Fig. 2: Schematic of multi-level disease transmission.

A schematic of the multi-level population dynamics model is depicted. Virus transmission occurs from an infected individual to susceptible individuals depending on the infected individual’s infectivity, which depends on their viral load. At each time step (i.e., day), the focal infected individual has contact with multiple susceptible individuals. Here the contact numbers are assumed to follow a negative binomial distribution, which does not depend on the viral load. The shape parameters k and θ for this binomial distribution are presented in Table S3. The sum of newly infected individuals (i.e., [\(c\left(t\right)\): number of contacted individuals per day (everybody is susceptible)] × [\(\rho \left(t\right)\): transmission probability per contacted individual]) during the infectious period is calculated as \({R}_{{TP}}\), called the “transmission potential”. Note that the focal infectious individuals are assigned one of two properties: symptomatic or asymptomatic. Whether being symptomatic or asymptomatic is randomly assigned by a constant probability f or 1-f, respectively. It is assumed that the transmission chains from the focal symptomatic infectious individuals are perfectly inhibited by isolation after symptom onset, \({T}^{*} < t\). Otherwise, \({R}_{{TP}}\) is calculated using the whole duration of viral shedding of the focal asymptomatic infectious individual. Thus, \({R}_{{TP}}\) for the symptomatic and asymptomatic individuals are different here.