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A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.
Wilkinson, Eduan; Giovanetti, Marta; Tegally, Houriiyah; San, James E; Lessells, Richard; Cuadros, Diego; Martin, Darren P; Rasmussen, David A; Zekri, Abdel-Rahman N; Sangare, Abdoul K; Ouedraogo, Abdoul-Salam; Sesay, Abdul K; Priscilla, Abechi; Kemi, Adedotun-Sulaiman; Olubusuyi, Adewunmi M; Oluwapelumi, Adeyemi O O; Hammami, Adnène; Amuri, Adrienne A; Sayed, Ahmad; Ouma, Ahmed E O; Elargoubi, Aida; Ajayi, Nnennaya A; Victoria, Ajogbasile F; Kazeem, Akano; George, Akpede; Trotter, Alexander J; Yahaya, Ali A; Keita, Alpha K; Diallo, Amadou; Kone, Amadou; Souissi, Amal; Chtourou, Amel; Gutierrez, Ana V; Page, Andrew J; Vinze, Anika; Iranzadeh, Arash; Lambisia, Arnold; Ismail, Arshad; Rosemary, Audu; Sylverken, Augustina; Femi, Ayoade; Ibrahimi, Azeddine; Marycelin, Baba; Oderinde, Bamidele S; Bolajoko, Bankole; Dhaala, Beatrice; Herring, Belinda L; Njanpop-Lafourcade, Berthe-Marie; Kleinhans, Bronwyn; McInnis, Bronwyn.
  • Wilkinson E; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Giovanetti M; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
  • Tegally H; Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.
  • San JE; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
  • Lessells R; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Cuadros D; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Martin DP; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
  • Rasmussen DA; Department of Geography and GIS, University of Cincinnati, Cincinnati, OH, USA.
  • Zekri AN; Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa.
  • Sangare AK; Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
  • Ouedraogo AS; Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA.
  • Sesay AK; Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.
  • Priscilla A; Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt.
  • Kemi AS; Centre d'Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali.
  • Olubusuyi AM; Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso.
  • Oluwapelumi AOO; MRCG at LSHTM Genomics Lab, Fajara, Gambia.
  • Hammami A; African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
  • Amuri AA; African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
  • Sayed A; Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria.
  • Ouma AEO; Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria.
  • Elargoubi A; CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia.
  • Ajayi NA; Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo.
  • Victoria AF; Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo.
  • Kazeem A; Genomics Research Program, Children's Cancer Hospital, Cairo, Egypt.
  • George A; Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia.
  • Trotter AJ; Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia.
  • Yahaya AA; Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia.
  • Keita AK; Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria.
  • Diallo A; African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
  • Kone A; African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
  • Souissi A; Irrua Specialist Teaching Hospital, Irrua, Nigeria.
  • Chtourou A; Quadram Institute Bioscience, Norwich, UK.
  • Gutierrez AV; World Health Organization, Africa Region, Brazzaville Congo.
  • Page AJ; Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea.
  • Vinze A; TransVIHMI, Montpellier University/IRD/INSERM, Montpellier, France.
  • Iranzadeh A; Virology Department, Institut Pasteur de Dakar, Dakar, Senegal.
  • Lambisia A; Mali-University Clinical Research Center (UCRC), Bamako, Mali.
  • Ismail A; Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.
  • Rosemary A; CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia.
  • Sylverken A; Quadram Institute Bioscience, Norwich, UK.
  • Femi A; Quadram Institute Bioscience, Norwich, UK.
  • Ibrahimi A; Broad Insitute of Harvard and MIT, Cambridge, MA, USA.
  • Marycelin B; Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa.
  • Oderinde BS; Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
  • Bolajoko B; KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya.
  • Dhaala B; National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa.
  • Herring BL; The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria.
  • Njanpop-Lafourcade BM; Institute of Virology, Charité - Universitätsmedizin, Berlin, Germany.
  • Kleinhans B; African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
  • McInnis B; Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco.
Science ; 374(6566): 423-431, 2021 Oct 22.
Article in English | MEDLINE | ID: covidwho-1483977
ABSTRACT
The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genomics / Pandemics / Epidemiological Monitoring / SARS-CoV-2 / COVID-19 Type of study: Observational study Topics: Variants Limits: Humans Country/Region as subject: Africa Language: English Journal: Science Year: 2021 Document Type: Article Affiliation country: Science.abj4336

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genomics / Pandemics / Epidemiological Monitoring / SARS-CoV-2 / COVID-19 Type of study: Observational study Topics: Variants Limits: Humans Country/Region as subject: Africa Language: English Journal: Science Year: 2021 Document Type: Article Affiliation country: Science.abj4336