Rahman Siddiq Ur, Hu Yikui, Rehman Hassan Ur, Alrashed May M, Attia Kotb A, Ullah Ubaid, Liang Huiying
Medical Big Data Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province 510080, PR China; Department of Computer Science & Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa, 27200, Pakistan.
Department of Neurology, Wuhan Wuchang Hospital, Wuhan, PR China.
Virus Res. 2025 Mar;353:199528. doi: 10.1016/j.virusres.2025.199528. Epub 2025 Jan 29.
Lassa virus genome consists of two single-stranded, negative-sense RNA segments that lie in the genus Arenavirus. The disease associated with the Lassa virus is distributed all over the world, with approximately 3,000,000-5,000,000 infections diagnosed annually in West Africa. It shows high health risks to the human being. Previous research used the evolutionary time scale and adaptive evolution to describe the Lassa virus population pattern. However, it is still unclear how the Lassa virus takes advantage of synonymous codons. In this study, we analyzed the codon usage bias in 162 Lassa virus strains by calculating and comparing the nucleotide contents, effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and others. The results disclosed that LASV strains are rich in A/T. The average ENC value indicated a low codon usage bias in LASVs. The ENC-plot, neutrality plot and parity rule 2 plot demonstrated that, besides mutational pressure, other factors like natural selection also contributed to codon usage bias. This study is significant because it described the pattern of codon usage in the genomes of the Lassa viruses and provided the information needed for a fundamental evolutionary study of them.
拉沙病毒基因组由位于沙粒病毒属的两个单链、负义RNA片段组成。与拉沙病毒相关的疾病在全球范围内均有分布，在西非地区每年约有300万至500万例感染被确诊。它对人类健康构成了很高的风险。以往的研究利用进化时间尺度和适应性进化来描述拉沙病毒群体模式。然而，拉沙病毒如何利用同义密码子仍不清楚。在本研究中，我们通过计算和比较核苷酸含量、有效密码子数（ENC）、密码子适应指数（CAI）、相对同义密码子使用情况（RSCU）等，分析了162株拉沙病毒的密码子使用偏好。结果显示，拉沙病毒株富含A/T。平均ENC值表明拉沙病毒的密码子使用偏好较低。ENC图、中性图和奇偶规则2图表明，除了突变压力外，自然选择等其他因素也对密码子使用偏好有影响。本研究具有重要意义，因为它描述了拉沙病毒基因组中的密码子使用模式，并为其基础进化研究提供了所需信息。
