The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Tegally, Houriiyah, San, James E., Cotten, Matthew, Moir, Monika, Tegomoh, Bryan, Mboowa, Gerald, Martin, Darren P., Baxter, Cheryl, Lambisia, Arnold W., Diallo, Amadou, Amoako, Daniel G., Diagne, Moussa M., Sisay, Abay, Zekri, Abdel-Rahman N., Gueye, Abdou Salam, Sangare, Abdoul K., Ouedraogo, Abdoul-Salam, Sow, Abdourahmane, Musa, Abdualmoniem O., Sesay, Abdul K., Abias, Abe G., Elzagheid, Adam I., Lagare, Adamou, Kemi, Adedotun-Sulaiman, Abar, Aden Elmi, Johnson, Adeniji A., Fowotade, Adeola, Oluwapelumi, Adeyemi O., Amuri, Adrienne A., Juru, Agnes, Kandeil, Ahmed, Mostafa, Ahmed, Rebai, Ahmed, Sayed, Ahmed, Kazeem, Akano, Balde, Aladje, Christoffels, Alan, Trotter, Alexander J., Campbell, Allan, Keita, Alpha K., Kone, Amadou, Bouzid, Amal, Souissi, Amal, Agweyu, Ambrose, Naguib, Amel, Gutierrez, Ana V., Nkeshimana, Anatole, Page, Andrew J., Yadouleton, Anges, Vinze, Anika, Happi, Anise N., Chouikha, Anissa, Iranzadeh, Arash, Maharaj, Arisha, Batchi-Bouyou, Armel L., Ismail, Arshad, Sylverken, Augustina A., Goba, Augustine, Femi, Ayoade, Sijuwola, Ayotunde E., Marycelin, Baba, Salako, Babatunde L., Oderinde, Bamidele S., Bolajoko, Bankole, Diarra, Bassirou, Herring, Belinda L., Tsofa, Benjamin, Lekana-Douki, Bernard, Mvula, Bernard, Njanpop-Lafourcade, Berthe-Marie, Marondera, Blessing T., Khaireh, Bouh Abdi, Kouriba, Bourema, Adu, Bright, Pool, Brigitte, McInnis, Bronwyn, Brook, Cara, Williamson, Carolyn, Nduwimana, Cassien, Anscombe, Catherine, Pratt, Catherine B., Scheepers, Cathrine, Akoua-Koffi, Chantal G., Agoti, Charles N., Mapanguy, Chastel M., Loucoubar, Cheikh, Onwuamah, Chika K., Ihekweazu, Chikwe, Malaka, Christian N., Peyrefitte, Christophe, Grace, Chukwa, Omoruyi, Chukwuma E., Rafaï, Clotaire D., Morang’a, Collins M., Erameh, Cyril, Lule, Daniel B., Bridges, Daniel J., Mukadi-Bamuleka, Daniel, Park, Danny, Rasmussen, David A., Baker, David, Nokes, David J., Ssemwanga, Deogratius, Tshiabuila, Derek, Amuzu, Dominic S. Y., Goedhals, Dominique, Grant, Donald S., Omuoyo, Donwilliams O., Maruapula, Dorcas, Wanjohi, Dorcas W., Foster-Nyarko, Ebenezer, Lusamaki, Eddy K., Simulundu, Edgar, Ong’era, Edidah M., Ngabana, Edith N., Abworo, Edward O., Otieno, Edward, Shumba, Edwin, Barasa, Edwine, Ahmed, El Bara, Ahmed, Elhadi A., Lokilo, Emmanuel, Mukantwari, Enatha, Philomena, Eromon, Belarbi, Essia, Simon-Loriere, Etienne, Anoh, Etilé A., Manuel, Eusebio, Leendertz, Fabian, Taweh, Fahn M., Wasfi, Fares, Abdelmoula, Fatma, Takawira, Faustinos T., Derrar, Fawzi, Ajogbasile, Fehintola V., Treurnicht, Florette, Onikepe, Folarin, Ntoumi, Francine, Muyembe, Francisca M., Ragomzingba, Frank E. Z., Dratibi, Fred A., Iyanu, Fred-Akintunwa, Mbunsu, Gabriel K., Thilliez, Gaetan, Kay, Gemma L., Akpede, George O., van Zyl, Gert U., Awandare, Gordon A., Kpeli, Grace S., Schubert, Grit, Maphalala, Gugu P., Ranaivoson, Hafaliana C., Omunakwe, Hannah E., Onywera, Harris, Abe, Haruka, Karray, Hela, Nansumba, Hellen, Triki, Henda, Kadjo, Herve Albéric Adje, Elgahzaly, Hesham, Gumbo, Hlanai, Mathieu, Hota, Kavunga-Membo, Hugo, Smeti, Ibtihel, Olawoye, Idowu B., Adetifa, Ifedayo M. 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T., Abid, Nabil, Rujeni, Nadine, Abuzaid, Nadir, Ismael, Nalia, Elguindy, Nancy, Top, Ndeye Marieme, Dia, Ndongo, Mabunda, Nédio, Hsiao, Nei-yuan, Silochi, Nelson Boricó, Francisco, Ngiambudulu M., Saasa, Ngonda, Bbosa, Nicholas, Murunga, Nickson, Gumede, Nicksy, Wolter, Nicole, Sitharam, Nikita, Ndodo, Nnaemeka, Ajayi, Nnennaya A., Tordo, Noël, Mbhele, Nokuzola, Razanajatovo, Norosoa H., Iguosadolo, Nosamiefan, Mba, Nwando, Kingsley, Ojide C., Sylvanus, Okogbenin, Femi, Oladiji, Adewumi, Olubusuyi M., Testimony, Olumade, Ogunsanya, Olusola A., Fakayode, Oluwatosin, Ogah, Onwe E., Oludayo, Ope-Ewe, Faye, Ousmane, Smith-Lawrence, Pamela, Ondoa, Pascale, Combe, Patrice, Nabisubi, Patricia, Semanda, Patrick, Oluniyi, Paul E., Arnaldo, Paulo, Quashie, Peter Kojo, Okokhere, Peter O., Bejon, Philip, Dussart, Philippe, Bester, Phillip A., Mbala, Placide K., Kaleebu, Pontiano, Abechi, Priscilla, El-Shesheny, Rabeh, Joseph, Rageema, Aziz, Ramy Karam, Essomba, René G., Ayivor-Djanie, Reuben, Njouom, Richard, Phillips, Richard O., Gorman, Richmond, Kingsley, Robert A., Neto Rodrigues, Rosa Maria D. 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A., Gargouri, Saba, Masmoudi, Saber, Bootsma, Sacha, Sankhe, Safietou, Mohamed, Sahra Isse, Femi, Saibu, Mhalla, Salma, Hosch, Salome, Kassim, Samar Kamal, Metha, Samar, Trabelsi, Sameh, Agwa, Sara Hassan, Mwangi, Sarah Wambui, Doumbia, Seydou, Makiala-Mandanda, Sheila, Aryeetey, Sherihane, Ahmed, Shymaa S., Ahmed, Side Mohamed, Elhamoumi, Siham, Moyo, Sikhulile, Lutucuta, Silvia, Gaseitsiwe, Simani, Jalloh, Simbirie, Andriamandimby, Soa Fy, Oguntope, Sobajo, Grayo, Solène, Lekana-Douki, Sonia, Prosolek, Sophie, Ouangraoua, Soumeya, van Wyk, Stephanie, Schaffner, Stephen F., Kanyerezi, Stephen, Ahuka-Mundeke, Steve, Rudder, Steven, Pillay, Sureshnee, Nabadda, Susan, Behillil, Sylvie, Budiaki, Sylvie L., van der Werf, Sylvie, Mashe, Tapfumanei, Mohale, Thabo, Le-Viet, Thanh, Velavan, Thirumalaisamy P., Schindler, Tobias, Maponga, Tongai G., Bedford, Trevor, Anyaneji, Ugochukwu J., Chinedu, Ugwu, Ramphal, Upasana, George, Uwem E., Enouf, Vincent, Nene, Vishvanath, Gorova, Vivianne, Roshdy, Wael H., Karim, Wasim Abdul, Ampofo, William K., Preiser, Wolfgang, Choga, Wonderful T., Ahmed, Yahaya Ali, Ramphal, Yajna, Bediako, Yaw, Naidoo, Yeshnee, Butera, Yvan, de Laurent, Zaydah R., Ouma, Ahmed E. O., von Gottberg, Anne, Githinji, George, Moeti, Matshidiso, Tomori, Oyewale, Sabeti, Pardis C., Sall, Amadou A., Oyola, Samuel O., Tebeje, Yenew K., Tessema, Sofonias K., de Oliveira, Tulio, Happi, Christian, Lessells, Richard, Nkengasong, John, Wilkinson, Eduan, Shibemba, Aaron L., Obong, Abasi Ene, Fadeyi, Abayomi, Anas, Abbad, Shabaan, Abd Elazeez, Adel, Abd Monaem, Shoka, Abd Moniem Ain, Abdelhamid, W., Laraqui, Abdelilah, Laatiris, Abdelkader, Bellefquih, Abdelkrim Meziane, Faouzi, Abdellah, Abdelmoulah, F., Essabbar, Abdelomunim, Bimouhen, Abderrahmane, Hilali, Abderraouf, Abdo, I., Padane, Abdou, Sangaré, Abdoul Karim, Soumah, Abdoul Karim, Djimde, Abdoulaye, Toure, Abdoulaye, Kanteh, Abdoulie, Bashein, Abdulla, Salama, Abdullah, Lojuan, Abe, Bayih, Abebe Genetu, Negash, Abel Abera, Lissom, Abel, Abid, N., Konou, Abla A., Shama, Abo, Abosede, O., Abouelnaga, S., Ali, Abraham, Anang, Abraham Kwabena, Tesfaye, Abraham, Khan, Adam K., Tayachew, Adamu, Mihret, Adane, AlEmam, Adba Alfatih, Hawi, Adede, Adesegun, A., Desta, Adey Feleke, Ghassan, Adib, Traoré, Adjaratou, Adjiratou Aissatou, B. 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B., Bahadoor, B. S., Bahnassy, A.A., Sanyang, Bakary, Bakry, U., Touré, Bamba Fatoumata, Iwalokun, Bamidele, Banda, R., Bane, S., Johnson, Bankole, Cisse, Barada, Murwira, Barbra, Munnink, Bas Oude, Batchi-Bouyou, Armel L., Batra, R., Dhaala, Beatrice, Lamiae, Belayachi, Belkhir, A.B., Ben Ayed, I., Morton, Ben, Moussa, Ben, Wulf, Ben, Ndeboko, Bénédicte, Rachid, Benhida, Lindsey, Benjamiin B., Foulkes, Benjamin H., Hounkpatin, Benjamin, Selekon, Benjamin, Bensaid, M., Mpairwe, Bernard, Bagaya, Bernard Ssentalo, Vanmechelen, Bert, Lell, Bertrand, Mutai, Beth, Adnew, Bethlehem, Makamure, Beuty, Bighignoli, B., Ndiaye, Birahim Piere, Adhikari, Bishwo N., Bitrou, S.M., Akenji, Blaise MBoringong, Shobayo, Bode, Zuze, Boitumelo, Nlavo, Bonifacio Manguire, Belfquih, Bouchra, Boujemla, Bouchra, Yatassaye, Bouna, Aymane, Bouzidi, Andika, Brian, Yemi, Bright K., Kleinhans, Bronwyn, Galvao, Bruna, Embaló, Bubacar Delgado Pinto, Manene, Bulelani, Pascal, Butoyi, Capel, Camille, Anu, Campbell, Tchibozo, Carine, Madeira, Carla, Cortes, Carlos, Elisabeth, Carniel, Kifude, Carol, Tayimetha, Carolle Yanique, Arnold, Catherine E., Okoi, Catherine, Waruhiu, Cecilia, Godwe, Celestin, Obiekea, Celestina, Nkenfou, Celine, Chabuka, L. B., Nejjari, Chakib, Chambaro, H., Chanda, D., Changula, K., Touzani, Charifa Drissi, Kayuki, Charles, Nyagupe, Charles, Ssuuna, Charles, Hicham, Charoute, Watters, Chaselynn M., Chawech, H., Sokhna, Cheikh, Mohamed, Chenaoui, Nwuba, Chiamaka, Chilufya, C., Chukwu, Chimaobi, Anyika, Chinyere, Chipimo, P.J., Chitanga, S., Chitenje, M., Chiwaula, M. J., Taha, Chouati, Mansell, Chris, Butel, Christelle, Devaux, Christian A., Drosten, Christian, Ranaivoson, Christian, Utpatel, Christian, Malabat, Christophe, Chtourou, A., Chukwu, G., Daubenberger, Claudia, Kakai, Clement G., Masakwe, Clement, Rafai, Clotaire Donatien, Chenwi, Collins, Misita, Collins M., Muli, Collins, GeurtsvanKessel, Corine H., Maufrais, Corinne, Mbegnan, Coulibaly, Crawford, M., Tato, Cristina M., Yiaba, Cyrus, D'Amore, N., Damilari, Dabiri, Ramadan, Dalia, Damena, D., Ouso, Daniel, Pisanelli, Daniela, Licastro, Danilo, Hammer, David, Nieuwenhuijse, David, Kateete, David Patrick, Wilkinson, David, Mouangala, Davy Leger, Alemayehu, Dawit Hailu, Dawood, R.M., De Sanctis, R., Mettle, Deborah N. A., Koita, Demba, Lodiongo, Dennis Kenyi, Laryea, Dennis, Wandera, Dennis N., Leta, Dereje, Noureddine, Dersi, Takou, Desire, Tefera, Dessalegn Abeje, Batra, Dhwani, Ndongo, Dia, Diab, A., Diagne, Diabou, Mabika, Diane A., Bamourou, Diané, Samaté, Dianke, Diarra, B., Raoult, Didier, Mutangana, Dieudonne, Nyepetsi, Dineo Emang Tshiamo. Gape, Ada, Diosdado Odjama Nseng, Salah, Djimabi, Cedola, Donatella, Harding, Doris, Yeboah-Manu, Dorothy, Ange, Dossou, Djomsi, Dowbiss Meta, Drinkovic, Dragana, Draper, C., Sahr, Dumbuya Foday, Odewale, Ebenezer, Sedjro, Eclou, Armand, Edang-Minko, Kigozi, Edgar, Koskei, Edith, Nkwembe, Edith, de Oliveira Filho, Edmilson F., Maria da Costa, Edmira, Kiritu, Edward, Lim, Efrem S., Ozer, Egon A., Egyir, B., Abuelenein, Ehab Abdelkader, Ngole, Eitel Mpoudi, Aissam, El Aliani, Zahra, El Ansari Fatima, Adil, El Hamouchi, Abdelmjid, El Oualid, El-Shaqnqery, H., El-Zayat, M., Abualas, Elamin, Hicham, Elannaz, Elargoubi, A., Kidane, Eleni, Rizgalla, Elham, Elhoseny, M.M., Elhosieny, F.W., Carniel, Elisabeth, Nyakarungu, Elizabeth, Elkhateeb, S.M., Benaissa, Elmostafa, El Fahime, Elmostafa, Elouanass, M., Elsissy, M.H., Mbongo-Nkama, Elvyre, Latif, Elwaleed M. 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H., Fuh-Neba, T., Gaaloul, I., Kabamba, Gabriel, Gutema, Gadissa, Emna, Gaies, Gadzama, Galadima, Mahmoud, Galal, Ouangole, Garba, Gargouri, S., Garry, R., McAuliffe, Gary, Kimita, Gathii, Manouana, Gédéon Prince, Tesfaye, Gelanew, Awinda, George, Kyei, George B., Michuki, George, Ondo, Georgelin Nguema, van Rooyen, Gerhard, Marais, Gert, Abichu, Getachew, Beyene, Getachew Tesfaye, Tollera, Getachew, Hailu, Getnet, Hamza, Ghamaz, Kayali, Ghazi, El Amin, Ghizlane, Mhlanga, Gibson, Kibet, Gilbert, Hounkanrin, Gildas, Giordani, F., Teka, Gizaw, Masete, Godfrey, Goldstone, R., Gomaa, C., Mokhtar, Gomaa, Lo, Gora, Gosnell, B. I., Gottberg, A., Belournou, Grace Angong, Oni, Grace, Vincent, Grace, Wani, Gregory, Barreh, Guedi Ali, Garcia, Guillermo, Deng, Guohong, Guseva, N. P., Mbembo, Guy Paterne Malonga, Padzys, Guy Stéphane, Gwayi, S., Ben Romdhane, Habiba, Naija, Habiba, Diallo, Haby, Hadad, A., Hafez, M.M., Ladhari, Hafsia, Elshora, Hagar, Dadi, Hailu, Mohammed, Hajjaji, Kabbaj, Hakima, Hafez, Hala, Halafawy, A., Tinto, Halidou, Ndiaye, Halimatou Diop, Assane, Hamadi, Hamdani, T.N., Hamdy, M.S., Namagembe, Hamidah, Hammad, M., Hammami, A., Gharmaz, Hamza, Andersson, Hana Sofia, Dakka, Hanae, El Jebari, Hanen, Soliman, Hany K., Houda, Harmak, Harvey, R., Benkirane, Hasnae, Aguenaou, Hassan, Ihazmad, Hassan, Hassan, R., Hassan, W., Ahmed, Hatem, Sogodogo, Heitzer, Seth-Smith, Helena, Razafimanjato, Helisoa, Koka, Hellen, Mouhssine, Hemlali, Mwebesa, Henry, Perez, Hermes, Tchoudjin, Herve Christian Paho, Elannaz, Hicham, Oumzil, Hicham, Frempong, Hilda Opoku, Fidelia, Hinson, Elarab, Hoda Ezz, Xie, Hong, Benrahma, Houda, Arrouchi, Housna, Guedouar, Houssem, Luo, Hu, Bassène, Hubert, Si, Huiqing, Goodfellow, Ian, Guindo, Ibrahima, Halilou, Ibrahima, 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Abstract

INTRODUCTION

Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic.

RATIONALE

We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs).

RESULTS

Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants.

CONCLUSION

Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Item Type:	Article
Subjects:	QU Biochemistry > Genetics > QU 460 Genomics. Proteomics WC Communicable Diseases > Virus Diseases > Viral Respiratory Tract Infections. Respirovirus Infections > WC 506 COVID-19
Faculty: Department:	Clinical Sciences & International Health > Malawi-Liverpool-Wellcome Programme (MLW)
Digital Object Identifer (DOI):	https://doi.org/10.1126/science.abq5358
SWORD Depositor:	JISC Pubrouter
Depositing User:	JISC Pubrouter
Date Deposited:	15 Nov 2022 14:59
Last Modified:	15 Nov 2022 14:59
URI:	https://archive.lstmed.ac.uk/id/eprint/21319

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