Data mining of coronavirus: SARS-CoV-2, SARS-CoV and MERS-CoV

• Published in: BMC research notes Vol. 14; no. 1; p. 150
• Main Authors: Huh, Jung Eun, Han, Seunghee, Yoon, Taeseon
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 20.04.2021; BioMed Central; BMC
• Subjects: Accuracy; Algorithms; Amino Acid Sequence; Amino acids; Apriori; Base Sequence; BLAST; Codons; Comparative analysis; Coronavirus; Coronaviruses; Data Mining; Decision trees; Disease transmission; Experiments; Genomes; Humans; Identification and classification; Learning algorithms; Machine Learning; MERS-CoV; Methods; Middle East respiratory syndrome; Middle East Respiratory Syndrome Coronavirus - genetics; Peptides; Research Note; SARS Virus - genetics; SARS-CoV; SARS-CoV-2; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; Viruses; United Kingdom; South Korea; SARS-CoV-2; Coronavirus; Decision Tree; SARS-CoV; MERS-CoV; Apriori; SVM; BLAST
• ISSN: 1756-0500; 1756-0500
• DOI: 10.1186/s13104-021-05561-4

In this study we compare the amino acid and codon sequence of SARS-CoV-2, SARS-CoV and MERS-CoV using different statistics programs to understand their characteristics. Specifically, we are interested in how differences in the amino acid and codon sequence can lead to different incubation periods and outbreak periods. Our initial question was to compare SARS-CoV-2 to different viruses in the coronavirus family using BLAST program of NCBI and machine learning algorithms. The result of experiments using BLAST, Apriori and Decision Tree has shown that SARS-CoV-2 had high similarity with SARS-CoV while having comparably low similarity with MERS-CoV. We decided to compare the codons of SARS-CoV-2 and MERS-CoV to see the difference. Though the viruses are very alike according to BLAST and Apriori experiments, SVM proved that they can be effectively classified using non-linear kernels. Decision Tree experiment proved several remarkable properties of SARS-CoV-2 amino acid sequence that cannot be found in MERS-CoV amino acid sequence. The consequential purpose of this paper is to minimize the damage on humanity from SARS-CoV-2. Hence, further studies can be focused on the comparison of SARS-CoV-2 virus with other viruses that also can be transmitted during latent periods.