Inferring diagnostic serial intervals to understand COVID-19 transmission dynamics in Hong Kong and Mainland China

Estimating the instantaneous reproduction numbers (Rt) requires inferring generation time (Rt>, the interval between successive infections in the transmission chain), often approximated by the serial interval (SI, the interval between successive onsets in the transmission chain). The serial interval based on clinical outcomes is subject to recall biases, and such clinical information is not always available. As a comparable metric, we defined the diagnostic serial interval (SId, the time between diagnostic reporting of case pairs in a transmission chain) and compared it with the traditional SI.

We analyzed confirmed COVID-19 cases from three ancestral waves in Hong Kong and the first wave in mainland China. Using Bayesian methods, we inferred the distributions of effective SI and SId, along with onset-to-reporting delays, and compared the resulting Rt estimates.

The distributions of SI and SId were comparable across waves, with shorter means observed in SId. Reporting delays for infectors were longer than those for infectees, which was identified as a key factor influencing the temporal variation in SI and SId. Additionally, factors such as public health and social measures (PHSMs), case profile, and demographics were found to significantly impact the estimates. Time-varying estimates of the reproduction number derived from both SI and SId were highly consistent, with median absolute differences ranging from 0.12 to 0.19.

The diagnostic serial interval shows potentials as a comparable metric to the traditional serial interval for estimating transmissibility in assessing COVID-19 transmission dynamics, and this approach could be extended for other respiratory viruses.