{"id":"W3128528355","doi":"10.1038/s41598-021-83355-1","title":"Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada","year":2021,"lang":"en","type":"article","venue":"Scientific Reports","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":14,"is_retracted":false,"has_abstract":true,"ca_institutions":"Kingston Health Sciences Centre; Queen's University","funders":"Bijzonder Onderzoeksfonds UGent","keywords":"Minion; Ion semiconductor sequencing; Phylogenetic tree; Genome; Phylogenomics; Biology; Phylogenetics; Transmission (telecommunications); Pandemic; Genetics; Evolutionary biology; Contact tracing; Virology; Clade; DNA sequencing; Gene; Infectious disease (medical specialty); Disease; Nanopore sequencing; Coronavirus disease 2019 (COVID-19); Medicine","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0003200757,0.0003484539,0.0004794869,0.001464726,0.002204127,0.001243058,0.0009029619,0.0005265634,0.002237727],"category_scores_gemma":[0.001406555,0.0003608585,0.0004213007,0.003388054,0.0006938984,0.0002572977,0.0007409733,0.0005649328,0.0003480094],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0183823,"about_ca_system_score_gemma":0.01591683,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.9830483,"about_ca_topic_score_gemma":0.9876207,"domain_scores_codex":[0.9993094,0.00003810338,0.00003303833,0.0001187964,0.0001302962,0.0003703993],"domain_scores_gemma":[0.9990343,0.00007825461,0.000191785,0.00004244093,0.000386329,0.0002669913],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.000177535,0.00001530803,0.9920649,0.00002215285,0.00002675691,0.0005493333,0.001003194,0.0001212768,0.0009204647,0.00010836,0.001249416,0.003741229],"study_design_scores_gemma":[0.000008493866,0.00002021818,0.9963943,0.00002277214,0.00001952912,0.0002678095,0.001798111,0.0004549829,0.00009834061,0.00003194166,0.0008734622,0.00001000206],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9932672,0.0004710903,0.0001466918,0.0003766119,0.000007040144,0.00003369882,0.00368286,0.00001299784,0.002001931],"genre_scores_gemma":[0.9965418,0.0003635893,0.0001965803,0.0001256136,0.000005475645,0.000009550859,0.002059105,0.00001142013,0.0006868672],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0183823,"threshold_uncertainty_score":0.1333736,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01769457538390799,"score_gpt":0.2708664076385486,"score_spread":0.2531718322546406,"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."}}