Indrabalan Uma Bharathi, Suresh Kuralayanapalya Puttahonnappa, Shivamallu Chandan, Patil Sharanagouda S
Spatial Epidemiology Laboratory, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru, Karnataka India.
Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysore, Karnataka India.
Virusdisease. 2021 Dec;32(4):810-822. doi: 10.1007/s13337-021-00719-x. Epub 2021 Jul 22.
African swine fever virus (ASFV) belongs to the family of to the genus ASF virus causes hemorrhage illness with a high mortality rate and hence, commercial loss in the swine community. The ASFV has been categorized by variation in codon usage that is caused by high mutation rates and natural selection. The evolution is caused mainly due to the mutation pressure and regulating the protein gene expression. Based on publicly accessible nucleotide sequences of the ASFV and its host (pig & tick), codon usage bias analysis was performed since an approved effective vaccination is not available to date, it is very important to analyze the codon usage bias of the , , and proteins of ASFV to produce an effective and efficient vaccine to control the disease. Even though the codon usage bias analyses have been evaluated earlier, the evaluation of the codon usage pattern specific to of ASFV is inadequate. In all the protein-coding sequences, nucleotide base and codons terminating with base T were most frequent and the mean effective number of codons (Nc) was high, indicating the presence of codon usage bias. The GC contents and dinucleotide frequencies also indicated the codon usage bias of the ASFV pig and tick. The Nc plot, parity plot, neutrality plot analysis, revealed natural selection, as well as mutation pressure, were the major constraints in altering the codon bias of ASF virus. codon usage bias analysis was performed with no substantial differences in codon usage of the ASFV in pig and tick.
The online version contains supplementary material available at 10.1007/s13337-021-00719-x.
非洲猪瘟病毒（ASFV）属于 科 属，该病毒会引发高死亡率的出血性疾病，从而给养猪业带来商业损失。由于高突变率和自然选择导致密码子使用的变化，ASFV已被分类。其进化主要是由突变压力和调节蛋白质基因表达引起的。基于ASFV及其宿主（猪和蜱）可公开获取的核苷酸序列进行了密码子使用偏好分析，由于目前尚无批准的有效疫苗，分析ASFV的 、 和 蛋白的密码子使用偏好对于生产有效且高效的疫苗以控制该疾病非常重要。尽管之前已经对密码子使用偏好进行了评估，但针对ASFV的 特定密码子使用模式的评估并不充分。在所有蛋白质编码序列中，以碱基T结尾的核苷酸碱基和密码子最为常见，密码子的平均有效数量（Nc）较高，表明存在密码子使用偏好。GC含量和二核苷酸频率也表明了ASFV在猪和蜱中的密码子使用偏好。Nc图、奇偶图、中性图分析表明，自然选择以及突变压力是改变ASF病毒密码子偏好的主要限制因素。对猪和蜱中ASFV的密码子使用情况进行了密码子使用偏好分析，结果无显著差异。
在线版本包含可在10.1007/s13337-021-00719-x获取的补充材料。
