{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00179336,0.0003157802,0.0003599142,0.00124203,0.0006014706,0.001832192,0.0002020004,0.0006070515,0.001124279],"category_scores_gemma":[0.005447337,0.0001778474,0.0003407185,0.002643928,0.0005077353,0.00193406,0.0009755117,0.001024602,0.000234281],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005503084,"about_ca_system_score_gemma":0.0008551743,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006473188,"about_ca_topic_score_gemma":0.009561797,"domain_scores_codex":[0.9993755,0.0002137096,0.00004169804,0.0001613454,0.00008519999,0.0001225913],"domain_scores_gemma":[0.99799,0.0005962609,0.0005202035,0.0004196186,0.0002604687,0.0002134383],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00113021,0.00006300628,0.7578232,0.0007142139,0.0004993665,0.001741556,0.007175082,0.004632082,0.02374144,0.005772831,0.0225736,0.1741335],"study_design_scores_gemma":[0.00002944903,0.0001628665,0.8645341,0.0005887038,0.0001637407,0.001576318,0.005762218,0.002453478,0.003230809,0.006010483,0.1154086,0.00007930626],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9678692,0.007422509,0.003615591,0.005564685,0.0002520565,0.00002275763,0.01261126,0.0001112233,0.002530736],"genre_scores_gemma":[0.9767132,0.004444511,0.005475035,0.001283399,0.0001799815,0.00001779079,0.01128541,0.00006891743,0.0005317232],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006473188,"threshold_uncertainty_score":0.01287103,"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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