College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China.
College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China.
Res Vet Sci. 2021 Jul;137:217-225. doi: 10.1016/j.rvsc.2021.05.008. Epub 2021 May 15.
HoBi-like pestivirus, an emerging species within the Pestivirus genus, is an important pathogen associated with a variety of clinical manifestations of ruminants, especially cattle. HoBi-like pestiviruses were identified in several countries and from different hosts, and raised concerns with regard to their acute and persistent infections, which is implicated in economic losses for cattle farmers. However, the transmission path, codon usage bias, and host adaptation of the virus has not been studied. Hence, we performed the analysis the spatio-temporal transmission based on the available 5'-UTR sequences of HoBi-like pestivirus, and then conducted codon analysis of the complete coding sequence of the virus. The results show the virus appeared in 1952 (95% HPD: 1905-1985) and may have originated in India. In addition, Italy is the hub for the spread of the virus. Moreover, six potential recombination events and two complex recombination events were discovered. Analysis of codon usage patterns revealed that the effective number of codon (ENC) values with an average of 50.85, and the codon usage bias is greatly affected by natural selection, which is different from the previous BVDV-1, 2. Finally, codon adaptation index (CAI) analysis shows that pigs may be the potential origin species of the HoBi-like pestivirus. These findings will contribute to more effective control of the spread of the virus, extend the knowledge about the genetic and evolutionary features of HoBi-like viruses and provide some information for vaccine research.
类 HoBi 瘟病毒是瘟病毒属中的一个新兴种，是与反刍动物（尤其是牛）多种临床表现相关的重要病原体。已在多个国家和不同宿主中鉴定出类 HoBi 瘟病毒，并对其急性和持续性感染引起关注，这与牛养殖户的经济损失有关。然而，该病毒的传播途径、密码子使用偏好和宿主适应性尚未得到研究。因此，我们根据现有的类 HoBi 瘟病毒 5'UTR 序列进行时空传播分析，然后对病毒的完整编码序列进行密码子分析。结果表明，该病毒出现在 1952 年（95% HPD：1905-1985），可能起源于印度。此外，意大利是该病毒传播的中心。此外，还发现了六个潜在的重组事件和两个复杂的重组事件。密码子使用模式分析表明，有效密码子数（ENC）平均值为 50.85，密码子使用偏好受自然选择的影响很大，这与之前的 BVDV-1、2 不同。最后，密码子适应指数（CAI）分析表明，猪可能是类 HoBi 瘟病毒的潜在起源物种。这些发现将有助于更有效地控制病毒的传播，扩展对类 HoBi 病毒遗传和进化特征的认识，并为疫苗研究提供一些信息。
