The first study on analysis of the codon usage bias and evolutionary analysis of the glycoprotein envelope E2 gene of seven .

BACKGROUND AND AIM

, 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 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 . 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 (n = 89), (n = 60), (n = 75), (n = 10), (n = 07), (n = 52), and (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 es using a complete E2 gene region.

RESULTS

The combined analysis of codon usage bias and evolutionary rate analysis revealed that the es , and 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 , and es and mutational pressure in , and es. The correspondence analysis revealed that axis-1 significantly contributes to the synonymous codon usage pattern. In this study, the evolutionary rate of , , and was very high. The most recent common ancestors of all lineages are 1997, 1975, 1946, 1990, 2004, 1990, and 1990 for , and , 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 . 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 .