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As the Omicron epidemic continues to expand in South Africa and as case counts and sequencing data continues to come in, we can better estimate the current transmission rate of Omicron. 1/19
Here, I am focused on two approaches to estimate this transmission rate. One is growth in frequency of Omicron compared to Delta in Gauteng and the other is growth in case counts attributable to Omicron. 2/19
If one variant is fitter than anther variant and is transmitting faster in the population we should expect to see it increase in frequency following logistic growth. See @TWenseleers for discussion of this approach. 3/19

A simple logistic growth fit to sequence data from specimens collected in Gauteng and shared to @GISAID gives a per day growth rate of 0.25 [95% CI 0.15-0.35]. 4/19
Assuming a generation time for infection-to-infection of 5.1 days, this estimates the relative transmission advantage of Omicron over Delta as exp(growth rate × generation time) = 3.5 [95% CI 2.1-5.9]. 5/19
These estimates are still changing often as genomic data produced by @nhls_sa, @ceri_news and @nicd_sa comes in daily. 6/19

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Good thread from @trvrb