Surveillance of SARS-CoV-2 immunogenicity: loss of immunodominant HLA-A*02-restricted epitopes that activate CD8+ T cells
Introduction and methodsIn this present work, coronavirus subfamilies and SARS-CoV-2 Variants of Concern (VOCs) were investigated for the presence of MHC-I immunodominant viral peptides using in silico and in vitro tools.ResultsIn our results, HLA-A*02 haplotype showed the highest number of immunodo...
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Frontiers Media S.A.
2023-11-01
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| 丛编: | Frontiers in Immunology |
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| 在线阅读: | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1229712/full |
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| author | Ágata Lopes-Ribeiro Patrícia de Melo Oliveira Henrique Morais Retes Edel Figueiredo Barbosa-Stancioli Flávio Guimarães da Fonseca Flávio Guimarães da Fonseca Moriya Tsuji Jordana Grazziela Alves Coelho-dos-Reis |
| author_facet | Ágata Lopes-Ribeiro Patrícia de Melo Oliveira Henrique Morais Retes Edel Figueiredo Barbosa-Stancioli Flávio Guimarães da Fonseca Flávio Guimarães da Fonseca Moriya Tsuji Jordana Grazziela Alves Coelho-dos-Reis |
| author_sort | Ágata Lopes-Ribeiro |
| collection | DOAJ |
| description | Introduction and methodsIn this present work, coronavirus subfamilies and SARS-CoV-2 Variants of Concern (VOCs) were investigated for the presence of MHC-I immunodominant viral peptides using in silico and in vitro tools.ResultsIn our results, HLA-A*02 haplotype showed the highest number of immunodominant epitopes but with the lowest combined prediction score. Furthermore, a decrease in combined prediction score was observed for HLA-A*02-restricted epitopes when the original strain was compared to the VOCs, indicating that the mutations on the VOCs are promoting escape from HLA-A2-mediated antigen presentation, which characterizes a immune evasion process. Additionally, epitope signature analysis revealed major immunogenic peptide loss for structural (S) and non-structural (ORF8) proteins of VOCs in comparison to the Wuhan sequence.DiscussionThese results may indicate that the antiviral CD8+ T-cell responses generated by original strains could not be sufficient for clearance of variants in either newly or reinfection with SARS-CoV-2. In contrast, N epitopes remain the most conserved and reactive peptides across SARS-CoV-2 VOCs. Overall, our data could contribute to the rational design and development of new vaccinal platforms to induce a broad cellular CD8+ T cell antiviral response, aiming at controlling viral transmission of future SARS-CoV-2 variants. |
| first_indexed | 2024-03-11T13:12:21Z |
| format | Article |
| id | doaj.art-2cdeea3db73c48fd89cfdb1e758f894b |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-03-11T13:12:21Z |
| publishDate | 2023-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-2cdeea3db73c48fd89cfdb1e758f894b2023-11-03T14:01:17ZengFrontiers Media S.A.Frontiers in Immunology1664-32242023-11-011410.3389/fimmu.2023.12297121229712Surveillance of SARS-CoV-2 immunogenicity: loss of immunodominant HLA-A*02-restricted epitopes that activate CD8+ T cellsÁgata Lopes-Ribeiro0Patrícia de Melo Oliveira1Henrique Morais Retes2Edel Figueiredo Barbosa-Stancioli3Flávio Guimarães da Fonseca4Flávio Guimarães da Fonseca5Moriya Tsuji6Jordana Grazziela Alves Coelho-dos-Reis7Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, BrazilLaboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, BrazilLaboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, BrazilLaboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, BrazilLaboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, BrazilCentro de Tecnologia (CT) Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, BrazilAaron Diamond AIDS Research Center, Irving Medical School, Columbia University, New York, NY, United StatesLaboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, BrazilIntroduction and methodsIn this present work, coronavirus subfamilies and SARS-CoV-2 Variants of Concern (VOCs) were investigated for the presence of MHC-I immunodominant viral peptides using in silico and in vitro tools.ResultsIn our results, HLA-A*02 haplotype showed the highest number of immunodominant epitopes but with the lowest combined prediction score. Furthermore, a decrease in combined prediction score was observed for HLA-A*02-restricted epitopes when the original strain was compared to the VOCs, indicating that the mutations on the VOCs are promoting escape from HLA-A2-mediated antigen presentation, which characterizes a immune evasion process. Additionally, epitope signature analysis revealed major immunogenic peptide loss for structural (S) and non-structural (ORF8) proteins of VOCs in comparison to the Wuhan sequence.DiscussionThese results may indicate that the antiviral CD8+ T-cell responses generated by original strains could not be sufficient for clearance of variants in either newly or reinfection with SARS-CoV-2. In contrast, N epitopes remain the most conserved and reactive peptides across SARS-CoV-2 VOCs. Overall, our data could contribute to the rational design and development of new vaccinal platforms to induce a broad cellular CD8+ T cell antiviral response, aiming at controlling viral transmission of future SARS-CoV-2 variants.https://www.frontiersin.org/articles/10.3389/fimmu.2023.1229712/fullCD8+ T cellsSARS-CoV-2HLA-A2peptide microarrayimmunoinformatics |
| spellingShingle | Ágata Lopes-Ribeiro Patrícia de Melo Oliveira Henrique Morais Retes Edel Figueiredo Barbosa-Stancioli Flávio Guimarães da Fonseca Flávio Guimarães da Fonseca Moriya Tsuji Jordana Grazziela Alves Coelho-dos-Reis Surveillance of SARS-CoV-2 immunogenicity: loss of immunodominant HLA-A*02-restricted epitopes that activate CD8+ T cells Frontiers in Immunology CD8+ T cells SARS-CoV-2 HLA-A2 peptide microarray immunoinformatics |
| title | Surveillance of SARS-CoV-2 immunogenicity: loss of immunodominant HLA-A*02-restricted epitopes that activate CD8+ T cells |
| title_full | Surveillance of SARS-CoV-2 immunogenicity: loss of immunodominant HLA-A*02-restricted epitopes that activate CD8+ T cells |
| title_fullStr | Surveillance of SARS-CoV-2 immunogenicity: loss of immunodominant HLA-A*02-restricted epitopes that activate CD8+ T cells |
| title_full_unstemmed | Surveillance of SARS-CoV-2 immunogenicity: loss of immunodominant HLA-A*02-restricted epitopes that activate CD8+ T cells |
| title_short | Surveillance of SARS-CoV-2 immunogenicity: loss of immunodominant HLA-A*02-restricted epitopes that activate CD8+ T cells |
| title_sort | surveillance of sars cov 2 immunogenicity loss of immunodominant hla a 02 restricted epitopes that activate cd8 t cells |
| topic | CD8+ T cells SARS-CoV-2 HLA-A2 peptide microarray immunoinformatics |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1229712/full |
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