Abstract
When responding to infectious disease outbreaks, rapid and accurate estimation of the epidemic trajectory is critical. However, two common data collection problems affect the reliability of the epidemiological data in real time: missing information on the time of first symptoms, and retrospective revision of historical information, including right censoring. Here, we propose an approach to construct epidemic curves in near real time that addresses these two challenges by 1) imputation of dates of symptom onset for reported cases using a dynamically-estimated “backward” reporting delay conditional distribution, and 2) adjustment for right censoring using the NobBS software package to nowcast cases by date of symptom onset. This process allows us to obtain an approximation of the time-varying reproduction number (Rt) in real time. We apply this approach to characterize the early SARS-CoV-2 outbreak in two Spanish regions between March and April 2020. We evaluate how these real-time estimates compare with more complete epidemiological data that became available later. We explore the impact of the different assumptions on the estimates, and compare our estimates with those obtained from commonly used surveillance approaches. Our framework can help improve accuracy, quantify uncertainty, and evaluate frequently unstated assumptions when recovering the epidemic curves from limited data obtained from public health systems in other locations.
Funder
Fundación Ramón Areces
National Institute of General Medical Sciences
NIH Office of the Director
Morris-Singer
centers for disease control and prevention
Publisher
Public Library of Science (PLoS)
Subject
Computational Theory and Mathematics,Cellular and Molecular Neuroscience,Genetics,Molecular Biology,Ecology,Modeling and Simulation,Ecology, Evolution, Behavior and Systematics
Reference29 articles.
1. Enhancing Situational Awareness to Prevent Infectious Disease Outbreaks from Becoming Catastrophic;M Lipsitch;Curr Top Microbiol Immunol,2019
2. Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV-2);R Li;Science,2020
3. Epidemiology of measles in Taiwan: dynamics of transmission and timeliness of reporting during an epidemic in 1988–9;MS Lee;Epidemiology and Infection,1995
4. Quantifying Reporting Timeliness to Improve Outbreak Control;AB Marinović;Emerging Infectious Diseases,2015
5. Adjustments for reporting delays and the prediction of occurred but not reported events;JF Lawless;Canadian Journal of Statistics,1994
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