Vet World Vol.15 July-2022 Article-34
Research Article
Veterinary World, 15(7): 1857-1868
https://doi.org/10.14202/vetworld.2022.1857-1868
The first study on analysis of the codon usage bias and evolutionary analysis of the glycoprotein envelope E2 gene of seven Pestiviruses
2. ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India.
3. Department of Surgery, Pirogov Russian National Research Medical University, 117997, Moscow, Russia.
4. School of Physical Sciences, Amrita Vishwa Vidyapeetham, Mysuru, India.
5. Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, India.
Background and Aim: Pestivirus, a genus of the Flaviviridae family, comprises viruses that affect bovines, sheep, and pigs. Symptoms, including hemorrhagic syndromes, abortion, respiratory complications, and deadly mucosal diseases, are produced in infected animals, which cause huge economic losses to the farmers. Bovine viral diarrhea virus-1, bovine viral diarrhea virus-2, classical swine fever virus, border disease virus, Bungowannah, Hobi-like, and atypical porcine pestivirus belonging to the Pestivirus genus were selected for the study. This study aimed to estimate the codon usage bias and the rate of evolution using the glycoprotein E2 gene. Furthermore, codon usage bias analysis was performed using publicly available nucleotide sequences of the E2 gene of all seven Pestiviruses. These nucleotide sequences might elucidate the disease epidemiology and facilitate the development of designing better vaccines.
Materials and Methods: Coding sequences of the E2 gene of Pestiviruses A (n = 89), B (n = 60), C (n = 75), D (n = 10), F (n = 07), H (n = 52), and K (n = 85) were included in this study. They were analyzed using different methods to estimate the codon usage bias and evolution. In addition, the maximum likelihood and Bayesian methodologies were employed to analyze a molecular dataset of seven Pestiviruses using a complete E2 gene region.
Results: The combined analysis of codon usage bias and evolutionary rate analysis revealed that the Pestiviruses A, B, C, D, F, H, and K have a codon usage bias in which mutation and natural selection have played vital roles. Furthermore, while the effective number of codons values revealed a moderate bias, neutrality plots indicated the natural selection in A, B, F, and H Pestiviruses and mutational pressure in C, D, and K Pestiviruses. The correspondence analysis revealed that axis-1 significantly contributes to the synonymous codon usage pattern. In this study, the evolutionary rate of Pestiviruses B, H, and K was very high. The most recent common ancestors of all Pestivirus lineages are 1997, 1975, 1946, 1990, 2004, 1990, and 1990 for Pestiviruses A, B, C, D, F, H, and K, respectively. This study confirms that both mutational pressure and natural selection have played a significant role in codon usage bias and evolutionary studies.
Conclusion: This study provides insight into the codon usage bias and evolutionary lineages of pestiviruses. It is arguably the first report of such kind. The information provided by the study can be further used to elucidate the respective host adaptation strategies of the viruses. In turn, this information helps study the epidemiology and control methods of pestiviruses. Keywords: codon usage bias, evolutionary analysis, Flaviviridae, glycoprotein E2, India, Pestivirus.
Keywords: codon usage bias, evolutionary analysis, Flaviviridae, glycoprotein E2, India, Pestivirus.
How to cite this article: Shueb M, Prasad SK, Suresh KP, Indrabalan UB, Beelagi MS, Shivamallu C, Silina E, Stupin V, Manturova N, Kollur SP, Shome BR, Achar RR, Patil SS (2022) The first study on analysis of the codon usage bias and evolutionary analysis of the glycoprotein envelope E2 gene of seven Pestiviruses, Veterinary World, 15(7): 1857–1868.
Received: 02-03-2022 Accepted: 21-06-2022 Published online: 29-07-2022
Corresponding author: Sharanagouda S. Patil and Raghu Ram Achar E-mail: sharanspin13@gmail.com and rracharya@jssuni.edu.in
DOI: 10.14202/vetworld.2022.1857-1868
Copyright: Shueb, et al. This article is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.