Fig. 1: Correlations between temporal distribution of Ct values and transmission dynamics of COVID-19 in Hong Kong.

a Local COVID-19 cases and the estimated incidence-based \({R}_{t}\). Gray bars indicate the number of laboratory-confirmed local cases by date of reporting. Black lines and shaded areas indicate the mean and 95% credible intervals (CrIs) for incidence-based \({R}_{t}\). b Ct distributions smoothed from a generalized additive model (GAM). Dark gray bars indicate the number of sample collections. Orange lines and shaded areas indicate the daily average and 95% confidence intervals (CIs) of Ct values that were estimated from a GAM (Eq. (2)) over the study period in Hong Kong. c Daily skewness of Ct values over the study period. Blue dots represent the mean of daily Ct skewness and vertical lines represent 95% CIs of daily Ct skewness that were calculated from 500 bootstraps. d, e Correlations between the daily incidence-based \({R}_{t}\) and the daily mean Ct (d) or skewness (e). Boxes represent the interquartile range (IQR; defined as differences between 25th and 75th percentiles, same for Fig. 2) and median of the incidence-based \({R}_{t}\), lower whiskers represent the minimum and upper whiskers represent either the maximum or the largest values that are within the distance of 1.5 times the IQR of all incidence-based \({R}_{t}\,\) under various Ct distribution intervals, dots represent values beyond the lower and upper whiskers (\(n=59\) and 146 daily Ct mean for wave 3 and 4 in panel (d), and \(n=57\) and 138 daily Ct skewness for wave 3 and 4 in panel (e), respectively).