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; +392 more...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 SY; 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 EZ; 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 MO; Odia, Ikponmwosa; Ben Boubaker, Ilhem Boutiba; Muhammad, Iluoreh Ahmed; Ssewanyana, Isaac; Wurie, Isatta; Konstantinus, Iyaloo S; Halatoko, Jacqueline Wemboo Afiwa; Ayei, James; Sonoo, Janaki; Makangara, Jean-Claude C; Tamfum, Jean-Jacques M; Heraud, Jean-Michel; Shaffer, Jeffrey G; Giandhari, Jennifer; Musyoki, Jennifer; Nkurunziza, Jerome; Uwanibe, Jessica N; Bhiman, Jinal N; Yasuda, Jiro; Morais, Joana; Kiconco, Jocelyn; Sandi, John D; Huddleston, John; Odoom, John K; Morobe, John M; Gyapong, John O; Kayiwa, John T; Okolie, Johnson C; Xavier, Joicymara S; Gyamfi, Jones; Wamala, Joseph F; Bonney, Joseph HK; Nyandwi, Joseph; Everatt, Josie; Nakaseegu, Joweria; Ngoi, Joyce M; Namulondo, Joyce; Oguzie, Judith U; Andeko, Julia C; Lutwama, Julius J; Mogga, Juma JH; O'Grady, Justin; Siddle, Katherine J; Victoir, Kathleen; Adeyemi, Kayode T; Tumedi, Kefentse A; Carvalho, Kevin S; Mohammed, Khadija Said; Dellagi, Koussay; Musonda, Kunda G; Duedu, Kwabena O; Fki-Berrajah, Lamia; Singh, Lavanya; Kepler, Lenora M; Biscornet, Leon; de Oliveira Martins, Leonardo; Chabuka, Lucious; Olubayo, Luicer; Ojok, Lul Deng; Deng, Lul Lojok; Ochola-Oyier, Lynette I; Tyers, Lynn; Mine, Madisa; Ramuth, Magalutcheemee; Mastouri, Maha; ElHefnawi, Mahmoud; Mbanne, Maimouna; Matsheka, Maitshwarelo I; Kebabonye, Malebogo; Diop, Mamadou; Momoh, Mambu; Lima Mendonça, Maria da Luz; Venter, Marietjie; Paye, Marietou F; Faye, Martin; Nyaga, Martin M; Mareka, Mathabo; Damaris, Matoke-Muhia; Mburu, Maureen W; Mpina, Maximillian G; Owusu, Michael; Wiley, Michael R; Tatfeng, Mirabeau Y; Ayekaba, Mitoha Ondo'o; Abouelhoda, Mohamed; Beloufa, Mohamed Amine; Seadawy, Mohamed G; Khalifa, Mohamed K; Matobo, Mooko Marethabile; Kane, Mouhamed; Salou, Mounerou; Mbulawa, Mphaphi B; Mwenda, Mulenga; Allam, Mushal; Phan, My VT; 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 DESA; Audu, Rosemary A; Carr, Rosina AA; 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; Africa Pathogen Genomics Initiative (Africa PGI)‡; Ouma, Ahmed EO; 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; and Wilkinson, Eduan
(2022)
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.
Science, 378 (6615).
eabq5358-.
ISSN 0036-8075
DOI: 10.1126/science.abq5358
; San, James E; Cotten, Matthew; Moir, Monika; Tegomoh, Bryan; Mboowa, Gerald; Martin, Darren P; Baxter, Cheryl; Lambisia, Arnold W; Diallo, Amadou; +392 more...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 SY; 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 EZ; 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 MO; Odia, Ikponmwosa; Ben Boubaker, Ilhem Boutiba; Muhammad, Iluoreh Ahmed; Ssewanyana, Isaac; Wurie, Isatta; Konstantinus, Iyaloo S; Halatoko, Jacqueline Wemboo Afiwa; Ayei, James; Sonoo, Janaki; Makangara, Jean-Claude C; Tamfum, Jean-Jacques M; Heraud, Jean-Michel; Shaffer, Jeffrey G; Giandhari, Jennifer; Musyoki, Jennifer; Nkurunziza, Jerome; Uwanibe, Jessica N; Bhiman, Jinal N; Yasuda, Jiro; Morais, Joana; Kiconco, Jocelyn; Sandi, John D; Huddleston, John; Odoom, John K; Morobe, John M; Gyapong, John O; Kayiwa, John T; Okolie, Johnson C; Xavier, Joicymara S; Gyamfi, Jones; Wamala, Joseph F; Bonney, Joseph HK; Nyandwi, Joseph; Everatt, Josie; Nakaseegu, Joweria; Ngoi, Joyce M; Namulondo, Joyce; Oguzie, Judith U; Andeko, Julia C; Lutwama, Julius J; Mogga, Juma JH; O'Grady, Justin; Siddle, Katherine J; Victoir, Kathleen; Adeyemi, Kayode T; Tumedi, Kefentse A; Carvalho, Kevin S; Mohammed, Khadija Said; Dellagi, Koussay; Musonda, Kunda G; Duedu, Kwabena O; Fki-Berrajah, Lamia; Singh, Lavanya; Kepler, Lenora M; Biscornet, Leon; de Oliveira Martins, Leonardo; Chabuka, Lucious; Olubayo, Luicer; Ojok, Lul Deng; Deng, Lul Lojok; Ochola-Oyier, Lynette I; Tyers, Lynn; Mine, Madisa; Ramuth, Magalutcheemee; Mastouri, Maha; ElHefnawi, Mahmoud; Mbanne, Maimouna; Matsheka, Maitshwarelo I; Kebabonye, Malebogo; Diop, Mamadou; Momoh, Mambu; Lima Mendonça, Maria da Luz; Venter, Marietjie; Paye, Marietou F; Faye, Martin; Nyaga, Martin M; Mareka, Mathabo; Damaris, Matoke-Muhia; Mburu, Maureen W; Mpina, Maximillian G; Owusu, Michael; Wiley, Michael R; Tatfeng, Mirabeau Y; Ayekaba, Mitoha Ondo'o; Abouelhoda, Mohamed; Beloufa, Mohamed Amine; Seadawy, Mohamed G; Khalifa, Mohamed K; Matobo, Mooko Marethabile; Kane, Mouhamed; Salou, Mounerou; Mbulawa, Mphaphi B; Mwenda, Mulenga; Allam, Mushal; Phan, My VT; 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 DESA; Audu, Rosemary A; Carr, Rosina AA; 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; Africa Pathogen Genomics Initiative (Africa PGI)‡; Ouma, Ahmed EO; 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; and Wilkinson, Eduan
(2022)
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.
Science, 378 (6615).
eabq5358-.
ISSN 0036-8075
DOI: 10.1126/science.abq5358
Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.
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