Background
Coronaviruses have repeatedly threatened humanity, particularly COVID-19, caused by the novel coronavirus SARS-CoV-2 (SARS-CoV-2), which poses a significant threat to global public health. SARS-CoV-2 continues to evolve through random mutations, resulting in a significant decrease in the efficacy of existing vaccines and neutralizing antibody drugs. It is crucial to assess immune escape caused by viral mutations and to develop broad-spectrum vaccines and neutralizing antibodies targeting conserved epitopes.
On April 22, 2024, researchers from the State Key Laboratory of Advanced Drug Delivery and Release Systems at the School of Pharmacy, Zhejiang University, published an article titled "CovEpiAb: a comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses" in BriefingsinBioinformatics. They developed a comprehensive database and analysis resource for immune epitopes and antibodies against human coronaviruses ( HCoVs ), CovEpiAb. CovEpiAb contains over 60,000 experimentally validated epitopes and information on antibodies against over 12,000 HCoVs and SARS-CoV-2 variants. CovEpiAb is freely accessible at https://pgx.zju.edu.cn/covepiab/.
Overview of the CovEpiAb Database
Raw data (including immune epitopes and antibodies against HCoVs, virological characteristics of SARS-CoV-2 variants, and in vitro activity data for various therapeutics) were collected from public databases and literature and then preprocessed. To facilitate epitope prediction and analysis, an online pipeline called COVEP was developed, integrating existing B cell and T cell epitope prediction tools. Finally, the CovEpiAb database was constructed using MySQL and Django tools, with browsing, search, visualization, and download capabilities.
HCoVs immune epitopes
Effective vaccine development relies on the precise identification and characterization of immune epitopes. The database has collected and annotated 66,210 experimentally confirmed B cell epitopes and 3,209 T cell epitopes. Statistical analysis shows that SARS-CoV and MERS-CoV possess the most B cell epitopes (approximately 15,000), followed by HCoV-OC43 and SARS-CoV-2 (over 9,000). Other HCoVs have approximately 5,000. Compared to other HCoVs, SARS-CoV-2 possesses a significantly higher number of T cell epitopes, totaling 2,802, primarily derived from the ORF1ab and S proteins.
Many peptides from other coronaviruses can trigger immune responses in COVID-19 patients. These peptides are called cross-reactive epitopes. Cross-reactive epitopes can elicit a broad immune response against a wide range of viral strains and are important for developing broad-spectrum vaccines. Users can enter a peptide segment and use BLAST to search for all similar epitopes. Alternatively, they can enter a protein sequence to filter for epitope fragments. Detailed information including sequence, object type, location, species, and molecular parentage is available. The report also describes the receptors that bind to the epitopes, receptor-associated epitopes and experiments, immune stimulation protocols and experimental methods, and references.
HCoV antibody characteristics and interaction profiles
The CovEpiAb database contains information on 12,613 anti-HCoV antibodies and provides experimental interaction profiles related to binding and neo-activation activity, with a total of 62,916 data points. Statistical analysis showed that 11,409 antibodies bound to SARS-CoV-2 and 6,710 antibodies had neutralizing activity. More than 3,000 antibodies showed binding and neutralizing activity against SARS-CoV-2 variants. By analyzing antibody gene usage, the top 50 most common V and J gene pairs in antibody heavy and light chains were listed. The most commonly used human heavy chain genes are IGKV3-30, IGHV1-69, IGHJ4, and IGHJ6, and the light chain genes are IGKV1-39, IGKV3-20, IGKJ1, and IGLJ3.
Users can search for antibodies through three modules: antibody type, gene and structure, binding and neutralizing activity. Click on the antibody ID to enter the antibody details page, which provides basic information about the antibody, including name, type, source, binding viral antigen or region and structure, as well as binding and neutralization properties against various virus strains. Structural analysis of antibody-antigen binding sites enables us to reveal molecular interactions and provide guidance for antibody design and optimization. Based on the complex structure, the binding residues on the antigen-antibody contact interface were mainly identified. Focus on the target site of the antibody on the spike protein, as this is critical to determining whether mutations in the spike protein affect antibody binding and function.
Virological characteristics and therapeutic effects of SARS-CoV-2 mutants
SARS-CoV-2 genome mutations may lead to increased transmissibility and infectivity, evasion of immune responses, and reduced efficacy of vaccines and therapeutic drugs. The mutations and virological characteristics of emerging SARS-CoV-2 variants need to be closely monitored . The database provides virological characteristics of SARS-CoV-2 variants, including the currently prevalent Omicron subvariant and other variants. Analysis of the sensitivity of SARS-CoV-2 variants to different treatments, including vaccines, neutralizing antibodies, and convalescent plasma samples , found that compared with other variants, the Omicron variants BQ and XBB showed a more significant reduction in neutralizing activity against various treatments , and this reduction was particularly evident in neutralizing antibodies.
Comparing spike protein mutations across different variants using lollipop plots provides information on all variants. The database annotates key functional sites of spike mutations, including receptor binding sites, mAb resistance sites, and conservation scores. This page provides information on changes in transmissibility, ACE2 binding affinity, fusogenicity, and infectivity compared to other variants. It also includes experimental methods, result descriptions, and data sources. Furthermore, the database allows for scatter plots to illustrate the sensitivity of the variant to various treatments and to assess the neutralizing activity of therapeutic agents against various variants.
Epitope prediction pipeline and site conservation analysis
Since many epitopes have not yet been verified, bioinformatics prediction is of great significance in identifying and characterizing epitopes. In this study, an integrated online pipeline COVEP for B cell and T cell epitope prediction was developed. COVEP was used to successfully predict candidate B cell and T cell epitopes in the entire proteome of 7 HCoVs. By aligning the conserved sequences of the S proteins of 7 HCoVs, it was found that all 9 conserved sequences on the S protein are located on the S2 subunit. Information about antibodies is provided on the "HCoV Conservation" page, which visualizes the spike protein conservation score and antibody binding sites together. Epitopes within evolutionarily conserved regions represent key targets for designing broad-spectrum vaccines against coronaviruses.
Summary
In this study, a functional database and analysis resource for HCoV immune epitopes and antibodies, CovEpiAb, was developed, which provides a comprehensive collection of information on more than 60,000 experimentally validated epitopes and 12,000 antibodies against HCoV and SARS-CoV-2 variants. The database provides cross-reactive epitope annotations, antibody molecular and experimental interaction profiles, virological characteristics and in vitro activity of SARS-CoV-2 variants, immune epitopes, antibody binding sites, and key functional sites of SARS-CoV-2 variant mutations. Online integrated pipelines and conservation analysis enable users to predict not only candidate conserved epitopes of HCoV, but also other epitopes. The CovEpiAb database is a unique and comprehensive resource for evaluating the adaptability and immune evasion of emerging SARS-CoV-2 variants, as well as for the design and development of broad-spectrum vaccines and neutralizing antibody drugs.
