Comprehensive modeling of COVID-19 effective reproduction number using GPS data in Tokyo metropolitan area

Abstract

COVID-19 has been raging around the world from the beginning of 2020 to as of January 2023, and it is socially important to build a model to predict and explain its expansion. In this study, we first estimate the number of social contacts within a city for each type of social contact using large-scale GPS data and fit the effective reproduction number to calculate the basic one-to-one effective infection rate. Based on this, mathematical modeling is performed to comprehensively incorporate the effects of delta and omicron variants, vaccination effect and its decay, and herd immunity. The fitting results using real data show that all parameters are consistent with clinical data and other sources and quantitatively clarify the components of the effective reproduction number of COVID-19.