Synonymous codon usage pattern among the S, M, and L segments in Crimean-congo hemorrhagic fever virus

Mallikarjun S Beelagi; Sr Santosh Kumar; Uma Bharathi Indrabalan; Sharanagouda S Patil; Ashwini Prasad; K P Suresh; Shiva Prasad Kollur; Veeresh Santhebennur Jayappa; Siddappa B Kakkalameli; Chandrashekar Srinivasa; Prabhakarareddy Anapalli Venkataravana; Chandan Shivamallu

doi:10.6026/97320630017479

Synonymous codon usage pattern among the S, M, and L segments in Crimean-congo hemorrhagic fever virus

Bioinformation. 2021 Apr 30;17(4):479-491. doi: 10.6026/97320630017479. eCollection 2021.

Affiliations

¹ Department of Biotechnology and Bioinformatics, Faculty of Life Sciences, JSS Academy of Higher Education & Research, Mysuru-570015, India.
² Department of Studies in Food Technology, Shivagangotri, Davangere University, Davangere Karnataka-577 007, India.
³ ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru-560064, India.
⁴ Department of Microbiology, Faculty of Life Sciences, JSS Academy of Higher Education & Research, Mysuru-570015, India.
⁵ Department of Sciences, Amrita School of Arts and Sciences, Mysuru, Amrita Vishwa Vidyapeetham, Karnataka - 570 026, India.
⁶ Department of Studies in Environmental Science, Shivagangotri, Davangere University, Davangere Karnataka-577 007, India.
⁷ Department of Studies in Botany, Davangere University, Shivagangotri, Davangere Karnataka - 577 007, India.
⁸ Department of Studies in Biotechnology, Davangere University, Shivagangotri, Davangere Karnataka-577 007, India.

Abstract

Crimean-Congo hemorrhagic fever (CCHF) virus is one among the major zoonosis viral diseases that use the Hyalomma ticks as their transmission vector to cause viral infection to the human and mammalian community. The fatality of infectious is high across the world especially in Africa, Asia, Middle East, and Europe. This study regarding codon usage bias of S, M, and L segments of the CCHF virus pertaining to the host Homo sapiens, reveals in-depth information about the evolutionary characteristics of CCHFV. Relative Synonymous Codon Usage (RSCU), Effective number of codons (ENC) were calculated, to determine the codon usage pattern in each segment. Correlation analysis between Codon adaptation index (CAI), GRAVY (Hydrophobicity), AROMO (Aromaticity), and nucleotide composition revealed bias in the codon usage pattern. There was no strong codon bias found among any segments of the CCHF virus, indicating both the factors i.e., natural selection and mutational pressure shapes the codon usage bias.

Keywords: CCHF virus; Codon usage bias; Homo sapiens; Host adaptation; Mutational pressure; Natural selection; S, M, L segments.