2024
Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines
Kovalchik K, Hamelin D, Kubiniok P, Bourdin B, Mostefai F, Poujol R, Paré B, Simpson S, Sidney J, Bonneil É, Courcelles M, Saini S, Shahbazy M, Kapoor S, Rajesh V, Weitzen M, Grenier J, Gharsallaoui B, Maréchal L, Wu Z, Savoie C, Sette A, Thibault P, Sirois I, Smith M, Decaluwe H, Hussin J, Lavallée-Adam M, Caron E. Machine learning-enhanced immunopeptidomics applied to T-cell epitope discovery for COVID-19 vaccines. Nature Communications 2024, 15: 10316. PMID: 39609459, PMCID: PMC11604954, DOI: 10.1038/s41467-024-54734-9.Peer-Reviewed Original ResearchConceptsT cell epitopesT cellsCD8+ T cell epitopesT cell immunityT cell epitope discoverySARS-CoV-2T-cell-directed vaccinationDesigning effective vaccinesB7 supertypePatient's proteomesSARS-CoV-2 variantsVaccine epitopesViral antigensSpike antigenVaccine developmentEffective vaccineEpitope discoveryCOVID-19 vaccineVaccineEpitopesAntigenic featuresOmicron variantAntigenCOVID-19CD8
2022
Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages
Mostefai F, Gamache I, N'Guessan A, Pelletier J, Huang J, Murall CL, Pesaranghader A, Gaonac'h-Lovejoy V, Hamelin DJ, Poujol R, Grenier JC, Smith M, Caron E, Craig M, Wolf G, Krishnaswamy S, Shapiro BJ, Hussin JG. Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages. Frontiers In Medicine 2022, 9: 826746. PMID: 35265640, PMCID: PMC8899026, DOI: 10.3389/fmed.2022.826746.Peer-Reviewed Original ResearchPopulation genomic approachesStandard phylogenetic approachesGenome sequencing dataHaplotype networkGenomic approachesPhylogenetic approachTajima's DHigh-quality consensus sequencesGenetic diversityPopulation geneticsGenomic variationConsensus sequenceLineage expansionSequencing dataSARS-CoV-2 diversityGenetic characterizationLineage identificationDiversity landscapeInfection pathwaySARS-CoV-2 lineagesRecurrent mutationsGISAID databaseSARS-CoV-2DiversityPathogens
2021
The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner
Hamelin D, Fournelle D, Grenier J, Schockaert J, Kovalchik K, Kubiniok P, Mostefai F, Duquette J, Saab F, Sirois I, Smith M, 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 Systems 2021, 13: 143-157.e3. PMID: 34637888, PMCID: PMC8492600, DOI: 10.1016/j.cels.2021.09.013.Peer-Reviewed Original ResearchConceptsSARS-CoV-2SARS-CoV-2 TSARS-CoV-2 variantsHLA-B allelesMutational landscapeFirst yearCell immunityCell immunosurveillanceCell epitopesMass vaccinationDelta variantCell targetsRNA levelsImmunodominant onesMutation typeEpitopesPrevalent mutantsPopulation levelCD8PandemicImmunosurveillanceVaccinationHLAYearsImmunity