title: Overall codon usage pattern of enterovirus 71.
abstract: Hand, foot, and mouth disease (HFMD) is a systemic illness in children and is usually caused by enterovirus 71 (EV71). To provide new insights into the genetic features of EV71 and the relationship between the overall codon usage pattern of this virus and that of humans, values for relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), and nucleotide composition were calculated and analyzed. The relationship between ENC values and (G+C)₃% suggests that, although nucleotide composition plays an important role in shaping the overall codon usage pattern of this virus, other factors also affect this pattern. In addition, the negative correlation between the CAI value and (G+C)₃% suggests that the secondary structure of the EV71 coding sequence caused by its nucleotide composition can affect gene expression. Moreover, there was no significant correlation between ENC and CAI, suggesting that gene expression does not play a role in shaping the overall codon usage pattern of EV71. The overall codon usage pattern of the EV71 virus is only partly similar to the general codon pattern of human, suggesting that, although EV71 has co-evolved with humans for extended periods, mutation pressure played an important role in shaping the virus's overall codon usage pattern. These results revealed that the EV71 virus has developed a subtle strategy during evolution for adapting to environmental changes in its host cells solely by means of mutation pressure.
authors.affiliation: Experimental Center of Medicine, Lanzhou General Hospital, Lanzhou Military Area Command, Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou, Gansu, China.
authors.forename: M R
authors.initials: MR
authors.lastname: Ma
authors.affiliation: Experimental Center of Medicine, Lanzhou General Hospital, Lanzhou Military Area Command, Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou, Gansu, China.
authors.forename: L
authors.initials: L
authors.lastname: Hui
authors.affiliation: Experimental Center of Medicine, Lanzhou General Hospital, Lanzhou Military Area Command, Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou, Gansu, China.
authors.forename: M L
authors.initials: ML
authors.lastname: Wang
authors.affiliation: Experimental Center of Medicine, Lanzhou General Hospital, Lanzhou Military Area Command, Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou, Gansu, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Tang
authors.affiliation: Experimental Center of Medicine, Lanzhou General Hospital, Lanzhou Military Area Command, Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou, Gansu, China.
authors.forename: Y W
authors.initials: YW
authors.lastname: Chang
authors.affiliation: Experimental Center of Medicine, Lanzhou General Hospital, Lanzhou Military Area Command, Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou, Gansu, China.
authors.forename: Q H
authors.initials: QH
authors.lastname: Jia
authors.affiliation: Experimental Center of Medicine, Lanzhou General Hospital, Lanzhou Military Area Command, Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou, Gansu, China.
authors.forename: X H
authors.initials: XH
authors.lastname: Wang
authors.affiliation: Experimental Center of Medicine, Lanzhou General Hospital, Lanzhou Military Area Command, Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou, Gansu, China.
authors.forename: W
authors.initials: W
authors.lastname: Yan
authors.affiliation: Experimental Center of Medicine, Lanzhou General Hospital, Lanzhou Military Area Command, Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou, Gansu, China.
authors.forename: X Q
authors.initials: XQ
authors.lastname: Ha
mesh_terms: D001482:Base Composition; D003062:Codon / Q000235:genetics*; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics*; D029821:Enterovirus A, Human / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation
chemical_list: D003062:Codon; D004279:DNA, Viral