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Article

Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa

1
Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
2
Tygerberg Business Unit, National Health Laboratory Service (NHLS), Cape Town 8000, South Africa
3
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
4
Centre for Aids Programme of Research in South Africa (CAPRISA), Durban 4000, South Africa
5
Department of Global Health, University of Washington, Seattle, WA 98195, USA
*
Authors to whom correspondence should be addressed.
Academic Editors: Luciana Barros de Arruda, Fabrício S. Campos and Flavio Guimaraes da Fonseca
Viruses 2021, 13(3), 526; https://doi.org/10.3390/v13030526
Received: 27 January 2021 / Revised: 10 March 2021 / Accepted: 16 March 2021 / Published: 22 March 2021
(This article belongs to the Special Issue Viral Infections in Developing Countries)
Cape Town was the first city in South Africa to experience the full impact of the coronavirus disease 2019 (COVID-19) pandemic. We acquired samples from all suspected cases and their contacts during the first month of the pandemic from Tygerberg Hospital. Nanopore sequencing generated SARS-CoV-2 whole genomes. Phylogenetic inference with maximum likelihood and Bayesian methods were used to determine lineages that seeded the local epidemic. Three patients were known to have travelled internationally and an outbreak was detected in a nearby supermarket. Sequencing of 50 samples produced 46 high-quality genomes. The sequences were classified as lineages: B, B.1, B.1.1.1, B.1.1.161, B.1.1.29, B.1.8, B.39, and B.40. All the sequences from persons under investigation (PUIs) in the supermarket outbreak (lineage B.1.8) fall within a clade from the Netherlands with good support (p > 0.9). In addition, a new mutation, 5209A>G, emerged within the Cape Town cluster. The molecular clock analysis suggests that this occurred around 13 March 2020 (95% confidence interval: 9–17 March). The phylogenetic reconstruction suggests at least nine early introductions of SARS-CoV-2 into Cape Town and an early localized transmission in a shopping environment. Genomic surveillance was successfully used to investigate and track the spread of early introductions of SARS-CoV-2 in Cape Town. View Full-Text
Keywords: betacoronavirus; SARS-CoV-2; COVID-19; genome sequencing; mutation; phylogenetics; Cape Town; Western Cape Province; South Africa; molecular epidemiology betacoronavirus; SARS-CoV-2; COVID-19; genome sequencing; mutation; phylogenetics; Cape Town; Western Cape Province; South Africa; molecular epidemiology
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MDPI and ACS Style

Engelbrecht, S.; Delaney, K.; Kleinhans, B.; Wilkinson, E.; Tegally, H.; Stander, T.; van Zyl, G.; Preiser, W.; de Oliveira, T. Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. Viruses 2021, 13, 526. https://doi.org/10.3390/v13030526

AMA Style

Engelbrecht S, Delaney K, Kleinhans B, Wilkinson E, Tegally H, Stander T, van Zyl G, Preiser W, de Oliveira T. Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. Viruses. 2021; 13(3):526. https://doi.org/10.3390/v13030526

Chicago/Turabian Style

Engelbrecht, Susan, Kayla Delaney, Bronwyn Kleinhans, Eduan Wilkinson, Houriiyah Tegally, Tania Stander, Gert van Zyl, Wolfgang Preiser, and Tulio de Oliveira. 2021. "Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa" Viruses 13, no. 3: 526. https://doi.org/10.3390/v13030526

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