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12 results on '"Hamelin, David J."'

1. Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines

Author

Kovalchik, Kevin A., Hamelin, David J., Kubiniok, Peter, Bourdin, Benoîte, Mostefai, Fatima, Poujol, Raphaël, Paré, Bastien, Simpson, Shawn M., Sidney, John, Bonneil, Éric, Courcelles, Mathieu, Saini, Sunil Kumar, Shahbazy, Mohammad, Kapoor, Saketh, Rajesh, Vigneshwar, Weitzen, Maya, Grenier, Jean-Christophe, Gharsallaoui, Bayrem, Maréchal, Loïze, Wu, Zhaoguan, Savoie, Christopher, Sette, Alessandro, Thibault, Pierre, Sirois, Isabelle, Smith, Martin A., Decaluwe, Hélène, Hussin, Julie G., Lavallée-Adam, Mathieu, and Caron, Etienne

Published
2024
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4. MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets

Author

Kovalchik, Kevin A., Ma, Qing, Wessling, Laura, Saab, Frederic, Duquette, Jérôme D., Kubiniok, Peter, Hamelin, David J., Faridi, Pouya, Li, Chen, Purcell, Anthony W., Jang, Anne, Paramithiotis, Eustache, Tognetti, Marco, Reiter, Lukas, Bruderer, Roland, Lanoix, Joël, Bonneil, Éric, Courcelles, Mathieu, Thibault, Pierre, Caron, Etienne, and Sirois, Isabelle

Published
2022
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10. Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages

Author

Mostefai, Fatima, primary, Gamache, Isabel, additional, N'Guessan, Arnaud, additional, Pelletier, Justin, additional, Huang, Jessie, additional, Murall, Carmen Lia, additional, Pesaranghader, Ahmad, additional, Gaonac'h-Lovejoy, Vanda, additional, Hamelin, David J., additional, Poujol, Raphaël, additional, Grenier, Jean-Christophe, additional, Smith, Martin, additional, Caron, Etienne, additional, Craig, Morgan, additional, Wolf, Guy, additional, Krishnaswamy, Smita, additional, Shapiro, B. Jesse, additional, and Hussin, Julie G., additional

Published
2022
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12. The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner

Author

Hamelin, David J., Fournelle, Dominique, Grenier, Jean-Christophe, Schockaert, Jana, Kovalchik, Kevin A., Kubiniok, Peter, Mostefai, Fatima, Duquette, Jérôme D., Saab, Frederic, Sirois, Isabelle, Smith, Martin A., Pattijn, Sofie, Soudeyns, Hugo, Decaluwe, Hélène, Hussin, Julie, and Caron, Etienne

Abstract

The rapid, global dispersion of SARS-CoV-2 has led to the emergence of a diverse range of variants. Here, we describe how the mutational landscape of SARS-CoV-2 has shaped HLA-restricted T cell immunity at the population level during the first year of the pandemic. We analyzed a total of 330,246 high-quality SARS-CoV-2 genome assemblies, sampled across 143 countries and all major continents from December 2019 to December 2020 before mass vaccination or the rise of the Delta variant. We observed that proline residues are preferentially removed from the proteome of prevalent mutants, leading to a predicted global loss of SARS-CoV-2 T cell epitopes in individuals expressing HLA-B alleles of the B7 supertype family; this is largely driven by a dominant C-to-U mutation type at the RNA level. These results indicate that B7-supertype-associated epitopes, including the most immunodominant ones, were more likely to escape CD8+T cell immunosurveillance during the first year of the pandemic.

Published
2021
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