{"id":"W3163838900","doi":"10.1126/science.abj4336","title":"A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa","year":2021,"lang":"en","type":"article","venue":"Science","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":236,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Common Fund; Faculty of Medicine and Health, University of Sydney; Biotechnology and Biological Sciences Research Council; NYU Grossman School of Medicine; Centers for Disease Control and Prevention; Fogarty International Center; National Institutes of Health; University of Health and Allied Sciences; Robert Koch Institut; Nigerian Institute of Medical Research; Foreign, Commonwealth and Development Office; Université de Tunis El Manar; European and Developing Countries Clinical Trials Partnership; Kwame Nkrumah University of Science and Technology; Medical Research Council; African Academy of Sciences; National Health Laboratory Service; ELMA Foundation; Quadram Institute Bioscience; Centre National pour la Recherche Scientifique et Technique; Université de Sfax; Universiteit van die Vrystaat; United States Agency for International Development; Japan International Cooperation Agency; Universiteit Stellenbosch; World Health Organization; Centre International de Recherches Médicales de Franceville; Science and Technology Research Partnership for Sustainable Development; South African Medical Research Council; Hebrew University of Jerusalem; National Research Centre; Belgisch Ontwikkelingsagentschap; Department for International Development; New Partnership for Africa's Development; Fondation Mérieux; King Faisal Specialist Hospital and Research Centre; Bundesministerium für Bildung und Forschung; Université de Tunis; Institut National de la Santé et de la Recherche Médicale; Université Mohammed V de Rabat; University of Ghana; National Institute of Allergy and Infectious Diseases; University of Warwick; London School of Hygiene and Tropical Medicine; York University; Institut Pasteur de Tunis; Centers for Disease Control and Prevention Foundation; Skoll Foundation; Drexel University; Department of Health and Social Care; Ain Shams University; Philanthropic Educational Organization; Australian Government; National Human Genome Research Institute; Alliance for Accelerating Excellence in Science in Africa; Innovative Genomics Institute; UK Research and Innovation; Japan Agency for Medical Research and Development; Government of the United Kingdom; National Institute for Health and Care Research; Fraternal Order of Eagles; Oxford Nanopore Technologies; Wellcome Trust; Cairo University; Directorate for Biological Sciences; Université Monastir; Tulane University; U.S. Department of Health and Human Services; Emory University; Open Philanthropy Project; Rockefeller Foundation; World Bank Group; University of Nebraska Medical Center; Bill and Melinda Gates Foundation","keywords":"Pandemic; Outbreak; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Transmission (telecommunications); Coronavirus disease 2019 (COVID-19); Coronavirus; 2019-20 coronavirus outbreak; Geography; Virology; Development economics; Biology; Medicine; Disease; Infectious disease (medical specialty); Economics","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":[0.001779001,0.00008230494,0.0002195634,0.0001398121,0.00007073538,0.00004081798,0.0004327569,0.00004220629,0.000005239322],"category_scores_gemma":[0.0009913504,0.00005680084,0.00005336245,0.001566102,0.0005998286,0.00008108811,0.0001748688,0.0001987172,0.00004500196],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001265047,"about_ca_system_score_gemma":0.001097388,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006170504,"about_ca_topic_score_gemma":0.0001435138,"domain_scores_codex":[0.9983978,0.00008481833,0.0001728529,0.0003411417,0.000595232,0.0004081176],"domain_scores_gemma":[0.9989986,0.0001703334,0.00005720479,0.0005473098,0.0002045772,0.0000219988],"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":[0.00002448736,0.00002642484,0.164978,0.00002287701,0.000003147956,0.00003347161,0.0003886978,1.64705e-7,0.8333339,0.00008602446,0.0001875295,0.0009153384],"study_design_scores_gemma":[0.0009077282,0.00008857602,0.4026889,0.00007995357,0.000005717412,0.00006711979,0.0005552004,0.0002425214,0.5713813,0.0009441813,0.02291464,0.0001242477],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9942106,0.0009118117,0.00001941276,0.001111514,0.00008225816,0.0001910456,0.000004357844,0.00001670206,0.003452301],"genre_scores_gemma":[0.9959099,0.00002224549,0.0001353132,0.003774909,0.00003670954,0.0000104644,2.804908e-7,0.000007066234,0.0001031512],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2619526,"threshold_uncertainty_score":0.2316271,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.08679951135869028,"score_gpt":0.3566879442484017,"score_spread":0.2698884328897114,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). 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