An improved method to estimate the effective reproduction number of the COVID-19 pandemic: lessons from its application in Greece

Lytras, T.; Sypsa, V.; Panagiotakos, D.; Tsiodras, S.

Introduction: Monitoring the time-varying effective reproduction number Rt is crucial for assessing the evolution of the COVID-19 pandemic. We present an improved method to estimate Rt and its application to routine surveillance data from Greece. Methods: Our method extends that of Cori et al (2013), adding Bayesian imputation of missing symptom onset dates, imputation of infection times using an external estimate of the incubation period, and an adjustment for reporting delay. To facilitate its use, we provide an R software package named "bayEStim". We applied the method to COVID-19 surveillance data from Greece, and examined the resulting Rt estimates in relation to control measures applied, in order to assess their effectiveness. We also associated Rt, as a measure of transmissibility, to population mobility as recorded in Google data and to ambient temperature. We used a serial interval between 4 and 7.5 days, and a median incubation period of 5.1 days. Results: In Greece Rt fell rapidly as the first control measures were introduced, dropping below 1 at least a week before a full lockdown came into effect. In mid-July Rt started increasing again, as increased mobility associated with tourism activity was observed. Each 10% of increase in relative mobility increased Rt by 8.1% (95% CrI 6.1-10.2%), whereas each unit celsius of temperature increase decreased Rt by 4.6% (95% CrI 5.4-13.7%). Conclusions: Mobility patterns significantly affect Rt. Most of the reduction in COVID-19 transmissibility in Greece occurred already before the lockdown, likely as a result of decreased population mobility. Lower viral transmissibility in summer does not appear sufficient to counterbalance the increased mobility due to tourism. Monitoring Rt is an essential component of COVID-19 surveillance, and it is crucial for correctly assessing the effect of control measures.