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

Tegally, H. and San, J. E. and Cotten, M. and Moir, M. and Tegomoh, B. and Mboowa, G. and Martin, D. P. and Baxter, C. and Lambisia, A. W. and Diallo, A. and Amoako, D. G. and Diagne, M. M. and Sisay, A. and Zekri, A. N. and Gueye, A. S. and Sangare, A. K. and Ouedraogo, A. S. and Sow, A. and Musa, A. O. and Sesay, A. K. and Abias, A. G. and Elzagheid, A. I. and Lagare, A. and Kemi, A. S. and Abar, A. E. and Johnson, A. A. and Fowotade, A. and Oluwapelumi, A. O. and Amuri, A. A. and Juru, A. and Kandeil, A. and Mostafa, A. and Rebai, A. and Sayed, A. and Kazeem, A. and Balde, A. and Christoffels, A. and Trotter, A. J. and Campbell, A. and Keita, A. K. and Kone, A. and Bouzid, A. and Souissi, A. and Agweyu, A. and Naguib, A. and Gutierrez, A. V. and Nkeshimana, A. and Page, A. J. and Yadouleton, A. and Vinze, A. and Happi, A. N. and Chouikha, A. and Iranzadeh, A. and Maharaj, A. and Batchi-Bouyou, A. L. and Ismail, A. and Sylverken, A. A. and Goba, A. and Femi, A. and Sijuwola, A. E. and Marycelin, B. and Salako, B. L. and Oderinde, B. S. and Bolajoko, B. and Diarra, B. and Herring, B. L. and Tsofa, B. and Lekana-Douki, B. and Mvula, B. and Njanpop-Lafourcade, B. M. and Marondera, B. T. and Khaireh, B. A. and Kouriba, B. and Adu, B. and Pool, B. and McInnis, B. and Brook, C. and Williamson, C. and Nduwimana, C. and Anscombe, C. and Pratt, C. B. and Scheepers, C. and Akoua-Koffi, C. G. and Agoti, C. N. and Mapanguy, C. M. and Loucoubar, C. and Onwuamah, C. K. and Ihekweazu, C. and Malaka, C. N. and Peyrefitte, C. and Grace, C. and Omoruyi, C. E. and Rafaï, C. D. and Morang'a, C. M. and Erameh, C. and Lule, D. B. and Bridges, D. J. and Mukadi-Bamuleka, D. and Park, D. and Rasmussen, D. A. and Baker, D. and Nokes, D. J. and Ssemwanga, D. and Tshiabuila, D. and Amuzu, D. S. Y. and Goedhals, D. and Grant, D. S. and Omuoyo, D. O. and Maruapula, D. and Wanjohi, D. W. and Foster-Nyarko, E. and Lusamaki, E. K. and Simulundu, E. and Ong'era, E. M. and Ngabana, E. N. and Abworo, E. O. and Otieno, E. and Shumba, E. and Barasa, E. and Ahmed, E. B. and Ahmed, E. A. and Lokilo, E. and Mukantwari, E. and Philomena, E. and Belarbi, E. and Simon-Loriere, E. and Anoh, E. A. and Manuel, E. and Leendertz, F. and Taweh, F. M. and Wasfi, F. and Abdelmoula, F. and Takawira, F. T. and Derrar, F. and Ajogbasile, F. V. and Treurnicht, F. and Onikepe, F. and Ntoumi, F. and Muyembe, F. M. and Ragomzingba, F. E. Z. and Dratibi, F. A. and Iyanu, F. A. and Mbunsu, G. K. and Thilliez, G. and Kay, G. L. and Akpede, G. O. and van Zyl, G. U. and Awandare, G. A. and Kpeli, G. S. and Schubert, G. and Maphalala, G. P. and Ranaivoson, H. C. and Omunakwe, H. E. and Onywera, H. and Abe, H. and Karray, H. and Nansumba, H. and Triki, H. and Kadjo, H. A. A. and Elgahzaly, H. and Gumbo, H. and Mathieu, H. and Kavunga-Membo, H. and Smeti, I. and Olawoye, I. B. and Adetifa, I. M. O. and Odia, I. and Ben Boubaker, I. B. and Mohammad, I. 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M. and Biscornet, L. and de Oliveira Martins, L. and Chabuka, L. and Olubayo, L. and Ojok, L. D. and Deng, L. L. and Ochola-Oyier, L. I. and Tyers, L. and Mine, M. and Ramuth, M. and Mastouri, M. and ElHefnawi, M. and Mbanne, M. and Matsheka, M. I. and Kebabonye, M. and Diop, M. and Momoh, M. and Lima Mendonça, M. D. L. and Venter, M. and Paye, M. F. and Faye, M. and Nyaga, M. M. and Mareka, M. and Damaris, M. M. and Mburu, M. W. and Mpina, M. G. and Owusu, M. and Wiley, M. R. and Tatfeng, M. Y. and Ayekaba, M. O. and Abouelhoda, M. and Beloufa, M. A. and Seadawy, M. G. and Khalifa, M. K. and Matobo, M. M. and Kane, M. and Salou, M. and Mbulawa, M. B. and Mwenda, M. and Allam, M. and Phan, M. V. T. and Abid, N. and Rujeni, N. and Abuzaid, N. and Ismael, N. and Elguindy, N. and Top, N. M. and Dia, N. and Mabunda, N. and Hsiao, N. Y. and Silochi, N. B. and Francisco, N. M. and Saasa, N. and Bbosa, N. and Murunga, N. and Gumede, N. and Wolter, N. and Sitharam, N. and Ndodo, N. and Ajayi, N. A. and Tordo, N. and Mbhele, N. and Razanajatovo, N. H. and Iguosadolo, N. and Mba, N. and Kingsley, O. C. and Sylvanus, O. and Femi, O. and Adewumi, O. M. and Testimony, O. and Ogunsanya, O. A. and Fakayode, O. and Ogah, O. E. and Oludayo, O. E. and Faye, O. and Smith-Lawrence, P. and Ondoa, P. and Combe, P. and Nabisubi, P. and Semanda, P. and Oluniyi, P. E. and Arnaldo, P. and Quashie, P. K. and Okokhere, P. O. and Bejon, P. and Dussart, P. and Bester, P. A. and Mbala, P. K. and Kaleebu, P. and Abechi, P. and El-Shesheny, R. and Joseph, R. and Aziz, R. K. and Essomba, R. G. and Ayivor-Djanie, R. and Njouom, R. and Phillips, R. O. and Gorman, R. and Kingsley, R. A. and Neto Rodrigues, Rmdesa and Audu, R. A. and Carr, R. A. A. and Gargouri, S. and Masmoudi, S. and Bootsma, S. and Sankhe, S. and Mohamed, S. I. and Femi, S. and Mhalla, S. and Hosch, S. and Kassim, S. K. and Metha, S. and Trabelsi, S. and Agwa, S. H. and Mwangi, S. W. and Doumbia, S. and Makiala-Mandanda, S. and Aryeetey, S. and Ahmed, S. S. and Ahmed, S. M. and Elhamoumi, S. and Moyo, S. and Lutucuta, S. and Gaseitsiwe, S. and Jalloh, S. and Andriamandimby, S. F. and Oguntope, S. and Grayo, S. and Lekana-Douki, S. and Prosolek, S. and Ouangraoua, S. and van Wyk, S. and Schaffner, S. F. and Kanyerezi, S. and Ahuka-Mundeke, S. and Rudder, S. and Pillay, S. and Nabadda, S. and Behillil, S. and Budiaki, S. L. and van der Werf, S. and Mashe, T. and Mohale, T. and Le-Viet, T. and Velavan, T. P. and Schindler, T. and Maponga, T. G. and Bedford, T. and Anyaneji, U. J. and Chinedu, U. and Ramphal, U. and George, U. E. and Enouf, V. and Nene, V. and Gorova, V. and Roshdy, W. H. and Karim, W. A. and Ampofo, W. K. and Preiser, W. and Choga, W. T. and Ahmed, Y. A. and Ramphal, Y. and Bediako, Y. and Naidoo, Y. and Butera, Y. and de Laurent, Z. R. and Ouma, A. E. O. and von Gottberg, A. and Githinji, G. and Moeti, M. and Tomori, O. and Sabeti, P. C. and Sall, A. A. and Oyola, S. O. and Tebeje, Y. K. and Tessema, S. K. and de Oliveira, T. and Happi, C. and Lessells, R. and Nkengasong, J. and Wilkinson, E.. (2022) The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance. Science, 378 (6615). eabq5358.

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Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time 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 shed light on 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 re-emerging 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.
Faculties and Departments:09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH)
09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Medical Parasitology and Infection Biology (MPI) > Clinical Immunology (Daubenberger)
UniBasel Contributors:Mpina, Maximillian and Hosch, Salome and Schindler, Tobias
Item Type:Article, refereed
Article Subtype:Research Article
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:27 Dec 2022 22:20
Deposited On:27 Dec 2022 22:20

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