{"id":"W4411161874","doi":"10.1093/ve/veaf027","title":"Comprehensive analysis of SARS-CoV-2 Spike evolution: epitope classification and immune escape prediction","year":2025,"lang":"en","type":"article","venue":"Virus Evolution","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal","funders":"Research England; National Institute of Allergy and Infectious Diseases; Université Laval","keywords":"Immune escape; Spike (software development); Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Epitope; Virology; Coronavirus disease 2019 (COVID-19); Immune system; Coronavirus; 2019-20 coronavirus outbreak; Immune recognition; Computational biology; Biology; Computer science; Antibody; Medicine; Immunology; Outbreak; Disease; Infectious disease (medical specialty)","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005444011,0.0005166637,0.0004305312,0.001008148,0.000290297,0.0003797156,0.0002806842,0.0003093722,0.0003888221],"category_scores_gemma":[0.0008198977,0.0001612514,0.0006033792,0.0009450097,0.0001734346,0.0003893102,0.0004629269,0.0003568733,0.0002070736],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003019811,"about_ca_system_score_gemma":0.0003906404,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001932847,"about_ca_topic_score_gemma":0.002634783,"domain_scores_codex":[0.9997676,0.00004670682,0.00001589001,0.00006094065,0.00007274823,0.00003620085],"domain_scores_gemma":[0.9997161,0.00005639799,0.0000661087,0.00004249125,0.00007607585,0.00004279075],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0008665025,0.0004668463,0.3381981,0.0004453938,0.0007078567,0.000899962,0.0004544714,0.1924732,0.3428294,0.002067596,0.004583728,0.1160069],"study_design_scores_gemma":[0.0000485396,0.0007019299,0.2647909,0.00003524004,0.0002990819,0.0008950821,0.0003520811,0.6773975,0.04629978,0.002785987,0.00632107,0.00007278067],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9937508,0.000417875,0.004387521,0.0000475159,0.000004159474,0.0000118073,0.0008311586,0.0001684898,0.00038069],"genre_scores_gemma":[0.9856166,0.0002271429,0.008002485,0.00003273917,0.000006537563,0.00001157814,0.005873436,0.00005119126,0.0001783463],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001932847,"threshold_uncertainty_score":0.003843188,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05099962767178771,"score_gpt":0.3531902622259591,"score_spread":0.3021906345541714,"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."}}