2021
DOI: 10.3390/v13030526
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Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa

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 outb… Show more

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Cited by 25 publications
(23 citation statements)
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“…In other studies, lineage B.1.1.29 was reported to have been commonly identified in Europe, particularly the UK [36,64]; this is supported by the findings of our study, in which the majority of the migration events of the B.1.1.x clade originated from the UK (Table 2, Figure 8). Interestingly, this lineage was also reported in March-April of 2020 in Cape Town, South Africa, and it was estimated to have been imported from the Netherlands [64]. However, the B.1.1.29 lineage was identified much less frequently in Cyprus after June 2020.…”
Section: Discussionsupporting
confidence: 92%
“…In other studies, lineage B.1.1.29 was reported to have been commonly identified in Europe, particularly the UK [36,64]; this is supported by the findings of our study, in which the majority of the migration events of the B.1.1.x clade originated from the UK (Table 2, Figure 8). Interestingly, this lineage was also reported in March-April of 2020 in Cape Town, South Africa, and it was estimated to have been imported from the Netherlands [64]. However, the B.1.1.29 lineage was identified much less frequently in Cyprus after June 2020.…”
Section: Discussionsupporting
confidence: 92%
“…Note that the African country which has been stricken the most by the disease is South Africa where the prevalence of AC is much higher. It has been observed (Engelbrecht et al, 2021) that in this country COVID-19 clusters have occurred there in closed supermarkets, most often equipped with AC .…”
Section: Viii4 Airborne Close Contactmentioning
confidence: 94%
“…Coronavirus Disease 2019 (COVID-19), 2021 ). In December 2020, new variants of concerns (VOC) were detected in other countries, including the UK and South Africa ( Cella et al., 2021 ; Engelbrecht et al., 2021 ; Fiorentini et al., 2021 ; Voloch et al., 2021 ). These strains were related to increased transmissibility and posed higher public health concerns.…”
Section: Introductionmentioning
confidence: 99%