Residue analysis of a CTL epitope of SARS-CoV spike protein by IFN-gamma production and bioinformatics prediction

Abstract

BackgroundSevere acute respiratory syndrome (SARS) is an emerging infectious disease caused by the novel coronavirus SARS-CoV. The T cell epitopes of the SARS CoV spike protein are well known, but no systematic evaluation of the functional and structural roles of each residue has been reported for these antigenic epitopes. Analysis of the functional importance of side-chains by mutational study may exaggerate the effect by imposing a structural disturbance or an unusual steric, electrostatic or hydrophobic interaction.ResultsWe demonstrated that N50 could induce significant IFN-gamma response from SARS-CoV S DNA immunized mice splenocytes by the means of ELISA, ELISPOT and FACS. Moreover, S366-374 was predicted to be an optimal epitope by bioinformatics tools: ANN, SMM, ARB and BIMAS, and confirmed by IFN-gamma response induced by a series of S358-374-derived peptides. Furthermore, each of S366-374 was replaced by alanine (A), lysine (K) or aspartic acid (D), respectively. ANN was used to estimate the binding affinity of single S366-374 mutants to H-2 Kd. Y367 and L374 were predicated to possess the most important role in peptide binding. Additionally, these one residue mutated peptides were synthesized, and IFN-gamma production induced by G368, V369, A371, T372 and K373 mutated S366-374 were decreased obviously.ConclusionsWe demonstrated that S366-374 is an optimal H-2 Kd CTL epitope in the SARS CoV S protein. Moreover, Y367, S370, and L374 are anchors in the epitope, while C366, G368, V369, A371, T372, and K373 may directly interact with TCR on the surface of CD8-T cells.

Identification of a dominant CD8+ CTL epitope in the SARS-associated coronavirus 2 spike protein

“…By contrast, a peptide of the homologous region on the SARS-CoV-2 S protein (CYGVSPTKL; aa 379–387) was not recognized by CTLs in our study. The replacement of residue A371 by K or D in this epitope of SARS-CoV led to decreased recognition of the peptide by CTLs, suggesting that residue A371 is critical for epitope recognition by CTLs [16] . To determine the minimal epitope(s) required, we synthesized five truncated peptides of peptide #10 (shown in Table 1 ) and used them to stimulate CTLs from the immunized mice in vitro.…”

Immunoinformatics‐aided identification of T cell and B cell epitopes in the surface glycoprotein of 2019‐nCoV

“…Collectively, these interactions indicate a potentially successful presentation of the epitopes by MHC class I molecules, thereby activating CTLs and generating immune responses. We compared the epitopes obtained in our study with epitopes predicted in the spike protein of MERS‐CoV and SARS‐CoV 22,23 . We found one overlapping CTL epitope between MERS‐CoV and 2019‐nCoV with one gap and one mismatch (YLQPRTFLL/YKLQPLTFLL), and no comparable epitopes with SARS‐CoV.…”

SARS‐CoV‐2‐mediated immune system activation and potential application in immunotherapy

“…Currently, a safe vaccine, which is dependent on the investigation of specific epitopes derived from SARS‐CoV‐2 structural proteins and the availability of sequence data, is the most effective intervention for suppressing SARS‐CoV‐2 infection. However, identified epitopes are unstable due to difficulties in epitope detection in glycoproteins, error‐prone SARS‐CoV‐2 replication, and the continuous evolution and the mutations of SARS‐CoV‐2 127 . Thus, epitopes should be further screened according to the conservative filtering principle, consequently producing a more accurate epitope set.…”