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

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. 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., 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. Nature, 603:679–686, jan, 2022.

Paper doi abstract bibtex

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants, respectively. 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) 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, predicted to influence antibody neutralization and spike function. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.

@article{Viana2022,
abstract = {The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants, respectively. 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) 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, predicted to influence antibody neutralization and spike function. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.},
author = {Viana, Raquel and Moyo, Sikhulile and Amoako, Daniel G and Tegally, Houriiyah and Scheepers, Cathrine and Althaus, Christian L and Anyaneji, Ugochukwu J and Bester, Phillip A and Boni, Maciej F. and Chand, Mohammed and Choga, Wonderful T. and Colquhoun, Rachel and Davids, Michaela and Deforche, Koen and Doolabh, Deelan and du Plessis, Louis and Engelbrecht, Susan and Everatt, Josie and Giandhari, Jennifer and Giovanetti, Marta and Hardie, Diana and Hill, Verity and Hsiao, Nei-Yuan and Iranzadeh, Arash and Ismail, Arshad and Joseph, Charity and Joseph, Rageema and Koopile, Legodile and {Kosakovsky Pond}, Sergei L. and Kraemer, Moritz U. G. and Kuate-Lere, Lesego and Laguda-Akingba, Oluwakemi and Lesetedi-Mafoko, Onalethatha and Lessells, Richard J. and Lockman, Shahin and Lucaci, Alexander G. and Maharaj, Arisha and Mahlangu, Boitshoko and Maponga, Tongai and Mahlakwane, Kamela and Makatini, Zinhle and Marais, Gert and Maruapula, Dorcas and Masupu, Kereng and Matshaba, Mogomotsi and Mayaphi, Simnikiwe and Mbhele, Nokuzola and Mbulawa, Mpaphi B. and Mendes, Adriano and Mlisana, Koleka and Mnguni, Anele and Mohale, Thabo and Moir, Monika and Moruisi, Kgomotso and Mosepele, Mosepele and Motsatsi, Gerald and Motswaledi, Modisa S. and Mphoyakgosi, Thongbotho and Msomi, Nokukhanya and Mwangi, Peter N. and Naidoo, Yeshnee and Ntuli, Noxolo and Nyaga, Martin and Olubayo, Lucier and Pillay, Sureshnee and Radibe, Botshelo and Ramphal, Yajna and Ramphal, Upasana and San, James E. and Scott, Lesley and Shapiro, Roger and Singh, Lavanya and Smith-Lawrence, Pamela and Stevens, Wendy and Strydom, Amy and Subramoney, Kathleen and Tebeila, Naume and Tshiabuila, Derek and Tsui, Joseph and van Wyk, Stephanie and Weaver, Steven and Wibmer, Constantinos K. and Wilkinson, Eduan and Wolter, Nicole and Zarebski, Alexander E. and Zuze, Boitumelo and Goedhals, Dominique and Preiser, Wolfgang and Treurnicht, Florette and Venter, Marietje and Williamson, Carolyn and Pybus, Oliver G. and Bhiman, Jinal and Glass, Allison and Martin, Darren P. and Rambaut, Andrew and Gaseitsiwe, Simani and von Gottberg, Anne and de Oliveira, Tulio},
doi = {10.1038/D41586-021-03832-5},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Viana et al. - 2022 - Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
keywords = {OA,fund{\_}ack,genomics{\_}fund{\_}ack,original},
mendeley-tags = {OA,fund{\_}ack,genomics{\_}fund{\_}ack,original},
month = {jan},
pages = {679--686},
pmid = {35042229},
title = {{Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa}},
url = {https://www.nature.com/articles/d41586-021-03832-5},
volume = {603},
year = {2022}
}

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