Comparative genomic signature representations of the emerging COVID-19 coronavirus and other coronaviruses: High identity and possible recombination between Bat and Pangolin coronaviruses

Rabeb Touati; Sondes Haddad-Boubaker; Imen Ferchichi; Imen Messaoudi; Afef Elloumi Ouesleti; Henda Triki; Zied Lachiri; Maher Kharrat

doi:10.1016/j.ygeno.2020.07.003

Comparative genomic signature representations of the emerging COVID-19 coronavirus and other coronaviruses: High identity and possible recombination between Bat and Pangolin coronaviruses

Genomics. 2020 Nov;112(6):4189-4202. doi: 10.1016/j.ygeno.2020.07.003. Epub 2020 Jul 6.

Authors

Rabeb Touati¹, Sondes Haddad-Boubaker², Imen Ferchichi³, Imen Messaoudi⁴, Afef Elloumi Ouesleti⁵, Henda Triki², Zied Lachiri⁶, Maher Kharrat³

Affiliations

¹ University of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis, Tunisia; University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, le Belvédère, 1002 Tunis, Tunisie. Electronic address: rabeb.touati@enit.utm.tn.
² University of Tunis El Manar, Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for EMRO region, Institut Pasteur de Tunis, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisie.
³ University of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis, Tunisia.
⁴ University of Carthage, Higher Institute of Information Technologies and Communications, Industrial Computing Department, Tunisia; University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, le Belvédère, 1002 Tunis, Tunisie.
⁵ University of Carthage, National School of Engineers of Carthage, Electrical Engineering Department, Tunisia; University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, le Belvédère, 1002 Tunis, Tunisie.
⁶ University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, le Belvédère, 1002 Tunis, Tunisie.

Abstract

Coronaviruses are responsible on respiratory diseases in animal and human. The combination of numerical encoding techniques and digital signal processing methods are becoming increasingly important in handling large genomic data. In this paper, we propose to analyze the SARS-CoV-2 genomic signature using the combination of different nucleotide representations and signal processing tools in the aim to identify its genetic origin. The sequence of SARS-CoV-2 was compared with 21 relevant sequences including Bat, Yak and Pangolin coronavirus sequences. In addition, we developed a new algorithm to locate the nucleotide modifications. The results show that the Bat and Pangolin coronaviruses were the most related to SARS-CoV-2 with 96% and 86% of identity all along the genome. Within the S gene sequence, the Pangolin sequence presents local highest nucleotide identity. Those findings suggest genesis of SARS-Cov-2 through evolution from Bat and Pangolin strains. This study offers new ways to automatically characterize viruses.

Keywords: Bat; COVID19; Genome signature; Pangolin; SARS-CoV-2; Yak.

Publication types

Comparative Study
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Animals
Chiroptera / virology*
Coronavirus / genetics*
Genome, Viral / genetics*
Genomics / methods
Humans
Pangolins / virology*
Recombination, Genetic*
SARS-CoV-2 / genetics*