Advancements in deep learning and availability of medical imaging data have led to the use of CNN-based architectures in disease diagnostic assisted systems. In spite of the abundant use of reverse transcription-polymerase chain reaction-based tests in COVID-19 diagnosis, CT images offer an applicable supplement with their high sensitivity rates. Here, we study the classification of COVID-19 pneumonia and non-COVID-19 pneumonia in chest CT scans using efficient deep learning methods to be readily implemented by any hospital. We report our deep network framework design that encompasses Convolutional Neural Networks and bidirectional Long Short Term Memory architectures. Our study achieved high specificity (COVID-19 pneumonia: 98.3%, non-COVID-19 pneumonia: 96.2% Healthy: 89.3%) and high sensitivity (COVID-19 pneumonia: 84.0%, non-COVID-19 pneumonia: 93.9% Healthy: 94.9%) in classifying COVID-19 pneumonia, non-COVID-19 pneumonia and healthy patients. Next, we provide visual explanations for the Convolutional Neural Network predictions with gradient-weighted class activation mapping (Grad-CAM). The results provided a model explainability by showing that Ground Glass Opacities, indicators of COVID-19 pneumonia disease, were captured by our convolutional neural network. Finally, we have implemented our approach in three hospitals proving its compatibility and efficiency.