778T in Gn protein, and H195R in NP protein displayed large deviation and fluctuation, and affected intramolecular interactions. In conclusion, we observed that point mutations could impact structure, stability, and host-virus interaction of protein, and might lead to evolution of new strains for better survival and drug resistance.

Zika virus precursor membrane peptides induce immune response in peripheral blood mononuclear cells

Zika virus is a re-merging flavivirus allied to serious mental health conditions in the fetuses. There is currently no preventives or treatment available for Zika infection. In this work, we have extended the in silico analysis by performing the molecular docking of previous reported three conserved Zika virus precursor membrane (prM) peptides (MP1, MP2 and MP3) with HLA complex (pHLA) and T cell receptors (TCR) and also evaluated the peptide specific immune response in human peripheral blood mononuclear cells (PBMC). Most of the CD8+ and CD4+ T cell peptides-HLA complexes demonstrated good binding energies (ΔG) and HADDOCK scores in molecular docking analysis. Immunogenic response of peptides is measured as human peripheral blood mononuclear cell (PBMC) proliferation and interferon-gamma (IFN-γ) production using a 3-(4,5- dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay and a sandwich enzyme-linked immunosorbent assay (ELISA) respectively on ten different healthy blood samples. Peptide MP3 exhibited significant results in eight (cell proliferation) and seven (IFN-γ secretion) healthy volunteers' blood samples out of ten. Additionally, peptides MP1 and MP2 presented significant cell proliferation and IFN-γ release in six healthy blood samples. Thus, the outcomes from in silico and in vitro studies showed the immunogenic potential of peptides which need to validated in different experimental system before considering as candidate vaccine against Zika virus infection.

Understanding immune checkpoints and PD-1/PD-L1-mediated immune resistance towards tumour immunotherapy

Immunotherapy has emerged as a transformative approach in the treatment of various cancers, offering new hope for patients previously faced with limited treatment options. A cornerstone of cancer immunotherapy lies in targeting immune checkpoints, particularly the programmed cell death protein-1 (PD-1) and programmed death-ligand 1 (PD-L1) pathway. Immune checkpoints serve as crucial regulators of the immune response, preventing excessive immune activity and maintaining self-tolerance. PD-1, expressed on the surface of T cells, and its ligand PD-L1, expressed on various cell types, including cancer cells and immune cells, play a central role in this regulatory process. Although the success rate associated with these immunotherapies is very promising, most patients still show intrinsic or acquired resistance. Since the mechanisms related to PD-1/PD-L1 resistance are not well understood, an in-depth analysis is necessary to improve the success rate of anti-PD-1/PD-L1 therapy. Hence, here we provide an overview of PD-1, its ligand PD-L1, and the resistance mechanism towards PD-1/PD-L1. Furthermore, we have discussed the plausible solution to increase efficacy and clinical response. For the following research, joint endeavours of clinicians and basic scientists are essential to address the limitation of resistance towards immunotherapy.

Assessment of kinetic and statistical models for predicting breakthrough curves of bio-colloid transport through saturated porous media

The microbial contamination of groundwater and its prevention is a widespread concern in developing countries. The present study simulated the transportation and interception of bio-colloid, Escherichia coli in porous media experimentally using packed columns to address certain aspects of underexplored sorption potential and validated using several kinetic models. The breakthrough curves obtained through experiments are observed to be in good agreement with its prediction using kinetic models namely Thomas, Yoon-Nelson and Modified Dose-Response. The overall comparisons of R2 among all the three models suggest that the MDR model fits more perfectly to experimental results. The combined effect of independent factors (column depth, particle size and alumina content) on response factors (maximum relative concentration and time required to achieve peak concentration) was investigated by using Box-Behnken Design under Response Surface Methodology (RSM) to check statistical significancy of independent factors. The R2 values for both response factors are observed to be 0.94 and 0.99, indicating a very high correlation between predicted and actual values. The results obtained in the present study also confirms that the travel distance and particle size are the statistically significant parameters that efficiently impact on sorption of Escherichia coli during their transport whereas the alumina content also affects the sorption but is observed to be a statistically non-significant.

Immunoinformatics-Based Identification of the Conserved Immunogenic Peptides Targeting of Zika Virus Precursor Membrane Protein

Zika virus infections lead to neurological complications such as congenital Zika syndrome and Guillain-Barré syndrome. Rising Zika infections in newborns and adults have triggered the need for vaccine development. In the current study, the precursor membrane (prM) protein of the Zika virus is explored for its functional importance and design of epitopes enriched conserved peptides with the usage of different immunoinformatics approach. Phylogenetic and mutational analyses inferred that the prM protein is highly conserved. Three conserved peptides containing multiple T and B cell epitopes were designed by employing different epitope prediction algorithms. IEDB population coverage analysis of selected peptides in six different continents has shown the population coverage of 60-99.8% (class I HLA) and 80-100% (class II HLA). Molecular docking of selected peptides/epitopes was carried out with each of class I and II HLA alleles using HADDOCK. A majority of peptide-HLA complex (pHLA) have HADDOCK scores found to be comparable and more than native-HLA complex representing the good binding interaction of peptides to HLA. Molecular dynamics simulation with best docked pHLA complexes revealed that pHLA complexes are stable with RMSD <5.5Å. Current work highlights the importance of prM as a strong antigenic protein and selected peptides have the potential to elicit humoral and cell-mediated immune responses.

Identification of conserved immunogenic peptides of SARS-CoV-2 nucleocapsid protein

The emergence of the new SARS-CoV-2 variants has led to major concern regarding the efficacy of approved vaccines. Nucleocapsid is a conserved structural protein essential for replication of the virus. This study focuses on identifying conserved epitopes on the nucleocapsid (N) protein of SARS-CoV-2. Using 510 unique amino acid sequences of SARS-CoV-2 N protein, two peptides (193 and 215 aa) with 90% conservancy were selected for T cell epitope prediction. Three immunogenic peptides containing multiple T cell epitopes were identified which were devoid of autoimmune and allergic immune response. These peptides were also conserved (100%) in recent Omicron variants reported in Jan-August 2023. HLA analysis reveals that these peptides are predicted as binding to large number of HLA alleles and 71-90% population coverage in six continents. Identified peptides displayed good binding score with both HLA class I and HLA class II molecules in the docking study. Also, a vaccine construct docked with TLR-4 receptor displays strong interaction with 20 hydrogen bonds and molecular simulation analysis reveals that docked complex are stable. Additionally, the immunogenicity of these N protein peptides was confirmed using SARS-CoV-2 convalescent serum samples. We conclude that the identified N protein peptides contain highly conserved and antigenic epitopes which could be used as a target for the future vaccine development against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Machine learning-based ensemble approach in prediction of lung cancer predisposition using XRCC1 gene polymorphism

The employment of machine learning approaches has shown promising results in predicting cancer. In the current study, polymorphisms data of five single nucleotide polymorphisms (SNPs) of DNA repair gene XRCC1 (XRCC1 399, XRCC1 194, XRCC1 206, XRCC1 632, XRCC1 280) of the north Indian population along with four smoking status data is considered as an input to the proposed ensemble model to predict the risk of individual susceptibility to the lung cancer. The prediction accuracy of the proposed ensemble model for cancer predisposition was found to be 85%. The model performance is also evaluated using sensitivity, specificity, precision and the Gini index, which is found in the range of 0.83-0.87. The proposed model also outperformed in all evaluation parameters when compared with the individual Model (LM, SVM, RF, KNN and baseline neural net). Collectively, current results suggest the potential of the proposed ensemble model in predicting the risk of cancer based on XRCC1 SNPs data.Communicated by Ramaswamy H. Sarma.

Hemorrhagic Fever with Renal Syndrome in Asia: History, Pathogenesis, Diagnosis, Treatment, and Prevention

Hemorrhagic Fever with Renal Syndrome (HFRS) is the most frequently diagnosed zoonosis in Asia. This zoonotic infection is the result of exposure to the virus-contaminated aerosols. Orthohantavirus infection may cause Hemorrhagic Fever with Renal Syndrome (HRFS), a disease that is characterized by acute kidney injury and increased vascular permeability. Several species of orthohantaviruses were identified as causing infection, where Hantaan, Puumala, and Seoul viruses are most common. Orthohantaviruses are endemic to several Asian countries, such as China, South Korea, and Japan. Along with those countries, HFRS tops the list of zoonotic infections in the Far Eastern Federal District of Russia. Recently, orthohantavirus circulation was demonstrated in small mammals in Thailand and India, where orthohantavirus was not believed to be endemic. In this review, we summarized the current data on orthohantaviruses in Asia. We gave the synopsis of the history and diversity of orthohantaviruses in Asia. We also described the clinical presentation and current understanding of the pathogenesis of orthohantavirus infection. Additionally, conventional and novel approaches for preventing and treating orthohantavirus infection are discussed.

Seasonal Changes in Serum Metabolites in Multiple Sclerosis Relapse

Multiple sclerosis (MS) is a debilitating chronic disease of unknown etiology. There are limited treatment options due to an incomplete understanding of disease pathology. The disease is shown to have seasonal exacerbation of clinical symptoms. The mechanisms of such seasonal worsening of symptoms remains unknown. In this study, we applied targeted metabolomics analysis of serum samples using LC-MC/MC to determine seasonal changes in metabolites throughout the four seasons. We also analyzed seasonal serum cytokine alterations in patients with relapsed MS. For the first time, we can demonstrate seasonal changes in various metabolites in MS compared to the control. More metabolites were affected in MS in the fall season followed by spring, while summer MS was characterized by the smallest number of affected metabolites. Ceramides were activated in all seasons, suggesting their central role in the disease pathogenesis. Substantial changes in glucose metabolite levels were found in MS, indicating a potential shift to glycolysis. An increased serum level of quinolinic acid was demonstrated in winter MS. Histidine pathways were affected, suggesting their role in relapse of MS in the spring and fall. We also found that spring and fall seasons had a higher number of overlapping metabolites affected in MS. This could be explained by patients having a relapse of symptoms during these two seasons.

Epidemiology of Ebolaviruses from an Etiological Perspective

Since the inception of the ebolavirus in 1976, 32 outbreaks have resulted in nearly 15,350 deaths in more than ten countries of the African continent. In the last decade, the largest (2013-2016) and second largest (2018-2020) ebolavirus outbreaks have occurred in West Africa (mainly Guinea, Liberia, and Sierra Leone) and the Democratic Republic of the Congo, respectively. The 2013-2016 outbreak indicated an alarming geographical spread of the virus and was the first to qualify as an epidemic. Hence, it is imperative to halt ebolavirus progression and develop effective countermeasures. Despite several research efforts, ebolaviruses' natural hosts and secondary reservoirs still elude the scientific world. The primary source responsible for infecting the index case is also unknown for most outbreaks. In this review, we summarize the history of ebolavirus outbreaks with a focus on etiology, natural hosts, zoonotic reservoirs, and transmission mechanisms. We also discuss the reasons why the African continent is the most affected region and identify steps to contain this virus.

Structural, functional analysis and association of MSH6 rs1800932, rs1042821 polymorphisms with clinical outcome in North Indian lung cancer patients treated with platinum-based doublet chemotherapy

BACKGROUND

In this study, we have done structural and functional analysis of rs1800932 rs1042821 polymorphisms and tried to estimate any association of these polymorphisms with clinical outcomes in north Indian lung cancer patients.

METHODS

Genotyping of 500 lung cancer patients was completed utilizing PCR-RFLP (Polymerase chain reaction- Restriction fragment length polymorphism). MedCalc statistical software was used to calculate adjusted and unadjusted odds ratios. Various computational tools like SIFT PROVEAN are used for functional analysis. Structural analysis was completed via MODELLER and CHIMERA.

RESULTS

In our study, patients suffering from small cell lung cancer (SCLC) and harboring heterozygous genotype (AG) for MSH6 (rs1800932) polymorphism have reported a significant increase in median survival time (MST) (20.6 vs. 7.6 months, p = 0.03). Furthermore, for MSH6 rs1042821 polymorphism, patients undergoing docetaxel and carbo/cisplatin combination chemotherapeutic regimen and carrying heterogeneous genotype (CT) reported a significant increase in MST (16.6 vs.8.36 months, p = 0.03) and a corresponding decrease in hazard ratio 0.42 (95% CI= 0.18-1.03). Structural and Functional analysis of rs1042821 polymorphism revealed that it is present in the non-coding region of MSH6 protein and is significantly associated with increased overall survival.

CONCLUSIONS

These results suggest that MSH6 rs1800932 rs1042821 polymorphisms are involved in increasing the overall survival of lung cancer patients, further confirmed by computational analysis.

Identification of SNPs in hMSH3/MSH6 interaction domain affecting the structure and function of MSH2 protein

MutS homolog 2 (MSH2) is a mismatch repair gene that plays a critical role in DNA repair pathways, and its mutations are associated with different cancers. The present study aimed to find out the single nucleotide polymorphisms (SNPs) of MSH2 protein associated with causing structural and functional changes leading to the development of cancer with the help of computational tools. Four different tools for predicting deleterious SNPs (SIFT, PROVEAN, PANTHER, and PolyPhen), two tools each for identifying disease association (PhD-SNP and SNP&GO) and estimating stability (I-mutant and MUPro) were employed. Homology modeling, energy minimization, and root mean square deviation calculation were used to estimate structural variations. Twenty-seven SNPs and five SNPs (double amino acid change) were identified based on a consensus approach that might be associated with the structural and functional change in MSH2 protein. Molecular docking reveals that six SNPs affect the interaction of MSH2 and MSH6. Twelve identified SNPs were reported to be linked with hereditary nonpolyposis, colorectal cancer, and Lynch syndrome. Further, selected SNPs need to be validated in an in vitro system for their precise association with cancer predisposition.

Advancement in magnetic hyperthermia-based targeted therapy for cancer treatment

Magnetic hyperthermia utilizing magnetic nanoparticles (MNPs) and an alternating magnetic field (AMF) represents a promising approach in the field of cancer treatment. Active targeting has emerged as a valuable strategy to enhance the effectiveness and specificity of drug delivery. Active targeting utilizes specific biomarkers that are predominantly found in abundance on cancer cells while being minimally expressed on healthy cells. Current comprehensive review provides an overview of several cancer-specific biomarkers, including human epidermal growth factor, transferrin, folate, luteinizing hormone-releasing hormone, integrin, cluster of differentiation (CD) receptors such as CD90, CD95, CD133, CD20, and CD44 also CXCR4 and vascular endothelial growth factor, these biomarkers bind to ligands present on the surface of MNPs, enabling precise targeting. Additionally, this review touches various combination therapies employed to combat cancer. Magnetic hyperthermia synergistically enhances the efficacy of conventional cancer treatments such as targeted chemotherapy, radiation therapy, gene therapy, and immunotherapy.

Autoreactive lymphocytes in multiple sclerosis: Pathogenesis and treatment target

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) characterized by destruction of the myelin sheath structure. The loss of myelin leads to damage of a neuron’s axon and cell body, which is identified as brain lesions on magnetic resonance image (MRI). The pathogenesis of MS remains largely unknown. However, immune mechanisms, especially those linked to the aberrant lymphocyte activity, are mainly responsible for neuronal damage. Th1 and Th17 populations of lymphocytes were primarily associated with MS pathogenesis. These lymphocytes are essential for differentiation of encephalitogenic CD8⁺ T cell and Th17 lymphocyte crossing the blood brain barrier and targeting myelin sheath in the CNS. B-lymphocytes could also contribute to MS pathogenesis by producing anti-myelin basic protein antibodies. In later studies, aberrant function of Treg and Th9 cells was identified as contributing to MS. This review summarizes the aberrant function and count of lymphocyte, and the contributions of these cell to the mechanisms of MS. Additionally, we have outlined the novel MS therapeutics aimed to amend the aberrant function or counts of these lymphocytes.

In vitro evaluation of bioactive properties of banana sap

Banana sap is currently designated as a waste subsequent to utilization of pseudo stem in pulp and paper industry as well as other applications which is contributing to the environmental pollution. In the present study, banana sap and its crude extracts were evaluated for antimicrobial, antioxidant and anticancer properties. The role of oxidized and un-oxidized banana sap for its antimicrobial potential against a microbial test panel comprising gram positive as well as gram negative bacteria and Candida albicans using in vitro micro broth dilution assay. The un-oxidized banana sap exhibited a significantly higher antibacterial potential as evident by a lower minimal inhibitory concentration (MIC) ranging between 15.625 to 62.5 mg/mL. In vitro radical scavenging activity of dichloromethane (DCM) extract of banana sap by DPPH method exhibited 54.62 ± 1.09 (µg/mL) IC₅₀ value at the concentration of 1 mg/mL. Dichloromethane extract of banana sap showed maximum cytotoxic effect with human breast cancer (MCF-7) cell proliferation at the concentration of 100 µg/mL which was 78.37 ± 0.05% and the cytotoxic effect significantly increased with increasing concentration of banana sap extract. Furthermore, LCMS studies revealed the presence of bioactive compounds in dichloromethane extract of banana sap, such as rescinnamine derivative, dihydrorescinnamine and epimedin A. The present study suggested that banana sap is a promising source of bioactive compounds with relevant antimicrobial, antioxidant and anticancer properties.

Computational design of immunogenic peptide constructs comprising multiple HLA restricted Dengue virus envelope epitopes

Dengue virus (DENV) is endemic in 100 countries with ability to impact nearly 50% of world population. DENV envelope (E) protein is responsible for viral attachment to host cells and has been target of various countermeasure development efforts. The current study focuses on a consensus computational approach to identify cross-reactive, immunogenic DENV-2 E peptides displaying promiscuity with a wide array of HLA molecules. Four conserved peptides (FP-1, FP-2, FP-3 and FP-4) containing multiple CD8⁺ and CD4⁺ T cell epitopes were identified by employment of various immunoinformatics tools. FP-1, FP-2, FP-3 and FP-4 were estimated to bind with 227, 1787, 1008 and 834 HLA alleles respectively. RMSD values obtained by Molecular docking (CABS-Dock) with 20 HLA alleles (10 each of HLA class I and II) resulted into comparable RMSD values of identified epitopes with native peptides which represents the natural presentation of epitopes to HLA molecules. These peptides were also found to be part of previous experimentally validated immunogenic peptides. Further, a dengue immunogenic peptide construct was generated by linking the four peptides, an adjuvant and a 6x histidine tag. The construct showed strong binding and stability with Toll-like receptor (TLR4). Collectively, these results provide strong evidence in the support of the immunogenic potential of the dengue immunogenic peptide construct. This article is protected by copyright. All rights reserved.

Antibody and T Cell Immune Responses to SARS-CoV-2 Peptides in COVID-19 Convalescent Patients

Identifying immunogenic targets of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is critical to advance diagnostic and disease control strategies. We analyzed humoral (ELISA) and T-cell (ELISpot) immune responses to spike (S) and nucleocapsid (N) SARS-CoV-2 proteins as well as to human endemic coronavirus (eCoV) peptides in serum from convalescent coronavirus disease 2019 (COVID-19) patients from Tatarstan, Russia. We identified multiple SARS-CoV-2 peptides that were reactive with serum antibodies and T cells from convalescent COVID-19. In addition, age and gender associated differences in the reactivity to S and N protein peptides were identified. Moreover, several SARS-CoV-2 peptides tested negatively correlated with disease severity and lung damage. Cross-reactivity to eCoV peptides was analyzed and found to be lower in COVID-19 compared to controls. In this study, we demonstrate the changing pattern of immunogenic peptide reactivity in COVID-19 serum based on age, gender and previous exposure to eCoVs. These data highlight how humoral immune responses and cytotoxic T cell responses to some of these peptides could contribute to SARS-CoV-2 pathogenesis.

Immunogenic SARS-CoV-2 S and N Protein Peptide and Cytokine Combinations as Biomarkers for Early Prediction of Fatal COVID-19

Early indications of the likelihood of severe coronavirus disease 2019 COVID-19 can influence treatments and could improve clinical outcomes. However, knowledge on the prediction markers of COVID-19 fatality risks remains limited. Here, we analyzed and quantified the reactivity of serum samples from acute (non-fatal and fatal) and convalescent COVID-19 patients with the spike surface glycoprotein (S protein) and nucleocapsid phosphoprotein (N protein) SARS-CoV-2 peptide libraries. Cytokine activation was also analyzed. We demonstrated that IgM from fatal COVID-19 serum reacted with several N protein peptides. In contrast, IgM from non-fatal serum reacted more with S protein peptides. Further, higher levels of pro-inflammatory cytokines were found in fatal COVID-19 serum compared to non-fatal. Many of these cytokines were pro-inflammatory and chemokines. Differences in IgG reactivity from fatal and non-fatal COVID-19 sera were also demonstrated. Additionally, the longitudinal analysis of IgG reactivity with SARS-CoV-2 S and N protein identified peptides with the highest longevity in humoral immune response. Finally, using IgM antibody reactivity with S and N SARS-CoV-2 peptides and selected cytokines, we have identified a panel of biomarkers specific to patients with a higher risk of fatal COVID-19 compared with that of patients who survive. This panel could be used for the early prediction of COVID-19 fatality risk.

Polymorphisms in the MSH2 gene predict poor survival of North Indian lung cancer patients undergoing chemotherapy

Aim: To estimate if MSH2 polymorphisms, viz. rs63749993, rs2303425, rs2303426, rs4987188, rs2303428 and rs17217772, have any association with clinical outcomes in North Indian lung cancer patients. Materials & methods: PCR-RFLP was used for genotyping 500 cases. Logistic regression and survival analysis was performed by utilizing MedCalc software. Results & conclusion: Our study concluded, adenocarcinoma subjects having heterozygous genotype for rs2303425 have increased survival time (MST = 12.43, p = 0.03). In lung cancer patients undergoing paclitaxel therapy, heterozygous carriers for the rs17217772 polymorphism have reduced survival time (MST = 7.96 vs 2.63 months; HR = 2.09; p = 0.02). For rs63749993 polymorphism undergoing irinotecan therapy, subjects having mutant genotype showed poor survival (13.26 vs 6.06 months; HR = 5.37; p = 0.0004). The results suggest that MSH2 polymorphisms are involved in decreasing overall survival for patients undergoing platinum-based chemotherapy.

Association of MLH1-93G>A polymorphisms toward lung cancer susceptibility and its association with clinical outcome in North Indian patients treated with platinum-based chemotherapy

Background

Lung cancer is one of the most prevalent and main causes of malignancy-related deaths worldwide, especially in developed countries. Epidemiological studies have demonstrated that individuals having alterations in a particular gene may have a high risk of developing certain types of cancer.

Materials and Methods

In the present study, 500 Indian lung cancer patients and 500 healthy controls were enrolled. Polymerase chain reaction-restriction fragment length polymorphism method was used to identify the genotype of enrolled individuals and MedCalc statistical package was used for carrying out statistical analysis.

Results

In this study, we found a reduced risk of developing adenocarcinoma in patients harboring variant (P = 0.0007) and combined type genotype (P = 0.008), whereas an increased risk for small-cell lung carcinoma (SCLC) development for those subject harboring GA genotypes (P = 0.03) was also observed. Further, heterozygous type and combined type genotype of heavy smokers for MLH1 polymorphism reported a 2-fold (P = 0.001) and 1.8-fold increased risk toward lung cancer development, respectively (P = 0.007). In case of females, the subjects harboring a variant allele have a significantly reduced risk for lung cancer development (P = 0.0001). For MLH1 polymorphism, reduced risk of developing tumor to T3 or T4 stage was observed (P = 0.04). Moreover, this is the first study reporting overall survival (OS) association for north Indian lung cancer patients with platinum-based doublet chemotherapy; for docetaxel, a three-fold increase in hazard ratio and corresponding low median standard survival time (8.4 months) for mutant and combined type genotype (P = 0.04) was observed.

Conclusions

These results suggest that MLH1-93G>A polymorphism is involved in modulating the risk toward lung cancer. Our study also concluded a negative association of OS in patients undergoing carboplatin/cisplatin and docetaxel chemotherapy.

Antiinflammatory phytochemicals against virus-induced hyperinflammatory responses: Scope, rationale, application, and limitations

Uncontrolled inflammatory responses or cytokine storm associated with viral infections results in deleterious consequences such as vascular leakage, severe hemorrhage, shock, immune paralysis, multi-organ failure, and even death. With the emerging new viral infections and lack of effective prophylactic vaccines, evidence-based complementary strategies that limit viral infection-mediated hyperinflammatory responses could be a promising approach to limit host tissue injury. The present review emphasizes the potentials of antiinflammatory phytochemicals in limiting hyperinflammatory injury caused by viral infections. The predominant phytochemicals along with their mechanism in limiting hyperimmune and pro-inflammatory responses under viral infection have been reviewed comprehensively. How certain phytochemicals can be effective in limiting hyper-inflammatory response indirectly by favorably modulating gut microbiota and maintaining a functional intestinal barrier has also been presented. Finally, we have discussed improved systemic bioavailability of phytochemicals, efficient delivery strategies, and safety measures for effective antiinflammatory phytotherapies, in addition to emphasizing the requirement of tightly controlled clinical studies to establish the antiinflammatory efficacy of the phytochemicals. Collectively, the review provides a scooping overview on the potentials of bioactive phytochemicals to mitigate pro-inflammatory injury associated with viral infections.

Oxidative Stress Induced Cytotoxicity of Colloidal Copper Nanoparticles on RAW 264.7 Macrophage Cell Line

Copper is an essential trace mineral that plays an important role in various physiological processes of human body and also possesses excellent antimicrobial properties, however its high dose results in the formation of free-radicals, which can induce cytotoxicity through chromosomal and DNA damage. Therefore, cytotoxicity of colloidal copper nanoparticles (CuNPs) on murine macrophage cell line (RAW 264.7) was studied to understand the correlation between the cytotoxicity and the nanoparticle yield. Three identical sets of CuNPs with similar physical properties having hydrodynamic particle size of 11-14 nm were prepared by chemical reduction method with target yield of 0.2 g, 0.3 g and 0.4 g. CuNPs exhibited dose-dependent (0.001-100 μg/mL) cytotoxicity due to the mitochondrial damage as indicated by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide) assay. Oxidative stress induced by reactive oxygen species (ROS) in RAW 246.7 macrophage cell lines exposed to CuNPs was the primary cause of observed cytotoxicity in all CuNPs test samples. Morphological changes in cells also indicated strong dose-dependent oxidative damage by CuNPs. IC₅₀ (half maximal inhibitory concentration) values of CuNPs were independent of nanoparticle yield. This suggests that per batch variation in CuNPs yield from 0.2 g to 0.4 g had no negative correlation with their toxicity that makes CuNPs a potential candidate for further development of nanotherapeutics and anticancer drugs.

Conserved immunogenic peptides of Ebola glycoprotein elicit immune response in human peripheral blood mononuclear cells

In the past 45 years, ebolaviruses have periodically caused epidemics on the African continent. In December 2019, approval of a recombinant vector-based EBOV vaccine, named Ervebo, came as encouraging news; still, there is a long way to go in the development of an accessible, global, and pan-ebolavirus vaccine. The current study expanded our previous in silico work which was conducted on ebolavirus glycoprotein and this resulted in the identification of three potentially immunogenic peptides (P1 - FKRTSFFLWVIILFQRTFSIPL, P2 - LANETTQALQLF, and P3 - RATTELRTFSILNRKAIDF). An analysis to estimate the number of expected human leukocyte antigen (HLA) responders revealed that P1, P2, and P3 can potentially interact with 2540, 2150, and 2802 HLA alleles, respectively. Further, these peptides were subject to in vitro analysis wherein the human peripheral blood mononuclear cell proliferation and interferon-gamma (IFN-γ) production by peptide stimulated cells was studied in 10 healthy human blood samples with the help of a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay and a sandwich enzyme-linked immunosorbent assay (ELISA) respectively. P3 presented the best results, a significant (P < 0.05) peptide induced cell proliferation and IFN-γ stimulation for 8 and 10 samples, respectively, followed by P1 (5 and 6) and P2 (5 and 7). The in silico and in vitro results obtained in this study indicate the immunogenic potential of these peptides and warrant exploration of the effects on other cytokines as well as in vivo experimental validation.

Cytokine, Chemokine, and Metalloprotease Activation in the Serum of Patients with Nephropathia Epidemica from the Republic of Tatarstan and the Republic of Mordovia, Russia

Nephropathia Epidemica (NE), endemic to several Volga regions of Russia, including the Republic of Tatarstan (RT) and the Republic of Mordovia (RM), is a mild form of hemorrhagic fever with renal syndrome caused by infection with rodent-borne orthohantaviruses. Although NE cases have been reported for decades, little is known about the hantavirus strains associated with human infection in these regions. There is also limited understanding of the pathogenesis of NE in the RT and the RM. To address these knowledge gaps, we conducted comparative analyses of patients with NE in the RT and the RM. Clinical symptoms were more severe in patients with NE from the RM with longer observed duration of fever symptoms and hospitalization. Analysis of patient sera showed changes in the levels of numerous cytokines, chemokines, and matrix metalloproteases (MMPs) in patients with NE from both the RT and the RM, suggesting leukocyte activation, extracellular matrix degradation, and leukocyte chemotaxis. Interestingly, levels of several cytokines were distinctly different between patients NE from the RT when compared with those from the RM. These differences were not related to the genetic variation of orthohantaviruses circulating in those regions, as sequence analysis showed that Puumala virus (PUUV) was the causative agent of NE in these regions. Additionally, only the “Russia” (RUS) genetic lineage of PUUV was detected in the serum samples of patients with NE from both the RT and the RM. We therefore conclude that differences in serum cytokine, chemokine, and MMP levels between the RT and the RM are related to environmental factors and lifestyle differences that influence individual immune responses to orthohantavirus infection.

Scenedesmus acutus extracellular polysaccharides produced under increased concentration of sulphur and phosphorus exhibited enhanced proliferation of peripheral blood mononuclear cells

Exopolysaccharides (EPS) isolated from microalgae are promising immune cell proliferation agents, that could be potentially used as immunostimulants. In the current study, Scenedesmus acutus (S. acutus) was grown under varying nutrient (sulphur and phosphorus) concentrations to enhance the EPS production, and the isolated EPS were assessed for their effect on cell proliferation using peripheral blood mononuclear cells (PBMC). Five different concentrations of MgSO₄ (0, 0.25, 0.5, 1.0 and 1.25 g/L) and K₂HPO₄ (0, 0.2, 0.6, 0.8 and 1.0 g/L) were taken as compared to the normal culture conditions (0.75 g/L MgSO₄ and 0.4 g/L K₂HPO₄) with the intention to enrich EPS secretion. LC–MS, FTIR and NMR analysis revealed that isolated EPS have the characteristic spectrum of hetero-polysaccharides (octa-saccharides). Immunostimulatory property of EPS was demonstrated by their ability to augment PBMC proliferation as measured by MTT assay. Further, increase in the glucose content and proliferative index was observed for EPS obtained under higher concentrations of MgSO₄ (1 and 1.25 g/L) and K₂HPO₄ (0.6 and 0.8 g/L) relative to normal culture conditions. Effects of the generated EPS under varying concentration of MgSO₄ (r = 0.84–0.99) and K₂HPO₄ (r = 0.76–0.97) remained strongly correlated with cell count, chlorophyll content, total biomass, glucose, proliferative index and its scavenging activity. Collectively, our data not only showed that EPS generated by S. acutus under higher concentration of K₂HPO₄ and MgSO₄ possess improved immunostimulatory properties, but also provides convincing evidence towards nutritional optimization of alga for enhanced EPS production with better bioactivities.

Immunological Perspective for Ebola Virus Infection and Various Treatment Measures Taken to Fight the Disease

Ebolaviruses, discovered in 1976, belongs to the Filoviridae family, which also includes Marburg and Lloviu viruses. They are negative-stranded RNA viruses with six known species identified to date. Ebola virus (EBOV) is a member of Zaire ebolavirus species and can cause the Ebola virus disease (EVD), an emerging zoonotic disease that results in homeostatic imbalance and multi-organ failure. There are three EBOV outbreaks documented in the last six years resulting in significant morbidity (> 32,000 cases) and mortality (> 13,500 deaths). The potential factors contributing to the high infectivity of this virus include multiple entry mechanisms, susceptibility of the host cells, employment of multiple immune evasion mechanisms and rapid person-to-person transmission. EBOV infection leads to cytokine storm, disseminated intravascular coagulation, host T cell apoptosis as well as cell mediated and humoral immune response. In this review, a concise recap of cell types targeted by EBOV and EVD symptoms followed by detailed run-through of host innate and adaptive immune responses, virus-driven regulation and their combined effects contributing to the disease pathogenesis has been presented. At last, the vaccine and drug development initiatives as well as challenges related to the management of infection have been discussed.

Mutational Frequencies of SARS-CoV-2 Genome during the Beginning Months of the Outbreak in USA

SARS-CoV-2 has spread very quickly from its first reported case on 19 January 2020 in the United Stated of America, leading WHO to declare pandemic by 11 March 2020. RNA viruses accumulate mutations following replication and passage in human population, which prompted us to determine the rate and the regions (hotspots) of the viral genome with high rates of mutation. We analyzed the rate of mutation accumulation over a period of 11 weeks (submitted between 19th January to 15 April 2020) in USA SARS-CoV-2 genome. Our analysis identified that majority of the viral genes accumulated mutations, although with varying rates and these included NSP2, NSP3, RdRp, helicase, Spike, ORF3a, ORF8, and Nucleocapsid protein. Sixteen mutations accumulated in Spike protein in which four mutations are located in the receptor binding domain. Intriguingly, we identified a fair number of viral proteins (NSP7, NSP9, NSP10, NSP11, Envelop, ORF6, and ORF7b proteins), which did not accumulate any mutation. Limited changes in these proteins may suggest that they have conserved functions, which are essential for virus propagation. This provides a basis for a better understanding of the genetic variation in SARS-CoV-2 circulating in the US, which could help in identifying potential therapeutic targets for controlling COVID-19.

An Immunoinformatics Approach in Design of Synthetic Peptide Vaccine Against Influenza Virus

Peptide-based vaccines are an appealing strategy which involves usage of short synthetic peptides to engineer a highly targeted immune response. These short synthetic peptides contain potential T- and B-cell epitopes. Experimental approaches in identifying these epitopes are time-consuming and expensive; hence immunoinformatics approach came into picture. Immuninformatics approach involves epitope prediction tools, molecular docking, and population coverage analysis in design of desired immunogenic peptides. In order to overcome the antigenic variation of viruses, conserved regions are targeted to find the potential epitopes. The present chapter demonstrates the use of immunoinformatics approach to select potential peptide containing multiple T- (CD8+ and CD4+) and B-cell epitopes from Avian H3N2 M1 Protein. Further, molecular docking (to analyse HLA-peptide interaction) and population coverage analysis have been used to verify the potential of peptide to be presented by polymorphic HLA molecules. In silico approach of epitope prediction has proven to be successful methodology in screening the putative epitopes among numerous possible vaccine targets in a given protein.

Hetero-Polysaccharides Secreted from Dunaliella salina Exhibit Immunomodulatory Activity Against Peripheral Blood Mononuclear Cells and RAW 264.7 Macrophages

Several species of microalgae have been known to produce exopolysaccharides (EPS) with potential immune activity. In the present investigation, ethyl acetate fraction of crude EPS secreted by Dunaliella salina was explored for immunomodulatory activity against peripheral blood mononuclear cells (PBMC) and RAW 264.7 macrophages. Effect of EPS on cell growth and cytokines production were measured using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay and ELISA respectively. Griess reagent was used for measuring the nitric oxide production in RAW 264.7 macrophages. FTIR analysis and mass spectroscopy were carried out for the characterization. Ethyl acetate fraction exhibited dose dependent increase in proliferative index and cytokines production (IFN-γ, TNF-α, TGF-β). At low concentration (250 and 500 µg/mL), it showed growth inhibition and at higher concentration (1000 and 1500 µg/mL), it enhanced the cell growth. Interestingly, the pronounced increased TNF-α production was observed in ethyl acetate fraction treated PBMC cells at higher concentration (750 and 1000 µg/mL) indicating the immunostimulatory effect. In RAW cells, concentration dependent diminished cell growth (IC₅₀ = 691 µg/mL) and nitric oxide production (IC₅₀ = 630 µg/mL) was observed. FTIR analysis showed the presence of polysaccharides due to the detection of hydroxyl (-OH), Carbonyl (C-O) and alkyl (C-H) groups. Mass spectroscopy results revealed ethyl acetate fraction as penta-saccharide (m/z = 887.56 and 886.54) which are confirmed to be hetero-polysaccharides consisting of hexoses and pentoses along with association of ions. These results suggest that penta-saccharide (ethyl acetate fraction) isolated from D. salina may have the potential to be used for therapeutic purpose as immunomodulatory agent.

Computational Intelligence Technique for Prediction of Multiple Sclerosis Based on Serum Cytokines

Multiple sclerosis (MS) is a neurodegenerative disease characterized by lesions in the central nervous system (CNS). Inflammation and demyelination are the leading causes of neuronal death and brain lesions formation. The immune reactivity is believed to be essential in the neuronal damage in MS. Cytokines play important role in differentiation of Th cells and recruitment of auto-reactive B and T lymphocytes that leads to neuron demyelination and death. Several cytokines have been found to be linked with MS pathogenesis. In the present study, serum level of eight cytokines (IL-1β, IL-2, IL-4, IL-8, IL-10, IL-13, IFN-γ, and TNF-α) was analyzed in USA and Russian MS to identify predictors for the disease. Further, the model was extended to classify MS into remitting and non-remitting by including age, gender, disease duration, Expanded Disability Status Scale (EDSS) and Multiple Sclerosis Severity Score (MSSS) into the cytokines datasets in Russian cohorts. The individual serum cytokines data for the USA cohort was generated by Z score percentile method using R studio, while serum cytokines of the Russian cohort were analyzed using multiplex immunoassay. Datasets were divided into training (70%) and testing (30%). These datasets were used as an input into four machine learning models (support vector machine, decision tree, random forest, and neural networks) available in R programming language. Random forest model was identified as the best model for diagnosis of MS as it performed remarkable on all the considered criteria i.e., Gini, accuracy, specificity, AUC, and sensitivity. RF model also performed best in predicting remitting and non-remitting MS. The present study suggests that the concentration of serum cytokines could be used as prognostic markers for the prediction of MS.

Metadherin: A Therapeutic Target in Multiple Cancers

Altered expression of many genes and proteins is essential for cancer development and progression. Recently, the affected expression of metadherin (MTDH), also known as AEG-1 (Astrocyte Elevated Gene 1) and Lyric, has been implicated in various aspects of cancer progression and metastasis. Elevated expression of MTDH/AEG-1 has been reported in many cancers including breast, prostate, liver, and esophageal cancers, whereas its expression is low or absent in non-malignant tissues. These expression studies suggest that MTDH may represent a potential tumor associated antigen. MTDH also regulates multiple signaling pathways including PI3K/Akt, NF-κB, Wnt/β-catenin, and MAPK which cooperate to promote the tumorigenic and metastatic potential of transformed cells. Several microRNA have also been found to be associated with the increased MTDH expression in different cancers. Increased MTDH levels were linked to the tumor chemoresistance making it an attractive novel therapeutic target. In this review, we summarize data on MTDH function in various cancers.

History of ZIKV Infections in India and Management of Disease Outbreaks

Zika virus (ZIKV) is an emerging arbovirus infection endemic in multiple countries spread from Asia, Africa to the Americas and Europe. Previously known to cause rare and fairly benign human infections, ZIKV has become a major international public health emergency after being linked to unexpected neurological complications, that includes fetal brain damage/death and microcephaly in babies born to infected mothers and Guillain-Barre syndrome (GBS) in adults. It appears that a single genetic mutation in the ZIKV genome, likely acquired during explosive ZIKV outbreak in French Polynesia (2013), made virus causing mild disease to target fetus brain. The Aedes mosquitoes are found to be the main carrier of ZIKV, passing the virus to humans. Originally isolated from patients in Africa in 1954 (African lineage), virus disseminated to Southeast Asia (Asian lineage), establishing new endemic foci, including one in India. Numerous cases of ZIKV infection have been reported in several locations in India and neighboring countries like Pakistan and Bangladesh since mid of the last century, suggesting that the virus reached this part of Asia soon after it was first discovered in Uganda in 1947. Although, the exact means by which ZIKV was introduced to India remains unknown, it appears that the ZIKV strain circulating in India possibly belongs to the "Asian lineage," which has not yet been associated with microcephaly and other neurological disorders. However, there still exists a threat that the contemporary ZIKV virulent strain from South America, carrying a mutation can return to Asia, posing a potential crisis to newborns and adult patients. Currently there is no specific vaccine or antiviral medication to combat ZIKV infection, thus, vector control and continuous monitoring of potential ZIKV exposure is essential to prevent the devastating consequences similar to the ones experienced in Brazil. However, the major obstacle faced by Indian healthcare agencies is that most cases of ZIKV infection have been reported in rural areas that lack access to rapid diagnosis of infection. In this review, we attempt to present a comprehensive analysis of what is currently known about the ZIKV infection in India and the neighboring countries.

Immune responses to highly conserved influenza A virus matrix 1 peptides

Influenza vaccine development is considered to be complicated and challenging. Constantly evolving influenza viruses require continuous global monitoring and reformulation of the vaccine strains. Peptides that are conserved among different strains and subtypes of influenza A virus are strongly considered to be attractive targets for development of cross protective influenza vaccines that stimulate cellular responses. In this study, three highly conserved (>90%) matrix 1 peptides that contain multiple T cell epitopes, ILGFVFTLTVPSERGLQRRRF (P_M 1), LIRHENRMVLASTTAKA (P_M 2) and LQAYQKRMGVQMQR (P_M 3), were assessed for their immunogenic potential in vitro by subjecting peripheral blood mononuclear cells from healthy volunteers to repetitive stimulation with these chemically synthesised peptides and measuring their IFN-γ concentrations, proliferation by ELISA, and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, respectively. Seven samples were screened for immunogenicity of P_M 1 and P_M 2, and six for that of P_M 3. All six samples had positive responses (IFN-γ secretion) to P_M 3 stimulation, as did five and three for P_M 2 and P_M 1 respectively. In contrast, seven (P_M 1 and P_M 2) and four (P_M 3) samples showed proliferative response as compared with unstimulated cells. The encouraging immunogenic response generated by these highly conserved matrix 1 peptides indicates they are prospective candidates for development of broadly reactive influenza vaccines.

Metadherin peptides containing CD4(+) and CD8(+) T cell epitopes as a therapeutic vaccine candidate against cancer

The concept of peptide-based vaccines against cancer has made noteworthy progress. Metadherin (MTDH) overexpression and its role in the development of diverse cancers make it an attractive target for cancer immunotherapy. In the current study, six different T cell epitope prediction tools were run to identify MTDH peptides with multiple immunogenic regions. Further, molecular docking was performed to assess HLA-peptide binding interactions. Nine and eleven peptides fragments containing multiple CD8 (+) and CD4 (+) T-cell epitopes, ranging from 9 to 20 amino acids, respectively, were obtained using a consensus immunoinformatics approach. The three peptides that were finally identified as having overlapping CD4 (+) and CD8 (+) T- cell epitopes are ARLREMLSVGLGFLRTELG, FLLGYGWAAACAGAR, YIDDEWSGLNGLSSADP. These peptides were found to not only have multiple T cell epitopes but also to have binding affinity with wide HLA molecules. A molecular docking study revealed that the predicted immunogenic peptides (with single or multiple T cell epitopes) of MTDH have comparable binding energies with naturally bound peptides for both HLA classes I and II. Thus, these peptides have the potential to induce immune responses that could be considered for developing synthetic peptide vaccines against multiple cancers.

Antioxidant and cytotoxic activity of carotenes produced by Dunaliella salina under stress

Context Dunaliella salina Teodoresco (Dunaliellaceae) is one of the promising microalgae consumed as food and medicine for many years. Objective Dunaliella salina was grown under different stress conditions for enhancing carotene production. The carotene enriched extract was evaluated for antioxidant and cytotoxic activity. Materials and methods Carotene content was calculated under salinity, nitrogen and temperature stress conditions. Antioxidant activity was determined through DPPH assay by incubating the samples for 45 min with 250 μg/mL of extract and reducing power assay was performed with 50, 100, 150 and 200 μg/mL of extract. Cytotoxicity was determined by incubating ∼2 × 10(4) MCF-7 (breast cancer) cells with 250 μg of extract in each well for 72 h by MTT assay. Result Carotene content was significantly increased to 9.8 (3.5 M NaCl), 13.9 (37 °C), 8.2 (250 mM KNO3) and 10.6 μg/mL (nitrogen-depleted medium) as compared with 3.2 μg/mL in normal conditions (1.7 M NaCl, 0.75 mM KNO3 and 28 °C). Free radical scavenging activity increased at 3.0 and 3.5 M NaCl (27.8 and 57.5%, respectively), 37 °C (31.4%) and in nitrogen-depleted medium (41.9%) compared with normal (15%) conditions. Carotene content and scavenging activity were positively correlated under salinity (r = 0.97), temperature (r = 0.85) and nitrogen (r = 0.7) stress conditions. Cytotoxicity against MCF-7 cell lines increased due to increase in carotene content suggesting that cytotoxicity may be associated with carotene accumulation. Discussion and conclusions Carotene content enhanced by D. salina under stress conditions increased the antioxidant and cytotoxic activity.

Fusarium tricinctum, An Endophytic Fungus Exhibits Cell Growth Inhibition and Antioxidant Activity

An endophytic fungus (strain T6) isolated from Taxus baccata was studied for its effect on the growth of human breast cancer cell line (MCF-7), human cervical cancer cell line (HeLa) and peripheral blood mononuclear cells (PBMCs) as well as for its antioxidant activity. Based on morphological characters and internal transcribed spacer (ITS) sequence analysis, this fungus (strain T6) was identified as Fusarium tricinctum. This fungus has shown inhibition in the growth of the MCF-7 and HeLa cancer cell lines. IC₅₀ values of the fungal extract were 225 ± 26 and 220 ± 18 μg ml^-1 for MCF-7 and HeLa cell lines, respectively. Further, F. tricinctum showed inhibition in the proliferation of concanavalin A stimulated PBMCs indicating its immunosuppressive potential (IC₅₀ value 110 ± 44 μg ml^-1). Tumour necrosis factor (TNF)-α production in concanavalin A stimulated PBMCs and MCF-7 were found to be inhibited which indicates that the antiproliferative effect may be associated with TNF-α. Free radical scavenging results revealed that this fungus also exhibited antioxidant activity (IC₅₀ value 482 ± 9 μg ml^-1). Present study results suggested that F. tricinctum has the potential to be used for therapeutic purposes because of its antiproliferative and antioxidant potential.

Identification of Conserved Peptides Comprising Multiple T Cell Epitopes of Matrix 1 Protein in H1N1 Influenza Virus

Cell mediated immune response plays a key role in combating viral infection and thus identification of new vaccine targets manifesting T cell mediated response may serve as an ideal approach for influenza vaccine. The present study involves the application of an immunoinformatics-based consensus approach for epitope prediction (three epitope prediction tools each for CD4+ and CD8+ T cell epitopes) and molecular docking to identify peptide sequences containing T cell epitopes using the conserved sequences from all the Matrix 1 protein sequences of H1N1 virus available until April 2015. Three peptides comprising CD4+ and CD8+ T cell epitopes were obtained, which were not exactly reported in earlier studies. Population coverage study of these multi-epitope peptides revealed that they are capable of inducing a potent immune response belonging to individuals from different populations and ethnicity distributed around the globe. Conservation study with other subtypes of influenza virus infecting humans (H2N2, H5N1, H7N9, and H3N2) revealed that these three peptides were conserved (>90%), with 100% identity in most of these strains. Hence, these peptides can impart immunity against H1N1 as well as other subtypes of influenza virus. A molecular docking study of the predicted peptides with class I and II human leukocyte antigen (HLA) molecules has shown that the majority of them have comparable binding energies to that of native peptides. Hence, these peptides from Matrix 1 protein of H1N1 appear to be promising candidates for universal vaccine design.

Conserved peptides containing overlapping CD4+ and CD8+ T-cell epitopes in the H1N1 influenza virus: an immunoinformatics approach

Pandemic threats of the H1N1 influenza virus have drawn attention to developing a universal vaccine against circulating and future strains of this virus. An immunoinformatics study was conducted to identify conserved peptides containing CD4+ and CD8+ T-cell epitopes from all the hemagglutinin (HA) and neuraminidase (NA) protein sequences available until February 2013 to cover the seasonal as well as the pandemic strains of the H1N1 virus. In the present study, six different immunoinformatics prediction programs were used in order to define the epitopes. Five conserved peptides of HA and six of NA protein were obtained that contained overlapping CD4+ and CD8+ T-cell epitopes. These identified peptides have a binding affinity for a large number of major histocompatibility complex (MHC) alleles. WHGSNRPWVSF of NA protein is a new peptide whose T-cell response has not been previously reported. Population coverage studies have shown that these peptide fragments have the capacity to induce a potent immune response among individuals from different populations around the world. Hence, these HA and NA peptides may be considered as interesting candidates for vaccine design.