Estimating the measles effective reproduction number in Australia from routine notification data
May Chiew, Heather F Gidding, Aditi Dey, James Wood, Nicolee Martin, Stephanie Davis & Peter McIntyre
To estimate the measles effective reproduction number (R) in Australia by modelling routinely collected notification data.
R was estimated for 2009–2011 by means of three methods, using data from Australia’s National Notifiable Disease Surveillance System. Method 1 estimated R as 1 − P, where P equals the proportion of cases that were imported, as determined from data on place of acquisition. The other methods estimated R by fitting a subcritical branching process that modelled the spread of an infection with a given R to the observed distributions of outbreak sizes (method 2) and generations of spread (method 3). Stata version 12 was used for method 2 and Matlab version R2012 was used for method 3. For all methods, calculation of 95% confidence intervals (CIs) was performed using a normal approximation based on estimated standard errors.
During 2009–2011, 367 notifiable measles cases occurred in Australia (mean annual rate: 5.5 cases per million population). Data were 100% complete for importation status but 77% complete for outbreak reference number. R was estimated as < 1 for all years and data types, with values of 0.65 (95% CI: 0.60–0.70) obtained by method 1, 0.64 (95% CI: 0.56–0.72) by method 2 and 0.47 (95% CI: 0.38–0.57) by method 3.
The fact that consistent estimates of R were obtained from all three methods enhances confidence in the validity of these methods for determining R.