tetano
Editor, Senior Moderator
Int J Biol Macromol
. 2023 Oct 9:127319.
doi: 10.1016/j.ijbiomac.2023.127319. Online ahead of print. Codon usage bias analysis of the spike protein of human coronavirus 229E and its host adaptability
Meng Lu[SUP] 1 [/SUP], Wenbo Wan[SUP] 1 [/SUP], Yuxing Li[SUP] 1 [/SUP], Haipeng Li[SUP] 1 [/SUP], Bowen Sun[SUP] 1 [/SUP], Kang Yu[SUP] 1 [/SUP], Jin Zhao[SUP] 1 [/SUP], Giovanni Franzo[SUP] 2 [/SUP], Shuo Su[SUP] 3 [/SUP]
Affiliations
Human coronavirus 229E (HCoV-229E) represents one of the known coronaviruses capable of infecting humans and cause mild respiratory symptoms. It is also considered to have a zoonotic source, originating from animals and being transmitted the humans. In this study, a comprehensive phylogenetic and codon usage analysis of the spike (S) gene of HCoV-229E was conducted. Utilizing phylogenetic analysis and principal component analysis, HCoV-229E was categorized into four distinct clusters, each demonstrating unique host affiliations. Furthermore, it was observed that the codon usage bias within the S gene of HCoV-229E is relatively low, primarily influenced by natural selection patterns, with contributions from mutation pressure and dinucleotide abundance. Comparative analysis involving Codon Adaptation Index (CAI) and Relative Codon Deoptimization Index (RCDI) revealed that the codon usage pattern of HCoV-229E mirrors more closely that of camels, as opposed to alpacas and humans. The elucidation of the codon usage pattern within HCoV-229E, which we have meticulously examined, offers valuable insights for a more comprehensive comprehension of viral features, history, and evolutionary trajectory.
Keywords: Codon usage bias; HCoV-229E; Spike protein.
. 2023 Oct 9:127319.
doi: 10.1016/j.ijbiomac.2023.127319. Online ahead of print. Codon usage bias analysis of the spike protein of human coronavirus 229E and its host adaptability
Meng Lu[SUP] 1 [/SUP], Wenbo Wan[SUP] 1 [/SUP], Yuxing Li[SUP] 1 [/SUP], Haipeng Li[SUP] 1 [/SUP], Bowen Sun[SUP] 1 [/SUP], Kang Yu[SUP] 1 [/SUP], Jin Zhao[SUP] 1 [/SUP], Giovanni Franzo[SUP] 2 [/SUP], Shuo Su[SUP] 3 [/SUP]
Affiliations
- PMID: 37820917
- DOI: 10.1016/j.ijbiomac.2023.127319
Human coronavirus 229E (HCoV-229E) represents one of the known coronaviruses capable of infecting humans and cause mild respiratory symptoms. It is also considered to have a zoonotic source, originating from animals and being transmitted the humans. In this study, a comprehensive phylogenetic and codon usage analysis of the spike (S) gene of HCoV-229E was conducted. Utilizing phylogenetic analysis and principal component analysis, HCoV-229E was categorized into four distinct clusters, each demonstrating unique host affiliations. Furthermore, it was observed that the codon usage bias within the S gene of HCoV-229E is relatively low, primarily influenced by natural selection patterns, with contributions from mutation pressure and dinucleotide abundance. Comparative analysis involving Codon Adaptation Index (CAI) and Relative Codon Deoptimization Index (RCDI) revealed that the codon usage pattern of HCoV-229E mirrors more closely that of camels, as opposed to alpacas and humans. The elucidation of the codon usage pattern within HCoV-229E, which we have meticulously examined, offers valuable insights for a more comprehensive comprehension of viral features, history, and evolutionary trajectory.
Keywords: Codon usage bias; HCoV-229E; Spike protein.