PMID- 36061090 OWN - NLM STAT- PubMed-not-MEDLINE VI - 419 TI - Analysis of COVID-19 in Japan with extended SEIR model and ensemble Kalman filter. PG - 114772 CI - © 2022 Elsevier B.V. All rights reserved. LA - eng PT - Journal Article PL - Belgium TA - J Comput Appl Math JT - Journal of computational and applied mathematics JID - 101538565 IS - 0377-0427 (Print) LID - 10.1016/j.cam.2022.114772 [doi] FAU - Sun, Q AU - Sun Q AD - Data Assimilation Research Team, RIKEN Center for Computational Science (R-CCS), Kobe 650-0047, Japan. AD - Graduate School of Mathematics, Nagoya University, Nagoya 464-8602, Japan. FAU - Miyoshi, T AU - Miyoshi T AD - Data Assimilation Research Team, RIKEN Center for Computational Science (R-CCS), Kobe 650-0047, Japan. AD - Prediction Science Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe 650-0047, Japan. AD - RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS), Wako 351-0198, Japan. FAU - Richard, S AU - Richard S AD - Data Assimilation Research Team, RIKEN Center for Computational Science (R-CCS), Kobe 650-0047, Japan. AD - Graduate School of Mathematics, Nagoya University, Nagoya 464-8602, Japan. IS - 0377-0427 (Linking) OTO - NOTNLM OT - 92-08 OT - 92C60 OT - COVID-19 OT - Data assimilation OT - Ensemble Kalman filter OT - Extended SEIR model PMC - PMC9420319 LR - 20230124 DP - 2023 Feb DEP - 20220828 AB - We introduce an extended SEIR infectious disease model with data assimilation for the study of the spread of COVID-19. In this framework, undetected asymptomatic and pre-symptomatic cases are taken into account, and the impact of their uncertain proportion is fully investigated. The standard SEIR model does not consider these populations, while their role in the propagation of the disease is acknowledged. An ensemble Kalman filter is implemented to assimilate reliable observations of three compartments in the model. The system tracks the evolution of the effective reproduction number and estimates the unobservable subpopulations. The analysis is carried out for three main prefectures of Japan and for the entire country of Japan. For these four communities, our estimated effective reproduction numbers are more stable than the corresponding ones estimated by a different method (Toyokeizai). We also perform sensitivity tests for different values of some uncertain medical parameters, like the relative infectivity of symptomatic/asymptomatic cases. The regional analysis results suggest the decreasing efficiency of the states of emergency.