Synthetic peptides derived from the genomes of SARS-CoV-2, the virus causing the COVID-19 disease, are useful tools for studying the biology, the structure-function of viral proteins, and the infection cycle of the virus. For example peptide libraries or pools allow the stimulation of SARS-CoV-2 (COVID-19) specific T cells to allow the development of therapeutic vaccines or drugs. After successful stimulation , T cells can be detected and isolated for further research, as needed. Combinatorial peptide libraries allow the characterization of critical features of B cell epitopes as well as MHC class I and class II binding epitopes, either natural or synthetic.
Coronaviruses are positive-sense single-stranded RNA viruses belonging to the family coronavirida. The typical organization of the genome is as follows: 5'-leader-UTR-replicase-S(Spike)-E(Envelope)-M(Membrane)-N(Nucleocapsid)-3'-UTR-poly(A) tail. The virus genome encodes structural proteins, as well as nonstructural proteins. Structural proteins are critical in viral RNA synthesis and referred to as replicase-transcriptase proteins. Non-structural proteins are thought as nonessential for virus replication in cell culture. These nonessential proteins appear to give the virus a selective advantage in vivo and are considered as niche-specific proteins. The niche-specific protein, nonstructural protein 2 (nsp2) together with the structural protein N, the nucleocapsid protein, take part in viral RNA synthesis. The 3'-end of the virus genome contains accessory genes scattered between structural genes. Accessory proteins appear not to be needed for replication in tissue culture but to be important in viral pathogenesis. The synthesis of polypeptide 1ab (pp1ab) involves programmed ribosomal frameshifting during translation of open reading frame 1a (orf1a).
Frame shifting results in a new reading frame that produces a trans-frame protein product. In coronaviruses, a fixed portion of the ribosomes translating orf1a change reading frame at a specific location now decoding information contained in orf1b. Synthetic peptides derived from both types of viral proteins, structural and non-structural, enable the study of SARS-CoV-2 infection and allow defining the biological roles of individual proteins or peptide during infection and pathogenesis.