tetano
Editor, Senior Moderator
Nature
. 2022 Jan 7.
doi: 10.1038/s41586-022-04411-y. Online ahead of print.
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Raquel Viana[SUP] #[/SUP][SUP] 1 [/SUP], Sikhulile Moyo[SUP] #[/SUP][SUP] 2 3 4 [/SUP], Daniel G Amoako[SUP] #[/SUP][SUP] 5 [/SUP], Houriiyah Tegally[SUP] #[/SUP][SUP] 6 [/SUP], Cathrine Scheepers[SUP] #[/SUP][SUP] 5 7 [/SUP], Christian L Althaus[SUP] 8 [/SUP], Ugochukwu J Anyaneji[SUP] 6 [/SUP], Phillip A Bester[SUP] 9 10 [/SUP], Maciej F Boni[SUP] 11 [/SUP], Mohammed Chand[SUP] 12 [/SUP], Wonderful T Choga[SUP] 3 [/SUP], Rachel Colquhoun[SUP] 13 [/SUP], Michaela Davids[SUP] 14 [/SUP], Koen Deforche[SUP] 15 [/SUP], Deelan Doolabh[SUP] 16 [/SUP], Louis du Plessis[SUP] 17 18 [/SUP], Susan Engelbrecht[SUP] 19 [/SUP], Josie Everatt[SUP] 5 [/SUP], Jennifer Giandhari[SUP] 6 [/SUP], Marta Giovanetti[SUP] 20 21 [/SUP], Diana Hardie[SUP] 16 22 [/SUP], Verity Hill[SUP] 13 [/SUP], Nei-Yuan Hsiao[SUP] 16 22 23 [/SUP], Arash Iranzadeh[SUP] 24 [/SUP], Arshad Ismail[SUP] 5 [/SUP], Charity Joseph[SUP] 12 [/SUP], Rageema Joseph[SUP] 16 [/SUP], Legodile Koopile[SUP] 2 [/SUP], Sergei L Kosakovsky Pond[SUP] 25 [/SUP], Moritz U G Kraemer[SUP] 17 [/SUP], Lesego Kuate-Lere[SUP] 26 [/SUP], Oluwakemi Laguda-Akingba[SUP] 27 28 [/SUP], Onalethatha Lesetedi-Mafoko[SUP] 29 [/SUP], Richard J Lessells[SUP] 6 [/SUP], Shahin Lockman[SUP] 2 30 [/SUP], Alexander G Lucaci[SUP] 25 [/SUP], Arisha Maharaj[SUP] 6 [/SUP], Boitshoko Mahlangu[SUP] 5 [/SUP], Tongai Maponga[SUP] 19 [/SUP], Kamela Mahlakwane[SUP] 19 31 [/SUP], Zinhle Makatini[SUP] 32 [/SUP], Gert Marais[SUP] 16 22 [/SUP], Dorcas Maruapula[SUP] 2 [/SUP], Kereng Masupu[SUP] 4 [/SUP], Mogomotsi Matshaba[SUP] 4 33 34 [/SUP], Simnikiwe Mayaphi[SUP] 35 [/SUP], Nokuzola Mbhele[SUP] 16 [/SUP], Mpaphi B Mbulawa[SUP] 36 [/SUP], Adriano Mendes[SUP] 14 [/SUP], Koleka Mlisana[SUP] 37 38 [/SUP], Anele Mnguni[SUP] 5 [/SUP], Thabo Mohale[SUP] 5 [/SUP], Monika Moir[SUP] 39 [/SUP], Kgomotso Moruisi[SUP] 26 [/SUP], Mosepele Mosepele[SUP] 4 40 [/SUP], Gerald Motsatsi[SUP] 5 [/SUP], Modisa S Motswaledi[SUP] 4 41 [/SUP], Thongbotho Mphoyakgosi[SUP] 36 [/SUP], Nokukhanya Msomi[SUP] 42 [/SUP], Peter N Mwangi[SUP] 10 43 [/SUP], Yeshnee Naidoo[SUP] 6 [/SUP], Noxolo Ntuli[SUP] 5 [/SUP], Martin Nyaga[SUP] 10 43 [/SUP], Lucier Olubayo[SUP] 23 24 [/SUP], Sureshnee Pillay[SUP] 6 [/SUP], Botshelo Radibe[SUP] 2 [/SUP], Yajna Ramphal[SUP] 6 [/SUP], Upasana Ramphal[SUP] 6 [/SUP], James E San[SUP] 6 [/SUP], Lesley Scott[SUP] 44 [/SUP], Roger Shapiro[SUP] 2 30 [/SUP], Lavanya Singh[SUP] 6 [/SUP], Pamela Smith-Lawrence[SUP] 26 [/SUP], Wendy Stevens[SUP] 44 [/SUP], Amy Strydom[SUP] 14 [/SUP], Kathleen Subramoney[SUP] 32 [/SUP], Naume Tebeila[SUP] 5 [/SUP], Derek Tshiabuila[SUP] 6 [/SUP], Joseph Tsui[SUP] 17 [/SUP], Stephanie van Wyk[SUP] 39 [/SUP], Steven Weaver[SUP] 25 [/SUP], Constantinos K Wibmer[SUP] 5 [/SUP], Eduan Wilkinson[SUP] 39 [/SUP], Nicole Wolter[SUP] 5 45 [/SUP], Alexander E Zarebski[SUP] 17 [/SUP], Boitumelo Zuze[SUP] 2 [/SUP], Dominique Goedhals[SUP] 10 46 [/SUP], Wolfgang Preiser[SUP] 19 31 [/SUP], Florette Treurnicht[SUP] 32 [/SUP], Marietje Venter[SUP] 14 [/SUP], Carolyn Williamson[SUP] 16 22 23 47 [/SUP], Oliver G Pybus[SUP] 17 [/SUP], Jinal Bhiman[SUP] 5 7 [/SUP], Allison Glass[SUP] 1 48 [/SUP], Darren P Martin[SUP] 23 47 [/SUP], Andrew Rambaut[SUP] 13 [/SUP], Simani Gaseitsiwe[SUP] 2 3 [/SUP], Anne von Gottberg[SUP] 5 45 [/SUP], Tulio de Oliveira[SUP] 49 50 51 [/SUP]
Affiliations
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[SUP]1-3[/SUP]. 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[SUP]4[/SUP]. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
. 2022 Jan 7.
doi: 10.1038/s41586-022-04411-y. Online ahead of print.
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Raquel Viana[SUP] #[/SUP][SUP] 1 [/SUP], Sikhulile Moyo[SUP] #[/SUP][SUP] 2 3 4 [/SUP], Daniel G Amoako[SUP] #[/SUP][SUP] 5 [/SUP], Houriiyah Tegally[SUP] #[/SUP][SUP] 6 [/SUP], Cathrine Scheepers[SUP] #[/SUP][SUP] 5 7 [/SUP], Christian L Althaus[SUP] 8 [/SUP], Ugochukwu J Anyaneji[SUP] 6 [/SUP], Phillip A Bester[SUP] 9 10 [/SUP], Maciej F Boni[SUP] 11 [/SUP], Mohammed Chand[SUP] 12 [/SUP], Wonderful T Choga[SUP] 3 [/SUP], Rachel Colquhoun[SUP] 13 [/SUP], Michaela Davids[SUP] 14 [/SUP], Koen Deforche[SUP] 15 [/SUP], Deelan Doolabh[SUP] 16 [/SUP], Louis du Plessis[SUP] 17 18 [/SUP], Susan Engelbrecht[SUP] 19 [/SUP], Josie Everatt[SUP] 5 [/SUP], Jennifer Giandhari[SUP] 6 [/SUP], Marta Giovanetti[SUP] 20 21 [/SUP], Diana Hardie[SUP] 16 22 [/SUP], Verity Hill[SUP] 13 [/SUP], Nei-Yuan Hsiao[SUP] 16 22 23 [/SUP], Arash Iranzadeh[SUP] 24 [/SUP], Arshad Ismail[SUP] 5 [/SUP], Charity Joseph[SUP] 12 [/SUP], Rageema Joseph[SUP] 16 [/SUP], Legodile Koopile[SUP] 2 [/SUP], Sergei L Kosakovsky Pond[SUP] 25 [/SUP], Moritz U G Kraemer[SUP] 17 [/SUP], Lesego Kuate-Lere[SUP] 26 [/SUP], Oluwakemi Laguda-Akingba[SUP] 27 28 [/SUP], Onalethatha Lesetedi-Mafoko[SUP] 29 [/SUP], Richard J Lessells[SUP] 6 [/SUP], Shahin Lockman[SUP] 2 30 [/SUP], Alexander G Lucaci[SUP] 25 [/SUP], Arisha Maharaj[SUP] 6 [/SUP], Boitshoko Mahlangu[SUP] 5 [/SUP], Tongai Maponga[SUP] 19 [/SUP], Kamela Mahlakwane[SUP] 19 31 [/SUP], Zinhle Makatini[SUP] 32 [/SUP], Gert Marais[SUP] 16 22 [/SUP], Dorcas Maruapula[SUP] 2 [/SUP], Kereng Masupu[SUP] 4 [/SUP], Mogomotsi Matshaba[SUP] 4 33 34 [/SUP], Simnikiwe Mayaphi[SUP] 35 [/SUP], Nokuzola Mbhele[SUP] 16 [/SUP], Mpaphi B Mbulawa[SUP] 36 [/SUP], Adriano Mendes[SUP] 14 [/SUP], Koleka Mlisana[SUP] 37 38 [/SUP], Anele Mnguni[SUP] 5 [/SUP], Thabo Mohale[SUP] 5 [/SUP], Monika Moir[SUP] 39 [/SUP], Kgomotso Moruisi[SUP] 26 [/SUP], Mosepele Mosepele[SUP] 4 40 [/SUP], Gerald Motsatsi[SUP] 5 [/SUP], Modisa S Motswaledi[SUP] 4 41 [/SUP], Thongbotho Mphoyakgosi[SUP] 36 [/SUP], Nokukhanya Msomi[SUP] 42 [/SUP], Peter N Mwangi[SUP] 10 43 [/SUP], Yeshnee Naidoo[SUP] 6 [/SUP], Noxolo Ntuli[SUP] 5 [/SUP], Martin Nyaga[SUP] 10 43 [/SUP], Lucier Olubayo[SUP] 23 24 [/SUP], Sureshnee Pillay[SUP] 6 [/SUP], Botshelo Radibe[SUP] 2 [/SUP], Yajna Ramphal[SUP] 6 [/SUP], Upasana Ramphal[SUP] 6 [/SUP], James E San[SUP] 6 [/SUP], Lesley Scott[SUP] 44 [/SUP], Roger Shapiro[SUP] 2 30 [/SUP], Lavanya Singh[SUP] 6 [/SUP], Pamela Smith-Lawrence[SUP] 26 [/SUP], Wendy Stevens[SUP] 44 [/SUP], Amy Strydom[SUP] 14 [/SUP], Kathleen Subramoney[SUP] 32 [/SUP], Naume Tebeila[SUP] 5 [/SUP], Derek Tshiabuila[SUP] 6 [/SUP], Joseph Tsui[SUP] 17 [/SUP], Stephanie van Wyk[SUP] 39 [/SUP], Steven Weaver[SUP] 25 [/SUP], Constantinos K Wibmer[SUP] 5 [/SUP], Eduan Wilkinson[SUP] 39 [/SUP], Nicole Wolter[SUP] 5 45 [/SUP], Alexander E Zarebski[SUP] 17 [/SUP], Boitumelo Zuze[SUP] 2 [/SUP], Dominique Goedhals[SUP] 10 46 [/SUP], Wolfgang Preiser[SUP] 19 31 [/SUP], Florette Treurnicht[SUP] 32 [/SUP], Marietje Venter[SUP] 14 [/SUP], Carolyn Williamson[SUP] 16 22 23 47 [/SUP], Oliver G Pybus[SUP] 17 [/SUP], Jinal Bhiman[SUP] 5 7 [/SUP], Allison Glass[SUP] 1 48 [/SUP], Darren P Martin[SUP] 23 47 [/SUP], Andrew Rambaut[SUP] 13 [/SUP], Simani Gaseitsiwe[SUP] 2 3 [/SUP], Anne von Gottberg[SUP] 5 45 [/SUP], Tulio de Oliveira[SUP] 49 50 51 [/SUP]
Affiliations
- PMID: 35042229
- DOI: 10.1038/s41586-022-04411-y
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[SUP]1-3[/SUP]. 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[SUP]4[/SUP]. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.