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We apply the Entire Atmosphere GLobal (EAGLE) model to investigate the upper atmosphere response to the January 2009 sudden stratospheric warming (SSW) event. The model successfully reproduces neutral temperature and total electron content (TEC) observations. Using both model and observational data, we identify a cooling in the tropical lower thermosphere caused by the SSW. This cooling affects the zonal electric field close to the equator, leading to an enhanced vertical plasma drift. We demonstrate that along with a SSW-related wind disturbance, which is the main source to form a dynamo electric field in the ionosphere, perturbations of the ionospheric conductivity also make a significant contribution to the formation of the electric field response to SSW. The post-sunset TEC enhancement and pre-sunrise electron content reduction are revealed as a response to the 2009 SSW. We show that at post-sunset hours the SSW affects low-latitude TEC via a disturbance of the meridional electric field. We also show that the phase change of the semidiurnal migrating solar tide (SW2) in the neutral wind caused by the 2009 SSW at the altitude of the dynamo electric field generation has a crucial importance for the SW2 phase change in the zonal electric field. Such changes lead to the appearance of anomalous diurnal variability of the equatorial electromagnetic plasma drift and subsequent low-latitudinal TEC disturbances in agreement with available observations. Plain Language Summary - Entire Atmosphere GLobal model (EAGLE) interactively calculates the troposphere, stratosphere, mesosphere, thermosphere, and plasmasphere-ionosphere system states and their response to various natural and anthropogenic forcing. In this paper, we study the upper atmosphere response to the major sudden stratospheric warming that occurred in January 2009. Our results agree well with the observed evolution of the neutral temperature in the upper atmosphere and with low-latitude ionospheric disturbances