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.

Rights

This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/. This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using such material.

Cite as

Tegally, H., San, J., Cotten, M., Moir, M., Tegomoh, B., Mboowa, G., Martin, D., Baxter, C., Lambisia, A., Diallo, A., Amoako, D., Diagne, M., Sisay, A., Zekri, A., Gueye, A., Sangare, A., Ouedraogo, A., Sow, A., Musa, A., Sesay, A., Abias, A., Elzagheid, A., Lagare, A., Kemi, A., Abar, A., Johnson, A., Fowotade, A., Oluwapelumi, A., Amuri, A., Juru, A., Kandeil, A., Mostafa, A., Rebai, A., Sayed, A., Kazeem, A., Balde, A., Christoffels, A., Trotter, A., Campbell, A., Keita, A., Kone, A., Bouzid, A., Souissi, A., Agweyu, A., Naguib, A., Gutierrez, A., Nkeshimana, A., Page, A., Yadouleton, A., Vinze, A., Happi, A., Chouikha, A., Iranzadeh, A., Maharaj, A., Batchi-Bouyou, A., Ismail, A., Sylverken, A., Goba, A., Femi, A., Sijuwola, A., Marycelin, B., Salako, B., Oderinde, B., Bolajoko, B., Diarra, B., Herring, B., Tsofa, B., Lekana-Douki, B., Mvula, B., Njanpop-Lafourcade, B., Marondera, B., Khaireh, B., Kouriba, B., Adu, B., Pool, B., McInnis, B., Brook, C., Williamson, C., Nduwimana, C., Anscombe, C., Pratt, C., Scheepers, C., Akoua-Koffi, C., Agoti, C., Mapanguy, C., Loucoubar, C., Onwuamah, C., Ihekweazu, C., Malaka, C., Peyrefitte, C., Grace, C., Omoruyi, C., Rafaï, C., Morang'a, C., Erameh, C., Lule, D., Bridges, D., Mukadi-Bamuleka, D., Park, D., Rasmussen, D., Baker, D., Nokes, D., Ssemwanga, D., Tshiabuila, D., Amuzu, D., Goedhals, D., Grant, D., Omuoyo, D., Maruapula, D., Wanjohi, D., Foster-Nyarko, E., Lusamaki, E., Simulundu, E., Ong'era, E., Ngabana, E., Abworo, E., Otieno, E., Shumba, E., Barasa, E., Ahmed, E., Ahmed, E., Lokilo, E., Mukantwari, E., Philomena, E., Belarbi, E., Simon-Loriere, E., Anoh, E., Manuel, E., Leendertz, F., Taweh, F., Wasfi, F., Abdelmoula, F., Takawira, F., Derrar, F., Ajogbasile, F., Treurnicht, F., Onikepe, F., Ntoumi, F., Muyembe, F., Ragomzingba, F., Dratibi, F., Iyanu, F., Mbunsu, G., Thilliez, G., Kay, G., Akpede, G., van Zyl, G., Awandare, G., Kpeli, G., Schubert, G., Maphalala, G., Ranaivoson, H., Omunakwe, H., Onywera, H., Abe, H., Karray, H., Nansumba, H., Triki, H., Kadjo, H., Elgahzaly, H., Gumbo, H., Mathieu, H., Kavunga-Membo, H., Smeti, I., Olawoye, I., Adetifa, I., Odia, I., Ben Boubaker, I., Mohammad, I., Ssewanyana, I., Wurie, I., Konstantinus, I., Halatoko, J., Ayei, J., Sonoo, J., Makangara, J., Tamfum, J., Heraud, J., Shaffer, J., Giandhari, J., Musyoki, J., Nkurunziza, J., Uwanibe, J., Bhiman, J., Yasuda, J., Morais, J., Kiconco, J., Sandi, J., Huddleston, J., Odoom, J., Morobe, J., Gyapong, J., Kayiwa, J., Okolie, J., Xavier, J., Gyamfi, J., Wamala, J., Bonney, J., Nyandwi, J., Everatt, J., Nakaseegu, J., Ngoi, J., Namulondo, J., Oguzie, J., Andeko, J., Lutwama, J., Mogga, J., O'Grady, J., Siddle, K., Victoir, K., Adeyemi, K., Tumedi, K., Carvalho, K., Mohammed, K., Dellagi, K., Musonda, K., Duedu, K., Fki-Berrajah, L., Singh, L., Kepler, L., Biscornet, L., de Oliveira Martins, L., Chabuka, L., Olubayo, L., Ojok, L., Deng, L., Ochola-Oyier, L., Tyers, L., Mine, M., Ramuth, M., Mastouri, M., ElHefnawi, M., Mbanne, M., Matsheka, M., Kebabonye, M., Diop, M., Momoh, M., Lima Mendonça, M., Venter, M., Paye, M., Faye, M., Nyaga, M., Mareka, M., Damaris, M., Mburu, M., Mpina, M., Owusu, M., Wiley, M., Tatfeng, M., Ayekaba, M., Abouelhoda, M., Beloufa, M., Seadawy, M., Khalifa, M., Matobo, M., Kane, M., Salou, M., Mbulawa, M., Mwenda, M., Allam, M., Phan, M., Abid, N., Rujeni, N., Abuzaid, N., Ismael, N., Elguindy, N., Top, N., Dia, N., Mabunda, N., Hsiao, N., Silochi, N., Francisco, N., Saasa, N., Bbosa, N., Murunga, N., Gumede, N., Wolter, N., Sitharam, N., Ndodo, N., Ajayi, N., Tordo, N., Mbhele, N., Razanajatovo, N., Iguosadolo, N., Mba, N., Kingsley, O., Sylvanus, O., Femi, O., Adewumi, O., Testimony, O., Ogunsanya, O., Fakayode, O., Ogah, O., Oludayo, O., Faye, O., Smith-Lawrence, P., Ondoa, P., Combe, P., Nabisubi, P., Semanda, P., Oluniyi, P., Arnaldo, P., Quashie, P., Okokhere, P., Bejon, P., Dussart, P., Bester, P., Mbala, P., Kaleebu, P., Abechi, P., El-Shesheny, R., Joseph, R., Aziz, R., Essomba, R., Ayivor-Djanie, R., Njouom, R., Phillips, R., Gorman, R., Kingsley, R., Neto Rodrigues, R., Audu, R., Carr, R., Gargouri, S., Masmoudi, S., Bootsma, S., Sankhe, S., Mohamed, S., Femi, S., Mhalla, S., Hosch, S., Kassim, S., Metha, S., Trabelsi, S., Agwa, S., Mwangi, S., Doumbia, S., Makiala-Mandanda, S., Aryeetey, S., Ahmed, S., Ahmed, S., Elhamoumi, S., Moyo, S., Lutucuta, S., Gaseitsiwe, S., Jalloh, S., Andriamandimby, S., Oguntope, S., Grayo, S., Lekana-Douki, S., Prosolek, S., Ouangraoua, S., van Wyk, S., Schaffner, S., Kanyerezi, S., Ahuka-Mundeke, S., Rudder, S., Pillay, S., Nabadda, S., Behillil, S., Budiaki, S., van der Werf, S., Mashe, T., Mohale, T., Le-Viet, T., Velavan, T., Schindler, T., Maponga, T., Bedford, T., Anyaneji, U., Chinedu, U., Ramphal, U., George, U., Enouf, V., Nene, V., Gorova, V., Roshdy, W., Karim, W., Ampofo, W., Preiser, W., Choga, W., Ahmed, Y., Ramphal, Y., Bediako, Y., Naidoo, Y., Butera, Y., de Laurent, Z., Ouma, A., von Gottberg, A., Githinji, G., Moeti, M., Tomori, O., Sabeti, P., Sall, A., Oyola, S., Tebeje, Y., Tessema, S., Happi, C., Lessells, R., Nkengasong, J., Wilkinson, E. & De Oliveira, T. 2022, 'The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance', Science. https://doi.org/10.1126/science.abq5358

Downloadable citations

Download HTML citationHTML Download BIB citationBIB Download RIS citationRIS
Last updated: 05 November 2022
Was this page helpful?