Cluster Analysis of Coronavirus Sequences using Computational Sequence Descriptors: With Applications to SARS, MERS and SARS-CoV-2 (CoVID-19)

Title:Cluster Analysis of Coronavirus Sequences using Computational Sequence Descriptors: With Applications to SARS, MERS and SARS-CoV-2 (CoVID-19)

Volume: 17 Issue: 7

Author(s): Marjan Vračko, Subhash C. Basak*, Tathagata Dey and Ashesh Nandy

Affiliation:

• Department of Chemistry and Biochemistry, University of Minnesota, Duluth, USA

Keywords: SARS-CoV-2 (CoVID-19), SARS, MERS, mathematical representation of sequences, clustering, Euclidean distance, Mahalanobis distance, principal component analysis, alignment-free sequenc descriptors.

Abstract: Introduction: Coronaviruses comprise a group of enveloped, positive-sense single-stranded RNA viruses that infect humans as well as a wide range of animals. The study was performed on a set of 573 sequences belonging to SARS, MERS and SARS-CoV-2 (CoVID-19) viruses. The sequences were represented with alignment-free sequence descriptors and analyzed with different chemometric methods: Euclidean/Mahalanobis distances, principal component analysis and self-organizing maps (Kohonen networks). We report the cluster structures of the data. The sequences are well-clustered regarding the type of virus; however, some of them show the tendency to belong to more than one virus type.

Background: This is a study of 573 genome sequences belonging to SARS, MERS and SARS-- CoV-2 (CoVID-19) coronaviruses.

Objectives: The aim was to compare the virus sequences, which originate from different places around the world.

Methods: The study used alignment free sequence descriptors for the representation of sequences and chemometric methods for analyzing clusters.

Results: Majority of genome sequences are clustered with respect to the virus type, but some of them are outliers.

Conclusion: We indicate 71 sequences, which tend to belong to more than one cluster.

Cite this article as:

Vračko Marjan , Basak C. Subhash*, Dey Tathagata and Nandy Ashesh , Cluster Analysis of Coronavirus Sequences using Computational Sequence Descriptors: With Applications to SARS, MERS and SARS-CoV-2 (CoVID-19), Current Computer-Aided Drug Design 2021; 17 (7) . https://dx.doi.org/10.2174/1573409917666210202092646