Abstract

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Wilkinson E Giovanetti M Tegally H San JE Lessells R Cuadros D Martin DP Rasmussen DA Zekri AN Sangare AK Ouedraogo AS Sesay AK Priscilla A Kemi AS Olubusuyi AM Oluwapelumi AOO Hammami A Amuri AA Sayed A Ouma AEO Elargoubi A Ajayi NA Victoria AF Kazeem A George A Trotter AJ Yahaya AA Keita AK Diallo A Kone A Souissi A Chtourou A Gutierrez AV Page AJ Vinze A Iranzadeh A Lambisia A Ismail A Rosemary A Sylverken A Femi A Ibrahimi A Marycelin B Oderinde BS Bolajoko B Dhaala B Herring BL Njanpop-Lafourcade BM Kleinhans B McInnis B Tegomoh B Brook C Pratt CB Scheepers C Akoua-Koffi CG Agoti CN Peyrefitte C Daubenberger C Morang'a CM Nokes DJ Amoako DG Bugembe DL Park D Baker D Doolabh D Ssemwanga D Tshiabuila D Bassirou D Amuzu DSY Goedhals D Omuoyo DO Maruapula D Foster-Nyarko E Lusamaki EK Simulundu E Ong'era EM Ngabana EN Shumba E El Fahime E Lokilo E Mukantwari E Philomena E Belarbi E Simon-Loriere E Anoh EA Leendertz F Ajili F Enoch FO Wasfi F Abdelmoula F Mosha FS Takawira FT Derrar F Bouzid F Onikepe F Adeola F Muyembe FM Tanser F Dratibi FA Mbunsu GK Thilliez G Kay GL Githinji G van Zyl G Awandare GA Schubert G Maphalala GP Ranaivoson HC Lemriss H Anise H Abe H Karray HH Nansumba H Elgahzaly HA Gumbo H Smeti I Ayed IB Odia I Ben Boubaker IB Gaaloul I Gazy I Mudau I Ssewanyana I Konstantinus I Lekana-Douk JB Makangara JC Tamfum JM Heraud JM Shaffer JG Giandhari J Li J Yasuda J Mends JQ Kiconco J Morobe JM Gyapong JO Okolie JC Kayiwa JT Edwards JA Gyamfi J Farah J Nakaseegu J Ngoi JM Namulondo J Andeko JC Lutwama JJ O'Grady J Siddle K Adeyemi KT Tumedi KA Said KM Hae-Young K Duedu KO Belyamani L Fki-Berrajah L Singh L Martins LO Tyers L Ramuth M Mastouri M Aouni M El Hefnawi M Matsheka MI Kebabonye M Diop M Turki M Paye M Nyaga MM Mareka M Damaris MM Mburu MW Mpina M Nwando M Owusu M Wiley MR Youtchou MT Ayekaba MO Abouelhoda M Seadawy MG Khalifa MK Sekhele M Ouadghiri M Diagne MM Mwenda M Allam M Phan MVT Abid N Touil N Rujeni N Kharrat N Ismael N Dia N Mabunda N Hsiao NY Silochi NB Nsenga N Gumede N Mulder N Ndodo N Razanajatovo NH Iguosadolo N Judith O Kingsley OC Sylvanus O Peter O Femi O Idowu O Testimony O Chukwuma OE Ogah OE Onwuamah CK Cyril O Faye O Tomori O Ondoa P Combe P Semanda P Oluniyi PE Arnaldo P Quashie PK Dussart P Bester PA Mbala PK Ayivor-Djanie R Njouom R Phillips RO Gorman R Kingsley RA Carr RAA El Kabbaj S Gargouri S Masmoudi S Sankhe S Lawal SB Kassim S Trabelsi S Metha S Kammoun S Lemriss S Agwa SHA Calvignac-Spencer S Schaffner SF Doumbia S Mandanda SM Aryeetey S Ahmed SS Elhamoumi S Andriamandimby S Tope S Lekana-Douki S Prosolek S Ouangraoua S Mundeke SA Rudder S Panji S Pillay S Engelbrecht S Nabadda S Behillil S Budiaki SL van der Werf S Mashe T Aanniz T Mohale T Le-Viet T Schindler T Anyaneji UJ Chinedu U Ramphal U Jessica U George U Fonseca V Enouf V Gorova V Roshdy WH Ampofo WK Preiser W Choga WT Bediako Y Naidoo Y Butera Y de Laurent ZR Sall AA Rebai A von Gottberg A Kouriba B Williamson C Bridges DJ Chikwe I Bhiman JN Mine M Cotten M Moyo S Gaseitsiwe S Saasa N Sabeti PC Kaleebu P Tebeje YK Tessema SK Happi C Nkengasong J de Oliveira T
Science. 2021;374423-431

Permenent descriptor

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.