Shueb Mohammad, Prasad Shashanka K, Suresh Kuralayanapalya Puttahonnappa, Indrabalan Uma Bharathi, Beelagi Mallikarjun S, Shivamallu Chandan, Silina Ekaterina, Stupin Victor, Manturova Natalia, Kollur Shiva Prasad, Shome Bibek Ranjan, Achar Raghu Ram, Patil Sharanagouda S
Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India.
ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India.
Vet World. 2022 Jul;15(7):1857-1868. doi: 10.14202/vetworld.2022.1857-1868. Epub 2022 Jul 29.
, 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.
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.
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.
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 .
黄病毒科的一个属，包含影响牛、羊和猪的病毒。感染动物会出现包括出血综合征、流产、呼吸并发症和致命性黏膜疾病等症状，给养殖户造成巨大经济损失。本研究选取了属于该属的牛病毒性腹泻病毒1型、牛病毒性腹泻病毒2型、经典猪瘟病毒、边界病病毒、邦戈瓦纳病毒、霍比样病毒和非典型猪瘟病毒。本研究旨在利用糖蛋白E2基因估计密码子使用偏好和进化速率。此外，使用所有七种病毒E2基因的公开核苷酸序列进行密码子使用偏好分析。这些核苷酸序列可能有助于阐明疾病流行病学并促进更好疫苗设计的发展。
本研究纳入了牛病毒性腹泻病毒1型（n = 89）、牛病毒性腹泻病毒2型（n = 60）、经典猪瘟病毒（n = 75）、边界病病毒（n = 10）、邦戈瓦纳病毒（n = 7）、霍比样病毒（n = 52）和非典型猪瘟病毒（n = 85）的E2基因编码序列。使用不同方法对它们进行分析以估计密码子使用偏好和进化情况。此外，采用最大似然法和贝叶斯方法，利用完整的E2基因区域分析七种病毒的分子数据集。
密码子使用偏好和进化速率分析的综合结果显示，牛病毒性腹泻病毒1型、牛病毒性腹泻病毒2型和经典猪瘟病毒存在密码子使用偏好，其中突变和自然选择发挥了重要作用。此外，虽然有效密码子数的值显示出中等偏好，但中性绘图表明牛病毒性腹泻病毒1型、牛病毒性腹泻病毒2型和经典猪瘟病毒中存在自然选择，而边界病病毒、邦戈瓦纳病毒和霍比样病毒中存在突变压力。对应分析表明，轴1对同义密码子使用模式有显著贡献。在本研究中，牛病毒性腹泻病毒1型、牛病毒性腹泻病毒2型和经典猪瘟病毒的进化速率非常高。所有病毒谱系的最近共同祖先分别是1997年、1975年、1946年、1990年、2004年、1990年和1990年。本研究证实，突变压力和自然选择在密码子使用偏好和进化研究中都发挥了重要作用。
本研究深入了解了该属病毒的密码子使用偏好和进化谱系。可以说是此类的首次报告。该研究提供的信息可进一步用于阐明病毒各自的宿主适应策略。反过来，这些信息有助于研究该属病毒的流行病学和控制方法。
