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For: Woolthuis RG, van Dorp CH, Keşmir C, de Boer RJ, van Boven M. Long-term adaptation of the influenza A virus by escaping cytotoxic T-cell recognition. Sci Rep 2016;6:33334. [PMID: 27629812 DOI: 10.1038/srep33334] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/23/2016] [Indexed: 11/24/2022]  Open
Number Cited by Other Article(s)
1
Hamelin D, Scicluna M, Saadie I, Mostefai F, Grenier J, Baron C, Caron E, Hussin J. Predicting pathogen evolution and immune evasion in the age of artificial intelligence. Comput Struct Biotechnol J 2025;27:1370-1382. [PMID: 40235636 PMCID: PMC11999473 DOI: 10.1016/j.csbj.2025.03.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Revised: 03/21/2025] [Accepted: 03/26/2025] [Indexed: 04/17/2025]  Open
2
Zornikova K, Dianov D, Ivanova N, Davydova V, Nenasheva T, Fefelova E, Bogolyubova A. Features of Highly Homologous T-Cell Receptor Repertoire in the Immune Response to Mutations in Immunogenic Epitopes. Int J Mol Sci 2024;25:12591. [PMID: 39684303 DOI: 10.3390/ijms252312591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Revised: 11/21/2024] [Accepted: 11/21/2024] [Indexed: 12/18/2024]  Open
3
Macchia I, La Sorsa V, Ciervo A, Ruspantini I, Negri D, Borghi M, De Angelis ML, Luciani F, Martina A, Taglieri S, Durastanti V, Altavista MC, Urbani F, Mancini F. T Cell Peptide Prediction, Immune Response, and Host-Pathogen Relationship in Vaccinated and Recovered from Mild COVID-19 Subjects. Biomolecules 2024;14:1217. [PMID: 39456150 PMCID: PMC11505848 DOI: 10.3390/biom14101217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/12/2024] [Accepted: 09/18/2024] [Indexed: 10/28/2024]  Open
4
Jansen JM, Meineke R, Molle A, van de Sandt CE, Saletti G, Rimmelzwaan GF. Selective pressure mediated by influenza virus M158-66 epitope-specific CD8+T cells promotes accumulation of extra-epitopic amino acid substitutions associated with viral resistance to these T cells. Virus Res 2024;343:199355. [PMID: 38490580 PMCID: PMC10955411 DOI: 10.1016/j.virusres.2024.199355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
5
Haque A, Pant AB. The coevolution of Covid-19 and host immunity. EXPLORATION OF MEDICINE 2024:167-184. [DOI: 10.37349/emed.2024.00214] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/15/2024] [Indexed: 01/05/2025]  Open
6
Radwan J, Kohi C, Ejsmond M, Paganini J, Pontarotti P. Integration of the immune memory into the pathogen-driven MHC polymorphism hypothesis. HLA 2023;102:653-659. [PMID: 37688391 DOI: 10.1111/tan.15216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/01/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023]
7
Khadri L, Ziraksaz MH, Barekzai AB, Ghauri B. T cell responses to SARS-CoV-2. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023;202:183-217. [PMID: 38237986 DOI: 10.1016/bs.pmbts.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
8
Wong KH, Lal SK. Alternative antiviral approaches to combat influenza A virus. Virus Genes 2023;59:25-35. [PMID: 36260242 PMCID: PMC9832087 DOI: 10.1007/s11262-022-01935-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/06/2022] [Indexed: 01/14/2023]
9
Chen J, Tan S, Avadhanula V, Moise L, Piedra PA, De Groot AS, Bahl J. Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus. PLoS Comput Biol 2023;19:e1010360. [PMID: 36626370 PMCID: PMC9870173 DOI: 10.1371/journal.pcbi.1010360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 01/23/2023] [Accepted: 12/07/2022] [Indexed: 01/11/2023]  Open
10
Shafqat A, Omer MH, Ahmad O, Niaz M, Abdulkader HS, Shafqat S, Mushtaq AH, Shaik A, Elshaer AN, Kashir J, Alkattan K, Yaqinuddin A. SARS-CoV-2 epitopes inform future vaccination strategies. Front Immunol 2022;13:1041185. [PMID: 36505475 PMCID: PMC9732895 DOI: 10.3389/fimmu.2022.1041185] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022]  Open
11
Dolton G, Rius C, Hasan MS, Wall A, Szomolay B, Behiry E, Whalley T, Southgate J, Fuller A, Morin T, Topley K, Tan LR, Goulder PJR, Spiller OB, Rizkallah PJ, Jones LC, Connor TR, Sewell AK. Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope. Cell 2022;185:2936-2951.e19. [PMID: 35931021 PMCID: PMC9279490 DOI: 10.1016/j.cell.2022.07.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 05/08/2022] [Accepted: 07/07/2022] [Indexed: 01/06/2023]
12
Hensen L, Illing PT, Rowntree LC, Davies J, Miller A, Tong SYC, Habel JR, van de Sandt CE, Flanagan K, Purcell AW, Kedzierska K, Clemens EB. T Cell Epitope Discovery in the Context of Distinct and Unique Indigenous HLA Profiles. Front Immunol 2022;13:812393. [PMID: 35603215 PMCID: PMC9121770 DOI: 10.3389/fimmu.2022.812393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022]  Open
13
Moss P. The T cell immune response against SARS-CoV-2. Nat Immunol 2022;23:186-193. [PMID: 35105982 DOI: 10.1038/s41590-021-01122-w] [Citation(s) in RCA: 834] [Impact Index Per Article: 278.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022]
14
de Silva TI, Liu G, Lindsey BB, Dong D, Moore SC, Hsu NS, Shah D, Wellington D, Mentzer AJ, Angyal A, Brown R, Parker MD, Ying Z, Yao X, Turtle L, Dunachie S, Maini MK, Ogg G, Knight JC, Peng Y, Rowland-Jones SL, Dong T. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells. iScience 2021;24:103353. [PMID: 34729465 PMCID: PMC8552693 DOI: 10.1016/j.isci.2021.103353] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 10/28/2022]  Open
15
Hamelin DJ, Fournelle D, Grenier JC, Schockaert J, Kovalchik KA, Kubiniok P, Mostefai F, Duquette JD, Saab F, Sirois I, Smith MA, Pattijn S, Soudeyns H, Decaluwe H, Hussin J, Caron E. The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner. Cell Syst 2021;13:143-157.e3. [PMID: 34637888 PMCID: PMC8492600 DOI: 10.1016/j.cels.2021.09.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/03/2021] [Accepted: 09/23/2021] [Indexed: 02/09/2023]
16
Schweininger J, Scherer M, Rothemund F, Schilling EM, Wörz S, Stamminger T, Muller YA. Cytomegalovirus immediate-early 1 proteins form a structurally distinct protein class with adaptations determining cross-species barriers. PLoS Pathog 2021;17:e1009863. [PMID: 34370791 PMCID: PMC8376021 DOI: 10.1371/journal.ppat.1009863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/19/2021] [Accepted: 08/03/2021] [Indexed: 01/12/2023]  Open
17
Intranasal Immunization with the Influenza A Virus Encoding Truncated NS1 Protein Protects Mice from Heterologous Challenge by Restraining the Inflammatory Response in the Lungs. Microorganisms 2021;9:microorganisms9040690. [PMID: 33810549 PMCID: PMC8067201 DOI: 10.3390/microorganisms9040690] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 11/26/2022]  Open
18
Fellay J, Pedergnana V. Exploring the interactions between the human and viral genomes. Hum Genet 2019;139:777-781. [PMID: 31729546 DOI: 10.1007/s00439-019-02089-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/31/2019] [Indexed: 12/20/2022]
19
Palmer DS, Turner I, Fidler S, Frater J, Goedhals D, Goulder P, Huang KHG, Oxenius A, Phillips R, Shapiro R, Vuuren CV, McLean AR, McVean G. Mapping the drivers of within-host pathogen evolution using massive data sets. Nat Commun 2019;10:3017. [PMID: 31289267 PMCID: PMC6616926 DOI: 10.1038/s41467-019-10724-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 05/20/2019] [Indexed: 11/09/2022]  Open
20
Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved? J Virol 2019;93:JVI.01534-18. [PMID: 30626684 PMCID: PMC6401462 DOI: 10.1128/jvi.01534-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/26/2018] [Indexed: 01/10/2023]  Open
21
Voskarides K, Christaki E, Nikolopoulos GK. Influenza Virus-Host Co-evolution. A Predator-Prey Relationship? Front Immunol 2018;9:2017. [PMID: 30245689 PMCID: PMC6137132 DOI: 10.3389/fimmu.2018.02017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/15/2018] [Indexed: 12/20/2022]  Open
22
Textor J, Fähnrich A, Meinhardt M, Tune C, Klein S, Pagel R, König P, Kalies K, Westermann J. Deep Sequencing Reveals Transient Segregation of T Cell Repertoires in Splenic T Cell Zones during an Immune Response. THE JOURNAL OF IMMUNOLOGY 2018;201:350-358. [PMID: 29884700 DOI: 10.4049/jimmunol.1800091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/19/2018] [Indexed: 11/19/2022]
23
Evolution of Influenza A Virus by Mutation and Re-Assortment. Int J Mol Sci 2017;18:ijms18081650. [PMID: 28783091 PMCID: PMC5578040 DOI: 10.3390/ijms18081650] [Citation(s) in RCA: 231] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/13/2022]  Open
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