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Preprint
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
medRxiv : the preprint server for health sciences
13 May 2021
Featured in Collection : UN Sustainable Development Goals @ Drexel
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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- Title
- A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
- Creators
- Eduan Wilkinson - University of KwaZulu-NatalMarta Giovanetti - Fundação Oswaldo CruzHouriiyah Tegally - University of KwaZulu-NatalJames E San - University of KwaZulu-NatalRichard Lessells - University of KwaZulu-NatalDiego Cuadros - Department of Geography and GIS, University of Cincinnati, Cincinnati, OH, USADarren P Martin - University of Cape TownDavid A Rasmussen - North Carolina State UniversityAbdel-Rahman N Zekri - Cairo UniversityAbdoul K Sangare - Centre d'Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, MaliAbdoul-Salam Ouedraogo - Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina FasoAbdul K Sesay - MRC Unit the GambiaAbechi Priscilla - Redeemer's UniversityAdedotun-Sulaiman Kemi - Redeemer's UniversityAdewunmi M Olubusuyi - University of IbadanAdeyemi O O Oluwapelumi - University of IlorinAdnène Hammami - University of SfaxAdrienne A Amuri - Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the CongoAhmad Sayed - Children Cancer HospitalAida Elargoubi - University of MonastirAhmed E O Ouma - Africa Centres for Disease Control and PreventionNnennaya A Ajayi - Federal Teaching Hospital AbakalikiAjogbasile F Victoria - Redeemer's UniversityAkano Kazeem - Redeemer's UniversityAkpede George - Irrua Specialist Teaching HospitalAlexander J Trotter - Quadram InstituteAli A Yahaya - World Health Organization Regional Office for AfricaAlpha K Keita - Institut de Recherche pour le DéveloppementAmadou Diallo - Institut Pasteur de DakarAmadou Kone - University of BamakoAmal Souissi - Centre of Biotechnology of SfaxAmel Chtourou - University of SfaxAna V Gutierrez - Quadram InstituteAndrew J Page - Quadram Institute Bioscience, Norwich, UKAnika Vinze - Broad InstituteArash Iranzadeh - University of Cape TownArnold Lambisia - Kenya Medical Research InstituteArshad Ismail - National Health Laboratory ServiceAudu Rosemary - Nigerian Institute of Medical ResearchAugustina Sylverken - Charité - Universitätsmedizin BerlinAyoade Femi - Redeemer's UniversityAzeddine Ibrahimi - Mohammed V UniversityBaba Marycelin - University of MaiduguriBamidele S Oderinde - University of MaiduguriBankole Bolajoko - Redeemer's UniversityBeatrice Dhaala - Uganda Virus Research InstituteBelinda L Herring - World Health Organization Regional Office for AfricaBerthe-Marie Njanpop-Lafourcade - World Health Organization Regional Office for AfricaBronwyn Kleinhans - Stellenbosch UniversityBronwyn McInnis - Cairo UniversityBryan Tegomoh - Université de Yaoundé ICara Brook - University of ChicagoCatherine B Pratt - University of Nebraska Medical CenterCathrine Scheepers - National Health Laboratory ServiceChantal G Akoua-Koffi - CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d'IvoireCharles N Agoti - Kenya Medical Research InstituteChristophe Peyrefitte - Institut Pasteur de DakarClaudia Daubenberger - Swiss Tropical and Public Health InstituteCollins M Morang'a - University of GhanaD James Nokes - Kenya Medical Research InstituteDaniel G Amoako - National Health Laboratory ServiceDaniel L Bugembe - Uganda Virus Research InstituteDanny Park - Broad InstituteDavid Baker - Quadram InstituteDeelan Doolabh - Wellcome Centre for Infectious Diseases Research in AfricaDeogratius Ssemwanga - Uganda Virus Research InstituteDerek Tshiabuila - University of KwaZulu-NatalDiarra Bassirou - Institut Pasteur de DakarDominic S Y Amuzu - University of GhanaDominique Goedhals - National Health Laboratory ServiceDonwilliams O Omuoyo - Kenya Medical Research InstituteDorcas Maruapula - Botswana Harvard AIDS Institute PartnershipEbenezer Foster-Nyarko - Quadram InstituteEddy K Lusamaki - Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the CongoEdgar Simulundu - University of ZambiaEdidah M Ong'era - Wellcome TrustEdith N Ngabana - National Institute of Biomedical ResearchEdwin Shumba - African Society for Laboratory MedicineElmostafa El Fahime - National Centre for Nuclear Energy, Science and TechnologyEmmanuel Lokilo - National Institute of Biomedical ResearchEnatha Mukantwari - Rwanda National Reference Laboratory, Kigali, RwandaEromon Philomena - Redeemer's UniversityEssia Belarbi - Robert Koch InstituteEtienne Simon-Loriere - Evolutionary Genomics (United States)Etilé A Anoh - CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d'IvoireFabian Leendertz - Robert Koch-Institute, Berlin, GermanyFaida Ajili - Military Hospital of TunisFakayode O Enoch - Department of Public Health, Ministry of Health, Ilorin, Kwara State, NigeriaFares Wasfi - Institut Pasteur de TunisFatma Abdelmoula - Centre of Biotechnology of SfaxFausta S Mosha - World Health Organization Regional Office for AfricaFaustinos T Takawira - National Blood Service ZimbabweFawzi Derrar - National Influenza Centre, Viral Respiratory Laboratory, Algiers, AlgeriaFeriel Bouzid - Centre of Biotechnology of SfaxFolarin Onikepe - Redeemer's UniversityFowotade Adeola - University of IbadanFrancisca M Muyembe - National Institute of Biomedical ResearchFrank Tanser - University of LincolnFred A Dratibi - World Health Organization Regional Office for AfricaGabriel K Mbunsu - University of KinshasaGaetan Thilliez - Quadram InstituteGemma L Kay - Quadram InstituteGeorge Githinji - Kenya Medical Research InstituteGert van Zyl - Stellenbosch UniversityGordon A Awandare - University of GhanaGrit Schubert - Robert Koch InstituteGugu P Maphalala - Ministry of HealthHafaliana C Ranaivoson - Institut Pasteur de MadagascarHajar Lemriss - Université Hassan 1erHappi Anise - Redeemer's UniversityHaruka Abe - Nagasaki UniversityHela H Karray - University of SfaxHellen Nansumba - Central Public Health Laboratories (CPHL), Kampala, UgandaHesham A Elgahzaly - Ain Shams UniversityHlanai Gumbo - National Blood Service ZimbabweIbtihel Smeti - Centre of Biotechnology of SfaxIkhlas B Ayed - University of SfaxIkponmwosa Odia - Irrua Specialist Teaching HospitalIlhem Boutiba Ben Boubaker - Hôpital Charles-NicolleImed Gaaloul - University of MonastirInbal Gazy - Hebrew University of JerusalemInnocent Mudau - Wellcome Centre for Infectious Diseases Research in AfricaIsaac Ssewanyana - Central Public Health Laboratories (CPHL), Kampala, UgandaIyaloo Konstantinus - Namibia Institute of PathologyJean B Lekana-Douk - Centre International de Recherches Médicales de FrancevilleJean-Claude C Makangara - Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the CongoJean-Jacques M Tamfum - Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the CongoJean-Michel Heraud - Institut Pasteur de MadagascarJeffrey G Shaffer - Tulane UniversityJennifer Giandhari - University of KwaZulu-NatalJingjing Li - Drexel University, Urban Health CollaborativeJiro Yasuda - Nagasaki UniversityJoana Q Mends - University of Health and Allied SciencesJocelyn Kiconco - Uganda Virus Research InstituteJohn M Morobe - Kenya Medical Research InstituteJohn O Gyapong - University of Health and Allied SciencesJohnson C Okolie - Redeemer's UniversityJohn T Kayiwa - Uganda Virus Research InstituteJohnathan A Edwards - University of LincolnJones Gyamfi - University of Health and Allied SciencesJouali Farah - Casablanca (Brazil)Joweria Nakaseegu - Uganda Virus Research InstituteJoyce M Ngoi - University of GhanaJoyce Namulondo - Uganda Virus Research InstituteJulia C Andeko - Centre International de Recherches Médicales de FrancevilleJulius J Lutwama - Uganda Virus Research InstituteJustin O'Grady - Quadram InstituteKatherine Siddle - Broad InstituteKayode T Adeyemi - Redeemer's UniversityKefentse A Tumedi - Botswana Institute for Technology Research and InnovationKhadija M Said - Kenya Medical Research InstituteKim Hae-Young - New York UniversityKwabena O Duedu - University of Health and Allied SciencesLahcen Belyamani - Mohammed V UniversityLamia Fki-Berrajah - University of SfaxLavanya Singh - KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South AfricaLeonardo de O Martins - Quadram InstituteLynn Tyers - Wellcome Centre for Infectious Diseases Research in AfricaMagalutcheemee Ramuth - Ministry of Health and Quality of LifeMaha Mastouri - University of MonastirMahjoub Aouni - University of MonastirMahmoud El Hefnawi - National Water Research CenterMaitshwarelo I Matsheka - Botswana Institute for Technology Research and InnovationMalebogo Kebabonye - Ministry of HealthMamadou Diop - Institut Pasteur de DakarManel Turki - Centre of Biotechnology of SfaxMarietou Paye - Broad InstituteMartin M Nyaga - University of the Free StateMathabo Mareka - National University of LesothoMatoke-Muhia Damaris - Kenya Medical Research InstituteMaureen W Mburu - Kenya Medical Research InstituteMaximillian Mpina - Swiss Tropical and Public Health InstituteMba Nwando - Nigeria Centre for Disease ControlMichael Owusu - Kumasi Centre for Collaborative Research in Tropical MedicineMichael R Wiley - University of Nebraska Medical CenterMirabeau T Youtchou - Niger Delta UniversityMitoha O Ayekaba - Laboratorio de Investigaciones de Baney, Baney, Equatorial GuineaMohamed Abouelhoda - Cairo UniversityMohamed G Seadawy - Biological Prevention Department, Main Chemical Laboratories, Egypt Army, Cairo, EgyptMohamed K Khalifa - Children Cancer HospitalMooko Sekhele - National University of LesothoMouna Ouadghiri - Mohammed V UniversityMoussa M Diagne - Institut Pasteur de DakarMulenga Mwenda - PATH, Lusaka, ZambiaMushal Allam - National Health Laboratory ServiceMy V T Phan - MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, UgandaNabil Abid - University of MonastirNadia Touil - Mohammed V UniversityNadine Rujeni - Rwanda Biomedical CenterNajla Kharrat - Centre of Biotechnology of SfaxNalia Ismael - Instituto Nacional de SaúdeNdongo Dia - Institut Pasteur de DakarNedio Mabunda - Instituto Nacional de SaúdeNei-Yuan Hsiao - Wellcome Centre for Infectious Diseases Research in AfricaNelson B Silochi - Laboratorio de Investigaciones de Baney, Baney, Equatorial GuineaNgoy Nsenga - World Health Organization Regional Office for AfricaNicksy Gumede - World Health Organization Regional Office for AfricaNicola Mulder - Wellcome Centre for Infectious Diseases Research in AfricaNnaemeka Ndodo - Nigeria Centre for Disease ControlNorosoa H Razanajatovo - Institut Pasteur de MadagascarNosamiefan Iguosadolo - Redeemer's UniversityOguzie Judith - Redeemer's UniversityOjide C Kingsley - Federal Teaching Hospital AbakalikiOkogbenin Sylvanus - Irrua Specialist Teaching HospitalOkokhere Peter - Irrua Specialist Teaching HospitalOladiji Femi - University of IlorinOlawoye Idowu - Redeemer's UniversityOlumade Testimony - Redeemer's UniversityOmoruyi E Chukwuma - University of IbadanOnwe E Ogah - Federal Teaching Hospital AbakalikiChika K Onwuamah - Nigerian Institute of Medical ResearchOshomah Cyril - Irrua Specialist Teaching HospitalOusmane Faye - Institut Pasteur de DakarOyewale Tomori - Redeemer's UniversityPascale Ondoa - African Society for Laboratory MedicinePatrice Combe - Mayotte Hospital Center, Mayotte, FrancePatrick Semanda - Central Public Health Laboratories (CPHL), Kampala, UgandaPaul E Oluniyi - Redeemer's UniversityPaulo Arnaldo - Instituto Nacional de SaúdePeter K Quashie - University of GhanaPhilippe Dussart - Institut Pasteur de MadagascarPhillip A Bester - National Health Laboratory ServicePlacide K Mbala - National Institute of Biomedical ResearchReuben Ayivor-Djanie - University of Health and Allied SciencesRichard Njouom - Centre Pasteur du CamerounRichard O Phillips - Kumasi Centre for Collaborative Research in Tropical MedicineRichmond Gorman - Kumasi Centre for Collaborative Research in Tropical MedicineRobert A Kingsley - Quadram InstituteRosina A A Carr - University of Health and Allied SciencesSaâd El Kabbaj - Laboratoire de Recherche et d'Analyses Médicales de la Gendarmerie Royale, Rabat, MoroccoSaba Gargouri - University of SfaxSaber Masmoudi - Centre of Biotechnology of SfaxSafietou Sankhe - Institut Pasteur de DakarSalako B Lawal - Nigerian Institute of Medical ResearchSamar Kassim - Ain Shams UniversitySameh Trabelsi - Tunis El Manar UniversitySamar Metha - Broad InstituteSami Kammoun - Hopital Universitaire Hedi ChakerSanaâ Lemriss - Laboratoire de Recherche et d’Analyses Médicales de la Fraternelle de la Gendarmerie RoyaleSara H A Agwa - Ain Shams UniversitySébastien Calvignac-Spencer - Robert Koch InstituteStephen F Schaffner - Broad InstituteSeydou Doumbia - University of BamakoSheila M Mandanda - National Institute of Biomedical ResearchSherihane Aryeetey - Central Laboratory For Agricultural Expert SystemsShymaa S Ahmed - Central Public Health Laboratories (CPHL), Cairo, EgyptSiham Elhamoumi - Broad InstituteSoafy Andriamandimby - Institut Pasteur de MadagascarSobajo Tope - Redeemer's UniversitySonia Lekana-Douki - Centre International de Recherches Médicales de FrancevilleSophie Prosolek - Quadram InstituteSoumeya Ouangraoua - Centre MurazSteve A Mundeke - National Institute of Biomedical ResearchSteven Rudder - Quadram InstituteSumir Panji - Wellcome Centre for Infectious Diseases Research in AfricaSureshnee Pillay - University of KwaZulu-NatalSusan Engelbrecht - Stellenbosch UniversitySusan Nabadda - Central Public Health Laboratories (CPHL), Kampala, UgandaSylvie Behillil - Institut PasteurSylvie L Budiaki - National University of LesothoSylvie van der Werf - Institut PasteurTapfumanei Mashe - National Blood Service ZimbabweTarik Aanniz - Mohammed V UniversityThabo Mohale - National Health Laboratory ServiceThanh Le-Viet - Quadram InstituteTobias Schindler - Swiss Tropical and Public Health InstituteUgochukwu J Anyaneji - University of KwaZulu-NatalUgwu Chinedu - Redeemer's UniversityUpasana Ramphal - University of KwaZulu-NatalUwanibe Jessica - Redeemer's UniversityUwem George - Redeemer's UniversityVagner Fonseca - University of KwaZulu-NatalVincent Enouf - Institut PasteurVivianne Gorova - Med24 Medical Centre, Ruwa, ZimbabweWael H Roshdy - Central Laboratory For Agricultural Expert SystemsWilliam K Ampofo - University of GhanaWolfgang Preiser - Stellenbosch UniversityWonderful T Choga - Botswana Harvard AIDS Institute PartnershipYaw Bediako - University of GhanaYeshnee Naidoo - University of KwaZulu-NatalYvan Butera - Rwanda Biomedical CenterZaydah R de Laurent - Kenya Medical Research InstituteAmadou A Sall - Institut Pasteur de DakarAhmed Rebai - Centre of Biotechnology of SfaxAnne von Gottberg - National Health Laboratory ServiceBourema Kouriba - Nazi Boni UniversityCarolyn Williamson - Wellcome Centre for Infectious Diseases Research in AfricaDaniel J Bridges - PATH, Lusaka, ZambiaIhekweazu Chikwe - Nigeria Centre for Disease ControlJinal N Bhiman - National Health Laboratory ServiceMadisa Mine - Botswana Vaccine Institute (Botswana)Matthew Cotten - Uganda Virus Research InstituteSikhulile Moyo - Harvard UniversitySimani Gaseitsiwe - Botswana Harvard AIDS Institute PartnershipNgonda Saasa - University of ZambiaPardis C Sabeti - Broad InstitutePontiano Kaleebu - Uganda Virus Research InstituteYenew K Tebeje - Africa Centres for Disease Control and PreventionSofonias K Tessema - Africa Centres for Disease Control and PreventionChristian Happi - Redeemer's UniversityJohn Nkengasong - Africa Centres for Disease Control and PreventionTulio de Oliveira - University of KwaZulu-Natal
- Publication Details
- medRxiv : the preprint server for health sciences
- Publisher
- American Physical Society (APS)
- Grant note
- MC_UU_00027/1 / Medical Research Council U2R TW010673 / FIC NIH HHS Wellcome Trust U01 HG007480 / NHGRI NIH HHS K24 AI131924 / NIAID NIH HHS K24 AI131928 / NIAID NIH HHS INV-018030 / Bill & Melinda Gates Foundation U51 IP000812 / NCIRD CDC HHS INV-018278 / Bill & Melinda Gates Foundation MC_UU_12014/12 / Medical Research Council U01 AI151698 / NIAID NIH HHS 001 / World Health Organization U41 HG006941 / NHGRI NIH HHS 203077 / Wellcome Trust U54 HG007480 / NHGRI NIH HHS INV-018978 / Bill & Melinda Gates Foundation U01IP001048 / ACL HHS MC_PC_19026 / Medical Research Council MR/J01477X/1 / Medical Research Council
- Resource Type
- Preprint
- Language
- English
- Academic Unit
- Urban Health Collaborative
- Web of Science ID
- WOS:000710251800038
- Other Identifier
- 991021864299304721
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- Biochemistry & Molecular Biology