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We propose a new method to estimate the time-varying effective (or instantaneous) reproduction number of the novel coronavirus disease (COVID-19). The method is based on a discrete-time stochastic augmented compartmental model that describes the virus transmission. A two-stage estimation method, which combines the Extended Kalman Filter (EKF) to estimate reported state variables (active and removed cases) and a low pass filter based on a rational transfer function to remove short termdoi:10.1101/2020.06.28.20142158 fatcat:3tuhfskmhrhvfbbuebwew5734u