Calculating confidence intervals of the cell-culture-positivity curve (in Fig 3C)

Similar as the procedures performed for predicting the confidence intervals of viral genome load trajectories, we randomly sampled 5000 sets of parameter combinations from the distribution specified by the best-fit population parameters of the best model, i.e. the saturation model assuming Km only has a fixed effect (Table S8). More specifically, we sampled parameters from a log-normal distribution for J and h, with their means and standard deviations at the best-fit values. Using the parameter combinations, we generated curves of probability of cell-culture positivity at CN values ranging between 10 and 40. The median and the 5^th and 95^th quantile of viral genome loads at each CN values are reported.