Serial interval of SARS-CoV-2 was shortened over time by nonpharmaceutical interventions

Abstract

Studies of novel coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have reported varying estimates of epidemiological parameters, including serial interval distributions-i.e., the time between illness onset in successive cases in a transmission chain-and reproduction numbers. By compiling a line-list database of transmission pairs in mainland China, we show that mean serial intervals of COVID-19 shortened substantially from 7.8 to 2.6 days within a month (9 January to 13 February 2020). This change was driven by enhanced nonpharmaceutical interventions, particularly case isolation. We also show that using real-time estimation of serial intervals allowing for variation over time provides more accurate estimates of reproduction numbers than using conventionally fixed serial interval distributions. These findings could improve our ability to assess transmission dynamics, forecast future incidence, and estimate the impact of control measures.

Fig. 1. Serial intervals of SARS-CoV-2 substantially shortened over time in mainland China.

(A) Empirical serial interval distributions. From top to bottom, transmission pairs were analyzed by selecting infectors who developed symptoms during 9 to 22 January 2020 (prepeak); 23 to 29 January 2020 (peak week); 30 January to 13 February 2020 (postpeak); and 9 January to 13 February 2020 (whole period), respectively. In each panel, vertical dashed lines in red and blue colors indicate the median and interquartile range (IQR), respectively. (B) Estimated serial interval distributions by fitting a normal distribution using MCMC. From top to bottom, each group of bars corresponds to the transmission pairs with infectors who developed symptoms during the prepeak (162 pairs), peak week (339 pairs), postpeak (176 pairs), and whole 36-day period (677 pairs), respectively. Colored dots and bars correspond to the transmission pairs within households (blue), outside households (yellow), with isolation delays shorter than the median isolation delay of each period (green), and with isolation delays longer than the median isolation delay of each period (orange), respectively. Dark gray bars correspond to transmission pairs with no stratification. Dots and bars indicate the estimated median and IQR, respectively.

Fig. 2. Real-time effective serial intervals and instantaneous reproduction number R_t.

(A) Estimated serial interval distribution for each 14-day running time window. Dark gray color indicates fitting data with no stratification, whereas green and orange indicate fitting data with isolation delay shorter and longer, respectively, than the median isolation delay of each running time window. Dots and bars indicate the estimated median and IQR, respectively. (B to D) Daily estimates of R_t by using real-time effective serial interval distributions [as in (A)] versus using a single fixed serial interval distribution. Red curves and light pink shaded regions indicate the median and 95% CrI, respectively, of daily R_t estimated using real-time effective serial interval distributions. Black dashed curves and light gray shaded regions indicate the median and 95% CrI, respectively, of daily R_t estimated using a single serial interval distribution fixed, with a mean of 7.1 and SD of 5.3 days in (B), a mean of 5.2 and SD of 4.7 days in (C), and a mean of 3.0 and SD of 4.1 days in (D).