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



Mallikarjun S Beelagi1, Sharanagouda S Patil2, Santhosh Kumar SR3, Ashwini Prasad4, KP Suresh2, Shiva Prasad Kollur5, Uma Bharathi Indrabalan2, Veeresh Santhebennur Jayappa6, Siddappa B. Kakkalameli7, Chandrashekar Srinivasa8 & Chandan Shivamallu1



1Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education & Research, Mysuru - 570015, India; 2ICAR - National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru - 560064, India. 3Department of Studies in Food Technology, Shivagangotri, Davangere University, Davangere, Karnataka-577 002, India; 4Department of Microbiology, Faculty of Life Sciences, JSS Academy of Higher Education & Research, Mysuru - 570015, India; 5Department of Sciences, Amrita School of Arts and Sciences, Mysuru, Amrita Vishwa Vidyapeetham, Karnataka 570026, India; 6Department of Studies in Environmental Science, Shivagangotri, Davangere University, Davangere, Karnataka - 577002, India; 7Department of Studies in Botany, Davangere University, Shivagangotri, Davangere Karnataka-577 002, India; 8Department of Studies in Biotechnology, Davangere University, Shivagangotri, Davangere Karnataka - 577 002, India. *Correspondence



chandans@jssuni.edu.in (CS)


Article Type

Research Article



Received February 28, 2021; Revised March 31, 2021; Accepted April 1, 2021, Published April 30, 2021



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.



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



Beelagi et al. Bioinformation 17(4): 479-491 (2021)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.