Machine learning-based analysis of genomes suggests associations between Wuhan 2019-nCoV and bat Betacoronaviruses
Gurjit S Randhawa, Maximillian P.M. Soltysiak, Hadi El Roz, Camila P.E. de Souza, Kathleen A. Hill, Lila Kari
doi: https://doi.org/10.1101/2020.02.03.932350
Abstract
As of February 3, 2020, the 2019 Novel Coronavirus (2019-nCoV) spread to 27 countries with 362 deaths and more than 17000 confirmed cases. 2019-nCoV is being compared to the infamous SARS coronavirus outbreak. Between November 2002 and July 2003, SARS resulted in 8098 confirmed cases worldwide with a 9.6% death rate and 774 deaths. Mainland China alone suffered 349 deaths and 5327 confirmed cases. Though 2019-nCoV has a death rate of 2.2% as of 3 February, the 174895 confirmed cases in a few weeks (December 8, 2019 to February 3, 2020) are alarming. Cases are likely under-reported given the comparatively longer incubation period. Such outbreaks demand rapid elucidation and analysis of the virus genomic sequence for timely treatment plans. We classify the 2019-nCoV using MLDSP and MLDSP-GUI, alignment-free methods that use Machine Learning (ML) and Digital Signal Processing (DSP) for genome analyses. Genomic sequences were mapped into their respective genomic signals (discrete numeric series) using a two-dimensional numerical representation (Chaos Game Representation). The magnitude spectra were computed by applying Discrete Fourier Transform on the genomic signals. The Pearson Correlation Coefficient was used to calculate a pairwise distance matrix. The feature vectors were constructed from the distance matrix and used as an input to the supervised machine learning algorithms. 10-fold cross-validation was applied to compute the average classification accuracy scores. The trained classifier models were used to predict the labels of 29 2019-nCoV sequences. The classification strategy used over 5000 genomes and tested associations at taxonomic levels of realm to species. From our machine learning-based alignment-free analyses using MLDSP-GUI, we corroborate the current hypothesis of a bat origin and classify 2019-nCoV as Sarbecovirus, within Betacoronavirus.
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