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Synonymous codon usage analysis of hand, foot and mouth disease viruses: A comparative study on coxsackievirus A6, A10, A16, and enterovirus 71 from 2008 to 2015.

Publication ,  Journal Article
Su, W; Li, X; Chen, M; Dai, W; Sun, S; Wang, S; Sheng, X; Sun, S; Gao, C; Hou, A; Zhou, Y; Sun, B; Gao, F; Xiao, J; Zhang, Z; Jiang, C
Published in: Infect Genet Evol
September 2017

Enterovirus 71 (EV71) and coxsackievirus A16 (CVA16) have been considered major pathogens of hand, foot and mouth disease (HFMD) throughout the world for decades. In recent years, coxsackievirus A6 (CVA6) and coxsackievirus A10 (CVA10) have raised attention as two other serious pathogens of HFMD. The present study focused on the synonymous codon usage of four viruses isolated from 2008 to 2015, with particular attention on P1 (encoding capsid proteins) and P2-P3 regions (both encoding non-structural proteins) in the genomic RNA. Relative synonymous codon usage, effective number of codons, neutrality and correspondence were analyzed. The results indicated that these viruses prefer A/T at the third position in codons rather than G/C. The most frequent codons of 4 essential and 2 semi-essential amino acids, as well as a key amino acid of metabolic junctions (Glu) used in the four viruses are also the most frequently used in humans. Effective number of codons (ENC) values indicated weak codon usage bias in all the viruses. Relatively, the force of mutation pressure in the P1 region was found to be stronger than that in the P2-P3 region, and this force in the P1 region of CVA6 and EV71 was stronger than that of CVA10 and A16. The neutrality analysis results implied that mutation pressure plays a minor role in shaping codon bias of these viruses. Correspondence analysis indicated that the codon usage of EV71 strains varied much more than that of other viruses. In conclusion, the present study provides novel and comparative insight into the evolution of HFMD pathogens at the codon level.

Duke Scholars

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Published In

Infect Genet Evol

DOI

EISSN

1567-7257

Publication Date

September 2017

Volume

53

Start / End Page

212 / 217

Location

Netherlands

Related Subject Headings

  • Viral Nonstructural Proteins
  • Sequence Analysis, DNA
  • Microbiology
  • Humans
  • Hand, Foot and Mouth Disease
  • Genome, Viral
  • Genetic Code
  • Gene Expression
  • Enterovirus A, Human
  • Codon
 

Citation

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MLA
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Su, W., Li, X., Chen, M., Dai, W., Sun, S., Wang, S., … Jiang, C. (2017). Synonymous codon usage analysis of hand, foot and mouth disease viruses: A comparative study on coxsackievirus A6, A10, A16, and enterovirus 71 from 2008 to 2015. Infect Genet Evol, 53, 212–217. https://doi.org/10.1016/j.meegid.2017.06.004
Su, Weiheng, Xue Li, Meili Chen, Wenwen Dai, Shiyang Sun, Shuai Wang, Xin Sheng, et al. “Synonymous codon usage analysis of hand, foot and mouth disease viruses: A comparative study on coxsackievirus A6, A10, A16, and enterovirus 71 from 2008 to 2015.Infect Genet Evol 53 (September 2017): 212–17. https://doi.org/10.1016/j.meegid.2017.06.004.
Su, Weiheng, et al. “Synonymous codon usage analysis of hand, foot and mouth disease viruses: A comparative study on coxsackievirus A6, A10, A16, and enterovirus 71 from 2008 to 2015.Infect Genet Evol, vol. 53, Sept. 2017, pp. 212–17. Pubmed, doi:10.1016/j.meegid.2017.06.004.
Su W, Li X, Chen M, Dai W, Sun S, Wang S, Sheng X, Gao C, Hou A, Zhou Y, Sun B, Gao F, Xiao J, Zhang Z, Jiang C. Synonymous codon usage analysis of hand, foot and mouth disease viruses: A comparative study on coxsackievirus A6, A10, A16, and enterovirus 71 from 2008 to 2015. Infect Genet Evol. 2017 Sep;53:212–217.
Journal cover image

Published In

Infect Genet Evol

DOI

EISSN

1567-7257

Publication Date

September 2017

Volume

53

Start / End Page

212 / 217

Location

Netherlands

Related Subject Headings

  • Viral Nonstructural Proteins
  • Sequence Analysis, DNA
  • Microbiology
  • Humans
  • Hand, Foot and Mouth Disease
  • Genome, Viral
  • Genetic Code
  • Gene Expression
  • Enterovirus A, Human
  • Codon