Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates

• Published in: PLoS computational biology Vol. 20; no. 4; p. e1012021
• Main Authors: Lison, Adrian, Abbott, Sam, Huisman, Jana, Stadler, Tanja
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.04.2024; Public Library of Science (PLoS)
• Subjects: Basic Reproduction Number - statistics & numerical data; Bayes Theorem; Bayesian analysis; Bias; Communicable diseases; Computational Biology - methods; Computer Simulation; COVID-19; COVID-19 - epidemiology; COVID-19 - transmission; Disease Outbreaks - statistics & numerical data; Disease transmission; Epidemics; Estimation; Humans; Infections; Infectious diseases; Modelling; Outbreaks; Pandemics; Public health; Qualitative analysis; Real time; Regularization; Reproduction; SARS-CoV-2; Uncertainty; United States; Switzerland

The time-varying effective reproduction number R t is a widely used indicator of transmission dynamics during infectious disease outbreaks. Timely estimates of R t can be obtained from reported cases counted by their date of symptom onset, which is generally closer to the time of infection than the...