We present the results of studying the state of the neutral upper atmosphere and the ionosphere over the Eastern Siberia region during minor winter sudden stratosphere warming (SSW) in early February, 2016 and final stratospheric warming in early March, 2016. We used the data from spectrometric measurements of OH (~87 km, 834.0 nm, (6-2)) and At O2 (~94 km, 864.5 nm, (0-1)) emissions from the Geophysical Observatory at the Institute of Solar-Terrestrial Physics SB RAS (51.8°N, 103.1°E, Tory). We also used the vertical sounding data on the peak electron density (NmF2), and on the peak height (hmF2). These data were obtained with the DPS-4 Irkutsk ionosonde (52.3°N, 104.3°E). For the analysis, we also involved the MLS Aura satellite data of measuring vertical temperature profiles and the MERRA reanalysis data. We found the MLT and ionospheric signatures for both analyzed SSWs. At MLT heights, a significant increase in the OH and O2 emission intensities, a decrease in the atmosphere temperature, and an increase in wave activity were found. In the F2-region, we revealed significant (up to ~80 %) NmF2 positive disturbances in the postmidnight hours, which are not associated with geomagnetic activity variations. The revealed effects can be caused by the intensification of the activity of atmospheric waves and the enhancement of vertical transport of atmospheric components caused by stratospheric warmings.