Electron beam irradiation degrades the toxicity and alters the protein structure of Staphylococcus aureus alpha-hemolysin.

α-Hemolysin (Hla) is a potent pore-forming toxin (PFT) produced by Staphylococcus aureus that exacerbates the pathogenesis of S. aureus enterotoxicity and plays a role in population food poisoning. Hla lyses cells by binding to host cell membranes and oligomerizing to form heptameric structures, thereby disrupting the cell barrier. Although the broad bactericidal effect of electron beam irradiation (EBI) has been demonstrated whether it has a damaging or degrading effect on Hla's remains unknown. In this study, EBI was found to have the effect of altering the secondary structure of Hla proteins, verifying that the damaging effect of EBI-treated Hla on intestinal and skin epithelial cell barriers was significantly reduced. It was noted by hemolysis and protein interactions that EBI treatment significantly disrupted the binding of Hla to its high-affinity receptor, but did not affect the binding between Hla monomers to form heptamers. Thus, EBI can effectively reduce the threat of Hla to food safety.

Designing a bioadjuvant candidate vaccine targeting infectious bursal disease virus (IBDV) using viral VP2 fusion and chicken IL-2 antigenic epitope: A bioinformatics approach.

Infectious Bursal Disease (IBD) is a common and contagious viral infection that significantly affects the poultry industry. This severely suppresses the immune system in chickens, thereby threating their health and well-being. Vaccination is the most effective strategy for preventing and controlling this infectious agent. The development of VP2-based DNA vaccines combined with biological adjuvants has recently received considerable attention due to their effectiveness in eliciting both humoral and cellular immune responses. In this study, we applied bioinformatics tools to design a fused bioadjuvant candidate vaccine from the full-length sequence of the VP2 protein of IBDV isolated in Iran using the antigenic epitope of chicken IL-2 (chiIL-2). Furthermore, to improve the antigenic epitope presentation and to maintain the three-dimensional structure of the chimeric gene construct, the P2A linker (L) was used to fuse the two fragments. Our in-silico analysis for the design of a candidate vaccine indicates that a continuous sequence of amino acid residues ranging from 105 to 129 in chiIL-2 is proposed as a B cell epitope by epitope prediction servers. The final 3D structure of the VP2-L-chiIL-2105-129 was subjected to physicochemical property determination, molecular dynamic simulation, and antigenic site determination. The results of these analyses led to the development of a stable candidate vaccine that is non-allergenic and has the potential for antigenic surface display potential and adjuvant activity. Finally, it is necessary to investigate the immune response induced by our proposed vaccine in avian hosts. Notably, increasing the immunogenicity of DNA vaccines can be achieved by combining antigenic proteins with molecular adjuvants using the principle of rational vaccine design.

Study on the Sensitization and Antigenic Epitopes of Tropomyosin from Antarctic Krill (Euphausia superba).

Antarctic krill (Euphausia superba), a shrimp-like marine crustacean, has become a beneficial source of high-quality animal protein. Meanwhile, a special focus has been placed on its potential sensitization issue. In this study, a 35 kDa protein was purified and identified to be Antarctic krill tropomyosin (AkTM) by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The purified TM showed a strong IgE-binding capacity to shrimp/crab-allergic patients' sera, indicating that TM is the primary allergen in Antarctic krill. Simulated gastrointestinal digestion revealed that the digestion stability of TM to pepsin was higher than that to trypsin. The strong degranulation triggered by TM in RBL-2H3 cells suggested that AkTM has a strong sensitization capacity. The TM-sensitized BALB/c mice displayed severe anaphylactic symptoms; high levels of TM-specific IgE, sIgG1, and histamine; and increased IL-4, indicating that AkTM could provoke IgE-mediated allergic reactions. Bioinformatics prediction, indirect competition ELISA, and mast cell degranulation assay were used to map the antigenic epitopes of AkTM. Finally, nine peptides of T43-58, T88-101, T111-125, T133-143, T144-155, T183-197, T223-236, T249-261, and T263-281 were identified as the linear epitopes of AkTM. The findings may help us develop efficient food processing techniques to reduce krill allergy and gain a deeper comprehension of the allergenicity of krill allergens.

TPBTE: A model based on convolutional Transformer for predicting the binding of TCR to epitope.

T cell receptors (TCRs) selectively bind to antigens to fight pathogens with specific immunity. Current tools focus on the nature of amino acids within sequences and take less into account the nature of amino acids far apart and the relationship between sequences, leading to significant differences in the results from different datasets. We propose TPBTE, a model based on convolutional Transformer for Predicting the Binding of TCR to Epitope. It takes epitope sequences and the complementary decision region 3 (CDR3) sequences of TCRß chain as inputs. And it uses a convolutional attention mechanism to learn amino acid representations between different positions of the sequences based on learning local features of the sequences. At the same time, it uses cross attention to learn the interaction information between TCR sequences and epitope sequences. A comprehensive evaluation of the TCR-epitope data shows that the average area under the curve of TPBTE outperforms the baseline model, and demonstrate an intentional performance. In addition, TPBTE can give the probability of binding TCR to epitopes, which can be used as the first step of epitope screening, narrowing the scope of epitope search and reducing the time of epitope search.

Pulsed Electric Field-Assisted Alcalase Treatment Reduces the Allergenicity and Eliminates the Antigenic Epitopes of Ovomucoid.

Physically assisted chemical modifications can effectively reduce the allergenicity of ovomucoid (OVM). However, only a few studies have used pulsed electric field (PEF)-assisted alcalase hydrolysis to reduce the allergenicity of OVM. Herein, we investigated the effect of PEF-assisted alcalase treatment on the spatial conformation, allergenicity, and antigenic epitopes of OVM based on multispectroscopic analyses, bioinformatics, and mass spectrometry. The results showed that PEF-assisted alcalase treatment promoted the hydrolysis of OVM; moreover, the α-helix content and surface hydrophobicity of OVM significantly decreased, which disordered its spatial conformation and weakened its intermolecular interactions. Additionally, enzyme-linked immunosorbent assay (ELISA) results showed that the PEF-assisted alcalase treatment significantly reduced the binding levels of IgE and IgG1, which were 47.66 and 36.41%, respectively. Finally, eight epitopes of OVM were obtained by immunoinformatic tools. Nano-high performance liquid chromatography coupled to tandem mass spectrometry (nano-HPLC MS/MS) results showed that the hydrolysate of OVM and alcalase (HOVM) had nine more peptide-containing epitopes than the hydrolysate of PEF-treated OVM and PEF-treated alcalase (HOVM-PP'), indicating that PEF could promote the elimination of linear epitopes in OVM, thereby reducing OVM allergenicity.

Identification of allergenic epitopes destroyed by two processing technologies of glycinin A2 from soybean.

BACKGROUND: Glycinin is one of the most highly allergenic proteins in soybeans, and G2 is one of the five allergenic subunits of glycinin. Compared with the alkaline chain, the acidic chain A2 of the G2 subunit has strong allergenicity. However, the precise epitopes of A2 and the epitopes destroyed during processing are still unknown. RESULTS: In the present study, preparation of two specific antibodies damaged by processing and phage display techniques were applied to locate the antigenic epitopes of glycinin A2 polypeptide chains disrupted by two processing techniques (thermal processing and ultra-high pressure combined thermal processing). Bioinformatics methods were used to predict the possible epitopes of the A2 chain. The A2 chain and its overlapping segments were introduced into T7 phages and expressed on phage shell by phage display. An indirect enzyme-linked immunosorbent assay was used to screen for antigenic epitopes that had been disrupted by the two processing technologies. The results showed that the dominant antigenic region disrupted by processing was located mainly in the A2-3-B fragment. The reacting experiment with the serum of allergic patients showed that the A2-3-B fragment protein was not only an antigenic region, but also an allergenic region. The two processing technologies destroyed the allergenic epitopes of A2 chain, thereby reducing the allergenicity of protein. The amino acids where the dominant allergenic region disrupted by processing was located were: 233 AIVTVKGGLRVTAPAMRKPQQEEDDDDEEEQPQCVE268 . CONCLUSION: Precise epitopes of the acidic chain A2 in glycinin were identified and epitopes destroyed in two common processing methods were also obtained. The application products of rapid detection of de-allergenicity effect of processed food can be developed according to the location of processed destruction allergenic region, which is of great significance with respect to preventing the occurrence of soybean allergenic diseases. © 2022 Society of Chemical Industry.

Immunogenicity and Immunoprotection of PCV2 Virus-like Particles Incorporating Dominant T and B Cell Antigenic Epitopes Paired with CD154 Molecules in Piglets and Mice.

Porcine circovirus type 2 (PCV2) is capable of causing porcine circovirus-associated disease (PCVAD) and is one of the major threats to the global pig industry. The nucleocapsid protein Cap encoded by the PCV2 ORF2 gene is an ideal antigen for the development of PCV2 subunit vaccines, and its N-terminal nuclear localization sequence (NLS) structural domain is essential for the formation of self-assembling VLPs. In the present study, we systematically expressed and characterized full-length PCV2 Cap proteins fused to dominant T and B cell antigenic epitopes and porcine-derived CD154 molecules using baculovirus and found that the Cap proteins fusing epitopes were still capable of forming virus-like particles (VLPs). Both piglet and mice experiments showed that the Cap proteins fusing epitopes or paired with the molecular adjuvant CD154 were able to induce higher levels of humoral and cellular responses, particularly the secretion of PCV2-specific IFN-γ and IL-4. In addition, vaccination significantly reduced clinical signs and the viral load of PCV2 in the blood and tissues of challenged piglets. The results of the study provide new ideas for the development of a more efficient, safe and broad-spectrum next-generation PCV2 subunit vaccine.

Detection and Molecular Characterization of Rotavirus Infections in Children and Adults with Gastroenteritis from Vojvodina, Serbia.

Rotaviruses (RV) are the leading cause of gastroenteritis in infants, young children, and adults, responsible for serious disease burden. In the period 2012-2018, a cross-sectional study was conducted using stool samples collected from patients with acute gastroenteritis from Vojvodina, Serbia. We described age and gender distribution, as well as seasonal patterns of RV prevalence. Out of 1853 included stool samples, RV was detected in 29%. Hospitalized children between 1-2 years old were especially affected by RV infection (45%). The highest prevalence of infection was observed during the colder, winter/spring months. We compared sequenced representative G and P genotypes circulating in Serbia with vaccine strains and determined their genetic similarity. Genotype combination G2P[4] was the most prevalent (34.6%), followed by G2P[8] (24.1%) and G1P[8] (21.1%). Given that several epitopes were conserved, neutralization motifs among circulating strains can be characterized as sufficiently matching vaccine strains Rotarix™ and RotaTeq™, but existing antigenic disparities should not be overlooked. The present results contribute to a better insight into the prevalence of rotavirus infection in our region and point out the need for epidemiological surveillance of rotaviruses before the introduction of vaccines. These data can help formulate future vaccine strategies in Serbia.

Protective antigenic epitopes revealed by immunosignatures after three doses of inactivated SARS-CoV-2 vaccine.

Background: SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has infected millions of people around the world. Vaccination is a pillar in the strategy to control transmission of the SARS-CoV-2 spread. Immune responses to vaccination require elucidation. Methods: The immune responses to vaccination with three doses of inactivated SARS-CoV-2 vaccine were followed in a cohort of 37 healthy adults (18-59 years old). Blood samples were collected at multiple time points and submitted to peptide array, machine learning modeling, and sequence alignment analyses, the results of which were used to generate vaccine-induced antibody-binding region (VIABR) immunosignatures (Registration number: ChiCTR2200058571). Results: Antibody spectrum signals showed vaccination stimulated antibody production. Sequence alignment analyses revealed that a third vaccine dose generated a new highly represented VIABR near the A570D mutation, and the whole process of inoculation enhanced the VIABR near the N501Y mutation. In addition, the antigen conformational epitopes varied between short- and long-term samples. The amino acids with the highest scores in the short-term samples were distributed primarily in the receptor binding domain (RBD) and N-terminal domain regions of spike (S) protein, while in the long-term samples (12 weeks after the 2nd dose), some new conformational epitopes (CEs) were localized to crevices within the head of the S protein trimer. Conclusion: Protective antigenic epitopes were revealed by immunosignatures after three doses of inactivated SARS-CoV-2 vaccine inoculation. A third dose results in a new top-10 VIABR near the A570D mutation site of S protein, and the whole process of inoculation enhanced the VIABR near the N501Y mutation, thus potentially providing protection from strains that have gained invasion and immune escape abilities through these mutation.

Phylogenetic analysis of the viral proteins VP4/VP7 of circulating human rotavirus strains in China from 2016 to 2019 and comparison of their antigenic epitopes with those of vaccine strains.

Group A rotaviruses (RVAs) are the most common etiological agents of severe acute diarrhea among children under 5 years old worldwide. At present, two live-attenuated RVA vaccines, LLR (G10P[15]) and RotaTeq (G1-G4, G6 P[8], P[5]), have been introduced to mainland China. Although RVA vaccines can provide homotypic and partially heterotypic protection against several strains, it is necessary to explore the genetic and antigenic variations between circulating RVAs and vaccine strains. In this study, we sequenced viral protein VP7 and VP4 outer capsid proteins of 50 RVA strains circulating in China from 2016 to 2019. The VP7 and VP4 sequences of almost all strains showed high homology to those of previously reported human strains and vaccine strains of the same genotype. However, in the presumed antigenic epitopes of the VP7 and VP4, multiple amino acid variations were found, regardless of the G and P genotypes of these strains. Moreover, all circulating G3 RVA strains in China potentially possess an extra N-linked glycosylation site compared with the G3 strain of RotaTeq. The potential N-linked glycosylation site at residues 69-71 was found in all G9 strains in China but not in the G9 strain of the Rotavac or Rotasill vaccine. These variations in antigenic sites might result in the selection of strains that escape the RVA neutralizing-antibody pressure imposed by vaccines. Furthermore, the G4 and P[6] genotypes in this study showed high homology to those of porcine strains, indicating the transmission of G4 and P[6] genotypes from pigs to humans in China. More genetic surveillance with antigenic evaluation in prevalent RVAs is necessary for developing and implementing rotavirus vaccines in China.

Using Self-Assembling ADDomer Platform to Display B and T Epitopes of Type O Foot-and-Mouth Disease Virus.

Foot-and-mouth disease virus (FMDV) is a highly contagious and devastating virus that infects cloven-hoofed livestock and various wildlife species. Vaccination is the best measure to prevent FMD. ADDomer, as a kind of non-infectious adenovirus-inspired nanoparticle, has the advantage of high thermal stability. In this study, two dominant B-cell antigen epitopes (residues 129~160 and 200~213) and a dominant T-cell antigen epitope (residues 16~44) of type O FMDV were inserted into the ADDomer variable loop (VL) and arginine-glycine-aspartic acid (RGD) loop. The 3D structure of the recombinant protein (ADDomer-RBT) was simulated by homology modeling. First, the recombinant proteins were expressed by the baculovirus expression system and detected by western blot and Q Exactive mass spectrometry. Then the formation of VLPs was observed under a transmission electron micrograph (TEM). Finally, we evaluated the immunogenicity of chimeric VLPs with a murine model. Bioinformatic software analysis preliminarily corroborated that the chosen epitopes were successfully exposed on the surface of ADDomer VLPs. The TEM assay demonstrated the structural integrity of the VLPs. After immunizing, it was found that FMDV-specific antibodies can be produced in mice to induce humoral and cellular immune responses. To sum up, the ADDomer platform can be used as an effective antigen carrier to deliver antigen epitopes. This study presents one of the candidate vaccines to prevent and control FMDV.

Predicting Antigenic Peptides from Rocio Virus NS1 Protein for Immunodiagnostic Testing Using Immunoinformatics and Molecular Dynamics Simulation.

The mosquito-borne disease caused by the Rocio virus is a neglected threat, and new immune inputs for serological testing are urgently required for diagnosis in low-resource settings and epidemiological surveillance. We used in silico approaches to identify a specific antigenic peptide (p_ROCV2) in the NS1 protein of the Rocio virus that was theoretically predicted to be stable and exposed on its surface, where it demonstrated key properties allowing it to interact with antibodies. These findings related to the molecular dynamics of this peptide provide important insights for advancing diagnostic platforms and investigating therapeutic alternatives.

Ferritin Light Chain: A Candidate Autoantigen in Immuno-Related Pancytopenia.

The characteristic feature of immune-related pancytopenia (IRP) is autoantibody-mediated bone marrow (BM) damage and peripheral blood cytopenia. We found that the potential antigen of IRP was Ferritin light chain (FTL) by SEREX (serological analysis of recombinant cDNA expression libraries) in the previous study. In this study, we tried to explore the antigenic epitopes of FTL and verify its antigenicity in IRP. We found the possible FTL epitope: VNLYLQASYTYLSLG by phage random peptide library. Through ELISPOT, it was found that peptide VNLYLQASYTYLSLG can significantly stimulate the production of interleukin-4 and cannot stimulate the production of interferon-γ, which suggested that the peptide can obviously activate Th2 cells. Peptide-major histocompatibility complex tetramer elicited antigen-specific T cell responses. The expression levels of FTL were significantly increased in the patients with untreated IRP (P < 0.05). In conclusion, we found that FTL is the target antigen for some patients with IRP. The peptide of VNLYLQASYTYLSLG is an epitope of the target antigen. The target antigen is abnormally overexpressed on the membrane of BM cells, especially on the surface of CD34+ BM cells of patients with IRP. In addition, it is related to the severity of disease. These results provide a possible new target for the treatment of IRP in the future.

Impact of Vaccination on Rotavirus Genotype Diversity: A Nearly Two-Decade-Long Epidemiological Study before and after Rotavirus Vaccine Introduction in Sicily, Italy.

Sicily was the first Italian region to introduce rotavirus (RV) vaccination with the monovalent G1P[8] vaccine Rotarix® in May 2012. In this study, the seasonal distribution and molecular characterization of RV strains detected over 19 years were compared to understand the effect of Rotarix® on the evolutionary dynamics of human RVs. A total of 7846 stool samples collected from children < 5 years of age, hospitalized with acute gastroenteritis, were tested for RV detection and genotyping. Since 2013, vaccine coverage has progressively increased, while the RV prevalence decreased from 36.1% to 13.3% with a loss of seasonality. The local distribution of RV genotypes changed over the time possibly due to vaccine introduction, with a drastic reduction in G1P[8] strains replaced by common and novel emerging RV strains, such as equine-like G3P[8] in the 2018−2019 season. Comparison of VP7 and VP4 amino acid (aa) sequences with the cognate genes of Rotarix® and RotaTeq® vaccine strains showed specific aa changes in the antigenic epitopes of VP7 and of the VP8* portion of VP4 of the Italian RV strains. Molecular epidemiological surveillance data are required to monitor the emergence of novel RV strains and ascertain if these strains may affect the efficacy of RV vaccines.

Molecular surveillance and genetic divergence of rotavirus A antigenic epitopes in Gabonese children with acute gastroenteritis.

BACKGROUND: Rotavirus A (RVA) causes acute gastroenteritis in children <5 years of age in sub-Saharan Africa. In this study, we described the epidemiology and genetic diversity of RVA infecting Gabonese children and examined the antigenic variability of circulating strains in relation to available vaccine strains to maximize the public health benefits of introducing rotavirus vaccine through the Expanded Programme on Immunization (EPI) in Gabon. METHODS: Stool samples were collected consecutively between April 2018 and November 2019 from all hospitalized children <5 years with gastroenteritis and community controls without gastroenteritis. Children were tested for rotavirus A by quantitative RT-PCR and subsequently sequenced to identify circulating rotavirus A genotypes in the most vulnerable population. The VP7 and VP4 (VP8*) antigenic epitopes were mapped to homologs of vaccine strains to assess structural variability and potential impact on antigenicity. FINDINGS: Infections were mostly acquired during the dry season. Rotavirus A was detected in 98/177 (55%) hospitalized children with gastroenteritis and 14/67 (21%) of the control children. The most common RVA genotypes were G1 (18%), G3 (12%), G8 (18%), G9 (2%), G12 (25%), with G8 and G9 reported for the first time in Gabon. All were associated either with P[6] (31%) or P[8] (38%) genotypes. Several non-synonymous substitutions were observed in the antigenic epitopes of VP7 (positions 94 and 147) and VP8* (positions 89, 116, 146 and 150), which may modulate the elicited immune responses. INTERPRETATION: This study contributes to the epidemiological surveillance of rotavirus A required before the introduction of rotavirus vaccination in the EPI for Gabonese children.

Hidden Patterns of Anti-HLA Class I Alloreactivity Revealed Through Machine Learning.

Detection of alloreactive anti-HLA antibodies is a frequent and mandatory test before and after organ transplantation to determine the antigenic targets of the antibodies. Nowadays, this test involves the measurement of fluorescent signals generated through antibody-antigen reactions on multi-beads flow cytometers. In this study, in a cohort of 1,066 patients from one country, anti-HLA class I responses were analyzed on a panel of 98 different antigens. Knowing that the immune system responds typically to "shared" antigenic targets, we studied the clustering patterns of antibody responses against HLA class I antigens without any a priori hypothesis, applying two unsupervised machine learning approaches. At first, the principal component analysis (PCA) projections of intra-locus specific responses showed that anti-HLA-A and anti-HLA-C were the most distantly projected responses in the population with the anti-HLA-B responses to be projected between them. When PCA was applied on the responses against antigens belonging to a single locus, some already known groupings were confirmed while several new cross-reactive patterns of alloreactivity were detected. Anti-HLA-A responses projected through PCA suggested that three cross-reactive groups accounted for about 70% of the variance observed in the population, while anti-HLA-B responses were mainly characterized by a distinction between previously described Bw4 and Bw6 cross-reactive groups followed by several yet undocumented or poorly described ones. Furthermore, anti-HLA-C responses could be explained by two major cross-reactive groups completely overlapping with previously described C1 and C2 allelic groups. A second feature-based analysis of all antigenic specificities, projected as a dendrogram, generated a robust measure of allelic antigenic distances depicting bead-array defined cross reactive groups. Finally, amino acid combinations explaining major population specific cross-reactive groups were described. The interpretation of the results was based on the current knowledge of the antigenic targets of the antibodies as they have been characterized either experimentally or computationally and appear at the HLA epitope registry.

In-silico identification of subunit vaccine candidates against lung cancer-associated oncogenic viruses.

Globally, ~20% of cancer malignancies are associated with virus infections. Lung cancer is the most prevalent cancer and has a 10% 5-year survival rate when diagnosed at stage IV. Cancer vaccines and oncolytic immunotherapy are promising treatment strategies for better clinical outcomes in advanced-stage cancer patients. Here, we used a reverse vaccinology approach to devise subunit vaccine candidates against lung cancer-causing oncogenic viruses. Protein components (945) from nine oncogenic virus species were systematically analyzed to identify epitope-based subunit vaccine candidates. Best vaccine candidates were identified based on their predicted ability to stimulate humoral and cell-mediated immunity and avoid self-tolerance. Using a rigorous integrative approach, we identified 125 best antigenic epitopes with predicted B-cell, T-cell, and/or MHC-binding capability and vaccine adjuvant potential. Thirty-two of these antigenic epitopes were predicted to have IL-4/IFN-gamma inducing potential and IL-10 non-inducing potential and were predicted to bind 15 MHC-type I and 49 MHC-type II alleles. All 32 epitopes were non-allergenic and 31 were non-toxic. The identified epitopes showed good conservancy and likely bind a broad class of human HLA alleles, indicating promiscuous potential. The majority of best antigenic epitopes were derived from Human papillomavirus and Epstein-Barr virus proteins. Of the 32 epitopes, 25 promiscuous epitopes were related to E1 and E6 envelope genes and were present in multiple viral strains/species, potentially providing heterologous immunity. Further validating our results, 38 antigenic epitopes were also present in the largest experimentally-validated epitope resource, Immune Epitope Database and Analysis Resource. We further narrowed the selection to 29 antigenic epitopes with the highest immunogenic/immune-boosting potential. These epitopes possess tremendous therapeutic potential as vaccines against lung cancer-causing viruses and should be validated in future experiments. All findings are available at https://webs.iiitd.edu.in/raghava/vlcvirus/.

Identification of ß-conglycinin α' subunit antigenic epitopes destroyed by thermal treatments.

In the present study, phage display technology (PDT) was used to examine ß-conglycinin α' subunit epitopes destroyed by heat treatments. The overlapping gene fragments of the α' subunits were amplified using a polymerase chain reaction (PCR) method, and then the recombinant T7 phages containing the target genes were expressed on the phage surface. In addition, an indirect enzyme-linked immunosorbent assay (iELISA) method was adopted to screen the α' subunit epitopes which had been damaged by the heat treatments. Then, after three rounds of the expression and screening processes, the C1-Y fragments (488PHFNSKAIVVLVINEGEANIELVG511) were identified as α' subunit damaged epitopes. In order to confirm the types of epitopes, three peptides of the C1-Y fragments were synthesized using a solid-phase peptide synthesis method. The results of the iELISA showed that there was a linear epitope of 488PHFNSKAIVVLV499 in the C1-Y fragments. The results obtained in this study confirmed that the C1-Y fragments contained both linear and conformational epitopes, and that the conformational epitopes could be destroyed by thermal treatments. However, it was found that the linear epitopes could not be destroyed. The phage display protein Pt-C1-Y, coupling peptide BSA-Pep-Y, BSA-Pep-1, BSA-Pep-2, and soybean allergy patients' serum reaction results showed that only the Pt-C1-Y had reacted positively with the soybean allergy patients' serum. These findings further indicated that heat treatments can reduce not only the antigenicity, but also the allergenicity, of α' subunits in ß-conglycinin.

Genetic diversity of G9 rotavirus strains circulating among diarrheic children in North India: A comparison with 116E rotavirus vaccine strain.

The parental rotavirus strain 116E (G9P[11]) used to generate Rotavac® vaccine was isolated in 1986 in New Delhi. Thenceforward, there is no comprehensive report on diversity of G9 rotavirus strains from 116E; therefore, the present study evaluates the VP7 gene sequence diversity of G9 strains (retrieved from GenBank) from different geographical regions (1987-2016). Additionally, 22 recently collected G9 strains from Himachal Pradesh and Delhi (2013-2016) were included in the phylogenetic analysis. Interestingly, unlike 116E which belong to lineage-II all other G9 rotavirus including these 22 samples clustered together in a separate lineage (III). Further, six amino acid substitutions including one novel, K143M (epitope 7-2) different from 116E were detected mostly in the neutralization epitopes of VP7 protein (neutralization escape mutants). Overall, the accumulation of identified substitutions in VP7 epitopes and evolution of G9 strains in India may have impact on Rotavac® efficacy.

Scrutinizing the SARS-CoV-2 protein information for designing an effective vaccine encompassing both the T-cell and B-cell epitopes.

Novel SARS coronavirus (SARS-CoV-2) has caused a pandemic condition worldwide. It has been declared as a public health emergency of international concern by WHO in a very short span of time. The community transmission of this highly infectious virus has severely affected various parts of China, Italy, Spain, India, and USA, among others. The prophylactic solution against SARS-CoV-2 infection is challenging due to the high mutation rate of its RNA genome. Herein, we exploited a next-generation vaccinology approach to construct a multi-epitope vaccine candidate against SARS-CoV-2 that is predicted to have high antigenicity, safety, and efficacy to combat this deadly infectious agent. The whole proteome was scrutinized for the screening of highly conserved, antigenic, non-allergen, and non-toxic epitopes having high population coverage that can elicit both humoral and cellular mediated immune response against COVID-19 infection. These epitopes along with four different adjuvants, were utilized to construct a multi-epitope-vaccine candidate that can generate strong immunological memory response having high efficacy in humans. Various physiochemical analyses revealed the formation of a stable vaccine product having a high propensity to form a protective solution against the detrimental SARS-CoV-2 strain with high efficacy. The vaccine candidate interacted with immunological receptor TLR3 with a high affinity depicting the generation of innate immunity. Further, the codon optimization and in silico expression show the plausibility of the high expression and easy purification of the vaccine product. Thus, this present study provides an initial platform for the rapid generation of an efficacious protective vaccine for combating COVID-19.