Time-varying reproduction numbers of COVID-19 in Georgia, USA, March 2-June 14, 2020: comparison of two estimation methods

Objective: In 2020, SARS-CoV-2 impacted Georgia, USA. Georgia announced state-wide shelter-in-place on April 2 (implemented the next day) and announced the partial lifting of restrictions on April 27. Time-varying reproduction number estimates might vary depending on methodology. Methods: Daily incidence of confirmed COVID-19 cases by reporting date, March 2-June 14, 2020, in Georgia, Metro Atlanta, and Dougherty County were analyzed. We estimated and compared the COVID-19 time-varying reproduction number, Rt, by R package EpiEstim (with a window of 1 and 2 weeks) and the renewal equation tied to the generalized growth model (GGM). Results: The EpiEstim Rt estimates are more sensitive to fluctuation in incident cases than the GGM estimates. The median EpiEstim Rt estimate (1-week window) in Georgia dropped from between 2 and 4 in mid-March, to <2 in late March and early April. The median Rt dropped <1 for the first time on April 15. Rt fluctuates around 1 from mid-April to June 14. The Rt estimate by GGM dropped below 2 on March 7 and stabilized to the range of 1 to 1.1 by March 31. Conclusions: GGM estimated Rt as an overall trend over a 3-month period, while EpiEstim is sensitive to daily variation in incidence.