Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study

Randhawa, Gurjit S.; Soltysiak, Maximillian P. M.; El Roz, Hadi; de Souza, Camila P. E.; Hill, Kathleen A.; Kari, Lila

doi:10.1371/journal.pone.0232391

Cited by 1,023Fractal and DNA sequence analysisGenomics and Phylogenetic StudiesMachine Learning in Bioinformatics

Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study

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Randhawa, Gurjit S., Soltysiak, Maximillian P. M., El Roz, Hadi, de Souza, Camila P. E., Hill, Kathleen A., Kari, Lila·2020·PLOS ONE

DOI 10.1371/journal.pone.0232391PMC PMC7182198

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Abstract

The 2019 novel coronavirus (renamed SARS-CoV-2, and generally referred to as the COVID-19 virus) has spread to 184 countries with over 1.5 million confirmed cases. Such major viral outbreaks demand early elucidation of taxonomic classification and origin of the virus genomic sequence, for strategic planning, containment, and treatment. This paper identifies an intrinsic COVID-19 virus genomic signature and uses it together with a machine learning-based alignment-free approach for an ultra-fast, scalable, and highly accurate classification of whole COVID-19 virus genomes. The proposed method combines supervised machine learning with digital signal processing (MLDSP) for genome analyses, augmented by a decision tree approach to the machine learning component, and a Spearman's rank correlation coefficient analysis for result validation. These tools are used to analyze a large dataset of over 5000 unique viral genomic sequences, totalling 61.8 million bp, including the 29 COVID-19 virus sequences available on January 27, 2020. Our results support a hypothesis of a bat origin and classify the COVID-19 virus as Sarbecovirus, within Betacoronavirus. Our method achieves 100% accurate classification of the COVID-19 virus sequences, and discovers the most relevant relationships among over 5000 viral genomes within a few minutes, ab initio, using raw DNA sequence data alone, and without any specialized biological knowledge, training, gene or genome annotations. This suggests that, for novel viral and pathogen genome sequences, this alignment-free whole-genome machine-learning approach can provide a reliable real-time option for taxonomic classification.

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Authors: Randhawa, G. S., Soltysiak, M. P. M., El Roz, H., de Souza, C. P. E., Hill, K. A., & Kari, L.
Affiliations: Western University (CA)
Corresponding author: Randhawa, Gurjit S.
ORCID: Randhawa, Gurjit S.
Soltysiak, Maximillian P. M.
El Roz, Hadi
Hill, Kathleen A.
Venue: PLOS ONE
Publisher: Public Library of Science (PLoS)
Published: 2020-04-24
Volume: 15
Issue: 4
Pages: e0232391
ISSN: 1932-6203 (ISSN-L)
DOI: 10.1371/journal.pone.0232391
PMC: PMC7182198
OpenAlex: W3019119825
Cited by: 1,023
References: 99
Citations by year: 2026: 47 · 2025: 105 · 2024: 103 · 2023: 151 · 2022: 221 · 2021: 266 · 2020: 130
FWCI: 62.23
Type: journal article
Language: en
Update notices: correction (2021-01-27)
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
Locations: PLoS ONE (publishedVersion, cc-by)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Informationszentrum Lebenswissenschaften (ZB MED) (submittedVersion, cc-by)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Figshare (submittedVersion, cc-by)
Funders: Natural Sciences and Engineering Research Council of Canada (R2824A01, R3511A12)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
Keywords: SARS-CoV-2, COVID-19 pandemic, viral genome classification, alignment-free classification, genomic signatures, decision tree, virus taxonomy, Sarbecovirus, Betacoronavirus
MeSH terms: Machine Learning, Betacoronavirus, COVID-19, SARS-CoV-2, Humans, Pneumonia, Viral, Genome, Viral, Coronavirus Infections, Genomics, Pandemics

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Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study

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