Title: Codon usage in conserved sites is more biased compared to variable sites in the SARS-CoV-2 genome

Authors: Madhusmita Dash; Annushree Kurmi; Preetisudha Meher; Siddhartha Sankar Satapathy; Nima D. Namsa

Addresses: Department of Electronics and Communication Engineering, NIT Arunachal Pradesh, Jote, District: Papum Pare, Arunachal Pradesh – 791113, India ' Department of Computer Science and Engineering, Tezpur University, Napaam, Sonitpur – 784028, Assam, India ' Department of Electronics and Communication Engineering, NIT Arunachal Pradesh, Jote, District: Papum Pare, Arunachal Pradesh – 791113, India ' Department of Computer Science and Engineering, Tezpur University, Napaam, Sonitpur – 784028, Assam, India ' Department of Molecular Biology and Biotechnology, Tezpur University, Napaam-784028, Assam, India

Abstract: High error rate in SARS-CoV-2 genome replication allows the virus to adapt to different environments and selective pressures. In this study, 35% of codons of the protein-coding sequences of the genome were observed to have undergone base substitution mutations. Machine learning based comparative analysis of usage between conserved codons and the remaining variable codons of the protein-coding genes revealed that the codon usage patterns between the two groups are significantly different. Codon usage values in the variable region resemble genome composition, whereas the values in the conserved regions were highly variable. This differential codon usage suggests that the conserved regions are under influence of selection pressure in this virus genome. Further, the selection pressure on codon usage and the nucleotide substitution biases act towards increasing A and T base composition in SARS-CoV-2 genome. Our observations on the base substitution will help us in understanding evolution of this SARS-CoV-2 virus genome.

Keywords: SARS-CoV2 genome; base substitution mutation; selection; conserved region; codon usage bias; CUB.

DOI: 10.1504/IJBRA.2024.137368

International Journal of Bioinformatics Research and Applications, 2024 Vol.20 No.1, pp.42 - 60

Received: 17 May 2023
Accepted: 19 Jul 2023

Published online: 14 Mar 2024 *

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