We first utilised the SI established from the aforementioned field investigations of the initial 100 cases in estimating R t , as described in method 2. When performing the analysis using the SI distribution observed for laboratory-confirmed pH1N1 secondary cases only (mean 2.3 days, SD 61.3, range 1-5) [22] , we found an initialR R t of 1.43 (95% CI: 1.38-1.49) ( Figure 3A) . When performing the analysis using the SI distribution observed for both confirmed and suspected secondary cases (mean 2.7 days, SD 61.5, range 1-6) [22] , we found an initialR R t of 1.49 (95% CI: 1.44-1.55) ( Figure 3B ). Figure 4 shows the variation inR R t with the progression of the outbreak over time. We observed relatively highR R t values following the introduction of pH1N1 virus into South Africa, corresponding to high rates of transmission and exponential growth of the local epidemic during this period.R R t peaked on the first day of the epidemic growth period (June 21) at 2.91 (95% CI: 0.85-3.99).R R t began to drop from July 27 onward and remained consistently below one after August 22. This corresponds with the decline in the daily incidence of new cases detected. Averaging the R t values obtained during the epidemic growth period (June 21 to August 3, 2009), we estimate initial R t to be 1.42 (95% CI: 1.20-1.71). 