Abstract

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Tegally H San JE Cotten M Moir M Tegomoh B Mboowa G Martin DP Baxter C Lambisia AW Diallo A Amoako DG Diagne MM Sisay A Zekri AN Gueye AS Sangare AK Ouedraogo AS Sow A Musa AO Sesay AK Abias AG Elzagheid AI Lagare A Kemi AS Abar AE Johnson AA Fowotade A Oluwapelumi AO Amuri AA Juru A Kandeil A Mostafa A Rebai A Sayed A Kazeem A Balde A Christoffels A Trotter AJ Campbell A Keita AK Kone A Bouzid A Souissi A Agweyu A Naguib A Gutierrez AV Nkeshimana A Page AJ Yadouleton A Vinze A Happi AN Chouikha A Iranzadeh A Maharaj A Batchi-Bouyou AL Ismail A Sylverken AA Goba A Femi A Sijuwola AE Marycelin B Salako BL Oderinde BS Bolajoko B Diarra B Herring BL Tsofa B Lekana-Douki B Mvula B Njanpop-Lafourcade BM Marondera BT Khaireh BA Kouriba B Adu B Pool B McInnis B Brook C Williamson C Nduwimana C Anscombe C Pratt CB Scheepers C Akoua-Koffi CG Agoti CN Mapanguy CM Loucoubar C Onwuamah CK Ihekweazu C Malaka CN Peyrefitte C Grace C Omoruyi CE Rafai CD Morang'a CM Erameh C Lule DB Bridges DJ Mukadi-Bamuleka D Park D Rasmussen DA Baker D Nokes DJ Ssemwanga D Tshiabuila D Amuzu DSY Goedhals D Grant DS Omuoyo DO Maruapula D Wanjohi DW Foster-Nyarko E Lusamaki EK Simulundu E Ong'era EM Ngabana EN Abworo EO Otieno E Shumba E Barasa E Ahmed EB Ahmed EA Lokilo E Mukantwari E Philomena E Belarbi E Simon-Loriere E Anoh EA Manuel E Leendertz F Taweh FM Wasfi F Abdelmoula F Takawira FT Derrar F Ajogbasile FV Treurnicht F Onikepe F Ntoumi F Muyembe FM Ragomzingba FEZ Dratibi FA Iyanu FA Mbunsu GK Thilliez G Kay GL Akpede GO van Zyl GU Awandare GA Kpeli GS Schubert G Maphalala GP Ranaivoson HC Omunakwe HE Onywera H Abe H Karray H Nansumba H Triki H Kadjo HAA Elgahzaly H Gumbo H Mathieu H Kavunga-Membo H Smeti I Olawoye IB Adetifa IMO Odia I Ben Boubaker IB Muhammad IA Ssewanyana I Wurie I Konstantinus IS Halatoko JWA Ayei J Sonoo J Makangara JC Tamfum JM Heraud JM Shaffer JG Giandhari J Musyoki J Nkurunziza J Uwanibe JN Bhiman JN Yasuda J Morais J Kiconco J Sandi JD Huddleston J Odoom JK Morobe JM Gyapong JO Kayiwa JT Okolie JC Xavier JS Gyamfi J Wamala JF Bonney JHK Nyandwi J Everatt J Nakaseegu J Ngoi JM Namulondo J Oguzie JU Andeko JC Lutwama JJ Mogga JJH O'Grady J Siddle KJ Victoir K Adeyemi KT Tumedi KA Carvalho KS Mohammed KS Dellagi K Musonda KG Duedu KO Fki-Berrajah L Singh L Kepler LM Biscornet L de Oliveira Martins L Chabuka L Olubayo L Ojok LD Deng LL Ochola-Oyier LI Tyers L Mine M Ramuth M Mastouri M ElHefnawi M Mbanne M Matsheka MI Kebabonye M Diop M Momoh M Lima Mendonca MDL Venter M Paye MF Faye M Nyaga MM Mareka M Damaris MM Mburu MW Mpina MG Owusu M Wiley MR Tatfeng MY Ayekaba MO Abouelhoda M Beloufa MA Seadawy MG Khalifa MK Matobo MM Kane M Salou M Mbulawa MB Mwenda M Allam M Phan MVT Abid N Rujeni N Abuzaid N Ismael N Elguindy N Top NM Dia N Mabunda N Hsiao NY Silochi NB Francisco NM Saasa N Bbosa N Murunga N Gumede N Wolter N Sitharam N Ndodo N Ajayi NA Tordo N Mbhele N Razanajatovo NH Iguosadolo N Mba N Kingsley OC Sylvanus O Femi O Adewumi OM Testimony O Ogunsanya OA Fakayode O Ogah OE Oludayo OE Faye O Smith-Lawrence P Ondoa P Combe P Nabisubi P Semanda P Oluniyi PE Arnaldo P Quashie PK Okokhere PO Bejon P Dussart P Bester PA Mbala PK Kaleebu P Abechi P El-Shesheny R Joseph R Aziz RK Essomba RG Ayivor-Djanie R Njouom R Phillips RO Gorman R Kingsley RA Neto Rodrigues Rmdesa Audu RA Carr RAA Gargouri S Masmoudi S Bootsma S Sankhe S Mohamed SI Femi S Mhalla S Hosch S Kassim SK Metha S Trabelsi S Agwa SH Mwangi SW Doumbia S Makiala-Mandanda S Aryeetey S Ahmed SS Ahmed SM Elhamoumi S Moyo S Lutucuta S Gaseitsiwe S Jalloh S Andriamandimby SF Oguntope S Grayo S Lekana-Douki S Prosolek S Ouangraoua S van Wyk S Schaffner SF Kanyerezi S Ahuka-Mundeke S Rudder S Pillay S Nabadda S Behillil S Budiaki SL van der Werf S Mashe T Mohale T Le-Viet T Velavan TP Schindler T Maponga TG Bedford T Anyaneji UJ Chinedu U Ramphal U George UE Enouf V Nene V Gorova V Roshdy WH Karim WA Ampofo WK Preiser W Choga WT Ahmed YA Ramphal Y Bediako Y Naidoo Y Butera Y de Laurent ZR Africa Pathogen Genomics Initiative double dagger Ouma AEO von Gottberg A Githinji G Moeti M Tomori O Sabeti PC Sall AA Oyola SO Tebeje YK Tessema SK de Oliveira T Happi C Lessells R Nkengasong J Wilkinson E
Science. 2022;378eabq5358

Permenent descriptor

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.