{"id":"W3095374256","doi":"10.1101/2020.10.23.20218511","title":"Large-scale population analysis of SARS-CoV-2 whole genome sequences reveals host-mediated viral evolution with emergence of mutations in the viral Spike protein associated with elevated mortality rates","year":2020,"lang":"en","type":"preprint","venue":"medRxiv","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":22,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Manitoba; Research Institute in Oncology and Hematology; CancerCare Manitoba","funders":"Canadian Institutes of Health Research; Research Manitoba","keywords":"Biology; Host (biology); Population; Viral evolution; Mutation; Genetics; Viral quasispecies; Viral entry; Evolutionary biology; Mutation rate; Genome; Viral replication; Virus; Gene; Medicine","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.001817202,0.0003911488,0.00121169,0.0007722418,0.0000951821,0.00003248266,0.0004762167,0.000280531,0.00001078905],"category_scores_gemma":[0.0009104747,0.0002661746,0.0002516411,0.004082588,0.000295283,0.000151616,0.0001363549,0.0008223125,0.000004471398],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002200106,"about_ca_system_score_gemma":0.00056663,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004984894,"about_ca_topic_score_gemma":0.00705758,"domain_scores_codex":[0.9954768,0.0007815495,0.001092283,0.0007495799,0.00143607,0.0004636865],"domain_scores_gemma":[0.9973024,0.0001449643,0.0009922705,0.0007430322,0.0007758955,0.00004142104],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0002436845,0.0002659356,0.5517241,0.0002036123,0.0008428389,0.00003466478,0.00110253,0.0001994872,0.4453614,0.00001690189,0.000002882003,0.000001984775],"study_design_scores_gemma":[0.0009770414,0.0004895215,0.9102186,0.0003834566,0.001501612,0.000001518854,0.0007247277,0.009894241,0.07515766,0.0003771994,0.000009938753,0.0002644715],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9956491,0.0001716995,0.0006855883,0.0003804953,0.00003264522,0.002260786,0.0006970804,0.00006532243,0.00005728308],"genre_scores_gemma":[0.9972093,0.000003562444,0.0001534997,0.0005322724,0.00004174807,0.00034131,0.00167673,0.00003531633,0.000006332227],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3702037,"threshold_uncertainty_score":0.999979,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05558281028146515,"score_gpt":0.3559167681752995,"score_spread":0.3003339578938343,"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."}}