Estimating the generation interval and inferring the latent period of COVID-19 from the contact tracing data

• Published in: Epidemics Vol. 36; p. 100482
• Main Authors: Zhao, Shi, Tang, Biao, Musa, Salihu S, Ma, Shujuan, Zhang, Jiayue, Zeng, Minyan, Yun, Qingping, Guo, Wei, Zheng, Yixiang, Yang, Zuyao, Peng, Zhihang, Chong, Marc KC, Javanbakht, Mohammad, He, Daihai, Wang, Maggie H.
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.09.2021; The Authors. Published by Elsevier B.V; Elsevier
• Subjects: Contact tracing; COVID-19; Generation interval; Incubation period; Infectious Disease; Internal Medicine; Latent period; Serial interval; Statistical inference; COVID-19; Incubation period; Generation interval; Contact tracing; Serial interval; Statistical inference; Latent period; contact tracing; incubation period; generation interval; serial interval; statistical inference; latent period
• ISSN: 1755-4365; 1878-0067; 1878-0067
• DOI: 10.1016/j.epidem.2021.100482

•We estimate the generation interval and incubation period simultaneously by using the contact tracing data of COVID-19 cases.•We infer the pre-symptomatic transmission proportion and latent period thereafter.•We estimate mean incubation period at 6.8 days (95 %CI: 6.2, 7.5), and mean generation interval at 6.7 days (95 %CI: 5.4, 7.6).•We estimated that 49.8 % (95 %CI: 33.3, 71.5) of the secondary cases are likely due to pre-symptomatic transmission.•Using the best estimates of model parameters, we further infer the mean latent period at 3.3 days (95 %CI: 0.2, 7.9). The coronavirus disease 2019 (COVID-19) emerged by end of 2019, and became a serious public health threat globally in less than half a year. The generation interval and latent period, though both are of importance in understanding the features of COVID-19 transmission, are difficult to observe, and thus they can rarely be learnt from surveillance data empirically. In this study, we develop a likelihood framework to estimate the generation interval and incubation period simultaneously by using the contact tracing data of COVID-19 cases, and infer the pre-symptomatic transmission proportion and latent period thereafter. We estimate the mean of incubation period at 6.8 days (95 %CI: 6.2, 7.5) and SD at 4.1 days (95 %CI: 3.7, 4.8), and the mean of generation interval at 6.7 days (95 %CI: 5.4, 7.6) and SD at 1.8 days (95 %CI: 0.3, 3.8). The basic reproduction number is estimated ranging from 1.9 to 3.6, and there are 49.8 % (95 %CI: 33.3, 71.5) of the secondary COVID-19 infections likely due to pre-symptomatic transmission. Using the best estimates of model parameters, we further infer the mean latent period at 3.3 days (95 %CI: 0.2, 7.9). Our findings highlight the importance of both isolation for symptomatic cases, and for the pre-symptomatic and asymptomatic cases.