A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
Eduan Wilkinson, Marta Giovanetti, Houriiyah Tegally, James Emmanuel San, Richard Lessells, Diego F. Cuadros, Darren P. Martin, David A. Rasmussen, Abdel‐Rahman N. Zekri, Abdoul Karim Sangaré, Abdoul–Salam Ouédraogo, Abdul Karim Sesay, Priscilla Abechi, Adedotun-Sulaiman Kemi, Adewunmi M. Olubusuyi, Oluwapelumi O. Adeyemi, Adnene Hammami, Adrienne Amuri-Aziza, Ahmad Sayed, Ahmed E. O. Ouma, Aida Elargoubi, Nnennaya Anthony Ajayi, Ajogbasile F. Victoria, Kazeem Akano, Akpede George, Alexander J. Trotter, Yahaya Ali Ahmed, Alpha Kabinet Kéita, Amadou Diallo, A. Koné, Amal Souissi, Amel Chtourou, Ana Victoria Gutiérrez, Andrew J. Page, Anika Vinzé, Arash Iranzadeh, Arnold W. Lambisia, Arshad Ismail, Rosemary Audu, Augustina Angelina Sylverken, Femi Ayoade, Azeddine Ibrahimi, Baba M, Bamidele Soji Oderinde, Bankole Bolajoko, Beatrice Dhaala, Belinda L. Herring, Berthe‐Marie Njanpop‐Lafourcade, Bronwyn Kleinhans, Bronwyn McInnis, Bryan Tegomoh, Cara E. Brook, Catherine Pratt, Cathrine Scheepers, Chantal Akoua‐Koffi, Charles N. Agoti, Christophe N. Peyrefitte, Claudia Daubenberger, Collins M. Morang’a, D. James Nokes, Daniel G. Amoako, Daniel Lule Bugembe, Daniel J. Park, David Baker, Deelan Doolabh, Deogratius Ssemwanga, Derek Tshiabuila, Bassirou Diarra, Dominic S. Y. Amuzu, Dominique Goedhals, Donwilliams O. Omuoyo, Dorcas Maruapula, Ebenezer Foster-Nyarko, Eddy Kinganda-Lusamaki, Edgar Simulundu, Edidah M. Ong’era, Edith Nkwembe Ngabana, Edwin Shumba, Elmostafa El Fahime, Emmanuel Lokilo, Enatha Mukantwari, Eromon Philomena, Essia Belarbi, Etienne Simon‐Lorière, Etilé A. Anoh, Fabian H. Leendertz, F. Ajili, Fakayode O. Enoch, Wasfi Farès, Fatma Abdelmoula, Fausta Mosha, Faustinos Tatenda Takawira, Fawzi Derrar, Fériel Bouzid, Onikepe Folarin, Fowotade Adeola, Francisca Muyembe, Frank Tanser, Fred Athanasius Dratibi, Gabriel K. Mbunsu
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.