Derivation of the effective reproduction number R for COVID-19 in relation to mobility restrictions and confinement

Alex Arenas; Wesley Cota; Jesus Gomez-Gardenes; Sergio Gomez; Clara Granell; Joan T. Matamalas; David Soriano-Panos; Benjamin Steinegger

The rationale of the model is the following. Susceptible individuals get infected by contacts with asymptomatic and infected agents, with a probability Πg i , becoming exposed. Exposed individuals turn into asymptomatic at a certain rate η g , which in turn become infected at a rate α g . Once infected, two paths emerge, which are reached at an escape rate µ g . The first option is requiring hospitalization in an ICU, with a certain probability γ g ; otherwise, the individuals become recovered. While being at ICU, individuals have a death probability ω g , which is reached at a rate ψ g . Finally, ICUs discharge at a rate χ g , leading to the recovered compartment. See in Supplementary Figure 1 a sketch of the compartmental epidemic model with all the transitions, and Supplementary Table 1 for a list of the parameters and their values to simulate the spreading of COVID-19 in Spain, which will be discussed in Supplementary Note 6.