Fig. 2: Viral kinetics model fits, simulated infection dynamics and population-wide viral load kinetics.

(A) Schematic of the viral kinetics and infection model. Individuals begin susceptible with no viral load (susceptible), acquire the virus from another infectious individual to become exposed but not yet infectious (exposed), experience an increase in viral load to become infectious and possibly develop symptoms (infected), and finally either recover following viral waning or die (removed). This process is simulated for many individuals. (B) Model fits to time-varying viral loads in swab samples. The black dots show observed log10 RNA copies per swab; black bars show positive but unquantified swab samples; solid lines show posterior median estimates; dark shaded regions show 95% credible intervals (CI) on model-predicted latent viral loads; light shaded regions show 95% CI on simulated viral loads with added observation noise. The blue region shows viral loads before symptom onset and red region shows time after symptom onset. The horizontal dashed line shows the limit of detection. (C, E) 25 and 500 simulated viral loads over time, respectively. The heatmap shows the viral load in each individual over time. The distribution of viral loads reflects the increase and subsequent decline of prevalence. We simulated from inferred distributions for the viral load parameters, thereby propagating substantial individual-level variability through the simulations. Marginal distributions of observed viral loads during the different epidemic phases are shown in fig. S4. (D) Simulated infection incidence and prevalence of virologically positive individuals from the SEIR model. Incidence was defined as the number of new infections per day divided by the population size. Prevalence was defined as the number of individuals with viral load > 100 (log10 viral load > 2) in the population divided by the population size on a given day.