{"id":"W4319294603","doi":"10.1099/mgen.0.000887","title":"The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Medical Research Council; Directorate for Biological Sciences; Imperial College London; Department of Health and Social Care; National Institute for Health Research Health Protection Research Unit; UK Dementia Research Institute; National Institute for Health and Care Research; NIHR Imperial Biomedical Research Centre; Biotechnology and Biological Sciences Research Council; Huo Family Foundation; MRC-PHE Centre for Environment and Health; UK Research and Innovation; British Heart Foundation; Wellcome Trust","keywords":"Lineage (genetic); Clade; Phylogenetic tree; Quarter (Canadian coin); Transmission (telecommunications); Biology; Demography; Alpha (finance); Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Competition (biology); Coronavirus disease 2019 (COVID-19); Evolutionary biology; Genetics; Medicine; Internal medicine; Disease; Gene; Geography; Ecology; Infectious disease (medical specialty)","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008241525,0.0002009391,0.0004786716,0.0002546167,0.0002280047,0.0001171712,0.0003550305,0.000103089,0.000005631318],"category_scores_gemma":[0.0005700893,0.0001717406,0.00007721713,0.0007143098,0.0002022743,0.00007693506,0.0007564008,0.0005391326,0.00007317324],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000129797,"about_ca_system_score_gemma":0.0002048566,"about_ca_topic_candidate":true,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.008618514,"about_ca_topic_score_gemma":0.01234234,"domain_scores_codex":[0.9980915,0.0004918068,0.0004620323,0.000344048,0.0002175962,0.000393048],"domain_scores_gemma":[0.9966406,0.002304384,0.00007240633,0.0007102505,0.0002149059,0.00005740478],"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":[0.001019264,0.0001141285,0.08841968,0.00004736015,0.0001033065,0.00004839301,0.005013463,0.00001483262,0.9011429,0.00003412179,0.002588367,0.001454223],"study_design_scores_gemma":[0.001844012,0.0003268095,0.1481966,0.0001321748,0.000041331,0.00001029087,0.00150842,0.0001465211,0.5332783,0.00007056694,0.3142237,0.0002212413],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9966597,0.0001136139,0.00009871902,0.001574897,0.0001750908,0.0008447496,0.0004270507,0.00002596582,0.00008021799],"genre_scores_gemma":[0.9800342,0.0001352588,0.004257861,0.01478352,0.0003456694,0.00003760991,0.0002803975,0.00005871558,0.0000667725],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3678645,"threshold_uncertainty_score":0.9979832,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1882129535716628,"score_gpt":0.3845554961234446,"score_spread":0.1963425425517818,"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."}}