XCNN-SC: Explainable CNN for SARS-CoV-2 variants classification and mutation detection

The COVID-19 pandemic spread rapidly all over the world in 2019, causing the deaths of millions of people. One of the main challenges in controlling the pandemic was the high rate of virus mutation, which evaded the immune system and reduced the vaccine's effectiveness. Due to the differences in symptoms, transmission and mortality rate, and effective prevention strategies of each variant, identifying and classifying different variants is a great necessity. In the present study, 82802 whole genomes of Alpha, Beta, Delta, Eta, Epsilon, Lota, and Omicron variants of SARS-CoV-2 were obtained from the NCBI database. The label encoding method was applied to convert the genomic sequences to numeric sequences. Then, a single-layer 1D-CNN model was used to classify seven variants of SARS-CoV-2 and achieved 99.78% accuracy, 97.98% precision, 97.66% sensitivity, 99.95% specificity, and 98.68% F1-score. The max pool layer feature maps of this network were investigated to discover the sequence discriminative regions in SARS-CoV-2 variants and their effect on biological functional differences. The feature map examination led to the detection of three mutations; one of them was a missense mutation, which has been reported previously. The rest of the detected mutations were silent mutations. In conclusion, the achieved results indicated that CNN models can extract effective features to discriminate several SARS-CoV-2 variants. Also, investigation of CNN feature maps led to an explainable CNN revealing the learned knowledge of the network from the training database. This knowledge helped us to detect mutations and their functional effects in different variants.