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

Susan Engelbrecht,Tulio De Oliveira,Bronwyn Kleinhans,Houriiyah Tegally,Gert Van Zyl,Eduan Wilkinson,Tania Stander,Kayla Delaney,Wolfgang Preiser

doi:10.3390/v13030526

Susan Engelbrecht, Tulio De Oliveira + Show 7 more

Open Access

https://doi.org/10.3390/v13030526

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Abstract

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.

Highlights

IntroductionThe first recorded pandemic, the plague of Athens, caused the death of ~100,000 people between 430–425 BCE [1]
Emerging infectious diseases have accompanied mankind for millennia
Using a phylogenetic and epidemiological approach with nanopore sequencing technology, we investigated the introduction and timing of severe acute respiratory syndrome (SARS)-CoV-2 in the Cape Town Metropole

Summary

Introduction

The first recorded pandemic, the plague of Athens, caused the death of ~100,000 people between 430–425 BCE [1]. Infectious diseases of viral origin have increased dramatically since the turn of the 21st century, with the emergence of severe acute respiratory syndrome (SARS) in 2002 [2], influenza H1N1 in 2009 [3,4], chikungunya in 2014 [5], Zika in 2015 [6], and the ongoing coronavirus disease 2019 (COVID-19). COVID-19 was declared a Public Health Emergency of International Concern (PHEIC) by the World Health Organization (WHO) on 31 January 2020, [7] and subsequently a pandemic on 11 March 2020 [8]. SARS-CoV-2 has infected 117,660,021 people worldwide with 2,612,176 deaths (https://coronavirus.jhu.edu/map.html, accessed on 10 March 2021) [10]

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