Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa
| Autor: | Gert U. van Zyl, Bronwyn Kleinhans, Kayla Delaney, Tania Stander, Susan Engelbrecht, Wolfgang Preiser, Tulio de Oliveira, Houriiyah Tegally, Eduan Wilkinson |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Adult
Male 0301 basic medicine Adolescent 030106 microbiology education lcsh:QR1-502 Genome Viral Disease cluster molecular epidemiology Article Western Cape Province lcsh:Microbiology Disease Outbreaks South Africa Young Adult 03 medical and health sciences Virology Cape Pandemic Humans Clade Molecular clock Phylogeny Aged Netherlands Aged 80 and over Travel betacoronavirus SARS-CoV-2 COVID-19 genome sequencing mutation phylogenetics Cape Town Whole Genome Sequencing biology Molecular epidemiology Outbreak Middle Aged biology.organism_classification 030104 developmental biology Infectious Diseases Geography Female Betacoronavirus Demography |
| Zdroj: | Viruses, Vol 13, Iss 526, p 526 (2021) Viruses Viruses; Volume 13; Issue 3; Pages: 526 |
| ISSN: | 1999-4915 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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