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A detailed analysis of codon usage patterns and influencing factors in Zika virus

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Abstract

Recent outbreaks of Zika virus (ZIKV) in Africa, Latin America, Europe, and Southeast Asia have resulted in serious health concerns. To understand more about evolution and transmission of ZIKV, detailed codon usage analysis was performed for all available strains. A high effective number of codons (ENC) value indicated the presence of low codon usage bias in ZIKV. The effect of mutational pressure on codon usage bias was confirmed by significant correlations between nucleotide compositions at third codon positions and ENCs. Correlation analysis between Gravy values, Aroma values and nucleotide compositions at third codon positions also indicated some influence of natural selection. However, the low codon adaptation index (CAI) value of ZIKV with reference to human and mosquito indicated poor adaptation of ZIKV codon usage towards its hosts, signifying that natural selection has a weaker influence than mutational pressure. Additionally, relative dinucleotide frequencies, geographical distribution, and evolutionary processes also influenced the codon usage pattern to some extent.

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Acknowledgements

We are thankful to Director, School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana for the support.

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Authors and Affiliations

  1. School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, 141004, India

    Niraj K. Singh

  2. College of Fisheries, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, 141004, India

    Anuj Tyagi

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  1. Niraj K. Singh
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  2. Anuj Tyagi
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Correspondence to Niraj K. Singh.

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Singh, N.K., Tyagi, A. A detailed analysis of codon usage patterns and influencing factors in Zika virus. Arch Virol 162, 1963–1973 (2017). https://doi.org/10.1007/s00705-017-3324-2

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