{"id":"W4221096923","doi":"10.1016/j.isci.2022.103880","title":"Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa","year":2022,"lang":"en","type":"article","venue":"iScience","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":14,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Applied Physics Laboratory, Johns Hopkins University; Fogarty International Center; National Institutes of Health; National Institute for Nanotechnology; U.S. Department of Health and Human Services","keywords":"Genetic diversity; Evolutionary biology; Pandemic; Diversity (politics); Phylogenetic tree; Phylogenetics; Biology; Genome; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Coronavirus disease 2019 (COVID-19); Molecular epidemiology; Epidemiology; 2019-20 coronavirus outbreak; Divergence (linguistics); Lineage (genetic); Public health; Genetics; Virology; Disease; Infectious disease (medical specialty); Gene; Population; Outbreak; Genotype; Medicine; Environmental health; Anthropology","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001017203,0.0000561119,0.0002030604,0.0001602636,0.0001896967,0.000002236854,0.0001913189,0.00002495514,0.000005274834],"category_scores_gemma":[0.0008273605,0.00005159108,0.00003048873,0.0005111211,0.0002902623,0.00003752811,0.0007895967,0.0001848473,0.000002577179],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00006022501,"about_ca_system_score_gemma":0.000102062,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005727467,"about_ca_topic_score_gemma":0.00002825024,"domain_scores_codex":[0.9988875,0.0001362719,0.0001828039,0.0002655049,0.0002549043,0.0002729829],"domain_scores_gemma":[0.9993949,0.0003275154,0.00005761251,0.0001722861,0.00003112754,0.0000165927],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00002103163,0.00003982979,0.7679145,0.00002557994,0.000002550549,0.00007501713,0.0009739108,0.00001341331,0.2277582,0.00005349205,0.00004532891,0.003077063],"study_design_scores_gemma":[0.0007681109,0.0003915465,0.9400749,0.00002654433,0.00001253505,0.0001281809,0.0006105767,0.01347596,0.0387742,0.001077503,0.004542343,0.0001176581],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9968557,0.001379128,0.0001783603,0.0003581556,0.0000433171,0.0001297059,0.000002968209,0.00001046601,0.001042205],"genre_scores_gemma":[0.9943141,0.00000409992,0.0005849837,0.005062673,0.00001489824,0.000007354257,1.676451e-7,0.000002993959,0.00000872196],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.188984,"threshold_uncertainty_score":0.2103823,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1552830695085003,"score_gpt":0.3879840723267848,"score_spread":0.2327010028182845,"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."}}