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Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data
Pablo Martinez de Salazar; Fred Lu; James A Hay; Diana Gomez-Barroso; Pablo Fernandez-Navarro; Elena Vanessa Martinez; Jenaro Astray-Mochales; Rocio Amillategui; Ana Garcia-Fulgueiras; Maria Dolores Chirlaque; Alonso Sanchez-Migallon; Amparo Larrauri; Maria Jose Sierra; Marc Lipsitch; Fernando Simon; Mauricio Santillana; Miguel Hernan.
Afiliación
  • Pablo Martinez de Salazar; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, United States
  • Fred Lu; Department of Pediatrics, Harvard Medical School, Harvard University, Boston, United States
  • James A Hay; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, United States
  • Diana Gomez-Barroso; Centro Nacional de Epidemiologia, Carlos III Health Institute, Madrid, Spain
  • Pablo Fernandez-Navarro; Centro Nacional de Epidemiologia, Carlos III Health Institute, Madrid, Spain
  • Elena Vanessa Martinez; Centro de Coordinacion de Alertas y Emergencias Sanitarias, Ministry of Health, Madrid, Spain
  • Jenaro Astray-Mochales; Directorate-General for Public Health, Madrid General Health Authority, Spain
  • Rocio Amillategui; Centro Nacional de Epidemiologia, Carlos III Health Institute, Madrid, Spain
  • Ana Garcia-Fulgueiras; Department of Epidemiology, Regional Health Council, IMIB-Arrixaca, Murcia, Spain CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
  • Maria Dolores Chirlaque; Department of Epidemiology, Regional Health Council, IMIB-Arrixaca, Murcia, Spain CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
  • Alonso Sanchez-Migallon; Department of Epidemiology, Regional Health Council, IMIB-Arrixaca, Murcia, Spain CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
  • Amparo Larrauri; Centro Nacional de Epidemiologia, Carlos III Health Institute, Madrid, Spain
  • Maria Jose Sierra; Centro de Coordinacion de Alertas y Emergencias Sanitarias, Ministry of Health, Madrid, Spain
  • Marc Lipsitch; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, United States
  • Fernando Simon; Centro de Coordinacion de Alertas y Emergencias Sanitarias, Ministry of Health, Madrid, Spain
  • Mauricio Santillana; Machine Intelligence Lab, Boston and Computational Health Informatics Program, Boston Childrens Hospital; Department of Pediatrics, Harvard Medical School, Har
  • Miguel Hernan; Department of Epidemiology and Department of Biostatistics, Harvard T.H. Chan School of Public Health; Harvard-MIT Division of Health Sciences and Technology, B
Preprint en En | PREPRINT-MEDRXIV | ID: ppmedrxiv-20230094
ABSTRACT
Designing public health responses to outbreaks requires close monitoring of population-level health indicators in real-time. Thus, an accurate estimation of the epidemic curve is critical. We propose an approach to reconstruct epidemic curves in near real time. We apply this approach to characterize the early SARS-CoV-2 outbreak in two Spanish regions between March and April 2020. We address two data collection problems that affected the reliability of the available real-time epidemiological data, namely, the frequent missing information documenting when a patient first experienced symptoms, and the frequent retrospective revision of historical information (including right censoring). This is done by using a novel back-calculating procedure based on imputing patients dates of symptom onset from reported cases, according to a dynamically-estimated "backward" reporting delay conditional distribution, and adjusting for right censoring using an existing package, NobBS, to estimate in real time (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. At each step, we evaluate how different assumptions affect the recovered epidemiological events and compare the proposed approach to the alternative procedure of merely using curves of case counts, by report day, to characterize the time-evolution of the outbreak. Finally, we assess how these real-time estimates compare with subsequently documented epidemiological information that is considered more reliable and complete that became available later in time. Our approach may help improve accuracy, quantify uncertainty, and evaluate frequently unstated assumptions when recovering the epidemic curves from limited data obtained from public health surveillance systems in other locations.
Licencia
cc_by_nc_nd
Texto completo: 1 Colección: 09-preprints Base de datos: PREPRINT-MEDRXIV Tipo de estudio: Experimental_studies / Observational_studies Idioma: En Año: 2021 Tipo del documento: Preprint
Texto completo: 1 Colección: 09-preprints Base de datos: PREPRINT-MEDRXIV Tipo de estudio: Experimental_studies / Observational_studies Idioma: En Año: 2021 Tipo del documento: Preprint