Beyond Spike: Identification of nine highly prevalent SARS-CoV-2-specific CD8 T-cell epitopes in a large Norwegian cohort
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Abstract
T-cell epitopes with broad population coverage may form the basis for a new generation of SARS-CoV-2 vaccines. However, published studies on immunoprevalence are limited by small test cohorts, low frequencies of antigen-specific cells and lack of data correlating eluted HLA ligands with T-cell responsiveness. As the protective role of pre-existing cross-reactivity to homologous peptides is unclear, we aimed to identify SARS-CoV-2-specific minimal epitopes recognized by CD8 T-cells among 48 peptides eluted from prevalent HLA alleles, and an additional 84 predicted binders, in a large cohort of convalescents (n=83) and pre-pandemic control samples (n=19). We identified nine conserved SARS-CoV-2-specific epitopes restricted by four of the most prevalent HLA class I alleles in the Norwegian study cohort, to which responding CD8 T cells were detected in 70-100% of convalescents expressing the relevant HLA allele. Only two of these were derived from the Spike protein, included in current vaccines. We found a strong correlation between immunoprevalence and immunodominance. Thus, the CD8 T-cell response to SARS-CoV-2 is more focused than previously believed. Using a new algorithm, we predict that a vaccine including these epitopes could induce a T-cell response in 83% of Caucasians.
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SciScore for 10.1101/2021.10.13.463911: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Three convalescents for whom a PCR test was lacking were included based on positive anti-RBD and anti-Nucleocapsid antibodies. anti-RBDsuggested: Noneanti-Nucleocapsidsuggested: NoneThere were no differences between convalescent individuals who had been hospitalized due to COVID-19 as compared to those who had not with respect to SARS-CoV-2 antibody titers or functional CD4 and CD8 T cell responses to peptide pools (Suppl Fig. 1B and 2C). SARS-CoV-2suggested: NonePlasma antibody titer determination: A multiplexed bead-based flow cytometric assay, referred to as microsphere affinity proteomics (MAP), was … SciScore for 10.1101/2021.10.13.463911: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Three convalescents for whom a PCR test was lacking were included based on positive anti-RBD and anti-Nucleocapsid antibodies. anti-RBDsuggested: Noneanti-Nucleocapsidsuggested: NoneThere were no differences between convalescent individuals who had been hospitalized due to COVID-19 as compared to those who had not with respect to SARS-CoV-2 antibody titers or functional CD4 and CD8 T cell responses to peptide pools (Suppl Fig. 1B and 2C). SARS-CoV-2suggested: NonePlasma antibody titer determination: A multiplexed bead-based flow cytometric assay, referred to as microsphere affinity proteomics (MAP), was adapted for detection of SARS-CoV-2 antibodies50. antibodies50suggested: NoneAfter staining with a PE anti-human HLA-A,B,C antibody, stable HLA expressing cell lines were sorted using the Sony SH800 cell sorter. anti-human HLA-Asuggested: NoneSubsequently, surface staining was performed by adding the following antibodies: PerCP/Cyanine5.5 anti-human CD3, Alexa Fluor® 700 anti-human CD4, FITC anti-human CD8a, BV605 anti-human HLA-DR, anti-human CD3suggested: Noneanti-human CD4suggested: Noneanti-human HLA-DRsuggested: NoneThereafter the following antibodies and LD-NIR (1:1000) were added to the sample for 30min at 4°C: FITC anti-human CD8a, LD-NIRsuggested: Noneanti-human CD8asuggested: NoneSubsequently, surface staining was performed by adding the following antibodies: PE anti-human-CD8a, anti-human-CD8asuggested: NoneSoftware and Algorithms Sentences Resources BV785 anti-human CD38, BV421 anti-human CD69 together with Live/Dear-near IR (1:1000; LD-NIR; ThermoFisher Scientific; Cat no L10119) for exclusion of dead cells. ThermoFisher Scientificsuggested: None24 h after UV-exchange, the following streptavidin-tagged fluorochromes were added at optimized ratios to the pMonomer solution: SA-PE (Invitrogen; Cat no S866; Lot no 2129894); SA-APC (Invitrogen; Cat no S868; Lot no 2105223), SA-BV421 (Biolegend; Cat no 405229; Lot no B202410), SA-BV605 (Biolegend; Cat no 405225; Lot no B267737), SA-BV421 (Biolegend; Cat no 405229; Lot no B202410), SA-PE Cy7 (BD Biosciences; Cat no 557598; Lot no 7325636), SA-PE-CF594 (BD Biosciences; Cat no 562284; Lot no 7138598), SA-PE-Cy5 (BD Biosciences; Cat no 554062; Lot no 7066693), SA-APC-R700 (BD Biosciences; Cat no 565144; Lot no 7179560), SA-BB790-P (BD Biosciences; prototype kindly provided by Bob Balderas from BD Biosciences; Lot no 8124567). BD Biosciencessuggested: (BD Biosciences, RRID:SCR_013311)Peptide sequence alignment with human common cold coronaviruses: Homology calculations were performed by aligning the sequence of SARS-CoV-2 epitopes with the corresponding protein sequences of common cold coronaviruses (OC43, NL63, HKU1,229E) using the Clustal Omega tool with default parameters. Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Data analysis and statistics: Flow cytometry data acquired on different BD Biosciences instruments were analyzed using FlowJo (TreeStar) version 10.6.2 software. FlowJosuggested: (FlowJo, RRID:SCR_008520)Statistical analysis was performed in R version 4.0.4 and GraphPad Prism version 8.3.0. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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