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

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

Blog Article

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 3 Piece King Bed 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 Bath Bomb 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.