A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
Wilkinson, Eduan
Giovanetti, Marta
Tegally, Houriiyah
San, James E.
Lessells, Richard
Cuadros, Diego
Martin, Darren P.
Rasmussen, David A.
Zerki, Abdel-Rahman N.
Sangare, Abdoul K.
Ouedraogo, Abdoul-Salam
Sesay, Abdul K.
Priscilla, Abechi
Kemi, Adedotun-Sulaiman
Olubusuyi, Adewunmi M.
Oluwapelumi, Adeyemi O. O.
Hammami, Adnène
Amuri, Adrienne A.
Sayed, Ahmad
Ouma, Ahmed E. O.
Elargoubi, Aida
Ajayi, Nnennaya A.
Victoria, Ajogbasile F.
Kazeem, Akano
George, Akpede
Trotter, Alexander J.
Yahaya, Ali A.
Keita, Alpha K.
Diallo, Amadou
Kone, Amadou
Souissi, Amal
Chtourou, Amel
Gutierrez, Ana V.
Page, Andrew J.
Vinze, Anika
Iranzadeh, Arash
Lambisia, Arnold
Ismail, Arshad
Rosemary, Audu
Sylverken, Augustina
Femi, Ayoade
Ibrahimi, Azeddine
Marycelin, Baba
Oderinde, Bamidele S.
Bolajoko, Bankole
Dhaala, Beatrice
Herring, Belinda L.
Njanpop-Lafourcade, Berthe-Marie
Kleinhans, Bronwyn
McInnis, Bronwyn
Tegomoh, Bryan
Brook, Cara
Pratt, Catherine B.
Scheepers, Cathrine
Akouka-Koffi, Chantal G.
Agoti, Charles N.
Peyrefitte, Christophe
Daubenberger, Claudia
Morang'a, Collins M.
Nokes, D. James
Amoako, Daniel G.
Bugembe, Daniel L.
Park, Danny
Baker, David
Doolabh, Deelan
Ssemwanga, Deogratius
Tshiabuila, Derek
Bassirou, Diarra
Amuzu, Dominic S. Y.
Goedhals, Dominique
Omouyo, Donwilliams O.
Maruapula, Doracs
Foster-Nyarko, Ebenezer
Lusamaki, Eddy K.
Simulundu, Edgar
Ong'era, Edidah M.
Ngabana, Edith N.
Shumba, Edwin
el Fahime, Elmostafa
Lokilo, Emmanuel
Mukantwari, Enatha
Philomena, Eromon
Belarbi, Essia
Simon-Loriere, Etienne
Anoh, Etilé A.
Leendertz, Fabian
Ajili, Faida
Enoch, Fakayode O.
Wasfi, Fares
Abdelmoula, Fatma
Mosha, Fausta S.
Takawira, Faustinos T.
Derrar, Fawzi
Bouzid, Feriel
Onikepe, Folarin
Adeola, Fowotade
Muyembe, Francisca M.
Tanser, Frank
Dratibi, Fred A.
Mbunsu, Gabriel K.
Thilliez, Gaean
Kay, Gemma L.
Githinji, George
van Zyl, Gert
Awandare, Gordon A.
Schubert, Grit
Maphalala, Gugu P.
Rannaivoson, Hafaliana C.
Lemriss, Hajar
Anise, Happi
Abe, Haruka
Karray, Hela H.
Nansumba, Hellen
Elgahzaly, Hesham A.
Gumbo, Hlanai
Smeti, Ibtihel
Ayed, Ikhlas B.
Odia, Ikponmwosa
Boubaker, Ilhem Boubita Ben
Gaaloul, Imed
Gazy, Inbal
Mudau, Innocent
Ssewanyana, Isaac
Konstantinus, Iyaloo
Lekana-Douk, Jean B.
Makangara, Jean-Claude C.
Tamfum, Jean-Jacques M.
Heraud, Jean-Michel
Shaffer, Jeffrey G.
Giandhari, Jennifer
Li, Jing Jing
Yasuda, Jiro
Mends, Joana Q.
Kiconco, Jocelyn
Morobe, John M.
Gyapong, John O.
Okolie, Johnson C.
Kayiwa, John T.
Edwards, Johnathan A.
Gyamfi, Jones
Farah, Jouali
Nakaseegu, Joweira
Ngoi, Joyce M.
Namulondo, Joyce
Andeko, Julia C.
Lutwama, Julius J.
O'Grady, Justin
Siddle, Katherine
Adeyemi, Kayode T.
Tumedi, Kefentse A.
Said, Khadija M.
Hae-Young, Kim
Duedu, Kwabena
Belyamani, Lahcen
Fki-Berrajah, Lamia
Singh, Lavanya
de Oliveira Martins, Leonardo
Tyers, Lynn
Ramuth, Magalutcheemee
Matsouri, Maha
Aouni, Mahjoub
el Hefnawi, Mahmoud
Matsheka, Maitshwarelo I.
Kebabonye, Malebogo
Diop, Mamadou
Turki, Manel
Paye, Marietou
Nyaga, Martin M.
Mareka, Mathabo
Damaris, Matoke-Muhia
Mburu, Maureen W.
Mpina, Maximillian
Nwando, Mba
Owusu, Michael
Wiley, Michael R.
Youtchou, Mirabeau T.
Ayekaba, Mitoha O.
Abouelhoda, Mohamed
Seadawy, Mohamed G.
Khalifa, Mohamed K.
Sekhele, Mooko
Ouadghiri, Mouna
Diagne, Moussa M.
Mwenda, Mulenga
Allam, Mushal
Phan, My V. T.
Abid, Nabil
Touil, Nadia
rujeni, Nadine
Kharrat, Najla
Ismael, Nalia
Dia, Ndongo
Mabunda, Neido
Hsiao, Nei-Yuan
Silochi, Nelson B.
Nsenga, Ngoy
Gumede, Nicksy
Mulder, Nicola
Ndodo, Nnaemeka
Razanajatovo, Norosoa H.
Iguosadolo, Nosamiefan
Judith, Oguzie
Kingsley, Ojide C.
Sylvanus, Okogbenin
Peter, Okokhere
Femi, Oladiji
Idowu, Olawoye
Testimony, Olumade
Chukwuma, Omoruyi E.
Ogah, Onwe E.
Onwuamah, Chika K.
Cyril, Oshomah
Faye, Ousmane
Tomori, Oyewale
Ondoa, Pascale
Combe, Patrice
Semanda, Patrick
Oluniyi, Paul E.
Arnaldo, Paulo
Quashie, Peter K.
Dussart, Philippe
Bester, Phillip A.
Mbala, Placide K.
Ayivor-Djanie, Reuben
Njouom, Richard
Phillips, Richard O.
Gorman, Richmond
Lemriss
Kingsley, Robert A.
Carr, Rosina A. A.
el Kabbaj, Saâd
Gargouri, Saba
Masmoudi, Saber
Sankhe, Safietou
Lawal, Salako B.
Kassim, Samar
Trabelsi, Sameh
Metha, Samar
Kammoun, Sami
Lemriss, Sanaâ
Agwa, Sara H. A.
Calvignac-Spencer, Sébastien
Schaffner, Stephen F.
Doumbia, Seydou
Mandanda, Sheila M.
Aryeetey, Sherihane
Ahmed, Shymaa S.
Elhamoumi, Siham
Andriamandimby, Soafy
Tope, Sobajo
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
Chinedu, Ugwu
Ramphal, Upasana
Jessica, Uwanibe
George, Uwem
Fonseca, Vagner
Enouf, Vincent
Gorova, Vivianne
Roshdy, Wael H.
Ampofo, William K.
Preiser, Wolfgang
Choga, Wonderful T.
Bediako, Yaw
Naidoo, Yeshnee
Butera, Yvan
de Laurent, Zaydah R..
Sall, Amadou A.
Rebai, Ahmed
von Gottberg, Anne
Kouriba, Bourema
Williamson, Carolyn
Bridges, Daniel J.
Chikwe, Ihkeweazu
Biman, Jinal N.
Mine, Madisa
Cotten, Matthew
Moyo, Sikhulile
Gaseitsiwe, Simani
Saasa, Ngonda
Sabeti, Pardis C.
Kaleebu, Pontiano
Tebeje, Yenew K.
Tessema, Sofonias K.
Happi, Christian
Nkengasong, John
de Oliveira, Tulio
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.
