{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006252427,0.0005196433,0.0003294095,0.001073262,0.002518307,0.00181211,0.000826922,0.0005271027,0.005678466],"category_scores_gemma":[0.00213225,0.0002350011,0.000468684,0.001557683,0.0007910836,0.000644856,0.000610081,0.0007296827,0.0003789515],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.02059014,"about_ca_system_score_gemma":0.02124592,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.9809049,"about_ca_topic_score_gemma":0.9890565,"domain_scores_codex":[0.9993135,0.00005209685,0.0000208613,0.0002231479,0.0001751457,0.000215336],"domain_scores_gemma":[0.9979281,0.0001982974,0.0003314966,0.0001028873,0.001128908,0.0003101523],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0002254627,0.00003264996,0.959537,0.0001631467,0.0001556552,0.0003611607,0.001002395,0.001848893,0.005608293,0.0006929582,0.006785773,0.0235866],"study_design_scores_gemma":[0.00001584912,0.00004687743,0.9776669,0.0001284758,0.0000883351,0.0001738576,0.001672122,0.003869034,0.001063436,0.0001440355,0.01509583,0.00003531633],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9650068,0.002087233,0.002988726,0.001087721,0.00008135087,0.0001245726,0.01549086,0.0001893737,0.01294343],"genre_scores_gemma":[0.9920835,0.0005452475,0.001285554,0.0003574589,0.00001223053,0.00001805406,0.003122797,0.00003348257,0.002541667],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02059014,"threshold_uncertainty_score":0.1493926,"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."}}