Fig. 1: Quantification of evolving SARS-CoV-2 infection dynamics.

Viral load data from upper respiratory specimens (i.e., nose and pharynx) of 86 patients infected with the pre-Alpha (non-VOI/VOCs) variant, 59 Alpha variant patients, and 80 Delta variant patients were used for parameter estimation of the viral dynamics model. a The inferred viral dynamics for pre-Alpha (black), Alpha (blue), and Delta (red) variants are plotted. The solid curves correspond to the solution of Eqs. (4, 5) using the best-fit population parameters, and the error bands represented as shadow regions indicate the 95% interquantile range of the inferred viral load interval for all individuals at each time point. The distribution of the peak viral load, peak time, and duration of viral shedding for each patient are also shown in b, c, and d, respectively. Solid bars are their mean values. e The relation between the duration of viral shedding and the cumulative log-transformed viral load is shown. The gray curve is the best-fitting curve for Eq. (7). The distributions illustrated alongside the top and right parts are for the cumulative viral load and the duration of viral shedding, respectively, and the bars are their mean values. f The time-dependent transmission probability of each variant is calculated. In all panels, pre-Alpha, Alpha, and Delta variants are colored in black, blue, and red, respectively.