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Backgrounds: A short sequence of viral protein or peptide, can be used as a potential vaccine for the treatment of that virus. Considering all variants of concern (VOC), vaccine design with peptide for Severe Acute Respiratory Syndrome coronavirus 2 (SARS CoV2) is a challenging job for scientists.
Materials & Methods: In this current study, an epitope containing peptide vaccine for nonstructural protein 4 (nsp 4) of SARS CoV2 coronavirus has been predicted. With the help of a modified method for both B and T call epitope prediction, verified by molecular docking studies, linear B cell and T cell epitopes for nsp4 protein, are predicted here. Predicted epitopes are analyzed further with population coverage calculation and epitope conservancy analysis.
Findings: A short peptide sequence   ⁷⁴QRGGSYTNDKA⁸⁴  has been selected as B cell epitope considering the scores for surface accessibility, hydrophilicity, beta turn prediction for each amino acid residues.
Similarly, the peptide sequences ³⁵⁹ FLAHIQWMV³⁶⁷ and   ³⁵⁹ FLAHIQWVMFTPLV³⁷³ are predicted as T cell epitopes for MHC-I and MHC-II molecules. These two potential epitopes can interest with HLA-A*02:01 and HLA-DRB*01:01, MHC allelic proteins respectively with lowest IC₅₀ values.
Furthermore, no amino acid mutations are observed in GISAD Global initiate on sharing all influenza data) database for alpha, beta, gamma and delta variance of concerns (VOC). Among seven amino acid point mutation of nsp 4 protein in Omicron variant, none of them is present in the peptide sequences of predicted epitope-based vaccines.
Conclusion: The short peptide sequences can be predicted as vaccines to prevent coronavirus infections for all variants of concerns.
 

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Foot and Mouth Disease (FMD) is a highly contagious and devastating disease that spreads rapidly and causes many economic damages. One of the important      methods for detection of FMD and particularly differentiation of vaccinated from infected animals, is the use of non-structural proteins as antigens in ELISA kits. The purpose of this study was cloning of the gene sequence and expression of the antigenic regions of 3D nonstructural protein as one of the diagnostic options. For amplification of the antigenic regions of FMD virus 3D protein, specific primers containing NdeI and EcoRI restriction sites were designed and the polymerase chain reaction was performed. The sequences cut by these two enzymes, were inserted into PET21a+ vectors. The recombinant plasmids were then transformed into E. coli (DH5α). Colony-PCR tests and enzymatic digestions were performed on the resulting colonies and the presence of the target gene was confirmed. The gene sequence was further confirmed after sequencing. For production of recombinant antigens, the recombinant vector was transferred to the expression host of E. coli-BL21. The bacteria containing the recombinant gene were induced with IPTG and the expression of the recombinant protein was confirmed using the SDS-PAGE method. The molecular weight of the recombinant protein was about 24 kDa, and it can be used in the design of ELISA diagnostic kit.

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Background:
HIV has at least six regulatory genes among which the Vif protein can control HIV replication. This study, as the first report, investigated the important mutations in VIF protein in sequences from Iranian patients and using immunoinformatics, conserved regions of this protein and B-Cell, T-Cell and CTL epitopes to stimulate the immune system, were determined.
Methods:
VIF sequences were obtained from NCBI GenBank, and tertiary structures, B-Cell, T-Cell and CTL epitopes were predicted by bioinformatics tools; besides, their antigenic and allergenic properties were studied.
Results:
The most prevalent mutations in Vif protein were related to S 49 P (90%), S 140 N and N 186 S (80%). Two substitutions at positions 41 and 42 were introduced which have effect on Vif binding to host factor. In addition, three regions were identified as the best epitope sequences with high potential to induce immune system and the lowest allergic properties, among which 5-32 region was suggested as the best vaccine candidate regions.
Conclusion:
This study as the first study from Iran using immunoinformatics tools to introduced a region with the high potential to induce humoral and cellular immune systems and lowest allergenic properties which can be used for further studies on HIV vaccines. 

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Objective: Animal studies show that vaccination with epitope-based peptides results in protective immunity. However, immunodominance should be regarded as a major challenge in this area. Considering the advantages of epitopic-vaccines against hepatitis C virus (HCV) infection, herein, we compared the occurrence of immunodominance following mice immunization with three different HCV epitopic-peptide formulations. Methods: We synthesized four CD8+ epitopic-peptides (C1,E6,N,E4) that were derived from HCV-antigens. A polytope-peptide (C1E6NE4) spanning fusion of epitopes was designed based on immunoinformatics analyses for optimum proteasomal cleavage. BALB/c mice received three subcutaneous injections that contained 10 µg of peptide (minimal epitopes, or mixture of four epitopes or long-polytope) formulated with CpG (50 µg) and Montanide-ISA720 (70%) adjuvants in the tail-base at three-week intervals. Considering the H2-Dd (BALB/c)-restriction of C1 and E4-epitopes, three weeks after the last injection splenocytes from vaccinated animals were subjected to IFNγ/IL4 ELISpot assays in the presence of C1 and E4-peptides. Results: All vaccinated animals promoted Th1-oriented responses as evidenced by detection of IFNγ-secreting cells and a low-level of IL4 secretion. Mice injected with minimal CTL-epitopes provoked stronger responses, however, due to the higher affinity of E4-epitope for H2-Dd, frequency of E4-specific cells was considerably higher than C1-specific ones, showing some level of immunodominance. Interestingly, animals vaccinated with polytope-peptide developed high-quality balanced responses against both C1and E4-epitopes, however at a lower intensity. Conclusion: These results supported the superiority of polytope-peptides over minimal epitopes, yet emphasized the key role of polytope design and optimization to avoid epitope dominancy.