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

Tegally, H. et al. (2022) The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance. Science, 378(6615), eabq5358. (doi: 10.1126/science.abq5358) (PMID:36108049) (PMCID:PMC9529057)

Abstract

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.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Cotten, Professor Matthew
• Authors: Tegally, H., San, J. E., Cotten, M., Moir, M., Tegomoh, B., Mboowa, G., Martin, D. P., Baxter, C., Lambisia, A. W., Diallo, A., Amoako, D. G., Diagne, M. M., Sisay, A., Zekri, A.-R. N., Gueye, A. S., Sangare, A. K., Ouedraogo, A.-S., Sow, A., Musa, A. O., Sesay, A. K., Abias, A. G., Elzagheid, A. I., Lagare, A., Kemi, A.-S., Abar, A. E., Johnson, A. A., Fowotade, A., Oluwapelumi, A. O., Amuri, A. A., Juru, A., Kandeil, A., Mostafa, A., Rebai, A., Sayed, A., Kazeem, A., Balde, A., Christoffels, A., Trotter, A. J., Campbell, A., Keita, A. K., Kone, A., Bouzid, A., Souissi, A., Agweyu, A., Naguib, A., Gutierrez, A. V., Nkeshimana, A., Page, A. J., Yadouleton, A., Vinze, A., Happi, A. N., Chouikha, A., Iranzadeh, A., Maharaj, A., Batchi-Bouyou, A. L., Ismail, A., Sylverken, A. A., Goba, A., Femi, A., Sijuwola, A. E., Marycelin, B., Salako, B. L., Oderinde, B. S., Bolajoko, B., Diarra, B., Herring, B. L., Tsofa, B., Lekana-Douki, B., Mvula, B., Njanpop-Lafourcade, B.-M., Marondera, B. T., Khaireh, B. A., Kouriba, B., Adu, B., Pool, B., McInnis, B., Brook, C., Williamson, C., Nduwimana, C., Anscombe, C., Pratt, C. B., Scheepers, C., Akoua-Koffi, C. G., Agoti, C. N., Mapanguy, C. M., Loucoubar, C., Onwuamah, C. K., Ihekweazu, C., Malaka, C. N., Peyrefitte, C., Grace, C., Omoruyi, C. E., Rafaï, C. D., Morang’a, C. M., Erameh, C., Lule, D. B., Bridges, D. J., Mukadi-Bamuleka, D., Park, D., Rasmussen, D. A., Baker, D., Nokes, D. J., Ssemwanga, D., Tshiabuila, D., Amuzu, D. S. Y., Goedhals, D., Grant, D. S., Omuoyo, D. O., Maruapula, D., Wanjohi, D. W., Foster-Nyarko, E., Lusamaki, E. K., Simulundu, E., Ong’era, E. M., Ngabana, E. N., Abworo, E. O., Otieno, E., Shumba, E., Barasa, E., Ahmed, E. B., Ahmed, E. A., Lokilo, E., Mukantwari, E., Philomena, E., Belarbi, E., Simon-Loriere, E., Anoh, E. A., Manuel, E., Leendertz, F., Taweh, F. M., Wasfi, F., Abdelmoula, F., Takawira, F. T., Derrar, F., Ajogbasile, F. V., Treurnicht, F., Onikepe, F., Ntoumi, F., Muyembe, F. M., Ragomzingba, F. E. Z., Dratibi, F. A., Iyanu, F.-A., Mbunsu, G. K., Thilliez, G., Kay, G. L., Akpede, G. O., van Zyl, G. U., Awandare, G. A., Kpeli, G. S., Schubert, G., Maphalala, G. P., Ranaivoson, H. C., Omunakwe, H. E., Onywera, H., Abe, H., Karray, H., Nansumba, H., Triki, H., Kadjo, H. A. A., Elgahzaly, H., Gumbo, H., Mathieu, H., Kavunga-Membo, H., Smeti, I., Olawoye, I. B., Adetifa, I. M. O., Odia, I., Ben Boubaker, I. B., Mohammad, I. A., Ssewanyana, I., Wurie, I., Konstantinus, I. S., Halatoko, J. W. A., Ayei, J., Sonoo, J., Makangara, J.-C. C., Tamfum, J.-J. M., Heraud, J.-M., Shaffer, J. G., Giandhari, J., Musyoki, J., Nkurunziza, J., Uwanibe, J. N., Bhiman, J. N., Yasuda, J., Morais, J., Kiconco, J., Sandi, J. D., Huddleston, J., Odoom, J. K., Morobe, J. M., Gyapong, J. O., Kayiwa, J. T., Okolie, J. C., Xavier, J. S., Gyamfi, J., Wamala, J. F., Bonney, J. H. K., Nyandwi, J., Everatt, J., Nakaseegu, J., Ngoi, J. M., Namulondo, J., Oguzie, J. U., Andeko, J. C., Lutwama, J. J., Mogga, J. J. H., O’Grady, J., Siddle, K. J., Victoir, K., Adeyemi, K. T., Tumedi, K. A., Carvalho, K. S., Mohammed, K. S., Dellagi, K., Musonda, K. G., Duedu, K. O., Fki-Berrajah, L., Singh, L., Kepler, L. M., Biscornet, L., de Oliveira Martins, L., Chabuka, L., Olubayo, L., Ojok, L. D., Deng, L. L., Ochola-Oyier, L. I., Tyers, L., Mine, M., Ramuth, M., Mastouri, M., ElHefnawi, M., Mbanne, M., Matsheka, M. I., Kebabonye, M., Diop, M., Momoh, M., Lima Mendonça, M. d. L., Venter, M., Paye, M. F., Faye, M., Nyaga, M. M., Mareka, M., Damaris, M.-M., Mburu, M. W., Mpina, M. G., Owusu, M., Wiley, M. R., Tatfeng, M. Y., Ayekaba, M. O.’o., Abouelhoda, M., Beloufa, M. A., Seadawy, M. G., Khalifa, M. K., Matobo, M. M., Kane, M., Salou, M., Mbulawa, M. B., Mwenda, M., Allam, M., Phan, M. V. T., Abid, N., Rujeni, N., Abuzaid, N., Ismael, N., Elguindy, N., Top, N. M., Dia, N., Mabunda, N., Hsiao, N.-y., Silochi, N. B., Francisco, N. M., Saasa, N., Bbosa, N., Murunga, N., Gumede, N., Wolter, N., Sitharam, N., Ndodo, N., Ajayi, N. A., Tordo, N., Mbhele, N., Razanajatovo, N. H., Iguosadolo, N., Mba, N., Kingsley, O. C., Sylvanus, O., Femi, O., Adewumi, O. M., Testimony, O., Ogunsanya, O. A., Fakayode, O., Ogah, O. E., Oludayo, O.-E., Faye, O., Smith-Lawrence, P., Ondoa, P., Combe, P., Nabisubi, P., Semanda, P., Oluniyi, P. E., Arnaldo, P., Quashie, P. K., Okokhere, P. O., Bejon, P., Dussart, P., Bester, P. A., Mbala, P. K., Kaleebu, P., Abechi, P., El-Shesheny, R., Joseph, R., Aziz, R. K., Essomba, R. G., Ayivor-Djanie, R., Njouom, R., Phillips, R. O., Gorman, R., Kingsley, R. A., Neto Rodrigues, R. M. D. E. S. A., Audu, R. A., Carr, R. A. A., Gargouri, S., Masmoudi, S., Bootsma, S., Sankhe, S., Mohamed, S. I., Femi, S., Mhalla, S., Hosch, S., Kassim, S. K., Metha, S., Trabelsi, S., Agwa, S. H., Mwangi, S. W., Doumbia, S., Makiala-Mandanda, S., Aryeetey, S., Ahmed, S. S., Ahmed, S. M., Elhamoumi, S., Moyo, S., Lutucuta, S., Gaseitsiwe, S., Jalloh, S., Andriamandimby, S. F., Oguntope, S., Grayo, S., Lekana-Douki, S., Prosolek, S., Ouangraoua, S., van Wyk, S., Schaffner, S. F., Kanyerezi, S., Ahuka-Mundeke, S., Rudder, S., Pillay, S., Nabadda, S., Behillil, S., Budiaki, S. L., van der Werf, S., Mashe, T., Mohale, T., Le-Viet, T., Velavan, T. P., Schindler, T., Maponga, T. G., Bedford, T., Anyaneji, U. J., Chinedu, U., Ramphal, U., George, U. E., Enouf, V., Nene, V., Gorova, V., Roshdy, W. H., Karim, W. A., Ampofo, W. K., Preiser, W., Choga, W. T., Ahmed, Y. A., Ramphal, Y., Bediako, Y., Naidoo, Y., Butera, Y., de Laurent, Z. R., Ouma, A. E. O., von Gottberg, A., Githinji, G., Moeti, M., Tomori, O., Sabeti, P. C., Sall, A. A., Oyola, S. O., Tebeje, Y. K., Tessema, S. K., de Oliveira, T., Happi, C., Lessells, R., Nkengasong, J., and Wilkinson, E.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Science
• Publisher: American Association for the Advancement of Science
• ISSN: 0036-8075
• ISSN (Online): 1095-9203
• Published Online: 15 September 2022
• Copyright Holders: Copyright © 2022 The Authors
• First Published: First published in Science 378(6615): eabq5358
• Publisher Policy: Reproduced under a Creative Commons License

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
310822		African COVID-19 Preparedness (AFRICO19)	David Robertson	Wellcome Trust (WELLCOTR)	2007-1894	Computing Science
172630014		Cross-Cutting Programme – Viral Genomics and Bioinformatics (Programme 9)	David Robertson	Medical Research Council (MRC)	MC_UU_12014/12	III - Centre for Virus Research