Nucleotide and codon usage biases involved in the evolution of African swine fever virus: A comparative genomics analysis

• Published in: Journal of basic microbiology Vol. 63; no. 5; pp. 499 - 518
• Main Authors: Pu, Feiyang, Wang, Rui, Yang, Xuanye, Hu, Xinyan, Wang, Jinqian, Zhang, Lijuan, Zhao, Yongqing, Zhang, Derong, Liu, Zewen, Liu, Junlin
• Format: Journal Article
• Language: English
• Published: Germany 01.05.2023
• Subjects: adenine; African swine fever virus; African Swine Fever Virus - genetics; Animals; Bias; Codon; Codon Usage; cytosine; entropy; Evolution, Molecular; evolutionary adaptation; evolutionary plasticity; Genomics; mutation; natural selection; nucleotide composition constraint; nucleotide skew; Nucleotides - genetics; Swine; synonymous codon usage; Thymine; viral genome; viruses; evolutionary plasticity; African swine fever virus; nucleotide skew; nucleotide composition constraint; synonymous codon usage
• ISSN: 0233-111X; 1521-4028; 1521-4028
• DOI: 10.1002/jobm.202200624

Since African swine fever virus (ASFV) replication is closely related to its host's machinery, codon usage of viral genome can be subject to selection pressures. A better understanding of codon usage can give new insights into viral evolution. We implemented information entropy and revealed that the nucleotide usage pattern of ASFV is significantly associated with viral isolation factors (region and time), especially the usages of thymine and cytosine. Despite the domination of adenine and thymine in the viral genome, we found that mutation pressure alters the overall codon usage pattern of ASFV, followed by selective forces from natural selection. Moreover, the nucleotide skew index at the gene level indicates that nucleotide usages influencing synonymous codon bias of ASFV are significantly correlated with viral protein hydropathy. Finally, evolutionary plasticity is proved to contribute to the weakness in synonymous codons with A‐ or T‐end serving as optimal codons of ASFV, suggesting that fine‐tuning translation selection plays a role in synonymous codon usages of ASFV for adapting host. Taken together, ASFV is subject to evolutionary dynamics on nucleotide selections and synonymous codon usage, and our detailed analysis offers deeper insights into the genetic characteristics of this newly emerging virus around the world.