Publication

Title: A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
Authors: Wilkinson E, Giovanetti M, Tegally H, San EJ, Lessells R, Abdoul K. Sangare, Abdoul-Salam Ouedraogo, Abdul K. Sesay, Abechi Priscilla, Adedotun-Sulaiman Kemi, Adewunmi M. Olubusuyi, Adeyemi O.O. Oluwapelumi, Adnène Hammami, Adrienne A. Amuri, Ahmad Sayed, Ahmed E.O. Ouma, Aida Elargoubi, Ajayi N. Anthony, Ajogbasile F. Victoria, Akano Kazeem, Akpede George, Alexander J. Trotter, Ali A. Yahaya, Alpha K. Keita, Amadou Diallo, Amadou Kone, Amal Souissi, Amel Chtourou, Ana V. Gutierrez, Andrew J. Page, Anika Vinze, Arash Iranzadeh, Arnold Lambisia, Arshad Ismail, Audu Rosemary, Augustina Sylverken, Ayoade Femi, Azeddine Ibrahimi, Baba Marycelin, Bamidele S. Oderinde, Bankole Bolajoko, Beatrice Dhaala, Belinda L. Herring, Berthe-Marie Njanpop-Lafourcade, Bronwyn Kleinhans, Bronwyn McInnis, Bryan Tegomoh, Cara Brook, Catherine B. Pratt, Cathrine Scheepers, Chantal G. Akoua-Koffi, Charles N. Agoti, Christophe Peyrefitte, Claudia Daubenberger, Collins M. Morang’a, D. James Nokes, Daniel G. Amoako, Daniel L. Bugembe, Danny Park, David Baker, Deelan Doolabh, Deogratius Ssemwanga, Derek Tshiabuila, Diarra Bassirou, Dominic S.Y. Amuzu, Dominique Goedhals, Donwilliams O. Omuoyo, Dorcas Maruapula, Ebenezer Foster-Nyarko, Eddy K. Lusamaki, Edgar Simulundu, Edidah M. Ong'era, Edith N. Ngabana, Edwin Shumba, Elmostafa El Fahime, Emmanuel Lokilo, Enatha Mukantwari, Eromon Philomena, Essia Belarbi, Etienne Simon-Loriere, Etilé A. Anoh, Fabian Leendertz, Faida Ajili, Fakayode O. Enoch, Fares Wasfi, Fatma Abdelmoula, Fausta S. Mosha, Faustinos T. Takawira, Fawzi Derrar, Feriel Bouzid, Folarin Onikepe, Fowotade Adeola, Francisca M. Muyembe, Frank Tanser, Fred A. Dratibi, Gabriel K. Mbunsu, Gaetan Thilliez, Gemma L. Kay, George Githinji, Gert van Zyl, Gordon A. Awandare, Grit Schubert, Gugu P. Maphalala, Hafaliana C. Ranaivoson, Hajar Lemriss, Happi Anise, Haruka Abe, Hela H. Karray, Hellen Nansumba, Hesham A. Elgahzaly, Hlanai Gumbo, Ibtihel Smeti, Ikhlas B. Ayed, Ikponmwosa Odia, Ilhem Boutiba-Ben Boubaker, Imed Gaaloul, Inbal Gazy, Innocent Mudau, Isaac Ssewanyana, Iyaloo Konstantinus, Jean B. Lekana-Douk, Jean-Claude C. Makangara, Jean-Jacques M. Tamfum, Jean-Michel Heraud, Jeffrey G. Shaffer, Giandhari J, Jingjing Li, Jiro Yasuda, Joana Q. Mends, Jocelyn Kiconco, John M. Morobe, John O. Gyapong, Johnson C. Okolie, John T. Kayiwa, Johnathan A. Edwards, Jones Gyamfi, Jouali Farah, Joweria Nakaseegu, Joyce M. Ngoi, Joyce Namulondo, Julia C. Andeko, Julius J. Lutwama, Justin O’Grady, Katherine Siddle, Kayode T. Adeyemi, Kefentse A. Tumedi, Khadija M. Said, Kim Hae-Young, Kwabena O. Duedu, Lahcen Belyamani, Lamia Fki-Berrajah, Lavanya Singh, Leonardo de O. Martins, Lynn Tyers, Magalutcheemee Ramuth, Maha Mastouri, Mahjoub Aouni, Mahmoud el Hefnawi, Maitshwarelo I. Matsheka, Malebogo Kebabonye, Mamadou Diop, Manel Turki, Marietou Paye, Martin M. Nyaga, Mathabo Mareka, Matoke-Muhia Damaris, Maureen W. Mburu, Maximillian Mpina, Mba Nwando, Michael Owusu, Michael R. Wiley, Mirabeau T. Youtchou, Mitoha O. Ayekaba, Mohamed Abouelhoda, Mohamed G. Seadawy, Mohamed K. Khalifa, Mooko Sekhele, Mouna Ouadghiri, Moussa M. Diagne, Mulenga Mwenda, Mushal Allam, My V.T. Phan, Nabil Abid, Nadia Touil, Nadine Rujeni, Najla Kharrat, Nalia Ismael, Ndongo Dia, Nedio Mabunda, Nei-yuan Hsiao, Nelson B. Silochi, Ngoy Nsenga, Nicksy Gumede, Nicola Mulder, Nnaemeka Ndodo, Norosoa H Razanajatovo, Nosamiefan Iguosadolo, Oguzie Judith, Ojide C. Kingsley, Okogbenin Sylvanus, Okokhere Peter, Oladiji Femi, Olawoye Idowu, Olumade Testimony, Omoruyi E. Chukwuma, Onwe E. Ogah, Onwuamah Chika, Oshomah Cyril, Ousmane Faye, Oyewale Tomori, Pascale Ondoa, Patrice Combe, Patrick Semanda, Paul E. Oluniyi, Paulo Arnaldo, Peter K. Quashie, Philippe Dussart, Phillip A. Bester, Placide K. Mbala, Reuben Ayivor-Djanie, Richard Njouom, Richard O. Phillips, Richmond Gorman, Robert A. Kingsley, Rosina A.A. Carr, Saâd El Kabbaj, Saba Gargouri, Saber Masmoudi, Safietou Sankhe, Salako B. Lawal, Samar Kassim, Sameh Trabelsi, Samar Metha, Sami Kammoun, Sanaâ Lemriss, Sara H.A. Agwa, Sébastien Calvignac-Spencer, Stephen F. Schaffner, Seydou Doumbia, Sheila M. Mandanda, Sherihane Aryeetey, Shymaa S. Ahmed, Siham Elhamoumi, Soafy Andriamandimby, Sobajo Tope, 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, Ugwu Chinedu, Ramphal U, Uwanibe Jessica, Uwem George, Fonseca V, Vincent Enouf, Vivianne Gorova, Wael H. Roshdy, William K. Ampofo, Wolfgang Preiser, Wonderful T. Choga, Yaw Bediako, Yeshnee Naidoo, Yvan Butera, Zaydah R. de Laurent, Amadou A. Sall, Ahmed Rebai, Anne von Gottberg, Bourema Kouriba, Carolyn Williamson, Daniel J. Bridges, Ihekweazu Chikwe, Jinal Bhiman, Madisa Mine, Matthew Cotten, Sikhulile Moyo, Simani Gaseitsiwe, Ngonda Saasa, Pardis C. Sabeti, Pontiano Kaleebu, Yenew K. Tebeje, Sofonias K. Tessema, Happi Christian, John Nkengasong, de Oliveira T.
Journal: Science,DOI: 10.1126/science.abj4336: (2021)

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.

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Citation: Wilkinson E, Giovanetti M, Tegally H, San EJ, Lessells R, Abdoul K. Sangare, Abdoul-Salam Ouedraogo, Abdul K. Sesay, Abechi Priscilla, Adedotun-Sulaiman Kemi, Adewunmi M. Olubusuyi, Adeyemi O.O. Oluwapelumi, Adnène Hammami, Adrienne A. Amuri, Ahmad Sayed, Ahmed E.O. Ouma, Aida Elargoubi, Ajayi N. Anthony, Ajogbasile F. Victoria, Akano Kazeem, Akpede George, Alexander J. Trotter, Ali A. Yahaya, Alpha K. Keita, Amadou Diallo, Amadou Kone, Amal Souissi, Amel Chtourou, Ana V. Gutierrez, Andrew J. Page, Anika Vinze, Arash Iranzadeh, Arnold Lambisia, Arshad Ismail, Audu Rosemary, Augustina Sylverken, Ayoade Femi, Azeddine Ibrahimi, Baba Marycelin, Bamidele S. Oderinde, Bankole Bolajoko, Beatrice Dhaala, Belinda L. Herring, Berthe-Marie Njanpop-Lafourcade, Bronwyn Kleinhans, Bronwyn McInnis, Bryan Tegomoh, Cara Brook, Catherine B. Pratt, Cathrine Scheepers, Chantal G. Akoua-Koffi, Charles N. Agoti, Christophe Peyrefitte, Claudia Daubenberger, Collins M. Morang’a, D. James Nokes, Daniel G. Amoako, Daniel L. Bugembe, Danny Park, David Baker, Deelan Doolabh, Deogratius Ssemwanga, Derek Tshiabuila, Diarra Bassirou, Dominic S.Y. Amuzu, Dominique Goedhals, Donwilliams O. Omuoyo, Dorcas Maruapula, Ebenezer Foster-Nyarko, Eddy K. Lusamaki, Edgar Simulundu, Edidah M. Ong'era, Edith N. Ngabana, Edwin Shumba, Elmostafa El Fahime, Emmanuel Lokilo, Enatha Mukantwari, Eromon Philomena, Essia Belarbi, Etienne Simon-Loriere, Etilé A. Anoh, Fabian Leendertz, Faida Ajili, Fakayode O. Enoch, Fares Wasfi, Fatma Abdelmoula, Fausta S. Mosha, Faustinos T. Takawira, Fawzi Derrar, Feriel Bouzid, Folarin Onikepe, Fowotade Adeola, Francisca M. Muyembe, Frank Tanser, Fred A. Dratibi, Gabriel K. Mbunsu, Gaetan Thilliez, Gemma L. Kay, George Githinji, Gert van Zyl, Gordon A. Awandare, Grit Schubert, Gugu P. Maphalala, Hafaliana C. Ranaivoson, Hajar Lemriss, Happi Anise, Haruka Abe, Hela H. Karray, Hellen Nansumba, Hesham A. Elgahzaly, Hlanai Gumbo, Ibtihel Smeti, Ikhlas B. Ayed, Ikponmwosa Odia, Ilhem Boutiba-Ben Boubaker, Imed Gaaloul, Inbal Gazy, Innocent Mudau, Isaac Ssewanyana, Iyaloo Konstantinus, Jean B. Lekana-Douk, Jean-Claude C. Makangara, Jean-Jacques M. Tamfum, Jean-Michel Heraud, Jeffrey G. Shaffer, Giandhari J, Jingjing Li, Jiro Yasuda, Joana Q. Mends, Jocelyn Kiconco, John M. Morobe, John O. Gyapong, Johnson C. Okolie, John T. Kayiwa, Johnathan A. Edwards, Jones Gyamfi, Jouali Farah, Joweria Nakaseegu, Joyce M. Ngoi, Joyce Namulondo, Julia C. Andeko, Julius J. Lutwama, Justin O’Grady, Katherine Siddle, Kayode T. Adeyemi, Kefentse A. Tumedi, Khadija M. Said, Kim Hae-Young, Kwabena O. Duedu, Lahcen Belyamani, Lamia Fki-Berrajah, Lavanya Singh, Leonardo de O. Martins, Lynn Tyers, Magalutcheemee Ramuth, Maha Mastouri, Mahjoub Aouni, Mahmoud el Hefnawi, Maitshwarelo I. Matsheka, Malebogo Kebabonye, Mamadou Diop, Manel Turki, Marietou Paye, Martin M. Nyaga, Mathabo Mareka, Matoke-Muhia Damaris, Maureen W. Mburu, Maximillian Mpina, Mba Nwando, Michael Owusu, Michael R. Wiley, Mirabeau T. Youtchou, Mitoha O. Ayekaba, Mohamed Abouelhoda, Mohamed G. Seadawy, Mohamed K. Khalifa, Mooko Sekhele, Mouna Ouadghiri, Moussa M. Diagne, Mulenga Mwenda, Mushal Allam, My V.T. Phan, Nabil Abid, Nadia Touil, Nadine Rujeni, Najla Kharrat, Nalia Ismael, Ndongo Dia, Nedio Mabunda, Nei-yuan Hsiao, Nelson B. Silochi, Ngoy Nsenga, Nicksy Gumede, Nicola Mulder, Nnaemeka Ndodo, Norosoa H Razanajatovo, Nosamiefan Iguosadolo, Oguzie Judith, Ojide C. Kingsley, Okogbenin Sylvanus, Okokhere Peter, Oladiji Femi, Olawoye Idowu, Olumade Testimony, Omoruyi E. Chukwuma, Onwe E. Ogah, Onwuamah Chika, Oshomah Cyril, Ousmane Faye, Oyewale Tomori, Pascale Ondoa, Patrice Combe, Patrick Semanda, Paul E. Oluniyi, Paulo Arnaldo, Peter K. Quashie, Philippe Dussart, Phillip A. Bester, Placide K. Mbala, Reuben Ayivor-Djanie, Richard Njouom, Richard O. Phillips, Richmond Gorman, Robert A. Kingsley, Rosina A.A. Carr, Saâd El Kabbaj, Saba Gargouri, Saber Masmoudi, Safietou Sankhe, Salako B. Lawal, Samar Kassim, Sameh Trabelsi, Samar Metha, Sami Kammoun, Sanaâ Lemriss, Sara H.A. Agwa, Sébastien Calvignac-Spencer, Stephen F. Schaffner, Seydou Doumbia, Sheila M. Mandanda, Sherihane Aryeetey, Shymaa S. Ahmed, Siham Elhamoumi, Soafy Andriamandimby, Sobajo Tope, 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, Ugwu Chinedu, Ramphal U, Uwanibe Jessica, Uwem George, Fonseca V, Vincent Enouf, Vivianne Gorova, Wael H. Roshdy, William K. Ampofo, Wolfgang Preiser, Wonderful T. Choga, Yaw Bediako, Yeshnee Naidoo, Yvan Butera, Zaydah R. de Laurent, Amadou A. Sall, Ahmed Rebai, Anne von Gottberg, Bourema Kouriba, Carolyn Williamson, Daniel J. Bridges, Ihekweazu Chikwe, Jinal Bhiman, Madisa Mine, Matthew Cotten, Sikhulile Moyo, Simani Gaseitsiwe, Ngonda Saasa, Pardis C. Sabeti, Pontiano Kaleebu, Yenew K. Tebeje, Sofonias K. Tessema, Happi Christian, John Nkengasong, de Oliveira T. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa Science,DOI: 10.1126/science.abj4336: (2021).


KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).


Location: K-RITH Tower Building
Nelson R Mandela School of Medicine, UKZN
719 Umbilo Road, Durban, South Africa.
Director: Prof. Tulio de Oliveira