A new estimation method for COVID-19 time-varying reproduction number using active cases [article]

Agus Hasan, Hadi Susanto, Venansius Tjahjono, Rudy Kusdiantara, Endah Putri, Panji Hadisoemarto, Nuning Nuraini
2020 medRxiv   pre-print
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 term
more » ... ns of the reported cases, is used with case uncertainties that are assumed to follow a Gaussian distribution. Our method does not require information regarding serial intervals, which makes the estimation procedure simpler without reducing the quality of the estimate. We show that the proposed method is comparable to common approaches, e.g., age-structured and new cases based sequential Bayesian models. We also apply it to COVID-19 cases in the Scandinavian countries: Denmark, Sweden, and Norway, where we see a delay of about four days in predicting the epidemic peak.
doi:10.1101/2020.06.28.20142158 fatcat:3tuhfskmhrhvfbbuebwew5734u