Review 1: "A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa"

M Hossain

doi:doi:10.1162/2e3983f5.80a73fb2

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

by Eduan Wilkinson, Marta Giovanetti, Houriiyah Tegally, James E. San, Richard Lessels, Diego Cuadros, Darren P. Martin, Abdel-Rahman N. Zekri, Abdoul K. Sangare, Abdoul-Salam Ouedraogo, Abdul K. Sesay, Adnène Hammami, Adrienne A. Amuri, Ahmad Sayed, Ahmed Rebai, Aida Elargoubi, Alexander J. Trotter, Alpha K. Keita, Amadou A. Sall, Amadou Kone, Amal Souissi, Ana V. Gutierrez, Andrew J. Page, Arash Iranzadeh, Arnold Lambisia, Augustina Sylverken, Azeddine Ibrahimi, Beatrice Dhaala, Bourema Kouriba, Bronwyn Kleinhans, Cara Brook, Carolyn Williamson, Catherine B. Pratt, Chantal G. Akoua-Koffi, Charles N. Agoti, Collins M. Morang’a, D. James Nokes, Daniel J. Bridges, Daniel L. Bugembe, David Baker, Deelan Doolabh, Deogratius Ssemwanga, Derek Tshabuila, Diarra Bassirou, Dominic S.Y. Amuzu, Dominique Goedhals, Dorcas Maruapula, Ebenezer Foster-Nyarko, Eddy K. Lusamaki, Edgar Simulundu, Edidah Moraa, Edith N. Ngabana, Elmostafa El Fahime, Emerald Jacob, Emmanuel Lokilo, Enatha Mukantwari, Essia Belarbi, Etienne Simon-Loriere, Etilé A. Anoh, Fabian Leendertz, Faida Ajili, Fares Wasfi, Faustinos T. Takawira, Fawzi Derrar, Feriel Bouzid, Francisca M. Muyembe, Frank Tanser, Gabriel K. Mbunsu, Gaetan Thilliez, Gemma Kay, George Githinji, Gert van Zyl, Gordon A. Awandare, Grit Schubert, Gugu P. Maphalala, Hafaliana C. Ranaivoson, Hajar Lemriss, Haruka Abe, Hela H. Karray, Hellen Nansumba, Hesham A. Elgahzaly, Hlanai Gumbo, Ibtihel Smeti, Ikhlas B. Ayed, Ilhem Boutiba-Ben Boubaker, Imed Gaaloul, Inbal Gazy, Isaac Ssewanyana, Jean B. Lekana-Douk, Jean-Claude C. Makangara, Jean-Jacques M. Tamfum, Jean-Michel Heraud, Jeffrey G. Shaffer, Jennifer Giandhari, Jingjing Li, Jiro Yasuda, Joana Q. Mends, Jocelyn Kiconco, John Morobe, John N. Nkengasong, John O. Gyapong, John T. 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, Kim Hae-Young, Kwabena O. Duedu, Lahcen Belyamani, Lavanya Singh, Leonardo de O. Martins, Madisa Mine, Magalutcheemee Ramuth, Maha Mastouri, Mahjoub Aouni, Mahmoud el Hefnawi, Maitshwarelo I. Matsheka, Malebogo Kebabonye, Manel Turki, Martin M. Nyaga, Mathabo Mareka, Matoke Damaris, Matthew Cotten, Maureen W. Mburu, Maximillian 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, Nalia Ismael, Nedio Mabunda, Nei-yuan Hsiao, Nelson B. Silochi, Ngonda Saasa, Nicola Mulder, Patrice Combe, Patrick Semanda, Paul E. Oluniyi, Paulo Arnaldo, Peter K. Quashie, Philip A. Bester, Philippe Dussart, Placide K. Mbala, Pontiano Kaleebu, Reuben Ayivor-Djanie, Richard Njouom, Richard O. Phillips, Richmond Gorman, Robert A. Kingsley, Rosina A.A. Carr, Saâd El Kabbaj, Saba Gargouri, Saber Masmoudi, Samar Kassim, Sameh Trabelsi, Sami Kammoun, Sanaâ Lemriss, Sara H. Agwa, Sébastien Calvignac-Spencer, Seydou Doumbia, Sheila M. Mandanda, Sherihane Aryeetey, Shymaa S. Ahmed, Sikhulile Moyo, Simani Gaseitsiwe, Sonia Lekana-Douki, Sophie Prosolek, Soumeya Ouangraoua, Steve A. 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 K. Ampofo, Wolfgang Preiser, Wonderful T. Choga, Yaw Bediako, Yenew K Tebeje, Yeshnee Naidoo, Zaydah R. de Laurent, Sofonias K. Tessema, and Tulio de Oliveira

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AbstractThe 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.

Review 1: "A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa"

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