Ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus strains is posing new COVID-19 diagnosis and treatment challenges. To help efforts to meet these challenges we examined data acquired from proteomic analyses of human SARS-CoV-2-infected cell lines and samples from COVID-19 patients. Initially, 129 unique peptides were identified, which were rigorously evaluated for repeats, disorders, polymorphisms, antigenicity, immunogenicity, toxicity, allergens, sequence similarity to human proteins, and contributions from other potential cross-reacting pathogenic species or the human saliva microbiome. We also screened SARS-CoV-2-infected NBHE and A549 cell lines for presence of antigenic peptides, and identified paratope peptides from crystal structures of SARS-CoV-2 antigen-antibody complexes. We then selected four antigen peptides for docking with known viral unbound T-cell receptor (TCR), class I and II peptide major histocompatibility complex (pMHC), and identified paratope sequences. We also tested the paratope binding affinity of SARS-CoV T- and B-cell peptides that had been previously experimentally validated. The resultant antigenic peptides have high potential for generating SARS-CoV-2-specific antibodies, and the paratope peptides can be directly used to develop a COVID-19 diagnostics assay. The presented genomics and proteomics-based in-silico approaches have apparent utility for identifying new diagnostic peptides that could be used to fight SARS-CoV-2.
【저자키워드】 SARS-CoV-2, docking, COVID-19 vaccines, TCR, MHC, diagnostic peptides, paratopes, 【초록키워드】 COVID-19, Treatment, Evolution, proteomics, coronavirus, immunogenicity, SARS-CoV, diagnostic, peptide, Toxicity, docking, severe acute respiratory syndrome Coronavirus, diagnostics, binding affinity, Antigen, Polymorphisms, Viral, COVID-19 diagnosis, human saliva, Microbiome, peptides, T-cell receptor, antigenicity, respiratory, crystal structure, in-silico, utility, SARS-CoV-2-specific antibodies, proteomic, COVID-19 patients, specific antibodies, B-cell, Analysis, crystal structures, major histocompatibility complex, allergens, acute respiratory syndrome, acute respiratory syndrome coronavirus, acute respiratory syndrome coronavirus 2, disorders, human proteins, help, effort, sequence similarity, A549 cell lines, pathogenic, cell line, virus strain, approach, antigenic peptides, virus strains, selected, tested, develop, examined, evaluated, screened, unique, complexes, histocompatibility complex, A549 cell line, antigenic peptide, Initially, 【제목키워드】 development, identification,