Patil Sharanagouda S, Indrabalan Uma Bharathi, Suresh Kuralayanapalya Puttahonnappa, Shome Bibek Ranjan
ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India.
Vet World. 2021 Jun;14(6):1450-1458. doi: 10.14202/vetworld.2021.1450-1458. Epub 2021 Jun 5.
Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious disease in pigs causing 100% mortality in susceptible adult pigs and piglets. High mortality rate in pigs causes huge economic loss to pig farmers. CSFV has a positive-sense RNA genome of 12.3 kb in length flanked by untranslated regions at 5' and 3' end. The genome codes for a large polyprotein of 3900 amino acids coding for 11 viral proteins. The 1300 codons in the polyprotein are coded by different combinations of three nucleotides which help the infectious agent to evolve itself and adapt to the host environment. This study performed and employed various methods/techniques to estimate the changes occurring in the process of CSFV evolution by analyzing the codon usage pattern.
The evolution of viruses is widely studied by analyzing their nucleotides and coding regions/codons using various methods. A total of 115 complete coding regions of CSFVs including one complete genome from our laboratory (MH734359) were included in this study and analysis was carried out using various methods in estimating codon usage bias and evolution. This study elaborates on the factors that influence the codon usage pattern.
The effective number of codons (ENC) and relative synonymous codon usage showed the presence of codon usage bias. The mononucleotide (A) has a higher frequency compared to the other mononucleotides (G, C, and T). The dinucleotides CG and CC are underrepresented and overrepresented. The codons CGT was underrepresented and AGG was overrepresented. The codon adaptation index value of 0.71 was obtained indicating that there is a similarity in the codon usage bias. The principal component analysis, ENC-plot, Neutrality plot, and Parity Rule 2 plot produced in this article indicate that the CSFV is influenced by the codon usage bias. The mutational pressure and natural selection are the important factors that influence the codon usage bias.
The study provides useful information on the codon usage analysis of CSFV and may be utilized to understand the host adaptation to virus environment and its evolution. Further, such findings help in new gene discovery, design of primers/probes, design of transgenes, determination of the origin of species, prediction of gene expression level, and gene function of CSFV. To the best of our knowledge, this is the first study on codon usage bias involving such a large number of complete CSFVs including one sequence of CSFV from India.
经典猪瘟（CSF）由猪瘟病毒（CSFV）引起，是猪的一种高度传染性疾病，可导致易感成年猪和仔猪100%死亡。猪的高死亡率给养猪户造成巨大经济损失。CSFV具有一个12.3kb长的正义RNA基因组，其5'和3'端侧翼为非翻译区。该基因组编码一个由3900个氨基酸组成的大的多聚蛋白，该多聚蛋白编码11种病毒蛋白。多聚蛋白中的1300个密码子由三个核苷酸的不同组合编码，这有助于感染因子自身进化并适应宿主环境。本研究通过分析密码子使用模式，运用多种方法/技术来估计CSFV进化过程中发生的变化。
通过使用各种方法分析病毒的核苷酸和编码区/密码子，对病毒的进化进行了广泛研究。本研究共纳入了115个CSFV的完整编码区，包括来自我们实验室的一个完整基因组（MH734359），并使用各种方法进行分析以估计密码子使用偏好和进化。本研究阐述了影响密码子使用模式的因素。
有效密码子数（ENC）和相对同义密码子使用情况表明存在密码子使用偏好。与其他单核苷酸（G、C和T）相比，单核苷酸（A）的频率更高。二核苷酸CG和CC的含量分别低于和高于预期。密码子CGT的含量低于预期，AGG的含量高于预期。获得的密码子适应指数值为0.71，表明密码子使用偏好存在相似性。本文所做的主成分分析、ENC图、中性图和奇偶规则2图表明CSFV受密码子使用偏好的影响。突变压力和自然选择是影响密码子使用偏好的重要因素。
该研究为CSFV的密码子使用分析提供了有用信息，可用于了解宿主对病毒环境的适应及其进化。此外，这些发现有助于新基因发现、引物/探针设计、转基因设计、物种起源确定、基因表达水平预测以及CSFV的基因功能研究。据我们所知，这是首次涉及如此大量完整CSFV（包括来自印度的一个CSFV序列）的密码子使用偏好研究。
