Fig. 1: Monitoring the SARS-CoV-2 epidemic in South Africa using genomic sequencing.
a, Epidemiological curve showing the progression of daily COVID-19 numbers in South Africa, changes in Re estimations (mean estimated median Re with upper and lower bounds of the 95% confidence interval shown), lockdown levels and the timing of genomic sampling in South Africa from the beginning of the epidemic to 15 September. b, Estimated numbers of introductions into South Africa colored by region of origin. c, Overall sampling of genomes in South Africa colored by whether the genomes are associated with introduction events (origins outside South Africa) or not (origins in South Africa). d, MCC tree of 7,213 global genomes including 1,365 South African sequences, indicating a period of early introductions and a period of peak infection separated by a period of emergence of new lineages. The three largest monophyletic lineage clusters in South Africa, along with the early B.1.106 South African lineage, are labeled.
