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

2021; Cold Spring Harbor Laboratory; Linguagem: Inglês

10.1101/2021.05.12.21257080

Eduan Wilkinson, Marta Giovanetti, Houriiyah Tegally, James Emmanuel San, Richard Lessels, Diego F. Cuadros, Darren P. Martin, Abdel‐Rahman N. Zekri, Abdoul Karim Sangaré, Abdoul–Salam Ouédraogo, Abdul Karim Sesay, Adnène Hammami, Adrienne Amuri-Aziza, Ahmad Sayed, Ahmed Rebaï, Aida Elargoubi, Alexander J. Trotter, Alpha Kabinet Keïta, Amadou A. Sall, A. Koné, Amal Souissi, Ana Victoria Gutiérrez, Andrew J. Page, Arash Iranzadeh, Arnold W. Lambisia, Augustina Angelina Sylverken, Azeddine Ibrahimi, Beatrice Dhaala, Bourèma Kouriba, Bronwyn Kleinhans, Cara E. Brook, Carolyn Williamson, Catherine Pratt, Chantal Akoua‐Koffi, Charles N. Agoti, Collins M. Morang’a, D. James Nokes, Daniel J. Bridges, Daniel Lule Bugembe, David Baker, Deelan Doolabh, Deogratius Ssemwanga, Derek Tshabuila, Bassirou Diarra, Dominic S. Y. Amuzu, Dominique Goedhals, Dorcas Maruapula, Ebenezer Foster-Nyarko, Eddy Kinganda-Lusamaki, Edgar Simulundu, Edidah O. Moraa, Edith N. Ngabana, Elmostafa El Fahime, Emerald Jacob, Emmanuel Lokilo, Enatha Mukantwari, Essia Belarbi, Etienne Simon‐Lorière, Etilé A. Anoh, Fabian H. Leendertz, F. Ajili, Wasfi Farès, Faustinos Tatenda Takawira, Fawzi Derrar, Fériel Bouzid, Francisca Muyembe, Frank Tanser, Gabriel K. Mbunsu, Gaetän Thilliez, Gemma L. Kay, George Githinji, Gert U. van Zyl, Gordon A. Awandare, Grit Schubert, Gugu Maphalala, Hafaliana C. Ranaivoson, Hajar Lemriss, Haruka Abe, Héla Karray, Hellen Nansumba, Hesham A. Elgahzaly, Hlanai Gumbo, Ibtihel Smeti, Ikhlas Ben Ayed, Ilhem Boutiba-Ben Boubaker, Imed Gaâloul, Inbal Gazy, Isaac Ssewanyana, Jean B. Lekana-Douk, Jean-Claude Makangara-Cigolo, Jean‐Jacques Muyembe Tamfum, Jean‐Michel Héraud, Jeffrey G. Shaffer, Jennifer Giandhari, Jingjing Li, Jiro Yasuda, Joana Q. Mends, Jocelyn Kiconco, John Mwita Morobe, John N. Nkengasong, John O. Gyapong, John Kayiwa, Johnathan A. Edwards, Jones Gyamfi, Jouali Farah, Joyce M. Ngoi, Joyce Namulondo, Julia C. Andeko, Julius J. Lutwama, Justin O’Grady, Kefentse A. Tumedi, Khadija M. Said, Hae‐Young Kim, Kwabena Obeng Duedu, Lahcen Belyamani, Lavanya Singh, Leonardo de Oliveira Martins, Madisa Mine, Magalutcheemee Ramuth, Maha Mastouri, Mahjoub Aouni, Mahmoud El Hefnawi, M.I. Matsheka, Malebogo Kebabonye, Manel Turki, Martin M. Nyaga, Mathabo Mareka, Damaris Matoke, Matthew Cotten, Maureen W. Mburu, Maxmillian Mpina, Michael Owusu, Michael R. Wiley, Mohamed A. Ali, Mohamed Abouelhoda, Mohamed G. Seadawy, Mohamed K. Khalifa, Mooko Sekhele, Mouna Ouadghiri, Mulenga Mwenda, Mushal Allam, My V. T. Phan, Nabil Abid, Nadia Touil, Najla Kharrat, Nália Ismael, Nédio Mabunda, Marvin Hsiao, Nelson Boricó Silochi, Ngonda Saasa, Nicola Mulder, P Combe, Patrick Semanda, Paul E. Oluniyi, Paulo Arnaldo, Peter K. Quashie, Philip Armand Bester, Philippe Dussart, Placide Mbala, Pontiano Kaleebu, Reuben Ayivor-Djanie, Richard Njouom, Richard Odame Phillips, Richmond Gorman, Robert A. Kingsley, Rosina Carr, Saâd El Kabbaj, Saba Gargouri, Saber Masmoudi, Samar K. Kassim, Sameh Trabelsi, S. Kammoun, Sanaâ Lemriss, Sara H. A. Agwa, Sébastien Calvignac‐Spencer, Seydou Doumbia, Sheila Makiala Mandanda, Sherihane Aryeetey, Shymaa S. Ahmed, Sikhulile Moyo, Simani Gaseitsiwe, Sonia Etenna Lekana-Douki, Sophie J. Prosolek, Soumeya Ouangraoua, Steve Ahuka Mundeke, Steven Rudder, Sumir Panji, Sureshnee Pillay, Susan Engelbrecht, Susan Nabadda, Sylvie Behillil, Sylvie L. Budiaki, Sylvie van der Werf, Tapfumanei Mashe, Tarik Aanniz, Thabo Mohale, Thanh Le-Viet, Tobias Schindler, Ugochukwu J. Anyaneji, Upasana Ramphal, Vagner Fonseca, Vincent Enouf, Vivianne Gorova, Wael H. Roshdy, William Ampofo, Wolfgang Preiser, Wonderful T. Choga, Yaw Bediako, Yenew Kebede Tebeje, Yeshnee Naidoo, Zaydah R. de Laurent, Sofonías K. Tessema, Túlio de Oliveira,

Immune responses and vaccinations

Abstract The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, 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 following 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 breeding ground for new variants.