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Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa (preprint)
Raquel Viana; Sikhulile Moyo; Daniel Gyamfi Amoako; Houriiyah Tegally; Cathrine Scheepers; Richard J Lessells; Jennifer Giandhari; Nicole Wolter; Josie Everatt; Andrew Rambaut; Christian Althaus; Eduan Wilkinson; Adriano Mendes; Amy Strydom; Michaela Davids; Simnikiwe Mayaphi; Simani Gaseitsiwe; Wonderful T Choga; Dorcas Maruapula; Boitumelo Zuze; Botshelo Radibe; Legodile Koopile; Roger Shapiro; Shahin Lockman; Mpaphi B. Mbulawa; Thongbotho Mphoyakgosi; Pamela Smith-Lawrence; Mosepele Mosepele; Mogomotsi Matshaba; Kereng Masupu; Mohammed Chand; Charity Joseph; Lesego Kuate-Lere; Onalethatha Lesetedi-Mafoko; Kgomotso Moruisi; Lesley Scott; Wendy Stevens; Constantinos Kurt Wibmer; Anele Mnguni; Arshad Ismail; Boitshoko Mahlangu; Darren P. Martin; Verity Hill; Rachel Colquhoun; Modisa S. Motswaledi; James Emmanuel San; Noxolo Ntuli; Gerald Motsatsi; Sureshnee Pillay; Thabo Mohale; Upasana Ramphal; Yeshnee Naidoo; Naume Tebeila; Marta Giovanetti; Koleka Mlisana; Carolyn Williamson; Nei-yuan Hsiao; Nokukhanya Msomi; Kamela Mahlakwane; Susan Engelbrecht; Tongai Maponga; Wolfgang Preiser; Zinhle Makatini; Oluwakemi Laguda-Akingba; Lavanya Singh; Ugochukwu J. Anyaneji; Monika Moir; Stephanie van Wyk; Derek Tshiabuila; Yajna Ramphal; Arisha Maharaj; Sergei Pond; Alexander G Lucaci; Steven Weaver; Maciej F Boni; Koen Deforche; Kathleen Subramoney; Diana Hardie; Gert Marais; Deelan Doolabh; Rageema Joseph; Nokuzola Mbhele; Luicer Olubayo; Arash Iranzadeh; Alexander E Zarebski; Joseph Tsui; Moritz UG Kraemer; Oliver G Pybus; Dominique Goedhals; Phillip Armand Bester; Martin M Nyaga; Peter N Mwangi; Allison Glass; Florette Treurnicht; Marietjie Venter; Jinal N. Bhiman; Anne von Gottberg; Tulio de Oliveira.
medrxiv; 2021.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2021.12.19.21268028
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 function4. 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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Full text: Available Collection: Preprints Database: medRxiv Main subject: Severe Acute Respiratory Syndrome Language: English Year: 2021 Document Type: Preprint

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Full text: Available Collection: Preprints Database: medRxiv Main subject: Severe Acute Respiratory Syndrome Language: English Year: 2021 Document Type: Preprint