{"id":"W3210167380","doi":"10.1186/s13073-021-00986-9","title":"A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada","year":2021,"lang":"en","type":"article","venue":"Genome Medicine","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":34,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ontario Genomics; Université de Montréal; McGill University; Institut National de Santé Publique du Québec; Compute Canada; McGill Genome Centre","funders":"Canadian Institutes of Health Research; Fonds de Recherche du Québec - Santé; Genome Canada; McGill University","keywords":"Transmission (telecommunications); Pandemic; Context (archaeology); Lineage (genetic); Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Phylogenetic tree; Evolutionary biology; Phylogeography; Phylogenetics; Coronavirus disease 2019 (COVID-19); Genome; Biology; Geography; Founder effect; Genetics; Medicine; Infectious disease (medical specialty); Haplotype; Gene; Computer science; Genotype","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003823094,0.0001836583,0.0007113487,0.0002189868,0.00003432619,0.000002828627,0.0001656541,0.00009747608,0.0001656257],"category_scores_gemma":[0.0004596131,0.000151062,0.00008062798,0.0009823465,0.0002219207,0.00003450308,0.00004741567,0.0003511874,0.000008582636],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002989924,"about_ca_system_score_gemma":0.003721196,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.8405376,"about_ca_topic_score_gemma":0.6658081,"domain_scores_codex":[0.9979078,0.00008124723,0.000664746,0.0003668967,0.0006195675,0.0003597575],"domain_scores_gemma":[0.9987103,0.0001760086,0.0001102179,0.0005190268,0.0004189755,0.00006543023],"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":[0.00036085,0.0001831221,0.0447439,0.0004128705,0.00008851197,0.0001994615,0.001509847,9.45054e-7,0.9466034,0.00002880269,0.002278016,0.003590326],"study_design_scores_gemma":[0.004046702,0.0003773127,0.04733847,0.0005739912,0.0001305174,0.0002063453,0.0008383414,0.00003541545,0.6663704,0.0000841797,0.2798305,0.0001678999],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9818735,0.002829261,0.0002060817,0.01096428,0.0002116259,0.0003071178,0.00001051155,0.00001674562,0.003580861],"genre_scores_gemma":[0.9893181,0.00004400015,0.0003310599,0.009545293,0.0003379732,0.00002025155,0.00001512387,0.00003172011,0.0003564486],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.280233,"threshold_uncertainty_score":0.6601243,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05046885515895317,"score_gpt":0.3266888692355523,"score_spread":0.2762200140765991,"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."}}