{"id":"W3202019442","doi":"10.1016/j.cels.2021.09.013","title":"The mutational landscape of SARS-CoV-2 variants diversifies T cell targets in an HLA-supertype-dependent manner","year":2021,"lang":"en","type":"article","venue":"Cell Systems","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":39,"is_retracted":false,"has_abstract":false,"ca_institutions":"Université de Montréal; Montreal Heart Institute; Centre Hospitalier Universitaire Sainte-Justine","funders":"Fonds de Recherche du Québec - Santé; Canadian Institutes of Health Research; Natural Sciences and Engineering Research Council of Canada; Institut de Valorisation des Données; Fondation Institut de Cardiologie de Montréal; Centre hospitalier universitaire Sainte-Justine; Fondation Charles-Bruneau; Canada Foundation for Innovation","keywords":"Biology; Immunosurveillance; Population; Pandemic; Genetics; Human leukocyte antigen; Immunogenicity; Genome; Epitope; Haplotype; Virology; Allele; Cell; Coronavirus disease 2019 (COVID-19); Immune system; Gene; Medicine; Antigen; Disease","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000501653,0.0001456255,0.0003039902,0.0001141422,0.0001083206,0.00006515504,0.0002173796,0.000121482,0.00001898397],"category_scores_gemma":[0.00006495332,0.0001029966,0.00008155695,0.0002583372,0.00006369404,0.000100512,0.00009690594,0.0002149786,0.000139304],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007435767,"about_ca_system_score_gemma":0.0003262364,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005430814,"about_ca_topic_score_gemma":0.0002198161,"domain_scores_codex":[0.9981622,0.0002045551,0.0003603173,0.0003237732,0.0006164737,0.0003327234],"domain_scores_gemma":[0.9989785,0.0001992819,0.00008119506,0.0004166682,0.0002895673,0.00003477209],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.000366672,0.0006587469,0.1052247,0.0008265456,0.00007781426,0.001176266,0.002010647,0.00003325278,0.8852447,0.0003576313,0.003764187,0.000258872],"study_design_scores_gemma":[0.003659928,0.0002680072,0.01266909,0.0001633378,0.00005768683,0.00009728683,0.007348383,0.005055916,0.9327936,0.00009982045,0.03752543,0.00026149],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9769552,0.004247435,0.00007015689,0.0001260219,0.0005430587,0.0003742636,0.00002227743,0.00002456774,0.01763703],"genre_scores_gemma":[0.9979602,0.00001876606,0.00002253015,0.0009695716,0.0001656696,0.0000309446,0.00002021218,0.0000228178,0.0007893299],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.09255557,"threshold_uncertainty_score":0.4200079,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04264930182184622,"score_gpt":0.3084451288067582,"score_spread":0.2657958269849119,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}