{"id":"W3160452114","doi":"10.1101/2021.05.08.21256867","title":"SARS-CoV-2 lineage dynamics in England from January to March 2021 inferred from representative community samples","year":2021,"lang":"en","type":"preprint","venue":"medRxiv","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":16,"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); Throat; Transmission (telecommunications); Phylogenetic tree; Biology; Demography; Quarter (Canadian coin); Clade; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Transmissibility (structural dynamics); Nose; Evolutionary biology; Virology; Coronavirus disease 2019 (COVID-19); Internal medicine; Medicine; Genetics; Geography; Disease; Gene; 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":["metaepi_narrow","research_integrity"],"consensus_categories":[],"category_scores_codex":[0.001568917,0.0007080637,0.001667374,0.0006806097,0.0001670057,0.0002431881,0.001250018,0.000801516,0.00009746433],"category_scores_gemma":[0.003744764,0.0007133814,0.0003848756,0.000862625,0.000259925,0.0001214152,0.004263713,0.005446234,0.0001344286],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009553395,"about_ca_system_score_gemma":0.001139693,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.1690513,"about_ca_topic_score_gemma":0.1153043,"domain_scores_codex":[0.9933668,0.002221109,0.001081683,0.001379374,0.001150847,0.0008001732],"domain_scores_gemma":[0.9927544,0.003154184,0.0002314622,0.003214667,0.000497101,0.0001482021],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001194018,0.0008698209,0.8545014,0.0002783801,0.000562844,0.001781799,0.01216785,0.000009603104,0.1246389,0.000009055591,0.0005151813,0.003471101],"study_design_scores_gemma":[0.00479607,0.0002624664,0.6082435,0.002040466,0.0002215818,0.00001330783,0.006400312,0.005498712,0.3545956,0.001525425,0.01536623,0.001036361],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9903927,0.000986701,0.001332457,0.00128192,0.0006766348,0.001579227,0.001604873,0.00009423841,0.002051228],"genre_scores_gemma":[0.9806868,0.0001078775,0.003306876,0.01126963,0.0007515914,0.0003640554,0.003349289,0.0001206632,0.00004324199],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2462579,"threshold_uncertainty_score":0.9995317,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1052231334214259,"score_gpt":0.394858017739099,"score_spread":0.289634884317673,"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."}}