Search

Inflammatory bowel disease (IBD) is a chronic manifestation of dysregulated immune response to the gut microbiota in genetically predisposed hosts. Nearly half of patients with Crohn's disease (CD) develop selective serum immunoglobulin (Ig)G response to flagellin proteins expressed by bacteria in the Lachnospiraceae family. This study aimed to identify the binding epitopes of these IgG antibodies and assess their relevance in CD and in homeostasis. Sera from an adult CD cohort, a treatment-naïve pediatric CD cohort, and 3 independent non-IBD infant cohorts were analyzed using novel techniques including a flagellin peptide microarray and a flagellin peptide cytometric bead array. A dominant B cell peptide epitope in patients with CD was identified, located in the highly conserved "hinge region" between the D0 and D1 domains at the amino-terminus of Lachnospiraceae flagellins. Elevated serum IgG reactivity to the hinge peptide was strongly associated with incidence of CD and the development of disease complications in children with CD up to 5 years in advance. Notably, high levels of serum IgG to the hinge epitope were also found in most infants from 3 different geographic regions (Uganda, Sweden, and the United States) at 1 year of age, which decrements rapidly afterward. These findings identified a distinct subset of patients with CD, united by a shared reactivity to a dominant commensal bacterial flagellin epitope, that may represent failure of a homeostatic response to the gut microbiota beginning in infancy. [Display omitted] Patients with Crohn's disease and healthy infants share a dominant immunoglobulin G antibody response to the "hinge region" of Lachnospiraceae flagellins, suggesting that failure of establishing homeostasis with the gut microbiota in infancy may contribute to the development of Crohn's disease later in life. [ABSTRACT FROM AUTHOR]

Objective To analyze the structure of CD36, search the possible B cell epitopes and prepare multi-antigen peptides(MAP) with B cell epitopes, so as to provide a preliminary experimental basis for the preparation of CD36 antibodies using MAP with B cell epitopes. Methods The potential B cell epitopes of CD36 were analyzed by bioinformatics methods, including physical and chemical properties, secondary structure, potential phosphorylation and glycosylation sites. Eight-branch MAP with CD36 B cell epitopes were synthesized by FMOC using polylysine as the core matrix. The purity of MAPs was analyzed by reverse high-performance liquid chromatography chromatography(RP-HPLC), and the molecular weight of MAPs was determined by mass spectrometry. Results CD36 is a stable and hydrophilic alkaline protein, with multiple phosphorylation and glycosylation sites and strong antigenicity, and its secondary structure is mainly characterized by irregular curls. Four potential B cell epitopes were obtained and 4 MAPs containing potential B cell epitopes were prepared. RP-HPLC analysis showed that the purity of the MAPs were above 85%, and the molecular weight of 3 MAPs was consistent with the expected theoretical molecular weight. Conclusion CD36 on platelet has strong antigenicity. MAPs containing CD36 B cell epitopes can provide the experimental basis for the preparation and related research of CD36 antibodies.

B cell epitopes must be visible for recognition by cognate B cells and/or antibodies. Here, we studied that premise for known linear B cell epitopes that were collected from the Immune Epitope Database as being recognized by humans during microbial infections. We found that the majority of such known B cell epitopes are virus-specific linear B cell epitopes (87.96%), and most are located in antigens that remain enclosed in host cells and/or virus particles, preventing antibody recognition (18,832 out of 29,225 epitopes). Moreover, we estimated that only a minority (32.72%) of the virus-specific linear B cell epitopes that are found in exposed viral regions (e.g., the ectodomains of envelope proteins) are solvent accessible on intact antigens. Hence, we conclude that ample degradation/processing of viral particles and/or infected cells must occur prior to B cell recognition, thus shaping the B cell epitope repertoire. [ABSTRACT FROM AUTHOR]

The surge in the clinical use of therapeutic antibodies has reshaped the landscape of pharmaceutical therapy for many diseases, including rare and challenging conditions. However, the administration of exogenous biologics could potentially trigger unwanted immune responses such as generation of anti-drug antibodies (ADAs). Real-world experiences have illuminated the clear correlation between the ADA occurrence and unsatisfactory therapeutic outcomes as well as immune-related adverse events. By retrospectively examining research involving immunogenicity analysis, we noticed the growing emphasis on elucidating the immunogenic epitope profiles of antibody-based therapeutics aiming for mechanistic understanding the immunogenicity generation and, ideally, mitigating the risks. As such, we have comprehensively summarized here the progress in both experimental and computational methodologies for the characterization of T and B cell epitopes of therapeutics. Furthermore, the successful practice of epitope-driven deimmunization of biotherapeutics is exceptionally highlighted in this article.

The zoonotic viruses pose significant threats to public health. Nipah virus (NiV) is an emerging virus transmitted from bats to humans. The NiV causes severe encephalitis and acute respiratory distress syndrome, leading to high mortality rates, with fatality rates ranging from 40% to 75%. The first emergence of the disease was found in Malaysia in 1998–1999 and later in Bangladesh, Cambodia, Timor‐Leste, Indonesia, Singapore, Papua New Guinea, Vietnam, Thailand, India, and other South and Southeast Asian nations. Currently, no specific vaccines or antiviral drugs are available. The potential advantages of epitope‐based vaccines include their ability to elicit specific immune responses while minimizing potential side effects. The epitopes have been identified from the conserved region of viral proteins obtained from the UniProt database. The selection of conserved epitopes involves analyzing the genetic sequences of various viral strains. The present study identified two B cell epitopes, seven cytotoxic T lymphocyte (CTL) epitopes, and seven helper T lymphocyte (HTL) epitope interactions from the NiV proteomic inventory. The antigenic and physiological properties of retrieved protein were analyzed using online servers ToxinPred, VaxiJen v2.0, and AllerTOP. The final vaccine candidate has a total combined coverage range of 80.53%. The tertiary structure of the constructed vaccine was optimized, and its stability was confirmed with the help of molecular simulation. Molecular docking was performed to check the binding affinity and binding energy of the constructed vaccine with TLR‐3 and TLR‐5. Codon optimization was performed in the constructed vaccine within the Escherichia coli K12 strain, to eliminate the danger of codon bias. However, these findings must require further validation to assess their effectiveness and safety. The development of vaccines and therapeutic approaches for virus infection is an ongoing area of research, and it may take time before effective interventions are available for clinical use. [ABSTRACT FROM AUTHOR]

Porcine circovirus type 2 (PCV2) is the main causative agent of porcine circovirus-associated disease (PCVAD) that profoundly impacts the swine industry worldwide. While most of the commercial PCV vaccines are developed based on PCV genotype 2a (PCV2a), PCV genotype 2b (PCV2b) has become predominant since 2003. In this study, we developed and evaluated DNA-based bivalent vaccines covering both PCV2a and PCV2b. We generated a new immunogen, PCV2b-2a, by combining consensus sequences of the PCV2a and PCV2b capsid proteins (Cap2a and Cap2b) in a form of fusion protein. We also examined whether modifications of the PCV2b-2a fusion protein with a signal sequence (SS) and granulocyte macrophage-colony stimulating factor (GM-CSF) fusing with interleukine-4 (IL-4) (GI) could further improve the vaccine immunogenicity. An immunogenicity study of BALB/cAJcl mice revealed that the DNA vector pVAX1 co-expressing PCV2b-2a and GI (pVAX1.PCV2b-2a-GI) was most potent at inducing both antibody and cellular immune responses against Cap2a and Cap2b. Interestingly, the vaccines skewed the immune response towards Th1 phenotype (IgG2a > IgG1). By performing ELISA and ELISpot with predicted epitope peptides, the three most immunogenic B cell epitopes and five putative T cell epitopes were identified on Cap2a and Cap2b. Importantly, our DNA vaccines elicited broad immune responses recognizing both genotype-specific and PCV2-conserved epitopes. Sera from mice immunized with the DNAs expressing PCV2b-2a and PCV2b-2a-GI significantly inhibited PCV2a cell entry at serum dilution 1:8. All these results suggest a great potential of our PCV2b-2a-based vaccines, which can be further developed for use in other vaccine platforms to achieve both vaccine efficacy and economical production cost. [ABSTRACT FROM AUTHOR]

Simple Summary: Research on the Cap protein is highly significant in the diagnosis, prevention, and control of porcine circovirus 3. In this study, we identified a novel B cell epitope of Cap protein using monoclonal antibody, and an epitope-blocking enzyme-linked immunosorbent assay was successfully developed to detect PCV3 antibodies in porcine sera. This established EB-ELISA has the advantages of being rapid, highly sensitive, re-producible, specific, and did not react with other porcine virus sera, which has great potential for the detection of PCV3 antiserum in porcine farms. Porcine circovirus type 3 (PCV3) is endemic in swine worldwide and causes reproductive disorders, dermatitis and nephrotic syndrome, and multi-organ inflammation. Currently, there is a growing need for rapid and accurate diagnostic methods in disease monitoring. In this study, four monoclonal antibodies (mAbs) against PCV3 capsid proteins were prepared (mAbs 2F6, 2G8, 6E2, and 7E3). MAb 7E3, which had the highest binding affinity for the Cap protein, was chosen for further investigation. A novel B cell epitope 110DLDGAW115 was identified using mAb 7E3. An epitope-blocking (EB) enzyme-linked immunosorbent assay (ELISA) was successfully developed using horseradish-peroxidase-labeled mAb 7E3 to detect PCV3 antibodies in porcine sera. Moreover, the EB-ELISA showed no specific reaction with other porcine disease sera, and the cut-off value was defined as 35%. Compared with the commercial ELISA, the percentage agreement was 95.59%. Overall, we have developed a novel EB-ELISA method that accurately and conveniently detects PCV3 in serum, making it a valuable tool for the clinical detection of PCV3 infection. [ABSTRACT FROM AUTHOR]

In recent years, the incidence of brucellosis has increased annually, causing tremendous economic losses to animal husbandry in a lot of countries. Therefore, developing rapid, sensitive, and specific diagnostic techniques is critical to control the spread of brucellosis. In this study, bioinformatics technology was used to predict the B cell epitopes of the main outer membrane proteins of Brucella, and the diagnostic efficacy of each epitope was verified by an indirect enzyme-linked immunosorbent assay (iELISA). Then, a fusion protein containing 22 verified epitopes was prokaryotically expressed and used as an antigen in paper-based ELISA (p-ELISA) for serodiagnosis of brucellosis. The multi-epitope-based p-ELISA was evaluated using a collection of brucellosis-positive and -negative sera collected from bovine and goat, respectively. Receiver operating characteristic (ROC) curve analysis showed that the sensitivity and specificity of detection-ELISA in diagnosing goat brucellosis were 98.85 and 98.51%. The positive and the negative predictive values were 99.29 and 98.15%, respectively. In diagnosing bovine brucellosis, the sensitivity and specificity of this method were 97.85 and 96.61%, with the positive and negative predictive values being identified as 98.28 and 97.33%, respectively. This study demonstrated that the B cell epitopes contained in major antigenic proteins of Brucella can be a very useful antigen source in developing a highly sensitive and specific method for serodiagnosis of brucellosis.

The African swine fever virus (ASFV) is one of the most important pathogens that causes huge damage to worldwide swine production. The pI215L protein is found within the virion and expressed at a high level in infected porcine alveolar macrophages (PAMs), indicating a possible role of pI215L protein in ASFV detection and surveillance. In the present study, female BALB/c mice (5–6-week-old) were immunized with rpI215L protein, and six hybridomas, 1C1, 2F6, 2F10, 3C8, 5E1 and 5B3, steadily secreted anti-pI215L monoclonal antibodies (mAbs). Among them, 1C4, 5E1, and 5B3 had the IgG1 isotype with a Lambda light chain, 2F10 and 3C8 had the IgG1 isotype with a Kappa light chain, and 2F6 had the IgG2a isotype with a Kappa light chain. Western blot showed a good reactivity of the six mAbs against ASFV. Eight truncated polypeptides were produced for epitope mapping. Two novel B cell epitopes, 67LTFTSEMWHPNIYS80 and 167IEYFKNAASN176, were identified by the mAbs. Further analysis revealed that 2F6 mAb could be widely used in ASFV surveillance and 5B3 mAb might serve as a tool in the distinguishment of different ASFV genotypes. This study provides tools of monoclonal antibodies for further study of I215L function and contributes to the development of serological diagnosis and vaccine research. [ABSTRACT FROM AUTHOR]

Effective countermeasures against the recent emergence and rapid expansion of the 2019 novel coronavirus (SARS-CoV-2) require the development of data and tools to understand and monitor its spread and immune responses to it. However, little information is available about the targets of immune responses to SARS-CoV-2. We used the Immune Epitope Database and Analysis Resource (IEDB) to catalog available data related to other coronaviruses. This includes SARS-CoV, which has high sequence similarity to SARS-CoV-2 and is the best-characterized coronavirus in terms of epitope responses. We identified multiple specific regions in SARS-CoV-2 that have high homology to the SARS-CoV virus. Parallel bioinformatic predictions identified a priori potential B and T cell epitopes for SARS-CoV-2. The independent identification of the same regions using two approaches reflects the high probability that these regions are promising targets for immune recognition of SARS-CoV-2. These predictions can facilitate effective vaccine design against this virus of high priority.

Aim: To predict the dominant B-cell epitope of the human cytomegalovirus UL138 gene and to provide a new assay for its latent infection. Methods: Recombinant plasmids were constructed with the predicted dominant epitopes, induced to be expressed and immunized in mice as a way to identify peptide antigenicity, immunogenicity and human serum. Results: Five potentially dominant B-cell epitopes were obtained. The positive rate of detection was found to be significantly higher in neonatal, adult and mouse serum specimens than in human cytomegalovirus (HCMV) (IgG, IgM) and UL138 gene DNA and cDNA assays (p < 0.05). Conclusion: The predicted dominant B-cell epitope is highly sensitive for the detection of human serum HCMV latent infection and can replace the traditional HCMV IgG assay. [ABSTRACT FROM AUTHOR]

Streptococcus agalactiae (Group B Streptococcus, GBS) is a multi-host pathogen, even causing life-threatening infections in newborns. Vaccination with GBS crossed serotypes vaccine is one of the best options for long-term infection control. Here we built a comprehensive in silico epitope-prediction workflow pipeline to design a multivalent multiepitope-based subunit vaccine containing 11 epitopes against Streptococcus agalactiae (MVSA). All epitopes in MVSA came from the proteins which were antigenic-confirmed, virulent-associated, surface-exposed and conserved in ten GBS serotypes. The in-silico analysis showed MVSA had potential to evoke strong immune responses and enable worldwide population coverage. To validate MVSA protection efficacy against GBS infection, immune protection experiments were performed in a mouse model. Importantly, MVSA induced a high titre of antibodies, significant proliferation of mice splenocytes and elicited strong protection against lethal-dose challenge with a survival rate of 100% in mice after three vaccinations. Meanwhile, the polyclonal antibody against MVSA did not only inhibit for growth of GBS from six crucial serotypes in vitro, but also protect 100% naive mice from GBS lethal challenge. These active and passive immunity assay results suggested that MVSA could therefore be an efficacious multi-epitope vaccine against GBS infection.

Spike (S) glycoprotein is the most significant structural protein of SARS-CoV-2 and a key target for neutralizing antibodies. In light of the on-going SARS-CoV-2 pandemic, identification and screening of epitopes of spike glycoproteins will provide vital progress in the development of sensitive and specific diagnostic tools. In the present study, NTD, RBD, and S2 genes were inserted into the pcDNA3.1(+) vector and designed with N-terminal 6× His-tag for fusion expression in HEK293F cells by transient transfection. Six monoclonal antibodies (4G, 9E, 4B, 7D, 8F, and 3D) were prepared using the expressed proteins by cell fusion technique. The characterization of mAbs was performed by indirect -ELISA, western blot, and IFA. We designed 49 overlapping synthesized peptides that cover the extracellular region of S protein in which 6 amino acid residues were offset between adjacent (S1–S49). Peptides S12, S19, and S49 were identified as the immunodominant epitope regions by the mAbs. These regions were further truncated and the peptides S12.2 286TDAVDCALDPLS297, S19.2 464FERDISTEIYQA475, and S49.4 1202ELGKYEQYIKWP1213 were identified as B- cell linear epitopes for the first time. Alanine scans showed that the D467, I468, E471, Q474, and A475 of the epitope S19.2 and K1205, Q1208, and Y1209 of the epitope S49.4 were the core sites involved in the mAbs binding. The multiple sequence alignment analysis showed that these three epitopes were highly conserved among the variants of concern (VOCs) and variants of interest (VOIs). Taken together, the findings provide a potential material for rapid diagnosis methods of COVID-19.

Abstract Background The variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harbor diverse spike (S) protein sequences, which can greatly influence the efficacies of therapeutics. Therefore, it would be of great value to develop neutralizing monoclonal antibodies (mAbs) that can broadly recognize multiple variants. Methods Using an mRNA-LNP immunization strategy, we generated several mAbs that specifically target the conserved S2 subunit of SARS-CoV-2 (B-S2-mAbs). These mAbs were assessed for their neutralizing activity with pseudotyped viruses and binding ability for SARS-CoV-2 variants. Results Among these mAbs, five exhibited strong neutralizing ability toward the Gamma variant and also recognized viral S proteins from the Wuhan, Alpha, Beta, Gamma, Delta and Omicron (BA.1, BA.2 and BA.5) variants. Furthermore, we demonstrated the broad reactivities of these B-S2-mAbs in several different applications, including immunosorbent, immunofluorescence and immunoblotting assays. In particular, B-S2-mAb-2 exhibited potent neutralization of Gamma variant (IC50 = 0.048 µg/ml) in a pseudovirus neutralization assay. The neutralizing epitope of B-S2-mAb-2 was identified by phage display as amino acid residues 1146–1152 (DSFKEEL) in the S2 subunit HR2 domain of SARS-CoV-2. Conclusion Since there are not many mAbs that can bind the S2 subunit of SARS-CoV-2 variants, our set of B-S2-mAbs may provide important materials for basic research and potential clinical applications. Importantly, our study results demonstrate that the viral S2 subunit can be targeted for the production of cross-reactive antibodies, which may be used for coronavirus detection and neutralization.

The present study aimed to generate antibodies against predicted B cell epitopic peptides encoding bAMH for developing different ELISA models. Sandwich ELISA was determined to be an excellent technique for assessing bAMH in bovine plasma based on sensitivity tests. The assay's specificity, sensitivity, inter- and intra-assay CV, recovery %, Lower limit of quantification (LLOQ), and Upper limit of quantification (ULOQ) were determined. The test was selective since it did not bind to AMH-related growth and differentiation factors (LH and FSH) or non-related components (BSA, progesterone). The intra-assay CV was 5.67%, 3.12%, 4.94%, 3.61% and 4.27% for 72.44, 183.11, 368.24, 522.24 and 732.25 pg/ml AMH levels, respectively. At the same time, the inter-assay CV was 8.77%, 7.87%, 4.53%, 5.76% and 6.70% for 79.30, 161.27, 356.30, 569.33 and 798.19 pg/ml AMH levels, respectively. The average (Mean ± SEM) recovery percentages were 88–100%. LLOQ was 5 pg/ml and ULOQ at 50 µg/ml (CV < 20%). In conclusion, we developed a new highly sensitive ELISA against bAMH using epitope specific antibodies. [ABSTRACT FROM AUTHOR]

To express the GapC protein of Staphylococcus aureus isolated from bovine milk and to predict and identify its B-cell epitope, GapC gene of S. aureus strain 15119 isolated by our lab was amplified and the recombinant expression plasmid pET-28a-GapC was constructed. The recombinant protein GapC with a molecular weight of 44 kD was induced and purified. Then, the purified protein was used to immunize New Zealand white rabbits to obtain polyclonal antibodies. And bioinformatics method was to analyze the secondary and tertiary structures of GapC protein and predict the B cell epitopes. The predicted and selected epitopes were identified by specific antibodies. The results showed that the GapC protein had promising immugenicity and 7 B cell epitopes were selected. Two of dominant B cell epitope PL5（221IPEIDGKLDGGAQRVP236）and PL7（264KNASNESFGYTEDEIVSSDVVGM286）were identified using specific polyclonal antibody. This data lays the foundation for the development of epitope vaccine [ABSTRACT FROM AUTHOR]

This study aims to establish a chemiluminescence immunoassay for the detection of anti-PPRV H protein antibody. Four epitope peptides of B cell epitope of H protein, with good reactivity, were used as the detection antigen after synthesized together. After determining the antigen concentration for coating and working dilution for serum, the optimization of the incubation time for serum and enzymelabeled secondary antibody, the ROC curve analysis was performed to determine the cut-off value of the assay. Thus the chemiluminescence immunoassay for the detection of anti-PPRV H protein was constructed, and the sensitivity, specificity and repeatability of this assay were evaluated. Results showed that the optimal coating concentration of antigen of this assay was 1.5×10-6 μg/well, the optimal working dilution of the serum to be tested were 1 : 100, and the incubation time of serum, and enzyme-labeled secondary antibody were 10 min respectively. The cut-off value of the assay was S/P=9.77%, the intra-assay and inter-assay coefficients of variation were tested to be < 10%. There was no crossreaction obtained when positive sera of FMD, sheep pox, BT, and contagious caprine pleuropneumonia were used to test the assay, indicating that the assay had reasonable specificity. The detection results of 247 field sera showed that the established assay had a relative coincidence rate of 94.33% and much more sensitivity when compared with commercially available PPRV c-ELISA kit. In conclusion, this study has developed a specific, sensitive and stable chemiluminescence immunoassay method for detecting antibodies of PPRV H protein, which can be used to detect PPRV antibodies in field serum samples. [ABSTRACT FROM AUTHOR]

Porcine circovirus type 2 (PCV2) is the main causative agent of porcine circovirus-associated disease (PCVAD) that profoundly impacts the swine industry worldwide. While most of the commercial PCV vaccines are developed based on PCV genotype 2a (PCV2a), PCV genotype 2b (PCV2b) has become predominant since 2003. In this study, we developed and evaluated DNA-based bivalent vaccines covering both PCV2a and PCV2b. We generated a new immunogen, PCV2b-2a, by combining consensus sequences of the PCV2a and PCV2b capsid proteins (Cap2a and Cap2b) in a form of fusion protein. We also examined whether modifications of the PCV2b-2a fusion protein with a signal sequence (SS) and granulocyte macrophage-colony stimulating factor (GM-CSF) fusing with interleukine-4 (IL-4) (GI) could further improve the vaccine immunogenicity. An immunogenicity study of BALB/cAJcl mice revealed that the DNA vector pVAX1 co-expressing PCV2b-2a and GI (pVAX1.PCV2b-2a-GI) was most potent at inducing both antibody and cellular immune responses against Cap2a and Cap2b. Interestingly, the vaccines skewed the immune response towards Th1 phenotype (IgG2a > IgG1). By performing ELISA and ELISpot with predicted epitope peptides, the three most immunogenic B cell epitopes and five putative T cell epitopes were identified on Cap2a and Cap2b. Importantly, our DNA vaccines elicited broad immune responses recognizing both genotype-specific and PCV2-conserved epitopes. Sera from mice immunized with the DNAs expressing PCV2b-2a and PCV2b-2a-GI significantly inhibited PCV2a cell entry at serum dilution 1:8. All these results suggest a great potential of our PCV2b-2a-based vaccines, which can be further developed for use in other vaccine platforms to achieve both vaccine efficacy and economical production cost.

The hepatitis B virus core antigen (HBcAg) tolerates insertion of foreign epitopes and maintains its ability to self‐assemble into virus‐like particles (VLPs). We constructed a ∆HBcAg‐based VLP vaccine expressing three predicted severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) B and T cell epitopes and determined its immunogenicity and protective efficacy. The recombinant ∆HBcAg‐SARS‐CoV‐2 protein was expressed in Escherichia coli, purified, and shown to form VLPs. K18‐hACE2 transgenic C57BL/6 mice were immunized intramuscularly with ∆HBcAg VLP control (n = 15) or ∆HBcAg‐SARS‐CoV‐2 VLP vaccine (n = 15). One week after the 2nd booster and before virus challenge, five ∆HBcAg‐SARS‐CoV‐2 vaccinated mice were euthanized to evaluate epitope‐specific immune responses. There is a statistically significant increase in epitope‐specific Immunoglobulin G (IgG) response, and statistically higher interleukin 6 (IL‐6) and monocyte chemoattractant protein‐1 (MCP‐1) expression levels in ∆HBcAg‐SARS‐CoV‐2 VLP‐vaccinated mice compared to ∆HBcAg VLP controls. While not statistically significant, the ∆HBcAg‐SARS‐CoV‐2 VLP mice had numerically more memory CD8+ T‐cells, and 3/5 mice also had numerically higher levels of interferon gamma (IFN‐γ) and tumor necrosis factor (TNF). After challenge with SARS‐CoV‐2, ∆HBcAg‐SARS‐CoV‐2 immunized mice had numerically lower viral RNA loads in the lung, and slightly higher survival, but the differences are not statistically significant. These results indicate that the ∆HBcAg‐SARS‐CoV‐2 VLP vaccine elicits epitope‐specific humoral and cell‐mediated immune responses but they were insufficient against SARS‐CoV‐2 infection. [ABSTRACT FROM AUTHOR]

Aim: Dengue and Zika viruses cause significant mortality globally. Considering high sequence similarity between the viral proteins, we designed common multi-epitope vaccine candidates against these pathogens. Methods: We identified multiple T and B cell epitope-rich conserved 'immunogenic hotspots' from highly antigenic and phylogenetically related viral proteins and used these to design the multi-epitope vaccine (MEV) candidates, ensuring high global population coverage. Results: Four MEV candidates containing conserved immunogenic hotspots from E and NS5 proteins with the highest structural integrity could favorably interact with TLR4-MD2 complex in molecular docking studies, indicating activation of TLR-mediated immune responses. MEVs also induced memory responses in silico, hallmarks of a good vaccine candidate. Conclusion: Conserved immunogenic hotspots can be utilized to design cross-protective MEV candidates. Dengue and Zika viruses cause significant illness globally. Interestingly, they belong to the same family of viruses and therefore are closely related to each other. The immune response developed against one can often protect against the other or in some cases exacerbate the infection. Considering these characteristics of these viruses, we have designed a common vaccine candidate using bioinformatics-based tools, taking care to exclude the infection enhancing factors. Common multi-epitope vaccine candidates against Dengue viral strains and Zika virus have been designed in silico by utilizing multiple T and B-cell epitope-rich 'immunogenic hotspots', derived from the most antigenic and phylogenetically-related conserved proteins. [ABSTRACT FROM AUTHOR]

African swine fever virus (ASFV) is a highly infectious viral pathogen that endangers the global pig industry, and no effective vaccine is available thus far. The CD2v protein is a glycoprotein on the outer envelope of ASFV, which mediates the transmission of the virus in the blood and recognition of the virus serotype, playing an important role in ASFV vaccine development and disease prevention. Here, we generated two specific monoclonal antibodies (mAbs), 6C11 and 8F12 (subtype IgG1/kappa-type), against the ASFV CD2v extracellular domain (CD2v-ex, GenBank: MK128995.1, 1–588 bp) and characterized their specificity. Peptide scanning technology was used to identify the epitopes recognized by mAbs 6C11 and 8F12. As a result, two novel B cell epitopes, 38DINGVSWN45 and 134GTNTNIY140, were defined. Amino acid sequence alignment showed that the defined epitopes were conserved in all referenced ASFV strains from various regions of China including the highly pathogenic, epidemic strain, Georgia2007/1 (NC_044959.2), with the same noted substitutions compared to the four foreign ASFV wild-type strains. This study provides important reference values for the design and development of an ASFV vaccine and useful biological materials for the functional study of the CD2v protein by deletion analysis. [ABSTRACT FROM AUTHOR]

Background: The variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harbor diverse spike (S) protein sequences, which can greatly influence the efficacies of therapeutics. Therefore, it would be of great value to develop neutralizing monoclonal antibodies (mAbs) that can broadly recognize multiple variants. Methods: Using an mRNA-LNP immunization strategy, we generated several mAbs that specifically target the conserved S2 subunit of SARS-CoV-2 (B-S2-mAbs). These mAbs were assessed for their neutralizing activity with pseudotyped viruses and binding ability for SARS-CoV-2 variants. Results: Among these mAbs, five exhibited strong neutralizing ability toward the Gamma variant and also recognized viral S proteins from the Wuhan, Alpha, Beta, Gamma, Delta and Omicron (BA.1, BA.2 and BA.5) variants. Furthermore, we demonstrated the broad reactivities of these B-S2-mAbs in several different applications, including immunosorbent, immunofluorescence and immunoblotting assays. In particular, B-S2-mAb-2 exhibited potent neutralization of Gamma variant (IC50 = 0.048 µg/ml) in a pseudovirus neutralization assay. The neutralizing epitope of B-S2-mAb-2 was identified by phage display as amino acid residues 1146–1152 (DSFKEEL) in the S2 subunit HR2 domain of SARS-CoV-2. Conclusion: Since there are not many mAbs that can bind the S2 subunit of SARS-CoV-2 variants, our set of B-S2-mAbs may provide important materials for basic research and potential clinical applications. Importantly, our study results demonstrate that the viral S2 subunit can be targeted for the production of cross-reactive antibodies, which may be used for coronavirus detection and neutralization. [ABSTRACT FROM AUTHOR]

Aspergillus fumigatus is a pathogenic microorganism that causes aspergillosis due to the presence of its allergenic proteins. During the last two years, a few clinical cases have been reported where allergic bronchopulmonary aspergillosis (ABPA) has been detected in COVID-19 patients. The administration of antifungal medicine did not provide satisfactory results. It is a challenging job for medical scientists to protect mankind by designing an epitope-based vaccine against the rare disease aspergillosis. Other than twenty-three allergenic proteins, this microorganism contains an extra-cellular cellulase CelA expansin protein (Afu5g08030), which is allergenic. To design a peptide vaccine against aspergillosis, the identification of B cell and T cell epitopes is state-of-the-art technology. In our latest research, probable T cell and B cell epitopes are predicted. Molecular docking analysis of these predicted epitopes with their receptors is performed. Here, the primary sequence of the expansin protein is extracted and analyzed. Then, its secondary and tertiary structures are predicted using a homology modeling method and validated. Considering the physicochemical properties of this antigenic protein, two short stretches of peptides, namely 80KPQADEDPNASSSSSSS96 and 286DGGKTWQGTTRTS298, are predicted as linear B cell epitopes. Similarly, based on its contacts with the highest number of alleles, the peptide sequence 221LDLFQNAFTQLADVS235 is chosen as the most possible T cell epitope for the protein present in Aspergillus fumigatus with the highest binding energy for MHC II allele HLA-DRB1* 01: 01. Considering the binding energy of the B cell epitope with IgE, the second epitope 286DGGKTWQGTTRTS298 is designated as the most potential epitope of B cells for this protein. Docking studies were performed with the T cell epitope with the human ternary complex of T cell receptor, CD4 receptor, and peptide-MHC II molecule (PDB ID 3T0E) with a binding energy of −192 Kcal/mole. For peptide-based vaccines, the proposed B cell and T cell epitopes may be used against aspergillosis after further experimental analysis. [ABSTRACT FROM AUTHOR]

Foot-and-mouth disease (FMD) is a highly contagious and economically devastating disease in cloven-hoofed animals. To prevent the spread of FMD virus (FMDV), traditional inactivated vaccines are used to immunize susceptible animals in disease-endemic countries. However, the inactivated FMD vaccine has several limitations, including safety concerns. To overcome these limitations, subunit proteins have been studied as alternative vaccine candidates. In this study, we designed two multiepitope recombinant proteins (OVM and AVM) containing antigenic sites (residue of VP1 132–162 and residue of VP1 192–212) of three topotypes of FMDV serotype O or three topotypes of FMDV serotype A. Each recombinant protein was efficiently expressed in Escherichia coli with high solubility, and the immunogenicity and protective efficacy of the proteins as FMD vaccine candidates were evaluated. The results showed that OVM and AVM emulsified with ISA201 adjuvant induced effective antigen-specific humoral and cell-mediated immune responses and successfully protected mice from O/Jincheon/SKR/2014, O/VET/2013, and A/Malaysia/97 viruses. In addition, intramuscular immunization of pigs with the OVM and AVM emulsified with ISA201 elicited effective levels of neutralizing antibodies to the viruses with homologous epitopes. Importantly, OVM-AVM emulsified with CAvant®SOE-X adjuvant conferred 100% protection against the O/Jincheon/SKR/2014 virus with homologous residues and 75% protection against A/SKR/GP/2018 with heterologous residues. The results presented in this study suggest that the combination of OVM and AVM protein with an effective adjuvant could yield an effective and safe vaccine candidate for the prevention and control of foot-and-mouth disease. In addition, our results provide a vaccine platform that can safely, cost-efficiently, and rapidly generate protective vaccine candidates against diverse FMDVs. [ABSTRACT FROM AUTHOR]

Infectious diseases, caused by various pathogens in the clinic, threaten the safety of human life, are harmful to physical and mental health, and also increase economic burdens on society. Infections are a complex mechanism of interaction between pathogenic microorganisms and their host. Identification of the causative agent of the infection is vital for the diagnosis and treatment of diseases. Etiological laboratory diagnostic tests are therefore essential to identify pathogens. However, due to its rapidity and automation, the serological diagnostic test is among the methods of great significance for the diagnosis of infections with the basis of detecting antigens or antibodies in body fluids clinically. Epitopes, as a special chemical group that determines the specificity of antigens and the basic unit of inducing immune responses, play an important role in the study of immune responses. Identifying the epitopes of a pathogen may contribute to the development of a vaccine to prevent disease, the diagnosis of the corresponding disease, and the determination of different stages of the disease. Moreover, both the preparation of neutralizing antibodies based on useful epitopes and the assembly of several associated epitopes can be used in the treatment of disease. Epitopes can be divided into B cell epitopes and T cell epitopes; B cell epitopes stimulate the body to produce antibodies and are therefore commonly used as targets for the design of serological diagnostic experiments. Meanwhile, epitopes can fall into two possible categories: linear and conformational. This article reviews the role of B cell epitopes in the clinical diagnosis of infectious diseases. [ABSTRACT FROM AUTHOR]

Clostridium perfringens type A frequently causes necrohaemorrhagic enteritis in cattle, a rapidly progressing disease with a high mortality rate, thus inflicting substantial economic losses in the cattle industry. Effective prevention and control of this disease rely on rapid detection and vaccination strategies, making the screening of antigenic proteins with diagnostic and vaccine potential particularly crucial. In this study, we conducted a pangenomic analysis of 15 bacterial strains, grounded in traditional reverse vaccinology and supplemented with B-cell linear and conformational epitope analysis tools. This approach led to the identification of 2304 core genes and 3606 accessory genes, among which 58 surface-exposed proteins, encoded by core genes, were identified Proteins lacking tertiary structure information were predicted via AlphaFold2, ultimately identifying four target proteins and 14 candidate proteins enriched with linear and conformational epitopes, including virulence proteins such as alpha-toxin, theta-toxin, and alpha-clostripain, and extracellular solute-binding proteins, rhodanese-like proteins, and the accessory gene-encoded lysozyme inhibitor LprI family protein. Our findings demonstrate that the combined use of multiple B-cell epitope analysis tools can help overcome the limitations of any single tool. The proteins selected in this study offer valuable references for rapid diagnostics and the development of genetically engineered vaccines. • Combined linear and conformational epitope predictions enhance the accuracy of antigen selection. • Identified novel surface proteins with high immunological potential using AlphaFold2. • Analyzed B-cell epitope tool biases to improve prediction reliability. • Multi-tool strategy reduces individual prediction biases, enhancing accuracy. [ABSTRACT FROM AUTHOR]

Porcine epidemic diarrhea virus (PEDV) is the pathogen of Porcine epidemic diarrhea (PED) and can mainly cause acute diarrhea, vomiting, dehydration and high mortality in neonatal piglets. The nucleocapsid (N) protein of PEDV is a highly conserved structural protein. In this study, 6–8-week-old BALB/c mice were immunized with purified PEDV, and three monoclonal antibodies (mAbs) against the PEDV N protein were generated, named 3C6,4F8,4C9. Among them, three new B cell epitopes, 235IGENPDKL242, 12KRVPLSLY19, 372DAFKTGNA380 were firstly identified in the viral N-protein. Among them, 4F8 and 4C9 had IgG1 isotype with Kappa light chain, while 3C6 had IgG2a isotype with Kappa light chain. Three monoclonal antibodies (mAbs) demonstrated specific reactivity with PEDV as evidenced by Western blot and indirect immunofluorescence assay. By studying the interaction between the mAbs and the N protein, we can gain insights into the protein's conformation and functional regions. This information will help develop fast and accurate PEDV diagnostic methods. • Three hybridoma cell lines that could stably secrete mAbs against N protein was prepared. • All mAbs have high anti-PEDV affinity, indicating the potential for the development of an ELISA diagnostic method. • Three B cell epitope on N protein are identificated for the first time. [ABSTRACT FROM AUTHOR]

Copyright of China Tropical Medicine is the property of China Tropical Medicine Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract The porcine epidemic diarrhea virus (PEDV) causes a highly contagious disease in pigs, which is one of the most devastating viral diseases of swine in the world. In China, PEDV was first confirmed in 1984 and PEDV infections occurred sporadically from 1984 to early 2010. From late 2010 until present, PEDV infections have swept every province or region in China. In this study, we analyzed a total of 186 full-length spike genes and deduced proteins of all available complete genomes of PEDVs isolated in China during 2007–2019. A total of 28 potential recombination events were identified in the spike genes of PEDVs in China. Spike gene recombination not only expanded the genetic diversity of PEDVs in the GII genogroup, but also resulted in the emergence of a new evolutional branch GI-c during 2016–2018. In addition, comparative analysis of spike proteins between GI-a prototype virulent CV777 and GII strain AJ1102 reveals that the amino acid variations could affect 20 potential linear B cell epitopes, demonstrating a dramatic antigen drift in the spike protein. These results provide a thorough view of the information about the genetic and antigenic diversity of PEDVs circulating in China and therefore could benefit the development of suitable strategies for disease control.

Bovine viral diarrhea virus (BVDV), causing bovine viral diarrhea (BVD) in cattle, is one of the highly contagious and devastating diseases of cattle. Since 1980, BVDV has been identified all-over China in a variety of animal species including cattle, camels, yaks, sheep, water buffalo, goats, Sika deer and pigs. In this study, 31 BVDV complete genomes reported in China (from 2004 to 2020) with other 112 genomes reported around the world were comparatively analyzed. Phylogenetic analysis shows that BVDV genomes reported worldwide clustered in three major clades i.e., BVDV-1, BVDV-2, and BVDV-3. The BVDV-1 is genetically the most diverged genotype and phylogenetically classified into 7 sub-clades in our study based on full-length genomes. The China BVDV genomes fall into all three major clades, e.g., BVDV-1, BVDV-2 and BVDV-3. China BVDV-1 clustered into five sub-clades, e.g., 1, 2, 3, 6 and 7, where sub-clade 7 clustered as a separate sub-clade. Full-length genome recombination analysis reveals that the BVDV-1 reported in China appears to be mainly involved in recombination events. In addition, comparative analysis of E2 proteins between BVDV-1, BVDV-2, and BVDV-3 reveals that the amino acid variations could affect 12 potential linear B cell epitopes, demonstrating a dramatic antigen drift in the E2 protein. These results provide a thorough view of the information about the genetic and antigenic diversity of BVDVs circulating in China and therefore could benefit the development of suitable strategies for disease control.

Biotherapeutics, and antimicrobial proteins in particular, are of increasing interest for human medicine. An important challenge in the development of such therapeutics is their potential immunogenicity, which can induce production of anti-drug-antibodies, resulting in altered pharmacokinetics, reduced efficacy, and potentially severe anaphylactic or hypersensitivity reactions. For this reason, the development and application of effective deimmunization methods for protein drugs is of utmost importance. Deimmunization may be achieved by unspecific shielding approaches, which include PEGylation, fusion to polypeptides (e.g., XTEN or PAS), reductive methylation, glycosylation, and polysialylation. Alternatively, the identification of epitopes for T cells or B cells and their subsequent deletion through site-directed mutagenesis represent promising deimmunization strategies and can be accomplished through either experimental or computational approaches. This review highlights the most recent advances and current challenges in the deimmunization of protein therapeutics, with a special focus on computational epitope prediction and deletion tools.

Canine adenovirus type 1 (CAdV-1) is a double-stranded DNA virus, which is the causative agent of fox encephalitis. The Fiber protein is one of the structural proteins in CAdV-1, which mediates virion binding to the coxsackievirus and adenovirus receptor on host cells. The suspected virus was cultured in the MDCK cells, and it was determined through the cytopathic effects, sequencing and electron microscopy. The informatics analysis of the Fiber was done using online bioinformatics servers. The CAdV-1-JL2021 strain was isolated successfully, and were most similar to the CAdV-1 strain circulating in Italy. The occurrence of negative selection and recombination were found in the CAdV-1-JL2021 and CAdV-2-AC_000020.1. Host cell membrane was its subcellular localization. The CAdV-1-JL2021 Fiber (ON164651) had 6 glycosylation sites and 107 phosphorylation sites, exerted adhesion receptor-mediated virion attachment to host cell, which was the same as CAdV-2-AC_000020.1 Fiber. The Fiber tertiary structure of the CAdV-1-JL2021 and CAdV-2-AC_000020.1 was different, but they had the same coxsackievirus and adenovirus receptor. "VATTSPTLTFAYPLIKNNNH" were predicted to be the potential CAdV-1 B cell linear epitope. The MHC-I binding peptide "KLGVKPTTY" were both presented in the CAdV-1-JL2021 and CAdV-2-AC_000020.1 Fiber and it is useful to design the canine adenovirus vaccine. [ABSTRACT FROM AUTHOR]

The outbreak of SARS-CoV-2 leading to the declaration of the COVID-19 global pandemic has led to the urgent development and deployment of several COVID-19 vaccines. Many of these new vaccines, including those based on mRNA and adenoviruses, are aimed to generate neutralizing antibodies against the spike glycoprotein, which is known to bind to the receptor angiotensin converting enzyme 2 (ACE2) in host cells via the receptor-binding domain (RBD). Antibodies binding to this domain can block the interaction with the receptor and prevent viral entry into the cells. Additionally, these vaccines can also induce spike-specific T cells which could contribute to providing protection against the virus. However, the emergence of new SARS-CoV-2 variants can impair the immunity generated by COVID-19 vaccines if mutations occur in cognate epitopes, precluding immune recognition. Here, we evaluated the chance of five SARS-CoV-2 variants of concern (VOCs), Alpha, Beta, Gamma, Delta and Omicron, to escape spike-specific immunity induced by vaccines. To that end, we examined the impact of the SARS-CoV-2 variant mutations on residues located on experimentally verified spike-specific epitopes, deposited at the Immune Epitope Database, that are targeted by neutralizing antibodies or recognized by T cells. We found about 300 of such B cell epitopes, which were largely overlapping, and could be grouped into 54 B cell epitope clusters sharing ≥ 7 residues. Most of the B cell epitope clusters map in the RBD domain (39 out of 54) and 20%, 50%, 37%, 44% and 57% of the total are mutated in SARS-CoV-2 Alpha, Beta, Gamma, Delta and Omicron variants, respectively. We also found 234 experimentally verified CD8 and CD4 T cell epitopes that were distributed evenly throughout the spike protein. Interestingly, in each SARS-CoV-2 VOC, over 87% and 79% of CD8 and CD4 T cell epitopes, respectively, are not mutated. These observations suggest that SARS-CoV-2 VOCs—particularly the Omicron variant—may be prone to escape spike-specific antibody immunity, but not cellular immunity, elicited by COVID-19 vaccines. [ABSTRACT FROM AUTHOR]

Canine adenovirus type 1 (CAdV-1) is a double-stranded DNA virus, which is the causative agent of fox encephalitis. The Fiber protein is one of the structural proteins in CAdV-1, which mediates virion binding to the coxsackievirus and adenovirus receptor on host cells. The suspected virus was cultured in the MDCK cells, and it was determined through the cytopathic effects, sequencing and electron microscopy. The informatics analysis of the Fiber was done using online bioinformatics servers. The CAdV-1-JL2021 strain was isolated successfully, and were most similar to the CAdV-1 strain circulating in Italy. The occurrence of negative selection and recombination were found in the CAdV-1-JL2021 and CAdV-2-AC_000020.1. Host cell membrane was its subcellular localization. The CAdV-1-JL2021 Fiber (ON164651) had 6 glycosylation sites and 107 phosphorylation sites, exerted adhesion receptor-mediated virion attachment to host cell, which was the same as CAdV-2-AC_000020.1 Fiber. The Fiber tertiary structure of the CAdV-1-JL2021 and CAdV-2-AC_000020.1 was different, but they had the same coxsackievirus and adenovirus receptor. “VATTSPTLTFAYPLIKNNNH” were predicted to be the potential CAdV-1 B cell linear epitope. The MHC-I binding peptide “KLGVKPTTY” were both presented in the CAdV-1-JL2021 and CAdV-2-AC_000020.1 Fiber and it is useful to design the canine adenovirus vaccine.

Porcine hemagglutinating encephalomyelitis virus (PHEV) is a Betacoronavirus characterized by neurological symptoms and a worldwide prevalence. Although PHEV is one of the earliest discovered porcine coronaviruses, it remains poorly studied. The full-length genome of the earliest PHEV strain collected in 1970 in the United States (PHEV/67 N/US/1970) was determined in October 2020. Using this virus as a prototype, we comparatively analyzed all available PHEV full-length sequences during 1970–2015. In phylogenetic trees based on PHEV full-length or spike glycoprotein open reading frame genomic sequences, PHEV/67 N/US/1970 was sorted into a clade different from that of viruses isolated in the United States in 2015. Intriguingly, United States and Belgium viruses isolated in 2015 and 2005, respectively, revealed multiple deletion mutation patterns compared to the strain PHEV/67 N/US/1970, leading to a truncated or a non-functional NS2A coding region. In addition, the genomic similarity analysis showed a hypervariability of the spike glycoprotein coding region, which can affect at least eight potential linear B cell epitopes located in the spike glycoprotein. This report indicates that PHEVs in the United States underwent a significant genetic drift, which might influence PHEV surveillance in other countries.

Porcine hemagglutinating encephalomyelitis virus (PHEV) is a Betacoronavirus characterized by neurological symptoms and a worldwide prevalence. Although PHEV is one of the earliest discovered porcine coronaviruses, it remains poorly studied. The full-length genome of the earliest PHEV strain collected in 1970 in the United States (PHEV/67 N/US/1970) was determined in October 2020. Using this virus as a prototype, we comparatively analyzed all available PHEV full-length sequences during 1970–2015. In phylogenetic trees based on PHEV full-length or spike glycoprotein open reading frame genomic sequences, PHEV/67 N/US/1970 was sorted into a clade different from that of viruses isolated in the United States in 2015. Intriguingly, United States and Belgium viruses isolated in 2015 and 2005, respectively, revealed multiple deletion mutation patterns compared to the strain PHEV/67 N/US/1970, leading to a truncated or a non-functional NS2A coding region. In addition, the genomic similarity analysis showed a hypervariability of the spike glycoprotein coding region, which can affect at least eight potential linear B cell epitopes located in the spike glycoprotein. This report indicates that PHEVs in the United States underwent a significant genetic drift, which might influence PHEV surveillance in other countries. [ABSTRACT FROM AUTHOR]

The development of autoimmune diseases following SARS-CoV-2 infection, including multisystem inflammatory syndrome, has been reported, and several mechanisms have been suggested, including molecular mimicry. We developed a scalable, comparative immunoinformatics pipeline called cross-reactive-epitope-search-using-structural-properties-of-proteins (CRESSP) to identify cross-reactive epitopes between a collection of SARS-CoV-2 proteomes and the human proteome using the structural properties of the proteins. Overall, by searching 4 911 245 proteins from 196 352 SARS-CoV-2 genomes, we identified 133 and 648 human proteins harboring potential cross-reactive B-cell and CD8+ T-cell epitopes, respectively. To demonstrate the robustness of our pipeline, we predicted the cross-reactive epitopes of coronavirus spike proteins, which were recognized by known cross-neutralizing antibodies. Using single-cell expression data, we identified PARP14 as a potential target of intermolecular epitope spreading between the virus and human proteins. Finally, we developed a web application (https://ahs2202.github.io/3M/) to interactively visualize our results. We also made our pipeline available as an open-source CRESSP package (https://pypi.org/project/cressp/), which can analyze any two proteomes of interest to identify potentially cross-reactive epitopes between the proteomes. Overall, our immunoinformatic resources provide a foundation for the investigation of molecular mimicry in the pathogenesis of autoimmune and chronic inflammatory diseases following COVID-19. [ABSTRACT FROM AUTHOR]

Objective To analyze the structure，physicochemical properties and B/T cell antigenic epitopes of the Tyrophagus putrescentiae group 3（Tyr p 3）. Methods The amino acid sequence of Tyr p 3 was obtained from NCBI da‑ tabase. The primary structure of Tyr p 3 was analyzed by ProtScale tools. The secondary structure of Tyr p 3 was analyzed by SOPMA. The homology modeling of the tertiary structure of Tyr p 3 was carried out by SWISS-MODEL，and the stabili‑ ty of the predicted tertiary structure model of Tyr p 3 protein was evaluated. The signal peptide of Tyr p 3 was predicted by‑ SignalP 4. 1. The location of the transmembrane region of Tyr p 3 was predicted by TMHMM2. 0. The physicochemical properties of Tyr p 3 were analyzed by ProtScale tools，including the hydrophobicity，instability index and theoretical iso‑ electric point（pI）of Tyr p 3. The phosphorylation site of Tyr p 3 was analyzed using NetPhos3. 1. The B cell epitope of Tyr p 3 was analyzed by using Protean software in DNASTAR Lasergene software，BCPreds and IEDB. The T cell epitope of Tyr p 3 was analyzed by NetMHC II 2. 2 and NetMHC II pan-3. 1. Results The primary structure of Tyr p 3 contained a total of 269 amino acids with a molecular weight of 28 380. 13 Da. The secondary structure of Tyr p 3 included α-helix （19. 65% of amino acids），β-turn（5. 96% of amino acids），extended chain（25. 61% of amino acids）and random coil （50. 19% of amino acids）. The tertiary structure of Tyr p 3 obtained by homology modeling was verified to be reasonable. The amino acids 1 to 16 of Tyr p 3 was the signal peptide of Tyr p 3. The amino acid starting position to ending position of the transmembrane domain of Tyr p 3 protein was 247-268. Tyr p 3 was a hydrophilic and physicochemically stable protein with a theoretical isoelectric point of 5. 63. Tyr p 3 contained 9 serine kinases，7 threonine kinases and 3 tyrosine kinase phosphorylation sites. The B cell epitope of Tyr p 3 had 5 peptide sequences，and the amino acid positions were 102-113， 145-150，161-170，207-221，and 237-242. The T cell epitope of Tyr p 3 had 3 peptide sequences，the amino acid posi‑ tions of which were 89-10，114-125，and 175-185. Conclusions Tyr p 3 was a hydrophilic protein with stable physico‑ chemical properties. The predicted B/T epitope provided a reference for the development of vaccines and peptide-ELISA detection kits. [ABSTRACT FROM AUTHOR]

House dust mites are one of the most important allergen sources worldwide and affect approximately 50% of asthmatic patients. Allergen-specific immunotherapy (AIT) is the only disease-modifying treatment for allergic diseases. However, clinical applications of allergen extract-based AIT were greatly restricted due to the potential adverse reactions. In order to improve the efficacy and reduce adverse effects, modified hypoallergens have been proposed for molecular forms of AIT. Therefore, in the present study, we converted the major house dust mite allergen Der f 34 into a B cell epitope-based hypoallergenic vaccine by the immunoinformatics and peptide-carrier fusion approaches. Initially, the physiochemical and structural properties of Der f 34 were analyzed. Accordingly, the linear and conformational B cell epitopes, as well as the helper T lymphocytes epitopes, were computed based on the properties of Der f 34. Three different fragments (residues 12–18, 83–89, and 98–116) of major allergen Der f 34 that containing candidate B cell epitope and that without T cell epitopes were linked at the N terminal and C terminal of the PreS carrier. The three-dimensional structure of the final vaccine was then predicted and the interaction with immune receptors (toll-like receptor-3) was evaluated by ligand-receptor docking. The immunogenic profiles and immune response of the final vaccine were in silico assessed after immunization, which represented the vaccine could induce an effective immune response. In addition, the codon sequences of the vaccine were cloned and expressed in E.coli, the vaccine was purified and exhibited a lower IgE-binding ability. Our results indicated that the Der f 34 hypoallergen could be a potential vaccine candidate for molecular forms of AIT in the house dust mite allergy. [ABSTRACT FROM AUTHOR]

Arginine kinase (AK) is an enzyme present in various invertebrates, as well as in some trypanosomatids such as T. cruzi , the etiological agent that causes Chagas disease. In invertebrates, this protein acts as an allergen inducing an IgE-type humoral immune response. Since AK is a highly conserved protein, we decided to study whether patients with chronic Chagas disease (CCD) produce specific antibodies against T. cruzi AK (Tc AK). Plasma from patients with CCD, with and without cardiac alterations and non-infected individuals were evaluated for the presence of anti- Tc AK IgG and IgE antibodies by ELISA, including detection of specific IgG subclasses. Our results showed that the levels of specific anti- Tc AK IgG and IgE were different between infected and non-infected individuals, but comparable between those with different clinical manifestations. Interestingly, anti- Tc AK IgG4 antibodies associated with IgE-mediated allergenic processes were also increased in CCD patients. Finally, we found that several of the predicted B cell epitopes in Tc AK matched allergenic peptides previously described for its homologues in other organisms. Our results revealed for the first time a parasite's specific IgE antibody target and suggest that Tc AK could contribute to delineate an inefficient B cell response by prompting a bias towards a Th2 profile. These findings also shed light on a potential allergenic response in the context of T. cruzi infection. [ABSTRACT FROM AUTHOR]

Foot-and-mouth disease (FMD) is a highly contagious and economically devastating disease in cloven-hoofed animals. To prevent the spread of FMD virus (FMDV), traditional inactivated vaccines are used to immunize susceptible animals in disease-endemic countries. However, the inactivated FMD vaccine has several limitations, including safety concerns. To overcome these limitations, subunit proteins have been studied as alternative vaccine candidates. In this study, we designed two multiepitope recombinant proteins (OVM and AVM) containing antigenic sites (residue of VP1 132–162 and residue of VP1 192–212) of three topotypes of FMDV serotype O or three topotypes of FMDV serotype A. Each recombinant protein was efficiently expressed in Escherichia coli with high solubility, and the immunogenicity and protective efficacy of the proteins as FMD vaccine candidates were evaluated. The results showed that OVM and AVM emulsified with ISA201 adjuvant induced effective antigen-specific humoral and cell-mediated immune responses and successfully protected mice from O/Jincheon/SKR/2014, O/VET/2013, and A/Malaysia/97 viruses. In addition, intramuscular immunization of pigs with the OVM and AVM emulsified with ISA201 elicited effective levels of neutralizing antibodies to the viruses with homologous epitopes. Importantly, OVM-AVM emulsified with CAvant®SOE-X adjuvant conferred 100% protection against the O/Jincheon/SKR/2014 virus with homologous residues and 75% protection against A/SKR/GP/2018 with heterologous residues. The results presented in this study suggest that the combination of OVM and AVM protein with an effective adjuvant could yield an effective and safe vaccine candidate for the prevention and control of foot-and-mouth disease. In addition, our results provide a vaccine platform that can safely, cost-efficiently, and rapidly generate protective vaccine candidates against diverse FMDVs.

In recent years, the incidence of brucellosis has increased annually, causing tremendous economic losses to animal husbandry in a lot of countries. Therefore, developing rapid, sensitive, and specific diagnostic techniques is critical to control the spread of brucellosis. In this study, bioinformatics technology was used to predict the B cell epitopes of the main outer membrane proteins of Brucella, and the diagnostic efficacy of each epitope was verified by an indirect enzyme-linked immunosorbent assay (iELISA). Then, a fusion protein containing 22 verified epitopes was prokaryotically expressed and used as an antigen in paper-based ELISA (p-ELISA) for serodiagnosis of brucellosis. The multi-epitope-based p-ELISA was evaluated using a collection of brucellosis-positive and -negative sera collected from bovine and goat, respectively. Receiver operating characteristic (ROC) curve analysis showed that the sensitivity and specificity of detection-ELISA in diagnosing goat brucellosis were 98.85 and 98.51%. The positive and the negative predictive values were 99.29 and 98.15%, respectively. In diagnosing bovine brucellosis, the sensitivity and specificity of this method were 97.85 and 96.61%, with the positive and negative predictive values being identified as 98.28 and 97.33%, respectively. This study demonstrated that the B cell epitopes contained in major antigenic proteins of Brucella can be a very useful antigen source in developing a highly sensitive and specific method for serodiagnosis of brucellosis.

Analysis of the bat viruses most closely related to SARS‐CoV‐2 indicated that the virus probably required limited adaptation to spread in humans. Nonetheless, since its introduction in human populations, SARS‐CoV‐2 must have been subject to the selective pressure imposed by the human immune system. We exploited the availability of a large number of high‐quality SARS‐CoV‐2 genomes, as well as of validated epitope predictions, to show that B cell epitopes in the spike glycoprotein (S) and in the nucleocapsid protein (N) have higher diversity than nonepitope positions. Similar results were obtained for other human coronaviruses and for sarbecoviruses sampled in bats. Conversely, in the SARS‐CoV‐2 population, epitopes for CD4+ and CD8+ T cells were not more variable than nonepitope positions. A significant reduction in epitope variability was instead observed for some of the most immunogenic proteins (S, N, ORF8 and ORF3a). Analysis over longer evolutionary time frames indicated that this effect is not due to differential constraints. These data indicate that SARS‐CoV‐2 evolves to elude the host humoral immune response, whereas recognition by T cells is not actively avoided by the virus. However, we also found a trend of lower diversity of T cell epitopes for common cold coronaviruses, indicating that epitope conservation per se is not directly linked to disease severity. We suggest that conservation serves to maintain epitopes that elicit tolerizing T cell responses or induce T cells with regulatory activity. [ABSTRACT FROM AUTHOR]

The Natural killer (NK) cells' ability to destroy cancerous cells is predominantly focused on the activation of the co-stimulatory and natural killer group two with receptor of member-D also called NKGD2/NKG2D. These identifies ligands that are MHC-Class1 structural homologs like that of the UL16 protein-binding type 2. The ULBP2 has been shown to mediate-natural resistance against the tumors mechanism in the condition of in-vitro, in-vivo, making it a possible target for producing the immune-therapeutic drugs for the diagnosis of the cancers and certain other viral diseases. In this present research, we created a stable and high-quality 3-D structure of the ULBP-2 protein through SWISS-Model also visualized by using UCSF-Chimera Tool. Moreover, the ULBP2 protein was prognosticated to be acts as antigenic, 11-discontinuous-B-Cell epitopes, 05 ULBP2 proteins antibody-based epitopes, and possible predicted the top hits of six linear B-cell epitopes. The ULBP2 protein carried seven cytotoxic-T lymphocytes (CTLs), two helper-T lymphocytes (HTLs), the LGKKLNVTTAWAQN is a promiscuous epitope MHC bounded to the T cells and with LRDIQLENY highest antigen scores in MHC molecule. Finally, the promising epitopes that could be successful in producing B-cell and T-cell mediated immunity against the required immune reaction to tumorigenesis were expected.

Infectious diseases, caused by various pathogens in the clinic, threaten the safety of human life, are harmful to physical and mental health, and also increase economic burdens on society. Infections are a complex mechanism of interaction between pathogenic microorganisms and their host. Identification of the causative agent of the infection is vital for the diagnosis and treatment of diseases. Etiological laboratory diagnostic tests are therefore essential to identify pathogens. However, due to its rapidity and automation, the serological diagnostic test is among the methods of great significance for the diagnosis of infections with the basis of detecting antigens or antibodies in body fluids clinically. Epitopes, as a special chemical group that determines the specificity of antigens and the basic unit of inducing immune responses, play an important role in the study of immune responses. Identifying the epitopes of a pathogen may contribute to the development of a vaccine to prevent disease, the diagnosis of the corresponding disease, and the determination of different stages of the disease. Moreover, both the preparation of neutralizing antibodies based on useful epitopes and the assembly of several associated epitopes can be used in the treatment of disease. Epitopes can be divided into B cell epitopes and T cell epitopes; B cell epitopes stimulate the body to produce antibodies and are therefore commonly used as targets for the design of serological diagnostic experiments. Meanwhile, epitopes can fall into two possible categories: linear and conformational. This article reviews the role of B cell epitopes in the clinical diagnosis of infectious diseases.

The porcine epidemic diarrhea virus (PEDV) causes a highly contagious disease in pigs, which is one of the most devastating viral diseases of swine in the world. In China, PEDV was first confirmed in 1984 and PEDV infections occurred sporadically from 1984 to early 2010. From late 2010 until present, PEDV infections have swept every province or region in China. In this study, we analyzed a total of 186 full-length spike genes and deduced proteins of all available complete genomes of PEDVs isolated in China during 2007–2019. A total of 28 potential recombination events were identified in the spike genes of PEDVs in China. Spike gene recombination not only expanded the genetic diversity of PEDVs in the GII genogroup, but also resulted in the emergence of a new evolutional branch GI-c during 2016–2018. In addition, comparative analysis of spike proteins between GI-a prototype virulent CV777 and GII strain AJ1102 reveals that the amino acid variations could affect 20 potential linear B cell epitopes, demonstrating a dramatic antigen drift in the spike protein. These results provide a thorough view of the information about the genetic and antigenic diversity of PEDVs circulating in China and therefore could benefit the development of suitable strategies for disease control. [ABSTRACT FROM AUTHOR]

African swine fever virus (ASFV), a re-emerging DNA virus, causes a highly contagious disease for domestic pigs. It is running rife worldwide and threatening the global swine industry. Protein p54 is an attractive candidate for ASFV diagnostic and vaccine design. In this work, we designed a peptide to mimic the N-terminal domain (NTD) of ASFV p54 and pretested it with sera from ASFV-infected pigs. The peptide could be well recognized by the sera, implying that the NTD of p54 contained some potential linear B cell epitopes. Then, the conjugates of the peptide with bovine serum albumin were used as the immunogen to generate monoclonal antibodies (mAbs). A total of six mAbs specific to the NTD of ASFV p54 protein were developed. Five of them well reacted with ASFV HLJ/18 strain and recognized a same linear B cell epitope 5FFQPV9. Furthermore, epitope 5FFQPV9 could be well recognized by ASFV-positive sera from natural infected pigs, suggesting that it was a natural linear B-cell epitope. Conservation analysis indicated that epitope 5FFQPV9 were highly conserved among ASFV epidemic isolates belonging to genotype I and II. Alanine-scanning mutagenesis further revealed that the residues (6F to 9V) of epitope 5FFQPV9 were the core binding sites for antibody recognition. This is the first research to characterize specific mAbs against NTD of p54 protein. These findings may help further understand the function of p54 protein and the improvement of ASFV diagnosis. [ABSTRACT FROM AUTHOR]

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)