A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
Authors: Wilkinson Eduan , Giovanetti Marta , Tegally Houriiyah , San James E. , Lessels Richard , Cuadros Diego , Martin Darren P. , Zekri Abdel-Rahman N. , Sangare Abdoul K. , Ouedraogo Abdoul-Salam , Sesay Abdul K. , Hammami Adnène , Amuri Adrienne A. , Sayed Ahmad , Rebai Ahmed , Elargoubi Aida , Trotter Alexander J. , Keita Alpha K. , Sall Amadou A. , Kone Amadou , Souissi Amal , Gutierrez Ana V. , Page Andrew J. , Iranzadeh Arash , Lambisia Arnold , Sylverken Augustina , Ibrahimi Azeddine , Dhaala Beatrice , Kouriba Bourema , Kleinhans Bronwyn , Brook Cara , Williamson Carolyn , Pratt Catherine B. , Akoua-Koffi Chantal G. , Agoti Charles N. , Morang’a Collins M. , Nokes D. James , Bridges Daniel J. , Bugembe Daniel L. , Baker David , Doolabh Deelan , Ssemwanga Deogratius , Tshabuila Derek , Bassirou Diarra , Amuzu Dominic S.Y. , Goedhals Dominique , Maruapula Dorcas , Foster-Nyarko Ebenezer , Lusamaki Eddy K. , Simulundu Edgar , Moraa Edidah , Ngabana Edith N. , Fahime Elmostafa El , Jacob Emerald , Lokilo Emmanuel , Mukantwari Enatha , Belarbi Essia , Simon-Loriere Etienne , Anoh Etilé A. , Leendertz Fabian , Ajili Faida , Wasfi Fares , Takawira Faustinos T. , Derrar Fawzi , Bouzid Feriel , Muyembe Francisca M. , Tanser Frank , Mbunsu Gabriel K. , Thilliez Gaetan , Kay Gemma , Githinji George , Zyl Gert van , Awandare Gordon A. , Schubert Grit , Maphalala Gugu P. , Ranaivoson Hafaliana C. , Lemriss Hajar , Abe Haruka , Karray Hela H. , Nansumba Hellen , Elgahzaly Hesham A. , Gumbo Hlanai , Smeti Ibtihel , Ayed Ikhlas B. , Boubaker Ilhem Boutiba-Ben , Gaaloul Imed , Gazy Inbal , Ssewanyana Isaac , Lekana-Douk Jean B. , Makangara Jean-Claude C. , Tamfum Jean-Jacques M. , Heraud Jean-Michel , Shaffer Jeffrey G. , Giandhari Jennifer , Li Jingjing , Yasuda Jiro , Mends Joana Q. , Kiconco Jocelyn , Morobe John , Nkengasong John N. , Gyapong John O. , Kayiwa John T. , Edwards Johnathan A. , Gyamfi Jones , Farah Jouali , Ngoi Joyce M. , Namulondo Joyce , Andeko Julia C. , Lutwama Julius J. , O’Grady Justin , Tumedi Kefentse A. , Said Khadija M. , Hae-Young Kim , Duedu Kwabena O. , Belyamani Lahcen , Singh Lavanya , Martins Leonardo de O. , Mine Madisa , Ramuth Magalutcheemee , Mastouri Maha , Aouni Mahjoub , Hefnawi Mahmoud el , Matsheka Maitshwarelo I. , Kebabonye Malebogo , Turki Manel , Nyaga Martin M. , Mareka Mathabo , Damaris Matoke , Cotten Matthew , Mburu Maureen W. , Mpina Maximillian , Owusu Michael , Wiley Michael R. , Ali Mohamed A. , Abouelhoda Mohamed , Seadawy Mohamed G. , Khalifa Mohamed K. , Sekhele Mooko , Ouadghiri Mouna , Mwenda Mulenga , Allam Mushal , Phan My V.T. , Abid Nabil , Touil Nadia , Kharrat Najla , Ismael Nalia , Mabunda Nedio , Hsiao Nei-yuan , Silochi Nelson B. , Saasa Ngonda , Mulder Nicola , Combe Patrice , Semanda Patrick , Oluniyi Paul E. , Arnaldo Paulo , Quashie Peter K. , Bester Philip A. , Dussart Philippe , Mbala Placide K. , Kaleebu Pontiano , Ayivor-Djanie Reuben , Njouom Richard , Phillips Richard O. , Gorman Richmond , Kingsley Robert A. , Carr Rosina A.A. , Kabbaj Saâd El , Gargouri Saba , Masmoudi Saber , Kassim Samar , Trabelsi Sameh , Kammoun Sami , Lemriss Sanaâ , Agwa Sara H. , Calvignac-Spencer Sébastien , Doumbia Seydou , Mandanda Sheila M. , Aryeetey Sherihane , Ahmed Shymaa S. , Moyo Sikhulile , Gaseitsiwe Simani , Lekana-Douki Sonia , Prosolek Sophie , Ouangraoua Soumeya , Mundeke Steve A. , Rudder Steven , Panji Sumir , Pillay Sureshnee , Engelbrecht Susan , Nabadda Susan , Behillil Sylvie , Budiaki Sylvie L. , van der Werf Sylvie , Mashe Tapfumanei , Aanniz Tarik , Mohale Thabo , Le-Viet Thanh , Schindler Tobias , Anyaneji Ugochukwu J. , Ramphal Upasana , Fonseca Vagner , Enouf Vincent , Gorova Vivianne , Roshdy Wael H. , Ampofo William K. , Preiser Wolfgang , Choga Wonderful T. , Bediako Yaw , Tebeje Yenew K , Naidoo Yeshnee , de Laurent Zaydah R. , Tessema Sofonias K. , de Oliveira Tulio 
Published: May 2021

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.