Codon usage bias of H9N2 avian influenza virus complete genomes and its influence factors

HUANG Weihong; CHEN Yongjie; SUN Yankuo; SUN Weidong

doi:10.7671/j.issn.1001-411X.201908020

Journal of South China Agricultural University > 2020 > 41(3): 15-22. > DOI: 10.7671/j.issn.1001-411X.201908020

HUANG Weihong, CHEN Yongjie, SUN Yankuo, et al. Codon usage bias of H9N2 avian influenza virus complete genomes and its influence factors[J]. Journal of South China Agricultural University, 2020, 41(3): 15-22. DOI: 10.7671/j.issn.1001-411X.201908020

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Codon usage bias of H9N2 avian influenza virus complete genomes and its influence factors

1.
College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
2.
Key Laboratory of Zoonosis Prevention and Control of Guangdong Province/College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China

More Information

Received Date: August 13, 2019
Available Online: May 17, 2023

Graphical Abstract

Abstract

Abstract

Objective
To study codon usage bias of H9N2 avian influenza virus (AIV) complete genomes and its influence factors.

Method
The complete genomes of Chinese epidemic H9N2 AIV strains from 2010 to 2018 were selected. The characteristics of base composition, optimal codons, influence factors of codon usage bias and adaption to the codon usage patterns of the host were analyzed.

Result
AU content was higher than GC content in the whole genomes of H9N2 AIV. Most of the optimal codons ended with A or U, and the average of effective number of codons (ENC) was 52.86, suggesting that codon usage bias existed, but the bias was low. The codon usage bias was mainly affected by mutation pressure and natural selection. Natural selection (accounting for 61.79%−76.15%) played a greater role than mutation pressure (accounting for 23.85%−38.21%). In addition, the average codon adaptation ind ex of H9N2 AIV to Homo sapiens ranged from 0.739 to 0.741, suggesting that H9N2 AIV might have adapted to human codon usage patterns.

Conclusion
The study provides a theoretical basis for genetic evolution analysis of H9N2 AIV, codon optimization of existing vaccines and development of new vaccines (codon deoptimization vaccine).
- H9N2 avian influenza virus,
- codon usage bias,
- natural selection,
- mutation pressure

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References (22)

References

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Codon usage bias of H9N2 avian influenza virus complete genomes and its influence factors

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