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Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

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Viana, Raquel, Moyo, Sikhulile, Amoako, Daniel G., Tegally, Houriiyah, Scheepers, Cathrine, Althaus, Christian L., Anyaneji, Ugochukwu J., Bester, Phillip A., Boni, Maciej F., Chand, Mohammed, Choga, Wonderful T., Colquhoun, Rachel, Davids, Michaela, Deforche, Koen, Doolabh, Deelan, du Plessis, Louis, Engelbrecht, Susan, Everatt, Josie, Giandhari, Jennifer, Giovanetti, Marta, Hardie, Diana, Hill, Verity, Hsiao, Nei-Yuan, Iranzadeh, Arash, Ismail, Arshad, Joseph, Charity, Joseph, Rageema, Koopile, Legodile, Kosakovsky Pond, Sergei L., Kraemer, Moritz U. G., Kuate-Lere, Lesego, Laguda-Akingba, Oluwakemi, Lesetedi-Mafoko, Onalethatha, Lessells, Richard J., Lockman, Shahin, Lucaci, Alexander G., Maharaj, Arisha, Mahlangu, Boitshoko, Maponga, Tongai, Mahlakwane, Kamela, Makatini, Zinhle, Marais, Gert, Maruapula, Dorcas, Masupu, Kereng, Matshaba, Mogomotsi, Mayaphi, Simnikiwe, Mbhele, Nokuzola, Mbulawa, Mpaphi B., Mendes, Adriano, Mlisana, Koleka, Mnguni, Anele, Mohale, Thabo, Moir, Monika, Moruisi, Kgomotso, Mosepele, Mosepele, Motsatsi, Gerald, Motswaledi, Modisa S., Mphoyakgosi, Thongbotho, Msomi, Nokukhanya, Mwangi, Peter N., Naidoo, Yeshnee, Ntuli, Noxolo, Nyaga, Martin, Olubayo, Lucier, Pillay, Sureshnee, Radibe, Botshelo, Ramphal, Yajna, Ramphal, Upasana, San, James E., Scott, Lesley, Shapiro, Roger, Singh, Lavanya, Smith-Lawrence, Pamela, Stevens, Wendy, Strydom, Amy, Subramoney, Kathleen, Tebeila, Naume, Tshiabuila, Derek, Tsui, Joseph, van Wyk, Stephanie, Weaver, Steven, Wibmer, Constantinos K., Wilkinson, Eduan, Wolter, Nicole, Zarebski, Alexander E., Zuze, Boitumelo, Goedhals, Dominique, Preiser, Wolfgang, Treurnicht, Florette, Venter, Marietje, Williamson, Carolyn, Pybus, Oliver G., Bhiman, Jinal, Glass, Allison, Martin, Darren P., Rambaut, Andrew, Gaseitsiwe, Simani, von Gottberg, Anne, de Oliveira, Tulio·2022·Nature
DOI 10.1038/s41586-022-04411-y
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Abstract

The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively 1–3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function 4. Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.

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Metadata

Authors
Viana, R., Moyo, S., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., Anyaneji, U. J., Bester, P. A., Boni, M. F., Chand, M., Choga, W. T., Colquhoun, R., Davids, M., Deforche, K., Doolabh, D., du Plessis, L., Engelbrecht, S., Everatt, J., Giandhari, J., Giovanetti, M., Hardie, D., Hill, V., Hsiao, N.-Y., Iranzadeh, A., Ismail, A., Joseph, C., Joseph, R., Koopile, L., Kosakovsky Pond, S. L., Kraemer, M. U. G., Kuate-Lere, L., Laguda-Akingba, O., Lesetedi-Mafoko, O., Lessells, R. J., Lockman, S., Lucaci, A. G., Maharaj, A., Mahlangu, B., Maponga, T., Mahlakwane, K., Makatini, Z., Marais, G., Maruapula, D., Masupu, K., Matshaba, M., Mayaphi, S., Mbhele, N., Mbulawa, M. B., Mendes, A., Mlisana, K., Mnguni, A., Mohale, T., Moir, M., Moruisi, K., Mosepele, M., Motsatsi, G., Motswaledi, M. S., Mphoyakgosi, T., Msomi, N., Mwangi, P. N., Naidoo, Y., Ntuli, N., Nyaga, M., Olubayo, L., Pillay, S., Radibe, B., Ramphal, Y., Ramphal, U., San, J. E., Scott, L., Shapiro, R., Singh, L., Smith-Lawrence, P., Stevens, W., Strydom, A., Subramoney, K., Tebeila, N., Tshiabuila, D., Tsui, J., van Wyk, S., Weaver, S., Wibmer, C. K., Wilkinson, E., Wolter, N., Zarebski, A. E., Zuze, B., Goedhals, D., Preiser, W., Treurnicht, F., Venter, M., Williamson, C., Pybus, O. G., Bhiman, J., Glass, A., Martin, D. P., Rambaut, A., Gaseitsiwe, S., von Gottberg, A., & de Oliveira, T.
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2022-01-07
Volume
603
Issue
7902
Pages
679-686
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-022-04411-y
OpenAlex
W4225691034
Cited by
1,690
References
25
FWCI
178.17
Type
journal article
Language
en
Open access
hybrid
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Viana, R., Moyo, S., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., Anyaneji, U. J., Bester, P. A., Boni, M. F., Chand, M., Choga, W. T., Colquhoun, R., Davids, M., Deforche, K., Doolabh, D., du Plessis, L., Engelbrecht, S., Everatt, J., Giandhari, J., . . . de Oliveira, T. (2022). Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature. https://doi.org/10.1038/s41586-022-04411-y

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