ABSTRACT
Coronaviruses are widespread in nature and can infect mammals and poultry, making them a public health concern. Globally, prevention and control of emerging and re-emerging animal coronaviruses is a great challenge. The mechanisms of virus-mediated immune responses have important implications for research on virus prevention and control. The antigenic epitope is a chemical group capable of stimulating the production of antibodies or sensitized lymphocytes, playing an important role in antiviral immune responses. Thus, it can shed light on the development of diagnostic methods and novel vaccines. Here, we have reviewed advances in animal coronavirus antigenic epitope research, aiming to provide a reference for the prevention and control of animal and human coronaviruses. Supplementary Information: The online version contains supplementary material available at 10.1186/s44149-023-00080-0.
ABSTRACT
The regional outbreak of the Swine acute diarrhea syndrome coronavirus (SADS-CoV) has seriously threatened the swine industry. There is an urgent need to discover safe and effective vaccines to contain them quickly. The coronavirus spike protein mediates virus entry into host cells, one of the most important antigenic determinants and a potential vaccine target. Therefore, this study aims to conduct a predictive analysis of the epitope of S protein B cells and T cells (MHC class I and class II) by immunoinformatics methods by screening and identifying protective antigenic epitopes that induce major neutralized antibodies and activate immune responses to construct epitope vaccines. The study explored primary, secondary, and tertiary structures, disulfide bonds, protein docking, immune response simulation, and seamless cloning of epitope vaccines. The results show that the spike protein dominant epitope of the screening has a high conservativeness and coverage of IFN-γ, IL-4-positive Th epitope, and CTL epitope. The constructed epitope vaccine interacts stably with TLR-3 receptors, and the immune response simulation shows good immunogenicity, which could effectively activate humoral and cellular immunity. After codon optimization, it was highly likely to be efficiently and stably expressed in the Escherichia coli K12 expression system. Therefore, the constructed epitope vaccine will provide a new theoretical basis for the design of SADS-CoV antiviral drugs and related research on coronaviruses such as SARS-CoV-2.
ABSTRACT
Although multiple vaccines have been developed and widely administered, several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have been reported to evade immune responses and spread diffusely. Here, 108 RNA-seq files from coronavirus disease 2019 (COVID-19) patients and healthy donors (HD) were downloaded to extract their TCR immune repertoire by MiXCR. Those extracted TCR repertoire were compared and it was found that disease progression was related negatively with diversity and positively with clonality. Specifically, greater proportions of high-abundance clonotypes were observed in active and severe COVID-19 samples, probably resulting from strong stimulation of SARS-CoV-2 epitopes and a continued immune response in host. To investigate the specific recognition between TCR CDR3 and SARS-CoV-2 epitopes, we constructed an accurate classifier CoV2-TCR with an AUC of 0.967 in an independent dataset, which outperformed several similar tools. Based on this model, we observed a huge range in the number of those TCR CDR3 recognizing those different peptides, including 28 MHC-I epitopes from SARS-CoV-2 and 22 immunogenic peptides from SARS-CoV-2 variants. Interestingly, their proportions of high-abundance, low-abundance and rare clonotypes were close for each peptide. To expand the potential application of this model, we established the webserver, CoV2-TCR, in which users can obtain those recognizing CDR3 sequences from the TCR repertoire of COVID-19 patients based on the 9-mer peptides containing mutation site(s) on the four main proteins of SARS-CoV-2 variants. Overall, this study provides preliminary screening for candidate antigen epitopes and the TCR CDR3 that recognizes them, and should be helpful for vaccine design on SARS-CoV-2 variants.
ABSTRACT
Bioinformatics methods were used to predict the hydrophilicity, hydrophobicity, antigen epitopes and analyse multiple sequence alignment of the nucleocapsid protein (N protein) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The recombinant plasmid pET28a/ N was constructed. In the prokaryotic expression system of Escherichia coli, the solubility and expression level of the protein were improved by adjusting the change of induction temperature and time, and the expressed recombinant N protein was purified and identified. The results showed that SARS-CoV-2 N encoded 419 amino acids, with an isoelectric point (PI) of 10.10, no transmembrane region, no signal peptide sequence, and strong local hydrophilicity. The full-length protein had a high antigenic index and was highly conserved, and its homology with SARS-CoV N protein was 90.5%. After fermentation with Escherichia coli prokaryotic expression system, the engineering strain BL21 (DE3)/pET28a/N was induced at 16 °C for 20 h with the final IPTG concentration of 0.2 mmol/L, and the protein was soluble and most pressed at this time, accounting for 70% of the total protein expression. The target protein purified by Ni-NTA affinity chromatography and gel filtration chromatography had a purity of 90% and a molecular weight of 55 kDa, which was specific. [ FROM AUTHOR] Copyright of Journal of Light Industry is the property of Journal of Zhengzhou University of Light Industry, Natural Science Edition 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 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 . (Copyright applies to all s.)
ABSTRACT
Porcine deltacoronavirus (PDCoV) mainly causes severe diarrhea and intestinal pathological damage in piglets and poses a serious threat to pig farms. Currently, no effective reagents or vaccines are available to control PDCoV infection. Single-chain fragment variable (scFv) antibodies can effectively inhibit virus infection and may be a potential therapeutic reagent for PDCoV treatment. In this study, a porcine phage display antibody library from the peripheral blood lymphocytes of piglets infected with PDCoV was constructed and used to select PDCoV-specific scFv. The library was screened with four rounds of biopanning using the PDCoV N protein, and the colony with the highest affinity to the PDCoV N protein was obtained (namely, N53). Then, the N53-scFv gene fragment was cloned into plasmid pFUSE-hIgG-Fc2 and expressed in HEK-293T cells. The scFv-Fc antibody N53 (namely, scFv N53) was purified using Protein A-sepharose. The reactive activity of the purified antibody with the PDCoV N protein was confirmed by indirect enzyme-linked immunosorbent assay (ELISA), western blot and indirect immunofluorescence assay (IFA). Finally, the antigenic epitopes that the scFv N53 recognized were identified by a series of truncated PDCoV N proteins. The amino acid residues 82GELPPNDTPATTRVT96 of the PDCoV N protein were verified as the minimal epitope that can be recognized by the scFv-Fc antibody N53. In addition, the interaction between the scFv-Fc antibody N53 and the PDCoV N protein was further analyzed by molecule docking. In conclusion, our research provides some references for the treatment and prevention of PDCoV.