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Presently, the world needs safe and effective vaccines to overcome the COVID-19 pandemic. Our work has focused on formulating two types of mRNA vaccines that differ in capacity to copy themselves inside the cell. These are non-amplifying mRNA (NRM) and self-amplifying mRNA (SAM) vaccines. Both the vaccine candidates encode an engineered viral replicon which can provoke an immune response. Hence we predicted and screened twelve epitopes from the spike glycoprotein of SARS-CoV-2. We used five CTL, four HTL, and three B-cell-activating epitopes to formulate each mRNA vaccine. Molecular docking revealed that these epitopes could combine with HLA molecules that are important for boosting immunogenicity. The B-cell epitopes were adjoined with GPGPG linkers, while CTL and HTL epitopes were linked with KK linkers. The entire protein chain was reverse translated to develop a specific NRM-based vaccine. We incorporate gene encoding replicase in the upstream region of CDS encoding antigen to design the SAM vaccine. Subsequently, signal sequences were added to human mRNA to formulate vaccines. Both vaccine formulations translated to produce the epitopes in host cells, initiate a protective immune cascade, and generate immunogenic memory, which can counter future SARS-CoV-2 viral exposures before the onset of infection. Supplementary Information The online version contains supplementary material available at 10.1007/s12033-021-00432-6.

Newly emerging significant SARS-CoV-2 variants such as B.1.1.7, B.1.351, and B.1.1.28 are the variant of concern (VOC) for the human race. These variants are getting challenging to contain from spreading worldwide. Because of these variants, the second wave has started in various countries and is threatening human civilization. Thus, we require efficient vaccines that can combat all emerging variants of SARS-CoV-2. Therefore, we took the initiative to develop a peptide-based next-generation vaccine using four variants (Wuhan variant, B.1.1.7, B.1.351, and B.1.1.28) that could potentially combat SARS-CoV-2 variants. We applied a series of computational tools, servers, and software to identify the most significant epitopes present on the mutagenic regions of SARS-CoV-2 variants. The immunoinformatics approaches were used to identify common B cell derived T cell epitopes, influencing the host immune system. Consequently, to develop a novel vaccine candidate, the antigenic epitopes were linked with a flexible and stable peptide linker, and the adjuvant was added at the N-terminal end. 3D vaccine candidate structure was refined, and quality was assessed using web servers. The physicochemical properties and safety parameters of the vaccine construct were assessed through bioinformatics and immunoinformatics tools. The molecular docking analysis between TLR4/MD2 and the proposed vaccine candidate demonstrated a satisfactory interaction. The molecular dynamics studies confirmed the stability of the vaccine candidate. Finally, we optimized the proposed vaccine through codon optimization and in silico cloning to study the expression. Our multi-epitopic next-generation peptide vaccine construct can boost immunity against the Wuhan variant and all significant mutant variants of SARS-CoV-2.

Helicobacter pylori is a highly potential pathogen to colonize in the human stomach. This bacterial strain is now alarming serious health concern all over the world. Combating through available drugs is a difficult task due to lack of appropriate common targets against genetically diverse strains. Therefore, the developments of effective targets vaccines require alternative strategies to eliminate the H. pylori infection. In this study, we developed a novel vaccine construct using B-cell derived T-cell epitopes from four target antigenic proteins (HpaA, FlaA, FlaB and Omp18), and found the induction of possible immune response using advanced immunoinformatics approaches. In order to boost immune system, we tagged adjuvant (50S ribosomal protein L7/L12) with a suitable linker at the N-terminus side of vaccine sequence. Protein–protein docking between human Toll like receptor 5 (TLR5) and vaccine construct help to predict the way of inductive signaling that leads to immune-response. The calculated negative score (− 151.4, + / − 8.7) of molecular docking complex signify the best binding interface. Molecular dynamics simulation studies confirmed the proper docking between TLR5 and vaccine candidate. Moreover, Normal mode analysis (NMA) calculates the molecular motion of the docking complex. The low eigenvalue (2.935e−05) indicates the stable and flexible molecular motion in the binding interaction side. Finally, in-silico cloning of vaccine candidate was performed using expression vector pET28b (+) with the optimized restriction sites. Supplementary Information The online version of this article (10.1007/s10989-020-10157-w) contains supplementary material, which is available to authorized users.

Bunyamwera orthobunyavirus and its serogroup can cause several diseases in humans, cattle, ruminants, and birds. The viral M-polyprotein helps the virus to enter the host body. Therefore, this protein might serve as a potential vaccine target against Bunyamwera orthobunyavirus. The present study applied the immunoinformatics technique to design an epitopic vaccine component that could protect against Bunyamwera infection. Phylogenetic analysis revealed the presence of conserved patterns of M-polyprotein within the viral serogroup. Three epitopes common for both B-cell and T-cell were identified, i.e., YQPTELTRS, YKAHDKEET, and ILGTGTPKF merged with a specific linker peptide to construct an active vaccine component. The low atomic contact energy value of docking complex between human TLR4 (TLR4/MD2 complex) and vaccine construct confirms the elevated protein–protein binding interaction. Molecular dynamic simulation and normal mode analysis illustrate the docking complex’s stability, especially by the higher Eigenvalue. In silico cloning of the vaccine construct was applied to amplify the desired vaccine component. Structural allocation of both the vaccine and epitopes also show the efficacy of the developed vaccine. Hence, the computational research design outcomes support that the peptide-based vaccine construction is a crucial drive target to limit the infection of Bunyamwera orthobunyavirus to an extent. Supplementary Information The online version contains supplementary material available at 10.1007/s10989-021-10322-9.

COVID-19 caused by SARS-CoV-2 was declared a global pandemic by WHO (World Health Organization) in March, 2020. Within 6 months, nearly 750,000 deaths are claimed by COVID-19 across the globe. This called for immediate social, scientific, technological, public and community interventions. Considering the severity of infection and the associated mortalities, global efforts are underway to develop preventive measures against SARS-CoV-2. Among the SARS-CoV-2 target proteins, Spike (S) glycoprotein (a.k.a S Protein) is the most studied target known to trigger strong host immune response. A detailed analysis of S protein-based epitopes enabled us to design a novel B-cell-derived T-cell Multi-epitope-based peptide (MEBP) vaccine candidate. This involved a systematic and comprehensive computational protocol consisting of prediction of dual-purpose epitopes and designing an MEBP vaccine construct. This was followed by 3D structure validation, MEBP complex interaction studies, in silico cloning and vaccine dose-based immune response simulation to evaluate the immunogenic potency of the vaccine construct. The dual-purpose epitope prediction protocol was designed such that the same epitope elicits both humoral and cellular immune response unlike the earlier designs. Further, the epitopes predicted were screened against stringent criteria to ensure selection of a potent candidate with maximum antigen coverage and best immune response. The vaccine dose-based immune response simulation studies revealed a rapid antigen clearance through antibody generation and elevated levels of cell-mediated immunity during repeated exposure of the vaccine. The favourable results of the analysis strongly indicate that the vaccine construct is indeed a potent vaccine candidate and ready to proceed to the next steps of experimental validation and efficacy studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-020-02574-x.

The present study was undertaken to detect the incidence of extended-spectrum-cephalosporinase gene possessing-Escherichia coli, its co-resistance pattern against other antimicrobials, and the clonal relationship of the isolates in healthy kuroiler birds. A total of 80 cloacal swabs from kuroilers were collected randomly from West Bengal, India. The use of costly antimicrobials (cephalosporins) was not practiced by farmers. Escherichia coli was isolated and identified by standard biochemical tests and 16SrRNA-PCR. All the E. coli isolates, including controls, were subjected to PCR for detection of blaCTX-M, blaTEM, blaSHV, and blaCMY-2 genes. By comparing the RAPD-banding pattern, the phylogenetic relationship among the isolates was established. All the isolates were tested for phenotypical resistance against other antibiotics. In total, 60 isolates were identified as E. coli from the kuroilers studied (n = 80). Among them, 12 (20%) isolates possessed one of the studied extended-spectrum cephalosporinase genes. Among the studied genes, blaTEM and blaSHV were detected in 6 (10%) and 12 (20%) E. coli isolates, respectively. None of the E. coli isolates possessed blaCTX-M and blaCMY-2. In phylogenetic analysis, the strains isolated from same localities with similar genetic profile were grouped into the same cluster. Resistance of extended-spectrum cephalosporinase gene possessing E. coli isolates was observed most frequently against ampicillin/cloxacillin, co-trimoxazole, amoxyclav, piperacillin, ceftriaxone, and tetracycline. Kuroiler birds with no cephalosporin usage profile may act as a reservoir of extended-spectrum cephalosporinase gene possessing E. coli. This is the first systematic study in kuroilers, to raise the awareness of consumers regarding the possibility of transmission of antimicrobial resistant E. coli from them., Istraživanje je poduzeto da se odredi incidencija bakterije E. coli koja posjeduje gene za cefalosporinaze proširenog spektra, a istodobno je rezistentna na druge antimikrobne tvari, te klonski odnos izolata u zdravih kokoši pasmine kuroiler. Ukupno je bilo nasumce prikupljeno 80 obrisaka kloake spomenute pasmine u Zapadnom Bengalu u Indiji. Skupe antimikrobne tvari (cefalosporini) nisu bile rabljene za liječenje. Izolati E. coli bili su identificirani standardnim biokemijskim testovima i 16SrRNA-PCR-om. Svi izolati bili su lančanom reakcijom polimerazom (PCR) pretraženi na prisutnost gena blaCTX-M, blaTEM, blaSHV i blaCMY-2. Filogenetska srodnost izolata bila je određena RAPD-om. Otpornost svih izolata bila je fenotipski pretražena i na druge antibiotike. Ukupno je izdvojeno 60 izolata E. coli iz 80 kuroiler kokoši. Od toga je u 12 (20 %) bio dokazan jedan od istraživanih gena za cefalosporinaze proširenog spektra. Među istraživanim genima, blaTEM je bio dokazan u 6 (10 %) izolata, a blaSHV u 12 (20 %) izolata E. coli. Nijedan od izolata nije posjedovao blaCTX-M i blaCMY-2. Filogenetskom analizom ustanovljeno je da su izolati iz istih lokaliteta sa sličnim genetičkim profilom bili grupirani u istu skupinu. Posjedovanje gena za cefalosporinaze proširenog spektra bilo je najčešće dokazano za antibiotike ampicilin/kloksacilin, kotrimoksazol, amoksiklav, piperacilin, ceftriakson i tetraciklin. Perad pasmine kuroiler kojoj nikad nisu davani cefalosporini može biti rezervoar E. coli koja ima gene za cefalosporinaze proširenog spektra. To je prvo sustavno istraživanje u pasmine kuroiler od značenja za svjesnost konzumenata o mogućnosti prijenosa bakterije E. coli otporne na antimikrobne tvari.