We have studied coupling between the neutral atmosphere and the ionospheric E region in the midlatitude by combining two numerical simulation models. Atmospheric gravity waves generated in the troposphere propagate through the stratosphere and the mesosphere and can reach the lower thermosphere. When a zonal wind shear that can accumulate a sporadic-E (Es) layer (eastward below and westward above) is applied, the accumulated Es layer is strongly modulated by the gravity waves, and polarization electric field due to the modulated Es layer produces wave-like patterns of plasma density in the upper E region. Since the eastward wind below the shear node filters out gravity waves with eastward phase velocity, those with westward phase velocity are dominant where the Es layer is accumulated. Because of the angle between phase front of gravity waves and the geomagnetic field line, gravity waves with southward phase velocity is more effective to generate polarization electric field than those with northward phase velocity. Since gravity waves with southwestward phase velocity have phase fronts aligned from northwest to southeast, polarization electric field also has the similar structure. This mechanism can explain the spatial structure of quasi-periodic (QP) echoes associated with plasma irregularities in the midlatitude E region which often shows northwest-southeast alignment.