We present an SIRD epidemic modelling for COVID-19 outbreak in the ASEAN member countries. The occurrence of a second wave in the region adds complexity to the parameter estimation of the SIRD model. In this case, a standard genetic algorithm cannot fully capture the dynamic transmission of the pandemic. We therefore introduce a genetic partial fitting algorithm (GPFA) of seven-day intervals. We show that our method outperforms the standard algorithm with a significant reduction in the Root Mean Square Error (RMSE) value. We also extend our study to produce a real-time estimation of the effective reproduction number with a confidence interval to incorporate uncertainties in the model.