Accurate Identification of SARS-CoV-2 from Viral Genome Sequences using Deep Learning

Abstract

One of the reasons for the fast spread of SARS-CoV-2 is the lack of accuracy in detection tools in the clinical field. Molecular techniques, such as quantitative real-time RT-PCR and nucleic acid sequencing methods, are widely used to identify pathogens. For this particular virus, however, they have an overall unsatisfying detection rate, due to its relatively recent emergence and still not completely understood features. In addition, SARS-CoV-2 is remarkably similar to other Coronaviruses, and it can present with other respiratory infections, making identification even harder. To tackle this issue, we propose an assisted detection test, combining molecular testing with deep learning. The proposed approach employs a state-of-the-art deep convolutional neural network, able to automatically create features starting from the genome sequence of the virus. Experiments on data from the Novel Coronavirus Resource (2019nCoVR) show that the proposed approach is able to correctly classify SARS-CoV-2, distinguishing it from other coronavirus strains, such as MERS-CoV, HCoV-NL63, HCoV-OC43, HCoV-229E, HCoV-HKU1, and SARS-CoV regardless of missing information and errors in sequencing (noise). From a dataset of 553 complete genome non-repeated sequences that vary from 1,260 to 31,029 bps in length, the proposed approach classifies the different coronaviruses with an average accuracy of 98.75% in a 10-fold cross-validation, identifying SARS-CoV-2 with an AUC of 98%, specificity of 0.9939 and sensitivity of 1.00 in a binary classification. Then, using the same basis, we classify SARS-CoV-2 from 384 complete viral genome sequences with human host, that contain the gene ORF1ab from the NCBI with a 10-fold accuracy of 98.17%, a specificity of 0.9797 and sensitivity of 1.00. These preliminary results seem encouraging enough to identify deep learning as a promising research venue to develop assisted detection tests for SARS-CoV-2. At this end the interaction between viromics and deep learning, will hopefully help to solve global infection problems. In addition, we offer our code and processed data to be used for diagnostic purposes by medical doctors, virologists and scientists involved in solving the SARS-CoV-2 pandemic. As more data become available we will update our system.