Superspreading is an important feature of COVID-19 transmission dynamics, but few studies have investigated this feature stratified by transmission setting. Using detailed clustering data comprising 8647 COVID-19 cases confirmed in Hong Kong between 2020 and 2021, we estimated the mean number of new infections expected in a transmission cluster ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub><mml:mrow><mml:mi>C</mml:mi></mml:mrow> <mml:mrow><mml:mi>Z</mml:mi></mml:mrow> </mml:msub> </mml:math…

Abstract The serial interval (SI) distribution of an epidemic is used to approximate the generation time distribution, an essential parameter for inferring the transmissibility (${R}_t$) of an infectious disease. However, SI distributions may change as an epidemic progresses. We examined detailed contact tracing data on laboratory-confirmed cases of COVID-19 in Hong Kong, China, during the 5 COVID-19 waves from January 2020 to July 2022. We reconstructed the transmission pairs and estimated time-varying effective …

Abstract Phylodynamics is central to understanding infectious disease dynamics through the integration of genomic and epidemiological data. Despite advancements, including the application of deep learning to overcome computational limitations, significant challenges persist due to data inadequacies and statistical unidentifiability of key parameters. These issues are particularly pronounced in poorly resolved phylogenies, commonly observed in outbreaks such as SARS-CoV-2. In this study, we conducted a thorough eva…

Testing inbound travellers at arrival and during quarantine can detect imported cases early, but may not prevent all COVID-19 introductions into the community. Public health measures should be adapted in response to the emergence of SARS-CoV-2 variants based on evidence from ongoing surveillance.

Abstract Deep learning has emerged as a powerful tool for phylodynamic analysis, addressing common computational limitations affecting existing methods. However, notable disparities exist between simulated phylogenetic trees used for training existing deep learning models and those derived from real-world sequence data, necessitating a thorough examination of their practicality. We conducted a comprehensive evaluation of model performance by assessing an existing deep learning inference tool for phylodynamics, Phy…